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WireEngine.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/WireEngine.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
/**
* Writes out the xml to configure the 'real' deduplication/matching process of this specific
* {@link Wire} instance.
*/
public class WireEngine {
Wire wire;
private final String[] defaultFalseList = new String[] {
"useInSelect", "useInNegativeSelect", "indexLength", "blanksMatch",
"addOriginalQueryValue", "addOriginalAuthorityValue",
"addTransformedQueryValue", "addTransformedAuthorityValue", "indexInitial",
"useWildcard"};
public WireEngine(Wire wire) {
this.wire = wire;
}
public ArrayList<String> toXML(int indentLevel) throws IllegalArgumentException, IllegalAccessException, NoSuchFieldException, SecurityException {
int shiftWidth = 4;
String shift = String.format("%" + shiftWidth + "s", " ");
String indent = "";
for (int i=0;i<indentLevel;i++) {
indent += shift;
}
ArrayList<String> outXML = new ArrayList<String>();
outXML.add(String.format("%s<bean class=\"org.kew.rmf.core.configuration.Property\"", indent));
outXML.add(String.format("%s%sp:queryColumnName=\"%s\"", indent, shift, this.wire.getQueryColumnName()));
if (this.wire.getAuthorityColumnName().length() > 0) {
outXML.add(String.format("%s%sp:authorityColumnName=\"%s\"", indent, shift, this.wire.getAuthorityColumnName()));
}
// all boolean attributes default to false and we only want to write them if they are set to true
for (String attr:this.defaultFalseList) {
boolean value = (boolean) this.wire.getClass().getField(attr).get(this.wire);
if (value) outXML.add(String.format("%s%sp:%s=\"%s\"", indent, shift, attr, value));
}
outXML.add(String.format("%s%sp:matcher-ref=\"%s\">", indent, shift, this.wire.getMatcher().getName()));
List<WiredTransformer> queryTransens = this.wire.getQueryTransformers();
if (queryTransens.size() > 0) {
outXML.add(String.format("%s%s<property name=\"queryTransformers\">", indent, shift));
outXML.add(String.format("%s%s%s<util:list id=\"1\">", indent, shift, shift));
Collections.sort(queryTransens);
for (WiredTransformer wTrans:queryTransens) {
outXML.add(String.format("%s%s%s%s<ref bean=\"%s\"/>", indent, shift,shift, shift, wTrans.getTransformer().getName()));
}
outXML.add(String.format("%s%s%s</util:list>", indent, shift, shift));
outXML.add(String.format("%s%s</property>", indent, shift));
}
List<WiredTransformer> authorityTransens = this.wire.getAuthorityTransformers();
if (authorityTransens.size() > 0) {
outXML.add(String.format("%s%s<property name=\"authorityTransformers\">", indent, shift));
outXML.add(String.format("%s%s%s<util:list id=\"1\">", indent, shift, shift));
Collections.sort(authorityTransens);
for (WiredTransformer wTrans:authorityTransens) {
outXML.add(String.format("%s%s%s%s<ref bean=\"%s\"/>", indent, shift,shift, shift, wTrans.getTransformer().getName()));
}
outXML.add(String.format("%s%s%s</util:list>", indent, shift, shift));
outXML.add(String.format("%s%s</property>", indent, shift));
}
outXML.add(String.format("%s</bean>", indent));
return outXML;
}
public ArrayList<String> toXML() throws IllegalArgumentException, IllegalAccessException, NoSuchFieldException, SecurityException {
return toXML(0);
}
}
| 4,471 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
Wire.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/Wire.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf;
import java.util.ArrayList;
import java.util.List;
import javax.persistence.CascadeType;
import javax.persistence.ManyToOne;
import javax.persistence.OneToMany;
import javax.persistence.Table;
import org.hibernate.annotations.Sort;
import org.hibernate.annotations.SortType;
import org.kew.rmf.matchconf.utils.GetterSetter;
import org.springframework.roo.addon.javabean.RooJavaBean;
import org.springframework.roo.addon.jpa.activerecord.RooJpaActiveRecord;
import org.springframework.roo.addon.tostring.RooToString;
/**
* This is the ORM equivalent to any implementation of
* {@link org.kew.rmf.core.configuration.Property}.
*
* It maps named columns to a {@link Matcher} per column and 0:n {@link Transformer}s per column.
* It also takes care of dealing with the separation of query- and authority- {@link Transformer}s.
*
* The link to the Transformers is via {@link WiredTransformer}s.
*/
@RooJavaBean
@RooToString
@Table(uniqueConstraints = @javax.persistence.UniqueConstraint(columnNames = { "configuration", "queryColumnName", "authorityColumnName" }))
@RooJpaActiveRecord(finders = { "findWiresByMatcher" })
public class Wire extends CloneMe<Wire> implements Comparable<Wire> {
static String[] CLONE_STRING_FIELDS = new String[] { "authorityColumnName", "queryColumnName" };
static String[] CLONE_BOOL_FIELDS = new String[] { "addOriginalQueryValue", "addOriginalAuthorityValue", "addTransformedAuthorityValue", "addTransformedQueryValue", "blanksMatch", "indexInitial", "indexLength", "useInNegativeSelect", "useInSelect", "useWildcard" };
private String queryColumnName;
private String authorityColumnName = "";
public Boolean useInSelect = false;
public Boolean useInNegativeSelect = false;
public Boolean indexLength = false;
public Boolean blanksMatch = false;
public Boolean addOriginalQueryValue = false;
public Boolean addOriginalAuthorityValue = false;
public Boolean addTransformedQueryValue = false;
public Boolean addTransformedAuthorityValue = false;
public Boolean indexInitial = false;
public Boolean useWildcard = false;
@ManyToOne
private Matcher matcher;
@ManyToOne
private Configuration configuration;
@OneToMany(cascade = CascadeType.ALL, orphanRemoval = true)
@Sort(type = SortType.NATURAL)
private List<WiredTransformer> queryTransformers = new ArrayList<WiredTransformer>();
@OneToMany(cascade = CascadeType.ALL, orphanRemoval = true)
private List<WiredTransformer> authorityTransformers = new ArrayList<WiredTransformer>();
public String getName() {
return this.getQueryColumnName() + "_" + this.getAuthorityColumnName();
}
@Override
public int compareTo(Wire w) {
return this.getName().compareTo(w.getName());
}
@Override
public String toString() {
return this.getName();
}
public Wire cloneMe(Configuration configClone) throws Exception {
Wire clone = new Wire();
// first the string attributes
for (String method : Wire.CLONE_STRING_FIELDS) {
clone.setattr(method, this.getattr(method, ""));
}
for (String method : Wire.CLONE_BOOL_FIELDS) {
clone.setattr(method, this.getattr(method, true));
}
// then the relational attributes
clone.setConfiguration(configClone);
clone.setMatcher(this.matcher.cloneMe(configClone));
for (WiredTransformer trans : this.getQueryTransformers()) {
clone.getQueryTransformers().add(trans.cloneMe(configClone));
}
for (WiredTransformer trans : this.getAuthorityTransformers()) {
clone.getAuthorityTransformers().add(trans.cloneMe(configClone));
}
return clone;
}
public WiredTransformer getWiredTransformer(String transformerType, String transformerName) throws Exception {
for (WiredTransformer wT : new GetterSetter<List<WiredTransformer>>().getattr(this, transformerType + "Transformers")) {
if (wT.getName().equals(transformerName)) return wT;
}
;
return null;
}
public WiredTransformer getQueryTransformerForName(String wiredTransformerName) {
for (WiredTransformer wiredTransformer : this.getQueryTransformers()) {
if (wiredTransformer.getName().equals(wiredTransformerName)) return wiredTransformer;
}
return null;
}
public WiredTransformer getAuthorityTransformerForName(String wiredTransformerName) {
for (WiredTransformer wiredTransformer : this.getAuthorityTransformers()) {
if (wiredTransformer.getName().equals(wiredTransformerName)) return wiredTransformer;
}
return null;
}
}
| 5,529 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
DictionaryEngine.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/DictionaryEngine.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf;
import java.util.ArrayList;
/**
* Writes out the xml to configure the 'real' deduplication/matching process of this specific
* {@link Dictionary} instance.
*/
public class DictionaryEngine {
Dictionary dict;
public DictionaryEngine(Dictionary dict) {
this.dict = dict;
}
public ArrayList<String> toXML(int indentLevel) throws Exception {
int shiftWidth = 4;
String shift = String.format("%" + shiftWidth + "s", " ");
String indent = "";
for (int i=0;i<indentLevel;i++) {
indent += shift;
}
ArrayList<String> outXML = new ArrayList<String>();
outXML.add(String.format("%s<bean id=\"%s\" class=\"org.kew.rmf.utils.CsvDictionary\"", indent, this.dict.getName()));
outXML.add(String.format("%s%sp:fileDelimiter=\"%s\"", indent, shift, this.dict.getFileDelimiter()));
// change path to unix-style for convencience, even if on windows..
outXML.add(String.format("%s%sp:filePath=\"%s\" />", indent, shift, this.dict.getFilePath().replace("\\\\", "/")));
return outXML;
}
}
| 1,809 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
BotEngine.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/BotEngine.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf;
import java.util.ArrayList;
/**
* Writes out the xml to configure the 'real' deduplication/matching process of this specific
* <?extends {@link Bot}> instance.
*/
public class BotEngine {
Bot bot;
public BotEngine(Bot bot) {
this.bot = bot;
}
/**
* Write out nicely formatted xml containing all necessary details for this instance.
*
* @param indentLevel
* @return
* @throws Exception
*/
public ArrayList<String> toXML(int indentLevel) throws Exception {
int shiftWidth = 4;
String shift = String.format("%" + shiftWidth + "s", " ");
String indent = "";
for (int i=0;i<indentLevel;i++) {
indent += shift;
}
ArrayList<String> outXML = new ArrayList<String>();
if (this.bot.getComposedBy().size() > 0) {
outXML.add(String.format("%s<bean id=\"%s\" class=\"%s.%s\">", indent, this.bot.getName(), this.bot.getPackageName(), this.bot.getClassName()));
outXML.add(String.format("%s%s<property name=\"%s\">", indent, shift, this.bot.getGroup()));
outXML.add(String.format("%s%s%s<util:list id=\"1\">", indent, shift, shift));
for (Bot bot:this.bot.getComposedBy()) {
outXML.addAll(new BotEngine(bot).toXML(indentLevel+3));
}
outXML.add(String.format("%s%s%s</util:list>", indent, shift, shift));
outXML.add(String.format("%s%s</property>", indent, shift));
outXML.add(String.format("%s</bean>", indent));
} else {
if (this.bot.getParams().length() > 0) {
outXML.add(String.format("%s<bean id=\"%s\" class=\"%s.%s\"", indent, this.bot.getName(), this.bot.getPackageName(), this.bot.getClassName()));
for (String param:this.bot.getParams().split(",")) {
String key, value;
String[] paramTuple = param.split("=");
if (paramTuple.length != 2) {
throw new Exception(String.format("Wrong params configuration for %s -- params format has to be like < param1=value1, param2=value2, ..>, but was: < %s >)", this.bot.getName(), this.bot.getParams()));
}
key = paramTuple[0].trim();
value = paramTuple[1].trim().replaceAll("(\"$)|(^\")", ""); // replace surounding quotes on the values of the params
if ((this.bot.getClassName().contains("Dict") || this.bot.getClassName().contains("LevenshteinMatcher")) && key.equals("dict")) {
outXML.add(String.format("%s%sp:dict-ref=\"%s\"", indent, shift, value));
} else outXML.add(String.format("%s%sp:%s=\"%s\"", indent, shift, key, value));
}
outXML.set(outXML.size()-1, outXML.get(outXML.size()-1) + "/>");
} else {
outXML.add(String.format("%s<bean id=\"%s\" class=\"%s.%s\" />", indent, this.bot.getName(), this.bot.getPackageName(), this.bot.getClassName()));
}
}
return outXML;
}
public ArrayList<String> toXML() throws Exception {
return toXML(0);
}
}
| 3,531 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
Transformer.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/Transformer.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf;
import java.util.ArrayList;
import java.util.List;
import javax.persistence.CascadeType;
import javax.persistence.ManyToMany;
import javax.persistence.ManyToOne;
import javax.persistence.Table;
import javax.persistence.Transient;
import javax.persistence.UniqueConstraint;
import org.hibernate.annotations.Sort;
import org.hibernate.annotations.SortType;
import org.springframework.roo.addon.javabean.RooJavaBean;
import org.springframework.roo.addon.jpa.activerecord.RooJpaActiveRecord;
import org.springframework.roo.addon.tostring.RooToString;
/**
* This is the ORM equivalent to any implementation of
* {@link org.kew.rmf.transformers.Transformer}.
*
* It can describe any matcher, the provided params are expected to be a comma-separated
* String of key=value pairs.
*/
@RooJavaBean
@RooToString
@RooJpaActiveRecord()
@Table(uniqueConstraints=@UniqueConstraint(columnNames={"configuration", "name"}))
public class Transformer extends Bot {
private String name;
private String packageName;
private String className;
private String params;
@Transient
private final String group = "transformers";
@ManyToMany(cascade = CascadeType.ALL)
@Sort(type=SortType.NATURAL)
private List<Transformer> composedBy = new ArrayList<>();
@ManyToOne
private Configuration configuration;
public String toString () {
return this.getName();
}
public Transformer cloneMe(Configuration configClone) throws Exception {
Transformer alreadyCloned = configClone.getTransformerForName(this.name);
if (alreadyCloned != null) return alreadyCloned;
Transformer clone = new Transformer();
// first the string attributes
for (String method:Bot.CLONE_STRING_FIELDS) {
clone.setattr(method, this.getattr(method, ""));
}
// then the relational attributes
clone.setConfiguration(configClone);
for (Transformer component:this.composedBy) {
Transformer compoClone = component.cloneMe(configClone);
clone.getComposedBy().add(compoClone);
}
return clone;
}
/**
* Helper method to deal with the problem of orphaned WiredTransformer instances.
* If this problem is sorted please delete!
*
* @throws Exception
*/
public void removeWiredTransformers() throws Exception {
try {
this.removeWiredTransformersLongWay();
} catch (Exception e) {
if (e instanceof Exception) {
throw new Exception(String.format("It seems that %s is still being used in a wire, please remove it there first in order to delete it.", this));
}
}
}
/**
* Helper method to deal with the problem of orphaned WiredTransformer instances.
* If this problem is sorted please delete!
*/
public Wire hasWiredTransformers() {
for (Wire wire:this.getConfiguration().getWiring()) {
for (WiredTransformer wt:wire.getQueryTransformers()) {
if (wt.getTransformer().getName().equals(this.getName())) {
return wire;
}
}
for (WiredTransformer wt:wire.getAuthorityTransformers()) {
if (wt.getTransformer().getName().equals(this.getName())) {
return wire;
}
}
}
return null;
}
/**
* Helper method to deal with the problem of orphaned WiredTransformer instances.
* If this problem is sorted please delete!
*/
public void removeOrphanedWiredTransformers() {
List<WiredTransformer> all_wts = WiredTransformer.findAllWiredTransformers();
for (WiredTransformer wt:all_wts) {
try {
if (wt.getTransformer().getName().equals(this.getName())) {
if (wt.isWireOrphan()) {
logger.warn("Still found orphaned WiredTransformer with id {}!!! trying to remove..", wt.getId());
wt.remove();
logger.info("Released orphaned WiredTransformer into, er, liberty.");
}
}
} catch (Exception e) {
if (wt.getTransformer() == null) {
logger.warn("Still found orphaned WiredTransformer with id {}!!! trying to remove..", wt.getId());
wt.remove();
logger.info("Released orphaned WiredTransformer into, er, liberty.");
} else throw e;
}
}
}
/**
* Helper method to deal with the problem of orphaned WiredTransformer instances.
* If this problem is sorted please delete!
*/
public void removeWiredTransformersLongWay() {
List<WiredTransformer> wts;
for (Wire wire:this.getConfiguration().getWiring()) {
wts = wire.getQueryTransformers();
for (WiredTransformer wt:new ArrayList<WiredTransformer>(wts)) {
if (wt.getTransformer().getName().equals(this.getName())) {
wts.remove(wt);
}
}
wts = wire.getAuthorityTransformers();
for (WiredTransformer wt:new ArrayList<WiredTransformer>(wts)) {
if (wt.getTransformer().getName().equals(this.getName())) wts.remove(wt);
}
wire.merge();
}
}
@Override
public String getGroup() {
return group;
}
}
| 6,261 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
CloneMe.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/CloneMe.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.List;
import javax.persistence.MappedSuperclass;
import javax.persistence.PostRemove;
import javax.persistence.PreRemove;
import org.kew.rmf.matchconf.utils.GetterSetter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.roo.addon.javabean.RooJavaBean;
import org.springframework.roo.addon.jpa.activerecord.RooJpaActiveRecord;
import org.springframework.roo.addon.tostring.RooToString;
/**
* Think of this abstract class as if it provided an abstract method 'cloneMe', I didn't get it
* working explicitely due to some conflicts between generics, raw types and the way the ORM is
* built, but this is how it's used.
*
* @param <T>
*/
@RooJavaBean
@RooToString
@MappedSuperclass
@RooJpaActiveRecord(mappedSuperclass=true)
public abstract class CloneMe<T> {
protected static Logger logger = LoggerFactory.getLogger(CloneMe.class);
public int getattr(String fieldName) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, NoSuchMethodException, SecurityException {
return new GetterSetter<Integer>().getattr(this, fieldName);
}
public Boolean getattr(String fieldName, Boolean b) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, NoSuchMethodException, SecurityException {
return new GetterSetter<Boolean>().getattr(this, fieldName);
}
public String getattr(String fieldName, String s) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, NoSuchMethodException, SecurityException {
return new GetterSetter<String>().getattr(this, fieldName);
}
public void setattr(String fieldName, int n) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, NoSuchMethodException, SecurityException {
new GetterSetter<Integer>().setattr(this, fieldName, n);;
}
public void setattr(String fieldName, Boolean b) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, NoSuchMethodException, SecurityException {
new GetterSetter<Boolean>().setattr(this, fieldName, b);
}
public void setattr(String fieldName, String s) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, NoSuchMethodException, SecurityException {
if (s!= null) new GetterSetter<String>().setattr(this, fieldName, s);
}
// conflict of Generics, inheritance and spring roo as far as I understand; have moved this method out of Roo's way,
// not using it anyway
public static List<CloneMe<Object>> findAllCloneMes() {
return new ArrayList<CloneMe<Object>>();
}
// conflict of Generics, inheritance and spring roo as far as I understand; have moved this method out of Roo's way,
// not using it anyway
public static List<CloneMe<Object>> findCloneMeEntries(int firstResult, int maxResults) {
return new ArrayList<CloneMe<Object>>();
}
@PreRemove
public void loggPreRemoval() {
logger.warn("Attempt to delete {} with id {}", this, this.getId());
}
@PostRemove
public void loggRemoval() {
logger.info("Deleted {}", this);
}
}
| 4,070 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
Matcher.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/Matcher.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf;
import java.util.ArrayList;
import java.util.List;
import javax.persistence.CascadeType;
import javax.persistence.ManyToMany;
import javax.persistence.ManyToOne;
import javax.persistence.Table;
import javax.persistence.Transient;
import javax.persistence.UniqueConstraint;
import org.hibernate.annotations.Sort;
import org.hibernate.annotations.SortType;
import org.springframework.roo.addon.javabean.RooJavaBean;
import org.springframework.roo.addon.jpa.activerecord.RooJpaActiveRecord;
import org.springframework.roo.addon.tostring.RooToString;
/**
* This is the ORM equivalent to any implementation of
* {@link org.kew.rmf.matchers.Matcher}.
*
* It can describe any matcher, the provided params are expected to be a comma-separated
* String of key=value pairs.
*/
@RooJavaBean
@RooToString
@RooJpaActiveRecord
@Table(uniqueConstraints=@UniqueConstraint(columnNames={"configuration", "name"}))
public class Matcher extends Bot {
private String name;
private String packageName;
private String className;
private String params;
@Transient
private final String group = "matchers";
@ManyToMany(cascade = CascadeType.ALL)
@Sort(type=SortType.NATURAL)
private List<Matcher> composedBy = new ArrayList<Matcher>();
@ManyToOne
private Configuration configuration;
public String toString () {
return this.getName();
}
public Matcher cloneMe(Configuration configClone) throws Exception {
Matcher alreadyCloned = configClone.getMatcherForName(this.name);
if (alreadyCloned != null) return alreadyCloned;
Matcher clone = new Matcher();
// first the string attributes
for (String method:Bot.CLONE_STRING_FIELDS) {
clone.setattr(method, this.getattr(method, ""));
}
// then the relational attributes
clone.setConfiguration(configClone);
for (Matcher component:this.composedBy) {
Matcher compoClone = component.cloneMe(configClone);
clone.getComposedBy().add(compoClone);
}
return clone;
}
@Override
public String getGroup() {
return group;
}
}
| 2,932 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ReporterEngine.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/ReporterEngine.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf;
import java.util.ArrayList;
/**
* Writes out the xml to configure the 'real' deduplication/matching process of this specific
* {@link Reporter} instance.
*/
public class ReporterEngine {
Reporter reporter;
public ReporterEngine(Reporter reporter) {
this.reporter = reporter;
}
public ArrayList<String> toXML(int indentLevel) {
int shiftWidth = 4;
String shift = String.format("%" + shiftWidth + "s", " ");
String indent = "";
for (int i=0;i<indentLevel;i++) {
indent += shift;
}
ArrayList<String> outXML = new ArrayList<String>();
outXML.add(String.format("%s<bean class=\"%s.%s\"", indent, this.reporter.getPackageName(), this.reporter.getClassName()));
outXML.add(String.format("%s%sp:name=\"%s\"", indent, shift, this.reporter.getName()));
outXML.add(String.format("%s%sp:configName=\"%s\"", indent, shift, this.reporter.getConfig().getName()));
// nameSpacePrefix: if not overwritten on reporter-level...
if (!this.reporter.getParams().contains("nameSpacePrefix")) {
// ..check if it's a dedup config..
if (this.reporter.getConfig().getClassName().equals("DeduplicationConfiguration")) {
// and tell it to name-space with the dedup-config's name
outXML.add(String.format("%s%sp:nameSpacePrefix=\"%s_\"", indent, shift, this.reporter.getConfig().getName()));
}
}
outXML.add(String.format("%s%sp:delimiter=\"%s\"", indent, shift, this.reporter.getDelimiter()));
outXML.add(String.format("%s%sp:idDelimiter=\"%s\"", indent, shift, this.reporter.getIdDelimiter()));
if (this.reporter.getParams().length() > 0) {
for (String param:this.reporter.getParams().split(",")) {
String key, value;
String[] paramTuple = param.split("=");
key = paramTuple[0];
value = paramTuple[1];
outXML.add(String.format("%s%sp:%s=\"%s\"", indent, shift, key, value));
}
}
outXML.set(outXML.size()-1, outXML.get(outXML.size()-1) + ">");
outXML.add(String.format("%s%s<property name=\"file\">", indent, shift));
outXML.add(String.format("%s%s%s<bean class=\"java.io.File\">", indent, shift, shift));
// change path to unix-style for convencience, even if on windows..
String rPath = String.format("%s/%s_%s",
this.reporter.getConfig().getWorkDirPath(),
this.reporter.getConfig().getName(),
this.reporter.getFileName()).replace("\\\\", "/");
outXML.add(String.format("%s%s%s%s<constructor-arg value=\"%s\" />", indent, shift, shift, shift, rPath));
outXML.add(String.format("%s%s%s</bean>", indent, shift, shift));
outXML.add(String.format("%s%s</property>", indent, shift));
outXML.add(String.format("%s</bean>", indent));
return outXML;
}
public ArrayList<String> toXML() {
return toXML(0);
}
}
| 3,853 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
GetterSetter.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/utils/GetterSetter.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.utils;
import java.lang.reflect.InvocationTargetException;
import org.apache.commons.lang3.StringUtils;
/**
* A helper class to get and set attributes via conventional getField and setField methods
* using generics.
*
* @param <ReturnType>
*/
public class GetterSetter<ReturnType> {
@SuppressWarnings("unchecked")
public <ObjClass> ReturnType getattr(ObjClass obj, String fieldName) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, NoSuchMethodException, SecurityException {
String method = "get" + StringUtils.capitalize(fieldName);
return (ReturnType) obj.getClass().getMethod(method).invoke(obj);
}
public <T> void setattr(T obj, String fieldName, int n) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, NoSuchMethodException, SecurityException {
String method = "set" + StringUtils.capitalize(fieldName);
obj.getClass().getMethod(method, int.class).invoke(obj, n);
}
public <T> void setattr(T obj, String fieldName, ReturnType b) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, NoSuchMethodException, SecurityException {
String method = "set" + StringUtils.capitalize(fieldName);
obj.getClass().getMethod(method, b.getClass()).invoke(obj, b);
}
}
| 2,125 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
WiredTransformerController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/WiredTransformerController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import org.kew.rmf.matchconf.WiredTransformer;
import org.springframework.roo.addon.web.mvc.controller.scaffold.RooWebScaffold;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMapping;
@RequestMapping("/wiredtransformers")
@Controller
@RooWebScaffold(path = "wiredtransformers", formBackingObject = WiredTransformer.class)
public class WiredTransformerController {
}
| 1,210 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
LibraryScanner.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/LibraryScanner.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import java.lang.reflect.Modifier;
import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;
import org.kew.rmf.matchers.Matcher;
import org.kew.rmf.reporters.Reporter;
import org.kew.rmf.transformers.Transformer;
import org.reflections.Reflections;
/**
* The LibraryScanner finds Transformers, Matchers and Reporters and produces a map that groups the classes in packages.
*/
public class LibraryScanner {
/**
* Produces a map that groups the classes in packages.
*/
public static Map<String, Map<String, Set<String>>> availableItems() {
Map<String, Map<String, Set<String>>> items = new TreeMap<>();
items.put("matchers", classesImplementingInterface(Matcher.class));
items.put("transformers", classesImplementingInterface(Transformer.class));
items.put("reporters", classesImplementingInterface(Reporter.class));
return items;
}
private static Map<String, Set<String>> classesImplementingInterface(Class<?> ınterface) {
Map<String, Set<String>> classesByPackage = new TreeMap<>();
Reflections reflections = new Reflections(ınterface.getPackage().getName());
for (Class<?> clazz : reflections.getSubTypesOf(ınterface)) {
if (Modifier.isAbstract(clazz.getModifiers())) continue;
String packageName = clazz.getPackage().getName();
if (classesByPackage.get(packageName) == null) classesByPackage.put(packageName, new TreeSet<String>());
classesByPackage.get(packageName).add(clazz.getSimpleName());
}
return classesByPackage;
}
}
| 2,308 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
package-info.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/package-info.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
/**
* This package contains the controllers for the matchconf-UI. You will notice
* that most of them are called Custom*.java, the Custom one being the one used
* as the original <Classname>Controller was created by Spring Roo and had to be
* customized.
*
* As Roo (given a roo shell is running) automatically updates the controllers
* after changes to the model it was convenient to keep the original
* <Classname>Controller classes.
*
* There is not documentation on most of them as it was to boring to document each
* delete, create, update, updateForm, show, list, populateEditForm,
* encodeUrlPathSegment, .. They all repeat for each controller, read the
* documentations for spring based web applications and spring roo.
*
* A major change I have made is to change the default id-based url-mapping to a
* name- or slug-based one. This seems to be much more eye friendly.
*
* Sometimes I added 'deleteByid', which is a work-around to delete entities based on
* their id rather than their name (this should be considered as deprecated now),
* and 'customValidation' which is a form validation specific to each controller.
*/
package org.kew.rmf.matchconf.web;
| 1,937 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
MatcherController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/MatcherController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import org.kew.rmf.matchconf.Matcher;
import org.kew.rmf.matchconf.Wire;
import org.springframework.roo.addon.web.mvc.controller.scaffold.RooWebScaffold;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.web.bind.annotation.RequestMapping;
@RequestMapping("/matchers")
@Controller
@RooWebScaffold(path = "matchers", formBackingObject = Matcher.class)
public class MatcherController {
void populateEditForm(Model uiModel, Matcher matcher) {
uiModel.addAttribute("matcher", matcher);
uiModel.addAttribute("matchers", Matcher.findAllMatchers());
uiModel.addAttribute("wires", Wire.findAllWires());
}
}
| 1,483 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ConfigurationController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/ConfigurationController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import org.kew.rmf.matchconf.Configuration;
import org.springframework.roo.addon.web.mvc.controller.scaffold.RooWebScaffold;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMapping;
@RequestMapping("/configurations")
@Controller
@RooWebScaffold(path = "configurations", formBackingObject = Configuration.class)
public class ConfigurationController {
}
| 1,195 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
CustomMatcherController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/CustomMatcherController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import java.io.UnsupportedEncodingException;
import java.util.List;
import javax.servlet.http.HttpServletRequest;
import javax.validation.Valid;
import org.kew.rmf.matchconf.Configuration;
import org.kew.rmf.matchconf.Matcher;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.validation.BindingResult;
import org.springframework.validation.ObjectError;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.util.UriUtils;
import org.springframework.web.util.WebUtils;
@Controller
public class CustomMatcherController {
// GET: matcher creation form for this configuration
@RequestMapping(value="/{configType}_configs/{configName}/matchers", params = "form", produces = "text/html")
public String createForm(@PathVariable("configType") String configType, @PathVariable("configName") String configName, Model uiModel,
@RequestParam(value = "className", required = false) String className,
@RequestParam(value = "packageName", required = false) String packageName) {
Matcher instance = new Matcher();
instance.setPackageName(packageName);
instance.setClassName(className);
populateEditForm(uiModel, configType, configName, instance);
return "config_matchers/create";
}
// POST to create an object and add it to this configuration
@RequestMapping(value="/{configType}_configs/{configName}/matchers", method = RequestMethod.POST, produces = "text/html")
public String create(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @Valid Matcher matcher, BindingResult bindingResult, Model uiModel, HttpServletRequest httpServletRequest) {
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
// assert unique_together:config&name
if (config.getMatcherForName(matcher.getName()) != null) {
bindingResult.addError(new ObjectError("matcher.name", "There is already a Matcher set up for this configuration with this name."));
}
this.customValidation(configName, matcher, bindingResult);
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, configType, configName, matcher);
return "config_matchers/create";
}
uiModel.asMap().clear();
matcher.setConfiguration(config);
matcher.persist();
config.getMatchers().add(matcher);
config.merge();
return "redirect:/{configType}_configs/" + encodeUrlPathSegment(configName, httpServletRequest) + "/matchers/" + encodeUrlPathSegment(matcher.getName(), httpServletRequest);
}
// GET indiviual matcher level
@RequestMapping(value="/{configType}_configs/{configName}/matchers/{matcherName}", produces = "text/html")
public String show(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("matcherName") String matcherName, Model uiModel) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
Matcher matcher = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getMatcherForName(matcherName);
uiModel.addAttribute("matcher", matcher);
uiModel.addAttribute("itemId", matcher.getName());
uiModel.addAttribute("configName", configName);
return "config_matchers/show";
}
// GET list of matchers for this config
@RequestMapping(value="/{configType}_configs/{configName}/matchers", produces = "text/html")
public String list(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @RequestParam(value = "page", required = false) Integer page, @RequestParam(value = "size", required = false) Integer size, Model uiModel) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
List<Matcher> matchers = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getMatchers();
if (page != null || size != null) {
int sizeNo = Math.min(size == null ? 10 : size.intValue(), matchers.size());
final int firstResult = page == null ? 0 : (page.intValue() - 1) * sizeNo;
uiModel.addAttribute("matchers", matchers.subList(firstResult, sizeNo));
float nrOfPages = (float) Matcher.countMatchers() / sizeNo;
uiModel.addAttribute("maxPages", (int) ((nrOfPages > (int) nrOfPages || nrOfPages == 0.0) ? nrOfPages + 1 : nrOfPages));
} else {
uiModel.addAttribute("matchers", matchers);
}
uiModel.addAttribute("configName", configName);
return "config_matchers/list";
}
// GET the update form for a specific matcher
@RequestMapping(value="/{configType}_configs/{configName}/matchers/{matcherName}", params = "form", produces = "text/html")
public String updateForm(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("matcherName") String matcherName, Model uiModel) {
Matcher matcher = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getMatcherForName(matcherName);
populateEditForm(uiModel, configType, configName, matcher);
return "config_matchers/update";
}
// PUT: update a specific matcher
@RequestMapping(value="/{configType}_configs/{configName}/matchers", method = RequestMethod.PUT, produces = "text/html")
public String update(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @Valid Matcher matcher, BindingResult bindingResult, Model uiModel, HttpServletRequest httpServletRequest) {
this.customValidation(configName, matcher, bindingResult);
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, configType, configName, matcher);
return "config_matchers/update";
}
uiModel.asMap().clear();
matcher.setConfiguration(Configuration.findConfigurationsByNameEquals(configName).getSingleResult());
matcher.merge();
return "redirect:/{configType}_configs/" + encodeUrlPathSegment(configName, httpServletRequest) + "/matchers/" + encodeUrlPathSegment(matcher.getName(), httpServletRequest);
}
// DELETE a specific matcher from a collection's list
@RequestMapping(value="/{configType}_configs/{configName}/matchers/{matcherName}", method = RequestMethod.DELETE, produces = "text/html")
public String delete(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("matcherName") String matcherName, @RequestParam(value = "page", required = false) Integer page, @RequestParam(value = "size", required = false) Integer size, Model uiModel) {
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
config.removeMatcher(matcherName);
uiModel.asMap().clear();
uiModel.addAttribute("page", (page == null) ? "1" : page.toString());
uiModel.addAttribute("size", (size == null) ? "10" : size.toString());
return "redirect:/{configType}_configs/" + configName.toString() + "/matchers/";
}
// DELETE by id
@RequestMapping(value="/{configType}_configs/{configName}/matchers/delete-by-id/{id}", method = RequestMethod.DELETE, produces = "text/html")
public String deleteById(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("id") long id, Model uiModel) {
Matcher toDelete = Matcher.findMatcher(id);
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
config.getMatchers().remove(toDelete);
config.merge();
return "redirect:/{configType}_configs/" + configName.toString() + "/matchers/";
}
void populateEditForm(Model uiModel, String configType, String configName, Matcher matcher) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
List<Matcher> matchers = config.getMatchers();
matchers.remove(matcher);
uiModel.addAttribute("matcher", matcher);
uiModel.addAttribute("matchers", matchers);
uiModel.addAttribute("configType", configType);
uiModel.addAttribute("configName", configName);
}
String encodeUrlPathSegment(String pathSegment, HttpServletRequest httpServletRequest) {
String enc = httpServletRequest.getCharacterEncoding();
if (enc == null) {
enc = WebUtils.DEFAULT_CHARACTER_ENCODING;
}
try {
pathSegment = UriUtils.encodePathSegment(pathSegment, enc);
} catch (UnsupportedEncodingException uee) {}
return pathSegment;
}
public void customValidation (String configName, Matcher matcher, BindingResult br) {
if (!FieldValidator.validSlug(matcher.getName())) {
br.addError(new ObjectError("matcher.name", "The name has to be set and can only contain ASCII letters and/or '-' and/or '_'"));
}
}
}
| 10,336 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
FieldValidator.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/FieldValidator.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import org.apache.commons.lang3.StringUtils;
public class FieldValidator {
/**
* We use many strings as part of the REST-ish url structure;
* These only want to contain ASCII letters and/or '-', '_'
* @param s
* @return
*/
public static boolean validSlug(String s) {
return !StringUtils.isBlank(s) && s.matches("[\\w-_]*");
}
}
| 1,163 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
TransformerController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/TransformerController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import org.kew.rmf.matchconf.Transformer;
import org.springframework.roo.addon.web.mvc.controller.scaffold.RooWebScaffold;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.web.bind.annotation.RequestMapping;
@RequestMapping("/transformers")
@Controller
@RooWebScaffold(path = "transformers", formBackingObject = Transformer.class)
public class TransformerController {
void populateEditForm(Model uiModel, Transformer transformer) {
uiModel.addAttribute("transformer", transformer);
uiModel.addAttribute("transformers", Transformer.findAllTransformers());
}
}
| 1,436 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
CustomReporterController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/CustomReporterController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import java.io.UnsupportedEncodingException;
import java.util.List;
import javax.servlet.http.HttpServletRequest;
import javax.validation.Valid;
import org.kew.rmf.matchconf.Configuration;
import org.kew.rmf.matchconf.Reporter;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.validation.BindingResult;
import org.springframework.validation.ObjectError;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.util.UriUtils;
import org.springframework.web.util.WebUtils;
@Controller
public class CustomReporterController {
@RequestMapping(value="/{configType}_configs/{configName}/reporters", params = "form", produces = "text/html")
public String createForm(@PathVariable("configType") String configType, @PathVariable("configName") String configName, Model uiModel,
@RequestParam(value = "className", required = false) String className,
@RequestParam(value = "packageName", required = false) String packageName) {
Reporter instance = new Reporter();
instance.setPackageName(packageName);
instance.setClassName(className);
populateEditForm(uiModel, configType, configName, instance);
return "config_reporters/create";
}
// Default Post
@RequestMapping(value="/{configType}_configs/{configName}/reporters", method = RequestMethod.POST, produces = "text/html")
public String create(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @Valid Reporter reporter, BindingResult bindingResult, Model uiModel, HttpServletRequest httpServletRequest) {
// assert unique_together:config&name
if (Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getReporterForName(reporter.getName()) != null) {
bindingResult.addError(new ObjectError("reporter.name", "There is already a LuceneReporter set up for this configuration with this name."));
}
this.customValidation(configName, reporter, bindingResult);
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, configType, configName, reporter);
return "config_reporters/create";
}
uiModel.asMap().clear();
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
reporter.setConfig(config);
reporter.persist();
config.getReporters().add(reporter);
config.merge();
return String.format("redirect:/%s_configs/", configType) + encodeUrlPathSegment(configName, httpServletRequest) + "/reporters/" + encodeUrlPathSegment(reporter.getName(), httpServletRequest);
}
// default GET indiviual reporter level
@RequestMapping(value="/{configType}_configs/{configName}/reporters/{reporterName}", produces = "text/html")
public String show(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("reporterName") String reporterName, Model uiModel) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
Reporter reporter = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getReporterForName(reporterName);
uiModel.addAttribute("reporter", reporter);
uiModel.addAttribute("itemId", reporter.getName());
uiModel.addAttribute("configName", configName);
uiModel.addAttribute("transformers", reporter.getConfig().getTransformers());
return "config_reporters/show";
}
@RequestMapping(value="/{configType}_configs/{configName}/reporters", produces = "text/html")
public String list(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @RequestParam(value = "page", required = false) Integer page, @RequestParam(value = "size", required = false) Integer size, Model uiModel) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
List<Reporter> reporters = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getReporters();
if (page != null || size != null) {
int sizeNo = Math.min(size == null ? 10 : size.intValue(), reporters.size());
final int firstResult = page == null ? 0 : (page.intValue() - 1) * sizeNo;
uiModel.addAttribute("reporters", reporters.subList(firstResult, sizeNo));
float nrOfPages = (float) reporters.size() / sizeNo;
uiModel.addAttribute("maxPages", (int) ((nrOfPages > (int) nrOfPages || nrOfPages == 0.0) ? nrOfPages + 1 : nrOfPages));
} else {
uiModel.addAttribute("reporters", reporters);
}
uiModel.addAttribute("configName", configName);
return "config_reporters/list";
}
@RequestMapping(value="/{configType}_configs/{configName}/reporters", method = RequestMethod.PUT, produces = "text/html")
public String update(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @Valid Reporter reporter, BindingResult bindingResult, Model uiModel, HttpServletRequest httpServletRequest) {
this.customValidation(configName, reporter, bindingResult);
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, configType, configName, reporter);
return String.format("%s_config_reporters/update", configType);
}
uiModel.asMap().clear();
reporter.setConfig(Configuration.findConfigurationsByNameEquals(configName).getSingleResult());
reporter.merge();
return String.format("redirect:/%s_configs/", configType) + encodeUrlPathSegment(configName, httpServletRequest) + "/reporters/" + encodeUrlPathSegment(reporter.getName(), httpServletRequest);
}
@RequestMapping(value="/{configType}_configs/{configName}/reporters/{reporterName}", params = "form", produces = "text/html")
public String updateForm(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("reporterName") String reporterName, Model uiModel) {
Reporter reporter = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getReporterForName(reporterName);
populateEditForm(uiModel, configType, configName, reporter);
return "config_reporters/update";
}
@RequestMapping(value="/{configType}_configs/{configName}/reporters/{reporterName}", method = RequestMethod.DELETE, produces = "text/html")
public String delete(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("reporterName") String reporterName, @RequestParam(value = "page", required = false) Integer page, @RequestParam(value = "size", required = false) Integer size, Model uiModel) {
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
config.removeReporter(reporterName);
uiModel.asMap().clear();
uiModel.addAttribute("page", (page == null) ? "1" : page.toString());
uiModel.addAttribute("size", (size == null) ? "10" : size.toString());
return String.format("redirect:/%s_configs/%s/reporters/", configType, configName.toString());
}
// DELETE by id
@RequestMapping(value="/{configType}_configs/{configName}/reporters/delete-by-id/{id}", method = RequestMethod.DELETE, produces = "text/html")
public String deleteById(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("id") long id, Model uiModel) {
Reporter toDelete = Reporter.findReporter(id);
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
config.getReporters().remove(toDelete);
config.merge();
return "redirect:/{configType}_configs/" + configName.toString() + "/reporters/";
}
void populateEditForm(Model uiModel, String configType, String configName, Reporter reporter) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
uiModel.addAttribute("reporter", reporter);
uiModel.addAttribute("configName", configName);
uiModel.addAttribute("configType", configType);
}
String encodeUrlPathSegment(String pathSegment, HttpServletRequest httpServletRequest) {
String enc = httpServletRequest.getCharacterEncoding();
if (enc == null) {
enc = WebUtils.DEFAULT_CHARACTER_ENCODING;
}
try {
pathSegment = UriUtils.encodePathSegment(pathSegment, enc);
} catch (UnsupportedEncodingException uee) {}
return pathSegment;
}
public void customValidation (String configName, Reporter reporter, BindingResult br) {
if (!FieldValidator.validSlug(reporter.getName())) {
br.addError(new ObjectError("reporter.name", "The name has to be set and can only contain ASCII letters and/or '-' and/or '_'"));
}
}
}
| 10,105 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
CustomWiredTransformerController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/CustomWiredTransformerController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import java.io.UnsupportedEncodingException;
import java.util.HashSet;
import java.util.List;
import javax.servlet.http.HttpServletRequest;
import javax.validation.Valid;
import org.kew.rmf.matchconf.Configuration;
import org.kew.rmf.matchconf.Wire;
import org.kew.rmf.matchconf.WiredTransformer;
import org.kew.rmf.matchconf.utils.GetterSetter;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.validation.BindingResult;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.util.UriUtils;
import org.springframework.web.util.WebUtils;
@Controller
public class CustomWiredTransformerController {
@SuppressWarnings("serial")
private final static HashSet<String> T_TYPES = new HashSet<String>() {{add("query"); add("authority");}};
@RequestMapping(value="/{configType}_configs/{configName}/wires/{wireName}/{transformerType}_transformers", method = RequestMethod.POST, produces = "text/html")
public String create(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("wireName") String wireName, @PathVariable("transformerType") String transformerType, @Valid WiredTransformer wiredTransformer, BindingResult bindingResult, Model uiModel, HttpServletRequest httpServletRequest) throws Exception {
if (!T_TYPES.contains(transformerType)) throw new Exception(String.format("The transformer type has to be of %s", T_TYPES));
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, configType, configName, wiredTransformer);
return "wiredtransformers/create";
}
uiModel.asMap().clear();
wiredTransformer.persist();
Wire wire = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getWireForName(wireName);
new GetterSetter<List<WiredTransformer>>().getattr(wire, transformerType + "Transformers").add(wiredTransformer);
wire.merge();
return String.format("redirect:/%s_configs/%s/wires/%s/%s_transformers/%s", configType, configName, wireName, transformerType, wiredTransformer.getName());
}
@RequestMapping(value="/{configType}_configs/{configName}/wires/{wireName}/{transformerType}_transformers", params = "form", produces = "text/html")
public String createForm(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("wireName") String wireName, @PathVariable("transformerType") String transformerType, Model uiModel) throws Exception {
if (!T_TYPES.contains(transformerType)) throw new Exception(String.format("The transformer type has to be of %s", T_TYPES));
WiredTransformer instance = new WiredTransformer();
populateEditForm(uiModel, configType, configName, instance);
return "wired_transformers/create";
}
@RequestMapping(value = "/{configType}_configs/{configName}/wires/{wireName}/{transformerType}_transformers/{wiredTransformerName}", produces = "text/html")
public String show(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("wireName") String wireName, @PathVariable("transformerType") String transformerType, @PathVariable("wiredTransformerName") String wiredTransformerName, Model uiModel) throws Exception {
if (!T_TYPES.contains(transformerType)) throw new Exception(String.format("The transformer type has to be of %s", T_TYPES));
Wire wire = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getWireForName(wireName);
WiredTransformer wTransformer = wire.getWiredTransformer(transformerType, wiredTransformerName);
uiModel.addAttribute("wiredTransformer", wTransformer);
uiModel.addAttribute("transformerType", transformerType);
uiModel.addAttribute("itemId", wiredTransformerName);
return "wired_transformers/show";
}
@RequestMapping(value = "/{configType}_configs/{configName}/wires/{wireName}/{transformerType}_transformers", produces = "text/html")
public String list(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("wireName") String wireName, @PathVariable("transformerType") String transformerType, @RequestParam(value = "page", required = false) Integer page, @RequestParam(value = "size", required = false) Integer size, Model uiModel) throws Exception {
Wire wire = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getWireForName(wireName);
List<WiredTransformer> wTransformers = new GetterSetter<List<WiredTransformer>>().getattr(wire, transformerType + "Transformers");
uiModel.addAttribute("transformerType", transformerType);
if (page != null || size != null) {
int sizeNo = size == null ? 10 : size.intValue();
final int firstResult = page == null ? 0 : (page.intValue() - 1) * sizeNo;
uiModel.addAttribute("wiredTransformers", wTransformers.subList(firstResult, Math.min(firstResult + sizeNo, wTransformers.size())));
float nrOfPages = (float) wTransformers.size() / sizeNo;
uiModel.addAttribute("maxPages", (int) ((nrOfPages > (int) nrOfPages || nrOfPages == 0.0) ? nrOfPages + 1 : nrOfPages));
} else {
uiModel.addAttribute("wiredTransformers", wTransformers);
}
return "wired_transformers/list";
}
@RequestMapping(value = "/{configType}_configs/{configName}/wires/{wireName}/{transformerType}_transformers", method = RequestMethod.PUT, produces = "text/html")
public String update(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("wireName") String wireName, @PathVariable("transformerType") String transformerType, @Valid WiredTransformer wiredTransformer, BindingResult bindingResult, Model uiModel, HttpServletRequest httpServletRequest) {
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, configType, configName, wiredTransformer);
return "wired_transformers/update";
}
uiModel.asMap().clear();
wiredTransformer.merge();
return String.format("redirect:/%s_configs/%s/wires/%s/%s_transformers/%s", configType, configName, wireName, transformerType, wiredTransformer.getName());
}
@RequestMapping(value = "/{configType}_configs/{configName}/wires/{wireName}/{transformerType}_transformers/{wiredTransformerName}", params = "form", produces = "text/html")
public String updateForm(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("wireName") String wireName, @PathVariable("transformerType") String transformerType, @PathVariable("wiredTransformerName") String wiredTransformerName, Model uiModel) throws Exception {
Wire wire = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getWireForName(wireName);
populateEditForm(uiModel, configType, configName, wire.getWiredTransformer(transformerType, wiredTransformerName));
return "wired_transformers/update";
}
@RequestMapping(value = "/{configType}_configs/{configName}/wires/{wireName}/{transformerType}_transformers/{wiredTransformerName}", method = RequestMethod.DELETE, produces = "text/html")
public String delete(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("wireName") String wireName, @PathVariable("transformerType") String transformerType, @PathVariable("wiredTransformerName") String wiredTransformerName, @RequestParam(value = "page", required = false) Integer page, @RequestParam(value = "size", required = false) Integer size, Model uiModel) throws Exception {
Wire wire = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getWireForName(wireName);
WiredTransformer wiredTransformer = wire.getWiredTransformer(transformerType, wiredTransformerName);
new GetterSetter<List<WiredTransformer>>().getattr(wire, transformerType + "Transformers").remove(wiredTransformer);
wire.merge();
uiModel.asMap().clear();
uiModel.addAttribute("page", (page == null) ? "1" : page.toString());
uiModel.addAttribute("size", (size == null) ? "10" : size.toString());
return String.format("redirect:/%s_configs/%s/wires/%s/%s_transformers", configType, configName, wireName, transformerType);
}
void populateEditForm(Model uiModel, String configType, String configName, WiredTransformer wTransformer) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
uiModel.addAttribute("wiredTransformer", wTransformer);
uiModel.addAttribute("transformers", Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getTransformers());
uiModel.addAttribute("configName", configName);
uiModel.addAttribute("configType", configType);
}
String encodeUrlPathSegment(String pathSegment, HttpServletRequest httpServletRequest) {
String enc = httpServletRequest.getCharacterEncoding();
if (enc == null) {
enc = WebUtils.DEFAULT_CHARACTER_ENCODING;
}
try {
pathSegment = UriUtils.encodePathSegment(pathSegment, enc);
} catch (UnsupportedEncodingException uee) {}
return pathSegment;
}
}
| 10,503 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
WireController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/WireController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import org.kew.rmf.matchconf.Wire;
import org.springframework.roo.addon.web.mvc.controller.scaffold.RooWebScaffold;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMapping;
@RequestMapping("/wires")
@Controller
@RooWebScaffold(path = "wires", formBackingObject = Wire.class)
public class WireController {
}
| 1,150 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
CustomWireController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/CustomWireController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import java.io.UnsupportedEncodingException;
import java.util.List;
import javax.servlet.http.HttpServletRequest;
import javax.validation.Valid;
import org.kew.rmf.matchconf.Configuration;
import org.kew.rmf.matchconf.Wire;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.validation.BindingResult;
import org.springframework.validation.ObjectError;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.util.UriUtils;
import org.springframework.web.util.WebUtils;
@Controller
public class CustomWireController {
@RequestMapping(value="/{configType}_configs/{configName}/wires", params = "form", produces = "text/html")
public String createForm(@PathVariable("configType") String configType, @PathVariable("configName") String configName, Model uiModel) {
populateEditForm(uiModel, configName, new Wire());
return String.format("%s_config_wires/create", configType);
}
// Default Post
@RequestMapping(value="/{configType}_configs/{configName}/wires", method = RequestMethod.POST, produces = "text/html")
public String create(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @Valid Wire wire, BindingResult bindingResult, Model uiModel, HttpServletRequest httpServletRequest) {
// assert unique_together:config&name
if (Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getWireForName(wire.getName()) != null) {
bindingResult.addError(new ObjectError("wire.name", "There is already a Wire set up for this configuration with this name."));
}
this.customValidation(configName, wire, bindingResult);
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, configName, wire);
return String.format("%s_config_wires/create", configType);
}
uiModel.asMap().clear();
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
wire.setConfiguration(config);
wire.persist();
config.getWiring().add(wire);
config.merge();
return String.format("redirect:/%s_configs/", configType) + encodeUrlPathSegment(configName, httpServletRequest) + "/wires/" + encodeUrlPathSegment(wire.getName(), httpServletRequest);
}
// default GET indiviual wire level
@RequestMapping(value="/{configType}_configs/{configName}/wires/{wireName}", produces = "text/html")
public String show(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("wireName") String wireName, Model uiModel) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
Wire wire = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getWireForName(wireName);
uiModel.addAttribute("wire", wire);
uiModel.addAttribute("itemId", wire.getName());
uiModel.addAttribute("configName", configName);
uiModel.addAttribute("transformers", wire.getConfiguration().getTransformers());
return String.format("%s_config_wires/show", configType);
}
@RequestMapping(value="/{configType}_configs/{configName}/wires", produces = "text/html")
public String list(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @RequestParam(value = "page", required = false) Integer page, @RequestParam(value = "size", required = false) Integer size, Model uiModel) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
List<Wire> wires = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getWiring();
if (page != null || size != null) {
int sizeNo = Math.min(size == null ? 10 : size.intValue(), wires.size());
final int firstResult = page == null ? 0 : (page.intValue() - 1) * sizeNo;
uiModel.addAttribute("wires", wires.subList(firstResult, sizeNo));
float nrOfPages = (float) wires.size() / sizeNo;
uiModel.addAttribute("maxPages", (int) ((nrOfPages > (int) nrOfPages || nrOfPages == 0.0) ? nrOfPages + 1 : nrOfPages));
} else {
uiModel.addAttribute("wires", wires);
}
uiModel.addAttribute("configName", configName);
return String.format("%s_config_wires/list", ConfigSwitch.getTypeForUrl(configName));
}
@RequestMapping(value="/{configType}_configs/{configName}/wires", method = RequestMethod.PUT, produces = "text/html")
public String update(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @Valid Wire wire, BindingResult bindingResult, Model uiModel, HttpServletRequest httpServletRequest) {
this.customValidation(configName, wire, bindingResult);
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, configName, wire);
return String.format("%s_config_wires/update", configType);
}
uiModel.asMap().clear();
wire.setConfiguration(Configuration.findConfigurationsByNameEquals(configName).getSingleResult());
wire.merge();
return String.format("redirect:/%s_configs/", configType) + encodeUrlPathSegment(configName, httpServletRequest) + "/wires/" + encodeUrlPathSegment(wire.getName(), httpServletRequest);
}
@RequestMapping(value="/{configType}_configs/{configName}/wires/{wireName}", params = "form", produces = "text/html")
public String updateForm(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("wireName") String wireName, Model uiModel) {
Wire wire = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getWireForName(wireName);
populateEditForm(uiModel, configName, wire);
return String.format("%s_config_wires/update", configType);
}
@RequestMapping(value="/{configType}_configs/{configName}/wires/{wireName}", method = RequestMethod.DELETE, produces = "text/html")
public String delete(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("wireName") String wireName, @RequestParam(value = "page", required = false) Integer page, @RequestParam(value = "size", required = false) Integer size, Model uiModel) {
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
config.removeWire(wireName);
uiModel.asMap().clear();
uiModel.addAttribute("page", (page == null) ? "1" : page.toString());
uiModel.addAttribute("size", (size == null) ? "10" : size.toString());
return String.format("redirect:/%s_configs/%s/wires/", configType, configName.toString());
}
// DELETE by id
@RequestMapping(value="/{configType}_configs/{configName}/wires/delete-by-id/{id}", method = RequestMethod.DELETE, produces = "text/html")
public String deleteById(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("id") long id, Model uiModel) {
Wire toDelete = Wire.findWire(id);
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
config.getWiring().remove(toDelete);
config.merge();
return "redirect:/{configType}_configs/" + configName.toString() + "/wires/";
}
void populateEditForm(Model uiModel, String configName, Wire wire) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
uiModel.addAttribute("wire", wire);
uiModel.addAttribute("configName", configName);
uiModel.addAttribute("matchers", config.getMatchers());
uiModel.addAttribute("queryTransformers", wire.getQueryTransformers());
uiModel.addAttribute("authorityTransformers", wire.getAuthorityTransformers());
}
String encodeUrlPathSegment(String pathSegment, HttpServletRequest httpServletRequest) {
String enc = httpServletRequest.getCharacterEncoding();
if (enc == null) {
enc = WebUtils.DEFAULT_CHARACTER_ENCODING;
}
try {
pathSegment = UriUtils.encodePathSegment(pathSegment, enc);
} catch (UnsupportedEncodingException uee) {}
return pathSegment;
}
public void customValidation (String configName, Wire wire, BindingResult br) {
if (!FieldValidator.validSlug(wire.getName())) {
br.addError(new ObjectError("wire.name", "The name can only contain ASCII letters and/or '-' and/or '_'"));
}
}
}
| 9,820 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
CustomTransformerController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/CustomTransformerController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import java.io.UnsupportedEncodingException;
import java.util.List;
import javax.servlet.http.HttpServletRequest;
import javax.validation.Valid;
import org.kew.rmf.matchconf.Configuration;
import org.kew.rmf.matchconf.Transformer;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.validation.BindingResult;
import org.springframework.validation.ObjectError;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.util.UriUtils;
import org.springframework.web.util.WebUtils;
@Controller
public class CustomTransformerController {
// GET: transformer creation form for this configuration
@RequestMapping(value="/{configType}_configs/{configName}/transformers", params = "form", produces = "text/html")
public String createForm(@PathVariable("configType") String configType, @PathVariable("configName") String configName, Model uiModel,
@RequestParam(value = "className", required = false) String className,
@RequestParam(value = "packageName", required = false) String packageName) {
Transformer instance = new Transformer();
instance.setPackageName(packageName);
instance.setClassName(className);
populateEditForm(uiModel, configType, configName, instance);
return "config_transformers/create";
}
// POST to create an object and add it to this configuration
@RequestMapping(value="/{configType}_configs/{configName}/transformers", method = RequestMethod.POST, produces = "text/html")
public String create(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @Valid Transformer transformer, BindingResult bindingResult, Model uiModel, HttpServletRequest httpServletRequest) {
// assert unique_together:config&name
if (Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getTransformerForName(transformer.getName()) != null) {
bindingResult.addError(new ObjectError("transformer.name", "There is already a Transformer set up for this configuration with this name."));
}
this.customValidation(configName, transformer, bindingResult);
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, configType, configName, transformer);
return "config_transformers/create";
}
uiModel.asMap().clear();
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
transformer.setConfiguration(config);
transformer.persist();
config.getTransformers().add(transformer);
config.merge();
return "redirect:/{configType}_configs/" + encodeUrlPathSegment(configName, httpServletRequest) + "/transformers/" + encodeUrlPathSegment(transformer.getName(), httpServletRequest);
}
// GET indiviual transformer level
@RequestMapping(value="/{configType}_configs/{configName}/transformers/{transformerName}", produces = "text/html")
public String show(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("transformerName") String transformerName, Model uiModel) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
Transformer transformer = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getTransformerForName(transformerName);
uiModel.addAttribute("transformer", transformer);
uiModel.addAttribute("itemId", transformer.getName());
uiModel.addAttribute("configName", configName);
return "config_transformers/show";
}
// GET list of transformers for this config
@RequestMapping(value="/{configType}_configs/{configName}/transformers", produces = "text/html")
public String list(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @RequestParam(value = "page", required = false) Integer page, @RequestParam(value = "size", required = false) Integer size, Model uiModel) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
List<Transformer> transformers = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getTransformers();
if (page != null || size != null) {
int sizeNo = Math.min(size == null ? 10 : size.intValue(), transformers.size());
final int firstResult = page == null ? 0 : (page.intValue() - 1) * sizeNo;
uiModel.addAttribute("transformers", transformers.subList(firstResult, sizeNo));
float nrOfPages = (float) Transformer.countTransformers() / sizeNo;
uiModel.addAttribute("maxPages", (int) ((nrOfPages > (int) nrOfPages || nrOfPages == 0.0) ? nrOfPages + 1 : nrOfPages));
} else {
uiModel.addAttribute("transformers", transformers);
}
uiModel.addAttribute("configName", configName);
return "config_transformers/list";
}
// GET the update form for a specific transformer
@RequestMapping(value="/{configType}_configs/{configName}/transformers/{transformerName}", params = "form", produces = "text/html")
public String updateForm(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("transformerName") String transformerName, Model uiModel) {
Transformer transformer = Configuration.findConfigurationsByNameEquals(configName).getSingleResult().getTransformerForName(transformerName);
populateEditForm(uiModel, configType, configName, transformer);
return "config_transformers/update";
}
// PUT: update a specific transformer
@RequestMapping(value="/{configType}_configs/{configName}/transformers", method = RequestMethod.PUT, produces = "text/html")
public String update(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @Valid Transformer transformer, BindingResult bindingResult, Model uiModel, HttpServletRequest httpServletRequest) {
this.customValidation(configName, transformer, bindingResult);
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, configType, configName, transformer);
return "config_transformers/update";
}
uiModel.asMap().clear();
transformer.setConfiguration(Configuration.findConfigurationsByNameEquals(configName).getSingleResult());
transformer.merge();
return "redirect:/{configType}_configs/" + encodeUrlPathSegment(configName, httpServletRequest) + "/transformers/" + encodeUrlPathSegment(transformer.getName(), httpServletRequest);
}
// DELETE a specific transformer from a collection's list
@RequestMapping(value="/{configType}_configs/{configName}/transformers/{transformerName}", method = RequestMethod.DELETE, produces = "text/html")
public String delete(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("transformerName") String transformerName, @RequestParam(value = "page", required = false) Integer page, @RequestParam(value = "size", required = false) Integer size, Model uiModel) throws Exception {
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
config.removeTransformer(transformerName);
uiModel.asMap().clear();
uiModel.addAttribute("page", (page == null) ? "1" : page.toString());
uiModel.addAttribute("size", (size == null) ? "10" : size.toString());
return "redirect:/{configType}_configs/" + configName.toString() + "/transformers/";
}
// DELETE by id
@RequestMapping(value="/{configType}_configs/{configName}/transformers/delete-by-id/{id}", method = RequestMethod.DELETE, produces = "text/html")
public String deleteById(@PathVariable("configType") String configType, @PathVariable("configName") String configName, @PathVariable("id") long id, Model uiModel) {
Transformer toDelete = Transformer.findTransformer(id);
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
config.getTransformers().remove(toDelete);
config.merge();
return "redirect:/{configType}_configs/" + configName.toString() + "/transformers/";
}
void populateEditForm(Model uiModel,String configType, String configName, Transformer transformer) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
uiModel.addAttribute("transformer", transformer);
uiModel.addAttribute("configName", configName);
uiModel.addAttribute("configType", configType);
}
String encodeUrlPathSegment(String pathSegment, HttpServletRequest httpServletRequest) {
String enc = httpServletRequest.getCharacterEncoding();
if (enc == null) {
enc = WebUtils.DEFAULT_CHARACTER_ENCODING;
}
try {
pathSegment = UriUtils.encodePathSegment(pathSegment, enc);
} catch (UnsupportedEncodingException uee) {}
return pathSegment;
}
public void customValidation (String configName, Transformer transformer, BindingResult br) {
if (!FieldValidator.validSlug(transformer.getName())) {
br.addError(new ObjectError("transformer.name", "The name has to be set and can only contain ASCII letters and/or '-' and/or '_'"));
}
}
}
| 10,544 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ConfigSwitch.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/ConfigSwitch.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import java.lang.reflect.InvocationTargetException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.kew.rmf.matchconf.Configuration;
public class ConfigSwitch {
@SuppressWarnings("serial")
static final Map<String,String> TYPE_CLASS_MAP = new HashMap<String,String>() {{
put("match", "MatchConfiguration");
put("dedup", "DeduplicationConfiguration");
}};
@SuppressWarnings("serial")
static final Map<String,String> CLASS_TYPE_MAP = new HashMap<String,String>() {{
put("MatchConfiguration", "match");
put("DeduplicationConfiguration", "dedup");
}};
public static String getTypeForUrl (String configName) {
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
return CLASS_TYPE_MAP.get(config.getClassName());
}
@SuppressWarnings("unchecked")
public static List<Configuration> findConfigEntries (int firstResult, int size, String configType) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, NoSuchMethodException, SecurityException {
String method = "findConfigurationEntries";
if (configType.equals("match")) method = "findMatchConfigEntries";
else if (configType.equals("dedup")) method = "findDedupConfigEntries";
return (List<Configuration>) Configuration.class.getMethod(method, int.class, int.class).invoke(null, firstResult, size);
}
public static long countConfigs(String className) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, NoSuchMethodException, SecurityException {
String method = "countConfigurations";
if (className.equals("match")) method = "countMatchConfigs";
else if (className.equals("dedup")) method = "countDedupConfigs";
return (long) Configuration.class.getMethod(method).invoke(null);
}
@SuppressWarnings("unchecked")
public static List<Configuration> findAllConfigs(String configType) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, NoSuchMethodException, SecurityException {
String method = "findAllConfigurations";
if (configType.equals("match")) method = "findAllMatchConfigs";
else if (configType.equals("dedup")) method = "findAllDedupConfigs";
return (List<Configuration>) Configuration.class.getMethod(method).invoke(null);
}
}
| 3,240 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
CustomConfigController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/CustomConfigController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import java.io.UnsupportedEncodingException;
import java.lang.reflect.InvocationTargetException;
import java.util.List;
import java.util.Map;
import javax.servlet.http.HttpServletRequest;
import javax.validation.Valid;
import org.kew.rmf.matchconf.Configuration;
import org.kew.rmf.matchconf.ConfigurationEngine;
import org.kew.rmf.matchconf.Transformer;
import org.springframework.orm.jpa.JpaSystemException;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.validation.BindingResult;
import org.springframework.validation.ObjectError;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.util.UriUtils;
import org.springframework.web.util.WebUtils;
@Controller
public class CustomConfigController {
// redirect root (/MatchConf) to default GET configs overview
@RequestMapping(value = "/", produces = "text/html")
public String root() {
return "redirect:/dedup_configs";
}
// default GET configs overview
@RequestMapping(value = "/{configType}_configs", produces = "text/html")
public String list(@PathVariable("configType") String configType,
@RequestParam(value = "page", required = false) Integer page,
@RequestParam(value = "size", required = false) Integer size, Model uiModel)
throws IllegalAccessException, IllegalArgumentException, InvocationTargetException, NoSuchMethodException, SecurityException {
List<Configuration> configurations;
if (page != null || size != null) {
int sizeNo = size == null ? 10 : size.intValue();
final int firstResult = page == null ? 0 : (page.intValue() - 1) * sizeNo;
configurations = ConfigSwitch.findConfigEntries(firstResult, sizeNo, configType);
float nrOfPages = (float) ConfigSwitch.countConfigs(configType) / sizeNo;
uiModel.addAttribute("maxPages", (int) ((nrOfPages > (int) nrOfPages || nrOfPages == 0.0) ? nrOfPages + 1 : nrOfPages));
} else {
configurations = ConfigSwitch.findAllConfigs(configType);
}
uiModel.addAttribute("configurations", configurations);
return String.format("%s_configs/list", configType);
}
// Default POST for configs
@RequestMapping(value = "/{configType}_configs", method = RequestMethod.POST, produces = "text/html")
public String create(@PathVariable("configType") String configType,
@Valid Configuration configuration, BindingResult bindingResult,
Model uiModel, HttpServletRequest httpServletRequest) {
configuration.setClassName(ConfigSwitch.TYPE_CLASS_MAP.get(configType));
this.customValidation(configuration, bindingResult);
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, configuration);
return configType + "_configs/create";
}
uiModel.asMap().clear();
configuration.persist();
return String.format("redirect:/%s_configs/", configType) + encodeUrlPathSegment(configuration.getName(), httpServletRequest);
}
@RequestMapping(value = "/{configType}_configs", params = "form", produces = "text/html")
public String create(@PathVariable String configType, Model uiModel) {
populateEditForm(uiModel, new Configuration());
return configType + "_configs/create";
}
// Default GET indiviual config level
@RequestMapping(value = "/{configType}_configs/{configName}", produces = "text/html")
public String show(@PathVariable("configType") String configType, @PathVariable("configName") String configName, Model uiModel) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
uiModel.addAttribute("configuration", config);
uiModel.addAttribute("itemId", config.getName());
return configType + "_configs/show";
}
@RequestMapping(value = "/{configType}_configs", method = RequestMethod.PUT, produces = "text/html")
public String update(@PathVariable String configType, @Valid Configuration configuration, BindingResult bindingResult, Model uiModel, HttpServletRequest httpServletRequest) {
uiModel.addAttribute("availableItems", LibraryScanner.availableItems());
configuration.setClassName(ConfigSwitch.TYPE_CLASS_MAP.get(configType));
this.customValidation(configuration, bindingResult);
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, configuration);
return configType + "_configs/update";
}
uiModel.asMap().clear();
configuration.merge();
return String.format("redirect:/%s_configs/", configType) + encodeUrlPathSegment(configuration.getName(), httpServletRequest);
}
@RequestMapping(value = "/{configType}_configs/{configName}", params = "form", produces = "text/html")
public String updateForm(@PathVariable String configType, @PathVariable("configName") String configName, Model uiModel) {
populateEditForm(uiModel, Configuration.findConfigurationsByNameEquals(configName).getSingleResult());
return configType + "_configs/update";
}
@RequestMapping(value = "/{configType}_configs/{configName}", method = RequestMethod.DELETE, produces = "text/html")
public String delete(@PathVariable String configType, @PathVariable("configName") String configName, @RequestParam(value = "page", required = false) Integer page, @RequestParam(value = "size", required = false) Integer size, Model uiModel) throws Exception {
Configuration configuration = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
try {
for (Transformer t:configuration.getTransformers()) t.removeOrphanedWiredTransformers(); // this is expensive and should go soon
configuration.remove();
} catch (JpaSystemException e) {
// assuming a possibly still exotically ocurring legacy error: a wire
// of a *different* config uses this matcher, hence it would have a
// foreign key into the void and complains so the matcher can't be
// deleted and this config neither..
configuration.fixMatchersForAlienWire();
configuration.getWiring().clear();
configuration.merge();
configuration.removeTransformers();
configuration = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
configuration.remove();
}
uiModel.asMap().clear();
uiModel.addAttribute("page", (page == null) ? "1" : page.toString());
uiModel.addAttribute("size", (size == null) ? "10" : size.toString());
return String.format("redirect:/%s_configs", configType);
}
// DELETE by id
@RequestMapping(value="/{configType}_configs/delete-by-id/{id}", method = RequestMethod.DELETE, produces = "text/html")
public String deleteById(@PathVariable("configType") String configType, @PathVariable("id") long id, Model uiModel) {
Configuration toDelete = Configuration.findConfiguration(id);
toDelete.remove();
return "redirect:/{configType}_configs/";
}
void populateEditForm(Model uiModel, Configuration configuration) {
uiModel.addAttribute("configuration", configuration);
uiModel.addAttribute("configName", configuration.getName());
uiModel.addAttribute("wiring", configuration.getWiring());
uiModel.addAttribute("transformers", configuration.getTransformers());
uiModel.addAttribute("matchers", configuration.getMatchers());
uiModel.addAttribute("reporters", configuration.getReporters());
}
String encodeUrlPathSegment(String pathSegment, HttpServletRequest httpServletRequest) {
String enc = httpServletRequest.getCharacterEncoding();
if (enc == null) {
enc = WebUtils.DEFAULT_CHARACTER_ENCODING;
}
try {
pathSegment = UriUtils.encodePathSegment(pathSegment, enc);
} catch (UnsupportedEncodingException uee) {}
return pathSegment;
}
public void customValidation (Configuration config, BindingResult br) {
// validation for all classes that have their name as part of a REST-ish url
if (!FieldValidator.validSlug(config.getName())) {
br.addError(new ObjectError("config.name", "The name has to be set and can only contain ASCII letters and/or '-' and/or '_'"));
}
// MatchConfig specific: has to specify a authorityFileName
if (config.getClassName().equals("MatchConfiguration") && config.getAuthorityFileName().equals("")) {
br.addError(new ObjectError("configuration.authorityFileName", "A Match Configuration needs to specify an authority File"));
}
}
@RequestMapping(value = "/{configType}_configs/{configName}/clone", produces = "text/html")
public String cloneConfig(@PathVariable("configType") String configType, @PathVariable("configName") String configName, Model model) throws Exception {
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
config.cloneMe();
return String.format("redirect:/%s_configs", configType);
}
@RequestMapping(value = "/{configType}_configs/{configName}/run", produces = "text/html")
public String runConfig(@PathVariable("configType") String configType, @PathVariable("configName") String configName, Model model) throws Exception {
Configuration config = Configuration.findConfigurationsByNameEquals(configName).getSingleResult();
Map<String, List<String>> infoMap = new ConfigurationEngine(config).runConfiguration();
model.addAttribute("engineMessages", infoMap.get("messages"));
model.addAttribute("config", config);
model.addAttribute("exception", infoMap.get("exception"));
model.addAttribute("stackTrace", infoMap.get("stackTrace"));
return "configurations/run/index";
}
}
| 11,230 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ReporterController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/ReporterController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import org.kew.rmf.matchconf.Reporter;
import org.springframework.roo.addon.web.mvc.controller.scaffold.RooWebScaffold;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMapping;
@RequestMapping("/reporters")
@Controller
@RooWebScaffold(path = "reporters", formBackingObject = Reporter.class)
public class ReporterController {
}
| 1,170 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
DictionaryController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/DictionaryController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import java.io.UnsupportedEncodingException;
import javax.servlet.http.HttpServletRequest;
import javax.validation.Valid;
import org.kew.rmf.matchconf.Dictionary;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.validation.BindingResult;
import org.springframework.validation.ObjectError;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.util.UriUtils;
import org.springframework.web.util.WebUtils;
@RequestMapping("/dictionaries")
@Controller
public class DictionaryController {
@RequestMapping(params = "form", produces = "text/html")
public String createForm(Model uiModel) {
populateEditForm(uiModel, new Dictionary());
return "dictionaries/create";
}
@RequestMapping(produces = "text/html")
public String list(@RequestParam(value = "page", required = false) Integer page, @RequestParam(value = "size", required = false) Integer size, Model uiModel) {
if (page != null || size != null) {
int sizeNo = size == null ? 10 : size.intValue();
final int firstResult = page == null ? 0 : (page.intValue() - 1) * sizeNo;
uiModel.addAttribute("dictionaries", Dictionary.findDictionaryEntries(firstResult, sizeNo));
float nrOfPages = (float) Dictionary.countDictionarys() / sizeNo;
uiModel.addAttribute("maxPages", (int) ((nrOfPages > (int) nrOfPages || nrOfPages == 0.0) ? nrOfPages + 1 : nrOfPages));
} else {
uiModel.addAttribute("dictionaries", Dictionary.findAllDictionarys());
}
return "dictionaries/list";
}
void populateEditForm(Model uiModel, Dictionary dictionary) {
uiModel.addAttribute("dictionary", dictionary);
}
String encodeUrlPathSegment(String pathSegment, HttpServletRequest httpServletRequest) {
String enc = httpServletRequest.getCharacterEncoding();
if (enc == null) {
enc = WebUtils.DEFAULT_CHARACTER_ENCODING;
}
try {
pathSegment = UriUtils.encodePathSegment(pathSegment, enc);
} catch (UnsupportedEncodingException uee) {}
return pathSegment;
}
@RequestMapping(value = "/{name}", produces = "text/html")
public String show(@PathVariable("name") String name, Model uiModel) {
uiModel.addAttribute("dictionary", Dictionary.findDictionariesByNameEquals(name).getSingleResult());
uiModel.addAttribute("itemId", name);
return "dictionaries/show";
}
@RequestMapping(method = RequestMethod.POST, produces = "text/html")
public String create(@Valid Dictionary dictionary, BindingResult bindingResult, Model uiModel, HttpServletRequest httpServletRequest) {
this.customValidation(dictionary, bindingResult);
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, dictionary);
return "dictionaries/create";
}
uiModel.asMap().clear();
dictionary.persist();
return "redirect:/dictionaries/" + encodeUrlPathSegment(dictionary.getName(), httpServletRequest);
}
@RequestMapping(method = RequestMethod.PUT, produces = "text/html")
public String update(@Valid Dictionary dictionary, BindingResult bindingResult, Model uiModel, HttpServletRequest httpServletRequest) {
this.customValidation(dictionary, bindingResult);
if (bindingResult.hasErrors()) {
populateEditForm(uiModel, dictionary);
return "dictionaries/update";
}
uiModel.asMap().clear();
dictionary.merge();
return "redirect:/dictionaries/" + encodeUrlPathSegment(dictionary.getName(), httpServletRequest);
}
@RequestMapping(value = "/{name}", params = "form", produces = "text/html")
public String updateForm(@PathVariable("name") String name, Model uiModel) {
populateEditForm(uiModel, Dictionary.findDictionariesByNameEquals(name).getSingleResult());
return "dictionaries/update";
}
@RequestMapping(value = "/{name}", method = RequestMethod.DELETE, produces = "text/html")
public String delete(@PathVariable("name") String name, @RequestParam(value = "page", required = false) Integer page, @RequestParam(value = "size", required = false) Integer size, Model uiModel) {
Dictionary dictionary = Dictionary.findDictionariesByNameEquals(name).getSingleResult();
dictionary.remove();
uiModel.asMap().clear();
uiModel.addAttribute("page", (page == null) ? "1" : page.toString());
uiModel.addAttribute("size", (size == null) ? "10" : size.toString());
return "redirect:/dictionaries";
}
public void customValidation (Dictionary dict, BindingResult br) {
if (!FieldValidator.validSlug(dict.getName())) {
br.addError(new ObjectError("dict.name", "The name has to be set and can only contain ASCII letters and/or '-' and/or '_'"));
}
}
}
| 5,958 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ApplicationConversionServiceFactoryBean.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/matchconf/src/main/java/org/kew/rmf/matchconf/web/ApplicationConversionServiceFactoryBean.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.matchconf.web;
import org.springframework.format.FormatterRegistry;
import org.springframework.format.support.FormattingConversionServiceFactoryBean;
import org.springframework.roo.addon.web.mvc.controller.converter.RooConversionService;
/**
* A central place to register application converters and formatters.
*/
@RooConversionService
public class ApplicationConversionServiceFactoryBean extends FormattingConversionServiceFactoryBean {
@Override
protected void installFormatters(FormatterRegistry registry) {
super.installFormatters(registry);
// Register application converters and formatters
}
}
| 1,384 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ConversionTest.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service-model/src/test/java/org/kew/rmf/refine/domain/ConversionTest.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.refine.domain;
import java.util.ArrayList;
import java.util.List;
import org.codehaus.jackson.map.ObjectMapper;
import org.junit.Assert;
import org.junit.Test;
import org.kew.rmf.refine.domain.metadata.Metadata;
import org.kew.rmf.refine.domain.metadata.MetadataView;
import org.kew.rmf.refine.domain.metadata.Type;
import org.kew.rmf.refine.domain.query.Property;
import org.kew.rmf.refine.domain.query.Query;
import org.kew.rmf.refine.domain.response.QueryResponse;
import org.kew.rmf.refine.domain.response.QueryResult;
public class ConversionTest {
/**
* Show that we can convert to / from JSON and the POJOs used in communication with reconciliation service.
*/
@Test
public void testConversion() {
// We use a Jackson object mapper:
ObjectMapper jsonMapper = new ObjectMapper();
/*
* Create a metadata object and set some values
* Using sample from:
* http://code.google.com/p/google-refine/wiki/ReconciliationServiceApi
* http://standard-reconcile.freebaseapps.com/reconcile?callback=jsonp
*/
Metadata metadata = new Metadata();
metadata.setName("Freebase Reconciliation Service");
metadata.setSchemaSpace("http://rdf.freebase.com/ns/type.object.mid");
metadata.setIdentifierSpace("http://rdf.freebase.com/ns/type.object.id");
MetadataView metadataView = new MetadataView();
metadataView.setUrl("http://www.freebase.com/view{{id}}");
metadata.setView(metadataView);
try {
System.out.println(metadata.toString());
System.out.println(jsonMapper.writeValueAsString(metadata));
}
catch (Exception e){
e.printStackTrace();
Assert.fail(e.getMessage());
}
/*
* Create a query object and set some values:
*/
Query query = new Query();
query.setQuery("Poa annua");
query.setLimit(3);
query.setType("/scientific_name");
query.setType_strict("any");
// Properties are a flexible way to pass more data into the service:
Property property = new Property();
property.setP("author");
property.setV("L.");
List<Property> properties = new ArrayList<Property>();
properties.add(property);
query.setProperties(properties.toArray(new Property[0]));
try {
System.out.println(query.toString());
String json = jsonMapper.writeValueAsString(query);
System.out.println(json);
// Now "round trip" it - i.e. use this JSON to build a new Java object representation:
Query query_roundtripped = jsonMapper.readValue(json, Query.class);
System.out.println(query_roundtripped.toString());
}
catch (Exception e) {
e.printStackTrace();
Assert.fail(e.getMessage());
}
/*
* Create a query response object and set some values:
*/
QueryResponse<QueryResult> queryResponse = new QueryResponse<>();
// A response can contain multiple queryresults
List<QueryResult> queryResults = new ArrayList<QueryResult>();
// Build one queryresult
QueryResult queryResult = new QueryResult();
queryResult.setId("12345");
queryResult.setName("Poa annua");
List<Type> types = new ArrayList<>();
types.add(new Type("/scientific_name", "Scientific name"));
queryResult.setType(types.toArray(new Type[0]));
queryResult.setScore(100);
queryResult.setMatch(true);
// Add to list
queryResults.add(queryResult);
// Set list of queryresults onto response
queryResponse.setResult(queryResults.toArray(new QueryResult[0]));
try {
System.out.println(queryResponse.toString());
String json = jsonMapper.writeValueAsString(queryResponse);
System.out.println(json);
// Now "round trip" it - i.e. use this JSON to build a new Java object representation:
QueryResponse<QueryResult> queryResponse_roundtripped = jsonMapper.readValue(json, QueryResponse.class);
System.out.println(queryResponse_roundtripped.toString());
}
catch (Exception e) {
e.printStackTrace();
Assert.fail(e.getMessage());
}
}
}
| 4,616 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
MetadataView.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service-model/src/main/java/org/kew/rmf/refine/domain/metadata/MetadataView.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.refine.domain.metadata;
public class MetadataView {
private String url;
@Override
public String toString() {
return "MetadataView [url="+url+"]";
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
MetadataView other = (MetadataView) obj;
if (url == null) {
if (other.url != null)
return false;
}
else if (!url.equals(other.url))
return false;
return true;
}
/* • Getters and setters • */
public String getUrl() { return url; }
public void setUrl(String url) { this.url = url; }
} | 1,415 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
MetadataSuggest.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service-model/src/main/java/org/kew/rmf/refine/domain/metadata/MetadataSuggest.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.refine.domain.metadata;
public class MetadataSuggest {
private MetadataSuggestDetails type;
private MetadataSuggestDetails property;
private MetadataSuggestDetails entity;
@Override
public String toString() {
return "MetadataSuggest ["
+ "type=" + type
+ ", property=" + property
+ ", entity=" + entity
+ "]";
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
MetadataSuggest other = (MetadataSuggest) obj;
if (entity == null) {
if (other.entity != null)
return false;
}
else if (!entity.equals(other.entity))
return false;
if (property == null) {
if (other.property != null)
return false;
}
else if (!property.equals(other.property))
return false;
if (type == null) {
if (other.type != null)
return false;
}
else if (!type.equals(other.type))
return false;
return true;
}
/* • Getters and setters • */
public MetadataSuggestDetails getType() { return type; }
public void setType(MetadataSuggestDetails type) { this.type = type; }
public MetadataSuggestDetails getProperty() { return property; }
public void setProperty(MetadataSuggestDetails property) { this.property = property; }
public MetadataSuggestDetails getEntity() { return entity; }
public void setEntity(MetadataSuggestDetails entity) { this.entity = entity; }
} | 2,217 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
MetadataPreview.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service-model/src/main/java/org/kew/rmf/refine/domain/metadata/MetadataPreview.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.refine.domain.metadata;
public class MetadataPreview {
private String url;
private int width;
private int height;
@Override
public String toString() {
return "MetadataPreview ["
+ "url=" + url
+ ", width=" + width
+ ", height=" + height
+ "]";
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
MetadataPreview other = (MetadataPreview) obj;
if (height != other.height)
return false;
if (url == null) {
if (other.url != null)
return false;
}
else if (!url.equals(other.url))
return false;
if (width != other.width)
return false;
return true;
}
/* • Getters and setters • */
public String getUrl() { return url; }
public void setUrl(String url) { this.url = url; }
public int getWidth() { return width; }
public void setWidth(int width) { this.width = width; }
public int getHeight() { return height; }
public void setHeight(int height) { this.height = height; }
} | 1,834 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
Type.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service-model/src/main/java/org/kew/rmf/refine/domain/metadata/Type.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.refine.domain.metadata;
public class Type {
private String id;
private String name;
public Type() {}
public Type(String id, String name) {
setId(id);
setName(name);
}
@Override
public String toString() {
return "Type "+id+" "+name;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Type other = (Type) obj;
if (id == null) {
if (other.id != null) {
return false;
}
}
else if (!id.equals(other.id)) {
return false;
}
if (name == null) {
if (other.name != null) {
return false;
}
}
else if (!name.equals(other.name)) {
return false;
}
return true;
}
/* • Getters and setters • */
public String getId() { return id; }
public void setId(String id) { this.id = id; }
public String getName() { return name; }
public void setName(String name) { this.name = name; }
}
| 1,735 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
Metadata.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service-model/src/main/java/org/kew/rmf/refine/domain/metadata/Metadata.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.refine.domain.metadata;
import java.util.Arrays;
import javax.xml.bind.annotation.XmlRootElement;
/**
* Represents the Metadata class of the OpenRefine Reconciliation Service API.
*
* See https://github.com/OpenRefine/OpenRefine/wiki/Reconciliation-Service-API
*/
@XmlRootElement
public class Metadata {
private String name;
private String identifierSpace;
private String schemaSpace;
private MetadataView view;
private MetadataPreview preview;
private MetadataSuggest suggest;
private Type[] defaultTypes;
@Override
public String toString() {
return "Metadata ["
+ "name=" + name
+ ", identifierSpace=" + identifierSpace
+ ", schemaSpace=" + schemaSpace
+ ", view=" + view
+ ", preview=" + preview
+ ", suggest=" + suggest
+ ", defaultTypes=" + defaultTypes
+ "]";
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Metadata other = (Metadata) obj;
if (!Arrays.equals(defaultTypes, other.defaultTypes))
return false;
if (identifierSpace == null) {
if (other.identifierSpace != null)
return false;
}
else if (!identifierSpace.equals(other.identifierSpace))
return false;
if (name == null) {
if (other.name != null)
return false;
}
else if (!name.equals(other.name))
return false;
if (preview == null) {
if (other.preview != null)
return false;
}
else if (!preview.equals(other.preview))
return false;
if (schemaSpace == null) {
if (other.schemaSpace != null)
return false;
}
else if (!schemaSpace.equals(other.schemaSpace))
return false;
if (suggest == null) {
if (other.suggest != null)
return false;
}
else if (!suggest.equals(other.suggest))
return false;
if (view == null) {
if (other.view != null)
return false;
}
else if (!view.equals(other.view))
return false;
return true;
}
/* • Getters and setters • */
public String getName() { return name; }
public void setName(String name) { this.name = name; }
public String getIdentifierSpace() { return identifierSpace; }
public void setIdentifierSpace(String identifierSpace) { this.identifierSpace = identifierSpace; }
public String getSchemaSpace() { return schemaSpace; }
public void setSchemaSpace(String schemaSpace) { this.schemaSpace = schemaSpace; }
public MetadataView getView() { return view; }
public void setView(MetadataView view) { this.view = view; }
public MetadataPreview getPreview() { return preview; }
public void setPreview(MetadataPreview preview) { this.preview = preview; }
public MetadataSuggest getSuggest() { return suggest; }
public void setSuggest(MetadataSuggest suggest) { this.suggest = suggest; }
public Type[] getDefaultTypes() { return defaultTypes; }
public void setDefaultTypes(Type[] defaultTypes) { this.defaultTypes = defaultTypes; }
}
| 3,711 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
MetadataSuggestDetails.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service-model/src/main/java/org/kew/rmf/refine/domain/metadata/MetadataSuggestDetails.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.refine.domain.metadata;
public class MetadataSuggestDetails {
private String service_url;
private String service_path;
private String flyout_service_url;
private String flyout_service_path;
@Override
public String toString() {
return "MetadataSuggestDetails ["
+ "service_url=" + service_url
+ ", service_path=" + service_path
+ ", flyout_service_url=" + flyout_service_url
+ ", flyout_service_path=" + flyout_service_path
+ "]";
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
MetadataSuggestDetails other = (MetadataSuggestDetails) obj;
if (flyout_service_path == null) {
if (other.flyout_service_path != null)
return false;
}
else if (!flyout_service_path.equals(other.flyout_service_path))
return false;
if (flyout_service_url == null) {
if (other.flyout_service_url != null)
return false;
}
else if (!flyout_service_url.equals(other.flyout_service_url))
return false;
if (service_path == null) {
if (other.service_path != null)
return false;
}
else if (!service_path.equals(other.service_path))
return false;
if (service_url == null) {
if (other.service_url != null)
return false;
}
else if (!service_url.equals(other.service_url))
return false;
return true;
}
/* • Getters and setters • */
public String getService_url() { return service_url; }
public void setService_url(String serviceUrl) { this.service_url = serviceUrl; }
public String getService_path() { return service_path; }
public void setService_path(String servicePath) { this.service_path = servicePath; }
public String getFlyout_service_url() { return flyout_service_url; }
public void setFlyout_service_url(String flyoutServiceUrl) { this.flyout_service_url = flyoutServiceUrl; }
public String getFlyout_service_path() { return flyout_service_path; }
public void setFlyout_service_path(String flyoutServicePath) { this.flyout_service_path = flyoutServicePath; }
} | 2,853 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
Query.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service-model/src/main/java/org/kew/rmf/refine/domain/query/Query.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.refine.domain.query;
import java.util.Arrays;
import javax.xml.bind.annotation.XmlRootElement;
@XmlRootElement
public class Query {
private String query;
private String type;
private Integer limit;
private String type_strict;
private Property[] properties;
@Override
public String toString() {
return "Query [query=" + query + ", type=" + type + ", limit=" + limit
+ ", type_strict=" + type_strict + ", properties="
+ Arrays.toString(properties) + "]";
}
/* • Getters and setters • */
public String getQuery() {
return query;
}
public void setQuery(String query) {
this.query = query;
}
public String getType() {
return type;
}
public void setType(String type) {
this.type = type;
}
public Integer getLimit() {
return limit;
}
public void setLimit(Integer limit) {
this.limit = limit;
}
public String getType_strict() {
return type_strict;
}
public void setType_strict(String type_strict) {
this.type_strict = type_strict;
}
public Property[] getProperties() {
return properties;
}
public void setProperties(Property[] properties) {
this.properties = properties;
}
}
| 1,910 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
Property.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service-model/src/main/java/org/kew/rmf/refine/domain/query/Property.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.refine.domain.query;
import javax.xml.bind.annotation.XmlRootElement;
@XmlRootElement
public class Property {
private String p;
private String pid;
private String v;
@Override
public String toString() {
return "Property [p=" + p + ", pid=" + pid + ", v=" + v + "]";
}
@Override
public boolean equals(Object obj) {
if (this == obj) return true;
if (obj == null) return false;
if (getClass() != obj.getClass()) return false;
Property other = (Property) obj;
if (p == null) {
if (other.p != null) return false;
}
else if (!p.equals(other.p)) return false;
if (pid == null) {
if (other.pid != null) return false;
}
else if (!pid.equals(other.pid)) return false;
if (v == null) {
if (other.v != null) return false;
}
else if (!v.equals(other.v)) return false;
return true;
}
/* • Getters and setters • */
public String getP() {
return p;
}
public void setP(String p) {
this.p = p;
}
public String getPid() {
return pid;
}
public void setPid(String pid) {
this.pid = pid;
}
public String getV() {
return v;
}
public void setV(String v) {
this.v = v;
}
}
| 1,905 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
FlyoutResponse.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service-model/src/main/java/org/kew/rmf/refine/domain/response/FlyoutResponse.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.refine.domain.response;
import javax.xml.bind.annotation.XmlRootElement;
/**
* The flyout response is simply HTML wrapped in JSON.
*/
@XmlRootElement
public class FlyoutResponse {
private String html;
public FlyoutResponse() {}
public FlyoutResponse(String html) {
this.html = html;
}
public String getHtml() {
return html;
}
public void setHtml(String html) {
this.html = html;
}
}
| 1,175 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
QueryResultComparator.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service-model/src/main/java/org/kew/rmf/refine/domain/response/QueryResultComparator.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.refine.domain.response;
import java.util.Comparator;
public class QueryResultComparator implements Comparator<QueryResult>{
@Override
public int compare(QueryResult o1, QueryResult o2) {
return Double.compare(o2.getScore(), o1.getScore());
}
}
| 1,022 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
QueryResult.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service-model/src/main/java/org/kew/rmf/refine/domain/response/QueryResult.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.refine.domain.response;
import java.util.Arrays;
import javax.xml.bind.annotation.XmlRootElement;
import org.kew.rmf.refine.domain.metadata.Type;
@XmlRootElement
public class QueryResult {
private String id;
private String name;
private Type[] type;
private double score;
private boolean match;
@Override
public String toString() {
return "QueryResult [id=" + id + ", name=" + name + ", type="
+ Arrays.toString(type) + ", score=" + score + ", match="
+ match + "]";
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
QueryResult other = (QueryResult) obj;
if (id == null) {
if (other.id != null)
return false;
}
else if (!id.equals(other.id))
return false;
if (match != other.match)
return false;
if (name == null) {
if (other.name != null)
return false;
}
else if (!name.equals(other.name))
return false;
if (Double.doubleToLongBits(score) != Double.doubleToLongBits(other.score))
return false;
if (!Arrays.equals(type, other.type))
return false;
return true;
}
/* • Getters and setters • */
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public Type[] getType() {
return type;
}
public void setType(Type[] type) {
this.type = type;
}
public double getScore() {
return score;
}
public void setScore(double score) {
this.score = score;
}
public boolean isMatch() {
return match;
}
public void setMatch(boolean match) {
this.match = match;
}
}
| 2,506 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
QueryResponse.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service-model/src/main/java/org/kew/rmf/refine/domain/response/QueryResponse.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.refine.domain.response;
import java.util.Arrays;
import javax.xml.bind.annotation.XmlRootElement;
@XmlRootElement
public class QueryResponse<T> {
private T[] result;
@Override
public String toString() {
return "QueryResponse [result=" + Arrays.toString(result) + "]";
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
QueryResponse<?> other = (QueryResponse<?>) obj;
if (!Arrays.equals(result, other.result))
return false;
return true;
}
/* • Getters and setters • */
public T[] getResult() {
return result;
}
public void setResult(T[] result) {
this.result = result;
}
}
| 1,507 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ScientificNameToPropertiesConverterTest.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/test/java/org/kew/rmf/reconciliation/queryextractor/ScientificNameToPropertiesConverterTest.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.queryextractor;
import static java.util.Arrays.asList;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.CoreMatchers.hasItems;
import static org.junit.Assert.assertThat;
import org.junit.Test;
import org.kew.rmf.refine.domain.query.Property;
public class ScientificNameToPropertiesConverterTest {
@Test
public void testExtractProperties() {
QueryStringToPropertiesExtractor extractor = new ScientificNameToPropertiesConverter();
Property expectedEpithet1 = new Property();
Property expectedEpithet2 = new Property();
Property expectedEpithet3 = new Property();
Property expectedBasionymAuthor = new Property();
Property expectedPublishingAuthor = new Property();
expectedEpithet1.setP("epithet_1");
expectedEpithet1.setPid("epithet_1");
expectedEpithet2.setP("epithet_2");
expectedEpithet2.setPid("epithet_2");
expectedEpithet3.setP("epithet_3");
expectedEpithet3.setPid("epithet_3");
expectedBasionymAuthor.setP("basionym_author");
expectedBasionymAuthor.setPid("basionym_author");
expectedPublishingAuthor.setP("publishing_author");
expectedPublishingAuthor.setPid("publishing_author");
// Fagaceae
expectedEpithet1.setV("Fagaceae");
assertThat(asList(extractor.extractProperties("Fagaceae")), hasItems(expectedEpithet1));
assertThat(asList(extractor.extractProperties("Fagaceae")).size(), equalTo(1));
// Fagaceae Juss.
expectedEpithet1.setV("Fagaceae");
expectedPublishingAuthor.setV("Juss.");
assertThat(asList(extractor.extractProperties("Fagaceae Juss.")), hasItems(expectedEpithet1, expectedPublishingAuthor));
assertThat(asList(extractor.extractProperties("Fagaceae Juss.")).size(), equalTo(2));
// Asteraceae subfam. Barnadesioidae K.Bremer & R.K.Jansen
expectedEpithet1.setV("Barnadesioidae");
expectedPublishingAuthor.setV("K.Bremer & R.K.Jansen");
assertThat(asList(extractor.extractProperties("Asteraceae subfam. Barnadesioidae K.Bremer & R.K.Jansen")), hasItems(expectedEpithet1, expectedPublishingAuthor));
assertThat(asList(extractor.extractProperties("Asteraceae subfam. Barnadesioidae K.Bremer & R.K.Jansen")).size(), equalTo(2));
// Barnadesioidae K.Bremer & R.K.Jansen
expectedEpithet1.setV("Barnadesioidae");
expectedPublishingAuthor.setV("K.Bremer & R.K.Jansen");
assertThat(asList(extractor.extractProperties("Barnadesioidae K.Bremer & R.K.Jansen")), hasItems(expectedEpithet1, expectedPublishingAuthor));
assertThat(asList(extractor.extractProperties("Barnadesioidae K.Bremer & R.K.Jansen")).size(), equalTo(2));
// Asteraceae trib. Chaenactideae B.G.Baldwin
expectedEpithet1.setV("Chaenactideae");
expectedPublishingAuthor.setV("B.G.Baldwin");
assertThat(asList(extractor.extractProperties("Asteraceae trib. Chaenactideae B.G.Baldwin")), hasItems(expectedEpithet1, expectedPublishingAuthor));
assertThat(asList(extractor.extractProperties("Asteraceae trib. Chaenactideae B.G.Baldwin")).size(), equalTo(2));
// Asteraceae subtrib. Chaenactidinae Rydb.
expectedEpithet1.setV("Chaenactideae");
expectedPublishingAuthor.setV("B.G.Baldwin");
assertThat(asList(extractor.extractProperties("Chaenactideae B.G.Baldwin")), hasItems(expectedEpithet1, expectedPublishingAuthor));
assertThat(asList(extractor.extractProperties("Chaenactideae B.G.Baldwin")).size(), equalTo(2));
// Asteraceae supersubtrib. Chaenactidodinae C.Jeffrey
expectedEpithet1.setV("Chaenactidodinae");
expectedPublishingAuthor.setV("C.Jeffrey");
assertThat(asList(extractor.extractProperties("Asteraceae supersubtrib. Chaenactidodinae C.Jeffrey")), hasItems(expectedEpithet1, expectedPublishingAuthor));
assertThat(asList(extractor.extractProperties("Asteraceae supersubtrib. Chaenactidodinae C.Jeffrey")).size(), equalTo(2));
// Quercus
expectedEpithet1.setV("Quercus");
assertThat(asList(extractor.extractProperties("Quercus")), hasItems(expectedEpithet1));
assertThat(asList(extractor.extractProperties("Quercus")).size(), equalTo(1));
// Quercus L.
expectedEpithet1.setV("Quercus");
expectedPublishingAuthor.setV("L.");
assertThat(asList(extractor.extractProperties("Quercus L.")), hasItems(expectedEpithet1, expectedPublishingAuthor));
assertThat(asList(extractor.extractProperties("Quercus L.")).size(), equalTo(2));
// Helichrysum sect. Chrysocephalum (Walp.) Benth.
expectedEpithet1.setV("Helichrysum");
expectedEpithet2.setV("Chrysocephalum");
expectedBasionymAuthor.setV("Walp.");
expectedPublishingAuthor.setV("Benth.");
assertThat(asList(extractor.extractProperties("Helichrysum sect. Chrysocephalum (Walp.) Benth.")), hasItems(expectedEpithet1, expectedEpithet2, expectedBasionymAuthor, expectedPublishingAuthor));
assertThat(asList(extractor.extractProperties("Helichrysum sect. Chrysocephalum (Walp.) Benth.")).size(), equalTo(4));
// Quercus alba
expectedEpithet1.setV("Quercus");
expectedEpithet2.setV("alba");
assertThat(asList(extractor.extractProperties("Quercus alba")), hasItems(expectedEpithet1, expectedEpithet2));
assertThat(asList(extractor.extractProperties("Quercus alba")).size(), equalTo(2));
// Quercus alba L.
expectedEpithet1.setV("Quercus");
expectedEpithet2.setV("alba");
expectedPublishingAuthor.setV("L.");
assertThat(asList(extractor.extractProperties("Quercus alba L.")), hasItems(expectedEpithet1, expectedEpithet2, expectedPublishingAuthor));
assertThat(asList(extractor.extractProperties("Quercus alba L.")).size(), equalTo(3));
// Quercus alba f. alba
expectedEpithet1.setV("Quercus");
expectedEpithet2.setV("alba");
expectedEpithet3.setV("alba");
assertThat(asList(extractor.extractProperties("Quercus alba f. alba")), hasItems(expectedEpithet1, expectedEpithet2, expectedEpithet3));
assertThat(asList(extractor.extractProperties("Quercus alba f. alba")).size(), equalTo(3));
// Quercus alba f. viridis Trel.
expectedEpithet1.setV("Quercus");
expectedEpithet2.setV("alba");
expectedEpithet3.setV("viridis");
expectedPublishingAuthor.setV("Trel.");
assertThat(asList(extractor.extractProperties("Quercus alba f. viridis Trel.")), hasItems(expectedEpithet1, expectedEpithet2, expectedEpithet3, expectedPublishingAuthor));
assertThat(asList(extractor.extractProperties("Quercus alba f. viridis Trel.")).size(), equalTo(4));
// Quercus alba f. latiloba (Sarg.) E.J.Palmer & Steyerm.
expectedEpithet1.setV("Quercus");
expectedEpithet2.setV("alba");
expectedEpithet3.setV("latiloba");
expectedBasionymAuthor.setV("Sarg.");
expectedPublishingAuthor.setV("E.J.Palmer & Steyerm.");
assertThat(asList(extractor.extractProperties("Quercus alba f. latiloba (Sarg.) E.J.Palmer & Steyerm.")), hasItems(expectedEpithet1, expectedEpithet2, expectedEpithet3, expectedBasionymAuthor, expectedPublishingAuthor));
assertThat(asList(extractor.extractProperties("Quercus alba f. latiloba (Sarg.) E.J.Palmer & Steyerm.")).size(), equalTo(5));
// Quercus alba L. f. latiloba (Sarg.) E.J.Palmer & Steyerm.
expectedEpithet1.setV("Quercus");
expectedEpithet2.setV("alba");
expectedEpithet3.setV("latiloba");
expectedBasionymAuthor.setV("Sarg.");
expectedPublishingAuthor.setV("E.J.Palmer & Steyerm.");
assertThat(asList(extractor.extractProperties("Quercus alba L. f. latiloba (Sarg.) E.J.Palmer & Steyerm.")), hasItems(expectedEpithet1, expectedEpithet2, expectedEpithet3, expectedBasionymAuthor, expectedPublishingAuthor));
assertThat(asList(extractor.extractProperties("Quercus alba L. f. latiloba (Sarg.) E.J.Palmer & Steyerm.")).size(), equalTo(5));
}
@Test
public void testExtractPropertiesMoreExamples() {
QueryStringToPropertiesExtractor extractor = new ScientificNameToPropertiesConverter();
Property expectedEpithet1 = new Property();
Property expectedEpithet2 = new Property();
Property expectedEpithet3 = new Property();
Property expectedBasionymAuthor = new Property();
Property expectedPublishingAuthor = new Property();
expectedEpithet1.setP("epithet_1");
expectedEpithet1.setPid("epithet_1");
expectedEpithet2.setP("epithet_2");
expectedEpithet2.setPid("epithet_2");
expectedEpithet3.setP("epithet_3");
expectedEpithet3.setPid("epithet_3");
expectedBasionymAuthor.setP("basionym_author");
expectedBasionymAuthor.setPid("basionym_author");
expectedPublishingAuthor.setP("publishing_author");
expectedPublishingAuthor.setPid("publishing_author");
// Fagaceæ — Æ ligature
expectedEpithet1.setV("Fagaceæ");
assertThat(asList(extractor.extractProperties("Fagaceæ")), hasItems(expectedEpithet1));
assertThat(asList(extractor.extractProperties("Fagaceæ")).size(), equalTo(1));
// Quercus alba L. f. latiloba (Sarg.) E.J.Palmer & Steyerm. — spaces are a mess
expectedEpithet1.setV("Quercus");
expectedEpithet2.setV("alba");
expectedEpithet3.setV("latiloba");
expectedBasionymAuthor.setV("Sarg.");
expectedPublishingAuthor.setV("E.J.Palmer & Steyerm.");
assertThat(asList(extractor.extractProperties(" Quercus alba L. f. latiloba (Sarg.) E.J.Palmer & Steyerm. ")), hasItems(expectedEpithet1, expectedEpithet2, expectedEpithet3, expectedBasionymAuthor, expectedPublishingAuthor));
assertThat(asList(extractor.extractProperties(" Quercus alba L. f. latiloba (Sarg.) E.J.Palmer & Steyerm. ")).size(), equalTo(5));
}
}
| 10,088 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
GenusSpeciesInfraspeciesToPropertiesConverterTest.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/test/java/org/kew/rmf/reconciliation/queryextractor/GenusSpeciesInfraspeciesToPropertiesConverterTest.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.queryextractor;
import static java.util.Arrays.asList;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.CoreMatchers.hasItems;
import static org.junit.Assert.assertThat;
import org.junit.Test;
import org.kew.rmf.refine.domain.query.Property;
public class GenusSpeciesInfraspeciesToPropertiesConverterTest {
@Test
public void testExtractProperties() {
QueryStringToPropertiesExtractor extractor = new GenusSpeciesInfraspeciesToPropertiesConverter();
Property expectedGenus = new Property();
Property expectedSpecies = new Property();
Property expectedInfraspecies = new Property();
Property expectedAuthors = new Property();
expectedGenus.setP("genus");
expectedGenus.setPid("genus");
expectedSpecies.setP("species");
expectedSpecies.setPid("species");
expectedInfraspecies.setP("infraspecies");
expectedInfraspecies.setPid("infraspecies");
expectedAuthors.setP("authors");
expectedAuthors.setPid("authors");
// Fagaceae
expectedGenus.setV("Fagaceae");
assertThat(asList(extractor.extractProperties("Fagaceae")), hasItems(expectedGenus));
assertThat(asList(extractor.extractProperties("Fagaceae")).size(), equalTo(1));
// Fagaceae Juss.
expectedGenus.setV("Fagaceae");
expectedAuthors.setV("Juss.");
assertThat(asList(extractor.extractProperties("Fagaceae Juss.")), hasItems(expectedGenus, expectedAuthors));
assertThat(asList(extractor.extractProperties("Fagaceae Juss.")).size(), equalTo(2));
// Asteraceae subfam. Barnadesioidae K.Bremer & R.K.Jansen
//expectedGenus.setV("Barnadesioidae");
//expectedAuthors.setV("K.Bremer & R.K.Jansen");
//assertThat(asList(extractor.extractProperties("Asteraceae subfam. Barnadesioidae K.Bremer & R.K.Jansen")), hasItems(expectedGenus, expectedAuthors));
//assertThat(asList(extractor.extractProperties("Asteraceae subfam. Barnadesioidae K.Bremer & R.K.Jansen")).size(), equalTo(2));
// Barnadesioidae K.Bremer & R.K.Jansen
expectedGenus.setV("Barnadesioidae");
expectedAuthors.setV("K.Bremer & R.K.Jansen");
assertThat(asList(extractor.extractProperties("Barnadesioidae K.Bremer & R.K.Jansen")), hasItems(expectedGenus, expectedAuthors));
assertThat(asList(extractor.extractProperties("Barnadesioidae K.Bremer & R.K.Jansen")).size(), equalTo(2));
// Asteraceae trib. Chaenactideae B.G.Baldwin
//expectedGenus.setV("Chaenactideae");
//expectedAuthors.setV("B.G.Baldwin");
//assertThat(asList(extractor.extractProperties("Asteraceae trib. Chaenactideae B.G.Baldwin")), hasItems(expectedGenus, expectedAuthors));
//assertThat(asList(extractor.extractProperties("Asteraceae trib. Chaenactideae B.G.Baldwin")).size(), equalTo(2));
// Asteraceae subtrib. Chaenactidinae Rydb.
expectedGenus.setV("Chaenactideae");
expectedAuthors.setV("B.G.Baldwin");
assertThat(asList(extractor.extractProperties("Chaenactideae B.G.Baldwin")), hasItems(expectedGenus, expectedAuthors));
assertThat(asList(extractor.extractProperties("Chaenactideae B.G.Baldwin")).size(), equalTo(2));
// Asteraceae supersubtrib. Chaenactidodinae C.Jeffrey
//expectedGenus.setV("Chaenactidodinae");
//expectedAuthors.setV("C.Jeffrey");
//assertThat(asList(extractor.extractProperties("Asteraceae supersubtrib. Chaenactidodinae C.Jeffrey")), hasItems(expectedGenus, expectedAuthors));
//assertThat(asList(extractor.extractProperties("Asteraceae supersubtrib. Chaenactidodinae C.Jeffrey")).size(), equalTo(2));
// Quercus
expectedGenus.setV("Quercus");
assertThat(asList(extractor.extractProperties("Quercus")), hasItems(expectedGenus));
assertThat(asList(extractor.extractProperties("Quercus")).size(), equalTo(1));
// Quercus L.
expectedGenus.setV("Quercus");
expectedAuthors.setV("L.");
assertThat(asList(extractor.extractProperties("Quercus L.")), hasItems(expectedGenus, expectedAuthors));
assertThat(asList(extractor.extractProperties("Quercus L.")).size(), equalTo(2));
// Helichrysum sect. Chrysocephalum (Walp.) Benth.
//expectedGenus.setV("Helichrysum");
//expectedSpecies.setV("Chrysocephalum");
//expectedAuthors.setV("(Walp.) Benth.");
//assertThat(asList(extractor.extractProperties("Helichrysum sect. Chrysocephalum (Walp.) Benth.")), hasItems(expectedGenus, expectedSpecies, expectedAuthors));
//assertThat(asList(extractor.extractProperties("Helichrysum sect. Chrysocephalum (Walp.) Benth.")).size(), equalTo(3));
// Quercus alba
expectedGenus.setV("Quercus");
expectedSpecies.setV("alba");
assertThat(asList(extractor.extractProperties("Quercus alba")), hasItems(expectedGenus, expectedSpecies));
assertThat(asList(extractor.extractProperties("Quercus alba")).size(), equalTo(2));
// Quercus alba L.
expectedGenus.setV("Quercus");
expectedSpecies.setV("alba");
expectedAuthors.setV("L.");
assertThat(asList(extractor.extractProperties("Quercus alba L.")), hasItems(expectedGenus, expectedSpecies, expectedAuthors));
assertThat(asList(extractor.extractProperties("Quercus alba L.")).size(), equalTo(3));
// Quercus alba f. alba
expectedGenus.setV("Quercus");
expectedSpecies.setV("alba");
expectedInfraspecies.setV("alba");
assertThat(asList(extractor.extractProperties("Quercus alba f. alba")), hasItems(expectedGenus, expectedSpecies, expectedInfraspecies));
assertThat(asList(extractor.extractProperties("Quercus alba f. alba")).size(), equalTo(3));
// Quercus alba f. viridis Trel.
expectedGenus.setV("Quercus");
expectedSpecies.setV("alba");
expectedInfraspecies.setV("viridis");
expectedAuthors.setV("Trel.");
assertThat(asList(extractor.extractProperties("Quercus alba f. viridis Trel.")), hasItems(expectedGenus, expectedSpecies, expectedInfraspecies, expectedAuthors));
assertThat(asList(extractor.extractProperties("Quercus alba f. viridis Trel.")).size(), equalTo(4));
// Quercus alba f. latiloba (Sarg.) E.J.Palmer & Steyerm.
expectedGenus.setV("Quercus");
expectedSpecies.setV("alba");
expectedInfraspecies.setV("latiloba");
expectedAuthors.setV("(Sarg.) E.J.Palmer & Steyerm.");
assertThat(asList(extractor.extractProperties("Quercus alba f. latiloba (Sarg.) E.J.Palmer & Steyerm.")), hasItems(expectedGenus, expectedSpecies, expectedInfraspecies, expectedAuthors));
assertThat(asList(extractor.extractProperties("Quercus alba f. latiloba (Sarg.) E.J.Palmer & Steyerm.")).size(), equalTo(4));
// Quercus alba L. f. latiloba (Sarg.) E.J.Palmer & Steyerm.
//expectedGenus.setV("Quercus");
//expectedSpecies.setV("alba");
//expectedInfraspecies.setV("latiloba");
//expectedAuthors.setV("(Sarg.) E.J.Palmer & Steyerm.");
//assertThat(asList(extractor.extractProperties("Quercus alba L. f. latiloba (Sarg.) E.J.Palmer & Steyerm.")), hasItems(expectedGenus, expectedSpecies, expectedInfraspecies, expectedAuthors));
//assertThat(asList(extractor.extractProperties("Quercus alba L. f. latiloba (Sarg.) E.J.Palmer & Steyerm.")).size(), equalTo(4));
// • Less-perfect examples
// Jaffueliobryum arsenei (Thér.) Thér.
// (Multiple spaces.)
expectedGenus.setV("Jaffueliobryum");
expectedSpecies.setV("arsenei");
expectedAuthors.setV("(Thér.) Thér.");
assertThat(asList(extractor.extractProperties("Jaffueliobryum arsenei (Thér.) Thér.")), hasItems(expectedGenus, expectedSpecies, expectedAuthors));
assertThat(asList(extractor.extractProperties("Jaffueliobryum arsenei (Thér.) Thér.")).size(), equalTo(3));
}
}
| 8,197 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
CitationToPropertiesConverterTest.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/test/java/org/kew/rmf/reconciliation/queryextractor/CitationToPropertiesConverterTest.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.queryextractor;
import static java.util.Arrays.asList;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.CoreMatchers.hasItems;
import static org.junit.Assert.assertThat;
import org.junit.Test;
import org.kew.rmf.refine.domain.query.Property;
public class CitationToPropertiesConverterTest {
@Test
public void testExtractProperties() {
QueryStringToPropertiesExtractor extractor = new CitationToPropertiesConverter();
Property expectedPublication = new Property();
Property expectedDate = new Property();
Property expectedAuthors = new Property();
expectedPublication.setP("publication");
expectedPublication.setPid(expectedPublication.getP());
expectedAuthors.setP("authors");
expectedAuthors.setPid(expectedAuthors.getP());
expectedDate.setP("date");
expectedDate.setPid(expectedDate.getP());
// Publication
expectedPublication.setV("Reconciliation Service");
assertThat(asList(extractor.extractProperties("Reconciliation Service")), hasItems(expectedPublication));
assertThat(asList(extractor.extractProperties("Reconciliation Service")).size(), equalTo(1));
// Publication and authors
expectedPublication.setV("Reconciliation Service");
expectedAuthors.setV("Matthew Blissett et. al.");
assertThat(asList(extractor.extractProperties("Reconciliation Service [Matthew Blissett et. al.]")), hasItems(expectedPublication, expectedAuthors));
assertThat(asList(extractor.extractProperties("Reconciliation Service [Matthew Blissett et. al.]")).size(), equalTo(2));
// Publication and date
expectedPublication.setV("Reconciliation Service");
expectedDate.setV("2014");
assertThat(asList(extractor.extractProperties("Reconciliation Service, (2014).")), hasItems(expectedPublication, expectedDate));
assertThat(asList(extractor.extractProperties("Reconciliation Service, (2014).")).size(), equalTo(2));
// All three
expectedPublication.setV("Reconciliation Service");
expectedAuthors.setV("Matthew Blissett et. al.");
expectedDate.setV("2014");
assertThat(asList(extractor.extractProperties("Reconciliation Service [Matthew Blissett et. al.], (2014).")), hasItems(expectedPublication, expectedDate, expectedAuthors));
assertThat(asList(extractor.extractProperties("Reconciliation Service [Matthew Blissett et. al.], (2014).")).size(), equalTo(3));
}
}
| 3,131 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
SpecimenCitationToPropertiesConverterTest.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/test/java/org/kew/rmf/reconciliation/queryextractor/SpecimenCitationToPropertiesConverterTest.java | /*
* Reconciliation and Matching Fram!ework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.queryextractor;
import static java.util.Arrays.asList;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.CoreMatchers.hasItems;
import static org.junit.Assert.assertThat;
import org.junit.Ignore;
import org.junit.Test;
import org.kew.rmf.refine.domain.query.Property;
public class SpecimenCitationToPropertiesConverterTest {
@Test @Ignore
public void testExtractProperties() {
QueryStringToPropertiesExtractor extractor = new SpecimenCitationToPropertiesConverter();
Property expectedCollectorName = new Property();
Property expectedCollectorNumber = new Property();
Property expectedCollectionDate = new Property();
Property expectedLocality = new Property();
Property expectedCountry = new Property();
Property expectedHerbarium = new Property();
expectedCollectorName.setP("collector_name");
expectedCollectorName.setPid("collector_name");
expectedCollectorNumber.setP("collector_number");
expectedCollectorNumber.setPid("collector_number");
expectedCollectionDate.setP("collection_date");
expectedCollectionDate.setPid("collection_date");
expectedLocality.setP("locality");
expectedLocality.setPid("locality");
expectedCountry.setP("country");
expectedCountry.setPid("country");
expectedHerbarium.setP("herbarium");
expectedHerbarium.setPid("herbarium");
// Zambia: c. 3 km west of Kalabo, foot of escarpment at edge of swamp bordering river, fl. 13.xi.1959, Drummond & Cookson 6442 (E; K; LISC; SRGH).
String citation = "Zambia: c. 3 km west of Kalabo, foot of escarpment at edge of swamp bordering river, fl. 13.xi.1959, Drummond & Cookson 6442 (E; K; LISC; SRGH).";
expectedCountry.setV("Zambia");
expectedLocality.setV("c. 3 km west of Kalabo, foot of escarpment at edge of swamp bordering river, fl.");
expectedCollectionDate.setV("13.xi.1959");
expectedCollectorName.setV("Drummond & Cookson");
expectedCollectorNumber.setV("6442");
expectedHerbarium.setV("E; K; LISC; SRGH");
assertThat(asList(extractor.extractProperties(citation)), hasItems(expectedCollectorName, expectedCollectorNumber, expectedCollectionDate, expectedLocality, expectedCountry, expectedHerbarium));
assertThat(asList(extractor.extractProperties(citation)).size(), equalTo(6));
}
}
| 3,045 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ReconciliationResultPropertyFormatterTest.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/test/java/org/kew/rmf/reconciliation/resultformatter/ReconciliationResultPropertyFormatterTest.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.resultformatter;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.junit.Assert.assertThat;
import java.util.Arrays;
import java.util.HashMap;
import org.junit.Test;
import org.kew.rmf.reconciliation.service.resultformatter.ReconciliationResultPropertyFormatter;
public class ReconciliationResultPropertyFormatterTest {
@Test
public void testFormatResult() {
ReconciliationResultPropertyFormatter formatter = new ReconciliationResultPropertyFormatter();
formatter.setFormat("%s * %s : '%s'");
formatter.setProperties(Arrays.asList(new String[]{"x", "a", "f"}));
HashMap<String, String> result = new HashMap<>();
result.put("x", "y");
result.put("a", "b");
result.put("f", "g");
result.put("m", "n");
String formattedResult = formatter.formatResult(result);
assertThat(formattedResult, equalTo("y * b : 'g'"));
}
}
| 1,648 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
WebInterfaceStepdefs.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/test/java/org/kew/rmf/reconciliation/ws/WebInterfaceStepdefs.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.ws;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
import static org.springframework.test.web.servlet.result.MockMvcResultHandlers.*;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
import java.util.List;
import java.util.Map;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.web.WebAppConfiguration;
import org.springframework.test.web.servlet.MockMvc;
import org.springframework.test.web.servlet.result.MockMvcResultMatchers;
import org.springframework.test.web.servlet.setup.MockMvcBuilders;
import org.springframework.web.context.WebApplicationContext;
import cucumber.api.PendingException;
import cucumber.api.java.Before;
import cucumber.api.java.en.Given;
import cucumber.api.java.en.Then;
import cucumber.api.java.en.When;
@WebAppConfiguration
@ContextConfiguration("classpath:/META-INF/spring/cucumber.xml")
public class WebInterfaceStepdefs {
//private static Logger log = LoggerFactory.getLogger(WebInterfaceStepdefs.class);
//private static final String TEXT_HTML_UTF8 = "text/html;charset=UTF-8";
@Autowired
private WebApplicationContext wac;
private MockMvc mockMvc;
//private MvcResult result;
//private Document html;
//private Element propertyTransformers;
//private Element propertyMatcher;
@Before
public void setup() {
mockMvc = MockMvcBuilders.webAppContextSetup(wac)
.build();
// TODO: Temporary fix to allow test configuration to have loaded.
// Once the ReconciliatioService allows querying for this, this should be replaced.
try {
Thread.sleep(2L * 1000L);
}
catch (InterruptedException e) {}
}
@Given("^I am on the about page for \"(.*?)\"$")
public void i_am_on_the_about_page_for(String configName) throws Throwable {
// Call
//result =
mockMvc.perform(get("/about/"+configName)) //.accept(MediaType.TEXT_HTML))
.andDo(print())
.andExpect(status().isOk())
//.andExpect(content().contentType(TEXT_HTML_UTF8))
.andExpect(view().name("about-matcher"))
.andExpect(MockMvcResultMatchers.model().attribute("configName", "generalTest"))
.andReturn();
// Because we are using JSPs it's not possible to check their execution — we need a servlet container to execute them.
//Document html = Jsoup.parse(result.getResponse().getContentAsString());
}
@When("^I look at the detail for the property \"(.*?)\"$")
public void i_look_at_the_detail_for_the_property(String property) throws Throwable {
throw new PendingException("Can't check contents of JSPs without a servlet container to execute them.");
//log.info("Want to select {}", "#"+property+"_transformers");
//propertyTransformers = html.select("#"+property+"_transformers").first();
//propertyMatcher = html.select("#"+property+"_matcher").first();
}
@Then("^the transformers are$")
public void the_transformers_are(List<Map<String,String>> values) throws Throwable {
//for (Element transformer : propertyTransformers.children()) {
// transformer.select("span").first().text().equals("Epithet Transformer");
// transformer.select("span").first().attr("title").equals("org.kew.stuff");
// transformer.select("span").get(1).text().equals("replacement: \"\"");
//}
throw new PendingException();
}
@Then("^the matcher is$")
public void the_matcher_is(List<Map<String,String>> values) throws Throwable {
throw new PendingException();
}
@When("^I type in the atomized name details:$")
public void i_type_in_the_atomized_name_details(Map<String,String> details) throws Throwable {
throw new PendingException();
}
@When("^run the query$")
public void run_the_query() throws Throwable {
throw new PendingException();
}
@Then("^the results are$")
public void the_results_are(Map<String,String> results) throws Throwable {
throw new PendingException();
}
@When("^I type in the unatomized name \"(.*?)\"$")
public void i_type_in_the_unatomized_name(String arg1) throws Throwable {
throw new PendingException();
}
}
| 4,892 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
RunCucumberWsTest.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/test/java/org/kew/rmf/reconciliation/ws/RunCucumberWsTest.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.ws;
import org.junit.runner.RunWith;
import cucumber.api.CucumberOptions;
import cucumber.api.junit.Cucumber;
@RunWith(Cucumber.class)
@CucumberOptions(format = {"pretty", "html:target/site/cukes/ws", "json:target/site/cukes/ws/cucumber.json"}, monochrome = false)
public class RunCucumberWsTest {
}
| 1,089 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
GeneralReconciliationServiceStepdefs.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/test/java/org/kew/rmf/reconciliation/ws/GeneralReconciliationServiceStepdefs.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.ws;
import static org.hamcrest.MatcherAssert.*;
import static org.hamcrest.Matchers.*;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
import java.util.Map;
import org.codehaus.jackson.map.ObjectMapper;
import org.codehaus.jackson.map.annotate.JsonSerialize.Inclusion;
import org.codehaus.jackson.type.TypeReference;
import org.hamcrest.Matchers;
import org.junit.Assert;
import org.kew.rmf.refine.domain.metadata.Metadata;
import org.kew.rmf.refine.domain.query.Query;
import org.kew.rmf.refine.domain.response.QueryResponse;
import org.kew.rmf.refine.domain.response.QueryResult;
import org.skyscreamer.jsonassert.JSONAssert;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.mock.web.MockMultipartFile;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.web.WebAppConfiguration;
import org.springframework.test.web.servlet.MockMvc;
import org.springframework.test.web.servlet.MvcResult;
import org.springframework.test.web.servlet.ResultActions;
import org.springframework.test.web.servlet.request.MockMvcRequestBuilders;
import org.springframework.test.web.servlet.setup.MockMvcBuilders;
import org.springframework.web.context.WebApplicationContext;
import org.springframework.web.servlet.config.annotation.WebMvcConfigurationSupport;
import cucumber.api.PendingException;
import cucumber.api.java.Before;
import cucumber.api.java.en.Then;
import cucumber.api.java.en.When;
@WebAppConfiguration
@ContextConfiguration("classpath:/META-INF/spring/cucumber.xml")
public class GeneralReconciliationServiceStepdefs extends WebMvcConfigurationSupport {
private static Logger log = LoggerFactory.getLogger(GeneralReconciliationServiceStepdefs.class);
private static final String JSON_UTF8_S = "application/json;charset=UTF-8";
private static final MediaType JSON_UTF8 = MediaType.parseMediaType(JSON_UTF8_S);
@Autowired
private WebApplicationContext wac;
private ObjectMapper mapper = new ObjectMapper();
private MockMvc mockMvc;
private String responseJson;
private ResultActions resultActions;
private MvcResult result;
public GeneralReconciliationServiceStepdefs() {
mapper.setSerializationInclusion(Inclusion.NON_NULL);
}
@Before
public void setup() {
mockMvc = MockMvcBuilders.webAppContextSetup(wac).build();
// TODO: Temporary fix to allow test configuration to have loaded.
// Once the ReconciliatioService allows querying for this, this should be replaced.
try {
Thread.sleep(2L * 1000L);
}
catch (InterruptedException e) {}
}
@When("^I query for metadata of the \"(.*?)\" reconciliation service$")
public void i_query_for_metadata_of_the_reconciliation_service(String configName) throws Throwable {
// Call
resultActions = mockMvc.perform(get("/reconcile/"+configName).accept(JSON_UTF8))
// .andExpect(status().isOk())
.andExpect(content().contentType(JSON_UTF8_S));
result = resultActions.andReturn();
if (result.getResponse().getStatus() == HttpStatus.OK.value()) {
responseJson = result.getResponse().getContentAsString();
log.debug("Response as string was {}", responseJson);
}
}
@Then("^I receive an HTTP (\\d+) result\\.$")
public void i_receive_an_HTTP_result(int expectedStatus) throws Throwable {
Assert.assertThat("Expected HTTP Status "+expectedStatus, result.getResponse().getStatus(), Matchers.equalTo(expectedStatus));
}
@Then("^cross-site access is permitted$")
public void cross_site_access_is_permitted() throws Throwable {
resultActions.andExpect(header().string("Access-Control-Allow-Origin", "*"));
}
@Then("^I receive the following metadata response:$")
public void i_receive_the_following_metadata_response(String expectedResponseString) throws Throwable {
Metadata responseMetadata = mapper.readValue(responseJson, Metadata.class);
// Check response
log.info("Received response {}", responseMetadata);
Metadata expectedResponse = new ObjectMapper().readValue(expectedResponseString, Metadata.class);
Assert.assertThat("Metadata response correct", responseMetadata, Matchers.equalTo(expectedResponse));
}
@When("^I make a match query for \"(.*?)\"$")
public void i_make_a_match_query_for(String queryString) throws Throwable {
// Call
resultActions = mockMvc.perform(get("/match/generalTest?"+queryString).accept(JSON_UTF8))
.andExpect(status().isOk())
.andExpect(content().contentType(JSON_UTF8_S));
result = resultActions.andReturn();
responseJson = result.getResponse().getContentAsString();
log.debug("Response as string was {}", responseJson);
}
@Then("^I receive the following match response:$")
public void i_receive_the_following_match_response(String expectedJson) throws Throwable {
JSONAssert.assertEquals(expectedJson, responseJson, true);
}
@When("^I make the reconciliation query:$")
public void i_make_the_reconciliation_query(String queryJson) throws Throwable {
Query query = mapper.readValue(queryJson, Query.class);
log.debug("Query is {}", "/reconcile/generalTest?query="+mapper.writeValueAsString(query));
resultActions = mockMvc.perform(post("/reconcile/generalTest?query={query}", mapper.writeValueAsString(query)).accept(JSON_UTF8))
.andExpect(status().isOk())
.andExpect(content().contentType(JSON_UTF8_S));
result = resultActions.andReturn();
responseJson = result.getResponse().getContentAsString();
log.debug("Response as string was {}", responseJson);
}
@Then("^I receive the following reconciliation response:$")
public void i_receive_the_following_reconciliation_response(String expectedResponseString) throws Throwable {
QueryResponse<QueryResult> actualResponse = mapper.readValue(responseJson, new TypeReference<QueryResponse<QueryResult>>(){});
// Check response
log.info("Received response {}", actualResponse);
QueryResponse<QueryResult> expectedResponse = mapper.readValue(expectedResponseString, new TypeReference<QueryResponse<QueryResult>>(){});
Assert.assertThat("QueryResponse<QueryResult> response correct", actualResponse, Matchers.equalTo(expectedResponse));
}
@When("^I make the reconciliation queries:$")
public void i_make_the_reconciliation_queries(String queriesJson) throws Throwable {
Map<String,Query> queries = mapper.readValue(queriesJson, new TypeReference<Map<String,Query>>() {});
log.debug("Query is {}", "/reconcile/generalTest?queries="+mapper.writeValueAsString(queries));
resultActions = mockMvc.perform(post("/reconcile/generalTest?queries={queries}", mapper.writeValueAsString(queries)).accept(JSON_UTF8))
.andExpect(status().isOk())
.andExpect(content().contentType(JSON_UTF8_S));
result = resultActions.andReturn();
responseJson = result.getResponse().getContentAsString();
log.debug("Response as string was {}", responseJson);
}
@Then("^I receive the following reconciliation multiple response:$")
public void i_receive_the_following_reconciliation_multiple_response(String expectedResponseString) throws Throwable {
Map<String,QueryResponse<QueryResult>> actualResponse = mapper.readValue(responseJson, new TypeReference<Map<String,QueryResponse<QueryResult>>>() {});
// Check response
log.info("Received response {}", actualResponse);
Map<String,QueryResponse<QueryResult>> expectedResponse = mapper.readValue(expectedResponseString, new TypeReference<Map<String,QueryResponse<QueryResult>>>() {});
Assert.assertThat("QueryResponse<QueryResult> multiple response correct", actualResponse, Matchers.equalTo(expectedResponse));
}
@When("^I make the reconciliation suggest query with prefix \"(.*?)\"$")
public void i_make_the_reconciliation_suggest_query_with_prefix(String prefix) throws Throwable {
resultActions = mockMvc.perform(get("/reconcile/generalTest?prefix="+prefix).accept(JSON_UTF8))
.andExpect(status().isOk())
.andExpect(content().contentType(JSON_UTF8_S));
result = resultActions.andReturn();
responseJson = result.getResponse().getContentAsString();
log.debug("Response as string was {}", responseJson);
}
@When("^I make the reconciliation suggest property query with prefix \"(.*?)\"$")
public void i_make_the_reconciliation_suggest_property_query_with_prefix(String prefix) throws Throwable {
resultActions = mockMvc.perform(get("/reconcile/generalTest/suggestProperty?prefix="+prefix).accept(JSON_UTF8))
.andExpect(status().isOk())
.andExpect(content().contentType(JSON_UTF8_S));
result = resultActions.andReturn();
responseJson = result.getResponse().getContentAsString();
log.debug("Response as string was {}", responseJson);
}
@When("^I make the reconciliation suggest type query with prefix \"(.*?)\"$")
public void i_make_the_reconciliation_suggest_type_query_with_prefix(String prefix) throws Throwable {
resultActions = mockMvc.perform(get("/reconcile/generalTest/suggestType?prefix="+prefix).accept(JSON_UTF8))
.andExpect(status().isOk())
.andExpect(content().contentType(JSON_UTF8_S));
result = resultActions.andReturn();
responseJson = result.getResponse().getContentAsString();
log.debug("Response as string was {}", responseJson);
}
@When("^I make a bulk match query with a file containing these rows:$")
public void i_make_a_bulk_match_query_with_a_file_containing_these_rows(String allRows) throws Throwable {
MockMultipartFile multipartFile = new MockMultipartFile("file", allRows.getBytes());
resultActions = mockMvc.perform(MockMvcRequestBuilders.fileUpload("/filematch/generalTest/")
.file(multipartFile)
.param("charset", "UTF-8"))
.andExpect(status().is(200));
result = resultActions.andReturn();
}
@Then("^I receive the following result file:$")
public void i_receive_the_following_result_file(String expectedFile) throws Throwable {
String fileName = result.getResponse().getHeader("X-File-Download");
resultActions = mockMvc.perform(get("/download/"+fileName))
.andExpect(status().is(200));
result = resultActions.andReturn();
String actualFile = result.getResponse().getContentAsString();
log.info("File received is\n{}", actualFile);
String[] expectedFileLines = expectedFile.split("\r?\n|\r");
String[] actualFileLines = actualFile.split("\r?\n|\r");
for (int i=0; i < expectedFileLines.length; i++) {
String expectedLine = expectedFileLines[i];
String actualLine = actualFileLines[i];
try {
log.debug("Expecting line «{}», got «{}»", expectedLine, actualLine);
assertThat(actualLine, is(expectedLine));
}
catch (IndexOutOfBoundsException e) {
throw new IndexOutOfBoundsException(String.format("→ line %s not found in match output.", expectedLine));
}
}
assertThat(actualFileLines.length, is(expectedFileLines.length));
}
@When("^I make the reconciliation suggest flyout request with id \"(.*?)\"$")
public void i_make_the_reconciliation_suggest_flyout_request_with_id(String id) throws Throwable {
throw new PendingException("Not bothering to add WireMock or similar to test something so simple.");
//result = mockMvc.perform(get("/reconcile/generalTest/flyout/"+id).accept(JSON_UTF8))
// .andExpect(status().isOk())
// .andExpect(content().contentType(JSON_UTF8_S))
// .andReturn();
//responseJson = result.getResponse().getContentAsString();
//log.debug("Response as string was {}", responseJson);
}
@Then("^I receive the following flyout response:$")
public void i_receive_the_following_flyout_response(String expectedJson) throws Throwable {
JSONAssert.assertEquals(expectedJson, responseJson, true);
}
}
| 12,593 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
MatchConfigurationTestingStepdefs.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/test/java/org/kew/rmf/reconciliation/configurations/MatchConfigurationTestingStepdefs.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.configurations;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang.StringUtils;
import org.hamcrest.Matchers;
import org.junit.Assert;
import org.kew.rmf.core.configuration.ReconciliationServiceConfiguration;
import org.kew.rmf.core.exception.MatchExecutionException;
import org.kew.rmf.core.exception.TooManyMatchesException;
import org.kew.rmf.core.lucene.LuceneMatcher;
import org.kew.rmf.reconciliation.queryextractor.QueryStringToPropertiesExtractor;
import org.kew.rmf.refine.domain.query.Property;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ConfigurableApplicationContext;
import org.springframework.context.support.GenericXmlApplicationContext;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.web.WebAppConfiguration;
import org.springframework.web.context.support.GenericWebApplicationContext;
import cucumber.api.java.en.Given;
import cucumber.api.java.en.Then;
import cucumber.api.java.en.When;
@WebAppConfiguration
@ContextConfiguration("classpath:/META-INF/spring/cucumber.xml")
public class MatchConfigurationTestingStepdefs {
private final static Logger logger = LoggerFactory.getLogger(MatchConfigurationTestingStepdefs.class);
@Autowired
private GenericWebApplicationContext wac;
LuceneMatcher currentMatcher;
List<Map<String,String>> queryResults;
@Given("^I have loaded the \"(.*?)\" configuration$")
public void i_have_loaded_the_configuration(String fileName) throws Throwable {
currentMatcher = getConfiguration(fileName);
Assert.assertNotNull("Failed to load matcher", currentMatcher);
}
@When("^I query for$")
public void i_query_for(List<Map<String,String>> queries) throws Throwable {
Assert.assertNotNull("No matcher selected", currentMatcher);
// Go through the list of queries one at a time, execute the query, store the result in a new key "result".
queryResults = new ArrayList<>();
for (Map<String,String> testQuery : queries) {
Map<String,String> result = doSingleTestQuery(testQuery);
logger.debug("Query result: {}", result);
queryResults.add(result);
}
}
@When("^I query with only a single string for$")
public void i_query_with_only_a_single_string_for(List<Map<String,String>> singleStringQueries) throws Throwable {
Assert.assertNotNull("No matcher selected", currentMatcher);
// Go through the list of queries one at a time, execute the query, store the result in a new key "result".
queryResults = new ArrayList<>();
for (Map<String,String> testQuery : singleStringQueries) {
Map<String,String> result = doSingleStringTestQuery(testQuery.get("queryId"), testQuery.get("queryString"));
logger.debug("Query result: {}", result);
queryResults.add(result);
}
}
@Then("^the results are$")
public void the_results_are(List<Map<String,String>> expectedResults) throws Throwable {
for (Map<String,String> expectedResult : expectedResults) {
checkResult(expectedResult);
}
}
private void checkResult(Map<String,String> expectedResult) {
String targetId = expectedResult.get("queryId");
Map<String,String> actualResult = null;
for (Map<String,String> result : queryResults) {
if (targetId.equals(result.get("queryId"))) {
actualResult = result;
break;
}
}
Assert.assertNotNull("No result found for query "+targetId, actualResult);
Assert.assertThat("Match results not correct for query "+expectedResult.get("queryId"), actualResult.get("results"), Matchers.equalTo(expectedResult.get("results")));
}
private Map<String,String> doSingleStringTestQuery(String queryId, String query) throws TooManyMatchesException, MatchExecutionException {
ReconciliationServiceConfiguration reconConfig = (ReconciliationServiceConfiguration) currentMatcher.getConfig();
QueryStringToPropertiesExtractor propertiesExtractor = reconConfig.getQueryStringToPropertiesExtractor();
Property[] properties = propertiesExtractor.extractProperties(query);
Map<String, String> suppliedRecord = new HashMap<String, String>();
suppliedRecord.put("queryId", queryId);
for (Property p : properties) {
logger.trace("Setting: {} to {}", p.getPid(), p.getV());
suppliedRecord.put(p.getPid(), p.getV());
}
return doSingleTestQuery(suppliedRecord);
}
private Map<String,String> doSingleTestQuery(Map<String,String> origQuery) throws TooManyMatchesException, MatchExecutionException {
// Copy the map, as Cucumber supplies an UnmodifiableMap
Map<String,String> query = new HashMap<>();
query.putAll(origQuery);
query.put("id", query.get("queryId")); // Means the id can show up in the debug output.
List<Map<String,String>> matches = currentMatcher.getMatches(query);
logger.debug("Found some matches: {}", matches.size());
if (matches.size() < 4) {
logger.debug("Matches for {} are {}", query, matches);
}
// Construct result string (list of ids)
ArrayList<String> matchedIds = new ArrayList<>();
for (Map<String,String> match : matches) {
matchedIds.add(match.get("id"));
}
Collections.sort(matchedIds);
query.put("results", StringUtils.join(matchedIds, " "));
return query;
}
private static final Map<String, LuceneMatcher> matchers = new HashMap<String, LuceneMatcher>();
private LuceneMatcher getConfiguration(String config) throws Throwable {
logger.debug("Considering initialising match controller with configuration {}", config);
// Load up the matchers from the specified files
if (!matchers.containsKey(config)){
String configurationFile = "/META-INF/spring/reconciliation-service/" + config + ".xml";
logger.debug("Loading configuration {} from {}", config, configurationFile);
ConfigurableApplicationContext context = new GenericXmlApplicationContext(configurationFile);
LuceneMatcher matcher = context.getBean("engine", LuceneMatcher.class);
matcher.loadData();
logger.debug("Loaded data for configuration {}", config);
matchers.put(config, matcher);
logger.debug("Stored matcher with name {} from configuration {}", matcher.getConfig().getName(), config);
}
return matchers.get(config);
}
}
| 7,088 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
RunCucumberMatchConfigurationTest.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/test/java/org/kew/rmf/reconciliation/configurations/RunCucumberMatchConfigurationTest.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.configurations;
import org.junit.runner.RunWith;
import cucumber.api.CucumberOptions;
import cucumber.api.junit.Cucumber;
@RunWith(Cucumber.class)
@CucumberOptions(format = {"pretty", "html:target/site/cukes/configurations", "json:target/site/cukes/configurations/cucumber.json"}, monochrome = false)
public class RunCucumberMatchConfigurationTest {
// TODO: These tests, and the configurations they test, do not depend on the webservice and should be refactored into a separate module.
}
| 1,279 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
QueryStringToPropertiesExtractor.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/queryextractor/QueryStringToPropertiesExtractor.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.queryextractor;
import org.kew.rmf.refine.domain.query.Property;
public interface QueryStringToPropertiesExtractor {
public Property[] extractProperties(String queryString);
}
| 965 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
SpecimenCitationToPropertiesConverter.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/queryextractor/SpecimenCitationToPropertiesConverter.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.queryextractor;
import java.util.ArrayList;
import java.util.List;
import org.kew.rmf.refine.domain.query.Property;
import org.perf4j.LoggingStopWatch;
import org.perf4j.slf4j.Slf4JStopWatch;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Converts a specimen citation into a set of properties.
*/
public class SpecimenCitationToPropertiesConverter implements QueryStringToPropertiesExtractor {
private static final Logger logger = LoggerFactory.getLogger(SpecimenCitationToPropertiesConverter.class);
// Zambia: c. 3 km west of Kalabo, foot of escarpment at edge of swamp bordering river, fl. 13.xi.1959, Drummond & Cookson 6442 (E; K; LISC; SRGH).
@Override
public Property[] extractProperties(String queryString) {
// Log the query if it takes more than 250ms.
LoggingStopWatch speedCheck = new Slf4JStopWatch("SpecimenCitationParsing:"+queryString, logger, Slf4JStopWatch.WARN_LEVEL).setTimeThreshold(250);
speedCheck.stop();
return makeProperties(queryString);
}
private Property[] makeProperties(String recordedBy) {
List<org.kew.rmf.refine.domain.query.Property> properties = new ArrayList<>();
if (recordedBy != null) {
org.kew.rmf.refine.domain.query.Property p = new org.kew.rmf.refine.domain.query.Property();
p.setP("recorded_by");
p.setPid("recorded_by");
p.setV(recordedBy);
properties.add(p);
}
return properties.toArray(new Property[properties.size()]);
}
}
| 2,225 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
GenusSpeciesInfraspeciesToPropertiesConverter.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/queryextractor/GenusSpeciesInfraspeciesToPropertiesConverter.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.queryextractor;
import java.util.ArrayList;
import java.util.List;
import org.kew.rmf.refine.domain.query.Property;
public class GenusSpeciesInfraspeciesToPropertiesConverter implements QueryStringToPropertiesExtractor {
@Override
public Property[] extractProperties(String queryString) {
/*
* Example scientific names:
* Fagaceae
* Fagaceae Juss.
* Quercus
* Quercus L.
* Quercus alba
* Quercus alba L.
* Quercus alba f. alba
* Quercus alba f. viridis Trel.
* Quercus alba f. latiloba (Sarg.) E.J.Palmer & Steyerm.
* Quercus alba L. f. latiloba (Sarg.) E.J.Palmer & Steyerm.
*
* For the moment, this is just a very basic implementation to satisfy the requirements of the
* Reconciliation Service "suggest" and "preview" queries.
*/
queryString = queryString.replace(" ", " ");
String[] parts = queryString.split(" ");
String genus = null, species = null, infraspecies = null, authors = null;
// Assume first part is generic epithet
genus = parts[0];
if (parts.length == 1) return makeProperties(genus, species, infraspecies, authors);
// If second part has capital letter or "(", assume rest of name is authors
if (isCapital(parts[1].charAt(0)) || parts[1].charAt(0) == '(') {
authors = joinRest(parts, 1);
}
// Otherwise, assume second part is species
else {
species = parts[1];
if (parts.length == 2) return makeProperties(genus, species, infraspecies, authors);
// If third part has capital letter or "(", assume rest of name is authors
if (isCapital(parts[2].charAt(0)) || parts[2].charAt(0) == '(') {
authors = joinRest(parts, 2);
}
// Otherwise, infraspecific rank (ignore) and infraspecific epithet
else {
// parts[2] is infraspecific rank
if (parts.length == 3) return makeProperties(genus, species, infraspecies, authors);
infraspecies = parts[3]; // bounds check
if (parts.length == 4) return makeProperties(genus, species, infraspecies, authors);
authors = joinRest(parts, 4);
}
}
return makeProperties(genus, species, infraspecies, authors);
}
private boolean isCapital(char letter) {
return letter >= 'A' && letter <= 'Z';
}
/**
* Joins from index'th to last element of array with space.
*
* If index is out of bounds, returns empty string.
*/
private String joinRest(String[] array, int index) {
StringBuilder joined = new StringBuilder();
while (index < array.length) {
if (joined.length() > 0) joined.append(' ');
joined.append(array[index]);
index++;
}
return joined.toString();
}
private Property[] makeProperties(String genus, String species, String infraspecies, String authors) {
List<org.kew.rmf.refine.domain.query.Property> properties = new ArrayList<>();
if (genus != null) {
org.kew.rmf.refine.domain.query.Property p = new org.kew.rmf.refine.domain.query.Property();
p.setP("genus");
p.setPid("genus");
p.setV(genus);
properties.add(p);
}
if (species != null) {
org.kew.rmf.refine.domain.query.Property p = new org.kew.rmf.refine.domain.query.Property();
p.setP("species");
p.setPid("species");
p.setV(species);
properties.add(p);
}
if (infraspecies != null) {
org.kew.rmf.refine.domain.query.Property p = new org.kew.rmf.refine.domain.query.Property();
p.setP("infraspecies");
p.setPid("infraspecies");
p.setV(infraspecies);
properties.add(p);
}
if (authors != null) {
org.kew.rmf.refine.domain.query.Property p = new org.kew.rmf.refine.domain.query.Property();
p.setP("authors");
p.setPid("authors");
p.setV(authors);
properties.add(p);
}
return properties.toArray(new Property[properties.size()]);
}
}
| 4,483 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ScientificNameToPropertiesConverter.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/queryextractor/ScientificNameToPropertiesConverter.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.queryextractor;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Pattern;
import org.gbif.api.model.checklistbank.ParsedName;
import org.gbif.nameparser.NameParser;
import org.gbif.nameparser.UnparsableException;
import org.kew.rmf.refine.domain.query.Property;
import org.kew.rmf.transformers.authors.StripBasionymAuthorTransformer;
import org.kew.rmf.transformers.authors.StripPublishingAuthorTransformer;
import org.perf4j.LoggingStopWatch;
import org.perf4j.slf4j.Slf4JStopWatch;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Converts a scientific name string — of any reasonable rank — into
* a first, second and third epithet, plus authors, using the GBIF {@link NameParser}.
*/
public class ScientificNameToPropertiesConverter implements QueryStringToPropertiesExtractor {
private static final Logger logger = LoggerFactory.getLogger(ScientificNameToPropertiesConverter.class);
private NameParser gbifNameParser = new NameParser();
private StripPublishingAuthorTransformer stripPublishingAuthor = new StripPublishingAuthorTransformer();
private StripBasionymAuthorTransformer stripBasionymAuthors = new StripBasionymAuthorTransformer();
@Override
public Property[] extractProperties(String queryString) {
// Log the query if it takes more than 250ms — there are suggestions the GBIF Name Parser may be slow in some cases.
LoggingStopWatch speedCheck = new Slf4JStopWatch("NameParsing:"+queryString, logger, Slf4JStopWatch.WARN_LEVEL).setTimeThreshold(250);
queryString = stripUnwantedFamilyEpithet(queryString);
try {
String epithet1, epithet2, epithet3, basionymAuthors, publishingAuthors;
ParsedName parsedName = gbifNameParser.parse(queryString);
/*
* May return combinations of genusOrAbove, infraGeneric, infraSpecific, specific.
*/
// genusOrAbove should always be present
epithet1 = parsedName.getGenusOrAbove();
// if infraGeneric is present it's the second epithet and the rank will be infrageneric
if (parsedName.getInfraGeneric() != null) {
epithet2 = parsedName.getInfraGeneric();
epithet3 = null;
}
// otherwise we may have species epithets
else {
epithet2 = parsedName.getSpecificEpithet();
epithet3 = parsedName.getInfraSpecificEpithet();
}
basionymAuthors = parsedName.getBracketAuthorship();
publishingAuthors = parsedName.getAuthorship();
//parsedName.getNomStatus();
//parsedName.getRank();
//parsedName.getRankMarker();
speedCheck.stop();
return makeProperties(epithet1, epithet2, epithet3, basionymAuthors, publishingAuthors);
}
catch (UnparsableException e) {
logger.info("GBIF NameParser couldn't handle «"+queryString+"»", e);
// Have a go at the fallback parsing
return fallbackParsing(queryString);
}
}
private Pattern unwantedFamilyEpithet = Pattern.compile(
"^" +
/*
* ICBN Art 18.1:
* The name of a family is a plural adjective used as a noun; … termination -aceae
*/
"(\\p{L}+aceae" +
/*
* ICBN Art 18.4:
* When a name of a family has been published with an improper Latin termination…
*/
/*
* ICBN Art. 18.5:
* <blockquote>
* The following names, of long usage, are treated as validly published:
* Palmae (Arecaceae; type, Areca L.);
* Gramineae (Poaceae; type, Poa L.);
* Cruciferae (Brassicaceae; type, Brassica L.);
* Leguminosae (Fabaceae; type, Faba Mill. [= Vicia L.]);
* Guttiferae (Clusiaceae; type, Clusia L.);
* Umbelliferae (Apiaceae; type, Apium L.);
* Labiatae (Lamiaceae; type, Lamium L.);
* Compositae (Asteraceae; type, Aster L.).
* When the Papilionaceae (Fabaceae; type, Faba Mill.) are regarded as a family distinct from the remainder of the
* Leguminosae, the name Papilionaceae is conserved against Leguminosae.
* </blockquote>
*/
"|Palmae" +
"|Gramineae" +
"|Cruciferae" +
"|Leguminosae" +
"|Guttiferae" +
"|Umbelliferae" +
"|Labiatae" +
"|Compositae)" +
/*
* Followed by an infrafamilial rank (subfam., supsubtrib. etc)
*/
"\\s+[a-z]+\\.");
/**
* Removes an initial family + infrafamilial rank from a string, so the GBIF name parser
* returns the rest of the name, not just a family.
*/
private String stripUnwantedFamilyEpithet(String s) {
if (s == null) return null;
return unwantedFamilyEpithet.matcher(s).replaceFirst("");
}
/**
* Fallback parsing, in case the GBIF parser fails.
*/
private Property[] fallbackParsing(String queryString) {
/*
* Example scientific names:
* Fagaceae
* Fagaceae Juss.
* Quercus
* Quercus L.
* Quercus alba
* Quercus alba L.
* Quercus alba f. alba
* Quercus alba f. viridis Trel.
* Quercus alba f. latiloba (Sarg.) E.J.Palmer & Steyerm.
* Quercus alba L. f. latiloba (Sarg.) E.J.Palmer & Steyerm.
*
* For the moment, this is just a very basic implementation to satisfy the requirements of the
* Reconciliation Service "suggest" and "preview" queries.
*/
queryString.replace(" ", " ");
String[] parts = queryString.split(" ");
String genus = null, species = null, infraspecies = null, authors = null;
// Assume first part is generic epithet
genus = parts[0];
if (parts.length == 1) return makeProperties(genus, species, infraspecies, authors);
// If second part has capital letter, assume rest of name is authors
if (isCapital(parts[1].charAt(0))) {
authors = joinRest(parts, 1);
}
// Otherwise, assume second part is species
else {
species = parts[1];
if (parts.length == 2) return makeProperties(genus, species, infraspecies, authors);
// If third part has capital letter, assume rest of name is authors
if (isCapital(parts[2].charAt(0))) {
authors = joinRest(parts, 2);
}
// Otherwise, infraspecific rank (ignore) and infraspecific epithet
else {
// parts[2] is infraspecific rank
if (parts.length == 3) return makeProperties(genus, species, infraspecies, authors);
infraspecies = parts[3]; // bounds check
if (parts.length == 4) return makeProperties(genus, species, infraspecies, authors);
authors = joinRest(parts, 4);
}
}
return makeProperties(genus, species, infraspecies, authors);
}
private boolean isCapital(char letter) {
return letter >= 'A' && letter <= 'Z';
}
/**
* Joins from index'th to last element of array with space.
*
* If index is out of bounds, returns empty string.
*/
private String joinRest(String[] array, int index) {
StringBuilder joined = new StringBuilder();
while (index < array.length) {
if (joined.length() > 0) joined.append(' ');
joined.append(array[index]);
index++;
}
return joined.toString();
}
private Property[] makeProperties(String genus, String species, String infraspecies, String authors) {
String basionymAuthors = stripPublishingAuthor.transform(authors);
String publishingAuthors = stripBasionymAuthors.transform(authors);
return makeProperties(genus, species, infraspecies, basionymAuthors, publishingAuthors);
}
private Property[] makeProperties(String genus, String species, String infraspecies, String basionymAuthors, String publishingAuthors) {
List<org.kew.rmf.refine.domain.query.Property> properties = new ArrayList<>();
if (genus != null) {
org.kew.rmf.refine.domain.query.Property p = new org.kew.rmf.refine.domain.query.Property();
p.setP("epithet_1");
p.setPid("epithet_1");
p.setV(genus);
properties.add(p);
}
if (species != null) {
org.kew.rmf.refine.domain.query.Property p = new org.kew.rmf.refine.domain.query.Property();
p.setP("epithet_2");
p.setPid("epithet_2");
p.setV(species);
properties.add(p);
}
if (infraspecies != null) {
org.kew.rmf.refine.domain.query.Property p = new org.kew.rmf.refine.domain.query.Property();
p.setP("epithet_3");
p.setPid("epithet_3");
p.setV(infraspecies);
properties.add(p);
}
if (basionymAuthors != null) {
org.kew.rmf.refine.domain.query.Property p = new org.kew.rmf.refine.domain.query.Property();
p.setP("basionym_author");
p.setPid("basionym_author");
p.setV(basionymAuthors);
properties.add(p);
}
if (publishingAuthors != null) {
org.kew.rmf.refine.domain.query.Property p = new org.kew.rmf.refine.domain.query.Property();
p.setP("publishing_author");
p.setPid("publishing_author");
p.setV(publishingAuthors);
properties.add(p);
}
return properties.toArray(new Property[properties.size()]);
}
}
| 9,325 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
CitationToPropertiesConverter.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/queryextractor/CitationToPropertiesConverter.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.queryextractor;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Pattern;
import org.kew.rmf.refine.domain.query.Property;
import com.google.common.base.Strings;
/**
* Extracts the publication, date and authors from a full reference.
*/
public class CitationToPropertiesConverter implements QueryStringToPropertiesExtractor {
Pattern pattern = Pattern.compile("^([^\\[,(]*)(\\[(.*)\\]|)(, \\((\\d*)\\)|)");
@Override
public Property[] extractProperties(String queryString) {
/*
* Expected format:
* Publication abbreviation [Authors], (YEAR).
*/
queryString.replace(" ", " ");
String publication = null, authors = null, date = null;
if (queryString != null) {
java.util.regex.Matcher m = pattern.matcher(queryString);
if (m.find()) {
publication = m.group(1).trim();
authors = Strings.emptyToNull(m.group(3));
date = Strings.emptyToNull(m.group(5));
}
}
return makeProperties(publication, authors, date);
}
private Property[] makeProperties(String publication, String authors, String date) {
List<org.kew.rmf.refine.domain.query.Property> properties = new ArrayList<>();
if (publication != null) {
org.kew.rmf.refine.domain.query.Property p = new org.kew.rmf.refine.domain.query.Property();
p.setP("publication");
p.setPid("publication");
p.setV(publication);
properties.add(p);
}
if (authors != null) {
org.kew.rmf.refine.domain.query.Property p = new org.kew.rmf.refine.domain.query.Property();
p.setP("authors");
p.setPid("authors");
p.setV(authors);
properties.add(p);
}
if (date != null) {
org.kew.rmf.refine.domain.query.Property p = new org.kew.rmf.refine.domain.query.Property();
p.setP("date");
p.setPid("date");
p.setV(date);
properties.add(p);
}
return properties.toArray(new Property[properties.size()]);
}
}
| 2,657 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
WebAppInitializer.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/config/WebAppInitializer.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.config;
import java.util.Set;
import javax.servlet.ServletContext;
import javax.servlet.ServletRegistration;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.web.WebApplicationInitializer;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.WebApplicationContext;
import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
import org.springframework.web.servlet.DispatcherServlet;
public class WebAppInitializer implements WebApplicationInitializer {
private static Logger log = LoggerFactory.getLogger(WebAppInitializer.class);
@Override
public void onStartup(ServletContext servletContext) {
WebApplicationContext rootContext = createRootContext(servletContext);
configureSpringMvc(servletContext, rootContext);
// Add Perf4J graphing servlet
ServletRegistration.Dynamic servletRegistration = servletContext.addServlet("perf4j", org.perf4j.logback.servlet.GraphingServlet.class);
servletRegistration.setInitParameter("graphNames", "graphOtherTimes,graphQueryTimes,graphQueriesPerSecond");
servletRegistration.addMapping("/perf4j");
}
private WebApplicationContext createRootContext(ServletContext servletContext) {
AnnotationConfigWebApplicationContext rootContext = new AnnotationConfigWebApplicationContext();
rootContext.register(CoreConfig.class);
rootContext.refresh();
servletContext.addListener(new ContextLoaderListener(rootContext));
servletContext.setInitParameter("defaultHtmlEscape", "true");
return rootContext;
}
private void configureSpringMvc(ServletContext servletContext, WebApplicationContext rootContext) {
AnnotationConfigWebApplicationContext mvcContext = new AnnotationConfigWebApplicationContext();
mvcContext.register(MvcConfig.class);
mvcContext.setParent(rootContext);
ServletRegistration.Dynamic appServlet = servletContext.addServlet("reconciliation-service", new DispatcherServlet(mvcContext));
appServlet.setLoadOnStartup(1);
Set<String> mappingConflicts = appServlet.addMapping("/");
if (!mappingConflicts.isEmpty()) {
for (String s : mappingConflicts) {
log.error("Mapping conflict: " + s);
}
throw new IllegalStateException("'webservice' cannot be mapped to '/'");
}
}
}
| 3,078 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
CoreConfig.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/config/CoreConfig.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.config;
import javax.annotation.Resource;
import org.springframework.context.annotation.Configuration;
import org.springframework.core.env.Environment;
@Configuration
//@EnableCaching
public class CoreConfig {
@Resource
private Environment env;
// Doesn't do anything yet. Custom beans can be defined here.
}
| 1,104 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
MvcConfig.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/config/MvcConfig.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.config;
import java.util.Properties;
import org.codehaus.jackson.map.ObjectMapper;
import org.kew.rmf.reconciliation.ws.ReconciliationExceptionResolver;
import org.perf4j.slf4j.aop.TimingAspect;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.EnableAspectJAutoProxy;
import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
import org.springframework.core.io.ClassPathResource;
import org.springframework.core.io.Resource;
import org.springframework.core.task.TaskExecutor;
import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
import org.springframework.ui.context.ThemeSource;
import org.springframework.ui.context.support.ResourceBundleThemeSource;
import org.springframework.web.multipart.MultipartResolver;
import org.springframework.web.multipart.commons.CommonsMultipartResolver;
import org.springframework.web.servlet.ThemeResolver;
import org.springframework.web.servlet.config.annotation.DefaultServletHandlerConfigurer;
import org.springframework.web.servlet.config.annotation.EnableWebMvc;
import org.springframework.web.servlet.config.annotation.InterceptorRegistry;
import org.springframework.web.servlet.config.annotation.ResourceHandlerRegistry;
import org.springframework.web.servlet.config.annotation.WebMvcConfigurerAdapter;
import org.springframework.web.servlet.handler.SimpleMappingExceptionResolver;
import org.springframework.web.servlet.theme.CookieThemeResolver;
import org.springframework.web.servlet.theme.ThemeChangeInterceptor;
import org.springframework.web.servlet.view.UrlBasedViewResolver;
import org.springframework.web.servlet.view.tiles2.TilesConfigurer;
import org.springframework.web.servlet.view.tiles2.TilesView;
@Configuration
@EnableWebMvc
@ComponentScan(basePackageClasses = {
org.kew.rmf.reconciliation.service.ReconciliationService.class,
org.kew.rmf.reconciliation.ws.BaseController.class
})
@EnableAspectJAutoProxy
public class MvcConfig extends WebMvcConfigurerAdapter {
static @Bean public PropertySourcesPlaceholderConfigurer myPropertySourcesPlaceholderConfigurer() {
PropertySourcesPlaceholderConfigurer p = new PropertySourcesPlaceholderConfigurer();
Resource[] resourceLocations = new Resource[] {
new ClassPathResource("/META-INF/spring/reconciliation-service.properties")
};
p.setLocations(resourceLocations);
return p;
}
@Bean
public ObjectMapper jsonMapper() {
return new ObjectMapper();
}
/**
* Increase maximum upload size.
* TODO: Test.
*/
@Bean
public MultipartResolver multipartResolver() {
CommonsMultipartResolver multipartResolver = new CommonsMultipartResolver();
multipartResolver.setMaxUploadSize(100 * 1024 * 1024);
return multipartResolver;
}
/**
* Static resources configuration
*/
@Override
public void addResourceHandlers(ResourceHandlerRegistry registry) {
registry.addResourceHandler("/css/**").addResourceLocations("/css/").setCachePeriod(3600 * 30);
registry.addResourceHandler("/img/**").addResourceLocations("/img/").setCachePeriod(3600 * 30);
registry.addResourceHandler("/js/**").addResourceLocations("/js/").setCachePeriod(3600 * 30);
}
/**
* Default servlet handler for resources
*/
@Override
public void configureDefaultServletHandling(DefaultServletHandlerConfigurer configurer) {
configurer.enable();
}
/**
* Theme source
*/
@Bean
public ThemeSource themeSource() {
ResourceBundleThemeSource themeSource = new ResourceBundleThemeSource();
themeSource.setBasenamePrefix("kew2014-");
return themeSource;
}
/**
* Theme resolver
*/
@Bean
public ThemeResolver themeResolver() {
CookieThemeResolver themeResolver = new CookieThemeResolver();
themeResolver.setDefaultThemeName("default");
return themeResolver;
}
/**
* Theme interceptor (optional, without it the theme won't be changed).
*/
@Override
public void addInterceptors(InterceptorRegistry registry) {
ThemeChangeInterceptor themeChangeInterceptor = new ThemeChangeInterceptor();
themeChangeInterceptor.setParamName("theme");
registry.addInterceptor(themeChangeInterceptor);
}
/**
* Tiles2 views configuration.
*/
@Bean
public TilesConfigurer tilesConfigurer() {
TilesConfigurer tilesConfig = new TilesConfigurer();
tilesConfig.setDefinitions(new String[] {
"/WEB-INF/kew-layouts/layouts.xml",
"/WEB-INF/layouts/layouts.xml",
"/WEB-INF/views/**/views.xml"
});
tilesConfig.setCheckRefresh(true);
return tilesConfig;
}
/**
* ViewResolver configuration for Tiles2-based views.
*/
@Bean
public UrlBasedViewResolver viewResolver() {
UrlBasedViewResolver viewResolver = new UrlBasedViewResolver();
viewResolver.setViewClass(TilesView.class);
viewResolver.setContentType("text/html;charset=UTF-8");
return viewResolver;
}
/**
* TaskExecutor for asynchronous pooled tasks
*/
@Bean
public TaskExecutor taskExecutor() {
ThreadPoolTaskExecutor taskExecutor = new ThreadPoolTaskExecutor();
taskExecutor.setCorePoolSize(2);
taskExecutor.setMaxPoolSize(2);
// Wait up to 30 seconds for the tasks to exit themselves, after receiving an interrupt from the executor.
taskExecutor.setDaemon(true);
taskExecutor.setAwaitTerminationSeconds(30);
taskExecutor.initialize();
return taskExecutor;
}
@Bean
public TimingAspect timingAspect() {
return new TimingAspect();
}
/**
* Generate error pages for unhandled exceptions.
*/
@Bean
public SimpleMappingExceptionResolver simpleMappingExceptionResolver() {
ReconciliationExceptionResolver r = new ReconciliationExceptionResolver();
Properties mappings = new Properties();
mappings.setProperty("UnknownReconciliationServiceException", "404");
r.setExceptionMappings(mappings);
r.setDefaultErrorView("500");
r.setDefaultStatusCode(500);
r.setPreventResponseCaching(true);
r.setWarnLogCategory("org.kew.rmf.reconciliation.error");
return r;
}
}
| 6,834 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ReconciliationService.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/service/ReconciliationService.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.service;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.annotation.PostConstruct;
import org.kew.rmf.core.configuration.MatchConfiguration;
import org.kew.rmf.core.configuration.ReconciliationServiceConfiguration;
import org.kew.rmf.core.exception.MatchExecutionException;
import org.kew.rmf.core.exception.TooManyMatchesException;
import org.kew.rmf.core.lucene.LuceneMatcher;
import org.kew.rmf.reconciliation.exception.ReconciliationServiceException;
import org.kew.rmf.reconciliation.exception.UnknownReconciliationServiceException;
import org.kew.rmf.reconciliation.queryextractor.QueryStringToPropertiesExtractor;
import org.kew.rmf.reconciliation.service.resultformatter.ReconciliationResultFormatter;
import org.kew.rmf.reconciliation.service.resultformatter.ReconciliationResultPropertyFormatter;
import org.kew.rmf.refine.domain.metadata.Metadata;
import org.perf4j.StopWatch;
import org.perf4j.aop.Profiled;
import org.perf4j.slf4j.Slf4JStopWatch;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.ConfigurableApplicationContext;
import org.springframework.context.support.GenericXmlApplicationContext;
import org.springframework.core.io.Resource;
import org.springframework.core.io.support.PathMatchingResourcePatternResolver;
import org.springframework.core.io.support.ResourcePatternResolver;
import org.springframework.core.task.TaskExecutor;
import org.springframework.stereotype.Service;
/**
* The ReconciliationService handles loading and using multiple reconciliation configurations.
*/
@Service
public class ReconciliationService {
private static final Logger logger = LoggerFactory.getLogger(ReconciliationService.class);
private static final Logger timingLogger = LoggerFactory.getLogger("org.kew.rmf.reconciliation.TimingLogger");
private static final String queryTimingLoggerName = "org.kew.rmf.reconciliation.QueryTimingLogger";
@Value("${environment:unknown}")
private String environment;
@Value("#{'${configurations}'.split(',')}")
private List<String> initialConfigurations;
@Autowired
private TaskExecutor taskExecutor;
private final Map<String,ConfigurationStatus> configurationStatuses = new HashMap<String,ConfigurationStatus>();
public enum ConfigurationStatus {
NOT_LOADED, LOADED, LOADING;
}
private final String CONFIG_BASE = "/META-INF/spring/reconciliation-service/";
private final String CONFIG_EXTENSION = ".xml";
private final Map<String, ConfigurableApplicationContext> contexts = new HashMap<String, ConfigurableApplicationContext>();
private final Map<String, LuceneMatcher> matchers = new HashMap<String, LuceneMatcher>();
private final Map<String, Integer> totals = new HashMap<String, Integer>();
/**
* Kicks off tasks (threads) to load the initial configurations.
*/
@PostConstruct
public void init() {
logger.debug("Initialising reconciliation service");
// Load up the matchers from the specified files
if (initialConfigurations != null) {
for (String config : initialConfigurations) {
try {
loadConfigurationInBackground(config + CONFIG_EXTENSION);
}
catch (ReconciliationServiceException e) {
throw new RuntimeException("Error kicking off data load for Reconciliation Service", e);
}
}
}
}
/**
* For loading a configuration in the background (i.e. in a thread).
*/
private class BackgroundConfigurationLoaderTask implements Runnable {
private String configFileName;
public BackgroundConfigurationLoaderTask(String configFileName) {
this.configFileName = configFileName;
}
@Override
public void run() {
try {
loadConfiguration(configFileName);
}
catch (ReconciliationServiceException e) {
logger.error(configFileName + ": Error while loading", e);
}
}
}
/**
* Lists the available configuration files from the classpath.
*/
public List<String> listAvailableConfigurationFiles() throws ReconciliationServiceException {
List<String> availableConfigurations = new ArrayList<>();
ResourcePatternResolver pmrpr = new PathMatchingResourcePatternResolver();
try {
Resource[] configurationResources = pmrpr.getResources("classpath*:"+CONFIG_BASE+"*Match.xml");
logger.debug("Found {} configuration file resources", configurationResources.length);
for (Resource resource : configurationResources) {
availableConfigurations.add(resource.getFilename());
}
}
catch (IOException e) {
throw new ReconciliationServiceException("Unable to list available configurations", e);
}
return availableConfigurations;
}
/**
* Loads a single configuration in the background.
*/
public void loadConfigurationInBackground(String configFileName) throws ReconciliationServiceException {
synchronized (configurationStatuses) {
ConfigurationStatus status = configurationStatuses.get(configFileName);
if (status == ConfigurationStatus.LOADED) {
throw new ReconciliationServiceException("Match configuration "+configFileName+" is already loaded.");
}
else if (status == ConfigurationStatus.LOADING) {
throw new ReconciliationServiceException("Match configuration "+configFileName+" is loading.");
}
configurationStatuses.put(configFileName, ConfigurationStatus.LOADING);
}
taskExecutor.execute(new BackgroundConfigurationLoaderTask(configFileName));
}
/**
* Loads a single configuration.
*/
private void loadConfiguration(String configFileName) throws ReconciliationServiceException {
synchronized (configurationStatuses) {
ConfigurationStatus status = configurationStatuses.get(configFileName);
assert (status == ConfigurationStatus.LOADING);
}
StopWatch sw = new Slf4JStopWatch(timingLogger);
String configurationFile = CONFIG_BASE + configFileName;
logger.info("{}: Loading configuration from file {}", configFileName, configurationFile);
ConfigurableApplicationContext context = new GenericXmlApplicationContext(configurationFile);
context.registerShutdownHook();
LuceneMatcher matcher = context.getBean("engine", LuceneMatcher.class);
String configName = matcher.getConfig().getName();
contexts.put(configFileName, context);
matchers.put(configName, matcher);
try {
matcher.loadData();
totals.put(configName, matcher.getIndexReader().numDocs());
logger.debug("{}: Loaded data", configName);
// Append " (environment)" to Metadata name, to help with interactive testing
Metadata metadata = getMetadata(configName);
if (metadata != null) {
if (!"prod".equals(environment)) {
metadata.setName(metadata.getName() + " (" + environment + ")");
}
}
synchronized (configurationStatuses) {
ConfigurationStatus status = configurationStatuses.get(configFileName);
if (status != ConfigurationStatus.LOADING) {
logger.error("Unexpected configuration status '"+status+"' after loading "+configFileName);
}
configurationStatuses.put(configFileName, ConfigurationStatus.LOADED);
}
}
catch (Exception e) {
logger.error("Problem loading configuration "+configFileName, e);
context.close();
totals.remove(configName);
matchers.remove(configName);
contexts.remove(configFileName);
synchronized (configurationStatuses) {
ConfigurationStatus status = configurationStatuses.get(configFileName);
if (status != ConfigurationStatus.LOADING) {
logger.error("Unexpected configuration status '"+status+"' after loading "+configFileName);
}
configurationStatuses.remove(configFileName);
}
sw.stop("LoadConfiguration:"+configFileName+".failure");
throw new ReconciliationServiceException("Problem loading configuration "+configFileName, e);
}
sw.stop("LoadConfiguration:"+configFileName+".success");
}
/**
* Unloads a single configuration.
*/
public void unloadConfiguration(String configFileName) throws ReconciliationServiceException {
synchronized (configurationStatuses) {
ConfigurationStatus status = configurationStatuses.get(configFileName);
if (status == ConfigurationStatus.LOADING) {
throw new ReconciliationServiceException("Match configuration "+configFileName+" is loading, wait until it has completed.");
}
else if (status == null) {
throw new ReconciliationServiceException("Match configuration "+configFileName+" is not loaded.");
}
StopWatch sw = new Slf4JStopWatch(timingLogger);
logger.info("{}: Unloading configuration", configFileName);
ConfigurableApplicationContext context = contexts.get(configFileName);
String configName = configFileName.substring(0, configFileName.length() - 4);
totals.remove(configName);
matchers.remove(configName);
contexts.remove(configFileName);
context.close();
configurationStatuses.remove(configFileName);
sw.stop("UnloadConfiguration:"+configFileName+".success");
}
}
/**
* Retrieve reconciliation service metadata.
* @throws UnknownReconciliationServiceException if the requested matcher doesn't exist.
* @throws MatchExecutionException if no default type is specified
*/
public Metadata getMetadata(String configName) throws UnknownReconciliationServiceException, MatchExecutionException {
ReconciliationServiceConfiguration reconcilationConfig = getReconciliationServiceConfiguration(configName);
if (reconcilationConfig != null) {
Metadata metadata = reconcilationConfig.getReconciliationServiceMetadata();
if (metadata.getDefaultTypes() == null || metadata.getDefaultTypes().length == 0) {
throw new MatchExecutionException("No default type specified, OpenRefine 2.6 would fail");
}
return metadata;
}
return null;
}
/**
* Convert single query string into query properties.
* @throws UnknownReconciliationServiceException if the requested matcher doesn't exist.
*/
public QueryStringToPropertiesExtractor getPropertiesExtractor(String configName) throws UnknownReconciliationServiceException {
ReconciliationServiceConfiguration reconcilationConfig = getReconciliationServiceConfiguration(configName);
if (reconcilationConfig != null) {
return reconcilationConfig.getQueryStringToPropertiesExtractor();
}
return null;
}
/**
* Formatter to convert result into single string.
* @throws UnknownReconciliationServiceException if the requested matcher doesn't exist.
*/
public ReconciliationResultFormatter getReconciliationResultFormatter(String configName) throws UnknownReconciliationServiceException {
ReconciliationServiceConfiguration reconcilationConfig = getReconciliationServiceConfiguration(configName);
if (reconcilationConfig != null) {
ReconciliationResultFormatter reconciliationResultFormatter = reconcilationConfig.getReconciliationResultFormatter();
if (reconciliationResultFormatter != null) {
return reconciliationResultFormatter;
}
else {
// Set it to the default one
ReconciliationResultPropertyFormatter formatter = new ReconciliationResultPropertyFormatter(reconcilationConfig);
reconcilationConfig.setReconciliationResultFormatter(formatter);
return formatter;
}
}
return null;
}
/**
* Perform match query against specified configuration.
*/
@Profiled(tag="MatchQuery:{$0}", logger=queryTimingLoggerName, logFailuresSeparately=true)
public synchronized List<Map<String,String>> doQuery(String configName, Map<String, String> userSuppliedRecord) throws TooManyMatchesException, UnknownReconciliationServiceException, MatchExecutionException {
List<Map<String,String>> matches = null;
LuceneMatcher matcher = getMatcher(configName);
if (matcher == null) {
// When no matcher specified with that configuration
logger.warn("Invalid match configuration «{}» requested", configName);
return null;
}
matches = matcher.getMatches(userSuppliedRecord);
// Just write out some matches to std out:
logger.debug("Found some matches: {}", matches.size());
if (matches.size() < 4) {
logger.debug("Matches for {} are {}", userSuppliedRecord, matches);
}
return matches;
}
/**
* Retrieve reconciliation service configuration.
* @throws UnknownReconciliationServiceException if the requested configuration doesn't exist.
*/
public ReconciliationServiceConfiguration getReconciliationServiceConfiguration(String configName) throws UnknownReconciliationServiceException {
MatchConfiguration matchConfig = getMatcher(configName).getConfig();
if (matchConfig instanceof ReconciliationServiceConfiguration) {
ReconciliationServiceConfiguration reconcilationConfig = (ReconciliationServiceConfiguration) matchConfig;
return reconcilationConfig;
}
return null;
}
/* • Getters and setters • */
public Map<String, LuceneMatcher> getMatchers() {
return matchers;
}
public LuceneMatcher getMatcher(String matcher) throws UnknownReconciliationServiceException {
if (matchers.get(matcher) == null) {
throw new UnknownReconciliationServiceException("No matcher called '"+matcher+"' exists.");
}
return matchers.get(matcher);
}
public List<String> getInitialConfigurations() {
return initialConfigurations;
}
public void setInitialConfigurations(List<String> initialConfigurations) {
this.initialConfigurations = initialConfigurations;
}
public Map<String, ConfigurationStatus> getConfigurationStatuses() {
return configurationStatuses;
}
public Map<String, Integer> getTotals() {
return totals;
}
}
| 14,349 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
DatabaseCursorRecordReader.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/service/DatabaseCursorRecordReader.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.service;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import javax.sql.DataSource;
import org.kew.rmf.core.DatabaseRecordSource;
/**
* Reads records from a database using a cursor.
*/
public class DatabaseCursorRecordReader implements DatabaseRecordSource {
private Connection connection;
private DataSource dataSource;
private String sql;
private String countSql;
private int fetchSize = 5000;
private PreparedStatement preparedStatement;
private ResultSet rs;
private void openCursor() throws SQLException {
preparedStatement = getConnection().prepareStatement(sql, ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY);
if (getConnection().getMetaData().getDatabaseProductName().equals("MySQL")) {
preparedStatement.setFetchSize(Integer.MIN_VALUE);
}
else {
preparedStatement.setFetchSize(fetchSize);
}
preparedStatement.setFetchDirection(ResultSet.FETCH_FORWARD);
this.rs = preparedStatement.executeQuery();
}
@Override
public int count() throws SQLException {
if (countSql == null) {
return -1;
}
Statement s = getConnection().createStatement();
ResultSet r = s.executeQuery(countSql);
r.next();
return r.getInt(1);
}
/* • Getters and setters */
private synchronized Connection getConnection() throws SQLException {
if (connection == null) {
connection = dataSource.getConnection();
connection.setAutoCommit(false); // Cursors in PostgreSQL (at least) don't work in autocommit mode.
}
return connection;
}
@Override
public ResultSet getResultSet() throws SQLException {
if (rs == null) {
openCursor();
}
return rs;
}
@Override
public void close() throws SQLException {
if (rs != null) {
rs.close();
}
if (preparedStatement != null) {
preparedStatement.close();
}
if (connection != null) {
connection.close();
}
}
public DataSource getDataSource() {
return dataSource;
}
public void setDataSource(DataSource dataSource) {
this.dataSource = dataSource;
}
public String getSql() {
return sql;
}
public void setSql(String sql) {
this.sql = sql;
}
public String getCountSql() {
return countSql;
}
public void setCountSql(String countSql) {
this.countSql = countSql;
}
public int getFetchSize() {
return fetchSize;
}
public void setFetchSize(int fetchSize) {
this.fetchSize = fetchSize;
}
}
| 3,233 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ReconciliationResultPropertyFormatter.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/service/resultformatter/ReconciliationResultPropertyFormatter.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.service.resultformatter;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.kew.rmf.core.configuration.Property;
import org.kew.rmf.core.configuration.ReconciliationServiceConfiguration;
/**
* Formats results according to the specified string format, with values chosen by property (result keys).
*/
public class ReconciliationResultPropertyFormatter implements ReconciliationResultFormatter {
private String format;
private List<String> properties;
private String stripRepeats;
public ReconciliationResultPropertyFormatter() {
}
/**
* Create a formatter based on the configured columns, in order, separated by commas.
*/
public ReconciliationResultPropertyFormatter(ReconciliationServiceConfiguration reconcilationConfig) {
properties = new ArrayList<>();
StringBuilder sbFormat = new StringBuilder();
List<Property> columns = reconcilationConfig.getProperties();
for (Property p : columns) {
properties.add(p.getAuthorityColumnName());
if (sbFormat.length() > 0) sbFormat.append(", ");
sbFormat.append("%s");
}
format = sbFormat.toString();
stripRepeats = null;
}
@Override
public String formatResult(Map<String, String> result) {
Object[] resultProperties = new Object[properties.size()];
for (int i = 0; i < resultProperties.length; i++) {
resultProperties[i] = result.get(properties.get(i));
}
if (stripRepeats != null) {
return String.format(getFormat(), resultProperties).replace(stripRepeats+stripRepeats, stripRepeats);
}
else {
return String.format(getFormat(), resultProperties);
}
}
/* • Getters and setters • */
public String getFormat() {
return format;
}
public void setFormat(String format) {
this.format = format;
}
public List<String> getProperties() {
return properties;
}
public void setProperties(List<String> properties) {
this.properties = properties;
}
public String getStripRepeats() {
return stripRepeats;
}
public void setStripRepeats(String stripRepeats) {
this.stripRepeats = stripRepeats;
}
}
| 2,845 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ReconciliationResultFormatter.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/service/resultformatter/ReconciliationResultFormatter.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.service.resultformatter;
import java.util.Map;
/**
* Defines how a result should be formatted in the JSON response to a reconciliation query.
*/
public interface ReconciliationResultFormatter {
public String formatResult(Map<String, String> result);
}
| 1,043 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
UnknownReconciliationServiceException.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/exception/UnknownReconciliationServiceException.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.exception;
public class UnknownReconciliationServiceException extends Exception {
private static final long serialVersionUID = 1L;
public UnknownReconciliationServiceException() {
super();
}
public UnknownReconciliationServiceException(String message) {
super(message);
}
public UnknownReconciliationServiceException(String message, Throwable cause) {
super(message, cause);
}
}
| 1,182 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ReconciliationServiceException.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/exception/ReconciliationServiceException.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.exception;
public class ReconciliationServiceException extends Exception {
private static final long serialVersionUID = 1L;
public ReconciliationServiceException() {
super();
}
public ReconciliationServiceException(String message) {
super(message);
}
public ReconciliationServiceException(String message, Throwable cause) {
super(message, cause);
}
}
| 1,154 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
OtherController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/ws/OtherController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.ws;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
/**
* Information, help pages etc.
*/
@Controller
public class OtherController {
//private static Logger logger = LoggerFactory.getLogger(OtherController.class);
@Autowired
private BaseController baseController;
@RequestMapping(produces="text/html", value = "/", method = RequestMethod.GET)
public String doWelcome(Model model) {
baseController.menuAndBreadcrumbs("/", model);
return "index";
}
@RequestMapping(produces="text/html", value = "/help", method = RequestMethod.GET)
public String doHelp(Model model) {
baseController.menuAndBreadcrumbs("/help", model);
return "help";
}
}
| 1,673 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ConfigurationController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/ws/ConfigurationController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.ws;
import java.io.IOException;
import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
import javax.servlet.http.HttpServletRequest;
import org.codehaus.jackson.JsonGenerationException;
import org.codehaus.jackson.map.JsonMappingException;
import org.kew.rmf.core.configuration.Property;
import org.kew.rmf.core.configuration.ReconciliationServiceConfiguration;
import org.kew.rmf.matchers.Matcher;
import org.kew.rmf.reconciliation.exception.ReconciliationServiceException;
import org.kew.rmf.reconciliation.exception.UnknownReconciliationServiceException;
import org.kew.rmf.reconciliation.service.ReconciliationService;
import org.kew.rmf.reconciliation.service.ReconciliationService.ConfigurationStatus;
import org.kew.rmf.reconciliation.ws.dto.DisplayBean;
import org.kew.rmf.transformers.Transformer;
import org.kew.rmf.transformers.WeightedTransformer;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
/**
* Administration, configuration information pages etc.
*/
@Controller
public class ConfigurationController {
private static Logger logger = LoggerFactory.getLogger(ConfigurationController.class);
@Autowired
private ReconciliationService reconciliationService;
@Autowired
private BaseController baseController;
private List<String> charsetNames = new ArrayList<>();
public ConfigurationController() {
// Initialise the list of available character sets.
for (String charsetName : Charset.availableCharsets().keySet()) {
if (!charsetName.startsWith("x-") && !charsetName.startsWith("X-")) {
charsetNames.add(charsetName);
}
}
}
@RequestMapping(produces="text/html", value = "/admin", method = RequestMethod.GET)
public String doConfigurationAdmin(Model model) throws ReconciliationServiceException {
logger.info("Request for configuration admin page");
Map<String,ConfigurationStatus> configurationStatuses = reconciliationService.getConfigurationStatuses();
logger.debug("Loaded/loading config files: {}", configurationStatuses);
Map<String,ConfigurationStatus> configurations = new TreeMap<>();
for (String configurationFileName : reconciliationService.listAvailableConfigurationFiles()) {
configurations.put(configurationFileName, configurationStatuses.get(configurationFileName) == null ? ConfigurationStatus.NOT_LOADED : configurationStatuses.get(configurationFileName));
}
model.addAttribute("configurations", configurations);
baseController.menuAndBreadcrumbs("/admin", model);
return "configuration-admin";
}
@RequestMapping(produces="text/html", value = "/admin", method = RequestMethod.POST)
public String doConfigurationAdmin(
HttpServletRequest request,
@RequestParam(required=false) String load,
@RequestParam(required=false) String reload,
@RequestParam(required=false) String unload,
Model model) throws JsonGenerationException, JsonMappingException, IOException, ReconciliationServiceException {
logger.info("Request for configuration loading L:{} R:{} U:{}", load, reload, unload);
if (reload != null) {
// TODO ••• Check user input! •••
String configName = reload;
logger.info("Request to reload {}", configName);
reconciliationService.unloadConfiguration(configName);
reconciliationService.loadConfigurationInBackground(configName);
}
if (unload != null) {
// TODO ••• Check user input! •••
String configName = unload;
logger.info("Request to unload {}", configName);
reconciliationService.unloadConfiguration(configName);
}
if (load != null) {
// TODO ••• Check user input! •••
String configName = load;
logger.info("Request to load {}", configName);
reconciliationService.loadConfigurationInBackground(configName);
}
return "redirect:/admin";
}
@RequestMapping(produces="text/html", value = "/about", method = RequestMethod.GET)
public String doWelcome(Model model) {
model.addAttribute("availableMatchers", reconciliationService.getMatchers().keySet());
baseController.menuAndBreadcrumbs("/about", model);
return "about-general";
}
@RequestMapping(produces="text/html", value = "/about/{configName}", method = RequestMethod.GET)
public String doAbout(@PathVariable String configName, Model model) throws UnknownReconciliationServiceException {
logger.info("Request for about page for {}", configName);
List<String> properties = new ArrayList<String>();
Map<String,DisplayBean<Matcher>> p_matchers = new HashMap<>();
Map<String,List<DisplayBean<Transformer>>> p_transformers = new HashMap<>();
ReconciliationServiceConfiguration configuration = reconciliationService.getReconciliationServiceConfiguration(configName);
model.addAttribute("reconciliationConfiguration", configuration);
for (Property p : configuration.getProperties()) {
properties.add(p.getQueryColumnName());
p_matchers.put(p.getQueryColumnName(), new DisplayBean<Matcher>(p.getMatcher()));
List<DisplayBean<Transformer>> p_t = new ArrayList<>();
for (Transformer t : p.getQueryTransformers()) {
// Ignore WeightedTransformers, use the wrapped transformer instead.
if (t instanceof WeightedTransformer) {
p_t.add(new DisplayBean<Transformer>(((WeightedTransformer)t).getTransformer()));
}
else {
p_t.add(new DisplayBean<Transformer>(t));
}
}
p_transformers.put(p.getQueryColumnName(), p_t);
}
model.addAttribute("total", reconciliationService.getTotals().get(configName));
model.addAttribute("configName", configName);
model.addAttribute("properties", properties);
model.addAttribute("matchers", p_matchers);
model.addAttribute("transformers", p_transformers);
model.addAttribute("charsetNames", charsetNames);
baseController.menuAndBreadcrumbs("/about/"+configName, model);
return "about-matcher";
}
}
| 7,077 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ReconciliationExceptionResolver.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/ws/ReconciliationExceptionResolver.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.ws;
import java.text.SimpleDateFormat;
import java.util.Date;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.handler.SimpleMappingExceptionResolver;
/**
* Adds the date, URL and contact email address details to exception messages. (Also, menu and breadcrumbs.)
*/
public class ReconciliationExceptionResolver extends SimpleMappingExceptionResolver {
@Autowired
private BaseController baseController;
private SimpleDateFormat simpleDateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss Z");
@Override
protected ModelAndView doResolveException(HttpServletRequest request, HttpServletResponse response, Object handler, Exception exception) {
ModelAndView mav = super.doResolveException(request, response, handler, exception);
mav.addObject("url", request.getRequestURL());
mav.addObject("datetime", simpleDateFormat.format(new Date()));
mav.addObject("contactemail", "[email protected]");
mav.addObject("statusCode", response.getStatus());
mav.addObject("statusMessage", HttpStatus.valueOf(response.getStatus()).getReasonPhrase());
baseController.menuAndBreadcrumbs("/#", mav);
return mav;
}
}
| 2,160 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
CsvMatchController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/ws/CsvMatchController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.ws;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.Reader;
import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.io.FileUtils;
import org.kew.rmf.core.configuration.Configuration;
import org.kew.rmf.core.configuration.Property;
import org.kew.rmf.core.exception.MatchExecutionException;
import org.kew.rmf.core.exception.TooManyMatchesException;
import org.kew.rmf.core.lucene.LuceneMatcher;
import org.kew.rmf.reconciliation.exception.UnknownReconciliationServiceException;
import org.kew.rmf.reconciliation.service.ReconciliationService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.multipart.MultipartFile;
import org.supercsv.io.CsvMapReader;
import org.supercsv.prefs.CsvPreference;
/**
* Implements a CSV query interface to the reconciliation configurations, providing file upload processing.
*/
@Controller
public class CsvMatchController {
private static Logger logger = LoggerFactory.getLogger(CsvMatchController.class);
private static String tmpDir = System.getProperty("java.io.tmpdir");
@Autowired
private ReconciliationService reconciliationService;
@Autowired
private BaseController baseController;
/**
* Matches the records in the uploaded file.
*
* Results are put into a temporary file (available for download) and also shown in the web page.
*/
@RequestMapping(value = "/filematch/{configName}", method = RequestMethod.POST)
public String doFileMatch (@PathVariable String configName, @RequestParam("file") MultipartFile file, @RequestParam("charset") String charset, HttpServletResponse response, Model model) throws UnknownReconciliationServiceException, IOException {
logger.info("{}: File match query {}, {}", configName, file, charset);
if (file.isEmpty()) {
logger.warn("File is empty");
baseController.menuAndBreadcrumbs("/filematch/"+configName, model);
model.addAttribute("error", "CSV file is empty.");
return "file-matcher-error";
}
logger.debug("Looking for: {}", configName);
LuceneMatcher matcher = reconciliationService.getMatcher(configName);
// Map of matches
// Key is the ID of supplied records
// Entries are a List of Map<String,String>
Map<String,List<Map<String,String>>> matches = new HashMap<String,List<Map<String,String>>>();
// Map of supplied data (useful for display)
List<Map<String,String>> suppliedData = new ArrayList<Map<String,String>>();
// Temporary file for results
File resultsFile;
OutputStreamWriter resultsFileWriter;
List<String> unusedCsvFields = new ArrayList<>();
// Property field names
List<String> properties = new ArrayList<String>();
for (Property p : matcher.getConfig().getProperties()) {
properties.add(p.getQueryColumnName());
}
// Open file and read first line to determine line ending
BufferedReader fileReader = new BufferedReader(new InputStreamReader(file.getInputStream(), Charset.forName(charset)));
String lineEnding;
String userLineEnding;
boolean crlf = useCrLfEndings(fileReader);
lineEnding = crlf ? "\r\n" : "\n";
userLineEnding = crlf ? "Windows (CR+LF)" : "Linux/Mac (LF)";
logger.debug("Line endings are {}", userLineEnding);
// Read CSV from file
CsvPreference customCsvPref = new CsvPreference.Builder('"', ',', lineEnding).build(); // lineEnding is only used for writing anyway.
CsvMapReader mr = new CsvMapReader(fileReader, customCsvPref);
final String[] header = mr.getHeader(true);
// Check CSV file has appropriate headers
// Need "id" and at least one from properties
if (!validateCsvFields(header, properties, unusedCsvFields)) {
mr.close();
fileReader.close();
logger.warn("Uploaded CSV doesn't contain id column.");
baseController.menuAndBreadcrumbs("/filematch/"+configName, model);
model.addAttribute("error", "CSV file doesn't contain 'id' column, or is corrupt.");
return "file-matcher-error";
}
// Open results file and write header
resultsFile = File.createTempFile("match-results-", ".csv");
resultsFileWriter = new OutputStreamWriter(new FileOutputStream(resultsFile), "UTF-8");
resultsFileWriter.write("queryId,matchId");
resultsFileWriter.write(lineEnding);
// Process each line of the input CSV, append results to output file
Map<String, String> record = null;
while ((record = mr.read(header)) != null) {
logger.debug("Next record is {}", record);
suppliedData.add(record);
try {
List<Map<String,String>> theseMatches = matcher.getMatches(record);
if (theseMatches != null) {
logger.debug("Record ID {}, matched: {}", record.get(Configuration.ID_FIELD_NAME), theseMatches.size());
}
else {
logger.debug("Record ID {}, matched: null", record.get(Configuration.ID_FIELD_NAME));
}
matches.put(record.get(Configuration.ID_FIELD_NAME), theseMatches);
// Append match results to file
StringBuilder sb = new StringBuilder();
for (Map<String,String> result : theseMatches) {
if (sb.length() > 0) sb.append('|');
sb.append(result.get(Configuration.ID_FIELD_NAME));
}
sb.insert(0, ',').insert(0, record.get(Configuration.ID_FIELD_NAME)).append(lineEnding);
resultsFileWriter.write(sb.toString());
}
catch (TooManyMatchesException | MatchExecutionException e) {
logger.warn("Problem handling match", e);
}
}
// Close file etc
mr.close();
resultsFileWriter.close();
model.addAttribute("resultsFile", resultsFile.getName());
response.setHeader("X-File-Download", resultsFile.getName()); // Putting this in a header saves the unit tests from needing to parse the HTML.
model.addAttribute("suppliedData", suppliedData);
model.addAttribute("matches", matches);
model.addAttribute("properties", properties);
model.addAttribute("unusedCsvFields", unusedCsvFields);
model.addAttribute("userLineEnding", userLineEnding);
model.addAttribute("charset", charset);
baseController.menuAndBreadcrumbs("/filematch/"+configName, model);
return "file-matcher-results";
}
/**
* Returns true if the input file's line endings are likely to be Windows-style (\r\n).
*/
private boolean useCrLfEndings(Reader inputStream) {
if (inputStream.markSupported()) {
try {
inputStream.mark(4096);
int i = 0;
int c;
while(i++ < 4096
&& inputStream.ready()
&& ((c = inputStream.read()) > 0)) {
if (c == '\n') {
inputStream.reset();
return false;
}
if (c == '\r') {
inputStream.reset();
return true;
}
}
logger.warn("Detecting line endings not possible, first line is very long");
return false;
}
catch (IOException e) {
logger.warn("Exception determining CSV input file line ending", e);
return false;
}
}
else {
logger.warn("Detecting line endings not possible, mark not supported");
return false;
}
}
/**
* Checks for the presence of an "id" field, and returns all strings in fields but not in properties.
*/
private boolean validateCsvFields(String[] fields, List<String> properties, List<String> unusedFields) {
boolean containsId = false;
if (fields == null) return false;
for (String f : fields) {
if (Configuration.ID_FIELD_NAME.equals(f)) {
containsId = true;
}
else {
if (!properties.contains(f)) {
unusedFields.add(f);
}
}
}
return containsId;
}
/**
* Downloads a match result file.
*/
@RequestMapping(value = "/download/{fileName}", method = RequestMethod.GET)
public ResponseEntity<String> doDownload(@PathVariable String fileName, Model model) {
logger.info("User attempting to download file named «{}»", fileName);
// Check for the user trying to do something suspicious
if (fileName.contains(File.separator)) {
logger.error("User attempting to download file named «{}»", fileName);
return new ResponseEntity<String>("Looks dodgy.", baseController.getResponseHeaders(), HttpStatus.FORBIDDEN);
}
// Put back the .csv, as Spring has chopped it off.
File downloadFile = new File(tmpDir, fileName + ".csv");
try {
if (downloadFile.canRead()) {
return new ResponseEntity<String>(FileUtils.readFileToString(downloadFile, "UTF-8"), baseController.getResponseHeaders(), HttpStatus.OK);
}
else {
logger.warn("User attempted to download file «{}» but it doesn't exist", fileName);
return new ResponseEntity<String>("This download does not exist", baseController.getResponseHeaders(), HttpStatus.NOT_FOUND);
}
}
catch (IOException e) {
logger.error("Exception when user attempted to download file «{}»", fileName);
return new ResponseEntity<String>("Error retrieving download: "+e.getMessage(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
}
}
| 10,301 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ReconciliationServiceController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/ws/ReconciliationServiceController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.ws;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.servlet.ServletContext;
import javax.servlet.http.HttpServletRequest;
import org.codehaus.jackson.JsonGenerationException;
import org.codehaus.jackson.map.JsonMappingException;
import org.codehaus.jackson.map.ObjectMapper;
import org.codehaus.jackson.type.TypeReference;
import org.kew.rmf.core.configuration.Configuration;
import org.kew.rmf.core.configuration.Property;
import org.kew.rmf.core.exception.MatchExecutionException;
import org.kew.rmf.core.exception.TooManyMatchesException;
import org.kew.rmf.reconciliation.exception.UnknownReconciliationServiceException;
import org.kew.rmf.reconciliation.queryextractor.QueryStringToPropertiesExtractor;
import org.kew.rmf.reconciliation.service.ReconciliationService;
import org.kew.rmf.refine.domain.metadata.Metadata;
import org.kew.rmf.refine.domain.metadata.Type;
import org.kew.rmf.refine.domain.query.Query;
import org.kew.rmf.refine.domain.response.FlyoutResponse;
import org.kew.rmf.refine.domain.response.QueryResponse;
import org.kew.rmf.refine.domain.response.QueryResult;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.client.RestTemplate;
/**
* Implements an <a href="https://github.com/OpenRefine/OpenRefine/wiki/Reconciliation-Service-Api">OpenRefine Reconciliation Service</a>
* on top of a match configuration.
*/
@Controller
public class ReconciliationServiceController {
private static Logger logger = LoggerFactory.getLogger(ReconciliationServiceController.class);
@Autowired
private ReconciliationService reconciliationService;
@Autowired
private BaseController baseController;
@Autowired
private ServletContext servletContext;
@Autowired
private ObjectMapper jsonMapper;
private RestTemplate template = new RestTemplate();
/**
* Retrieve reconciliation service metadata.
*/
@RequestMapping(value = "/reconcile/{configName}", method={RequestMethod.GET,RequestMethod.POST}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> getMetadata(HttpServletRequest request, @PathVariable String configName, @RequestParam(value="callback",required=false) String callback, Model model) throws JsonGenerationException, JsonMappingException, IOException {
logger.info("{}: Get Metadata request", configName);
String myUrl = request.getScheme() + "://" + request.getServerName() + (request.getServerPort() == 80 ? "" : (":" + request.getServerPort()));
String basePath = servletContext.getContextPath() + "/reconcile/" + configName;
Metadata metadata;
try {
metadata = reconciliationService.getMetadata(configName);
}
catch (UnknownReconciliationServiceException e) {
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.NOT_FOUND);
}
catch (MatchExecutionException e) {
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
if (metadata != null) {
String metadataJson = jsonMapper.writeValueAsString(metadata).replace("LOCAL", myUrl).replace("BASE", basePath);
return new ResponseEntity<String>(wrapResponse(callback, metadataJson), baseController.getResponseHeaders(), HttpStatus.OK);
}
return null;
}
/**
* Perform multiple reconciliation queries (no callback)
*/
@RequestMapping(value = "/reconcile/{configName}", method={RequestMethod.GET,RequestMethod.POST}, params={"queries"}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> doMultipleQueries(@PathVariable String configName, @RequestParam("queries") String queries) {
return doMultipleQueries(configName, queries, null);
}
/**
* Perform multiple reconciliation queries (no callback)
*/
@RequestMapping(value = "/reconcile/{configName}", method={RequestMethod.GET,RequestMethod.POST}, params={"queries","callback"}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> doMultipleQueries(@PathVariable String configName, @RequestParam("queries") String queries, @RequestParam(value="callback",required=false) String callback) {
logger.info("{}: Multiple query request {}", configName, queries);
String jsonres = null;
Map<String,QueryResponse<QueryResult>> res = new HashMap<>();
try {
// Convert JSON to map of queries
Map<String,Query> qs = jsonMapper.readValue(queries, new TypeReference<Map<String,Query>>() {});
for (String key : qs.keySet()) {
try {
Query q = qs.get(key);
QueryResult[] qres = doQuery(q, configName);
QueryResponse<QueryResult> response = new QueryResponse<>();
response.setResult(qres);
res.put(key,response);
}
catch (MatchExecutionException | TooManyMatchesException e) {
// Only fail the one query, not the whole batch
logger.warn("{}: Query with key {} of multiple query call failed: {}", configName, key, e.getMessage());
}
}
jsonres = jsonMapper.writeValueAsString(res);
}
catch (Exception e) {
logger.error(configName + ": Error with multiple query call", e);
}
return new ResponseEntity<String>(wrapResponse(callback, jsonres), baseController.getResponseHeaders(), HttpStatus.OK);
}
/**
* Single reconciliation query, no callback.
*/
@RequestMapping(value = "/reconcile/{configName}", method={RequestMethod.GET,RequestMethod.POST}, params={"query"}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> doSingleQuery(@PathVariable String configName, @RequestParam("query") String query) {
return doSingleQuery(configName, query, null);
}
/**
* Single reconciliation query.
*/
@RequestMapping(value = "/reconcile/{configName}", method={RequestMethod.GET,RequestMethod.POST}, params={"query","callback"}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> doSingleQuery(@PathVariable String configName, @RequestParam("query") String query, @RequestParam(value="callback",required=false) String callback) {
logger.info("{}: Single query request {}", configName, query);
String jsonres = null;
try {
Query q = jsonMapper.readValue(query, Query.class);
QueryResult[] qres = doQuery(q, configName);
QueryResponse<QueryResult> response = new QueryResponse<>();
response.setResult(qres);
jsonres = jsonMapper.writeValueAsString(response);
}
catch (JsonMappingException | JsonGenerationException e) {
logger.warn(configName + ": Error parsing JSON query", e);
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
catch (IOException e) {
logger.error(configName + ": Query failed:", e);
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
catch (UnknownReconciliationServiceException e) {
logger.warn(configName + ": Query failed:", e);
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.NOT_FOUND);
}
catch (MatchExecutionException e) {
logger.error(configName + ": Query failed:", e);
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
catch (TooManyMatchesException e) {
logger.warn(configName + ": Query failed:", e);
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.CONFLICT);
}
return new ResponseEntity<String>(wrapResponse(callback, jsonres), baseController.getResponseHeaders(), HttpStatus.OK);
}
/**
* Single suggest query, no callback.
*/
@RequestMapping(value = "/reconcile/{configName}", method={RequestMethod.GET,RequestMethod.POST}, params={"prefix"}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> doSuggest(@PathVariable String configName, @RequestParam("prefix") String prefix) {
return doSuggest(configName, prefix, null);
}
/**
* Single suggest query.
*/
@RequestMapping(value = "/reconcile/{configName}", method={RequestMethod.GET,RequestMethod.POST}, params={"prefix","callback"}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> doSuggest(@PathVariable String configName, @RequestParam("prefix") String prefix, @RequestParam(value="callback",required=false) String callback) {
logger.info("{}: Suggest query, prefix {}", configName, prefix);
Query q = new Query();
q.setQuery(prefix);
try {
return doSingleQuery(configName, jsonMapper.writeValueAsString(q), callback);
}
catch (IOException e) {
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
}
/**
* Type suggest, no callback.
*/
@RequestMapping(value = "/reconcile/{configName}/suggestType", method={RequestMethod.GET,RequestMethod.POST}, params={"prefix"}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> doSuggestType(@PathVariable String configName, @RequestParam("prefix") String prefix) {
return doSuggestType(configName, prefix, null);
}
/**
* Type suggest.
*/
@RequestMapping(value = "/reconcile/{configName}/suggestType", method={RequestMethod.GET,RequestMethod.POST}, params={"prefix","callback"}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> doSuggestType(@PathVariable String configName, @RequestParam("prefix") String prefix, @RequestParam(value="callback",required=false) String callback) {
logger.info("{}: Type suggest query, prefix {}", configName, prefix);
String jsonres = null;
try {
Type[] defaultTypes = reconciliationService.getMetadata(configName).getDefaultTypes();
QueryResponse<Type> response = new QueryResponse<>();
response.setResult(defaultTypes);
jsonres = jsonMapper.writeValueAsString(response);
}
catch (JsonMappingException | JsonGenerationException e) {
logger.warn(configName + ": Error parsing JSON query", e);
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
catch (IOException e) {
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
catch (UnknownReconciliationServiceException e) {
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.NOT_FOUND);
}
catch (MatchExecutionException e) {
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
return new ResponseEntity<String>(wrapResponse(callback, jsonres), baseController.getResponseHeaders(), HttpStatus.OK);
}
/**
* Type suggest flyout
*/
@RequestMapping(value = "/reconcile/{configName}/flyoutType/{id:.+}", method={RequestMethod.GET,RequestMethod.POST}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> doTypeFlyout(@PathVariable String configName, @PathVariable String id, @RequestParam(value="callback",required=false) String callback) {
logger.info("{}: Type flyout for id {}", configName, id);
try {
Type[] defaultTypes = reconciliationService.getMetadata(configName).getDefaultTypes();
Type type = null;
for (Type t : defaultTypes) {
if (t.getId().equals(id)) {
type = t;
}
}
String html = "<html><body><ul><li>"+type.getName()+" ("+type.getId()+")</li></ul></body></html>\n";
FlyoutResponse jsonWrappedHtml = new FlyoutResponse(html);
return new ResponseEntity<String>(wrapResponse(callback, jsonMapper.writeValueAsString(jsonWrappedHtml)), baseController.getResponseHeaders(), HttpStatus.OK);
}
catch (IOException e) {
logger.warn(configName + ": Error in type flyout for id "+id, e);
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
catch (UnknownReconciliationServiceException e) {
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.NOT_FOUND);
}
catch (MatchExecutionException | NullPointerException e) {
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
}
/**
* Properties suggest, no callback.
*/
@RequestMapping(value = "/reconcile/{configName}/suggestProperty", method={RequestMethod.GET,RequestMethod.POST}, params={"prefix"}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> doSuggestProperty(@PathVariable String configName, @RequestParam("prefix") String prefix) {
return doSuggestProperty(configName, prefix, null);
}
/**
* Properties suggest.
*/
@RequestMapping(value = "/reconcile/{configName}/suggestProperty", method={RequestMethod.GET,RequestMethod.POST}, params={"prefix","callback"}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> doSuggestProperty(@PathVariable String configName, @RequestParam("prefix") String prefix, @RequestParam(value="callback",required=false) String callback) {
logger.info("{}: Property suggest query, prefix {}", configName, prefix);
String jsonres = null;
try {
List<Type> filteredProperties = new ArrayList<>();
List<Property> properties = reconciliationService.getReconciliationServiceConfiguration(configName).getProperties();
for (Property p : properties) {
String name = p.getQueryColumnName();
// Filter by prefix
if (name != null && name.toUpperCase().startsWith(prefix.toUpperCase())) {
Type t = new Type();
t.setId(name);
t.setName(name);
filteredProperties.add(t);
}
}
logger.debug("Suggest Property query for {} filtered {} properties to {}", prefix, properties.size(), filteredProperties);
QueryResponse<Type> response = new QueryResponse<>();
response.setResult(filteredProperties.toArray(new Type[1]));
jsonres = jsonMapper.writeValueAsString(response);
}
catch (JsonMappingException | JsonGenerationException e) {
logger.warn(configName + ": Error parsing JSON query", e);
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
catch (IOException e) {
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
catch (UnknownReconciliationServiceException e) {
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.NOT_FOUND);
}
return new ResponseEntity<String>(wrapResponse(callback, jsonres), baseController.getResponseHeaders(), HttpStatus.OK);
}
/**
* Properties suggest flyout
*/
@RequestMapping(value = "/reconcile/{configName}/flyoutProperty/{id:.+}", method={RequestMethod.GET,RequestMethod.POST}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> doPropertiesFlyout(@PathVariable String configName, @PathVariable String id, @RequestParam(value="callback",required=false) String callback) {
logger.info("{}: In property flyout for id {}", configName, id);
try {
String html = "<html><body><ul><li>"+id+"</li></ul></body></html>\n";
FlyoutResponse jsonWrappedHtml = new FlyoutResponse(html);
return new ResponseEntity<String>(wrapResponse(callback, jsonMapper.writeValueAsString(jsonWrappedHtml)), baseController.getResponseHeaders(), HttpStatus.OK);
}
catch (IOException e) {
logger.warn(configName + ": Error in properties flyout for id "+id, e);
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
}
/**
* Entity suggest flyout.
* <br/>
* Either calls the URL provided in the configuration, or generates an HTML snippet containing the known Property fields (in order) in a table.
*/
@RequestMapping(value = "/reconcile/{configName}/flyout/{id:.+}", method={RequestMethod.GET,RequestMethod.POST}, produces="application/json; charset=UTF-8")
public ResponseEntity<String> doSuggestFlyout(@PathVariable String configName, @PathVariable String id, @RequestParam(value="callback",required=false) String callback) {
logger.info("{}: Suggest flyout request for {}", configName, id);
// TODO: This should be replaced by a class which is customisable, e.g. to return HTML, or transform RDF.
String targetUrl;
try {
targetUrl = reconciliationService.getReconciliationServiceConfiguration(configName).getSuggestFlyoutUrl();
}
catch (UnknownReconciliationServiceException e) {
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.NOT_FOUND);
}
// If the configuration has a flyout configured use it
if (targetUrl != null) {
try {
ResponseEntity<String> httpResponse = template.getForEntity(targetUrl, String.class, id);
if (httpResponse.getStatusCode() != HttpStatus.OK) {
logger.debug("{}: Received HTTP {} from URL {} with id {}", configName, httpResponse.getStatusCode(), targetUrl, id);
}
String domainUpToSlash = targetUrl.substring(0, targetUrl.indexOf('/', 10));
String html = httpResponse.getBody();
html = html.replaceFirst("</head>", "<base href='"+domainUpToSlash+"/'/></head>");
FlyoutResponse jsonWrappedHtml = new FlyoutResponse(html);
logger.debug("JSON response is {}", wrapResponse(callback, jsonMapper.writeValueAsString(jsonWrappedHtml)));
return new ResponseEntity<String>(wrapResponse(callback, jsonMapper.writeValueAsString(jsonWrappedHtml)), baseController.getResponseHeaders(), httpResponse.getStatusCode());
}
catch (NullPointerException e) {
logger.info(configName + ": Not found when retrieving URL for id "+id, e);
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.NOT_FOUND);
}
catch (IOException e) {
logger.warn(configName + ": Exception retrieving URL for id "+id, e);
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
}
// Otherwise create something very simple from the Properties
else {
try {
StringBuilder flyout = new StringBuilder();
flyout.append("<!DOCTYPE HTML><html><body><table>\n");
Map<String,String> doc = reconciliationService.getMatcher(configName).getRecordById(id);
List<Property> properties = reconciliationService.getReconciliationServiceConfiguration(configName).getProperties();
for (Property p : properties) {
String name = p.getQueryColumnName();
flyout.append("<tr><th>");
flyout.append(name);
flyout.append("</th><td>");
flyout.append(doc.get(name));
flyout.append("</td></tr>\n");
}
flyout.append("</table></body></html>\n");
FlyoutResponse jsonWrappedHtml = new FlyoutResponse(flyout.toString());
logger.debug("JSON response is {}", wrapResponse(callback, jsonMapper.writeValueAsString(jsonWrappedHtml)));
return new ResponseEntity<String>(wrapResponse(callback, jsonMapper.writeValueAsString(jsonWrappedHtml)), baseController.getResponseHeaders(), HttpStatus.OK);
}
catch (UnknownReconciliationServiceException e) {
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.NOT_FOUND);
}
catch (IOException e) {
logger.warn(configName + ": Exception creating entity flyout for id "+id, e);
return new ResponseEntity<String>(e.toString(), baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
}
}
/**
* Wrap response into JSON-P if necessary.
*/
private String wrapResponse(String callback, String jsonres){
if (callback != null) {
return callback + "(" + jsonres + ")";
}
else {
return jsonres;
}
}
/**
* Perform match query against specified configuration.
*/
private QueryResult[] doQuery(Query q, String configName) throws TooManyMatchesException, MatchExecutionException, UnknownReconciliationServiceException {
ArrayList<QueryResult> qr = new ArrayList<QueryResult>();
org.kew.rmf.refine.domain.query.Property[] properties = q.getProperties();
// If user didn't supply any properties, try converting the query string into properties.
if (properties == null || properties.length == 0) {
QueryStringToPropertiesExtractor propertiesExtractor = reconciliationService.getPropertiesExtractor(configName);
if (propertiesExtractor != null) {
properties = propertiesExtractor.extractProperties(q.getQuery());
logger.debug("No properties provided, parsing query «{}» into properties {}", q.getQuery(), properties);
}
else {
logger.info("No properties provided, no properties resulted from parsing query string «{}»", q.getQuery());
}
}
else {
// If the user supplied some properties, but didn't supply the key property, then it comes from the query
String keyColumnName = reconciliationService.getReconciliationServiceConfiguration(configName).getProperties().get(0).getQueryColumnName();
if (!containsProperty(properties, keyColumnName)) {
properties = Arrays.copyOf(properties, properties.length + 1);
org.kew.rmf.refine.domain.query.Property keyProperty = new org.kew.rmf.refine.domain.query.Property();
keyProperty.setP(keyColumnName);
keyProperty.setPid(keyColumnName);
keyProperty.setV(q.getQuery());
logger.debug("Key property {} taken from query {}", keyColumnName, q.getQuery());
properties[properties.length-1] = keyProperty;
}
}
if (properties == null || properties.length == 0) {
logger.info("No properties provided for query «{}», query fails", q.getQuery());
// no query
return null;
}
// Build a map by looping over each property in the config, reading its value from the
// request object, and applying any transformations specified in the config
Map<String, String> userSuppliedRecord = new HashMap<String, String>();
for (org.kew.rmf.refine.domain.query.Property p : properties) {
if (logger.isTraceEnabled()) { logger.trace("Setting: {} to {}", p.getPid(), p.getV()); }
userSuppliedRecord.put(p.getPid(), p.getV());
}
List<Map<String,String>> matches = reconciliationService.doQuery(configName, userSuppliedRecord);
logger.debug("Found {} matches", matches.size());
for (Map<String,String> match : matches) {
QueryResult res = new QueryResult();
res.setId(match.get("id"));
// Set match to true if there's only one (which allows OpenRefine to autoselect it), false otherwise
res.setMatch(matches.size() == 1);
// Set score to 100 * match score (which is in range 0..1)
res.setScore(100 * Double.parseDouble(match.get(Configuration.MATCH_SCORE)));
// Set name according to format
res.setName(reconciliationService.getReconciliationResultFormatter(configName).formatResult(match));
// Set type to default type
res.setType(reconciliationService.getMetadata(configName).getDefaultTypes());
qr.add(res);
}
return qr.toArray(new QueryResult[qr.size()]);
}
private boolean containsProperty(org.kew.rmf.refine.domain.query.Property[] properties, String property) {
if (property == null) return false;
for (org.kew.rmf.refine.domain.query.Property p : properties) {
if (property.equals(p.getPid())) return true;
}
return false;
}
}
| 24,642 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
BaseController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/ws/BaseController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.ws;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.List;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.kew.rmf.reconciliation.service.ReconciliationService;
import org.kew.web.model.MenuItem;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.servlet.ModelAndView;
import com.google.common.base.Throwables;
@Controller
public class BaseController {
private static Logger logger = LoggerFactory.getLogger(BaseController.class);
@Autowired
private ReconciliationService reconciliationService;
private SimpleDateFormat simpleDateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss Z");
private HttpHeaders responseHeaders = new HttpHeaders();
/* • Constructors • */
public BaseController() {
responseHeaders.set("Access-Control-Allow-Origin", "*");
}
/* • HTTP • */
public HttpHeaders getResponseHeaders() {
return responseHeaders;
}
/* • Menus • */
public void menuAndBreadcrumbs(String activeHref, Model model) {
MenuItem menu = makeMenu(activeHref);
List<MenuItem> breadcrumbs = menu.toBreadcrumbTrail();
model.addAttribute("menu", menu);
model.addAttribute("breadcrumbs", breadcrumbs);
}
public void menuAndBreadcrumbs(String activeHref, ModelAndView mav) {
MenuItem menu = makeMenu(activeHref);
List<MenuItem> breadcrumbs = menu.toBreadcrumbTrail();
mav.addObject("menu", menu);
mav.addObject("breadcrumbs", breadcrumbs);
}
/**
* Generates the website menu with the active trail set accordingly.
*/
private MenuItem makeMenu(String activeHref) {
MenuItem topMenu = new MenuItem("http://www.kew.org/science-conservation/research-data/resources", "Resources and databases");
MenuItem mainMenu = new MenuItem("/#", "Reconciliation Service");
mainMenu.add(new MenuItem("/", "Introduction"));
MenuItem aboutMenu = new MenuItem("/about", "Available configurations");
if (reconciliationService.getMatchers() != null) {
for (String matcher : reconciliationService.getMatchers().keySet()) {
aboutMenu.add(
new MenuItem("/about/" + matcher, matcher)
);
}
}
mainMenu.add(aboutMenu);
MenuItem helpMenu = new MenuItem("/help", "Usage");
helpMenu.add(new MenuItem("/help#installation", "Overview and installation"));
helpMenu.add(new MenuItem("/help#data-preparation", "Data preparation"));
helpMenu.add(new MenuItem("/help#reconciling", "Querying the Reconciliation Service"));
helpMenu.add(new MenuItem("/help#extending", "Extending data using MQL"));
helpMenu.add(new MenuItem("/help#exporting", "Exporting data"));
helpMenu.add(new MenuItem("/help#troubleshooting", "Troubleshooting"));
helpMenu.add(new MenuItem("/help#advanced", "Advanced data manipulation"));
helpMenu.add(new MenuItem("/help#sourcecode", "Source code"));
mainMenu.add(helpMenu);
topMenu.add(mainMenu);
topMenu.setActiveTrail(activeHref);
return topMenu;
}
/* • Errors • */
/**
* Error handler for things not caught by the Exception Resolver.
*/
@RequestMapping("/error")
public String customError(HttpServletRequest request, HttpServletResponse response, Model model) {
// retrieve some useful information from the request
Integer statusCode = (Integer) request.getAttribute("javax.servlet.error.status_code");
if (statusCode == null) statusCode = 500;
Throwable throwable = (Throwable) request.getAttribute("javax.servlet.error.exception");
String exceptionMessage = getExceptionMessage(throwable, statusCode);
String requestUri = (String) request.getAttribute("javax.servlet.error.request_uri");
if (requestUri == null) {
requestUri = "Unknown";
}
logger.warn("Web error {} {}: {}", statusCode, requestUri, exceptionMessage);
model.addAttribute("url", requestUri);
model.addAttribute("datetime", simpleDateFormat.format(new Date()));
model.addAttribute("contactemail", "[email protected]");
model.addAttribute("statusCode", statusCode);
model.addAttribute("statusMessage", HttpStatus.valueOf(statusCode).getReasonPhrase());
menuAndBreadcrumbs("/#", model);
if (statusCode == 404) {
return "404";
}
else {
return "500";
}
}
private String getExceptionMessage(Throwable throwable, Integer statusCode) {
if (throwable != null) {
return Throwables.getRootCause(throwable).getMessage();
}
HttpStatus httpStatus = HttpStatus.valueOf(statusCode);
return httpStatus.getReasonPhrase();
}
}
| 5,576 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
MatchController.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/ws/MatchController.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.ws;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.kew.rmf.core.exception.MatchExecutionException;
import org.kew.rmf.core.exception.TooManyMatchesException;
import org.kew.rmf.reconciliation.exception.UnknownReconciliationServiceException;
import org.kew.rmf.reconciliation.service.ReconciliationService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
/**
* Implements a custom HTTP query interface to the reconciliation configurations, providing JSON responses.
*/
@Controller
public class MatchController {
private static Logger logger = LoggerFactory.getLogger(MatchController.class);
@Autowired
private ReconciliationService reconciliationService;
@Autowired
private BaseController baseController;
/**
* Performs a single match query.
*/
@RequestMapping(value = "/match/{configName}", method = RequestMethod.GET)
public ResponseEntity<List<Map<String,String>>> doMatch (@PathVariable String configName, @RequestParam Map<String,String> requestParams, Model model) throws UnknownReconciliationServiceException {
logger.info("{}: Match query {}", configName, requestParams);
// Build a map by looping over each property in the config, reading its value from the
// request object, and applying any transformations specified in the config
Map<String, String> userSuppliedRecord = new HashMap<String, String>();
for (String key : requestParams.keySet()) {
userSuppliedRecord.put(key, requestParams.get(key));
if (logger.isTraceEnabled()) { logger.trace("Setting: {} to {}", key, requestParams.get(key)); }
}
List<Map<String, String>> matches = null;
try {
matches = reconciliationService.doQuery(configName, userSuppliedRecord);
logger.debug("Found {} matches", matches.size());
if (matches.size() < 4) {
logger.debug("Matches for {} are {}", requestParams, matches);
}
}
catch (TooManyMatchesException | MatchExecutionException e) {
logger.error(configName + ": Problem handling match", e);
return new ResponseEntity<List<Map<String,String>>>(null, baseController.getResponseHeaders(), HttpStatus.INTERNAL_SERVER_ERROR);
}
// TODO: Reporter is needed to cause only configured properties to be returned in the JSON.
// matches will be returned as JSON
return new ResponseEntity<List<Map<String,String>>>(matches, baseController.getResponseHeaders(), HttpStatus.OK);
}
}
| 3,672 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
DisplayBean.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/reconciliation/ws/dto/DisplayBean.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.reconciliation.ws.dto;
import java.beans.BeanInfo;
import java.beans.IntrospectionException;
import java.beans.Introspector;
import java.beans.PropertyDescriptor;
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.List;
import org.kew.rmf.utils.Dictionary;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Generates properties necessary to display a bean nicely in the web interface.
*/
public class DisplayBean<T> {
private static Logger logger = LoggerFactory.getLogger(DisplayBean.class);
private String name;
private String qualifiedName;
private List<String> configuration;
public DisplayBean(T javaBean) {
Class<? extends Object> clazz = javaBean.getClass();
setName(clazz.getSimpleName().replaceAll("([a-z])([A-Z])", "$1 $2"));
setQualifiedName(clazz.getCanonicalName());
List<String> configuration = new ArrayList<>();
// Find getter/setter pairs, display the name and value.
try {
BeanInfo beanInfo = Introspector.getBeanInfo(clazz, Object.class);
for (PropertyDescriptor descriptor : beanInfo.getPropertyDescriptors()) {
String configurationItem;
try {
Method getter = descriptor.getReadMethod();
Method setter = descriptor.getWriteMethod();
if (setter != null) {
configurationItem = descriptor.getName().replaceAll("([a-z])([A-Z])", "$1 $2").toLowerCase();
if (getter != null) {
Class<?> propertyType = descriptor.getPropertyType();
// Quote string values
if (propertyType.equals(String.class)) {
configurationItem += ": \"<code>" + getter.invoke(javaBean) + "</code>\"";
}
// Recurse for lists
else if (Iterable.class.isAssignableFrom(propertyType)) {
Iterable<?> l = (Iterable<?>) getter.invoke(javaBean);
configurationItem += ": {\n";
for (Object li : l) {
DisplayBean<?> dto = new DisplayBean<Object>(li);
configurationItem += "\t• " + dto.getName();
if (dto.getConfiguration() != null && dto.getConfiguration().size() > 0) {
configurationItem += " " + dto.getConfiguration();
}
configurationItem += ";\n";
}
configurationItem = configurationItem.substring(0, configurationItem.length()-2);
configurationItem += "\n}";
}
// Dictionaries
else if (propertyType.equals(Dictionary.class)) {
configurationItem += ": \"<code>" + getter.invoke(javaBean) + "</code>\"";
}
// Otherwise
else {
configurationItem += ": <code>" + getter.invoke(javaBean) + "</code>";
}
}
else {
configurationItem += ": [Unknown]";
}
configuration.add(configurationItem);
}
}
catch (ReflectiveOperationException | IllegalArgumentException e) {
logger.warn("Error retrieving property details of "+javaBean+"."+descriptor, e);
}
}
}
catch (IntrospectionException e) {
logger.warn("Error retrieving properties of "+javaBean, e);
}
setConfiguration(configuration);
}
/* • Getters and setters • */
public String getName() { return name; }
public void setName(String name) { this.name = name; }
public String getQualifiedName() { return qualifiedName; }
public void setQualifiedName(String qualifiedName) { this.qualifiedName = qualifiedName; }
public List<String> getConfiguration() { return configuration; }
public void setConfiguration(List<String> configuration) { this.configuration = configuration; }
}
| 4,277 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
ReconciliationServiceConfiguration.java | /FileExtraction/Java_unseen/RBGKew_Reconciliation-and-Matching-Framework/reconciliation-service/src/main/java/org/kew/rmf/core/configuration/ReconciliationServiceConfiguration.java | /*
* Reconciliation and Matching Framework
* Copyright © 2014 Royal Botanic Gardens, Kew
*
* This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.kew.rmf.core.configuration;
import java.util.List;
import org.kew.rmf.reconciliation.queryextractor.QueryStringToPropertiesExtractor;
import org.kew.rmf.reconciliation.service.resultformatter.ReconciliationResultFormatter;
import org.kew.rmf.refine.domain.metadata.Metadata;
import org.kew.rmf.refine.domain.metadata.MetadataPreview;
import org.kew.rmf.refine.domain.metadata.MetadataSuggest;
import org.kew.rmf.refine.domain.metadata.MetadataSuggestDetails;
import org.kew.rmf.refine.domain.metadata.MetadataView;
import org.kew.rmf.refine.domain.metadata.Type;
import org.springframework.beans.factory.InitializingBean;
import org.springframework.context.ApplicationContext;
public class ReconciliationServiceConfiguration extends MatchConfiguration implements InitializingBean {
private ApplicationContext context;
private Metadata reconciliationServiceMetadata;
private QueryStringToPropertiesExtractor queryStringToPropertiesExtractor;
private ReconciliationResultFormatter reconciliationResultFormatter;
private String description;
// Metadata values
private String title;
private String identifierSpace;
private String schemaSpace;
private String viewUrl;
private String previewUrl;
private int previewWidth;
private int previewHeight;
private List<Type> defaultTypes;
private String suggestFlyoutUrl;
@Override
public void afterPropertiesSet() throws Exception {
// Generate Metadata object
reconciliationServiceMetadata = new Metadata();
reconciliationServiceMetadata.setName(title);
reconciliationServiceMetadata.setIdentifierSpace(identifierSpace);
reconciliationServiceMetadata.setSchemaSpace(schemaSpace);
if (viewUrl != null) {
MetadataView metadataView = new MetadataView();
metadataView.setUrl(viewUrl);
reconciliationServiceMetadata.setView(metadataView);
}
if (previewUrl != null) {
MetadataPreview metadataPreview = new MetadataPreview();
metadataPreview.setUrl(previewUrl);
metadataPreview.setWidth(previewWidth);
metadataPreview.setHeight(previewHeight);
reconciliationServiceMetadata.setPreview(metadataPreview);
}
MetadataSuggestDetails metadataSuggestTypeDetails = new MetadataSuggestDetails();
metadataSuggestTypeDetails.setService_url("LOCAL");
metadataSuggestTypeDetails.setService_path("BASE/suggestType");
metadataSuggestTypeDetails.setFlyout_service_url("LOCAL");
metadataSuggestTypeDetails.setFlyout_service_path("BASE/flyoutType/${id}");
MetadataSuggestDetails metadataSuggestPropertyDetails = new MetadataSuggestDetails();
metadataSuggestPropertyDetails.setService_url("LOCAL");
metadataSuggestPropertyDetails.setService_path("BASE/suggestProperty");
metadataSuggestPropertyDetails.setFlyout_service_url("LOCAL");
metadataSuggestPropertyDetails.setFlyout_service_path("BASE/flyoutProperty/${id}");
MetadataSuggestDetails metadataSuggestEntityDetails = new MetadataSuggestDetails();
metadataSuggestEntityDetails.setService_url("LOCAL");
metadataSuggestEntityDetails.setService_path("BASE");
metadataSuggestEntityDetails.setFlyout_service_url("LOCAL");
metadataSuggestEntityDetails.setFlyout_service_path("BASE/flyout/${id}");
MetadataSuggest metadataSuggest = new MetadataSuggest();
metadataSuggest.setType(metadataSuggestTypeDetails);
metadataSuggest.setProperty(metadataSuggestPropertyDetails);
metadataSuggest.setEntity(metadataSuggestEntityDetails);
reconciliationServiceMetadata.setSuggest(metadataSuggest);
reconciliationServiceMetadata.setDefaultTypes(defaultTypes.toArray(new Type[defaultTypes.size()]));
}
/* ••• Getters and setters ••• */
public ApplicationContext getContext() {
return context;
}
public void setContext(ApplicationContext context) {
this.context = context;
}
public Metadata getReconciliationServiceMetadata() {
return reconciliationServiceMetadata;
}
protected void setReconciliationServiceMetadata(Metadata reconciliationServiceMetadata) {
this.reconciliationServiceMetadata = reconciliationServiceMetadata;
}
public QueryStringToPropertiesExtractor getQueryStringToPropertiesExtractor() {
return queryStringToPropertiesExtractor;
}
/**
* Turns a single query into a set of properties for matching.
*/
public void setQueryStringToPropertiesExtractor(QueryStringToPropertiesExtractor queryStringToPropertiesExtractor) {
this.queryStringToPropertiesExtractor = queryStringToPropertiesExtractor;
}
public ReconciliationResultFormatter getReconciliationResultFormatter() {
return reconciliationResultFormatter;
}
/**
* Formats results for JSON responses.
*/
public void setReconciliationResultFormatter(ReconciliationResultFormatter reconciliationResultFormatter) {
this.reconciliationResultFormatter = reconciliationResultFormatter;
}
public String getDescription() {
return description;
}
/**
* Longer description of the purpose of the service, for display etc.
*/
public void setDescription(String description) {
this.description = description;
}
public String getTitle() {
return title;
}
/**
* The Metadata service title for the service.
*/
public void setTitle(String title) {
this.title = title;
}
public String getIdentifierSpace() {
return identifierSpace;
}
/**
* Metadata identifier space.
*/
public void setIdentifierSpace(String identifierSpace) {
this.identifierSpace = identifierSpace;
}
public String getSchemaSpace() {
return schemaSpace;
}
/**
* Metadata schema space.
*/
public void setSchemaSpace(String schemaSpace) {
this.schemaSpace = schemaSpace;
}
public String getViewUrl() {
return viewUrl;
}
/**
* URL to view web page for record.
*/
public void setViewUrl(String viewUrl) {
this.viewUrl = viewUrl;
}
public String getPreviewUrl() {
return previewUrl;
}
/**
* URL for preview web page, should be compact as it's shown in a popup.
*/
public void setPreviewUrl(String previewUrl) {
this.previewUrl = previewUrl;
}
public Integer getPreviewWidth() {
return previewWidth;
}
/**
* Preview popup width.
*/
public void setPreviewWidth(Integer previewWidth) {
this.previewWidth = previewWidth;
}
public Integer getPreviewHeight() {
return previewHeight;
}
/**
* Preview popup height.
*/
public void setPreviewHeight(Integer previewHeight) {
this.previewHeight = previewHeight;
}
public List<Type> getDefaultTypes() {
return defaultTypes;
}
/**
* Default type(s) used by the service.
*/
public void setDefaultTypes(List<Type> defaultTypes) {
this.defaultTypes = defaultTypes;
}
public String getSuggestFlyoutUrl() {
return suggestFlyoutUrl;
}
/**
* URL template for suggest entity flyouts. <code>{id}</code> will be replaced with the entity id.
* <br/>
* <strong>Do not have Javascript or wide-ranging CSS in here — it could break OpenRefine.</strong>
*/
public void setSuggestFlyoutUrl(String suggestFlyoutUrl) {
this.suggestFlyoutUrl = suggestFlyoutUrl;
}
}
| 7,724 | Java | .java | RBGKew/Reconciliation-and-Matching-Framework | 28 | 3 | 9 | 2014-09-24T13:39:19Z | 2017-04-18T13:37:52Z |
AlternateUsbInterfaceTest.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/usbxfer/src/test/java/info/martinmarinov/usbxfer/AlternateUsbInterfaceTest.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.usbxfer;
import android.hardware.usb.UsbDeviceConnection;
import android.hardware.usb.UsbInterface;
import org.junit.Test;
import static java.util.Arrays.asList;
import static java.util.Collections.singletonList;
import static org.hamcrest.core.IsEqual.equalTo;
import static org.junit.Assert.assertThat;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
public class AlternateUsbInterfaceTest {
@Test
public void getAlternateSetting() throws Exception {
UsbDeviceConnection usbDeviceConnection = mockConnectionWithRawDescriptors(new byte[] {
18, 1, 0, 2, 0, 0, 0, 64, -38, 11, 56, 40, 0, 1, 1, 2, 3, 1, // Device Descriptor
9, 2, 34, 0, 2, 1, 4, -128, -6, // Configuration Descriptor
9, 4, 0, 0, 1, -1, -1, -1, 5, // Interface Descriptor for interface 0 with alternate setting 0
9, 4, 0, 1, 1, -1, -1, -1, 5, // Interface Descriptor for interface 0 with alternate setting 1
7, 5, -127, 2, 0, 2, 0, // Endpoint Descriptor
9, 4, 1, 0, 0, -1, -1, -1, 5 // Interface Descriptor for interface 1 with alternate setting 0
});
// Interface 0 has alternate settings {0, 1}
UsbInterface i0 = mockInterface(0);
assertThat(AlternateUsbInterface.forUsbInterface(usbDeviceConnection, i0),
equalTo(asList(new AlternateUsbInterface(i0, 0), new AlternateUsbInterface(i0, 1))));
// Interface 1 has alternate settings {0}
UsbInterface i1 = mockInterface(1);
assertThat(AlternateUsbInterface.forUsbInterface(usbDeviceConnection, i1),
equalTo(singletonList(new AlternateUsbInterface(i1, 0))));
}
private static UsbInterface mockInterface(int id) {
UsbInterface usbInterface = mock(UsbInterface.class);
when(usbInterface.getId()).thenReturn(id);
return usbInterface;
}
private static UsbDeviceConnection mockConnectionWithRawDescriptors(byte[] rawDescriptors) {
UsbDeviceConnection usbDeviceConnection = mock(UsbDeviceConnection.class);
when(usbDeviceConnection.getRawDescriptors()).thenReturn(rawDescriptors);
return usbDeviceConnection;
}
} | 3,115 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
AlternateUsbInterface.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/usbxfer/src/main/java/info/martinmarinov/usbxfer/AlternateUsbInterface.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.usbxfer;
import android.hardware.usb.UsbDeviceConnection;
import android.hardware.usb.UsbInterface;
import androidx.annotation.VisibleForTesting;
import java.util.ArrayList;
import java.util.List;
/**
* Sometimes there could be multiple UsbInterfaces with same ID. Android API only allows
* using the UsbInterface#getAlternateSettings after Android 5.0 so this is a compatibility layer
*/
public class AlternateUsbInterface {
public static List<AlternateUsbInterface> forUsbInterface(UsbDeviceConnection deviceConnection, UsbInterface usbInterface) {
byte[] rawDescriptors = deviceConnection.getRawDescriptors();
List<AlternateUsbInterface> alternateSettings = new ArrayList<>(2);
int offset = 0;
while(offset < rawDescriptors.length) {
int bLength = rawDescriptors[offset] & 0xFF;
int bDescriptorType = rawDescriptors[offset + 1] & 0xFF;
if (bDescriptorType == 0x04) {
// interface descriptor, we are not interested
int bInterfaceNumber = rawDescriptors[offset + 2] & 0xFF;
int bAlternateSetting = rawDescriptors[offset + 3] & 0xFF;
if (bInterfaceNumber == usbInterface.getId()) {
alternateSettings.add(new AlternateUsbInterface(usbInterface, bAlternateSetting));
}
}
// go to next structure
offset += bLength;
}
if (alternateSettings.size() < 1) throw new IllegalStateException();
return alternateSettings;
}
private final UsbInterface usbInterface;
private final int alternateSettings;
@VisibleForTesting
AlternateUsbInterface(UsbInterface usbInterface, int alternateSettings) {
this.usbInterface = usbInterface;
this.alternateSettings = alternateSettings;
}
public UsbInterface getUsbInterface() {
return usbInterface;
}
int getAlternateSettings() {
return alternateSettings;
}
@SuppressWarnings("SimplifiableIfStatement")
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
AlternateUsbInterface that = (AlternateUsbInterface) o;
if (alternateSettings != that.alternateSettings) return false;
return usbInterface != null ? usbInterface.equals(that.usbInterface) : that.usbInterface == null;
}
@Override
public int hashCode() {
int result = usbInterface != null ? usbInterface.hashCode() : 0;
result = 31 * result + alternateSettings;
return result;
}
}
| 3,542 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
IoctlUtils.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/usbxfer/src/main/java/info/martinmarinov/usbxfer/IoctlUtils.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.usbxfer;
import java.io.IOException;
class IoctlUtils {
/**
* Handles return value of an ioctl request and throws an exception if necessary
* @param ioctlRes
* @throws IOException if return value is negative
*/
public static void res(int ioctlRes) throws IOException {
if (ioctlRes < 0) throw new IOException("ioctl returned "+ioctlRes);
}
}
| 1,272 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
ByteSink.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/usbxfer/src/main/java/info/martinmarinov/usbxfer/ByteSink.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.usbxfer;
import java.io.IOException;
public interface ByteSink {
void consume(byte[] data, int length) throws IOException;
}
| 1,019 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
UsbBulkSource.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/usbxfer/src/main/java/info/martinmarinov/usbxfer/UsbBulkSource.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.usbxfer;
import android.hardware.usb.UsbDeviceConnection;
import android.hardware.usb.UsbEndpoint;
import java.io.IOException;
public class UsbBulkSource implements ByteSource {
private final static int INITIAL_DELAY_BEFORE_BACKOFF = 1_000;
private final static int MAX_BACKOFF = 10;
private final UsbDeviceConnection usbDeviceConnection;
private final UsbEndpoint usbEndpoint;
private final AlternateUsbInterface usbInterface;
private final int numRequests;
private final int numPacketsPerReq;
private UsbHiSpeedBulk usbHiSpeedBulk;
private int backoff = -INITIAL_DELAY_BEFORE_BACKOFF;
public UsbBulkSource(UsbDeviceConnection usbDeviceConnection, UsbEndpoint usbEndpoint, AlternateUsbInterface usbInterface, int numRequests, int numPacketsPerReq) {
this.usbDeviceConnection = usbDeviceConnection;
this.usbEndpoint = usbEndpoint;
this.usbInterface = usbInterface;
this.numRequests = numRequests;
this.numPacketsPerReq = numPacketsPerReq;
}
@Override
public void open() throws IOException {
usbHiSpeedBulk = new UsbHiSpeedBulk(usbDeviceConnection, usbEndpoint, numRequests, numPacketsPerReq);
usbHiSpeedBulk.setInterface(usbInterface);
usbDeviceConnection.claimInterface(usbInterface.getUsbInterface(), true);
usbHiSpeedBulk.start();
}
@Override
public void readNext(ByteSink sink) throws IOException, InterruptedException {
UsbHiSpeedBulk.Buffer read = usbHiSpeedBulk.read(false);
if (read == null) {
backoff++;
if (backoff > 0) {
Thread.sleep(backoff);
} else {
if (backoff % 3 == 0) Thread.sleep(1);
}
if (backoff > MAX_BACKOFF) {
backoff = MAX_BACKOFF;
}
} else {
backoff = -INITIAL_DELAY_BEFORE_BACKOFF;
sink.consume(read.getData(), read.getLength());
}
}
@Override
public void close() throws IOException {
usbHiSpeedBulk.stop();
usbHiSpeedBulk.unsetInterface(usbInterface);
usbDeviceConnection.releaseInterface(usbInterface.getUsbInterface());
}
}
| 3,104 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
ByteSource.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/usbxfer/src/main/java/info/martinmarinov/usbxfer/ByteSource.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.usbxfer;
import java.io.Closeable;
import java.io.IOException;
public interface ByteSource extends Closeable {
void open() throws IOException;
void readNext(ByteSink sink) throws IOException, InterruptedException;
}
| 1,114 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
IsoRequest.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/usbxfer/src/main/java/info/martinmarinov/usbxfer/IsoRequest.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.usbxfer;
import android.hardware.usb.UsbDeviceConnection;
import android.hardware.usb.UsbEndpoint;
import java.io.IOException;
class IsoRequest {
private final long urbPtr;
private final int fd;
IsoRequest(UsbDeviceConnection usbDeviceConnection, UsbEndpoint usbEndpoint, int id, int maxPackets, int packetSize) {
this.fd = usbDeviceConnection.getFileDescriptor();
urbPtr = jni_allocate_urb(usbEndpoint.getAddress(), id, maxPackets, packetSize);
jni_reset_urb(urbPtr);
}
void reset() {
jni_reset_urb(urbPtr);
}
void submit() throws IOException {
IoctlUtils.res(jni_submit(urbPtr, fd));
}
void cancel() throws IOException {
IoctlUtils.res(jni_cancel(urbPtr, fd));
}
int read(byte[] data) {
return jni_read(urbPtr, data);
}
static int getReadyRequestId(UsbDeviceConnection usbDeviceConnection, boolean wait) {
return jni_get_ready_packet_id(usbDeviceConnection.getFileDescriptor(), wait);
}
@Override
protected void finalize() throws Throwable {
super.finalize();
jni_free_urb(urbPtr);
}
private static native long jni_allocate_urb(int endpointAddr, int id, int maxPackets, int packetSize);
private static native void jni_reset_urb(long ptr);
private static native void jni_free_urb(long ptr);
private static native int jni_submit(long ptr, int fd);
private static native int jni_cancel(long ptr, int fd);
private static native int jni_read(long ptr, byte[] data);
private static native int jni_get_ready_packet_id(int fd, boolean wait);
}
| 2,513 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
UsbHiSpeedBulk.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/usbxfer/src/main/java/info/martinmarinov/usbxfer/UsbHiSpeedBulk.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.usbxfer;
import android.hardware.usb.UsbDeviceConnection;
import android.hardware.usb.UsbEndpoint;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
/**
* Android USB API drops packets when high speeds are needed.
*
* This is why we need this framework to allow us to use the kernel to handle the transfer for us
*
* Inspired by http://www.source-code.biz/snippets/java/UsbIso
*
* This is not thread safe! Call only from one thread.
*/
public class UsbHiSpeedBulk {
public final static boolean IS_PLATFORM_SUPPORTED;
static {
boolean isPlatformSupported = false;
try {
System.loadLibrary("UsbXfer");
isPlatformSupported = true;
} catch (Throwable t) {
t.printStackTrace();
}
IS_PLATFORM_SUPPORTED = isPlatformSupported;
}
private final int fileDescriptor;
private final UsbDeviceConnection usbDeviceConnection;
private final List<IsoRequest> requests;
private final int nrequests, packetsPerRequests, packetSize;
private final UsbEndpoint usbEndpoint;
private final Buffer buffer;
public UsbHiSpeedBulk(UsbDeviceConnection usbDeviceConnection, UsbEndpoint usbEndpoint, int nrequests, int packetsPerRequests) {
this.usbDeviceConnection = usbDeviceConnection;
this.fileDescriptor = usbDeviceConnection.getFileDescriptor();
this.nrequests = nrequests;
this.requests = new ArrayList<>(nrequests);
this.packetSize = usbEndpoint.getMaxPacketSize();
this.usbEndpoint = usbEndpoint;
this.packetsPerRequests = packetsPerRequests;
this.buffer = new Buffer(packetsPerRequests * packetSize);
}
// API
public void setInterface(AlternateUsbInterface usbInterface) throws IOException {
IoctlUtils.res(jni_setInterface(fileDescriptor, usbInterface.getUsbInterface().getId(), usbInterface.getAlternateSettings()));
}
public void unsetInterface(AlternateUsbInterface usbInterface) throws IOException {
// According to original UsbHiSpeedBulk alternatesetting of 0 stops the streaming
IoctlUtils.res(jni_setInterface(fileDescriptor, usbInterface.getUsbInterface().getId(), 0));
}
public void start() throws IOException {
for (int i = 0; i < nrequests; i++) {
IsoRequest req = new IsoRequest(usbDeviceConnection, usbEndpoint, i, packetsPerRequests, packetSize);
try {
req.submit();
requests.add(req);
} catch (IOException e) {
// No more memory for allocating packets
e.printStackTrace();
break;
}
}
if (requests.isEmpty()) throw new IOException("Cannot initialize any USB requests");
}
/**
* Buffer is not immutable! Next time you call #read, its value will be invalid and overwriten.
* The buffer is reused for efficiency.
* @param wait whther to block until data is available
* @return a buffer or null if nothing is available
* @throws IOException
*/
public Buffer read(boolean wait) throws IOException {
IsoRequest req = getReadyRequest(wait);
if (req == null) return null;
buffer.length = req.read(buffer.data);
req.reset();
req.submit();
return buffer;
}
public void stop() throws IOException {
for (IsoRequest r : requests) {
r.cancel();
}
requests.clear();
}
public class Buffer {
private final byte[] data;
private int length;
private Buffer(int bufferSize) {
this.data = new byte[bufferSize];
}
public byte[] getData() {
return data;
}
public int getLength() {
return length;
}
}
// helpers
private IsoRequest getReadyRequest(boolean wait) throws IOException {
int readyRequestId = IsoRequest.getReadyRequestId(usbDeviceConnection, wait);
if (readyRequestId < 0) return null;
return requests.get(readyRequestId);
}
// native
private static native int jni_setInterface(int fd, int interfaceId, int alternateSettings);
}
| 5,133 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
RequestTest.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/test/java/info/martinmarinov/dvbservice/RequestTest.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice;
import android.util.Log;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.Mock;
import org.powermock.core.classloader.annotations.PowerMockIgnore;
import org.powermock.core.classloader.annotations.PrepareForTest;
import org.powermock.modules.junit4.PowerMockRunner;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import info.martinmarinov.drivers.DvbDevice;
import info.martinmarinov.drivers.DvbStatus;
import info.martinmarinov.drivers.tools.SetUtils;
import info.martinmarinov.drivers.DeliverySystem;
import static info.martinmarinov.drivers.tools.SetUtils.setOf;
import static org.hamcrest.CoreMatchers.is;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.mockito.Answers.RETURNS_DEEP_STUBS;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
import static org.mockito.MockitoAnnotations.initMocks;
import static org.powermock.api.mockito.PowerMockito.mockStatic;
@RunWith(PowerMockRunner.class)
@PrepareForTest({Log.class})
@PowerMockIgnore("jdk.internal.reflect.*")
public class RequestTest {
@Mock(answer = RETURNS_DEEP_STUBS)
private DvbDevice dvbDevice;
@Before
public void setUp() {
initMocks(this);
mockStatic(Log.class);
}
@Test
public void testProtocolVersion() {
long[] response = getRawResponse(0);
assertThat(response.length, is(3));
assertThat(response[0], is(1L)); // success
assertThat(response[1], is(0L)); // version of protocol
assertThat(response[2], is((long) Request.values().length)); // number of available requests
}
@Test
public void testExit() {
long[] response = getRawResponse(1);
assertThat(response.length, is(1));
assertThat(response[0], is(1L)); // success
}
@Test
public void testTune() throws Exception {
long[] response = getRawResponse(2, 506_000_000L, 8_000_000L, 1L);
assertThat(response.length, is(1));
assertThat(response[0], is(1L)); // success
// verify hardware was called
verify(dvbDevice).tune(506_000_000L, 8_000_000L, DeliverySystem.DVBT2);
}
@Test
public void testGetStatus() throws Exception {
when(dvbDevice.getStatus()).thenReturn(setOf(DvbStatus.FE_HAS_SIGNAL, DvbStatus.FE_HAS_CARRIER, DvbStatus.FE_HAS_VITERBI));
when(dvbDevice.readBitErrorRate()).thenReturn(123);
when(dvbDevice.readDroppedUsbFps()).thenReturn(456);
when(dvbDevice.readRfStrengthPercentage()).thenReturn(10);
when(dvbDevice.readSnr()).thenReturn(300);
long[] response = getRawResponse(3);
assertThat(response.length, is(9));
assertThat(response[0], is(1L)); // success
assertThat(response[1], is(300L)); // SNR
assertThat(response[2], is(123L)); // BER
assertThat(response[3], is(456L)); // Dropped FPS
assertThat(response[4], is(10L)); // RF strength as percentage
assertThat(response[5], is(1L)); // has signal
assertThat(response[6], is(1L)); // has carrier
assertThat(response[7], is(0L)); // no sync
assertThat(response[8], is(0L)); // no lock
}
@Test
public void setPids() throws Exception {
long[] response = getRawResponse(4, 0x1FF0L, 0x1277L, 0x0010L);
assertThat(response.length, is(1));
assertThat(response[0], is(1L)); // success
// verify hardware was called
verify(dvbDevice).setPidFilter(0x1FF0, 0x1277, 0x0010);
}
@Test
public void testGetCapabilities() throws Exception {
when(dvbDevice.readCapabilities().getFrequencyMin()).thenReturn(174000000L);
when(dvbDevice.readCapabilities().getFrequencyMax()).thenReturn(862000000L);
when(dvbDevice.readCapabilities().getFrequencyStepSize()).thenReturn(166667L);
when(dvbDevice.readCapabilities().getSupportedDeliverySystems()).thenReturn(SetUtils.setOf(DeliverySystem.DVBT, DeliverySystem.DVBT2, DeliverySystem.DVBC));
when(dvbDevice.getDeviceFilter().getVendorId()).thenReturn(0x0BDA);
when(dvbDevice.getDeviceFilter().getProductId()).thenReturn(0x2838);
long[] response = getRawResponse(5);
assertThat(response.length, is(7));
assertThat(response[0], is(1L)); // success
assertThat(response[1], is(0x7L)); // Capabilities flags
assertThat(response[2], is(174000000L)); // freq min
assertThat(response[3], is(862000000L)); // freq max
assertThat(response[4], is(166667L)); // step
assertThat(response[5], is(0x0BDAL)); // USB vendor id
assertThat(response[6], is(0x2838L)); // USB product id
}
/** Helper to do serialization/deserialization to bytes */
private long[] getRawResponse(int requestOrdinal, long ... reqArgs) {
try {
// Serialize request into bytes
ByteArrayOutputStream reqArgStream = new ByteArrayOutputStream();
DataOutputStream reqArgsWriter = new DataOutputStream(reqArgStream);
reqArgsWriter.write(requestOrdinal);
reqArgsWriter.write(reqArgs.length);
for (Long arg : reqArgs) reqArgsWriter.writeLong(arg);
byte[] requestBytes = reqArgStream.toByteArray();
// Run request
ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); // to store output
DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(requestBytes));
DataOutputStream dataOutputStream = new DataOutputStream(outputStream);
Request.parseAndExecute(dataInputStream, dataOutputStream, dvbDevice);
// De-serialize response
DataInputStream payloadStream = new DataInputStream(new ByteArrayInputStream(outputStream.toByteArray()));
assertThat(payloadStream.read(), is(requestOrdinal));
int size = payloadStream.readByte();
long[] rawPayload = new long[size];
for (int i = 0; i < size; i++) rawPayload[i] = payloadStream.readLong();
assertThat(payloadStream.available(), is(0));
// Some cleanup
dataInputStream.close();
dataOutputStream.close();
payloadStream.close();
reqArgStream.close();
return rawPayload;
} catch (Exception e) {
throw new RuntimeException(e);
}
}
} | 7,441 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
TsDumpFileUtilsTest.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/test/java/info/martinmarinov/dvbservice/tools/TsDumpFileUtilsTest.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice.tools;
import android.content.Context;
import org.junit.Before;
import org.junit.Test;
import org.mockito.Mock;
import java.io.File;
import java.util.Calendar;
import java.util.Date;
import java.util.GregorianCalendar;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.CoreMatchers.is;
import static org.hamcrest.CoreMatchers.nullValue;
import static org.junit.Assert.assertThat;
import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import static org.mockito.MockitoAnnotations.initMocks;
public class TsDumpFileUtilsTest {
private final static File ROOT = new File("/imaginary/root");
@Mock
private Context context;
@Before
public void setUp() {
initMocks(this);
when(context.getExternalFilesDir(anyString())).thenReturn(ROOT);
}
@Test
public void testNameCreation() {
File actual = TsDumpFileUtils.getFor(context, 506_000_000L, 8_000_000L, date(2017, 1, 10, 13, 4, 24));
assertThat(actual, equalTo(new File(ROOT, "mux_506000000_8000000_20170110130424.ts")));
}
@SuppressWarnings("ConstantConditions") // yeah I know res could be know
@Test
public void testParsing() {
TsDumpFileUtils.FreqBandwidth res =
TsDumpFileUtils.getFreqAndBandwidth(new File(ROOT, "mux_506000000_8000000_20170110130424.ts"));
assertThat(res.freq, is(506_000_000L));
assertThat(res.bandwidth, is(8_000_000L));
}
@SuppressWarnings("ConstantConditions") // yeah I know res could be know
@Test
public void testParsing_withoutDate() {
TsDumpFileUtils.FreqBandwidth res =
TsDumpFileUtils.getFreqAndBandwidth(new File(ROOT, "mux_506000000_8000000_randomSuffix.ts"));
assertThat(res.freq, is(506_000_000L));
assertThat(res.bandwidth, is(8_000_000L));
}
@Test
public void testUnparseable_RandomString() {
TsDumpFileUtils.FreqBandwidth res =
TsDumpFileUtils.getFreqAndBandwidth(new File(ROOT, "fsdjfmadjk3312"));
assertThat(res, nullValue());
}
@Test
public void testUnparseable_noExt() {
TsDumpFileUtils.FreqBandwidth res =
TsDumpFileUtils.getFreqAndBandwidth(new File(ROOT, "mux_506000000_8000000_20170110130424"));
assertThat(res, nullValue());
}
@Test
public void testUnparseable_noPrefix() {
TsDumpFileUtils.FreqBandwidth res =
TsDumpFileUtils.getFreqAndBandwidth(new File(ROOT, "506000000_8000000_20170110130424.ts"));
assertThat(res, nullValue());
}
private static Date date(int year, int month, int day, int hour, int minute, int second) {
Calendar c = new GregorianCalendar();
c.set(Calendar.YEAR, year);
c.set(Calendar.MONTH, month - 1);
c.set(Calendar.DAY_OF_MONTH, day);
c.set(Calendar.HOUR_OF_DAY, hour);
c.set(Calendar.MINUTE, minute);
c.set(Calendar.SECOND, second);
return c.getTime();
}
} | 3,932 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
StackTraceSerializerTest.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/test/java/info/martinmarinov/dvbservice/tools/StackTraceSerializerTest.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice.tools;
import org.junit.Test;
import java.io.IOException;
import static junit.framework.Assert.assertTrue;
public class StackTraceSerializerTest {
@Test
public void testSerialize() throws Exception {
String serialization = StackTraceSerializer.serialize(new IOException("Test message"));
assertTrue(serialization.startsWith("java.io.IOException: Test message\n" +
"\tat "+StackTraceSerializerTest.class.getName()+"."));
}
} | 1,371 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
Response.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/main/java/info/martinmarinov/dvbservice/Response.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice;
import java.io.IOException;
import java.io.OutputStream;
/**
* This is send to the client as a result of every Request received
*
* byte 0 will be the Request.ordinal of the Request
* byte 1 will be N the number of longs in the payload
* byte 3 to byte 6 will be the success flag (0 or 1). This indicates whether the request was succesful.
* byte 7 till the end the rest of the longs in the payload follow
*
* Basically the success flag is always part of the payload, so the payload
* always consists of at least one value.
*/
class Response {
static Response ERROR = error();
static Response SUCCESS = success();
private final boolean success;
private final long[] payload;
static Response success(long... payload) {
return new Response(true, payload);
}
private static Response error(long... payload) {
return new Response(false, payload);
}
private Response(boolean success, long ... payload) {
this.success = success;
this.payload = payload;
}
private static void writeLong(byte[] buff, int off, long v) {
buff[off] = (byte)(v >>> 56);
buff[off+1] = (byte)(v >>> 48);
buff[off+2] = (byte)(v >>> 40);
buff[off+3] = (byte)(v >>> 32);
buff[off+4] = (byte)(v >>> 24);
buff[off+5] = (byte)(v >>> 16);
buff[off+6] = (byte)(v >>> 8);
buff[off+7] = (byte)(v);
}
void serialize(Request request, OutputStream dataOutputStream) throws IOException {
byte[] payload_raw = new byte[2 + 8 + payload.length * 8];
payload_raw[0] = (byte) request.ordinal(); // what request called it
payload_raw[1] = (byte) (payload.length + 1); // the success flag is part of the payload
writeLong(payload_raw, 2, success ? 1 : 0); // success flag
for (int i = 0; i < payload.length; i++) {
writeLong(payload_raw, 2 + 8 + i * 8, payload[i]); // write actual payload if any
}
dataOutputStream.write(payload_raw); // raw payload in one chunk to avoid any TCP partitioning
dataOutputStream.flush(); // force send over the pipe, don't wait
}
}
| 3,060 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
Request.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/main/java/info/martinmarinov/dvbservice/Request.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice;
import android.util.Log;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.net.SocketException;
import java.util.Set;
import info.martinmarinov.drivers.DeliverySystem;
import info.martinmarinov.drivers.DvbCapabilities;
import info.martinmarinov.drivers.DvbDevice;
import info.martinmarinov.drivers.DvbException;
import info.martinmarinov.drivers.DvbStatus;
/**
* The client sends a command consisting of a variable number of Longs in the following format:
* <p>
* byte 0 will be the Request.ordinal of the request
* byte 1 will be N the number of longs in the payload
* byte 2 to 8*N+1 will consist the actual values of the payload
* <p>
* After the request has been processed it returns a Response, which is in a similar format.
* Please refer to the Response documentation for more info
* <p>
* Warning: For backwards compatibility order of the enum will be always preserved
*/
enum Request {
REQ_PROTOCOL_VERSION(
new Executor() {
@Override
public Response execute(DvbDevice dvbDevice, long... payload) throws DvbException {
// Clients can use it to determine whether new features
// are available.
// WARNING: Backward compatibility should always be ensured
return Response.success(
0L, // parameter 1, version, when adding capabilities, change that number.
ALL_REQUESTS.length // parameter 2, can be useful for determining supported commands
);
}
}
),
REQ_EXIT(new Executor() {
@Override
public Response execute(DvbDevice dvbDevice, long... payload) {
Log.d(TAG, "Client requested to close the connection");
return Response.SUCCESS;
}
}),
REQ_TUNE(new Executor() {
@Override
public Response execute(DvbDevice dvbDevice, long... payload) throws DvbException {
long frequency = payload[0]; // frequency in herz
long bandwidth = payload[1]; // bandwidth in herz.
// Typical value for DVB-T is 8_000_000
DeliverySystem deliverySystem = DeliverySystem.values()[(int) payload[2]];
// Check enum for actual values
Log.d(TAG, "Client requested tune to " + frequency + " Hz with bandwidth " + bandwidth + " Hz with delivery system " + deliverySystem);
dvbDevice.tune(frequency, bandwidth, deliverySystem);
return Response.SUCCESS;
}
}),
REQ_GET_STATUS(new Executor() {
@Override
public Response execute(DvbDevice dvbDevice, long... ignored) throws DvbException {
int snr = dvbDevice.readSnr();
int bitErrorRate = dvbDevice.readBitErrorRate();
int droppedUsbFps = dvbDevice.readDroppedUsbFps();
int rfStrengthPercentage = dvbDevice.readRfStrengthPercentage();
Set<DvbStatus> status = dvbDevice.getStatus();
boolean hasSignal = status.contains(DvbStatus.FE_HAS_SIGNAL);
boolean hasCarrier = status.contains(DvbStatus.FE_HAS_CARRIER);
boolean hasSync = status.contains(DvbStatus.FE_HAS_SYNC);
boolean hasLock = status.contains(DvbStatus.FE_HAS_LOCK);
return Response.success(
(long) snr, // parameter 1
(long) bitErrorRate, // parameter 2
(long) droppedUsbFps, // parameter 3
(long) rfStrengthPercentage, // parameter 4
hasSignal ? 1L : 0L, // parameter 5
hasCarrier ? 1L : 0L, // parameter 6
hasSync ? 1L : 0L, // parameter 7
hasLock ? 1L : 0L // parameter 8
);
}
}),
REQ_SET_PIDS(new Executor() {
@Override
public Response execute(DvbDevice dvbDevice, long... payload) throws DvbException {
int[] pids = new int[payload.length];
for (int i = 0; i < payload.length; i++) pids[i] = (int) payload[i];
dvbDevice.setPidFilter(pids);
return Response.SUCCESS;
}
}),
REQ_GET_CAPABILITIES(new Executor() {
@Override
public Response execute(DvbDevice dvbDevice, long... payload) throws DvbException {
DvbCapabilities frontendProperties = dvbDevice.readCapabilities();
// Only up to 62 deliverySystems are supported under current encoding method
if (frontendProperties.getSupportedDeliverySystems().size() > 62)
throw new IllegalStateException();
long supportedDeliverySystems = 0;
for (DeliverySystem deliverySystem : frontendProperties.getSupportedDeliverySystems()) {
supportedDeliverySystems |= 1 << deliverySystem.ordinal();
}
return Response.success(
supportedDeliverySystems, // parameter 1
frontendProperties.getFrequencyMin(), // parameter 2
frontendProperties.getFrequencyMax(), // parameter 3
frontendProperties.getFrequencyStepSize(), // parameter 4
(long) dvbDevice.getDeviceFilter().getVendorId(), // parameter 5
(long) dvbDevice.getDeviceFilter().getProductId() // parameter 6
);
}
});
private final static String TAG = Request.class.getSimpleName();
private final static Request[] ALL_REQUESTS = values();
private final Executor executor;
Request(Executor executor) {
this.executor = executor;
}
private Response execute(DvbDevice dvbDevice, long... payload) {
try {
return executor.execute(dvbDevice, payload);
} catch (Exception e) {
e.printStackTrace();
return Response.ERROR;
}
}
private static void readBytes(InputStream inputStream, byte[] read_buffer) throws IOException {
int bytesRead = 0;
while (bytesRead < read_buffer.length) {
int count = inputStream.read(read_buffer, bytesRead, read_buffer.length - bytesRead);
if (count < 0) {
throw new SocketException("End of stream reached before reading required number of bytes");
}
bytesRead += count;
}
}
private static long readLongAtByte(byte[] read_buffer, int offset) {
return (((long) read_buffer[offset] << 56) +
((long) (read_buffer[offset + 1] & 255) << 48) +
((long) (read_buffer[offset + 2] & 255) << 40) +
((long) (read_buffer[offset + 3] & 255) << 32) +
((long) (read_buffer[offset + 4] & 255) << 24) +
((read_buffer[offset + 5] & 255) << 16) +
((read_buffer[offset + 6] & 255) << 8) +
((read_buffer[offset + 7] & 255)));
}
private static long[] parsePayload(InputStream inputStream, int size) throws IOException {
byte[] payload_buffer = new byte[size * 8];
readBytes(inputStream, payload_buffer);
long[] payload = new long[size];
for (int i = 0; i < payload.length; i++) {
payload[i] = readLongAtByte(payload_buffer, i * 8);
}
return payload;
}
public static Request parseAndExecute(InputStream inputStream, OutputStream outputStream, DvbDevice dvbDevice) throws IOException {
Request req = null;
byte[] head_buffer = new byte[2];
readBytes(inputStream, head_buffer);
int ordinal = head_buffer[0] & 0xFF;
int size = head_buffer[1] & 0xFF;
long[] payload = parsePayload(inputStream, size);
if (ordinal < ALL_REQUESTS.length) {
req = ALL_REQUESTS[ordinal];
// This command is recognized, execute and get response
Response r = req.execute(dvbDevice, payload);
// Send response back over the wire
r.serialize(req, outputStream);
}
return req;
}
private interface Executor {
Response execute(DvbDevice dvbDevice, long... payload) throws DvbException;
}
}
| 9,172 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
DvbServerPorts.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/main/java/info/martinmarinov/dvbservice/DvbServerPorts.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice;
import java.io.Serializable;
class DvbServerPorts implements Serializable {
private final int controlPort;
private final int transferPort;
DvbServerPorts(int controlPort, int transferPort) {
this.controlPort = controlPort;
this.transferPort = transferPort;
}
int getControlPort() {
return controlPort;
}
int getTransferPort() {
return transferPort;
}
} | 1,321 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
UsbDelegate.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/main/java/info/martinmarinov/dvbservice/UsbDelegate.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice;
import android.app.Activity;
import android.content.ActivityNotFoundException;
import android.content.Intent;
import android.hardware.usb.UsbDevice;
import android.hardware.usb.UsbManager;
import android.os.Bundle;
import android.util.Log;
public class UsbDelegate extends Activity {
private static final String TAG = UsbDelegate.class.getSimpleName();
private static final String ACTION_DVB_DEVICE_ATTACHED = "info.martinmarinov.dvbdriver.DVB_DEVICE_ATTACHED";
@Override
public void onCreate(Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
Intent intent = getIntent();
if (UsbManager.ACTION_USB_DEVICE_ATTACHED.equals(intent.getAction())) {
UsbDevice usbDevice = intent.getParcelableExtra(UsbManager.EXTRA_DEVICE);
Log.d(TAG, "USB DVB-T attached: " + usbDevice.getDeviceName());
Intent newIntent = new Intent(ACTION_DVB_DEVICE_ATTACHED);
newIntent.putExtra(UsbManager.EXTRA_DEVICE, usbDevice);
try {
startActivity(newIntent);
} catch (ActivityNotFoundException e) {
Log.d(TAG, "No activity found for DVB-T handling");
}
}
finish();
}
} | 2,134 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
DvbServer.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/main/java/info/martinmarinov/dvbservice/DvbServer.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice;
import java.io.Closeable;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.net.InetAddress;
import java.net.InetSocketAddress;
import java.net.ServerSocket;
import java.net.Socket;
import java.net.SocketException;
import info.martinmarinov.drivers.DvbDevice;
import info.martinmarinov.drivers.DvbException;
class DvbServer implements Closeable {
private final static int SOCKET_TIMEOUT_MS = 60 * 1_000;
private final ServerSocket controlSocket = new ServerSocket();
private final ServerSocket transferSocket = new ServerSocket();
private final DvbDevice dvbDevice;
DvbServer(DvbDevice dvbDevice) throws IOException {
this.dvbDevice = dvbDevice;
}
DvbServerPorts bind(InetAddress address) throws IOException {
return bind(new InetSocketAddress(address, 0));
}
private DvbServerPorts bind(InetSocketAddress address) throws IOException {
try {
controlSocket.bind(address);
transferSocket.bind(address);
controlSocket.setSoTimeout(SOCKET_TIMEOUT_MS);
transferSocket.setSoTimeout(SOCKET_TIMEOUT_MS);
if (!controlSocket.getInetAddress().equals(transferSocket.getInetAddress()))
throw new IllegalStateException();
return new DvbServerPorts(controlSocket.getLocalPort(), transferSocket.getLocalPort());
} catch (IOException e) {
close();
throw e;
}
}
void open() throws DvbException {
dvbDevice.open();
}
@Override
public void close() {
quietClose(dvbDevice);
quietClose(controlSocket);
quietClose(transferSocket);
}
void serve() throws IOException {
InputStream inputStream = null;
OutputStream outputStream = null;
Socket control = null;
try {
control = controlSocket.accept();
control.setTcpNoDelay(true);
inputStream = control.getInputStream();
outputStream = control.getOutputStream();
final InputStream finInputStream = inputStream;
TransferThread worker = new TransferThread(dvbDevice, transferSocket, new TransferThread.OnClosedCallback() {
@Override
public void onClosed() {
// Close input stream to cancel the request parsing
quietClose(finInputStream);
}
});
try {
worker.start();
while (worker.isAlive() && !Thread.currentThread().isInterrupted()) {
Request c = Request.parseAndExecute(inputStream, outputStream, dvbDevice);
if (c == Request.REQ_EXIT) break;
}
} catch (SocketException e) {
IOException workerException = worker.signalAndWaitToDie();
if (workerException != null) throw workerException;
throw e;
}
// Finish successfully due to exit command, if worker failed for anything other
// than a socket exception, throw it
IOException workerException = worker.signalAndWaitToDie();
if (workerException != null && !(workerException instanceof SocketException)) throw workerException;
} finally {
quietClose(inputStream);
quietClose(outputStream);
quietClose(control);
}
}
private static void quietClose(Closeable c) {
if (c != null) {
try {
c.close();
} catch (IOException e) {
e.printStackTrace();
}
}
}
private static void quietClose(Socket socket) {
if (socket != null) {
try {
socket.close();
} catch (IOException e) {
e.printStackTrace();
}
}
}
private static void quietClose(ServerSocket socket) {
if (socket != null) {
try {
socket.close();
} catch (IOException e) {
e.printStackTrace();
}
}
}
}
| 5,087 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
DvbService.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/main/java/info/martinmarinov/dvbservice/DvbService.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice;
import android.app.Activity;
import android.app.Notification;
import android.app.NotificationChannel;
import android.app.NotificationManager;
import android.app.Service;
import android.content.Context;
import android.content.Intent;
import android.os.Build;
import android.os.IBinder;
import androidx.annotation.Nullable;
import androidx.core.app.NotificationCompat;
import androidx.localbroadcastmanager.content.LocalBroadcastManager;
import android.util.Log;
import java.io.Serializable;
import java.util.List;
import info.martinmarinov.drivers.DeviceFilter;
import info.martinmarinov.drivers.DvbDevice;
import info.martinmarinov.drivers.DvbException;
import info.martinmarinov.drivers.usb.DvbUsbDeviceRegistry;
import info.martinmarinov.dvbservice.tools.InetAddressTools;
import info.martinmarinov.dvbservice.tools.TsDumpFileUtils;
import static info.martinmarinov.drivers.DvbException.ErrorCode.CANNOT_OPEN_USB;
public class DvbService extends Service {
private static final String TAG = DvbService.class.getSimpleName();
private final static int ONGOING_NOTIFICATION_ID = 743713489; // random id
public static final String BROADCAST_ACTION = "info.martinmarinov.dvbservice.DvbService.BROADCAST";
private final static String DEVICE_FILTER = "DeviceFilter";
private final static String STATUS_MESSAGE = "StatusMessage";
private static Thread worker;
static void requestOpen(Activity activity, DeviceFilter deviceFilter) {
Intent intent = new Intent(activity, DvbService.class)
.putExtra(DEVICE_FILTER, deviceFilter);
activity.startService(intent);
}
static StatusMessage parseMessage(Intent intent) {
return (StatusMessage) intent.getSerializableExtra(STATUS_MESSAGE);
}
@Override
public int onStartCommand(Intent intent, int flags, int startId) {
final DeviceFilter deviceFilter = (DeviceFilter) intent.getSerializableExtra(DEVICE_FILTER);
// Kill existing connection
if (worker != null && worker.isAlive()) {
worker.interrupt();
try {
worker.join(15_000L);
} catch (InterruptedException ignored) {}
if (worker != null && worker.isAlive()) {
throw new RuntimeException("Cannot stop existing service");
}
}
worker = new Thread() {
@Override
public void run() {
DvbServer dvbServer = null;
try {
dvbServer = new DvbServer(getDeviceFromFilter(deviceFilter));
DvbServerPorts dvbServerPorts = dvbServer.bind(InetAddressTools.getLocalLoopback());
dvbServer.open();
// Device was opened! Tell client it's time to connect
broadcastStatus(new StatusMessage(null, dvbServerPorts, deviceFilter));
startForeground();
dvbServer.serve();
} catch (Exception e) {
e.printStackTrace();
broadcastStatus(new StatusMessage(e, null, deviceFilter));
} finally {
if (dvbServer != null) dvbServer.close();
}
Log.d(TAG, "Finished");
worker = null;
stopSelf();
}
};
worker.start();
return START_NOT_STICKY;
}
private void startForeground() {
NotificationManager notificationManager = (NotificationManager) getSystemService(Context.NOTIFICATION_SERVICE);
String NOTIFICATION_CHANNEL_ID = "DvbDriver";
if (notificationManager != null && Build.VERSION.SDK_INT >= Build.VERSION_CODES.O) {
NotificationChannel notificationChannel = new NotificationChannel(
NOTIFICATION_CHANNEL_ID, "DVB-T driver notifications",
NotificationManager.IMPORTANCE_HIGH
);
// Configure the notification channel.
notificationChannel.setDescription("When DVB-T driver operates");
notificationChannel.enableVibration(false);
notificationManager.createNotificationChannel(notificationChannel);
}
NotificationCompat.Builder builder = new NotificationCompat.Builder(this, NOTIFICATION_CHANNEL_ID)
.setAutoCancel(false)
.setOngoing(true)
.setContentTitle(getText(R.string.app_name))
.setContentText(getText(R.string.driver_description))
.setSmallIcon(R.drawable.ic_notification);
if (android.os.Build.VERSION.SDK_INT >= android.os.Build.VERSION_CODES.JELLY_BEAN) {
builder = builder
.setPriority(Notification.PRIORITY_MAX);
}
startForeground(ONGOING_NOTIFICATION_ID, builder.build());
}
private DvbDevice getDeviceFromFilter(DeviceFilter deviceFilter) throws DvbException {
List<DvbDevice> dvbDevices = DvbUsbDeviceRegistry.getUsbDvbDevices(this);
dvbDevices.addAll(TsDumpFileUtils.getDevicesForAllRecordings(this));
for (DvbDevice dvbDevice : dvbDevices) {
if (dvbDevice.getDeviceFilter().equals(deviceFilter)) return dvbDevice;
}
throw new DvbException(CANNOT_OPEN_USB, getString(R.string.device_no_longer_available));
}
private void broadcastStatus(StatusMessage statusMessage) {
Intent intent = new Intent(BROADCAST_ACTION)
.putExtra(STATUS_MESSAGE, statusMessage);
LocalBroadcastManager.getInstance(this).sendBroadcast(intent);
}
@Nullable
@Override
public IBinder onBind(Intent intent) {
return null;
}
static class StatusMessage implements Serializable {
final Exception exception;
final DvbServerPorts serverAddresses;
final DeviceFilter deviceFilter;
private StatusMessage(Exception exception, DvbServerPorts serverAddresses, DeviceFilter deviceFilter) {
this.exception = exception;
this.serverAddresses = serverAddresses;
this.deviceFilter = deviceFilter;
}
}
}
| 7,069 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
DeviceChooserActivity.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/main/java/info/martinmarinov/dvbservice/DeviceChooserActivity.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice;
import android.content.BroadcastReceiver;
import android.content.Context;
import android.content.Intent;
import android.content.IntentFilter;
import android.hardware.usb.UsbDevice;
import android.hardware.usb.UsbManager;
import android.os.Bundle;
import androidx.annotation.NonNull;
import androidx.fragment.app.FragmentActivity;
import androidx.fragment.app.FragmentActivity;
import androidx.localbroadcastmanager.content.LocalBroadcastManager;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import info.martinmarinov.drivers.DeviceFilter;
import info.martinmarinov.drivers.DvbDevice;
import info.martinmarinov.drivers.DvbException;
import info.martinmarinov.drivers.usb.DvbUsbDeviceRegistry;
import info.martinmarinov.dvbservice.dialogs.ListPickerFragmentDialog;
import info.martinmarinov.dvbservice.tools.StackTraceSerializer;
import info.martinmarinov.dvbservice.tools.TsDumpFileUtils;
import static info.martinmarinov.drivers.DvbException.ErrorCode.NO_DVB_DEVICES_FOUND;
public class DeviceChooserActivity extends FragmentActivity implements ListPickerFragmentDialog.OnSelected<DeviceFilter> {
private final static int RESULT_ERROR = RESULT_FIRST_USER;
private final static String CONTRACT_ERROR_CODE = "ErrorCode";
private final static String CONTRACT_CONTROL_PORT = "ControlPort";
private final static String CONTRACT_TRANSFER_PORT = "TransferPort";
private final static String CONTRACT_DEVICE_NAME = "DeviceName";
private final static String CONTRACT_RAW_TRACE = "RawTrace";
private final static String CONTRACT_USB_PRODUCT_IDS = "ProductIds";
private final static String CONTRACT_USB_VENDOR_IDS = "VendorIds";
private final Intent response = new Intent();
@Override
protected void onCreate(Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
setContentView(R.layout.progress);
// Set to receive info from the DvbService
IntentFilter statusIntentFilter = new IntentFilter(DvbService.BROADCAST_ACTION);
LocalBroadcastManager.getInstance(this).registerReceiver(new DvbServiceResponseReceiver(), statusIntentFilter);
}
@Override
protected void onStart() {
super.onStart();
try {
List<DvbDevice> dvbDevices = DvbUsbDeviceRegistry.getUsbDvbDevices(this);
List<DvbDevice> dvbFileDevices = TsDumpFileUtils.getDevicesForAllRecordings(this); // these are only for debugging purposes
dvbDevices.addAll(dvbFileDevices);
if (dvbDevices.isEmpty()) throw new DvbException(NO_DVB_DEVICES_FOUND, getString(info.martinmarinov.drivers.R.string.no_devices_found));
List<DeviceFilter> deviceFilters = new ArrayList<>(dvbDevices.size());
for (DvbDevice dvbDevice : dvbDevices) {
deviceFilters.add(dvbDevice.getDeviceFilter());
}
if (deviceFilters.size() > 1 || !dvbFileDevices.isEmpty()) {
ListPickerFragmentDialog.showOneInstanceOnly(getSupportFragmentManager(), deviceFilters);
} else {
DvbService.requestOpen(this, deviceFilters.get(0));
}
} catch (DvbException e) {
handleException(e);
}
}
@Override
public void onListPickerDialogItemSelected(@NonNull DeviceFilter deviceFilter) {
DvbService.requestOpen(this, deviceFilter);
}
@Override
public void onListPickerDialogCanceled() {
finishWith(RESULT_CANCELED);
}
// Open selected device
private class DvbServiceResponseReceiver extends BroadcastReceiver {
@Override
public void onReceive(Context context, Intent intent) {
DvbService.StatusMessage statusMessage = DvbService.parseMessage(intent);
if (statusMessage.exception != null) {
Exception exception = statusMessage.exception;
if (exception instanceof DvbException) {
handleException((DvbException) exception);
} else if (exception instanceof IOException) {
handleException(new DvbException(DvbException.ErrorCode.IO_EXCEPTION, exception));
} else if (exception instanceof RuntimeException) {
throw (RuntimeException) exception;
} else {
throw new RuntimeException(exception);
}
} else {
handleSuccess(statusMessage.deviceFilter, statusMessage.serverAddresses);
}
}
}
// API for returning response to caller
private void handleSuccess(DeviceFilter deviceFilter, DvbServerPorts addresses) {
int[] productIds = new int[] {deviceFilter.getProductId()};
int[] vendorIds = new int[] {deviceFilter.getVendorId()};
response.putExtra(CONTRACT_DEVICE_NAME, deviceFilter.getName());
response.putExtra(CONTRACT_USB_PRODUCT_IDS, productIds);
response.putExtra(CONTRACT_USB_VENDOR_IDS, vendorIds);
response.putExtra(CONTRACT_CONTROL_PORT, addresses.getControlPort());
response.putExtra(CONTRACT_TRANSFER_PORT, addresses.getTransferPort());
finishWith(RESULT_OK);
}
private void handleException(DvbException e) {
UsbManager manager = (UsbManager) getSystemService(Context.USB_SERVICE);
Collection<UsbDevice> availableDevices = manager.getDeviceList().values();
int[] productIds = new int[availableDevices.size()];
int[] vendorIds = new int[availableDevices.size()];
int id = 0;
for (UsbDevice usbDevice : availableDevices) {
productIds[id] = usbDevice.getProductId();
vendorIds[id] = usbDevice.getVendorId();
id++;
}
response.putExtra(CONTRACT_ERROR_CODE, e.getErrorCode().name());
response.putExtra(CONTRACT_RAW_TRACE, StackTraceSerializer.serialize(e));
response.putExtra(CONTRACT_USB_PRODUCT_IDS, productIds);
response.putExtra(CONTRACT_USB_VENDOR_IDS, vendorIds);
finishWith(RESULT_ERROR);
}
private void finishWith(int code) {
if (getParent() == null) {
setResult(code, response);
} else {
getParent().setResult(code, response);
}
finish();
}
}
| 7,241 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
TransferThread.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/main/java/info/martinmarinov/dvbservice/TransferThread.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice;
import java.io.Closeable;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.net.ServerSocket;
import java.net.Socket;
import info.martinmarinov.drivers.DvbDevice;
class TransferThread extends Thread {
private final DvbDevice dvbDevice;
private final ServerSocket serverSocket;
private final OnClosedCallback callback;
private IOException lastException = null;
private InputStream transportStream;
TransferThread(DvbDevice dvbDevice, ServerSocket serverSocket, OnClosedCallback callback) {
this.dvbDevice = dvbDevice;
this.serverSocket = serverSocket;
this.callback = callback;
}
@Override
public void interrupt() {
super.interrupt();
quietClose(serverSocket);
quietClose(transportStream);
}
@Override
public void run() {
setName(TransferThread.class.getSimpleName());
setPriority(NORM_PRIORITY);
OutputStream os = null;
Socket socket = null;
try {
socket = serverSocket.accept();
socket.setTcpNoDelay(true);
byte[] buf = new byte[5 * 188];
os = socket.getOutputStream();
transportStream = dvbDevice.getTransportStream(new DvbDevice.StreamCallback() {
@Override
public void onStreamException(IOException exception) {
lastException = exception;
interrupt();
}
@Override
public void onStoppedStreaming() {
interrupt();
}
});
while (!isInterrupted()) {
int inlength = transportStream.read(buf);
if (inlength > 0) {
os.write(buf, 0, inlength);
} else {
// No data, sleep for a bit until available
quietSleep(10);
}
}
} catch (IOException e) {
lastException = e;
} finally {
quietClose(os);
quietClose(socket);
quietClose(transportStream);
callback.onClosed();
}
}
private void quietSleep(long ms) {
try {
Thread.sleep(ms);
} catch (InterruptedException e) {
interrupt();
}
}
private void quietClose(Closeable c) {
if (c != null) {
try {
c.close();
} catch (IOException e) {
if (lastException == null) lastException = e;
}
}
}
private void quietClose(Socket s) {
if (s != null) {
try {
s.close();
} catch (IOException e) {
if (lastException == null) lastException = e;
}
}
}
private void quietClose(ServerSocket s) {
if (s != null) {
try {
s.close();
} catch (IOException e) {
if (lastException == null) lastException = e;
}
}
}
IOException signalAndWaitToDie() {
if (isAlive()) {
interrupt();
try {
join();
} catch (InterruptedException e) {
e.printStackTrace();
}
}
return lastException;
}
interface OnClosedCallback {
void onClosed();
}
}
| 4,362 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
StackTraceSerializer.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/main/java/info/martinmarinov/dvbservice/tools/StackTraceSerializer.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice.tools;
import java.io.ByteArrayOutputStream;
import java.io.PrintStream;
import java.io.UnsupportedEncodingException;
public class StackTraceSerializer {
public static String serialize(Throwable t) {
ByteArrayOutputStream buff = new ByteArrayOutputStream();
PrintStream ps = new PrintStream(buff);
t.printStackTrace(ps);
try {
return buff.toString("UTF-8");
} catch (UnsupportedEncodingException e) {
throw new RuntimeException(e);
}
}
}
| 1,419 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
InetAddressTools.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/main/java/info/martinmarinov/dvbservice/tools/InetAddressTools.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice.tools;
import java.net.InetAddress;
import java.net.UnknownHostException;
public class InetAddressTools {
private final static InetAddress LOCAL_LOOPBACK;
static {
try {
LOCAL_LOOPBACK = InetAddress.getByName("127.0.0.1");
} catch (UnknownHostException e) {
throw new RuntimeException(e);
}
}
public static InetAddress getLocalLoopback() {
return LOCAL_LOOPBACK;
}
} | 1,345 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
TsDumpFileUtils.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/main/java/info/martinmarinov/dvbservice/tools/TsDumpFileUtils.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice.tools;
import android.content.Context;
import android.content.res.Resources;
import androidx.annotation.VisibleForTesting;
import android.util.Log;
import java.io.File;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.LinkedList;
import java.util.List;
import java.util.Locale;
import info.martinmarinov.drivers.DvbDevice;
import info.martinmarinov.drivers.file.DvbFileDevice;
public class TsDumpFileUtils {
private final static String TAG = TsDumpFileUtils.class.getSimpleName();
private final static Locale DEFAULT_LOCALE = Locale.US;
private final static DateFormat DATE_FORMAT = new SimpleDateFormat("yyyyMMddHHmmss", DEFAULT_LOCALE);
private static File getRoot(Context ctx) {
return ctx.getExternalFilesDir(null);
}
public static File getFor(Context ctx, long freq, long bandwidth, Date date) {
File root = getRoot(ctx);
String timestamp = DATE_FORMAT.format(date);
String filename = String.format(DEFAULT_LOCALE, "mux_%d_%d_%s.ts", freq, bandwidth, timestamp);
return new File(root, filename);
}
public static List<DvbDevice> getDevicesForAllRecordings(Context ctx) {
LinkedList<DvbDevice> devices = new LinkedList<>();
Resources resources = ctx.getResources();
File root = getRoot(ctx);
if (root == null) return devices;
Log.d(TAG, "You can place ts files in "+root.getPath());
File[] files = root.listFiles();
for (File file : files) {
FreqBandwidth freqAndBandwidth = getFreqAndBandwidth(file);
if (freqAndBandwidth != null) {
devices.add(new DvbFileDevice(resources, file, freqAndBandwidth.freq, freqAndBandwidth.bandwidth));
}
}
return devices;
}
@VisibleForTesting
static FreqBandwidth getFreqAndBandwidth(File file) {
if (!"ts".equals(getExtension(file))) return null;
String[] parts = file.getName().toLowerCase().split("_");
if (parts.length != 4) return null;
if (!"mux".equals(parts[0])) return null;
try {
long freq = Long.parseLong(parts[1]);
long bandwidth = Long.parseLong(parts[2]);
return new FreqBandwidth(freq, bandwidth);
} catch (NumberFormatException ignored) {
return null;
}
}
private static String getExtension(File file) {
String[] parts = file.getName().toLowerCase().split("\\.");
if (parts.length == 0) return null;
return parts[parts.length-1];
}
@VisibleForTesting
static class FreqBandwidth {
@VisibleForTesting
final long freq, bandwidth;
private FreqBandwidth(long freq, long bandwidth) {
this.freq = freq;
this.bandwidth = bandwidth;
}
}
}
| 3,765 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
ShowOneInstanceFragmentDialog.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/main/java/info/martinmarinov/dvbservice/dialogs/ShowOneInstanceFragmentDialog.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice.dialogs;
import android.os.Bundle;
import androidx.appcompat.app.AppCompatDialogFragment;
import androidx.fragment.app.Fragment;
import androidx.fragment.app.FragmentManager;
import androidx.fragment.app.FragmentTransaction;
public class ShowOneInstanceFragmentDialog extends AppCompatDialogFragment {
public void showOneInstanceOnly(FragmentManager fragmentManager, String tag, Bundle args) {
// ensure only one instance is present and close existing instances
FragmentTransaction ft = fragmentManager.beginTransaction();
Fragment prev = fragmentManager.findFragmentByTag(tag);
if (prev != null) ft.remove(prev);
ft.addToBackStack(null);
// set arguments and launch
setArguments(args);
try {
show(ft, tag);
} catch (IllegalStateException e) {
// If we try to show an exception while driver is dying
e.printStackTrace();
}
}
}
| 1,854 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
ListPickerFragmentDialog.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/main/java/info/martinmarinov/dvbservice/dialogs/ListPickerFragmentDialog.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice.dialogs;
import android.app.AlertDialog;
import android.app.Dialog;
import android.content.Context;
import android.content.DialogInterface;
import android.os.Bundle;
import androidx.annotation.NonNull;
import androidx.fragment.app.FragmentManager;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
public class ListPickerFragmentDialog<T extends Serializable> extends ShowOneInstanceFragmentDialog {
private static final String DIALOG_TAG = ListPickerFragmentDialog.class.getSimpleName();
private static final String ARGS_SIZE = "argsSize";
private static final String ARG_ID = "arg";
private static String getArgKey(int id) {
return ARG_ID + id;
}
public static <T extends Serializable> void showOneInstanceOnly(FragmentManager fragmentManager, List<T> options) {
ListPickerFragmentDialog<T> dialog = new ListPickerFragmentDialog<>();
Bundle args = new Bundle();
args.putInt(ARGS_SIZE, options.size());
for (int i = 0; i < options.size(); i++) {
args.putSerializable(getArgKey(i), options.get(i));
}
dialog.showOneInstanceOnly(fragmentManager, DIALOG_TAG, args);
}
private OnSelected<T> callback;
private List<T> options;
@SuppressWarnings("unchecked")
@Override
public void onCreate(Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
Bundle args = getArguments();
int size = args.getInt(ARGS_SIZE);
options = new ArrayList<>(size);
for (int i = 0; i < size; i++) {
options.add((T) args.getSerializable(getArgKey(i)));
}
}
@SuppressWarnings("unchecked")
@Override
public void onAttach(Context context) {
super.onAttach(context);
callback = (OnSelected<T>) getActivity();
}
@Override
public @NonNull Dialog onCreateDialog(Bundle savedInstanceState) {
String[] strings = new String[options.size()];
for (int i = 0; i < strings.length; i++) strings[i] = options.get(i).toString();
return new AlertDialog.Builder(getActivity())
.setCancelable(true)
.setItems(strings, new DialogInterface.OnClickListener() {
@Override
public void onClick(DialogInterface dialog, int which) {
callback.onListPickerDialogItemSelected(options.get(which));
}
})
.create();
}
@Override
public void onCancel(DialogInterface dialog) {
callback.onListPickerDialogCanceled();
}
public interface OnSelected<T> {
void onListPickerDialogItemSelected(T item);
void onListPickerDialogCanceled();
}
}
| 3,664 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
DeviceFilterXmlEquivalenceTester.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/dvbservice/src/androidTest/java/info/martinmarinov/dvbservice/DeviceFilterXmlEquivalenceTester.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbservice;
import static androidx.test.core.app.ApplicationProvider.getApplicationContext;
import android.content.res.Resources;
import android.content.res.XmlResourceParser;
import android.util.AttributeSet;
import android.util.Xml;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.xmlpull.v1.XmlPullParser;
import java.util.HashSet;
import java.util.Set;
import info.martinmarinov.drivers.DeviceFilter;
import info.martinmarinov.drivers.usb.DvbUsbDevice;
import info.martinmarinov.drivers.usb.DvbUsbDeviceRegistry;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.core.IsEqual.equalTo;
import androidx.test.ext.junit.runners.AndroidJUnit4;
import androidx.test.filters.MediumTest;
@RunWith(AndroidJUnit4.class)
@MediumTest
public class DeviceFilterXmlEquivalenceTester {
@Test
public void allDevicesAreInXml() {
Set<DeviceFilter> devicesInXml = getDeviceData(getApplicationContext().getResources(), R.xml.device_filter);
Set<DeviceFilter> supportedDecvices = getDevicesInApp();
if (!supportedDecvices.equals(devicesInXml)) {
System.out.println("Devices needed to be added to the xml");
for (DeviceFilter supportedDevice : supportedDecvices) {
if (!devicesInXml.contains(supportedDevice)) {
System.out.printf(" <usb-device vendor-id=\"0x%x\" product-id=\"0x%x\"/> <!-- %s -->\n",
supportedDevice.getVendorId(), supportedDevice.getProductId(), supportedDevice.getName()
);
}
}
System.out.println("Devices in xml but not supported");
for (DeviceFilter deviceInXml : devicesInXml) {
if (!supportedDecvices.contains(deviceInXml)) {
System.out.printf("vendor-id=0x%x, product-id=0x%x\n",
deviceInXml.getVendorId(), deviceInXml.getProductId()
);
}
}
}
assertThat(supportedDecvices, equalTo(devicesInXml));
}
private static HashSet<DeviceFilter> getDevicesInApp() {
HashSet<DeviceFilter> supportedDevices = new HashSet<>();
for (DvbUsbDevice.Creator d : DvbUsbDeviceRegistry.AVAILABLE_DRIVERS) {
supportedDevices.addAll(d.getSupportedDevices());
}
return supportedDevices;
}
private static Set<DeviceFilter> getDeviceData(Resources resources, int xmlResourceId) {
Set<DeviceFilter> ans = new HashSet<>();
try {
XmlResourceParser xml = resources.getXml(xmlResourceId);
xml.next();
int eventType;
while ((eventType = xml.getEventType()) != XmlPullParser.END_DOCUMENT) {
if (eventType == XmlPullParser.START_TAG) {
if (xml.getName().equals("usb-device")) {
AttributeSet as = Xml.asAttributeSet(xml);
Integer vendorId = parseInt(as.getAttributeValue(null, "vendor-id"));
Integer productId = parseInt(as.getAttributeValue(null, "product-id"));
ans.add(new DeviceFilter(vendorId, productId, null));
}
}
xml.next();
}
} catch (Exception e) {
throw new RuntimeException(e);
}
return ans;
}
private static Integer parseInt(String number) {
if (number.startsWith("0x")) {
return Integer.valueOf( number.substring(2), 16);
} else {
return Integer.valueOf( number, 10);
}
}
} | 4,554 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
WelcomeActivity.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/app/src/main/java/info/martinmarinov/dvbdriver/WelcomeActivity.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbdriver;
import android.content.Intent;
import android.net.Uri;
import android.os.Bundle;
import android.app.Activity;
import android.view.View;
public class WelcomeActivity extends Activity {
private final static Uri SOURCE_URL = Uri.parse("https://github.com/signalwareltd/AndroidDvbDriver");
@Override
protected void onCreate(Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
setContentView(R.layout.activity_welcome);
findViewById(R.id.btn_close).setOnClickListener(v -> finish());
findViewById(R.id.btn_advanced_mode).setOnClickListener(v -> startActivity(new Intent(WelcomeActivity.this, DvbFrontendActivity.class)));
findViewById(R.id.btn_source_code).setOnClickListener(v -> startActivity(new Intent(Intent.ACTION_VIEW, SOURCE_URL)));
findViewById(R.id.btn_license).setOnClickListener(v -> startActivity(new Intent(WelcomeActivity.this, GplLicenseActivity.class)));
}
}
| 1,855 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |
DeviceController.java | /FileExtraction/Java_unseen/signalwareltd_AndroidDvbDriver/app/src/main/java/info/martinmarinov/dvbdriver/DeviceController.java | /*
* This is an Android user space port of DVB-T Linux kernel modules.
*
* Copyright (C) 2022 by Signalware Ltd <driver at aerialtv.eu>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
package info.martinmarinov.dvbdriver;
import java.io.IOException;
import java.util.List;
import java.util.Set;
import info.martinmarinov.drivers.DvbDevice;
import info.martinmarinov.drivers.DvbException;
import info.martinmarinov.drivers.DvbStatus;
import info.martinmarinov.drivers.DeliverySystem;
import info.martinmarinov.drivers.usb.DvbUsbDeviceRegistry;
import static info.martinmarinov.drivers.DvbException.ErrorCode.NO_DVB_DEVICES_FOUND;
class DeviceController extends Thread {
private final DvbFrontendActivity dvbFrontendActivity;
private volatile long desiredFreq, desiredBand;
private volatile long currFreq, currBand;
private volatile DeliverySystem currDelSystem, desiredDelSystem;
private DataHandler dataHandler;
DeviceController(DvbFrontendActivity dvbFrontendActivity, long desiredFreq, long desiredBand, DeliverySystem deliverySystem) {
this.dvbFrontendActivity = dvbFrontendActivity;
tuneTo(desiredFreq, desiredBand, deliverySystem);
}
void tuneTo(long desiredFreq, long desiredBand, DeliverySystem deliverySystem) {
// Avoid accessing the DvbDevice from multiple threads
this.desiredFreq = desiredFreq;
this.desiredBand = desiredBand;
this.desiredDelSystem = deliverySystem;
}
DataHandler getDataHandler() {
return dataHandler;
}
@Override
public void run() {
try {
List<DvbDevice> availableFrontends = DvbUsbDeviceRegistry.getUsbDvbDevices(dvbFrontendActivity.getApplicationContext());
if (availableFrontends.isEmpty())
throw new DvbException(NO_DVB_DEVICES_FOUND, dvbFrontendActivity.getString(R.string.no_devices_found));
DvbDevice dvbDevice = availableFrontends.get(0);
dvbDevice.open();
dvbFrontendActivity.announceOpen(true, dvbDevice.getDebugString());
dataHandler = new DataHandler(dvbFrontendActivity, dvbDevice.getTransportStream(new DvbDevice.StreamCallback() {
@Override
public void onStreamException(IOException e) {
dvbFrontendActivity.handleException(e);
}
@Override
public void onStoppedStreaming() {
interrupt();
}
}));
dataHandler.start();
try {
while (!isInterrupted()) {
if (desiredFreq != currFreq || desiredBand != currBand || desiredDelSystem != currDelSystem) {
dvbDevice.tune(desiredFreq, desiredBand, desiredDelSystem);
dvbDevice.disablePidFilter();
currFreq = desiredFreq;
currBand = desiredBand;
currDelSystem = desiredDelSystem;
dataHandler.setFreqAndBandwidth(currFreq, currBand);
dataHandler.reset();
}
int snr = dvbDevice.readSnr();
int qualityPercentage = Math.round(100.0f * (0xFFFF - dvbDevice.readBitErrorRate()) / (float) 0xFFFF);
int droppedUsbFps = dvbDevice.readDroppedUsbFps();
int rfStrength = dvbDevice.readRfStrengthPercentage();
Set<DvbStatus> status = dvbDevice.getStatus();
boolean hasSignal = status.contains(DvbStatus.FE_HAS_SIGNAL);
boolean hasCarrier = status.contains(DvbStatus.FE_HAS_CARRIER);
boolean hasSync = status.contains(DvbStatus.FE_HAS_SYNC);
boolean hasLock = status.contains(DvbStatus.FE_HAS_LOCK);
dvbFrontendActivity.announceMeasurements(snr, qualityPercentage, droppedUsbFps, rfStrength, hasSignal, hasCarrier, hasSync, hasLock);
Thread.sleep(1_000);
}
} catch (InterruptedException ie) {
// Interrupted exceptions are ok
} finally {
dataHandler.interrupt();
//noinspection ThrowFromFinallyBlock
dataHandler.join();
try {
dvbDevice.close();
} catch (IOException e) {
dvbFrontendActivity.handleException(e);
}
}
} catch (Exception e) {
dvbFrontendActivity.handleException(e);
} finally {
dvbFrontendActivity.announceOpen(false, null);
}
}
}
| 5,382 | Java | .java | signalwareltd/AndroidDvbDriver | 183 | 65 | 39 | 2017-02-22T15:41:19Z | 2023-04-29T01:10:41Z |