Add limit arg and test install ruby gem for name parsing

Dockerfile

@@ -17,8 +17,16 @@ RUN ls -l /data
 RUN unzip /data/gbif-occs.zip -d /data
 RUN ls -l /data
 COPY ./tab2csv.py /code/tab2csv.py
+
+# Setup to parse collector names using Bionomia utils (reqs Ruby)
+# Install ruby
+RUN \
+  apt-get update && \
+  apt-get install -y ruby
+RUN gem install dwc_agent
+
 #COPY ./extractcollectorname.py /code/extractcollectorname.py
-RUN python tab2csv.py --createcols /data/${GBIF_DOWNLOAD_ID}.csv /data/gbifocc-temp.csv 
+RUN python tab2csv.py --limit 1000 --createcols /data/${GBIF_DOWNLOAD_ID}.csv /data/gbifocc-temp.csv 
 #RUN python extractcollectorname.py /data/gbifocc-temp.csv /data/gbifocc.csv 
 RUN csvs-to-sqlite /data/gbifocc.csv /code/gbifocc.db
 RUN ls -l /code

tab2csv.py

@@ -17,6 +17,7 @@ if __name__ == '__main__':
     parser = argparse.ArgumentParser()
     parser.add_argument("inputfile")
     parser.add_argument("-c","--createcols", action='store_true')
+    parser.add_argument("-l","--limit", type='int')
     parser.add_argument("outputfile")    
     args = parser.parse_args()
 
@@ -24,7 +25,8 @@ if __name__ == '__main__':
                     encoding='utf8', 
                     keep_default_na=False, 
                     on_bad_lines='skip', 
-                    sep='\t')
+                    sep='\t',
+                    nrows=args.limit)
     if args.createcols:
         # Extract unique recordedBy values
         df_rb = df[['recordedBy']].drop_duplicates()