change to nginx for serving

50x.html

@@ -0,0 +1 @@
+System Error

conf/dev/Dockerfile

@@ -1,6 +1,9 @@
-# serve the data with busybox
-FROM busybox:1.36.1
-RUN adduser -D static
-USER static
-WORKDIR /home/static
+# serve the data with nginx
+FROM nginx:alpine
+
+# set the working folder in the container
+WORKDIR /usr/share/nginx/html
+
+# copy the nginx configuration
 COPY ./index.html ./
+COPY ./50x.html ./

conf/dev/default.conf

@@ -0,0 +1,33 @@
+server {
+ listen 80;
+ listen [::]:80;
+ server_name localhost;
+
+ location / {
+ root /usr/share/nginx/html;
+ index index.html index.htm;
+
+ # Enable CORS for specific origin and allow credentials
+ add_header 'Access-Control-Allow-Origin' 'http://localhost:5273' always;
+ add_header 'Access-Control-Allow-Methods' 'GET, POST, OPTIONS, PUT, DELETE';
+ add_header 'Access-Control-Allow-Headers' 'Origin, X-Requested-With, Content-Type, Accept, Authorization';
+ add_header 'Access-Control-Allow-Credentials' 'true' always;
+
+ # Handle preflight requests
+ if ($request_method = OPTIONS) {
+ add_header 'Access-Control-Allow-Origin' 'http://localhost:5273';
+ add_header 'Access-Control-Allow-Methods' 'GET, POST, OPTIONS, PUT, DELETE';
+ add_header 'Access-Control-Allow-Headers' 'Origin, X-Requested-With, Content-Type, Accept, Authorization';
+ add_header 'Access-Control-Allow-Credentials' 'true';
+ return 204;
+ }
+ }
+
+ # redirect server error pages to the static page /50x.html
+ #
+ error_page 500 502 503 504 /50x.html;
+ location = /50x.html {
+ root /usr/share/nginx/html;
+ }
+}
+

conf/dev/docker-compose.yml

@@ -6,14 +6,14 @@ services:
  context: ../../
  dockerfile: ./conf/dev/Dockerfile
  container_name: bike-ds
- working_dir: /home/static
- command: busybox httpd -f -v -p 28256
+ working_dir: /usr/share/nginx/html
  environment:
  NODE_ENV: dev
  volumes:
- - ../../data:/home/static/dataset
+ - ./default.conf:/etc/nginx/conf.d/default.conf
+ - ../../data:/usr/share/nginx/html/dataset
  ports:
- - 28256:28256
+ - 28256:80
  restart: always
  networks:
  - bikenet

conf/medviz/Dockerfile

@@ -1,6 +1,9 @@
-# serve the data with busybox
-FROM busybox:1.36.1
-RUN adduser -D static
-USER static
-WORKDIR /home/static
-COPY ./index.html ./
+# serve the data with nginx
+FROM nginx:alpine
+
+# set the working folder in the container
+WORKDIR /usr/share/nginx/html
+
+# copy the nginx configuration
+COPY ./index.html ./
+COPY ./50x.html ./

conf/medviz/default.conf

@@ -0,0 +1,33 @@
+server {
+ listen 80;
+ listen [::]:80;
+ server_name localhost;
+
+ location / {
+ root /usr/share/nginx/html;
+ index index.html index.htm;
+
+ # Enable CORS for specific origin and allow credentials
+ add_header 'Access-Control-Allow-Origin' 'https://medviz.org' always;
+ add_header 'Access-Control-Allow-Methods' 'GET, POST, OPTIONS, PUT, DELETE';
+ add_header 'Access-Control-Allow-Headers' 'Origin, X-Requested-With, Content-Type, Accept, Authorization';
+ add_header 'Access-Control-Allow-Credentials' 'true' always;
+
+ # Handle preflight requests
+ if ($request_method = OPTIONS) {
+ add_header 'Access-Control-Allow-Origin' 'https://medviz.org';
+ add_header 'Access-Control-Allow-Methods' 'GET, POST, OPTIONS, PUT, DELETE';
+ add_header 'Access-Control-Allow-Headers' 'Origin, X-Requested-With, Content-Type, Accept, Authorization';
+ add_header 'Access-Control-Allow-Credentials' 'true';
+ return 204;
+ }
+ }
+
+ # redirect server error pages to the static page /50x.html
+ #
+ error_page 500 502 503 504 /50x.html;
+ location = /50x.html {
+ root /usr/share/nginx/html;
+ }
+}
+

conf/medviz/docker-compose.yml

@@ -6,14 +6,14 @@ services:
  context: ../../
  dockerfile: ./conf/medviz/Dockerfile
  container_name: bike-ds
- working_dir: /home/static
- command: busybox httpd -f -v -p 28256
+ working_dir: /usr/share/nginx/html
  environment:
  NODE_ENV: medviz
  volumes:
- - ../../data:/home/static/dataset
+ - ./default.conf:/etc/nginx/conf.d/default.conf
+ - ../../data:/usr/share/nginx/html/dataset
  ports:
- - 28256:28256
+ - 28256:80
  restart: always
  networks:
  - bikenet

conf/spinup/Dockerfile

@@ -1,6 +1,9 @@
-# serve the data with busybox
-FROM busybox:1.36.1
-RUN adduser -D static
-USER static
-WORKDIR /home/static
+# serve the data with nginx
+FROM nginx:alpine
+
+# set the working folder in the container
+WORKDIR /usr/share/nginx/html
+
+# copy the nginx configuration
 COPY ./index.html ./
+COPY ./50x.html ./

conf/spinup/default.conf

@@ -0,0 +1,33 @@
+server {
+ listen 80;
+ listen [::]:80;
+ server_name localhost;
+
+ location / {
+ root /usr/share/nginx/html;
+ index index.html index.htm;
+
+ # Enable CORS for specific origin and allow credentials
+ add_header 'Access-Control-Allow-Origin' 'https://spinup-0028ce.spinup.yale.edu' always;
+ add_header 'Access-Control-Allow-Methods' 'GET, POST, OPTIONS, PUT, DELETE';
+ add_header 'Access-Control-Allow-Headers' 'Origin, X-Requested-With, Content-Type, Accept, Authorization';
+ add_header 'Access-Control-Allow-Credentials' 'true' always;
+
+ # Handle preflight requests
+ if ($request_method = OPTIONS) {
+ add_header 'Access-Control-Allow-Origin' 'https://spinup-0028ce.spinup.yale.edu';
+ add_header 'Access-Control-Allow-Methods' 'GET, POST, OPTIONS, PUT, DELETE';
+ add_header 'Access-Control-Allow-Headers' 'Origin, X-Requested-With, Content-Type, Accept, Authorization';
+ add_header 'Access-Control-Allow-Credentials' 'true';
+ return 204;
+ }
+ }
+
+ # redirect server error pages to the static page /50x.html
+ #
+ error_page 500 502 503 504 /50x.html;
+ location = /50x.html {
+ root /usr/share/nginx/html;
+ }
+}
+

conf/spinup/docker-compose.yml

@@ -6,14 +6,14 @@ services:
  context: ../../
  dockerfile: ./conf/spinup/Dockerfile
  container_name: bike-ds
- working_dir: /home/static
- command: busybox httpd -f -v -p 28256
+ working_dir: /usr/share/nginx/html
  environment:
  NODE_ENV: spinup
  volumes:
- - ../../data:/home/static/dataset
+ - ./default.conf:/etc/nginx/conf.d/default.conf
+ - ../../data:/usr/share/nginx/html/dataset
  ports:
- - 28256:28256
+ - 28256:80
  restart: always
  networks:
  - bikenet

data/medviz/HCP-438k.json

@@ -9,8 +9,8 @@
  "description": "Publications with high citations indexed by PubMed",
 
  "final_dataset": {
- "points_tsv": "/dataset/HCP-438k.tsv",
- "topics_json": "/dataset/PD1-46k.topics.json"
+ "points_tsv": "/dataset/medviz/HCP-438k.tsv",
+ "topics_json": "/dataset/medviz/PD1-46k.topics.json"
  },
 
  "config": {

data/medviz/NS-290k.json

@@ -9,7 +9,7 @@
  "description": "Publications from Nature and Science in the past 100 years",
 
  "final_dataset": {
- "points_tsv": "/dataset/NS-290k.tsv",
+ "points_tsv": "/dataset/medviz/NS-290k.tsv",
  "topics_json": ""
  },
 

data/medviz/PD1-46k.json

@@ -9,8 +9,8 @@
  "description": "This dataset contains the data of PD-1 and PD-L1 studies.",
 
  "final_dataset": {
- "points_tsv": "/dataset/PD1-46k.tsv",
- "topics_json": "/dataset/PD1-46k.topics.json"
+ "points_tsv": "/dataset/medviz/PD1-46k.tsv",
+ "topics_json": "/dataset/medviz/PD1-46k.topics.json"
  },
 
  "config": {