Merge pull request #78 from EMResearch/session-service

added session-service SUT

Author: arcuri82

.gitignore

@@ -269,3 +269,6 @@ dotnet_3/em/embedded/rest/ScsDriver/generated-tests/
 /jdk_17_maven/em/embedded/grpc/signal-registration/target/
 /jdk_17_maven/em/external/grpc/signal-registration/target/
 /jdk_17_maven/em/external/web/spring-petclinic/target/
+/jdk_8_maven/cs/rest/original/session-service/target/
+/jdk_8_maven/em/embedded/rest/session-service/target/
+/jdk_8_maven/em/external/rest/session-service/target/

README.md

@@ -72,6 +72,8 @@ More details (e.g., #LOCs and used databases) on these APIs can be found [in thi
 
 ### REST: Java/Kotlin
 
+* Session Service (not-known license), [jdk_8_maven/cs/rest/original/session-service](jdk_8_maven/cs/rest/original/session-service), from [https://github.com/cBioPortal/session-service](https://github.com/cBioPortal/session-service)
+
 * Bibliothek (MIT), [jdk_17_gradle/cs/rest/bibliothek](jdk_17_gradle/cs/rest/bibliothek), from [https://github.com/PaperMC/bibliothek](https://github.com/PaperMC/bibliothek)
 
 * Reservations API (not-known license), [jdk_11_gradle/cs/rest/reservations-api](jdk_11_gradle/cs/rest/reservations-api), from [https://github.com/cyrilgavala/reservations-api](https://github.com/cyrilgavala/reservations-api)

jdk_8_maven/cs/rest/original/pom.xml

@@ -19,6 +19,7 @@
         <module>catwatch</module>
         <module>languagetool</module>
         <module>restcountries</module>
+        <module>session-service</module>
     </modules>
 
 

jdk_8_maven/cs/rest/original/session-service/Dockerfile

@@ -0,0 +1,16 @@
+#
+# Copyright (c) 2019 The Hyve B.V.
+# This code is licensed under the GNU Affero General Public License (AGPL),
+# version 3, or (at your option) any later version.
+#
+
+FROM maven:3-eclipse-temurin-11 as build
+COPY $PWD /session-service
+WORKDIR /session-service
+RUN mvn package -DskipTests -Dpackaging.type=jar
+
+FROM eclipse-temurin:11
+# copy over target/session_service-x.y.z.jar ignore *-model.jar, that jar is
+# used by cbioportal/cbioportal to import the models
+COPY --from=build /session-service/target/*[0-9].jar /app.war
+CMD java ${JAVA_OPTS} -jar /app.war

jdk_8_maven/cs/rest/original/session-service/Procfile

@@ -0,0 +1 @@
+web: SERVER_PORT=${PORT} java $JAVA_OPTS -Dspring.data.mongodb.uri=${MONGODB_URI} -jar target/*[0-9].jar

jdk_8_maven/cs/rest/original/session-service/README.md

@@ -0,0 +1,334 @@
+[![Deploy](https://www.herokucdn.com/deploy/button.svg)](https://heroku.com/deploy)
+
+# session-service
+
+RESTful API to cBioPortal/cbioportal sessions in MongoDB.  
+
+Session information is stored in JSON, so this API generalizes to any JSON objects.
+
+
+## Run with Docker
+```
+docker-compose up
+```
+You can also run it in detached mode with:
+```
+docker-compose up -d
+```
+In that case, to stop it one runs:
+```
+docker-compose down
+```
+If you want to rebuild the session service image after having made changes in
+development:
+```
+docker-compose up --build
+```
+Check http://localhost:8080/info to confirm session service is running. It
+should show a version number.
+
+Test whether a session can be created like this:
+
+```
+curl -H "Content-Type: application/json" --user user:pass -X POST http://localhost:8080/api/sessions/test_portal/main_session --data '{"title": "my main portal session", "description": "this is an example"}'
+```
+
+The mongo database port is not exposed by default. One can connect to the
+mongo database like this:
+```
+docker exec -it session-service_db_1 mongo mongodb://localhost:27017
+```
+
+
+
+## Run without docker
+### Requirements
+
+JDK 1.7 or later: http://www.oracle.com/technetwork/java/javase/downloads/index.html
+
+Maven 3.0+: http://maven.apache.org/download.cgi
+
+MongoDB: https://docs.mongodb.org/manual/
+
+### Installation and setup
+
+Create database 'session_service' using the 'mongo' shell interface to MongoDB:
+
+```
+$ mongo
+
+> use session_service
+```
+Clone repository, compile, run tests, and start server:
+```
+$ git clone https://github.com/cBioPortal/session-service.git
+
+$ cd session-service
+
+session-service$ mvn package -Dpackaging.type=jar && java -Dspring.data.mongodb.uri=mongodb://localhost:27017/session-service -jar target/session_service-0.1.0.jar 
+```
+To generate war file with a configuration file:
+
+```
+$ cd session-service
+
+session-service$ mkdir src/main/resources/
+
+session-service$ cp /path/to/myapp.config src/main/resources/
+
+session-service$ mvn package
+```
+
+An example properties file:
+
+```
+spring.data.mongodb.database=session_service
+spring.data.mongodb.host=localhost
+spring.data.mongodb.port=27017
+```
+
+To have a context root that is not "/", add to the properties file:
+
+```
+server.contextPath=/session_service
+server.port=8080 # change this if u want to use a different port
+```
+
+One can use session-service with or without basic authentication. It's
+disabled by default. To enable basic authentication set:
+
+```
+security.basic.enabled=true
+spring.security.user.name=user
+spring.security.user.password=pass
+```
+
+By default the server runs on port 8080. This can be overridden by setting the
+process's SERVER_PORT environment variable.
+
+```
+session-service$ export set SERVER_PORT=8090; mvn package -Dpackaging.type=jar && java -Dspring.data.mongodb.uri=mongodb://localhost:27017/session-service -jar target/session_service-0.1.0.jar
+```
+
+## Sentry support
+
+Sentry is already included as a dependency of this project, one can add the following this [Sentry official documentation](https://docs.sentry.io/platforms/java/guides/spring-boot/configuration/#setting-the-dsn) to enable sentry.
+For example, for Run without docker, add the following when starting the server:
+```
+-Dsentry.dsn=https://examplePublicKey@o0.ingest.sentry.io/0
+```
+And example command for Run with docker also included in the docker-compoase.yaml file, please refer that command to enable sentry.
+
+## API
+
+Swagger documentation will be found here: http://[url]:[port]/swagger-ui.html e.g. http://localhost:8090/swagger-ui.html
+
+If basic auth is enabled note that one should pass the username password to access these endpoints e.g. with curl:
+
+```
+curl --user user:pass
+```
+
+### Create
+
+### Valid Type
+
+| Type  | Description  |
+|---|---|
+| main_session | represent result's page query |
+| virtual_study | represent a subset for samples saved from study summary page |
+| group | similar to virtual study except its used in comparison page |
+| comparison_session | represent comparison page query |
+| settings | represent cbio page settings. page type is identified by a field `page` in it |
+| custom_data | holds study-view page custom charts data |
+| genomic_chart | represents genomic chart added by user in study-view page |
+| custom_gene_list | represents custom gene list added by user in query page |
+
+#### POST http://localhost:8080/api/sessions/{source}/{type}/
+Creates a session.  Returns status 200 and the session id in response body
+on success.  The session is saved in a collection named {type}. Both
+source and type are saved in the session document. If a session with the same source, type,
+and data already exists in the database returns the session id of that session
+instead of creating a duplicate.  
+
+WARNING: This is case sensitive. You should always use the same case
+for source and type.
+
+Example body for POST http://localhost:8080/api/sessions/msk_portal/main_session/
+```
+{"title": "my main portal session", "description": "this is an example"}
+```
+Example response:
+```
+{
+  "id": "57167a52ef86d81afb415aba"
+}
+```
+If no JSON data passed in request body or an invalid type is sent returns 400 status
+with something like the following in the body:
+```
+{
+  "timestamp": 1461093154793,
+  "status": 400,
+  "error": "Bad Request",
+  "exception": "org.springframework.web.method.annotation.MethodArgumentTypeMismatchException",
+  "message": "valid types are: main_session, virtual_study, group, comparison_session, custom_data, genomic_chart",
+  "path": "/api/sessions/msk_portal/invalid_type/"
+}
+```
+Sending invalid JSON in the request body returns a 400 status
+with something like the following in the body:
+```
+{
+  "timestamp": 1461090997119,
+  "status": 400,
+  "error": "Bad Request",
+  "exception": "org.cbioportal.session_service.domain.exception.SessionInvalidException",
+  "message": "\n{\"portal-session\": blah blah blah}\n                   ^",
+  "path": "/api/sessions/msk_portal/main_session/"
+}
+```
+
+### Read
+
+#### GET http://localhost:8080/api/sessions/{source}/{type}/
+Returns all sessions for source and type.  Returns "[]" if no sessions.  
+Example response for GET http://localhost:8080/api/sessions/msk_portal/main_session/
+```
+[
+  {
+    "id": "57167a52ef86d81afb415aba",
+    "data": {
+      "title": "my main portal session",
+      "description": "this is an example"
+    },
+    "source": "msk_portal",
+    "type": "main_session"
+  },
+  {
+    "id": "57167c69ef86fdfcec850342",
+    "data": {
+      "title": "my main portal session",
+      "description": "this is another example"
+    },
+    "source": "msk_portal",
+    "type": "main_session"
+  }
+]
+```
+
+#### GET http://localhost:8080/api/sessions/{source}/{type}/{id}
+Returns single session given source, type, and id.
+Example response for GET http://localhost:8080/api/sessions/msk_portal/main_session/57167a52ef86d81afb415aba
+```
+{
+  "id": "57167a52ef86d81afb415aba",
+  "data": {
+    "title": "my main portal session",
+    "description": "this is an example"
+  },
+  "source": "msk_portal",
+  "type": "main_session"
+}
+```
+If no session is found returns status 404 with a request body like this:
+```
+{
+  "timestamp": 1462379207301,
+  "status": 404,
+  "error": "Not Found",
+  "exception": "org.cbioportal.session_service.service.exception.SessionNotFoundException",
+  "message": "Session not found",
+  "path": "/api/sessions/msk_portal/main_session/test"
+}
+```
+WARNING: This is case sensitive.
+GET http://localhost:8080/api/sessions/MSK_portal/main_session/57167a52ef86d81afb415aba
+and
+GET http://localhost:8080/api/sessions/msk_portal/Main_Session/57167a52ef86d81afb415aba 
+are NOT equivalent.
+
+#### GET http://localhost:8080/api/sessions/{source}/{type}/query?field={field}&value={value}
+Returns all sessions matching a query for source and type. Returns
+200 status on success.
+Example response for GET http://localhost:8080/api/sessions/msk_portal/main_session/query?field=data.title&value=my%20main%20portal%20session
+```
+[
+  {
+    "id": "57167c69ef86fdfcec850342",
+    "data": {
+      "title": "my main portal session",
+      "description": "this is another example"
+    },
+    "source": "msk_portal",
+    "type": "main_session"
+  }
+]
+```
+
+### Update
+
+#### PUT http://localhost:8080/api/sessions/{source}/{type}/{id}
+Updates a session given the source, type, and id.  Returns status 200
+on success with empty request body. 
+Example body for PUT http://localhost:8080/api/sessions/msk_portal/main_session/57167a52ef86d81afb415aba
+```
+{
+    "title": "my UPDATED main portal session",
+    "description": "this is an example"
+}
+```
+If no JSON data passed in request body returns status 400 with a request
+body like this:
+```
+{
+  "timestamp": 1461092375741,
+  "status": 400,
+  "error": "Bad Request",
+  "exception": "org.springframework.http.converter.HttpMessageNotReadableException",
+  "message": "Required request body is missing: public void org.cbioportal.session_service.web.SessionServiceController.updateSession(java.lang.String,java.lang.String,java.lang.String,java.lang.String)",
+  "path": "/api/sessions/msk_portal/main_session/57167a52ef86d81afb415aba"
+}
+```
+If an invalid id is passed returns status 404 with a request body like this:
+```
+{
+  "timestamp": 1462379078498,
+  "status": 404,
+  "error": "Not Found",
+  "exception": "org.cbioportal.session_service.service.exception.SessionNotFoundException",
+  "message": "Session not found",
+  "path": "/api/sessions/msk_portal/main_session/test"
+}
+```
+Sending invalid JSON in the request body returns a 400 status
+with something like the following in the body:
+```
+{
+  "timestamp": 1461092440979,
+  "status": 400,
+  "error": "Bad Request",
+  "exception": "org.cbioportal.session_service.domain.exception.SessionInvalidException",
+  "message": "\n{\n    \"title\": \"my UPDATED main portal session\",\n    \"description\": blah blah blah\n}\n                                                                    ^",
+  "path": "/api/sessions/msk_portal/main_session/57167a52ef86d81afb415aba"
+}
+```
+
+### Delete
+
+#### DELETE http://localhost:8080/api/sessions/{source}/{type}/{id}
+Deletes a session with source, type, and id.
+Returns 200 status on success with empty request body. 
+Example URL for DELETE http://localhost:8080/api/sessions/msk_portal/main_session/57167c69ef86fdfcec850342
+
+If an invalid id is passed returns status 404 with a request body like this:
+```
+{
+  "timestamp": 1462379146105,
+  "status": 404,
+  "error": "Not Found",
+  "exception": "org.cbioportal.session_service.service.exception.SessionNotFoundException",
+  "message": "Session not found",
+  "path": "/api/sessions/msk_portal/main_session/test"
+}
+```