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cBioPortal/session-service

Name: session-service

Owner: cBioPortal

Description: null

Created: 2015-09-28 15:22:50.0

Updated: 2017-11-13 18:55:14.0

Pushed: 2017-11-15 16:17:39.0

Homepage: null

Size: 89

Language: Java

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README

session-service

RESTful API to cBioPortal/cbioportal sessions in MongoDB.

Session information is stored in JSON, so this API generalizes to any JSON objects.

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:

ngo

e session_service

Clone repository, compile, run tests, and start server:

t clone https://github.com/cBioPortal/session-service.git

 session-service

ion-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:

 session-service

ion-service$ mkdir src/main/resources/

ion-service$ cp /path/to/myapp.config src/main/resources/

ion-service$ mvn package

An example properties file:

ng.data.mongodb.database=session_service
ng.data.mongodb.host=localhost
ng.data.mongodb.port=27017

To have a context root that is not “/“, add to the properties file:

er.contextPath=/session_service
er.port=8080

Assumes you want to run the server on port 8080. This can be overridden by setting the process's SERVER_PORT environment variable.

ion-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

API

Swagger documentation will be found here: http://[url]:[port]/swagger-ui.html e.g. http://localhost:8090/swagger-ui.html

Create

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. Valid types are: main_session and virtual_study. 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/

tle": "my main portal session", "description": "this is an example"}

Example response:


d": "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:


imestamp": 1461093154793,
tatus": 400,
rror": "Bad Request",
xception": "org.cbioportal.session_service.domain.exception.SessionInvalidException",
essage": "valid types are: 'main_session' and 'virtual_study';",
ath": "/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:


imestamp": 1461090997119,
tatus": 400,
rror": "Bad Request",
xception": "org.cbioportal.session_service.domain.exception.SessionInvalidException",
essage": "\n{\"portal-session\": blah blah blah}\n                   ^",
ath": "/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


d": "57167a52ef86d81afb415aba",
ata": {
"title": "my main portal session",
"description": "this is an example"

ource": "msk_portal",
ype": "main_session"

If no session is found returns status 404 with a request body like this:


imestamp": 1462379207301,
tatus": 404,
rror": "Not Found",
xception": "org.cbioportal.session_service.service.exception.SessionNotFoundException",
essage": "Session not found",
ath": "/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:


imestamp": 1461092375741,
tatus": 400,
rror": "Bad Request",
xception": "org.springframework.http.converter.HttpMessageNotReadableException",
essage": "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)",
ath": "/api/sessions/msk_portal/main_session/57167a52ef86d81afb415aba"

If an invalid id is passed returns status 404 with a request body like this:


imestamp": 1462379078498,
tatus": 404,
rror": "Not Found",
xception": "org.cbioportal.session_service.service.exception.SessionNotFoundException",
essage": "Session not found",
ath": "/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:


imestamp": 1461092440979,
tatus": 400,
rror": "Bad Request",
xception": "org.cbioportal.session_service.domain.exception.SessionInvalidException",
essage": "\n{\n    \"title\": \"my UPDATED main portal session\",\n    \"description\": blah blah blah\n}\n                                                                    ^",
ath": "/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:


imestamp": 1462379146105,
tatus": 404,
rror": "Not Found",
xception": "org.cbioportal.session_service.service.exception.SessionNotFoundException",
essage": "Session not found",
ath": "/api/sessions/msk_portal/main_session/test"

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.