genomizer / genomizer-server

A system for storing and analyzing DNA sequences (server component).

Genomizer Server

This is the main repository for the server side of the Genomizer system.

##Downloads

Auto-generated binary snapshots are uploaded by the Travis build bot to the genomizer-downloads repository after each successful build.

The following downloads are available:

• master branch:
• genomizer-server.jar
• genomizer-server-tester.jar
• develop branch:
• genomizer-server.jar
• genomizer-server-tester.jar
• Resources (common for both branches):
• genomizer-server-resources.tar.xz

NB: The genomizer-server-resources.tar.xz archive is updated manually due to its large size. GitHub Releases feature is used to host it.

##Building

To build the server.jar file manually, run ant jar from the console. To just compile the sources, use ant build or ant compile. To run tests, use ant test. To run individual tests or test groups, use an IDE (e.g. in Eclipse you can import the project with 'File > New > Project > Java > Java Project from Existing Ant Buildfile'). To produce a HTML report with test results, run ant junitreport. The report will be put under junit/index.html. To build and run the server in one step (useful during development), use ant run.

##Usage

The server requires Java 1.7 to run. This is the default on lab computers, so you can just use

java -jar server.jar

to run the Genomizer server. The full path to the Java 7 executable is /usr/lib/jvm/java-7-openjdk-amd64/bin/java.

The program can be run with the following options:

-p [NUMBER]    The listening port for the server, default is 7000

-f [FILE]      Use a custom config file instead of settings.cfg.

-nri       "No remove inactive", don't remove inactive users that are
           logged in.

-debug         Print out various debug information.

If no options are used the server will listen on port 7000 and look for a file named "settings.cfg" in the current folder to read settings from.

##Development

The main development branch is called develop. New feature development is done on separate feature branches. When a feature is completed, the feature branch is merged into develop after a code review. The develop branch is itself regularly merged into master (usually before a delivery).

More on this branching model can be found here. A guide for merging in Git can be found here.

##Overview

The server uses HTTP with a RESTful interface for client-server communication. Full documentation for the API can be found on Apiary. Since HTTP is based around non-persistent connections a token is generated for users when logging in, which must then be passed with all following requests. The authorization token should be passed in in the Authorization headr (or, alternatively, using a ?token= URL parameter) of all requests except login requests.

###Example: logging in

The client sends username and password in a JSON object and receives an authorization token from the server. The HTTP response code is used to notify the client if the operation was successful. 200 means OK.

Request

POST /login HTTP/1.1
Content-Length: XXXX

{"username":"yuri","password":"epicgenie"}

Response

HTTP/1.1 200 OK
Content-Length: XXXX

{"token":"abca44db68cd2ffg2293"}

###Example: fetching annotation list

Using the authorization token from the login request, the client can then make other requests, such as fetching a list of all annotation types in the database.

Request

GET /annotation HTTP/1.1
Authorization: abca44db68cd2ffg2293

Response

HTTP/1.1 200 OK
Content-Length: XXXX

[
 {
  "id": 1,
  "name": "pubmedId",
  "value": "freetext",
  "forced": true
 },
 {
  "id": 2,
  "name": "type",
  "value": "freetext",
  "forced": true
 },
 {
  "id": 3,
  "name": "specie",
  "value": ["fly", "human", "rat"],
  "forced": true
 }
]

##Links Client-Server API

Git merge instructions