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genesearcher

REST Application to allow users to get gene name suggestions for a given partial gene name.

Dependencies

  • Rebar3 & Erlang 21 The Service main language is erlang, you must install this if you want to develop and/or execute the service directly in your machine. See (http://www.erlang.org/downloads, http://www.rebar3.org/)

  • Docker This Service has been designed to be Dockerized. You can compile and execute it automatically inside a Docker container. see Running Docker Image

Getting the code

Just clone it or download it directly from github

$ git clone https://github.com/cfclavijo/genesearcher.git

Docker-ish

Building the Docker Image

This process will download a base image (erlang 21), upload the code, build it inside and install the Service. This workflow gives us the advantage of deploying the code through different OS.

First we need to build and generate a release of the code for linux. Then proceed to create a Docker image called genesearcher

$ make docker-image

Running Docker Image

With the service Dockerized it becomes easy to launch it in a proper environment (server or locally) by simply running

$ make docker-run

Development

Build

$ make

Execute

The service will start under port 8080.

$ make run

Configuration

Update erl.config according to the required parameters.

{genesearcher, [
    {'http_port', 8080},
    {'ensembldb_pool_size', 5},
    {'ensembldb_pool_max_overflow', 10},
    {'ensembldb_host', "ensembldb.ensembl.org"},
    {'ensembldb_port', 3306},
    {'ensembldb_database', "ensembl_website_90"},
    {'ensembldb_user', <<"anonymous">>},
    {'ensembldb_password', undefined},
    {'gene_suggest_limit', <<"10">>}
]}

Tests

The test suite will also generate Cobertura coverage XML report for Jenkins.

$ make test

Usage

-The service does not require authentication.-

gene_suggest

Given a partial name of a GENE and target species, returns a list of suggested gene names.

Example Usage
$ curl -H 'content-type:application/json' http://localhost:8080/gensearcher/v1/gene_suggest/ -d '{"query":"brc", "species": ["homo_sapiens"], "limit": "13"}'
JSON Request Body Properties
  • query:String. The Partial query typed by the user.
  • species:List(String). The name of the target species.
  • limit:Integer. Optional The maximum number of suggestions to return.
Content Type
application/json
200 Ok
{
    "suggestions": [
        "BRCA1",
        "BRCA2",
        "BRCC3",
        "BRCC3P1"
    ]
}
400 Invalid Parameters

If query or species parameters are invalid, the service will return a message indicating which parameter is invalid

{
    "error_type": "missing_parameter",
    "message": [
      [
        "species"
      ]
    ]
}