Coge

Viewing a Genome File in CoGe

A genome file may be submitted to CoGe for viewing within their genome viewer. This endpoint will share the given genome files with the CoGe user, then submit those paths to their "genome load" service. This service will return a URL where the authenticated user may view the genome viewer's progress, and the genome visualization once processing is done.

URL Path: /coge/genomes/load

HTTP Method: POST

Error Codes: ERR_NOT_A_USER, ERR_BAD_OR_MISSING_FIELD, ERR_DOES_NOT_EXIST, ERR_NOT_OWNER

Request Query Parameters:

Request Body:

{
    "paths": [
        "/iplant/home/ipctest/simple.fasta"
    ]
}

Response Body:

{
    "coge_genome_url": "http://bit.ly/CoGeSample"
}

Curl Command:

curl -sH "$AUTH_HEADER" -d '{"paths":["/iplant/home/ipctest/simple.fasta"]}' http://127.0.0.1:3000/coge/genomes/load

Searching for Genomes in CoGe

A user may search for genome information in CoGe in order to retrieve a text representation of that genome for use in DE analyses.

URL Path: /coge/genomes

HTTP Method: GET

Error Codes: ERR_REQUEST_FAILED

Request Query Parameters:

• search - The string to search for.

Response Body:

{
    "genomes": [
        {
            "chromosome_count": 35,
            "description": null,
            "id": 9716,
            "info": "Actinomyces coleocanis strain DSM 15436 (v1, id9716): unmasked",
            "link": null,
            "name": null,
            "organism": {
                "description": "Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales; Actinomycineae; Actinomycetaceae; Actinomyces",
                "id": 23534,
                "name": "Actinomyces coleocanis strain DSM 15436"
            },
            "organism_id": 23534,
            "restricted": false,
            "sequence_type": {
                "description": "unmasked sequence data",
                "id": "1",
                "name": "unmasked"
            },
            "version": "1"
        },
        ...
    }
}

Note: the response body from CoGe is passed back to the caller without modification.

Curl Command:

$ curl -sH "$AUTH_HEADER" "http://127.0.0.1:3000/coge/genomes?search=canis" | python -mjson.tool

Exporting CoGe Genome Data to iRODS

Once a user has found an interesting genome, he or she may request a text representation of the genome to be stored in the iPlant Data Store for processing in the DE.

URL Path: /coge/genomes/{genome-id}/export-fasta

HTTP Method: POST

Error Codes: ERR_REQUEST_FAILED

Request Query Parameters:

• notify - If present and set to "true" the user's email address will be forwarded to CoGe.
• overwrite - If present and set to "true" the output file will be overwritten if it exists.

Response Body:

{
    "id": 30702,
    "success": true
}

Note: the response body from CoGe is passed back to the caller without modification.