Rest Api

Submit a job

POST /api/v1/job/submit

Submit a job

Example request:

{
  'configuration' : {
    'profile': 'bacteria-gram+'
  },
  'sequence': 'MKKKQTTKALLVTCITDHKQDFYRLAFSYVKNQDDALDIVQESIKKALSSVETVRNPGTIKSWFYKILVRTAIDFLRKQKKIRVMDDETIEFLSKGKEDHYKDTDLHEALDELPYRYKTIIILRFFEDLKLEEIAEITGENTNTVKTRLYRALKLMRIQLTKEDLS'
}

Example response:

{
  "id": "5be12dcd-f74f-41d0-9abd-41527553a13a",
  "created": "2019-05-14T13:58:18.892507Z",
  "lastUpdated": "2019-05-14T13:58:18.906208Z",
  "deleteAt": "2019-05-15T13:58:18.892507Z",
  "step": "fasta-validator",
  "request": {
    "type": "sequence",
    "configuration": {
      "profile": "bacteria-gram+"
    },
    "sequence": "FDSJKLFJDSFKLJDFHADJKLFHDSJKLFHDAFJKLDHFJKLDASFHDJKLFHDSAJKLFHDAKLFJDHSAFKLDLSNCDJKLFENFIUPERWDJKPCNVDFPIEHFDCFJDKOWFPDJWFKLXSJFDWFIPUAENDCXAMSFNDUAFIDJFDLKSAFJDSAKFLJDSADJFDWFIPUAENDCXAMSFNDAAAAAAAAAAAFJDSAKAA\n"
  },
  "files": [
    {
      "location": "input.fas",
      "name": "input.fas",
      "type": "Input"
    }
  ],
  "state": {
    "name": "waiting",
    "type": "Waiting"
  }
}

Request JSON Object

sequence – The protein sequence, either raw or as fasta string
configuration.profile – The profile for the computation
source_app – An identifier of the app sends the request (optional)

Status Codes

200 OK – no error
400 Bad Request – the request is invalid

Get job status

GET /api/v1/job/(jobid)

Get the job object

Example request:

Example response:

{
  "id": "5be12dcd-f74f-41d0-9abd-41527553a13a",
  "created": "2019-05-14T13:58:18.892507Z",
  "lastUpdated": "2019-05-14T13:58:18.906208Z",
  "deleteAt": "2019-05-15T13:58:18.892507Z",
  "step": "fasta-validator",
  "request": {
    "type": "sequence",
    "configuration": {
      "profile": "bacteria-gram+"
    },
    "sequence": "FDSJKLFJDSFKLJDFHADJKLFHDSJKLFHDAFJKLDHFJKLDASFHDJKLFHDSAJKLFHDAKLFJDHSAFKLDLSNCDJKLFENFIUPERWDJKPCNVDFPIEHFDCFJDKOWFPDJWFKLXSJFDWFIPUAENDCXAMSFNDUAFIDJFDLKSAFJDSAKFLJDSADJFDWFIPUAENDCXAMSFNDAAAAAAAAAAAFJDSAKAA\n"
  },
  "files": [
    {
      "location": "input.fas",
      "name": "input.fas",
      "type": "Input"
    }
  ],
  "state": {
    "name": "waiting",
    "type": "Waiting"
  }
}

Parameters

jobid – The job id

Status Codes

200 OK – no error
404 Not Found – the job does not exist

Delete a job

DELETE /api/v1/job/(jobid)

Deletes the job

Example request:

Example response:

Parameters

jobid – The job id

Status Codes

200 OK – no error

Retrieve a job file

GET /api/v1/job/(jobid)/file/(filename)

Get the job object

Example request:

Example response:

>seq
AAAA

Parameters

jobid – The job id
filename – The filename

Status Codes

200 OK – no error
404 Not Found – the job or file does not exist

Access the eventbus

GET /api/v1/job/eventbus: Join the eventbus. Use the appropriate vertx library to access the eventbus.

Resolve the representations of a dbxref

GET /api/v1/dbxref/resolve/(dbxref)

Get the locations where you can find representations of the dbxref.

Example request:

GET /api/v1/dbxref/retrieve/taxon:100 HTTP/1.1
Host: psos-staging.computational.bio
Accept: application/json, text/javascript

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

[
  {"dbxref": "taxon:100",
   "locations": {
     "html": ["http://www.uniprot.org/taxonomy/100"],
     "json": ["https://www.ebi.ac.uk/ena/data/taxonomy/v1/taxon/tax-id/100"],
     "xml": ["http://www.uniprot.org/taxonomy/100.rdf"],
     "xml_ncbi": ["https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=100"]},
   "status": "found"}
]

Parameters

dbxref – The dbxref

Status Codes

200 OK – no error
404 Not Found – no information about the dbxref found

Retrieve a dbxref as json

GET /api/v1/dbxref/retrieve/(dbxref)

Retrieve a json representation of the dbxref.

Example request:

GET /api/v1/dbxref/retrieve/taxon:100 HTTP/1.1
Host: psos-staging.computational.bio
Accept: application/json, text/javascript

Example response:

HTTP/1.1 200 OK
Content-Type: application/json

[
  {
    "id": "Taxon:100",
    "scientificName": "Ancylobacter aquaticus",
    "lineage": ["Bacteria", "Proteobacteria", "Alphaproteobacteria", "Rhizobiales", "Xanthobacteraceae", "Ancylobacter"],
    "rank": "species",
    "geneticCodes": {
      "geneticCode": "11"
    }
  }
]

Parameters

dbxref – The dbxref

Status Codes

200 OK – no error
404 Not Found – no information about the dbxref found

Redirect to a html representation of a dbxref

GET /api/v1/dbxref/redirect/(dbxref)

Redirect to a html representation of the dbxref.

Example request:

GET /api/v1/dbxref/redirect/taxon:100 HTTP/1.1
Host: psos-staging.computational.bio
Accept: application/json, text/javascript

Example response:

HTTP/1.1 303 See Other
Location: http://www.uniprot.org/taxonomy/100

Parameters

dbxref – The dbxref

Status Codes

303 See Other – no error, html representation found
404 Not Found – database in dbxref not supported