Expression Tests

This page outlines the success and failure criteria for all tests of Expression resources.

Expression API Tests

Expression API tests assert the correct configuration of expression-related API routes. In order for a test case to succeed, the following conditions must be met when evaluating the response:

  • For all cases, Content-Type checking is enforced. The response MUST have a Content-Type header of application/vnd.ga4gh.rnaget.v1.0.0+json OR application/json

  • For all cases, Status Code checking is enforced. The response MUST have the expected status code

  • For all cases, schema checking is enforced. The json object in the response body MUST conform to a pre-defined schema of required fields and data types, which is specific to each API route

Expression API Test Cases

Get Supported Expression Formats

  • Route: /expressions/formats

  • Description: Requests the available expression data file formats on the server. Expects an array of strings to be returned in the response body.

  • Rationale: Asserts that /expressions/formats returns an array of strings, indicating which expression file formats the server supports

  • Request:

GET /expressions/formats
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 200 OK
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

[
  "loom",
  "tsv"
]

  • Success Criteria: Status Code == 200 AND response body is an array of strings in json format

  • Failure Criteria: Status Code != 200 OR response body is NOT an array of strings in json format

Expression Filters

  • Route: /expressions/filters

  • Description: Requests the filters that can be used to narrow search results for a list of Expressions

  • Rationale: Asserts that the endpoint returns an array of filter objects

  • Request:

GET /expressions/filters
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 200 OK
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

[
  {
    "fieldType": "string",
    "values": [
      "1.0"
    ],
    "filter": "version",
    "description": "version to search for"
  },
  {
    "fieldType": "string",
    "filter": "studyID",
    "description": "parent studyID"
  }
]

  • Success Criteria: Status Code == 200 AND response body is array of filters

  • Failure Criteria: Status Code != 200 OR response body is NOT array of filters

Get Test Expression Ticket

  • Route: /expressions/<id>/ticket

  • Description: Requests test expression ticket by its id. Expects the returned expression to match the ticket json schema.

  • Rationale: Asserts that the /expressions/<id>/ticket endpoint returns a valid ticket.

  • Request:

GET /expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 200 OK
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

{
  "id": "ac3e9279efd02f1c98de4ed3d335b98e",
  "version": "1.0",
  "studyID": "f3ba0b59bed0fa2f1030e7cb508324d1",
  "url": "https://url/to/expression/file",
  "units": "TPM",
  "fileType": "loom/tsv"
}

  • Success Criteria: Status Code == 200 AND response body is valid ticket

  • Failure Criteria: Status Code != 200 OR response body is NOT valid ticket

Single Expression Ticket - Not Found

  • Route: /expressions/<id>/ticket

  • Description: Requests an expression ticket with an invalid id, that is, an id that does not correspond to any Expression on the server. Expects a 404 Not Found status code in the response, and a response body with an error message.

  • Rationale: Asserts that the /expressions/<id>/ticket endpoint does not return arbitrary ticket.

  • Request:

GET /expressions/nonexistentid9999999999999999999/ticket
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 404 Not Found
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

{
  "message": "Entry not found in database."
}

  • Success Criteria: Status Code == 404 AND response body is valid Error json

  • Failure Criteria: Status Code != 404 OR response body is NOT valid Error json

Get Test Expression Bytes

  • Route: /expressions/<id>/bytes

  • Description: Requests test expression matrix as bytes by its id.

  • Rationale: Asserts that the /expressions/<id>/bytes endpoint returns matrix bytes.

  • Request:

GET /expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes
Accept: application/octet-stream, application/vnd.loom, text/tab-separated-values

  • Successful Response:

HTTP/1.1 200 OK
Content-Type: application/octet-stream

  • Success Criteria: Status Code == 200

  • Failure Criteria: Status Code != 200

Single Expression Bytes - Not Found

  • Route: /expressions/<id>/bytes

  • Description: Requests expression matrix bytes with an invalid id that doesn’t correspond to any Expression on the server. Expects a 404 Not Found status code and an error message in response body.

  • Rationale: Asserts that the /expressions/<id>/bytes endpoint does not return arbitrary matrix.

  • Request:

GET /expressions/nonexistentid9999999999999999999/bytes
Accept: application/octet-stream, application/vnd.loom, text/tab-separated-values

  • Successful Response:

HTTP/1.1 404 Not Found
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

{
  "message": "Entry not found in database."
}

  • Success Criteria: Status Code == 404 AND response body is valid Error json

  • Failure Criteria: Status Code != 404 OR response body is NOT valid Error json

Expression Ticket by Format

  • Route: /expressions/ticket

  • Description: Requests joined matrix, specifying only the required ‘format’ parameter. Expects ticket response.

  • Rationale: Asserts that the /expressions/ticket returns a valid ticket.

  • Request:

GET /expressions/ticket?format=loom
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 200 OK
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

 {
   "studyID": "6cccbbd76b9c4837bd7342dd616d0fec",
   "url": "/path/to/E-MTAB-5423-query-results.tpms.loom",
   "units": "TPM",
   "version": "1.0",
   "fileType": "loom"
 }

  • Success Criteria: Status Code == 200 AND response body is ticket

  • Failure Criteria: Status Code != 200 OR response body is NOT ticket

Expression Ticket - All Filters

  • Route: /expressions/ticket

  • Description: Requests joined matrix, using all filtering parameters associated with test expression. Expects ticket.

  • Rationale: Asserts that /expressions/ticket returns ticket when specifying filters.

  • Request:

GET /expressions/ticket?format=loom&version=1.0&studyID=f3ba0b59bed0fa2f1030e7cb508324d1
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 200 OK
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

 {
   "url": "https://path/to/expression.loom",
   "units": "TPM",
   "fileType": "loom"
 }

  • Success Criteria: Status Code == 200 AND response body is ticket

  • Failure Criteria: Status Code != 200 OR response body is NOT ticket

Expression Ticket - Single Filter, 1

  • Route: /expressions/ticket

  • Description: Requests joined matrix using only 1 filtering parameter associated with test expression (in addition to format). Expects ticket.

  • Rationale: Asserts filtering parameters can be used independently of one another, and that each filter yields a valid ticket.

  • Requests:

GET /expressions/ticket?format=loom&version=1.0
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 200 OK
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

 {
   "url": "https://path/to/expression.loom",
   "units": "TPM",
   "version": "1.0",
   "fileType": "loom"
 }

  • Success Criteria: Status Code == 200 AND response body is ticket

  • Failure Criteria: Status Code != 200 OR response body is NOT ticket

Expression Ticket - Single Filter, 2

  • Route: /expressions/ticket

  • Description: Requests joined matrix using only 1 filtering parameter (a different filter than above) associated with test expression (in addition to format). Expects ticket.

  • Rationale: Asserts filtering parameters can be used independently of one another, and that each filter yields a valid ticket.

  • Requests:

GET /expressions/ticket?format=loom&studyID=f3ba0b59bed0fa2f1030e7cb508324d1
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 200 OK
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

 {
   "studyID": "f3ba0b59bed0fa2f1030e7cb508324d1",
   "url": "/path/to/expression.loom",
   "units": "TPM",
   "fileType": "loom"
 }

  • Success Criteria: Status Code == 200 AND response body is ticket.

  • Failure Criteria: Status Code != 200 OR response body is NOT ticket.

Expression Ticket - Format Not Specified

  • Route: /expressions/ticket

  • Description: Requests joined matrix WITHOUT specifying the required format parameter. Expects a 4xx response with error message.

  • Rationale: As the format parameter is required to specify file format for the /expressions/ticket endpoint, this test asserts malformed requests raise an error.

  • Request:

GET /expressions/ticket
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 400 Bad Request
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

{
  "message": "Input payload validation failed"
}

  • Success Criteria: Status Code == 4xx AND response body is valid Error json

  • Failure Criteria: Status Code != 4xx AND response body is NOT valid Error json

Expression Ticket - Filetype Matches

  • Route: /expressions/ticket

  • Description: Requests joined matrix, only specifying the required format parameter. Checks that ticket has a fileType matching requested format.

  • Rationale: Asserts that the /expressions/ticket endpoint returns ticket with fileType matching the request.

  • Request:

GET /expressions/ticket?format=loom
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 200 OK
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

 {
   "url": "/path/to/E-MTAB-5423-query-results.tpms.loom",
   "units": "TPM",
   "fileType": "loom"
 }

  • Success Criteria: Status Code == 200 AND response body is ticket AND fileType matches requested format

  • Failure Criteria: Status Code != 200 OR response body is NOT ticket OR fileType DOES NOT match requested format

Expression Bytes by Format

  • Route: /expressions/bytes

  • Description: Requests joined matrix bytes, only specifying the required format parameter.

  • Rationale: Asserts that the /expressions/bytes endpoint returns matrix bytes.

  • Request:

GET /expressions/bytes?format=loom
Accept: application/octet-stream, application/vnd.loom, text/tab-separated-values

  • Successful Response:

HTTP/1.1 200 OK
Content-Type: application/octet-stream

  • Success Criteria: Status Code == 200

  • Failure Criteria: Status Code != 200

Expression Bytes - All Filters

  • Route: /expressions/bytes

  • Description: Requests joined matrix bytes using all expression filters.

  • Rationale: Asserts that the /expressions/bytes endpoint returns matrix bytes when all filters are provided.

  • Request:

GET /expressions/bytes?format=loom&version=1.0&studyID=f3ba0b59bed0fa2f1030e7cb508324d1
Accept: application/octet-stream, application/vnd.loom, text/tab-separated-values

  • Successful Response:

HTTP/1.1 200 OK
Content-Type: application/octet-stream

  • Success Criteria: Status Code == 200

  • Failure Criteria: Status Code != 200

Expression Bytes - Single Filter, 1

  • Route: /expressions/bytes

  • Description: Requests joined matrix bytes using one expression filter (in addition to format).

  • Rationale: Asserts filter parameters can be used independently of one another.

  • Request:

GET /expressions/bytes?format=loom&version=1.0
Accept: application/octet-stream, application/vnd.loom, text/tab-separated-values

  • Successful Response:

HTTP/1.1 200 OK
Content-Type: application/octet-stream

  • Success Criteria: Status Code == 200

  • Failure Criteria: Status Code != 200

Expression Bytes - Single Filter, 2

  • Route: /expressions/bytes

  • Description: Requests joined matrix bytes using one expression filter (different than above), in addition to format.

  • Rationale: Asserts filter parameters can be used independently of one another.

  • Request:

GET /expressions/bytes?format=loom&studyID=f3ba0b59bed0fa2f1030e7cb508324d1
Accept: application/octet-stream, application/vnd.loom, text/tab-separated-values

  • Successful Response:

HTTP/1.1 200 OK
Content-Type: application/octet-stream

  • Success Criteria: Status Code == 200

  • Failure Criteria: Status Code != 200

Expression Bytes - Format Not Specified

  • Route: /expressions/bytes

  • Description: Requests joined matrix bytes WITHOUT specifying required format parameter. Expects a 4xx response with error message.

  • Rationale: As the format parameter is required to specify file format for the /expressions/bytes endpoint, this test asserts malformed requests raise an error.

  • Request:

GET /expressions/bytes
Accept: application/octet-stream, application/vnd.loom, text/tab-separated-values

  • Successful Response:

HTTP/1.1 400 Bad Request
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

{
  "message": "Input payload validation failed"
}

  • Success Criteria: Status Code == 4xx AND response body is valid Error json

  • Failure Criteria: Status Code != 4xx AND response body is NOT valid Error json

Expression API Non-Implemented Test Cases

Expression Formats Not Implemented

  • Route: /expressions/formats

  • Description: If the Expressions endpoint is specified as Not Implemented in the config file, then this test will be run. Requests the /expressions/formats endpoint, expecting a 501 Not Implemented status code response

  • Rationale: Asserts that Expression related endpoints are correctly non-implemented according to the spec

  • Request:

GET /expressions/formats
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 501 Not Implemented
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

  • Success Criteria: Status Code == 501

  • Failure Criteria: Status Code != 501

Expression Ticket by Id Not Implemented

  • Route: /expressions/<id>/ticket

  • Description: If expressions endpoints are Not Implemented, this test will request /expressions/<id>/ticket, expecting a 501 Not Implemented status code response

  • Rationale: Asserts Expression related endpoints are correctly non-implemented

  • Request:

GET /expressions/nonexistentid9999999999999999999/ticket
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 501 Not Implemented
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

  • Success Criteria: Status Code == 501

  • Failure Criteria: Status Code != 501

Expression Bytes by Id Not Implemented

  • Route: /expressions/<id>/bytes

  • Description: If expressions endpoints are Not Implemented, this test will request /expressions/<id>/bytes, expecting a 501 Not Implemented status code response

  • Rationale: Asserts Expression related endpoints are correctly non-implemented

  • Request:

GET /expressions/nonexistentid9999999999999999999/bytes
Accept: application/octet-stream, application/vnd.loom, text/tab-separated-values

  • Successful Response:

HTTP/1.1 501 Not Implemented
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

  • Success Criteria: Status Code == 501

  • Failure Criteria: Status Code != 501

Expression Filters Not Implemented

  • Route: /expressions/filters

  • Description: If expressions endpoints are Not Implemented, this test will request /expressions/filters, expecting a 501 Not Implemented status code response

  • Rationale: Asserts that Expression related endpoints are correctly non-implemented

  • Request:

GET /expressions/filters
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 501 Not Implemented
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

  • Success Criteria: Status Code == 501

  • Failure Criteria: Status Code != 501

Expression Ticket Not Implemented

  • Route: /expressions/ticket

  • Description: If expressions endpoints are Not Implemented, this test will request /expressions/ticket, expecting a 501 Not Implemented status code response

  • Rationale: Asserts that Expression related endpoints are correctly non-implemented

  • Request:

GET /expressions/ticket
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Successful Response:

HTTP/1.1 501 Not Implemented
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

  • Success Criteria: Status Code == 501

  • Failure Criteria: Status Code != 501

Expression Bytes Not Implemented

  • Route: /expressions/bytes

  • Description: If expressions endpoints are Not Implemented, this test will request /expressions/bytes, expecting a 501 Not Implemented status code response

  • Rationale: Asserts that Expression related endpoints are correctly non-implemented

  • Request:

GET /expressions/bytes
Accept: application/octet-stream, application/vnd.loom, text/tab-separated-values

  • Successful Response:

HTTP/1.1 501 Not Implemented
Content-Type: application/vnd.ga4gh.rnaget.v1.0.0+json

  • Success Criteria: Status Code == 501

  • Failure Criteria: Status Code != 501

Expression Content Tests

Expression content tests assert that expression matrices downloaded from the RNAget server contain the expected content/results based on the request. Matrix rows, columns, and values are cross-referenced against the request to ensure the correct data has been returned.

Expression Content Test Cases

Expression Ticket by Id Content Test Cases

  • Route: /expressions/<id>/ticket

  • Description: Download test expression by ticket multiple times (sometimes slicing by featureIDList, featureNameList, sampleIDList).

  • Rationale: Asserts correct matrix file is associated with the test expression id. Validates expression values match expected. Validates returned columns/rows match expected based on slice parameters.

  • Request:

GET /expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Success Criteria: Test expression matrix columns, rows, values match expected

  • Failure Criteria: Test expression matrix columns, rows, values DO NOT match expected

Expression Bytes by Id Content Test Cases

  • Route: /expressions/<id>/bytes

  • Description: Download test expression by bytes multiple times (sometimes slicing by featureIDList, featureNameList, sampleIDList).

  • Rationale: Asserts correct matrix file is associated with the test expression id. Validates expression values match expected. Validates returned columns/rows match expected based on slice parameters.

  • Request:

GET /expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Success Criteria: Test expression matrix columns, rows, values match expected

  • Failure Criteria: Test expression matrix columns, rows, values DO NOT match expected

Expression Ticket Content Test Cases

  • Route: /expressions/ticket

  • Description: Download joined expression matrix by ticket multiple times (sometimes slicing by featureIDList, featureNameList, sampleIDList).

  • Rationale: Asserts joined matrix. Validates expression values match expected. Validates returned columns/rows match expected based on slice parameters.

  • Request:

GET /expressions/ticket?format=loom
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Success Criteria: Joined expression matrix columns, rows, values match expected

  • Failure Criteria: Joined expression matrix columns, rows, values DO NOT match expected

Expression Bytes Content Test Cases

  • Route: /expressions/bytes

  • Description: Download joined expression matrix by bytes multiple times (sometimes slicing by featureIDList, featureNameList, sampleIDList).

  • Rationale: Asserts joined matrix. Validates expression values match expected. Validates returned columns/rows match expected based on slice parameters.

  • Request:

GET /expressions/bytes?format=loom
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

  • Success Criteria: Joined expression matrix columns, rows, values match expected

  • Failure Criteria: Joined expression matrix columns, rows, values DO NOT match expected