Preamble¶

Welcome to the RNAget Server Compliance documentation.

This documentation (and associated compliance testing application) determines a server’s compliance with the RNAget API specification for serving RNAseq datasets. The specification, developed by the Global Alliance for Genomics and Health, serves to provide a standardized API framework and data structure to allow for interoperability of datasets hosted at different institutions.

RNAget Servers¶

RNAget Servers enable access to RNAseq datasets and their metadata using unique identifiers for each object in a hierarchical data model. Servers can be queried for expression matrices, as well as project and study information associated with the raw RNAseq data. Servers support the slicing of expression and continuous signal intensity matrices by various parameters, so that only subsets of large matrix files need to be transferred. Expression matrices can be subsetted by gene, sample, and/or expression value thresholds. Continuous signal intensity matrices can be subsetted by chromosome and start/end base positions.

Compliance Document¶

This documentation is for implementers of RNAget servers. Implementers MUST adhere to this documentation during development of RNAget-compliant servers, as the compliance tests outlined herein conform with the RNAget specification. The testing suite performs API testing on all routes discussed in the specification. Reference server responses MUST comply with the correct responses in this document for requests made to each route/endpoint.

RNAget maintains an up-to-date report of the compliance status of its reference implementers. Click here to view the latest report.

Click here to learn more about the API Specification

Table of Contents¶

API Specification¶

The RNAget specification describes, at maximum, 18 API routes. These routes are subdivided into 4 groups according to the data type they serve. These routes, broken down by data type, are as follows:

Projects: Serves project-related information. 3 Routes
- /projects/:id
- /projects
- /projects/filters
Studies: Serves study-related information. 3 Routes
- /studies/:id
- /studies
- /studies/filters
Expressions: Handles requests for querying, slicing, and downloading expression matrix data by gene name/id. 6 Routes
- /expressions/formats
- /expressions/filters
- /expressions/:id/ticket
- /expressions/:id/bytes
- /expressions/ticket
- /expressions/bytes
Continuous: Handles requests for querying, slicing, and downloading expression matrix data by genomic coordinate. 6 Routes
- /continuous/formats
- /continuous/filters
- /continuous/:id/ticket
- /continuous/:id/bytes
- /continuous/ticket
- /continuous/bytes

Detailed descriptions of each route are available in the specification document.

Important points:

A server MAY implement all 18 API routes
A server MAY have unimplemented routes from the Expressions and/or Continuous data type groups. If a data type group is unimplemented, then ALL of the associated routes MUST be unplemented. In other words, a server MUST NOT implement only some routes for a data type group.

Test Dataset¶

This page contains links to test dataset files. The compliance suite expects the test dataset project, study, expression, and continuous resources to be available on the server and accessible by all relevant routes.

Project json
- Download project.json
- id: 9c0eba51095d3939437e220db196e27b
- Format: json
- How to Prepare for Compliance Testing
  
  upload project.json to RNAget server
  
  project.json MUST be accessible by its id, ie. /projects/9c0eba51095d3939437e220db196e27b
  
  project.json MUST appear in /projects/search results array
  
  project.json MUST be filterable by implemented search filters
Study json
- Download
- id: f3ba0b59bed0fa2f1030e7cb508324d1
- Format: json
- How to Prepare for Compliance Testing
  
  upload study.json to RNAget server
  
  study.json MUST be accessible by its id, ie. /studies/f3ba0b59bed0fa2f1030e7cb508324d1
  
  study.json MUST appear in /studies/search results array
  
  study.json MUST be filterable by implemented search filters
Expression ticket json
- Download
- id: ac3e9279efd02f1c98de4ed3d335b98e
- Format: json
- How to Prepare for Compliance Testing
  
  modify expression_ticket.json url property, so that it points to the test expression matrix file on the server
  
  modify expression_ticket.json fileType property to indicate test expression matrix file format (ie. ‘loom’ if loom, ‘tsv’ if tsv)
  
  upload modified expression_ticket.json to RNAget server
  
  expression_ticket.json MUST be accessible by its id, ie. /expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket
  
  a valid ticket must be returned for requests for an expression ticket pertaining to the compliance dataset (e.g. /expressions/ticket?format=loom&studyID=f3ba0b59bed0fa2f1030e7cb508324d1
Expression loom
- Download
- id: ac3e9279efd02f1c98de4ed3d335b98e
- Format: loom
- How to Prepare for Compliance Testing
  
  upload expression.loom ONLY if expression_ticket.json fileType property was set to ‘loom’
  
  if uploaded, make expression.loom accessible by the url in the url property of expression_ticket.json
  
  if uploaded, expression.loom must be sliceable by all subsetting parameters (featureIDList, featureNameList, sampleIDList)
Expression tsv
- Download
- id: ac3e9279efd02f1c98de4ed3d335b98e
- Format: tsv
- How to Prepare for Compliance Testing
  
  upload expression.tsv ONLY if expression_ticket.json fileType property was set to ‘tsv’
  
  if uploaded, make expression.tsv accessible by the url in the url property of expression_ticket.json
  
  if uploaded, expression.tsv must be sliceable by all subsetting parameters (featureIDList, featureNameList, sampleIDList)
Continuous ticket json
- Download
- id: 5e22e009f41fc53cbea094a41de8798f
- Format: json
- How to Prepare for Compliance Testing
  
  modify continuous_ticket.json url property, so that it points to the test continuous matrix file on the server
  
  modify continuous_ticket.json fileType property to indicate test continuous matrix file format (ie. ‘loom’ if loom, ‘tsv’ if tsv)
  
  upload modified continuous_ticket.json to RNAget server
  
  continuous_ticket.json MUST be accessible by its id, ie. /continuous/5e22e009f41fc53cbea094a41de8798f/ticket
  
  a valid ticket must be returned for requests for a continuous ticket pertaining to the compliance dataset (e.g. /continuous/ticket?format=loom&studyID=f3ba0b59bed0fa2f1030e7cb508324d1
Continuous loom
- Download
- id: 5e22e009f41fc53cbea094a41de8798f
- Format: loom
- How to Prepare for Compliance Testing
  
  upload continuous.loom ONLY if continuous_ticket.json fileType property was set to ‘loom’
  
  if uploaded, make continuous.loom accessible by the url in the url property of continuous_ticket.json
  
  if uploaded, continuous.loom must be sliceable by all subsetting parameters (chr, start, end)
Continuous tsv
- Download
- id: 5e22e009f41fc53cbea094a41de8798f
- Format: tsv
- How to Prepare for Compliance Testing
  
  upload continuous.tsv ONLY if continuous_ticket.json fileType property was set to ‘tsv’
  
  if uploaded, make continuous.tsv accessible by the url in the url property of continuous_ticket.json
  
  if uploaded, continuous.tsv must be sliceable by all subsetting parameters (chr, start, end)
Filter json
- Download
- Format: json
- How to Prepare for Compliance Testing
  
  filter.json is an example, this file does not need to be uploaded, but requests for supported filters must respond with an array of valid filter objects
Error json
- Download
- Format: json
- How to Prepare for Compliance Testing
  
  error.json is an example, this file does not need to be uploaded, but requests that produce an error must respond with a valid Error json object
  
  valid Error json objects MUST at least contain a “message” property

Project Tests¶

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

Project API Tests¶

Project API tests assert the correct configuration of project-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

Project API Test Cases¶

Get Test Project
Project Not Found
Project Filters
Search Projects Without Filters
Search Projects With All Filters
Search Projects With Single Filter, 1
Search Projects With Single Filter, 2
Project Search Filters Non-Matching Resources

Get Test Project¶

Route: /projects/<id>
Description: Requests test project by its id. Expects the returned project to match the Project json schema.
Rationale: Asserts that the /projects/<id> endpoint returns one valid project object, with id matching the request.
Request:

GET /projects/9c0eba51095d3939437e220db196e27b
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": "9c0eba51095d3939437e220db196e27b",
   "version": "1.0",
   "name": "RNAgetTestProject0",
   "description": "Test project object used by RNAget compliance testing suite."
}

Success Criteria: Status Code == 200 AND response body is valid Project json
Failure Criteria: Status Code != 200 OR response body is NOT valid Project json

Project Not Found¶

Route: /projects/<id>
Description: Requests a project with an invalid id, that is, an id that does not correspond to any Project on the server. Expects a 404 Not Found status code in the response, and a response body with a message explaining that the specified resource could not be found.
Rationale: Asserts that the /projects/<id> endpoint does not return arbitrary Project objects, and only returns a Project when the id matches.
Request:

GET /projects/nonexistentid9999999999999999999
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

Project Filters¶

Route: /projects/filters
Description: Requests the filters that can be used to narrow search results for a list of Projects
Rationale: Asserts that the endpoint returns an array of Filter objects
Request:

GET /projects/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",
    "values": [
      "PCAWG",
      "RNAgetTestProject0"
    ],
    "filter": "name",
    "description": "name of project"
  }
]

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

Search Projects Without Filters¶

Route: /projects
Description: Searches for all projects, without specifying any filtering parameters. Expects an array of Projects in the response body.
Rationale: Asserts that /projects returns an array, and that each element in the array is a Project.
Request:

GET /projects
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": "9c0eba51095d3939437e220db196e27b",
    "version": "1.0",
    "name": "RNAgetTestProject0",
    "description": "Test project object used by RNAget compliance testing suite."
  },
  {
    "description": "Pan Cancer Analysis of Whole Genomes test data from Expression Atlas E-MTAB-5423",
    "id": "43378a5d48364f9d8cf3c3d5104df560",
    "name": "PCAWG",
    "version": "1.0"
  }
]

Success Criteria: Status Code == 200 AND response body is array of Project json AND Array Length >= 1
Failure Criteria: Status Code != 200 OR response body is NOT array of Project json OR Array Length < 1

Search Projects With All Filters¶

Route: /projects
Description: Searches projects, using all filtering parameters associated with test project. Expects an array of Projects to be returned in the response body. Array must contain at least 1 object.
Rationale: Asserts that /projects returns an array of Projects even when specifying filters. The returned array MUST have at least 1 object, as the parameter filters must match the attributes of the test project.
Request:

GET /projects?version=1.0&name=RNAgetTestProject0
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": "9c0eba51095d3939437e220db196e27b",
    "version": "1.0",
    "name": "RNAgetTestProject0",
    "description": "Test project object used by RNAget compliance testing suite."
  }
]

Success Criteria: Status Code == 200 AND response body is array of Project json AND Array Length >= 1
Failure Criteria: Status Code != 200 OR response body is NOT array of Project json OR Array Length < 1

Search Projects With Single Filter, 1¶

Route: /projects
Description: Searches projects using only 1 filtering parameter associated with test project. Expects an array of Projects, with length of 1 or greater.
Rationale: Asserts filtering parameters can be used independently of one another, and that each filter yields the test Project in the search results.
Requests:

GET /projects?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

[
  {
    "id": "9c0eba51095d3939437e220db196e27b",
    "version": "1.0",
    "name": "RNAgetTestProject0",
    "description": "Test project object used by RNAget compliance testing suite."
  }
]

Success Criteria: Status Code == 200 AND response body is array of Project json AND Array Length >= 1
Failure Criteria: Status Code != 200 OR response body is NOT array of Project json OR Array Length < 1

Search Projects With Single Filter, 2¶

Route: /projects
Description: Searches projects using only 1 filtering parameter (a different filter than above) associated with test project. Expects an array of Projects, with length of 1 or greater.
Rationale: Asserts filtering parameters can be used independently of one another, and that each filter yields the test Project in the search results.
Requests:

GET /projects?name=RNAgetTestProject0
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": "9c0eba51095d3939437e220db196e27b",
    "version": "1.0",
    "name": "RNAgetTestProject0",
    "description": "Test project object used by RNAget compliance testing suite."
  }
]

Success Criteria: Status Code == 200 AND response body is array of Project json AND Array Length >= 1
Failure Criteria: Status Code != 200 OR response body is NOT array of Project json OR Array Length < 1

Project Get Not Implemented¶

Route: /projects/<id>
Description: If the Projects endpoint is specified as Not Implemented in the config file, then this test will be run. Requests the /projects/<id> endpoint, expecting a 501 Not Implemented status code response
Rationale: Asserts that Project related endpoints are correctly non-implemented according to the spec
Request:

GET /projects/nonexistentid9999999999999999999
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

Project Search Not Implemented¶

Route: /projects
Description: If the Projects endpoint is specified as Not Implemented in the config file, then this test will be run. Requests the /projects endpoint, expecting a 501 Not Implemented status code response
Rationale: Asserts that Project related endpoints are correctly non-implemented according to the spec
Request:

GET /projects
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

Project Filters Not Implemented¶

Route: /projects/filters
Description: If the Projects endpoint is specified as Not Implemented in the config file, then this test will be run. Requests the /projects/filters endpoint, expecting a 501 Not Implemented status code response
Rationale: Asserts that Project related endpoints are correctly non-implemented according to the spec
Request:

GET /projects/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

Study Tests¶

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

Study API Tests¶

Study API tests assert the correct configuration of study-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

Study API Test Cases¶

Get Test Study
Study Not Found
Study Filters
Search Studies Without Filters
Search Studies With All Filters
Search Studies With Single Filter, 1
Search Studies With Single Filter, 2
Study Search Filters Non-Matching Resources

Get Test Study¶

Route: /studies/<id>
Description: Requests test study by its id. Expects the returned study to match the Study json schema.
Rationale: Asserts that the /studies/<id> endpoint returns one valid study object, with id matching the request.
Request:

GET /studies/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

{
  "id": "f3ba0b59bed0fa2f1030e7cb508324d1",
  "version": "1.0",
  "name": "RNAgetTestStudy0",
  "description": "Test study object used by RNAget compliance testing suite.",
  "parentProjectID": "9c0eba51095d3939437e220db196e27b"
}

Success Criteria: Status Code == 200 AND response body is valid Study json
Failure Criteria: Status Code != 200 OR response body is NOT valid Study json

Study Not Found¶

Route: /studies/<id>
Description: Requests a study with an invalid id, that is, an id that does not correspond to any Study on the server. Expects a 404 Not Found status code in the response, and a response body with a message explaining that the specified resource could not be found.
Rationale: Asserts that the /studies/<id> endpoint does not return arbitrary Study objects, and only returns a Study when the id matches.
Request:

GET /studies/nonexistentid9999999999999999999
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

Study Filters¶

Route: /studies/filters
Description: Requests the filters that can be used to narrow search results for a list of Studies
Rationale: Asserts that the endpoint returns an array of filter objects
Request:

GET /studies/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",
    "values": [
      "PCAWG",
      "RNAGetTestStudy0"
    ],
    "filter": "name",
    "description": "name of study"
  }
]

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

Search Studies Without Filters¶

Route: /studies
Description: Searches for all studies, without specifying any filtering parameters. Expects an array of Studies in the response body.
Rationale: Asserts that the /studies returns an array, and that each element in the array is a Study.
Request:

GET /studies
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": "6cccbbd76b9c4837bd7342dd616d0fec",
    "parentProjectID": "43378a5d48364f9d8cf3c3d5104df560",
    "name": "PCAWG",
    "description": "PCAWG study",
    "version": "1.0"
  },
  {
    "id": "f3ba0b59bed0fa2f1030e7cb508324d1",
    "parentProjectID": "9c0eba51095d3939437e220db196e27b",
    "name": "RNAgetTestStudy0",
    "description": "Test study object used by RNAget compliance testing suite.",
    "version": "1.0"
  }
]

Success Criteria: Status Code == 200 AND response body is array of Study json AND Array Length >= 1
Failure Criteria: Status Code != 200 OR response body is NOT array of Study json OR Array Length < 1

Search Studies With All Filters¶

Route: /studies
Description: Searches studies, using all filtering parameters associated with test study. Expects an array of Studies to be returned in the response body. Array must contain at least 1 object.
Rationale: Asserts that /studies returns an array of Studies even when specifying filters. The returned array MUST have at least 1 object, as the parameter filters must match the attributes of the test study.
Request:

GET /studies?version=1.0&name=RNAgetTestStudy0
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": "f3ba0b59bed0fa2f1030e7cb508324d1",
    "parentProjectID": "9c0eba51095d3939437e220db196e27b",
    "name": "RNAgetTestStudy0",
    "description": "Test study object used by RNAget compliance testing suite.",
    "version": "1.0"
  }
]

Success Criteria: Status Code == 200 AND response body is array of Study json AND Array Length >= 1
Failure Criteria: Status Code != 200 OR response body is NOT array of Study json OR Array Length < 1

Search Studies With Single Filter, 1¶

Route: /studies
Description: Searches studies using only 1 filtering parameter associated with test study. Expects an array of Studies, with length of 1 or greater.
Rationale: Asserts filtering parameters can be used independently of one another, and that each filter yields the test Study in the search results.
Requests:

GET /studies?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

[
  {
    "id": "f3ba0b59bed0fa2f1030e7cb508324d1",
    "parentProjectID": "9c0eba51095d3939437e220db196e27b",
    "name": "RNAgetTestStudy0",
    "description": "Test study object used by RNAget compliance testing suite.",
    "version": "1.0"
  }
]

Success Criteria: Status Code == 200 AND response body is array of Study json AND Array Length >= 1
Failure Criteria: Status Code != 200 OR response body is NOT array of Study json OR Array Length < 1

Search Studies With Single Filter, 2¶

Route: /studies
Description: Searches studies using only 1 filtering parameter (a different filter than above) associated with test study. Expects an array of Studies, with length of 1 or greater.
Rationale: Asserts filtering parameters can be used independently of one another, and that each filter yields the test Study in the search results.
Requests:

GET /studies?name=RNAgetTestStudy0
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": "f3ba0b59bed0fa2f1030e7cb508324d1",
    "parentProjectID": "9c0eba51095d3939437e220db196e27b",
    "name": "RNAgetTestStudy0",
    "description": "Test study object used by RNAget compliance testing suite.",
    "version": "1.0"
  }
]

Success Criteria: Status Code == 200 AND response body is array of Study json AND Array Length >= 1
Failure Criteria: Status Code != 200 OR response body is NOT array of Study json OR Array Length < 1

Study API Non-Implemented Test Cases¶

Study Get Not Implemented
Study Search Not Implemented
Study Search Filters Not Implemented

Study Get Not Implemented¶

Route: /studies/<id>
Description: If the Studies endpoint is specified as Not Implemented in the config file, then this test will be run. Requests the /studies/<id> endpoint, expecting a 501 Not Implemented status code response
Rationale: Asserts that Study related endpoints are correctly non-implemented according to the spec
Request:

GET /studies/nonexistentid9999999999999999999
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

Study Search Not Implemented¶

Route: /studies
Description: If the Studies endpoint is specified as Not Implemented in the config file, then this test will be run. Requests the /studies endpoint, expecting a 501 Not Implemented status code response
Rationale: Asserts that Study related endpoints are correctly non-implemented according to the spec
Request:

GET /studies
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 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
Expression Filters
Get Test Expression Ticket
Single Expression Ticket - Not Found
Get Test Expression Bytes
Single Expression Bytes - Not Found
Expression Ticket by Format
Expression Ticket - All Filters
Expression Ticket - Single Filter, 1
Expression Ticket - Single Filter, 2
Expression Ticket - Format Not Specified
Expression Ticket - Filetype Matches
Expression Bytes by Format
Expression Bytes - All Filters
Expression Bytes - Single Filter, 1
Expression Bytes - Single Filter, 2
Expression Bytes - Format Not Specified

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
Expression Ticket by Id Not Implemented
Expression Bytes by Id Not Implemented
Expression Filters Not Implemented
Expression Ticket Not Implemented
Expression Bytes Not Implemented

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
Expression Bytes by Id Content Test Cases
Expression Ticket Content Test Cases
Expression Bytes 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

Continuous Tests¶

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

Continuous API Tests¶

Continuous API tests assert the correct configuration of continuous-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. For most routes, a value of application/vnd.ga4gh.rnaget.v1.0.0+json OR application/json is expected. For the /continuous/<id> endpoint, a content type matching the format of the file attachment is expected.

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

Continuous API Test Cases¶

Get Supported Continuous Formats
Continuous Filters
Get Test Continuous Ticket
Single Continuous Ticket - Not Found
Single Continuous Ticket - Start Specified Without Chr
Single Continuous Ticket - End Specified Without Chr
Single Continuous Ticket - Start Greater Than End
Get Test Continuous Bytes
Single Continuous Bytes - Not Found
Single Continuous Bytes - Start Specified Without Chr
Single Continuous Bytes - End Specified Without Chr
Single Continuous Bytes - Start Greater Than End
Continuous Ticket by Format
Continuous Ticket - All Filters
Continuous Ticket - Single Filter, 1
Continuous Ticket - Single Filter, 2
Continuous Ticket - Format Not Specified
Continuous Ticket - Filetype Matches
Continuous Ticket - Start Specified Without Chr
Continuous Ticket - End Specified Without Chr
Continuous Ticket - Start Greater Than End
Continuous Bytes by Format
Continuous Bytes - All Filters
Continuous Bytes - Single Filter, 1
Continuous Bytes - Single Filter, 2
Continuous Bytes - Format Not Specified
Continuous Bytes - Start Specified Without Chr
Continuous Bytes - End Specified Without Chr
Continuous Bytes - Start Greater Than End

Get Supported Continuous Formats¶

Route: /continuous/formats
Description: Requests the available continuous file formats on the server. Expects an array of strings to be returned in the response body.
Rationale: Asserts that /continuous/formats returns an array of strings, indicating which continuous file formats the server supports
Request:

GET /continuous/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

Continuous Filters¶

Route: /continuous/filters
Description: Requests the filters that can be used to narrow search results for a list of Continuous
Rationale: Asserts that the endpoint returns an array of filters
Request:

GET /continuous/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 Continuous Ticket¶

Route: /continuous/<id>/ticket
Description: Requests continuous ticket by its id. Expects valid ticket.
Rationale: Asserts that /continuous/<id>/ticket returns valid ticket.
Request:

GET /continuous/5e22e009f41fc53cbea094a41de8798f/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": "5e22e009f41fc53cbea094a41de8798f",
  "version": "1.0",
  "studyID": "f3ba0b59bed0fa2f1030e7cb508324d1",
  "url": "https://url/to/continuous/file",
  "units": "TPM",
  "fileType": "loom/tsv"
}

Success Criteria: Status Code == 200 AND response is ticket
Failure Criteria: Status Code != 200 OR response is NOT ticket

Single Continuous Ticket - Not Found¶

Route: /continuous/<id>/ticket
Description: Requests continuous ticket with an invalid id. Expects a 404 Not Found status code in the response, and error message.
Rationale: Asserts that the /continuous/<id>/ticket endpoint does not return arbitrary ticket.
Request:

GET /continuous/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

Single Continuous Ticket - Start Specified Without Chr¶

Route: /continuous/<id>/ticket
Description: Requests continuous ticket by its id, specifying a start position without a chromosome. Expects a 400 Bad Request status code in the response, and an error message
Rationale: Asserts that the /continuous/<id>/ticket endpoint raises an error when start is specified without chr
Request:

GET /continuous/5e22e009f41fc53cbea094a41de8798f/ticket?start=5
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": "chr required if either start or end is specified"
}

Success Criteria: Status Code == 400 AND response body is valid Error json
Failure Criteria: Status Code != 400 OR response body is NOT valid Error json

Single Continuous Ticket - End Specified Without Chr¶

Route: /continuous/<id>/ticket
Description: Requests test continuous by its id, specifying an end position without a chromosome. Expects a 400 Bad Request status code in the response, and an error message
Rationale: Asserts that the /continuous/<id>/ticket endpoint raises an error when end is specified without chr
Request:

GET /continuous/5e22e009f41fc53cbea094a41de8798f/ticket?end=1000
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": "chr required if either start or end is specified"
}

Success Criteria: Status Code == 400 AND response body is valid Error json
Failure Criteria: Status Code != 400 OR response body is NOT valid Error json

Single Continuous Ticket - Start Greater Than End¶

Route: /continuous/<id>/ticket
Description: Requests test continuous ticket by its id, specifying chr, start, and end, however, start position is greater than end. Expects a 400 Bad Request status code in the response, and an error message
Rationale: Asserts that the /continuous/<id>/ticket endpoint raises an error when start is greater than end
Request:

GET /continuous/5e22e009f41fc53cbea094a41de8798f/ticket?chr=1&start=200&end=100
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": "start cannot be greater than end"
}

Success Criteria: Status Code == 400 AND response body is valid Error json
Failure Criteria: Status Code != 400 OR response body is NOT valid Error json

Get Test Continuous Bytes¶

Route: /continuous/<id>/bytes
Description: Requests continuous matrix bytes by its id.
Rationale: Asserts that /continuous/<id>/bytes returns matrix bytes.
Request:

GET /continuous/5e22e009f41fc53cbea094a41de8798f/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 Continuous Bytes - Not Found¶

Route: /continuous/<id>/bytes
Description: Requests continuous bytes with an invalid id. Expects a 404 Not Found status code in the response, and error message.
Rationale: Asserts that the /continuous/<id>/bytes endpoint does not return arbitrary matrix.
Request:

GET /continuous/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

Single Continuous Bytes - Start Specified Without Chr¶

Route: /continuous/<id>/bytes
Description: Requests continuous matrix bytes by its id, specifying a start position without a chromosome. Expects a 400 Bad Request status code in the response, and an error message
Rationale: Asserts that the /continuous/<id>/bytes endpoint raises an error when start is specified without chr
Request:

GET /continuous/5e22e009f41fc53cbea094a41de8798f/bytes?start=5
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": "chr required if either start or end is specified"
}

Success Criteria: Status Code == 400 AND response body is valid Error json
Failure Criteria: Status Code != 400 OR response body is NOT valid Error json

Single Continuous Bytes - End Specified Without Chr¶

Route: /continuous/<id>/bytes
Description: Requests test continuous matrix bytes by its id, specifying an end position without a chromosome. Expects a 400 Bad Request status code in the response, and an error message
Rationale: Asserts that the /continuous/<id>/bytes endpoint raises an error when end is specified without chr
Request:

GET /continuous/5e22e009f41fc53cbea094a41de8798f/bytes?end=1000
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": "chr required if either start or end is specified"
}

Success Criteria: Status Code == 400 AND response body is valid Error json
Failure Criteria: Status Code != 400 OR response body is NOT valid Error json

Single Continuous Bytes - Start Greater Than End¶

Route: /continuous/<id>/bytes
Description: Requests test continuous matrix bytes by its id, specifying chr, start, and end, however, start position is greater than end. Expects a 400 Bad Request status code in the response, and an error message
Rationale: Asserts that the /continuous/<id>/bytes endpoint raises an error when start is greater than end
Request:

GET /continuous/5e22e009f41fc53cbea094a41de8798f/bytes?chr=1&start=200&end=100
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": "start cannot be greater than end"
}

Success Criteria: Status Code == 400 AND response body is valid Error json
Failure Criteria: Status Code != 400 OR response body is NOT valid Error json

Continuous Ticket by Format¶

Route: /continuous/ticket
Description: Requests joined continuous matrix, specifying only the required ‘format’ parameter. Expects ticket.
Rationale: Asserts that /continuous/ticket returns a ticket with which the matrix can be downloaded.
Request:

GET /continuous/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/signal-query-results.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

Continuous Ticket - All Filters¶

Route: /continuous/ticket
Description: Requests joined continuous matrix, using all filtering parameters. Expects ticket.
Rationale: Asserts that /continuous/ticket returns ticket when specifying filters.
Request:

GET /continuous/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

{
  "studyID": "f3ba0b59bed0fa2f1030e7cb508324d1",
  "url": "/path/to/continuous.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

Continuous Ticket - Single Filter, 1¶

Route: /continuous/ticket
Description: Requests joined continuous matrix, using only 1 filtering parameter associated with test continuous (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 /continuous/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": "/path/to/signal-query-results.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.

Continuous Ticket - Single Filter, 2¶

Route: /continuous/ticket
Description: Requests joined continuous matrix, using only 1 filtering parameter (different than above) associated with test continuous (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 /continuous/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": "6cccbbd76b9c4837bd7342dd616d0fec",
  "url": "/path/to/signal-query-results.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.

Continuous Ticket - Format Not Specified¶

Route: /continuous/ticket
Description: Requests joined continuous 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 /continuous/ticket endpoint, this test asserts malformed requests raise an error.
Request:

GET /continuous/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

Continuous Ticket - Filetype Matches¶

Route: /continuous/ticket
Description: Request joined continuous matrix, only specifying the required format parameter. Checks that ticket has a fileType matching requested format.
Rationale: Asserts that the /continuous/ticket endpoint returns ticket with fileType matching the request.
Request:

GET /continuous/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": "/woldlab/castor/home/sau/public_html/rnaget/signal-query-results.loom",
  "units": "TPM",
  "version": "1.0",
  "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

Continuous Ticket - Start Specified Without Chr¶

Route: /continuous/ticket
Description: Requests joined continuous matrix ticket, specifying a start position without a chromosome. Expects a 400 Bad Request status code in the response, and an error message
Rationale: Asserts that the /continuous/ticket endpoint raises an error when start is specified without chr
Request:

GET /continuous/ticket?format=loom&start=5
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": "chr required if either start or end is specified"
}

Success Criteria: Status Code == 400 AND response body is valid Error json
Failure Criteria: Status Code != 400 OR response body is NOT valid Error json

Continuous Ticket - End Specified Without Chr¶

Route: /continuous/ticket
Description: Requests joined continuous matrix ticket, specifying an end position without a chromosome. Expects a 400 Bad Request status code in the response, and an error message
Rationale: Asserts that the /continuous/ticket endpoint raises an error when end is specified without chr
Request:

GET /continuous/ticket?format=loom&end=1000
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": "chr required if either start or end is specified"
}

Success Criteria: Status Code == 400 AND response body is valid Error json
Failure Criteria: Status Code != 400 OR response body is NOT valid Error json

Continuous Ticket - Start Greater Than End¶

Route: /continuous/ticket
Description: Requests joined continuous matrix ticket, specifying chr, start, and end, however, start position is greater than end. Expects a 400 Bad Request status code in the response, and an error message
Rationale: Asserts that the /continuous/ticket endpoint raises an error when start is greater than end
Request:

GET /continuous/ticket?format=loom&chr=1&start=200&end=100
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": "start cannot be greater than end"
}

Success Criteria: Status Code == 400 AND response body is valid Error json
Failure Criteria: Status Code != 400 OR response body is NOT valid Error json

Continuous Bytes by Format¶

Route: /continuous/bytes
Description: Requests joined continuous matrix as bytes, specifying only the required ‘format’ parameter.
Rationale: Asserts that /continuous/bytes returns matrix bytes.
Request:

GET /continuous/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

Continuous Bytes - All Filters¶

Route: /continuous/bytes
Description: Requests joined continuous matrix as bytes, using all filtering parameters.
Rationale: Asserts that /continuous/ticket returns matrix bytes when specifying filters.
Request:

GET /continuous/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

Continuous Bytes - Single Filter, 1¶

Route: /continuous/bytes
Description: Requests joined continuous matrix as bytes, using only 1 filtering parameter associated with test continuous (in addition to format).
Rationale: Asserts filtering parameters can be used independently of one another.
Requests:

GET /continuous/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

Continuous Bytes - Single Filter, 2¶

Route: /continuous/bytes
Description: Requests joined continuous matrix as bytes, using only 1 filtering parameter (different than above) associated with test continuous (in addition to format).
Rationale: Asserts filtering parameters can be used independently of one another.
Requests:

GET /continuous/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

Continuous Bytes - Format Not Specified¶

Route: /continuous/bytes
Description: Requests joined continuous matrix as bytes 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 /continuous/bytes endpoint, this test asserts malformed requests raise an error.
Request:

GET /continuous/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

Continuous Bytes - Start Specified Without Chr¶

Route: /continuous/bytes
Description: Requests joined continuous matrix as bytes, specifying a start position without a chromosome. Expects a 400 Bad Request status code in the response, and an error message
Rationale: Asserts that the /continuous/bytes endpoint raises an error when start is specified without chr
Request:

GET /continuous/bytes?format=loom&start=5
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": "chr required if either start or end is specified"
}

Success Criteria: Status Code == 400 AND response body is valid Error json
Failure Criteria: Status Code != 400 OR response body is NOT valid Error json

Continuous Bytes - End Specified Without Chr¶

Route: /continuous/bytes
Description: Requests joined continuous matrix as bytes, specifying an end position without a chromosome. Expects a 400 Bad Request status code in the response, and an error message
Rationale: Asserts that the /continuous/bytes endpoint raises an error when end is specified without chr
Request:

GET /continuous/bytes?format=loom&end=1000
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": "chr required if either start or end is specified"
}

Success Criteria: Status Code == 400 AND response body is valid Error json
Failure Criteria: Status Code != 400 OR response body is NOT valid Error json

Continuous Bytes - Start Greater Than End¶

Route: /continuous/bytes
Description: Requests joined continuous matrix as bytes, specifying chr, start, and end, however, start position is greater than end. Expects a 400 Bad Request status code in the response, and an error message
Rationale: Asserts that the /continuous/bytes endpoint raises an error when start is greater than end
Request:

GET /continuous/bytes?format=loom&chr=1&start=200&end=100
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": "start cannot be greater than end"
}

Success Criteria: Status Code == 400 AND response body is valid Error json
Failure Criteria: Status Code != 400 OR response body is NOT valid Error json

Continuous API Non-Implemented Test Cases¶

Continuous Formats Not Implemented
Continuous Ticket by Id Not Implemented
Continuous Bytes by Id Not Implemented
Continuous Filters Not Implemented
Continuous Ticket Not Implemented
Continuous Bytes Not Implemented

Continuous Formats Not Implemented¶

Route: /continuous/formats
Description: If Continuous endpoints are Not Implemented, then request /continuous/formats, expecting a 501 Not Implemented status code response
Rationale: Asserts that Continuous related endpoints are correctly non-implemented
Request:

GET /continuous/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

Continuous Ticket By Id Not Implemented¶

Route: /continuous/<id>/ticket
Description: If Continuous endpoints are Not Implemented, then request /continuous/<id>/ticket, expecting a 501 Not Implemented status code response
Rationale: Asserts that Continuous related endpoints are correctly non-implemented
Request:

GET /continuous/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

Continuous Bytes By Id Not Implemented¶

Route: /continuous/<id>/bytes
Description: If Continuous endpoints are Not Implemented, then request /continuous/<id>/bytes, expecting a 501 Not Implemented status code response
Rationale: Asserts that Continuous related endpoints are correctly non-implemented
Request:

GET /continuous/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

Continuous Filters Not Implemented¶

Route: /continuous/filters
Description: If Continuous endpoints are Not Implemented, then request /continuous/filters, expecting a 501 Not Implemented status code response
Rationale: Asserts that Continuous related endpoints are correctly non-implemented
Request:

GET /continuous/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

Continuous Ticket Not Implemented¶

Route: /continuous/ticket
Description: If Continuous endpoints are Not Implemented, then request /continuous/ticket, expecting a 501 Not Implemented status code response
Rationale: Asserts that Continuous related endpoints are correctly non-implemented
Request:

GET /continuous/ticket?format=loom
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

Continuous Bytes Not Implemented¶

Route: /continuous/bytes
Description: If Continuous endpoints are Not Implemented, then request /continuous/bytes, expecting a 501 Not Implemented status code response
Rationale: Asserts that Continuous related endpoints are correctly non-implemented
Request:

GET /continuous/bytes?format=loom
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

Continuous Content Tests¶

Continuous content tests assert that continuous matrices downloaded from the RNAget server contain the expected content based on the request. Continuous file tracks, positions, and intensity values are cross-referenced against the request to ensure the expected data has been returned.

Continuous Content Test Cases¶

Continuous Ticket by Id Content Test Cases
Continuous Bytes by Id Content Test Cases
Continuous Ticket Content Test Cases
Continuous Bytes Content Test Cases

Continuous Ticket by Id Content Test Cases¶

Route: /continuous/<id>/ticket
Description: Download test continuous matrix by ticket multiple times (sometimes slicing by chr, start, end).
Rationale: Asserts correct matrix file is associated with the test continuous id. Validates signal intensity values match expected. Validates returned columns/rows match expected based on slice parameters.
Request:

GET /continuous/5e22e009f41fc53cbea094a41de8798f/ticket
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

Success Criteria: Test continuous matrix columns, rows, values match expected
Failure Criteria: Test continuous matrix columns, rows, values DO NOT match expected

Continuous Bytes by Id Content Test Cases¶

Route: /continuous/<id>/bytes
Description: Download test continuous matrix bytes multiple times (sometimes slicing by chr, start, end).
Rationale: Asserts correct matrix file is associated with the test continuous id. Validates signal intensity values match expected. Validates returned columns/rows match expected based on slice parameters.
Request:

GET /continuous/5e22e009f41fc53cbea094a41de8798f/bytes
Accept: application/vnd.ga4gh.rnaget.v1.0.0+json, application/json

Success Criteria: Test continuous matrix columns, rows, values match expected
Failure Criteria: Test continuous matrix columns, rows, values DO NOT match expected

Continuous Ticket Content Test Cases¶

Route: /continuous/ticket
Description: Download joined continuous matrix by ticket multiple times (sometimes slicing by chr, start, end).
Rationale: Asserts joined matrix. Validates signal intensity values match expected. Validates returned columns/rows match expected based on slice parameters.
Request:

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

Success Criteria: Joined continuous matrix columns, rows, values match expected
Failure Criteria: Joined continuous matrix columns, rows, values DO NOT match expected

Continuous Bytes Content Test Cases¶

Route: /continuous/bytes
Description: Download joined continuous matrix as bytes multiple times (sometimes slicing by chr, start, end).
Rationale: Asserts joined matrix. Validates signal intensity values match expected. Validates returned columns/rows match expected based on slice parameters.
Request:

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

Success Criteria: Joined continuous matrix columns, rows, values match expected
Failure Criteria: Joined continuous matrix columns, rows, values DO NOT match expected

Getting Started¶

The RNAget compliance tool provides insight into how compliant a server is with the specification. The tool can be installed and executed from the command line, and can be configured to run compliance tests against any RNAget server of interest.

When run, the compliance tool generates a report, indicating which test cases succeeded and failed, as well as messages explaining why a test may have failed.

The next article provides instructions on how to install the RNAget compliance tool.

Installation¶

This section provides instructions on how to install the RNAget compliance suite application.

As a prerequisite, python 3 and pip must be installed on your system. The application can be installed by running the following from the command line.

Clone the latest build from https://github.com/ga4gh-rnaseq/rnaget-compliance-suite

git clone https://github.com/ga4gh-rnaseq/rnaget-compliance-suite

Enter rnaget-compliance-suite directory and install

cd rnaget-compliance-suite
python setup.py install

Confirm installation by executing the rnaget-compliance command

rnaget-compliance report

The next article explains how to run the compliance application.

Usage¶

The application can be run from the command line with the following command:

rnaget-compliance report

Command line parameters are as follows:

rnaget-compliance report command line parameters¶
Parameter	Short Name	Required?	Description
–user-config	-c	Yes	Path to yaml file, indicating which server(s), project(s), expression(s), etc. to query
–output_dir	-o	No	Output directory to write report results and web files. Directory must not already exist. Defaults to ./rnaget-compliance-results if not specified
–serve	N/A	No	Flag. If set, the program will spin up a local server serving the HTML report after all compliance tests are completed
–uptime	-u	No	Integer. The local report server will shut down automatically after this time in seconds
–no-tar	N/A	No	Flag. If set, the program will not write a .tar.gz archive of report results
–force	-f	No	Flag. If set, the program will overwrite the output directory if it exists

User Config YAML File¶

The compliance application requires configurations to be written to a YAML file, which is specified on the command line. The following is a template of the config file, which can be modified to query different servers, projects, studies, etc.

servers:
  - server_name: Caltech
    base_url: https://felcat.caltech.edu/rnaget/
    implemented:
      projects: true
      studies: true
      expressions: true
      continuous: true

The .yml config file contains the following important features, which must be taken into consideration when modifying it for a different server:

servers must be the root property. The value of servers is a list of server definitions (ie the application can query multiple servers in a single run).
Each server definition requires the following parameters:
- server_name: a string uniquely identifying the server
- base_url: the base url at which the RNAget API can be reached
If a server requires client authentication, then a server definition can include the OAuth 2.0 bearer access token under the “token” property:

servers:
   - server_name: Caltech
     base_url: https://felcat.caltech.edu/rnaget/
     token: abcdefghijklmnop
     implemented:
       projects: true
       studies: true
       expressions: true
       continuous: true

The token will be used for all API tests executed by the compliance suite.

A server’s implemented property indicates which routes (projects, studies, expressions, continuous) have been implemented. This property can be removed if all routes are implemented, as routes are expected to be implemented by default. Use ${ROUTENAME}: false to indicate non-implemented routes.

Basic Usage¶

The program requires, at minimum, a YAML config file to be specified in order to execute:

rnaget-compliance report -c user_config_template.yaml

The user can also specify the location at which to create the output report directory. The program will only run if the output directory does not already exist (will not overwrite existing files):

rnaget-compliance report -c user_config_template.yaml -o ./results/output

The program creates a series of web files at the output directory, which can be used to view the compliance results as an HTML report. A web server can be started manually at the output directory to serve the report. By specifying the --serve option, the report server will be started automatically upon completion of the compliance tests:

rnaget-compliance report -c user_config_template.yaml -o ./results/output --serve

The next article explains how to view the compliance report, including how to diagnose errors (compliance failures)

Report¶

Once the compliance report has been generated, the HTML report can be accessed by first starting a web server at the output directory, then navigating to the page via web browser.

Viewing the Report¶

Report: Index¶

The report index page displays a tabular overview of test successes/failures by tested servers and API routes. An example report index is displayed below:

Clicking on any of the Pass/Fail buttons will take you to an in-depth report of the status of all tests for that server.

Report: Test Status¶

This page shows a more detailed report of all tests run on a particular server, organized by API route and test case. For any given test, clicking the Info button will display information for that test, including the request url, parameters, and the response body. The Info window is also helpful in diagnosing failed compliance tests, as it reports the type of error encountered and related debug messages.

Below is an example of Projects test results for one server in the test status page:

Clicking the Info button shows test information, displayed below:

Test results can also be viewed as a matrix:

Preamble¶

RNAget Servers¶

Compliance Document¶

Table of Contents¶

API Specification¶

Test Dataset¶

Project Tests¶

Project API Tests¶

Project API Test Cases¶

Get Test Project¶

Project Not Found¶

Project Filters¶

Search Projects Without Filters¶

Search Projects With All Filters¶

Search Projects With Single Filter, 1¶

Search Projects With Single Filter, 2¶

Project Search Filters Non-Matching Resources¶

Project API Non-Implemented Test Cases¶

Project Get Not Implemented¶

Project Search Not Implemented¶

Project Filters Not Implemented¶

Study Tests¶

Study API Tests¶

Study API Test Cases¶

Get Test Study¶

Study Not Found¶

Study Filters¶

Search Studies Without Filters¶

Search Studies With All Filters¶

Search Studies With Single Filter, 1¶

Search Studies With Single Filter, 2¶

Study Search Filters Non-Matching Resources¶

Study API Non-Implemented Test Cases¶

Study Get Not Implemented¶

Study Search Not Implemented¶

Study Search Filters Not Implemented¶

Expression Tests¶

Expression API Tests¶

Expression API Test Cases¶

Get Supported Expression Formats¶

Expression Filters¶

Get Test Expression Ticket¶

Single Expression Ticket - Not Found¶

Get Test Expression Bytes¶

Single Expression Bytes - Not Found¶

Expression Ticket by Format¶

Expression Ticket - All Filters¶

Expression Ticket - Single Filter, 1¶

Expression Ticket - Single Filter, 2¶

Expression Ticket - Format Not Specified¶

Expression Ticket - Filetype Matches¶

Expression Bytes by Format¶

Expression Bytes - All Filters¶

Expression Bytes - Single Filter, 1¶

Expression Bytes - Single Filter, 2¶

Expression Bytes - Format Not Specified¶

Expression API Non-Implemented Test Cases¶

Expression Formats Not Implemented¶

Expression Ticket by Id Not Implemented¶

Expression Bytes by Id Not Implemented¶

Expression Filters Not Implemented¶

Expression Ticket Not Implemented¶

Expression Bytes Not Implemented¶

Expression Content Tests¶

Expression Content Test Cases¶

Expression Ticket by Id Content Test Cases¶

Expression Bytes by Id Content Test Cases¶

Expression Ticket Content Test Cases¶

Expression Bytes Content Test Cases¶

Continuous Tests¶

Continuous API Tests¶

Continuous API Test Cases¶

Get Supported Continuous Formats¶

Continuous Filters¶

Get Test Continuous Ticket¶

Single Continuous Ticket - Not Found¶

Single Continuous Ticket - Start Specified Without Chr¶

Single Continuous Ticket - End Specified Without Chr¶

Single Continuous Ticket - Start Greater Than End¶

Get Test Continuous Bytes¶