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RNAGet Implementation Compliance Report

Server: CanDIG

Base URL: https://candig.bcgsc.ca/rnaget/

Total tests: 13

Total tests passed: 11

Total tests failed: 2

Total tests skipped: 0

Total warnings generated: 2

Projects

Project 1 id: 9c0eba51095d3939437e220db196e27b

Tests

Test: Project Get - PASSED

description: Requests the /projects/:id endpoint

summary: 'Get Project by Id' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Get Test Project - PASSED

case description: request /projects/:id using test project id. checks content type and status code (200). validates response body matches Project object schema.

case summary: Test project successfully retrieved

Request: https://candig.bcgsc.ca/rnaget/projects/9c0eba51095d3939437e220db196e27b

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "created": "2019-08-22T16:40:52.366284Z", "description": "Test project object used by RNAget compliance testing suite.", "id": "9c0eba51095d3939437e220db196e27b", "name": "RNAgetTestProject0", "tags": [ "RNAgetCompliance" ], "version": "1.0" }

API Test Case: Project Not Found - PASSED

case description: request /projects/:id using a project id known to not exist. Checks content type and status code (4xx). Validates response body matches Error schema.

case summary: Server sends correct response when requested project not found

Request: https://candig.bcgsc.ca/rnaget/projects/nonexistentid9999999999999999999

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "code": 404, "message": "id parameters must be correctly formatted UUID strings" }

Test: Project Filters - PASSED

description: requests the /projects/filters endpoint

summary: 'Project Filters' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Project Filters - PASSED

case description: request /projects/filters. checks content type and status code (200). validates response body matches search filter array schema.

case summary: Project filters successfully retrieved

Request: https://candig.bcgsc.ca/rnaget/projects/filters

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: [ { "description": "Version to return", "fieldType": "string", "filter": "version" } ]

Test: Project Search - PASSED

description: Requests the /projects endpoint

summary: 'Project Search' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Search Projects Without Filters - PASSED

case description: request /projects without any parameter filters. checks content type and status code (200). validates response body matches project array schema.

case summary: Projects can be searched without filters

Request: https://candig.bcgsc.ca/rnaget/projects

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: [ { "created": "2019-08-22T16:40:52.366284Z", "description": "Test project object used by RNAget compliance testing suite.", "id": "9c0eba51095d3939437e220db196e27b", "name": "RNAgetTestProject0", "tags": [ "RNAgetCompliance" ], "version": "1.0" } ]

API Test Case: Search Projects With All Filters - PASSED

case description: request /projects using all server-supported project filters. checks content type and status code (200). validates response body matches project array schema.

case summary: Projects can be searched with all filters specified

Request: https://candig.bcgsc.ca/rnaget/projects

Params: {'version': '1.0'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: [ { "created": "2019-08-22T16:40:52.366284Z", "description": "Test project object used by RNAget compliance testing suite.", "id": "9c0eba51095d3939437e220db196e27b", "name": "RNAgetTestProject0", "tags": [ "RNAgetCompliance" ], "version": "1.0" } ]

API Test Case: Search Projects With Single Filter, 1 - PASSED

case description: request /projects using the first parameter filter supported by server. checks type and status code (200). validates response body matches project array schema

case summary: Projects can be searched when first filter parameter is supplied

Request: https://candig.bcgsc.ca/rnaget/projects

Params: {'version': '1.0'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: [ { "created": "2019-08-22T16:40:52.366284Z", "description": "Test project object used by RNAget compliance testing suite.", "id": "9c0eba51095d3939437e220db196e27b", "name": "RNAgetTestProject0", "tags": [ "RNAgetCompliance" ], "version": "1.0" } ]

API Test Case: Search Projects With Single Filter, 2 - PASSED

case description: request /projects using the second parameter filter supported by server. checks type and status code (200). validates response body matches project array schema

case summary: Projects can be searched when second filter parameter is supplied

Request: https://candig.bcgsc.ca/rnaget/projects

Params: {'version': '1.0'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: [ { "created": "2019-08-22T16:40:52.366284Z", "description": "Test project object used by RNAget compliance testing suite.", "id": "9c0eba51095d3939437e220db196e27b", "name": "RNAgetTestProject0", "tags": [ "RNAgetCompliance" ], "version": "1.0" } ]

API Test Case: Project Search Filters Non-Matching Resources - PASSED

case description: request /projects using filters that do not apply to any project. checks content type and status code (200). validates response body is an empty array.

case summary: Project search endpoint filters non-matching resources

Request: https://candig.bcgsc.ca/rnaget/projects

Params: {'version': 'nonexistentid9999999999999999999'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: []

Studies

Study 1 id: f3ba0b59bed0fa2f1030e7cb508324d1

Tests

Test: Study Get - PASSED

description: Requests the /studies/id endpoint

summary: 'Get Study by Id' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Get Test Study - PASSED

case description: request /studies/:id using test study id. checks content type and status code (200). validates response body matches Study object schema.

case summary: Test study successfully retrieved

Request: https://candig.bcgsc.ca/rnaget/studies/f3ba0b59bed0fa2f1030e7cb508324d1

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "created": "2019-08-22T16:44:17.958554Z", "description": "Test study object used by RNAget compliance testing suite.", "id": "f3ba0b59bed0fa2f1030e7cb508324d1", "name": "RNAgetTestStudy0", "parentProjectID": "9c0eba51095d3939437e220db196e27b", "tags": [ "RNAgetCompliance" ], "version": "1.0" }

API Test Case: Study Not Found - PASSED

case description: request /studies/:id using a study id known to not exist. Checks content type and status code (4xx). Validates response body matches Error schema.

case summary: Server sends correct response when requested study not found

Request: https://candig.bcgsc.ca/rnaget/studies/nonexistentid9999999999999999999

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "code": 404, "message": "studyID parameters must be correctly formatted UUID strings" }

Test: Study Filters - PASSED

description: requests the /studies/filters endpoint

summary: 'Study Filters' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Study Filters - PASSED

case description: request /studies/filters. checks content type and status code (200). validates response body matches search filter array schema.

case summary: Study filters successfully retrieved

Request: https://candig.bcgsc.ca/rnaget/studies/filters

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: [ { "description": "Version to return", "fieldType": "string", "filter": "version" } ]

Test: Study Search - PASSED

description: Requests the /studies endpoint

summary: 'Study Search' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Search Studies Without Filters - PASSED

case description: request /studies without any parameter filters. checks content type and status code (200). validates response body matches study array schema.

case summary: Studies can be searched without filters

Request: https://candig.bcgsc.ca/rnaget/studies

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: [ { "created": "2019-08-22T16:44:17.958554Z", "description": "Test study object used by RNAget compliance testing suite.", "id": "f3ba0b59bed0fa2f1030e7cb508324d1", "name": "RNAgetTestStudy0", "parentProjectID": "9c0eba51095d3939437e220db196e27b", "tags": [ "RNAgetCompliance" ], "version": "1.0" } ]

API Test Case: Search Studies With All Filters - PASSED

case description: request /studies using all server-supported study filters. checks content type and status code (200). validates response body matches study array schema.

case summary: Studies can be searched with all filters specified

Request: https://candig.bcgsc.ca/rnaget/studies

Params: {'version': '1.0'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: [ { "created": "2019-08-22T16:44:17.958554Z", "description": "Test study object used by RNAget compliance testing suite.", "id": "f3ba0b59bed0fa2f1030e7cb508324d1", "name": "RNAgetTestStudy0", "parentProjectID": "9c0eba51095d3939437e220db196e27b", "tags": [ "RNAgetCompliance" ], "version": "1.0" } ]

API Test Case: Search Studies With Single Filter, 1 - PASSED

case description: request /studies using the first parameter filter supported by server. checks type and status code (200). validates response body matches study array schema

case summary: Studies can be searched when first filter parameter is supplied

Request: https://candig.bcgsc.ca/rnaget/studies

Params: {'version': '1.0'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: [ { "created": "2019-08-22T16:44:17.958554Z", "description": "Test study object used by RNAget compliance testing suite.", "id": "f3ba0b59bed0fa2f1030e7cb508324d1", "name": "RNAgetTestStudy0", "parentProjectID": "9c0eba51095d3939437e220db196e27b", "tags": [ "RNAgetCompliance" ], "version": "1.0" } ]

API Test Case: Search Studies With Single Filter, 2 - PASSED

case description: request /studies using the second parameter filter supported by server. checks type and status code (200). validates response body matches study array schema

case summary: Studies can be searched when second filter parameter is supplied

Request: https://candig.bcgsc.ca/rnaget/studies

Params: {'version': '1.0'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: [ { "created": "2019-08-22T16:44:17.958554Z", "description": "Test study object used by RNAget compliance testing suite.", "id": "f3ba0b59bed0fa2f1030e7cb508324d1", "name": "RNAgetTestStudy0", "parentProjectID": "9c0eba51095d3939437e220db196e27b", "tags": [ "RNAgetCompliance" ], "version": "1.0" } ]

API Test Case: Study Search Filters Non-Matching Resources - PASSED

case description: request /studies using filters that do not apply to any project. checks content type and status code (200). validates response body is an empty array.

case summary: Study search endpoint filters non-matching resources

Request: https://candig.bcgsc.ca/rnaget/studies

Params: {'version': 'nonexistentid9999999999999999999'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: []

Expressions

Expression 1 id: ac3e9279efd02f1c98de4ed3d335b98e

Tests

Test: Expression Formats - PASSED

description: Requests the /expressions/formats endpoint

summary: 'Expression Formats' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Get Supported Expression Formats - PASSED

case description: request /expressions/formats. checks content type and status code (200). validates response body is an array of strings.

case summary: Expression formats successfully retrieved

Request: https://candig.bcgsc.ca/rnaget/expressions/formats

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: [ "json", "h5", "loom" ]

Test: Single Expression Ticket - FAILED

description: Requests the /expressions/:id/ticket endpoint

summary: 'Single Expression Ticket by Id' endpoint NOT correctly implemented

API Route Test Cases - PASSED

API Test Case: Get Test Expression Ticket - PASSED

case description: request /expressions/:id/ticket using test expression id. checks content type and status code (200). validates response body matches Ticket schema.

case summary: Test expression ticket successfully retrieved

Request: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "created": "2019-08-22T16:49:45.174886Z", "fileType": "loom", "id": "ac3e9279efd02f1c98de4ed3d335b98e", "md5": "71aa84a6a188e195a0ba6d1c4a920dec", "studyID": "f3ba0b59bed0fa2f1030e7cb508324d1", "tags": [ "RNAgetCompliance" ], "units": "TPM", "url": "https://candig.bcgsc.ca/rnaget/download/d648c550-3180-11ea-817d-1402ec895c5c", "version": "1.0" }

API Test Case: Single Expression Ticket - Not Found - PASSED

case description: request /expressions/:id/ticket using an expression id known to not exist. Checks content type and status code (4xx). validates response body matches Error schema.

case summary: Server sends correct response when requested expression not found

Request: https://candig.bcgsc.ca/rnaget/expressions/nonexistentid9999999999999999999/ticket

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "code": 404, "message": "id parameters must be correctly formatted UUID strings" }

File Content Test Cases - FAILED

Content Test Case: Single Expression Ticket - Expression Value 1 - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - Expression Value 2 - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - Expression Value 3 - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - Expression Value 4 - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - Expression Value 5 - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - Expression Value 6 - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - Expression Value 7 - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - Expression Value 8 - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - Expression Value 9 - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - Expression Value 10 - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - Slice by featureIDList - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {'featureIDList': 'ENSG00000037965,ENSG00000243503,ENSG00000259285'}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - Slice by featureNameList - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {'featureNameList': 'PGLYRP3,PRSS50,SNRPFP1,OR5AC4P,CLIC1,RF00092,AC100827.4'}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - Slice by sampleIDList - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {'sampleIDList': 'DO22935 - primary tumour,DO20604 - primary tumour,DO48516 - primary tumour,DO42881 - primary tumour,DO6144 - primary tumour,DO40948 - primary tumour,DO472 - primary tumour,DO48505 - primary tumour'}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - slice by featureIDList and sampleIDList - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {'featureIDList': 'ENSG00000106278,ENSG00000142025,ENSG00000171487,ENSG00000184471,ENSG00000213719,ENSG00000239589', 'sampleIDList': 'DO52655 - primary tumour,DO52685 - primary tumour,DO25887 - primary tumour'}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Single Expression Ticket - slice by featureNameList and sampleIDList - FAILED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content DOES NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {'featureNameList': 'SH3BP1,APOL5,RN7SL592P', 'sampleIDList': 'DO1249 - primary tumour,DO28763 - primary tumour,DO33408 - primary tumour,DO219961 - primary tumour,DO2995 - primary tumour,DO18671 - primary tumour,DO219106 - primary tumour'}

Unable to create file (unable to open file: name = 'single_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Test: Single Expression Bytes - PASSED

description: Requests the /expressions/:id/bytes endpoint

summary: 'Single Expression Bytes by Id' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Get Test Expression Bytes - PASSED

case description: request /expressions/:id/bytes using test expression id. checks content type and status code (200).

case summary: Test expression bytes successfully retrieved

Request: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/octet-stream, application/vnd.loom, text/tab-separated-values;'}

API Test Case: Single Expression Bytes - Not Found - PASSED

case description: request /expressions/:id/bytes using an expression id known to not exist. Checks content type and status code (4xx). validates response body matches Error schema.

case summary: Server sends correct response when requested expression not found

Request: https://candig.bcgsc.ca/rnaget/expressions/nonexistentid9999999999999999999/bytes

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "code": 404, "message": "id parameters must be correctly formatted UUID strings" }

File Content Test Cases - PASSED

Content Test Case: Single Expression Bytes - Expression Value 1 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Single Expression Bytes - Expression Value 2 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Single Expression Bytes - Expression Value 3 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Single Expression Bytes - Expression Value 4 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Single Expression Bytes - Expression Value 5 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Single Expression Bytes - Expression Value 6 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Single Expression Bytes - Expression Value 7 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Single Expression Bytes - Expression Value 8 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Single Expression Bytes - Expression Value 9 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Single Expression Bytes - Expression Value 10 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Single Expression Bytes - Slice by featureIDList - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {'featureIDList': 'ENSG00000037965,ENSG00000243503,ENSG00000259285'}

asserting number of rows matches number of supplied GeneIDs

asserting returned GeneIDs match supplied GeneIDs

Content Test Case: Single Expression Bytes - Slice by featureNameList - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {'featureNameList': 'PGLYRP3,PRSS50,SNRPFP1,OR5AC4P,CLIC1,RF00092,AC100827.4'}

asserting number of rows matches number of supplied GeneNames

asserting returned GeneNames match supplied GeneNames

Content Test Case: Single Expression Bytes - Slice by sampleIDList - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {'sampleIDList': 'DO22935 - primary tumour,DO20604 - primary tumour,DO48516 - primary tumour,DO42881 - primary tumour,DO6144 - primary tumour,DO40948 - primary tumour,DO472 - primary tumour,DO48505 - primary tumour'}

asserting number of columns matches number of supplied Samples

asserting returned Samples match supplied Samples

Content Test Case: Single Expression Bytes - slice by featureIDList and sampleIDList - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {'featureIDList': 'ENSG00000106278,ENSG00000142025,ENSG00000171487,ENSG00000184471,ENSG00000213719,ENSG00000239589', 'sampleIDList': 'DO52655 - primary tumour,DO52685 - primary tumour,DO25887 - primary tumour'}

asserting number of rows matches number of supplied GeneIDs

asserting returned GeneIDs match supplied GeneIDs

asserting number of columns matches number of supplied Samples

asserting returned Samples match supplied Samples

Content Test Case: Single Expression Bytes - slice by featureNameList and sampleIDList - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {'featureNameList': 'SH3BP1,APOL5,RN7SL592P', 'sampleIDList': 'DO1249 - primary tumour,DO28763 - primary tumour,DO33408 - primary tumour,DO219961 - primary tumour,DO2995 - primary tumour,DO18671 - primary tumour,DO219106 - primary tumour'}

asserting number of rows matches number of supplied GeneNames

asserting returned GeneNames match supplied GeneNames

asserting number of columns matches number of supplied Samples

asserting returned Samples match supplied Samples

Test: Expression Filters - PASSED

description: Requests the /expressions/filters endpoint.

summary: 'Expression Filters' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Expression Filters - PASSED

case description: request /expressions/filters. checks content type and status code (200). validates response body matches search filter array schema.

case summary: Expression filters successfully retrieved

Request: https://candig.bcgsc.ca/rnaget/expressions/filters

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: [ { "description": "return only results with expression values less than listed threshold for each corresponding feature in the array", "fieldType": "string", "filter": "maxExpression" }, { "description": "return only results with expression values greater than listed threshold for each corresponding feature in the array", "fieldType": "string", "filter": "minExpression" }, { "description": "return only values for listed feature ID values", "fieldType": "string", "filter": "featureIDList" }, { "description": "return only values for listed gene symbols", "fieldType": "string", "filter": "featureNameList" }, { "description": "sampleID to match", "fieldType": "string", "filter": "sampleID" }, { "description": "project to filter on", "fieldType": "string", "filter": "projectID" }, { "description": "study to filter on", "fieldType": "string", "filter": "studyID" }, { "description": "Comma separated tag list to filter by", "fieldType": "string", "filter": "tags" }, { "description": "Version to return", "fieldType": "string", "filter": "version" } ]

Test: Multi Expression Ticket - FAILED

description: Requests the /expressions/ticket endpoint.

summary: 'Expression Ticket' endpoint NOT correctly implemented

API Route Test Cases - PASSED

API Test Case: Expression Ticket by Format - PASSED

case description: requests /expressions/ticket, only specifying the required 'format' parameter. checks content type and status code (200). validates response body matches ticket schema

case summary: Expression Ticket can be retrieved

Request: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'format': 'loom'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "created": "2019-08-22T16:49:45.174886Z", "fileType": "loom", "id": "ac3e9279efd02f1c98de4ed3d335b98e", "md5": "71aa84a6a188e195a0ba6d1c4a920dec", "studyID": "f3ba0b59bed0fa2f1030e7cb508324d1", "tags": [ "RNAgetCompliance" ], "units": "TPM", "url": "https://candig.bcgsc.ca/rnaget/download/d648c550-3180-11ea-817d-1402ec895c5c", "version": "1.0" }

API Test Case: Expression Ticket - All Filters - PASSED

case description: request /expressions/ticket using all server-supported expression filters. checks content type and status code (200). validates response body matches ticket schema.

case summary: Expression Ticket retrieved when all filters specified

Request: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "created": "2019-08-22T16:49:45.174886Z", "fileType": "loom", "id": "ac3e9279efd02f1c98de4ed3d335b98e", "md5": "71aa84a6a188e195a0ba6d1c4a920dec", "studyID": "f3ba0b59bed0fa2f1030e7cb508324d1", "tags": [ "RNAgetCompliance" ], "units": "TPM", "url": "https://candig.bcgsc.ca/rnaget/download/d648c550-3180-11ea-817d-1402ec895c5c", "version": "1.0" }

API Test Case: Expression Ticket - Single Filter, 1 - PASSED

case description: request /expressions/ticket using the first filter supported by server (in addition to format). checks type and status code (200). validates response body matches ticket schema

case summary: Expression Ticket retrieved when first filter supplied

Request: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'format': 'loom'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "created": "2019-08-22T16:49:45.174886Z", "fileType": "loom", "id": "ac3e9279efd02f1c98de4ed3d335b98e", "md5": "71aa84a6a188e195a0ba6d1c4a920dec", "studyID": "f3ba0b59bed0fa2f1030e7cb508324d1", "tags": [ "RNAgetCompliance" ], "units": "TPM", "url": "https://candig.bcgsc.ca/rnaget/download/d648c550-3180-11ea-817d-1402ec895c5c", "version": "1.0" }

API Test Case: Expression Ticket - Single Filter, 2 - PASSED

case description: request /expressions/ticket using the second filter supported by server (in addition to format). checks type and status code (200). validates response body matches ticket schema

case summary: Expression Ticket retrieved when second filter supplied

Request: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'tags': 'RNAgetCompliance', 'format': 'loom'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "created": "2019-08-22T16:49:45.174886Z", "fileType": "loom", "id": "ac3e9279efd02f1c98de4ed3d335b98e", "md5": "71aa84a6a188e195a0ba6d1c4a920dec", "studyID": "f3ba0b59bed0fa2f1030e7cb508324d1", "tags": [ "RNAgetCompliance" ], "units": "TPM", "url": "https://candig.bcgsc.ca/rnaget/download/d648c550-3180-11ea-817d-1402ec895c5c", "version": "1.0" }

API Test Case: Expression Ticket - Format Not Specified - PASSED

case description: request /expressions/ticket endpoint without specifying the required 'format' parameter. checks content type and status code (4xx). validates response body matches error schema.

case summary: Server returns error when format not specified

Request: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: {"code": 400, "message": "Missing query parameter 'format'"}

API Test Case: Expression Ticket - Filetype Matches - PASSED

case description: request /expressions/ticket endpoint with 'format' parameter specified. checks content type and status code (200). validates ticket fileType matches requested format.

case summary: Expression Ticket fileType matches request format

Request: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'format': 'loom'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "created": "2019-08-22T16:49:45.174886Z", "fileType": "loom", "id": "ac3e9279efd02f1c98de4ed3d335b98e", "md5": "71aa84a6a188e195a0ba6d1c4a920dec", "studyID": "f3ba0b59bed0fa2f1030e7cb508324d1", "tags": [ "RNAgetCompliance" ], "units": "TPM", "url": "https://candig.bcgsc.ca/rnaget/download/d648c550-3180-11ea-817d-1402ec895c5c", "version": "1.0" }

File Content Test Cases - FAILED

Content Test Case: Multi Expression Ticket - Expression Value 1 - FAILED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to /expressions/ticket

case summary: Sliced expression matrix rows, columns, and values DO NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom'}

Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Multi Expression Ticket - Expression Value 2 - FAILED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to /expressions/ticket

case summary: Sliced expression matrix rows, columns, and values DO NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom'}

Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Multi Expression Ticket - Expression Value 3 - FAILED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to /expressions/ticket

case summary: Sliced expression matrix rows, columns, and values DO NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom'}

Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Multi Expression Ticket - Expression Value 4 - FAILED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to /expressions/ticket

case summary: Sliced expression matrix rows, columns, and values DO NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom'}

Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Multi Expression Ticket - Expression Value 5 - FAILED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to /expressions/ticket

case summary: Sliced expression matrix rows, columns, and values DO NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom'}

Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Multi Expression Ticket - Slice by featureIDList - FAILED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to /expressions/ticket

case summary: Sliced expression matrix rows, columns, and values DO NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom', 'featureIDList': 'ENSG00000037965,ENSG00000243503,ENSG00000259285'}

Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Multi Expression Ticket - Slice by featureNameList - FAILED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to /expressions/ticket

case summary: Sliced expression matrix rows, columns, and values DO NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom', 'featureNameList': 'PGLYRP3,PRSS50,SNRPFP1,OR5AC4P,CLIC1,RF00092,AC100827.4'}

Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Multi Expression Ticket - Slice by sampleIDList - FAILED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to /expressions/ticket

case summary: Sliced expression matrix rows, columns, and values DO NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom', 'sampleIDList': 'DO22935 - primary tumour,DO20604 - primary tumour,DO48516 - primary tumour,DO42881 - primary tumour,DO6144 - primary tumour,DO40948 - primary tumour,DO472 - primary tumour,DO48505 - primary tumour'}

Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Multi Expression Ticket - slice by featureIDList and sampleIDList - FAILED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to /expressions/ticket

case summary: Sliced expression matrix rows, columns, and values DO NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom', 'featureIDList': 'ENSG00000106278,ENSG00000142025,ENSG00000171487,ENSG00000184471,ENSG00000213719,ENSG00000239589', 'sampleIDList': 'DO52655 - primary tumour,DO52685 - primary tumour,DO25887 - primary tumour'}

Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Content Test Case: Multi Expression Ticket - slice by featureNameList and sampleIDList - FAILED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to /expressions/ticket

case summary: Sliced expression matrix rows, columns, and values DO NOT match expected

error message: Error parsing expression json and download url: Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Ticket URL: https://candig.bcgsc.ca/rnaget/expressions/ticket

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom', 'featureNameList': 'SH3BP1,APOL5,RN7SL592P', 'sampleIDList': 'DO1249 - primary tumour,DO28763 - primary tumour,DO33408 - primary tumour,DO219961 - primary tumour,DO2995 - primary tumour,DO18671 - primary tumour,DO219106 - primary tumour'}

Unable to create file (unable to open file: name = 'multi_expression_ticket_content_test.loom', errno = 17, error message = 'File exists', flags = 15, o_flags = c2)

Test: Multi Expression Bytes - PASSED

description: Requests the /expressions/bytes endpoint.

summary: 'Expression Bytes' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Expression Bytes by Format - PASSED

case description: requests /expressions/bytes, only specifying the required 'format' parameter. checks content type and status code (200).

case summary: Expression Bytes can be retrieved

Request: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'format': 'loom'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/octet-stream, application/vnd.loom, text/tab-separated-values;'}

API Test Case: Expression Bytes - All Filters - PASSED

case description: request /expressions/bytes using all server-supported expression filters. checks content type and status code (200).

case summary: Expression Bytes retrieved when all filters specified

Request: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/octet-stream, application/vnd.loom, text/tab-separated-values;'}

API Test Case: Expression Bytes - Single Filter, 1 - PASSED

case description: request /expressions/bytes using the first filter supported by server (in addition to format). checks type and status code (200).

case summary: Expression Bytes retrieved when first filter supplied

Request: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'format': 'loom'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/octet-stream, application/vnd.loom, text/tab-separated-values;'}

API Test Case: Expression Bytes - Single Filter, 2 - PASSED

case description: request /expressions/bytes using the second filter supported by server (in addition to format). checks type and status code (200).

case summary: Expression Bytes retrieved when second filter supplied

Request: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'tags': 'RNAgetCompliance', 'format': 'loom'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/octet-stream, application/vnd.loom, text/tab-separated-values;'}

API Test Case: Expression Bytes - Format Not Specified - PASSED

case description: request /expressions/bytes endpoint without specifying the required 'format' parameter. checks content type and status code (4xx). validates response body matches error schema.

case summary: Server returns error when format not specified

Request: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: {"code": 400, "message": "Missing query parameter 'format'"}

File Content Test Cases - PASSED

Content Test Case: Multi Expression Bytes - Expression Value 6 - PASSED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to endpoint

case summary: Sliced expression matrix rows, columns, and values match expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom'}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Multi Expression Bytes - Expression Value 7 - PASSED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to endpoint

case summary: Sliced expression matrix rows, columns, and values match expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom'}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Multi Expression Bytes - Expression Value 8 - PASSED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to endpoint

case summary: Sliced expression matrix rows, columns, and values match expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom'}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Multi Expression Bytes - Expression Value 9 - PASSED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to endpoint

case summary: Sliced expression matrix rows, columns, and values match expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom'}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Multi Expression Bytes - Expression Value 10 - PASSED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to endpoint

case summary: Sliced expression matrix rows, columns, and values match expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom'}

Asserting observed GeneName(s) match expected

Asserting observed GeneID(s) match expected

Asserting observed Condition(s) match expected

Asserting observed Tissue(s) match expected

Asserting observed Sample(s) match expected

Asserting observed Value(s) match expected

Content Test Case: Multi Expression Bytes - Slice by featureIDList - PASSED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to endpoint

case summary: Sliced expression matrix rows, columns, and values match expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom', 'featureIDList': 'ENSG00000037965,ENSG00000243503,ENSG00000259285'}

asserting number of rows matches number of supplied GeneIDs

asserting returned GeneIDs match supplied GeneIDs

Content Test Case: Multi Expression Bytes - Slice by featureNameList - PASSED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to endpoint

case summary: Sliced expression matrix rows, columns, and values match expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom', 'featureNameList': 'PGLYRP3,PRSS50,SNRPFP1,OR5AC4P,CLIC1,RF00092,AC100827.4'}

asserting number of rows matches number of supplied GeneNames

asserting returned GeneNames match supplied GeneNames

Content Test Case: Multi Expression Bytes - Slice by sampleIDList - PASSED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to endpoint

case summary: Sliced expression matrix rows, columns, and values match expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom', 'sampleIDList': 'DO22935 - primary tumour,DO20604 - primary tumour,DO48516 - primary tumour,DO42881 - primary tumour,DO6144 - primary tumour,DO40948 - primary tumour,DO472 - primary tumour,DO48505 - primary tumour'}

asserting number of columns matches number of supplied Samples

asserting returned Samples match supplied Samples

Content Test Case: Multi Expression Bytes - slice by featureIDList and sampleIDList - PASSED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to endpoint

case summary: Sliced expression matrix rows, columns, and values match expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom', 'featureIDList': 'ENSG00000106278,ENSG00000142025,ENSG00000171487,ENSG00000184471,ENSG00000213719,ENSG00000239589', 'sampleIDList': 'DO52655 - primary tumour,DO52685 - primary tumour,DO25887 - primary tumour'}

asserting number of rows matches number of supplied GeneIDs

asserting returned GeneIDs match supplied GeneIDs

asserting number of columns matches number of supplied Samples

asserting returned Samples match supplied Samples

Content Test Case: Multi Expression Bytes - slice by featureNameList and sampleIDList - PASSED

case description: Asserts correct slicing/subsetting of expression matrix when slice parameters are passed to endpoint

case summary: Sliced expression matrix rows, columns, and values match expected

Bytes URL: https://candig.bcgsc.ca/rnaget/expressions/bytes

Params: {'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', 'tags': 'RNAgetCompliance', 'version': '1.0', 'format': 'loom', 'featureNameList': 'SH3BP1,APOL5,RN7SL592P', 'sampleIDList': 'DO1249 - primary tumour,DO28763 - primary tumour,DO33408 - primary tumour,DO219961 - primary tumour,DO2995 - primary tumour,DO18671 - primary tumour,DO219106 - primary tumour'}

asserting number of rows matches number of supplied GeneNames

asserting returned GeneNames match supplied GeneNames

asserting number of columns matches number of supplied Samples

asserting returned Samples match supplied Samples

Continuous not implemented by server

Continuous 1 id: NA

Tests

Test: Continuous Endpoint Not Implemented - PASSED

description: Requests various /continuous routes, expecting the service to respond with a 'Not Implemented' status code

summary: Continuous endpoints correctly non-implemented

API Route Test Cases - PASSED

API Test Case: Continuous Formats Not Implemented - PASSED

case description: request /continuous/formats, expecting 501 status code

case summary: Continuous Formats correctly non-implemented

Request: https://candig.bcgsc.ca/rnaget/continuous/formats

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "code": 501, "message": "Not implemented" }

API Test Case: Continuous Ticket by Id Not Implemented - PASSED

case description: request /continuous/:id/ticket, expecting 501 status code

case summary: Continuous Ticket by Id correctly non-implemented

Request: https://candig.bcgsc.ca/rnaget/continuous/nonexistentid9999999999999999999/ticket

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "code": 501, "message": "Not implemented" }

API Test Case: Continuous Bytes by Id Not Implemented - PASSED

case description: request /continuous/:id/bytes, expecting 501 status code

case summary: Continuous Bytes by Id correctly non-implemented

Request: https://candig.bcgsc.ca/rnaget/continuous/nonexistentid9999999999999999999/bytes

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "code": 501, "message": "Not implemented" }

API Test Case: Continuous Filters Not Implemented - PASSED

case description: request /continuous/filters, expecting 501 status code

case summary: Continuous Filters correctly non-implemented

Request: https://candig.bcgsc.ca/rnaget/continuous/filters

Params: {}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "code": 501, "message": "Not implemented" }

API Test Case: Continuous Ticket Not Implemented - PASSED

case description: request /continuous/ticket, expecting 501 status code

case summary: Continuous Ticket correctly non-implemented

Request: https://candig.bcgsc.ca/rnaget/continuous/ticket

Params: {'format': 'tsv'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "code": 501, "message": "Not implemented" }

API Test Case: Continuous Bytes Not Implemented - PASSED

case description: request /continuous/bytes, expecting 501 status code

case summary: Continuous Bytes correctly non-implemented

Request: https://candig.bcgsc.ca/rnaget/continuous/bytes

Params: {'format': 'tsv'}

Headers: {'Authorization': 'omitted', 'Accept': 'application/vnd.ga4gh.rnaget.v1.0.0+json, application/json;'}

Response Body: { "code": 501, "message": "Not implemented" }

Server name Object and Id Test case Status
CanDIG Projects: 9c0eba51095d3939437e220db196e27b Project Get PASSED
CanDIG Projects: 9c0eba51095d3939437e220db196e27b Project Filters PASSED
CanDIG Projects: 9c0eba51095d3939437e220db196e27b Project Search PASSED
CanDIG Studies: f3ba0b59bed0fa2f1030e7cb508324d1 Study Get PASSED
CanDIG Studies: f3ba0b59bed0fa2f1030e7cb508324d1 Study Filters PASSED
CanDIG Studies: f3ba0b59bed0fa2f1030e7cb508324d1 Study Search PASSED
CanDIG Expressions: ac3e9279efd02f1c98de4ed3d335b98e Expression Formats PASSED
CanDIG Expressions: ac3e9279efd02f1c98de4ed3d335b98e Single Expression Ticket FAILED
CanDIG Expressions: ac3e9279efd02f1c98de4ed3d335b98e Single Expression Bytes PASSED
CanDIG Expressions: ac3e9279efd02f1c98de4ed3d335b98e Expression Filters PASSED
CanDIG Expressions: ac3e9279efd02f1c98de4ed3d335b98e Multi Expression Ticket FAILED
CanDIG Expressions: ac3e9279efd02f1c98de4ed3d335b98e Multi Expression Bytes PASSED
CanDIG Continuous: NA Continuous Endpoint Not Implemented PASSED