RNAget API Compliance Report

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://felcat.caltech.edu/rnaget/projects/9c0eba51095d3939437e220db196e27b

Params: {}

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

Response Body: {"version": "1.0", "description": "Test project object used by RNAget compliance testing suite.", "studies": [{"version": "1.0", "parentProjectID": "9c0eba51095d3939437e220db196e27b", "description": "Test study object used by RNAget compliance testing suite.", "tags": ["RNAgetCompliance"], "id": "f3ba0b59bed0fa2f1030e7cb508324d1", "name": "RNAgetTestStudy0"}], "tags": ["RNAgetCompliance"], "id": "9c0eba51095d3939437e220db196e27b", "name": "RNAgetTestProject0"}

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://felcat.caltech.edu/rnaget/projects/nonexistentid9999999999999999999

Params: {}

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

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

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://felcat.caltech.edu/rnaget/projects/filters

Params: {}

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

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

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://felcat.caltech.edu/rnaget/projects

Params: {}

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

Response Body: [{"version": "1.0", "description": "Pan Cancer Analysis of Whole Genomes test data from Expression Atlas E-MTAB-5423", "id": "43378a5d48364f9d8cf3c3d5104df560", "tags": ["PCAWG", "cancer"], "name": "PCAWG"}, {"version": "1.0", "description": "Test project object used by RNAget compliance testing suite.", "id": "9c0eba51095d3939437e220db196e27b", "tags": ["RNAgetCompliance"], "name": "RNAgetTestProject0"}, {"version": "1.0", "description": "The Cancer Genome Atlas", "id": "0dc1cb6327844b5aa6a1a4eed3f64607", "tags": ["TCGA"], "name": "TCGA"}]

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://felcat.caltech.edu/rnaget/projects

Params: {'version': '1.0'}

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

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://felcat.caltech.edu/rnaget/projects

Params: {'version': '1.0'}

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

Response Body: [{"id": "43378a5d48364f9d8cf3c3d5104df560", "tags": ["PCAWG", "cancer"], "version": "1.0", "description": "Pan Cancer Analysis of Whole Genomes test data from Expression Atlas E-MTAB-5423", "name": "PCAWG"}, {"id": "9c0eba51095d3939437e220db196e27b", "tags": ["RNAgetCompliance"], "version": "1.0", "description": "Test project object used by RNAget compliance testing suite.", "name": "RNAgetTestProject0"}, {"id": "0dc1cb6327844b5aa6a1a4eed3f64607", "tags": ["TCGA"], "version": "1.0", "description": "The Cancer Genome Atlas", "name": "TCGA"}]

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://felcat.caltech.edu/rnaget/projects

Params: {'version': '1.0'}

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

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://felcat.caltech.edu/rnaget/projects

Params: {'version': 'nonexistentid9999999999999999999'}

Headers: {'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://felcat.caltech.edu/rnaget/studies/f3ba0b59bed0fa2f1030e7cb508324d1

Params: {}

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

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

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://felcat.caltech.edu/rnaget/studies/nonexistentid9999999999999999999

Params: {}

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

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

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://felcat.caltech.edu/rnaget/studies/filters

Params: {}

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

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

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://felcat.caltech.edu/rnaget/studies

Params: {}

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

Response Body: [{"version": "1.0", "parentProjectID": "43378a5d48364f9d8cf3c3d5104df560", "description": "PCAWG study", "tags": ["PCAWG", "cancer"], "id": "6cccbbd76b9c4837bd7342dd616d0fec", "name": "PCAWG"}, {"version": "1.0", "parentProjectID": "9c0eba51095d3939437e220db196e27b", "description": "Test study object used by RNAget compliance testing suite.", "tags": ["RNAgetCompliance"], "id": "f3ba0b59bed0fa2f1030e7cb508324d1", "name": "RNAgetTestStudy0"}, {"version": "1.0", "parentProjectID": "0dc1cb6327844b5aa6a1a4eed3f64607", "description": "The Cancer Genome Atlas", "tags": ["TCGA"], "id": "3912338463b344ada95b88d26576abb3", "name": "TCGA"}]

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://felcat.caltech.edu/rnaget/studies

Params: {'version': '1.0'}

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

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://felcat.caltech.edu/rnaget/studies

Params: {'version': '1.0'}

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

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://felcat.caltech.edu/rnaget/studies

Params: {'version': '1.0'}

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

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://felcat.caltech.edu/rnaget/studies

Params: {'version': 'nonexistentid9999999999999999999'}

Headers: {'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://felcat.caltech.edu/rnaget/expressions/formats

Params: {}

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

Response Body: ["loom"]

Test: Single Expression Ticket - PASSED

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

summary: 'Single Expression Ticket by Id' endpoint 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://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

Params: {}

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

Response Body: {"url": "http://woldlab.caltech.edu/~sau/rnaget/expression.loom", "version": "1.0", "units": "TPM", "studyID": "f3ba0b59bed0fa2f1030e7cb508324d1", "id": "ac3e9279efd02f1c98de4ed3d335b98e", "tags": ["RNAgetCompliance"], "fileType": "loom"}

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://felcat.caltech.edu/rnaget/expressions/nonexistentid9999999999999999999/ticket

Params: {}

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

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

File Content Test Cases - PASSED

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

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

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 Ticket - Expression Value 2 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

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 Ticket - Expression Value 3 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

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 Ticket - Expression Value 4 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

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 Ticket - Expression Value 5 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

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 Ticket - Expression Value 6 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

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 Ticket - Expression Value 7 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

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 Ticket - Expression Value 8 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

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 Ticket - Expression Value 9 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

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 Ticket - Expression Value 10 - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

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 Ticket - Slice by featureIDList - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

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 Ticket - Slice by featureNameList - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

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 Ticket - Slice by sampleIDList - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/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'}

asserting number of columns matches number of supplied Samples

asserting returned Samples match supplied Samples

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

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/ticket

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 Ticket - slice by featureNameList and sampleIDList - PASSED

case description: Asserts correct expression values and slicing operations

case summary: Expression matrix content matches expected

Ticket URL: https://felcat.caltech.edu/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'}

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: 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://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

Params: {}

Headers: {'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://felcat.caltech.edu/rnaget/expressions/nonexistentid9999999999999999999/bytes

Params: {}

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

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

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://felcat.caltech.edu/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://felcat.caltech.edu/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://felcat.caltech.edu/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://felcat.caltech.edu/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://felcat.caltech.edu/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://felcat.caltech.edu/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://felcat.caltech.edu/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://felcat.caltech.edu/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://felcat.caltech.edu/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://felcat.caltech.edu/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://felcat.caltech.edu/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://felcat.caltech.edu/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://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

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://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

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://felcat.caltech.edu/rnaget/expressions/ac3e9279efd02f1c98de4ed3d335b98e/bytes

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://felcat.caltech.edu/rnaget/expressions/filters

Params: {}

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

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

Test: Multi Expression Ticket - PASSED

description: Requests the /expressions/ticket endpoint.

summary: 'Expression Ticket' endpoint 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://felcat.caltech.edu/rnaget/expressions/ticket

Params: {'format': 'loom'}

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

Response Body: {"studyID": "6cccbbd76b9c4837bd7342dd616d0fec", "units": "TPM", "tags": [], "url": "http://woldlab.caltech.edu/~sau/rnaget/E-MTAB-5423-query-results.tpms.loom", "version": "1.0", "fileType": "loom", "id": "2a7ab5533ef941eaa59edbfe887b58c4"}

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://felcat.caltech.edu/rnaget/expressions/ticket

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

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

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://felcat.caltech.edu/rnaget/expressions/ticket

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

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

Response Body: {"studyID": "f3ba0b59bed0fa2f1030e7cb508324d1", "units": "TPM", "tags": ["RNAgetCompliance"], "url": "http://woldlab.caltech.edu/~sau/rnaget/expression.loom", "version": "1.0", "fileType": "loom", "id": "ac3e9279efd02f1c98de4ed3d335b98e"}

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://felcat.caltech.edu/rnaget/expressions/ticket

Params: {'version': '1.0', 'format': 'loom'}

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

Response Body: {"url": "http://woldlab.caltech.edu/~sau/rnaget/E-MTAB-5423-query-results.tpms.loom", "version": "1.0", "units": "TPM", "studyID": "6cccbbd76b9c4837bd7342dd616d0fec", "id": "2a7ab5533ef941eaa59edbfe887b58c4", "tags": [], "fileType": "loom"}

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://felcat.caltech.edu/rnaget/expressions/ticket

Params: {}

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

Response Body: {"message": "Input payload validation failed", "errors": {"format": "format of data to return"}}

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://felcat.caltech.edu/rnaget/expressions/ticket

Params: {'format': 'loom'}

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

File Content Test Cases - PASSED

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

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 match expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ticket

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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 Ticket - Expression Value 2 - PASSED

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 match expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ticket

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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 Ticket - Expression Value 3 - PASSED

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 match expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ticket

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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 Ticket - Expression Value 4 - PASSED

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 match expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ticket

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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 Ticket - Expression Value 5 - PASSED

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 match expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ticket

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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 Ticket - Slice by featureIDList - PASSED

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 match expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ticket

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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 Ticket - Slice by featureNameList - PASSED

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 match expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ticket

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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 Ticket - Slice by sampleIDList - PASSED

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 match expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ticket

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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 Ticket - slice by featureIDList and sampleIDList - PASSED

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 match expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ticket

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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 Ticket - slice by featureNameList and sampleIDList - PASSED

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 match expected

Ticket URL: https://felcat.caltech.edu/rnaget/expressions/ticket

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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

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://felcat.caltech.edu/rnaget/expressions/bytes

Params: {'format': 'loom'}

Headers: {'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://felcat.caltech.edu/rnaget/expressions/bytes

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

Headers: {'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://felcat.caltech.edu/rnaget/expressions/bytes

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

Headers: {'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://felcat.caltech.edu/rnaget/expressions/bytes

Params: {'version': '1.0', 'format': 'loom'}

Headers: {'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://felcat.caltech.edu/rnaget/expressions/bytes

Params: {}

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

Response Body: {"message": "Input payload validation failed", "errors": {"format": "format of data to return"}}

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://felcat.caltech.edu/rnaget/expressions/bytes

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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://felcat.caltech.edu/rnaget/expressions/bytes

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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://felcat.caltech.edu/rnaget/expressions/bytes

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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://felcat.caltech.edu/rnaget/expressions/bytes

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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://felcat.caltech.edu/rnaget/expressions/bytes

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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://felcat.caltech.edu/rnaget/expressions/bytes

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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://felcat.caltech.edu/rnaget/expressions/bytes

Params: {'version': '1.0', 'studyID': 'f3ba0b59bed0fa2f1030e7cb508324d1', '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://felcat.caltech.edu/rnaget/expressions/bytes

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://felcat.caltech.edu/rnaget/expressions/bytes

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://felcat.caltech.edu/rnaget/expressions/bytes

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

Continuous 1 id: 5e22e009f41fc53cbea094a41de8798f

Tests

Test: Continuous Formats - PASSED

description: Requests the /continuous/formats endpoint

summary: 'Continuous Formats' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Get Supported Continuous Formats - PASSED

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

case summary: Continuous formats successfully retrieved

Request: https://felcat.caltech.edu/rnaget/continuous/formats

Params: {}

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

Response Body: ["loom"]

Test: Single Continuous Ticket - PASSED

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

summary: 'Single Continuous Ticket by Id' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Get Test Continuous Ticket - PASSED

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

case summary: Test continuous ticket successfully retrieved

Request: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/ticket

Params: {}

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

Response Body: {"url": "https://woldlab.caltech.edu/~sau/rnaget/continuous.loom", "version": "1.0", "units": "counts", "studyID": "f3ba0b59bed0fa2f1030e7cb508324d1", "id": "5e22e009f41fc53cbea094a41de8798f", "tags": ["RNAgetCompliance"], "fileType": "loom"}

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

case description: request /continuous/:id/ticket using a continuous 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 continuous not found

Request: https://felcat.caltech.edu/rnaget/continuous/nonexistentid9999999999999999999/ticket

Params: {}

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

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

API Test Case: Single Continuous Ticket - Start Specified Without Chr - PASSED

case description: request /continuous/:id/ticket, specifying start parameter without chr. checks content type and status code (400). validates response body matches error schema

case summary: Server sends correct response when start is specified without chr

Request: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/ticket

Params: {'start': '5'}

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

Response Body: {"message": "chr required if either start or end is specified"}

API Test Case: Single Continuous Ticket - End Specified Without Chr - PASSED

case description: request /continuous/:id/ticket, specifying end parameter without chr. checks content type and status code (400). validates response body matches error schema

case summary: Server sends correct response when end is specified without chr

Request: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/ticket

Params: {'end': '1000'}

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

Response Body: {"message": "chr required if either start or end is specified"}

API Test Case: Single Continuous Ticket - Start Greater Than End - PASSED

case description: request /continuous/:id/ticket, specifying chr, start, and end parameters, but start is greater than end. checks content type and status code (501). validates response body matches error schema

case summary: Server sends correct response when start is greater than end

Request: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/ticket

Params: {'chr': '1', 'start': '200', 'end': '100'}

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

Response Body: {"message": "end < start is not implemented"}

File Content Test Cases - PASSED

Content Test Case: Single Continuous Ticket - Continuous Value 1 - PASSED

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/ticket

Params: {}

asserting observed Track: 61729_test equals expected: 61729_test

asserting observed Position: chr1:20 equals expected: chr1:20

asserting observed Value: 8.904 equals expected: 8.904

Content Test Case: Single Continuous Ticket - Continuous Value 2 - PASSED

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/ticket

Params: {}

asserting observed Track: 61721_test equals expected: 61721_test

asserting observed Position: chr1:5 equals expected: chr1:5

asserting observed Value: 6.205 equals expected: 6.205

Content Test Case: Single Continuous Ticket - Continuous Value 3 - PASSED

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/ticket

Params: {}

asserting observed Track: 61733_test equals expected: 61733_test

asserting observed Position: chr5:143 equals expected: chr5:143

asserting observed Value: 8.779 equals expected: 8.779

Content Test Case: Single Continuous Ticket - Continuous Slice by chr, 1 - PASSED

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/ticket

Params: {'chr': 'chr1'}

asserting returned chromosome matches request

Content Test Case: Single Continuous Ticket - Continuous Slice by chr, start, 1 - PASSED

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/ticket

Params: {'chr': 'chr1', 'start': '32'}

asserting returned chromosome matches request

asserting start position is greater than or equal to request 'start' parameter

Content Test Case: Single Continuous Ticket - Continuous Slice by chr, end, 1 - PASSED

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/ticket

Params: {'chr': 'chr1', 'end': '22'}

asserting returned chromosome matches request

asserting end position is less than request 'end' parameter

Content Test Case: Single Continuous Ticket - Continuous Slice by chr, start, end, 1 - PASSED

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/ticket

Params: {'chr': 'chr1', 'start': '30', 'end': '50'}

asserting returned chromosome matches request

asserting start position is greater than or equal to request 'start' parameter

asserting end position is less than request 'end' parameter

Test: Single Continuous Bytes - PASSED

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

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

API Route Test Cases - PASSED

API Test Case: Get Test Continuous Bytes - PASSED

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

case summary: Test continuous bytes successfully retrieved

Request: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/bytes

Params: {}

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

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

case description: request /continuous/:id/bytes using a continuous 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 continuous not found

Request: https://felcat.caltech.edu/rnaget/continuous/nonexistentid9999999999999999999/bytes

Params: {}

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

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

API Test Case: Single Continuous Bytes - Start Specified Without Chr - PASSED

case description: request /continuous/:id/bytes, specifying start parameter without chr. checks content type and status code (400). validates response body matches error schema

case summary: Server sends correct response when start is specified without chr

Request: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/bytes

Params: {'start': '5'}

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

Response Body: {"message": "chr required if either start or end is specified"}

API Test Case: Single Continuous Bytes - End Specified Without Chr - PASSED

case description: request /continuous/:id/bytes, specifying end parameter without chr. checks content type and status code (400). validates response body matches error schema

case summary: Server sends correct response when end is specified without chr

Request: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/bytes

Params: {'end': '1000'}

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

Response Body: {"message": "chr required if either start or end is specified"}

API Test Case: Single Continuous Bytes - Start Greater Than End - PASSED

case description: request /continuous/:id/bytes, specifying chr, start, and end parameters, but start is greater than end. checks content type and status code (501). validates response body matches error schema

case summary: Server sends correct response when start is greater than end

Request: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/bytes

Params: {'chr': '1', 'start': '200', 'end': '100'}

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

Response Body: {"message": "end < start is not implemented"}

File Content Test Cases - PASSED

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

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/bytes

Params: {}

asserting observed Track: 61733_test equals expected: 61733_test

asserting observed Position: chr5:143 equals expected: chr5:143

asserting observed Value: 8.779 equals expected: 8.779

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

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/bytes

Params: {}

asserting observed Track: 61737_test equals expected: 61737_test

asserting observed Position: chr5:90 equals expected: chr5:90

asserting observed Value: 24.704 equals expected: 24.704

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

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/bytes

Params: {}

asserting observed Track: 61729_test equals expected: 61729_test

asserting observed Position: chr1:66 equals expected: chr1:66

asserting observed Value: 6.975 equals expected: 6.975

Content Test Case: Single Continuous Bytes - Continuous Slice by chr, 2 - PASSED

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/bytes

Params: {'chr': 'chr5'}

asserting returned chromosome matches request

Content Test Case: Single Continuous Bytes - Continuous Slice by chr, start, 2 - PASSED

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/bytes

Params: {'chr': 'chr5', 'start': '100'}

asserting returned chromosome matches request

asserting start position is greater than or equal to request 'start' parameter

Content Test Case: Single Continuous Bytes - Continuous Slice by chr, end, 2 - PASSED

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/bytes

Params: {'chr': 'chr5', 'end': '49'}

asserting returned chromosome matches request

asserting end position is less than request 'end' parameter

Content Test Case: Single Continuous Bytes - Continuous Slice by chr, start, end, 2 - PASSED

case description: Assert continuous rows, columns, and cell values match expected

case summary: Continuous matrix content matches expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/5e22e009f41fc53cbea094a41de8798f/bytes

Params: {'chr': 'chr5', 'start': '69', 'end': '117'}

asserting returned chromosome matches request

asserting start position is greater than or equal to request 'start' parameter

asserting end position is less than request 'end' parameter

Test: Continuous Filters - PASSED

description: Requests the /continuous/filters endpoint.

summary: 'Continuous Filters' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Continuous Filters - PASSED

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

case summary: Continuous filters successfully retrieved

Request: https://felcat.caltech.edu/rnaget/continuous/filters

Params: {}

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

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

Test: Multi Continuous Ticket - PASSED

description: Requests the /continuous/ticket endpoint.

summary: 'Continuous Ticket' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Continuous Ticket by Format - PASSED

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

case summary: Continuous Ticket can be retrieved

Request: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'format': 'loom'}

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

API Test Case: Continuous Ticket - All Filters - PASSED

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

case summary: Continuous Ticket retrieved when all filters specified

Request: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'version': '1.0', 'format': 'loom'}

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

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

case description: request /continuous/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: Continuous Ticket retrieved when first filter supplied

Request: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'version': '1.0', 'format': 'loom'}

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

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

case description: request /continuous/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: Continuous Ticket retrieved when second filter supplied

Request: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'version': '1.0', 'format': 'loom'}

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

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

case description: request /continuous/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://felcat.caltech.edu/rnaget/continuous/ticket

Params: {}

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

Response Body: {"message": "Input payload validation failed", "errors": {"format": "format of data to return"}}

API Test Case: Continuous Ticket - Filetype Matches - PASSED

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

case summary: Continuous Ticket fileType matches request format

Request: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'format': 'loom'}

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

API Test Case: Continuous Ticket - Start Specified Without Chr - PASSED

case description: request /continuous/ticket, specifying start parameter without chr. checks content type and status code (400). validates response body matches error schema

case summary: Server sends correct response when start is specified without chr

Request: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'start': '5', 'version': '1.0', 'format': 'loom'}

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

Response Body: {"message": "chr required if either start or end is specified"}

API Test Case: Continuous Ticket - End Specified Without Chr - PASSED

case description: request /continuous/ticket, specifying end parameter without chr. checks content type and status code (400). validates response body matches error schema

case summary: Server sends correct response when end is specified without chr

Request: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'end': '1000', 'version': '1.0', 'format': 'loom'}

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

Response Body: {"message": "chr required if either start or end is specified"}

API Test Case: Continuous Ticket - Start Greater Than End - PASSED

case description: request /continuous/ticket, specifying chr, start, and end parameters, but start is greater than end. checks content type and status code (501). validates response body matches error schema

case summary: Server sends correct response when start is greater than end

Request: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'chr': '1', 'start': '200', 'end': '100', 'version': '1.0', 'format': 'loom'}

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

Response Body: {"message": "end < start is not implemented"}

File Content Test Cases - PASSED

Content Test Case: Multi Continuous Ticket - Continuous Value 1 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'version': '1.0', 'format': 'loom'}

asserting observed Track: 61729_test equals expected: 61729_test

asserting observed Position: chr1:20 equals expected: chr1:20

asserting observed Value: 8.904 equals expected: 8.904

Content Test Case: Multi Continuous Ticket - Continuous Value 3 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'version': '1.0', 'format': 'loom'}

asserting observed Track: 61733_test equals expected: 61733_test

asserting observed Position: chr5:143 equals expected: chr5:143

asserting observed Value: 8.779 equals expected: 8.779

Content Test Case: Multi Continuous Ticket - Continuous Value 5 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'version': '1.0', 'format': 'loom'}

asserting observed Track: 61729_test equals expected: 61729_test

asserting observed Position: chr1:66 equals expected: chr1:66

asserting observed Value: 6.975 equals expected: 6.975

Content Test Case: Multi Continuous Ticket - Continuous Slice by chr, 1 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'version': '1.0', 'format': 'loom', 'chr': 'chr1'}

asserting returned chromosome matches request

Content Test Case: Multi Continuous Ticket - Continuous Slice by chr, start, 1 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'version': '1.0', 'format': 'loom', 'chr': 'chr1', 'start': '32'}

asserting returned chromosome matches request

asserting start position is greater than or equal to request 'start' parameter

Content Test Case: Multi Continuous Ticket - Continuous Slice by chr, end, 1 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'version': '1.0', 'format': 'loom', 'chr': 'chr1', 'end': '22'}

asserting returned chromosome matches request

asserting end position is less than request 'end' parameter

Content Test Case: Multi Continuous Ticket - Continuous Slice by chr, start, end, 1 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Ticket URL: https://felcat.caltech.edu/rnaget/continuous/ticket

Params: {'version': '1.0', 'format': 'loom', 'chr': 'chr1', 'start': '30', 'end': '50'}

asserting returned chromosome matches request

asserting start position is greater than or equal to request 'start' parameter

asserting end position is less than request 'end' parameter

Test: Multi Continuous Bytes - PASSED

description: Requests the /continuous/bytes endpoint.

summary: 'Continuous Bytes' endpoint correctly implemented

API Route Test Cases - PASSED

API Test Case: Continuous Bytes by Format - PASSED

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

case summary: Continuous Bytes can be retrieved

Request: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'format': 'loom'}

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

API Test Case: Continuous Bytes - All Filters - PASSED

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

case summary: Continuous Bytes retrieved when all filters specified

Request: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'version': '1.0', 'format': 'loom'}

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

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

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

case summary: Continuous Bytes retrieved when first filter supplied

Request: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'version': '1.0', 'format': 'loom'}

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

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

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

case summary: Continuous Bytes retrieved when second filter supplied

Request: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'version': '1.0', 'format': 'loom'}

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

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

case description: request /continuous/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://felcat.caltech.edu/rnaget/continuous/bytes

Params: {}

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

Response Body: {"message": "Input payload validation failed", "errors": {"format": "format of data to return"}}

API Test Case: Continuous Bytes - Start Specified Without Chr - PASSED

case description: request /continuous/bytes, specifying start parameter without chr. checks content type and status code (400). validates response body matches error schema

case summary: Server sends correct response when start is specified without chr

Request: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'start': '5', 'version': '1.0', 'format': 'loom'}

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

Response Body: {"message": "chr required if either start or end is specified"}

API Test Case: Continuous Bytes - End Specified Without Chr - PASSED

case description: request /continuous/bytes, specifying end parameter without chr. checks content type and status code (400). validates response body matches error schema

case summary: Server sends correct response when end is specified without chr

Request: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'end': '1000', 'version': '1.0', 'format': 'loom'}

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

Response Body: {"message": "chr required if either start or end is specified"}

API Test Case: Continuous Bytes - Start Greater Than End - PASSED

case description: request /continuous/bytes, specifying chr, start, and end parameters, but start is greater than end. checks content type and status code (501). validates response body matches error schema

case summary: Server sends correct response when start is greater than end

Request: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'chr': '1', 'start': '200', 'end': '100', 'version': '1.0', 'format': 'loom'}

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

Response Body: {"message": "end < start is not implemented"}

File Content Test Cases - PASSED

Content Test Case: Multi Continuous Bytes - Continuous Value 2 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'version': '1.0', 'format': 'loom'}

asserting observed Track: 61721_test equals expected: 61721_test

asserting observed Position: chr1:5 equals expected: chr1:5

asserting observed Value: 6.205 equals expected: 6.205

Content Test Case: Multi Continuous Bytes - Continuous Value 4 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'version': '1.0', 'format': 'loom'}

asserting observed Track: 61737_test equals expected: 61737_test

asserting observed Position: chr5:90 equals expected: chr5:90

asserting observed Value: 24.704 equals expected: 24.704

Content Test Case: Multi Continuous Bytes - Continuous Value 5 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'version': '1.0', 'format': 'loom'}

asserting observed Track: 61729_test equals expected: 61729_test

asserting observed Position: chr1:66 equals expected: chr1:66

asserting observed Value: 6.975 equals expected: 6.975

Content Test Case: Multi Continuous Bytes - Continuous Slice by chr, 2 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'version': '1.0', 'format': 'loom', 'chr': 'chr5'}

asserting returned chromosome matches request

Content Test Case: Multi Continuous Bytes - Continuous Slice by chr, start, 2 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'version': '1.0', 'format': 'loom', 'chr': 'chr5', 'start': '100'}

asserting returned chromosome matches request

asserting start position is greater than or equal to request 'start' parameter

Content Test Case: Multi Continuous Bytes - Continuous Slice by chr, end, 2 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'version': '1.0', 'format': 'loom', 'chr': 'chr5', 'end': '49'}

asserting returned chromosome matches request

asserting end position is less than request 'end' parameter

Content Test Case: Multi Continuous Bytes - Continuous Slice by chr, start, end, 2 - PASSED

case description: Asserts correct values of continuous matrix, and correct of matrix by parameters (chr, start, end).

case summary: Continuous matrix tracks, positions, and values match expected

Bytes URL: https://felcat.caltech.edu/rnaget/continuous/bytes

Params: {'version': '1.0', 'format': 'loom', 'chr': 'chr5', 'start': '69', 'end': '117'}

asserting returned chromosome matches request

asserting start position is greater than or equal to request 'start' parameter

asserting end position is less than request 'end' parameter

Server name	Object and Id	Test case	Status
Caltech	Projects: 9c0eba51095d3939437e220db196e27b	Project Get	PASSED
Caltech	Projects: 9c0eba51095d3939437e220db196e27b	Project Filters	PASSED
Caltech	Projects: 9c0eba51095d3939437e220db196e27b	Project Search	PASSED
Caltech	Studies: f3ba0b59bed0fa2f1030e7cb508324d1	Study Get	PASSED
Caltech	Studies: f3ba0b59bed0fa2f1030e7cb508324d1	Study Filters	PASSED
Caltech	Studies: f3ba0b59bed0fa2f1030e7cb508324d1	Study Search	PASSED
Caltech	Expressions: ac3e9279efd02f1c98de4ed3d335b98e	Expression Formats	PASSED
Caltech	Expressions: ac3e9279efd02f1c98de4ed3d335b98e	Single Expression Ticket	PASSED
Caltech	Expressions: ac3e9279efd02f1c98de4ed3d335b98e	Single Expression Bytes	PASSED
Caltech	Expressions: ac3e9279efd02f1c98de4ed3d335b98e	Expression Filters	PASSED
Caltech	Expressions: ac3e9279efd02f1c98de4ed3d335b98e	Multi Expression Ticket	PASSED
Caltech	Expressions: ac3e9279efd02f1c98de4ed3d335b98e	Multi Expression Bytes	PASSED
Caltech	Continuous: 5e22e009f41fc53cbea094a41de8798f	Continuous Formats	PASSED
Caltech	Continuous: 5e22e009f41fc53cbea094a41de8798f	Single Continuous Ticket	PASSED
Caltech	Continuous: 5e22e009f41fc53cbea094a41de8798f	Single Continuous Bytes	PASSED
Caltech	Continuous: 5e22e009f41fc53cbea094a41de8798f	Continuous Filters	PASSED
Caltech	Continuous: 5e22e009f41fc53cbea094a41de8798f	Multi Continuous Ticket	PASSED
Caltech	Continuous: 5e22e009f41fc53cbea094a41de8798f	Multi Continuous Bytes	PASSED

RNAGet Implementation Compliance Report

Server: Caltech

Base URL: https://felcat.caltech.edu/rnaget/

Projects

Project 1 id: 9c0eba51095d3939437e220db196e27b

Studies

Study 1 id: f3ba0b59bed0fa2f1030e7cb508324d1

Expressions

Expression 1 id: ac3e9279efd02f1c98de4ed3d335b98e

Continuous

Continuous 1 id: 5e22e009f41fc53cbea094a41de8798f