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openapi-appengine.v2.pub.yaml
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# [START swagger]
swagger: "2.0"
info:
description: "IDC API Endpoints, version 2"
title: "IDC API"
version: "2.0"
consumes:
- "application/json"
produces:
- "application/json"
- "application/xml"
schemes:
# ***********Uncomment https and comment http for deploymwnt***********
#- "https"
- "http"
tags:
- name: about
- name: data model
- name: cohorts
- name: manifests
- name: users
paths:
/about:
get:
tags:
- about
description: "Get links to the IDC API Swagger UI and IDC documentation"
operationId: "root-get"
produces:
- "application/json"
responses:
200:
description: "API Description and link to SwaggerUI interface."
schema:
$ref: "#/definitions/aboutResponse"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
/swagger:
get:
tags:
- about
description: "Swagger UI of the API spec"
operationId: "swaggerUI"
produces:
- "text/html"
responses:
200:
description: "Swagger UI of the API spec"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
/oauth2callback:
get:
description: "OAuth2 Redirect URI"
operationId: "oauth2redirect"
produces:
- "text/html"
responses:
200:
description: "OAuth2 Redirect URI"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
/versions:
get:
description: "Returns a list of IDC data versions and activation dates"
tags:
- data model
operationId: "getVersions"
produces:
- "application/json"
responses:
200:
description: "A list of IDC data versions and metadata"
schema:
$ref: "#/definitions/versionsListResponse"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
/collections:
get:
description: "Returns a list of collections, and associated metadata, in the current IDC data version. "
tags:
- data model
operationId: "getCollections"
produces:
- "application/json"
responses:
200:
description: "A list of collections"
schema:
$ref: "#/definitions/collectionsListResponse"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
/analysis_results:
get:
description: "Returns a list of the analysis results, and associated metadata, in the current IDC data version"
tags:
- data model
operationId: "getAnalysisResults"
produces:
- "application/json"
responses:
200:
description: "A list of analysis results"
schema:
$ref: "#/definitions/analysisResultsListResponse"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
/filters:
get:
description: "Returns a list of 'filters', organized by data source (BQ table), for the current IDC data version. An IDC cohort is defined by a 'filterset', a set of (filter,[values]) pairs, and the IDC version against which the filterset is applied. The returned data is grouped by source (the BQ table that contains the corresponding filter values). For each filter, its data type and units, when available, are reported."
tags:
- data model
operationId: "getFilters"
produces:
- "application/json"
responses:
200:
description: "A list of filters"
schema:
$ref: "#/definitions/filtersListResponse"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
/filters/values/{filter}:
get:
description: "Return a list of the values accepted for a 'categorical filter'. A categorical filter is a filter having a data type of 'Categorical String' or 'Categorical Number'. "
tags:
- data model
operationId: "getFilterValues"
produces:
- "application/json"
parameters:
- name: filter
in: path
description: "Categorical filter whose values are to be returned"
type: "string"
required: true
responses:
200:
description: "A list of accepted values"
schema:
$ref: "#/definitions/filterValues"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
/fields/{version}:
get:
description: "Return a list of queryable manifest fields."
tags:
- data model
operationId: "getFields"
produces:
- "application/json"
parameters:
- name: version
in: path
description: "IDC data version whose data is to be returned. If the version is 'current', the fields of the current IDC version are returned."
type: "string"
required: true
responses:
200:
description: "A list of fields"
schema:
$ref: "#/definitions/fieldsListResponse"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
/cohorts:
get:
description: "Returns a list of the user's cohorts and associated metadata. Authorization is required in order to access this endpoint."
tags:
- cohorts
operationId: "getCohorts"
produces:
- "application/json"
responses:
200:
description: "A list of the user's cohorts."
schema:
$ref: "#/definitions/cohortsListResponse"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
security:
- google_id_token: []
post:
description: "Create a cohort as defined by a specified 'filterset' and IDC version. Authorization is required in order to access this endpoint."
tags:
- cohorts
operationId: "cohortCreate"
consumes:
- "application/json"
produces:
- "application/json"
parameters:
- in: body
name: "cohort_def"
required: true
description: "Filters, name, and description used to create this cohort."
schema:
$ref: "#/definitions/cohortSpec"
responses:
200:
description: "Summary information about the cohort created."
schema:
$ref: "#/definitions/cohortCreateResponse"
400:
description: "Bad request"
schema:
$ref: "#/definitions/errorMessage"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
security:
- google_id_token: []
delete:
description: "Delete a list of the user's cohorts. Authorization is required in order to access this endpoint."
tags:
- cohorts
operationId: "cohortsDelete"
consumes:
- "application/json"
produces:
- "application/json"
parameters:
- in: body
name: "cohort_list"
required: true
description: "List of IDs of cohorts to be deleted."
schema:
$ref: "#/definitions/cohortIdList"
responses:
200:
description: "Summary of cohort deletion."
schema:
$ref: "#/definitions/cohortDeleteResponse"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
security:
- google_id_token: []
/cohorts/{cohort_id}:
delete:
description: "Delete a specified cohort. Authorization is required in order to access this endpoint."
tags:
- cohorts
operationId: "cohortDelete"
produces:
- "application/json"
parameters:
- in: path
name: "cohort_id"
required: true
description: "ID of cohort to be deleted."
type: "integer"
responses:
200:
description: "A list of the user's remaining cohorts."
schema:
$ref: "#/definitions/cohortDeleteResponse"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
security:
- google_id_token: []
/cohorts/manifest/preview:
post:
description: "Returns a manifest of a 'previewed cohort' as defined by a specified filterset. The filterset is always applied to the current IDC version. The metadata to be returned in the manifest is configurable. A previewed cohort is not saved in the user's IDC account."
tags:
- manifests
operationId: "cohortManifestPreview"
produces:
- "application/json"
parameters:
- name: "manifestPreviewBody"
in: body
description: "Cohort definition and list of fields to query."
schema:
$ref: "#/definitions/manifestPreviewBody"
required: true
responses:
200:
description: "Preview cohort spec and manifest"
schema:
$ref: "#/definitions/manifestPreviewResponse"
202:
description: "Timeout waiting for BQ job to complete"
schema:
$ref: "#/definitions/timeoutResponse"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
/cohorts/manifest/{cohort_id}:
post:
description: "Returns a manifest of a cohort that was previously saved under the user's IDC account. The metadata to be returned in the manifest is configurable. Authorization is required in order to access this endpoint."
tags:
- manifests
operationId: "cohortManifest"
produces:
- "application/json"
parameters:
- name: cohort_id
in: path
description: "IDC Cohort ID"
type: integer
required: true
- name: manifestBody
in: body
description: "List of fields to return."
schema:
$ref: "#/definitions/manifestBody"
required: true
responses:
200:
description: "Cohort spec and anifest"
schema:
$ref: "#/definitions/manifestResponse"
202:
description: "Timeout waiting for BQ job to complete"
schema:
$ref: "#/definitions/timeoutResponse"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
security:
- google_id_token: []
/cohorts/manifest/preview/nextPage:
get:
description: "Returns the next page of a /cohorts/manifest/preview request, when additional data is available."
tags:
- manifests
operationId: "cohortManifestPreviewNextPage"
produces:
- "application/json"
parameters:
- name: next_page
in: query
description: "The next_page token returned by a previous access of the /cohorts/manifest/preview endpoint. The token identifies the next page to be retrieved"
type: "string"
required: true
- name: page_size
in: query
description: "The maximum number of rows to be returned. If the manifest contains additional rows, another 'next_page' token is returned."
type: "integer"
required: false
default: 1000
responses:
200:
description: "Preview manifest page"
schema:
$ref: "#/definitions/manifestNextPageResponse"
202:
description: "Timeout waiting for BQ job to complete"
schema:
$ref: "#/definitions/timeoutResponse"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
/cohorts/manifest/nextPage:
get:
description: "Returns the next page of a /cohorts/manifest request, when additional data is available. Authorization is required in order to access this endpoint."
tags:
- manifests
operationId: "cohortManifestNextPage"
produces:
- "application/json"
parameters:
- name: next_page
in: query
description: "The next_page token returned by a previous access of the /cohorts/manifest endpoint. The token identifies the next page to be retrieved"
type: "string"
required: true
- name: page_size
in: query
description: "The maximum number of rows to be returned. If the manifest contains additional rows, another 'next_page' token is returned."
type: "integer"
required: false
default: 1000
responses:
200:
description: "manifest page"
schema:
$ref: "#/definitions/manifestNextPageResponse"
202:
description: "Timeout waiting for BQ job to complete"
schema:
$ref: "#/definitions/timeoutResponse"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
security:
- google_id_token: []
/users/account_details:
get:
description: "Retrieve user's account information. Authorization is required in order to access this endpoint."
tags:
- users
operationId: "getUserAccountDetails"
produces:
- "application/json"
responses:
200:
description: "Current account information for the validated user."
schema:
$ref: "#/definitions/accountDetailsResponse"
400:
description: "Invalid request error message"
schema:
$ref: "#/definitions/errorMessage"
403:
description: "Unauthorized. User not registered with the IDC web app"
schema:
$ref: "#/definitions/errorMessage"
500:
description: "Server error message"
schema:
$ref: "#/definitions/errorMessage"
security:
- google_id_token: []
definitions:
aboutResponse:
type: "object"
properties:
message:
type: "string"
documentation:
type: "string"
code:
type: "integer"
versionsListResponse:
type: "object"
properties:
idc_data_versions:
type: "array"
items:
type: "object"
properties:
idc_data_version:
type: "string"
date_active:
type: "string"
active:
type: "string"
code:
type: "integer"
collectionsListResponse:
type: "object"
properties:
collections:
type: "array"
items:
$ref: "#/definitions/collectionMetadata"
code:
type: "integer"
analysisResultsListResponse:
type: "object"
properties:
analysisResults:
type: "array"
items:
$ref: "#/definitions/analysisResultsMetadata"
code:
type: "integer"
dataSetType:
type: "array"
items:
type: "string"
enum: ['Clinical, Biospecimen, and Mutation Data', 'Image Data', 'Derived Data']
data_source:
type: "object"
properties:
name:
type: "string"
data_type:
type: "string"
enum: ["Image Data", "Clinical, Biospecimen, and Mutation Data", "Derived Data"]
filtersListResponse:
type: "object"
properties:
idc_data_version:
type: "string"
data_sources:
type: "array"
items:
$ref: "#/definitions/data_source_filters"
code:
type: "integer"
data_source_filters:
type: "object"
properties:
data_source:
type: "string"
filters:
type: "array"
items:
$ref: "#/definitions/filter"
filter:
type: "object"
properties:
name:
type: "string"
data_type:
type: "string"
enum: ["CONTINUOUS_NUMERIC", "CATEGORICAL_NUMERIC", "CATEGORICAL_STRING", "TEXT", "STRING"]
units:
type: "string"
filterValues:
type: "object"
properties:
values:
type: "array"
items:
type: "string"
fieldsListResponse:
type: "object"
properties:
idc_data_version:
type: "string"
data_sources:
type: "array"
items:
$ref: "#/definitions/data_source_fields"
code:
type: "integer"
data_source_fields:
type: "object"
properties:
data_source:
type: "string"
fields:
type: "array"
items:
type: "string"
collectionMetadata:
type: "object"
properties:
collection_id:
type: "string"
cancer_type:
type: "string"
date_updated:
type: "string"
description:
type: "string"
source_doi:
type: "string"
source_url:
type: "string"
image_types:
type: "string"
location:
type: "string"
species:
type: "string"
subject_count:
type: "integer"
supporting_data:
type: "string"
analysisResultsMetadata:
type: "object"
properties:
analysis_result_id:
type: "string"
analysisArtifacts:
type: "string"
cancer_type:
type: "string"
collections:
type: "string"
date_updated:
type: "string"
description:
type: "string"
doi:
type: "string"
location:
type: "string"
subjects:
type: "integer"
title:
type: "string"
cohortsListResponse:
type: "object"
properties:
cohorts:
type: "array"
items:
$ref: "#/definitions/cohortMetadata"
cohortDeleteResponse:
type: "object"
properties:
cohorts:
type: "array"
items:
type: "object"
properties:
cohort_id:
type: integer
result:
type: "string"
cohortMetadata:
type: "object"
properties:
cohort_id:
type: "integer"
name:
type: "string"
description:
type: "string"
owner:
type: "string"
permission:
type: "string"
enum: ["OWNER","READER"]
filterSet:
$ref: "#/definitions/filterSet"
cohortSpec:
type: "object"
properties:
name:
type: "string"
default: ""
description:
type: "string"
default: ""
filters:
$ref: "#/definitions/filters"
required:
- filters
example:
name: "mycohort"
description: "Example description"
filters:
collection_id: ["tcga_luad", "tcga_kirc"]
Modality: ["CT", "MR"]
race: ["WHITE"]
age_at_diagnosis_btw: [65, 75]
cohortIdList:
type: "object"
properties:
cohorts:
type: "array"
items:
type: "integer"
minItems: 1
cohortCreateResponse:
type: "object"
properties:
cohort_properties:
type: "object"
properties:
cohort_id:
type: "string"
name:
type: "string"
description:
type: "string"
filter:
$ref: "#/definitions/filterSet"
code:
type: "integer"
timeoutResponse:
type: "object"
properties:
next_page:
type: "string"
message:
type: "string"
code:
type: "integer"
filterSet:
type: "object"
properties:
idc_data_version:
type: "string"
filters:
$ref: '#/definitions/filters'
filters:
type: "object"
properties:
project_short_name:
type: "array"
items:
type: "string"
minItems: 1
sample_type:
type: "array"
items:
type: "string"
minItems: 1
age_at_diagnosis_btw:
type: "array"
items:
type: "integer"
minItems: 2
maxItems: 2
age_at_diagnosis_ebtw:
type: "array"
items:
type: "integer"
minItems: 2
maxItems: 2
age_at_diagnosis_btwe:
type: "array"
items:
type: "integer"
minItems: 2
maxItems: 2
age_at_diagnosis_ebtwe:
type: "array"
items:
type: "integer"
minItems: 2
maxItems: 2
age_at_diagnosis_gte:
type: "array"
items:
type: "integer"
minItems: 1
maxItems: 1
age_at_diagnosis_lte:
type: "array"
items:
type: "integer"
minItems: 1
maxItems: 1
age_at_diagnosis_gt:
type: "array"
items:
type: "integer"
minItems: 1
maxItems: 1
age_at_diagnosis_lt:
type: "array"
items:
type: "integer"
minItems: 1
maxItems: 1
age_at_diagnosis_eq:
type: "array"
items:
type: "integer"
minItems: 1
maxItems: 1
bmi_btw:
type: "array"
items:
type: "number"
minItems: 2
maxItems: 2
bmi_ebtw:
type: "array"
items:
type: "number"
minItems: 2
maxItems: 2
bmi_btwe:
type: "array"
items:
type: "number"
minItems: 2
maxItems: 2
bmi_ebtwe:
type: "array"
items:
type: "number"
minItems: 2
maxItems: 2
bmi_gte:
type: "array"
items:
type: "number"
minItems: 1
maxItems: 1
bmi_lte:
type: "array"
items:
type: "number"
minItems: 1
maxItems: 1
bmi_gt:
type: "array"
items:
type: "number"
minItems: 1
maxItems: 1
bmi_lt:
type: "array"
items:
type: "number"
minItems: 1
maxItems: 1
bmi_eq:
type: "array"
items:
type: "number"
minItems: 1
maxItems: 1
country:
type: "array"
items:
type: "string"
minItems: 1
disease_code:
type: "array"
items:
type: "string"
minItems: 1
ethnicity:
type: "array"
items:
type: "string"
minItems: 1
gender:
type: "array"
items:
type: "string"
minItems: 1
histological_type:
type: "array"
items:
type: "string"
minItems: 1
pathologic_stage:
type: "array"
items:
type: "string"
minItems: 1
project_name:
type: "array"
items:
type: "string"
minItems: 1
race:
type: "array"
items:
type: "string"
minItems: 1
tumor_tissue_site:
type: "array"
items:
type: "string"
minItems: 1
vital_status:
type: "array"
items:
type: "string"
minItems: 1
analysis_results_id:
type: "array"
items:
type: "string"
minItems: 1
AnatomicRegionSequence:
type: "array"
items:
type: "string"
minItems: 1
Apparent_Diffusion_Coefficient_btw:
type: "array"
items:
type: "number"
minItems: 2
maxItems: 2
Apparent_Diffusion_Coefficient_ebtw:
type: "array"
items:
type: "number"
minItems: 2
maxItems: 2
Apparent_Diffusion_Coefficient_btwe:
type: "array"
items:
type: "number"
minItems: 2
maxItems: 2
Apparent_Diffusion_Coefficient_ebtwe:
type: "array"
items:
type: "number"
minItems: 2
maxItems: 2
Apparent_Diffusion_Coefficient_gte:
type: "array"
items:
type: "number"
minItems: 1
maxItems: 1
Apparent_Diffusion_Coefficient_lte:
type: "array"
items:
type: "number"
minItems: 1
maxItems: 1
Apparent_Diffusion_Coefficient_gt:
type: "array"
items:
type: "number"
minItems: 1
maxItems: 1
Apparent_Diffusion_Coefficient_lt:
type: "array"
items:
type: "number"
minItems: 1
maxItems: 1
Apparent_Diffusion_Coefficient_eq:
type: "array"
items:
type: "number"
minItems: 1
maxItems: 1
BodyPartExamined:
type: "array"
items:
type: "string"
minItems: 1
Calcification:
type: "array"
items:
type: "string"
minItems: 1
CancerType:
type: "array"
items:
type: "string"
minItems: 1
collection_id:
type: "array"
items:
type: "string"
minItems: 1
Diameter_btw:
type: "array"
items:
type: "number"
minItems: 2