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openapi_public.yaml
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openapi_public.yaml
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openapi: 3.0.1
info:
title: ICA Rest API
description: "This API can be used to interact with Illumina Connected Analytics.<br>\n\
<h2>Authentication</h2>\n<p>\nAuthentication to the API can be done in multiple\
\ ways:<br>\n<ul><li>For the entire API, except for the POST /tokens endpoint:\
\ API-key + JWT</li>\n<li>Only for the POST /tokens endpoint: API-key + Basic\
\ Authentication</li></ul>\n</p>\n<p>\n<h4>API-key</h4>\nAPI keys are managed\
\ within the Illumina portal where you can manage your profile after you have\
\ logged on. The API-key has to be provided in the X-API-Key header parameter\
\ when executing API calls to ICA. In the background, a JWT will be requested\
\ at the IDP of Illumina to create a session. A good practice is to not use the\
\ API-key for every API call, but to first generate a JWT and to use that for\
\ authentication in subsequent calls.<br>\n</p>\n<p>\n<h4>JWT</h4>\nTo avoid using\
\ an API-key for each call, we recommend to request a JWT via the POST /tokens\
\ endpoint using this API-key. The JWT will expire after a pre-configured period\
\ specified by a tenant administrator through the IAM console in the Illumina\
\ portal. The JWT is the preferred way for authentication.<br>A not yet expired,\
\ still valid JWT could be refreshed using the POST /tokens:refresh endpoint.<br>Refreshing\
\ the JWT is not possible if the JWT was generated by using an API-key.<br>\n\
</p>\n<p>\n<h4>Basic Authentication</h4>\nBasic authentication is only supported\
\ by the POST /tokens endpoint for generating a JWT. Use \"Basic base64encoded(emailaddress:password)\"\
\ in the \"Authorization\" header parameter for this authentication method. In\
\ case having access to multiple tenants using the same email-address, also provide\
\ the \"tenant\" request parameter to indicate what tenant you would like to request\
\ a JWT for.\n</p>\n<p>\n<h2>Compression</h2>\nIf the API client provides request\
\ header 'Accept-Encoding' with value 'gzip', then the API applies GZIP compression\
\ on the JSON response. This significantly reduces the size and thus the download\
\ time of the response, which results in faster end-to-end API calls. In case\
\ of compression, the API also provides response header 'Content-Encoding' with\
\ value 'gzip', as indication for the client that decompression is required.\n\
</p>\n"
version: "3"
servers:
- url: /ica/rest
security:
- JwtAuth: []
- ApiKeyAuth: []
paths:
/api/analysisStorages:
get:
tags:
- Analysis Storage
summary: Retrieve the list of analysis storage options.
operationId: getAnalysisStorageOptions
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"200":
description: The list of analysis storage options is successfully retrieved.
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/AnalysisStorageList'
/api/bundles:
get:
tags:
- Bundle
summary: Retrieve a list of bundles.
operationId: getBundles
parameters:
- name: search
in: query
description: Search
schema:
type: string
- name: userTags
in: query
description: User tags to filter on
schema:
type: string
- name: technicalTags
in: query
description: Technical tags to filter on
schema:
type: string
- name: pageOffset
in: query
description: The amount of rows to skip in the result. Ideally this is a multiple
of the size parameter. Offset-based pagination has a result limit of 200K
rows and does not guarantee unique results across pages
schema:
type: string
- name: pageToken
in: query
description: The cursor to get subsequent results. The value to use is returned
in the result when using cursor-based pagination. Cursor-based pagination
guarantees complete and unique results across all pages.
schema:
type: string
- name: pageSize
in: query
description: The amount of rows to return. Use in combination with the offset
or cursor parameter to get subsequent results.
schema:
type: string
- name: sort
in: query
description: "Which field to order the results by. The default order is ascending,\
\ suffix with ' desc' to sort descending (suffix ' asc' also works for ascending).\
\ Multiple values should be separated with commas. An example: \"?sort=dateCreated,\
\ lastName desc\"\n\nThe attributes for which sorting is supported:\n- name\n\
- shortDescription"
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"200":
description: The list of bundles is successfully retrieved.
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/BundlePagedList'
post:
tags:
- Bundle
summary: Create a new bundle
operationId: createBundle
requestBody:
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/CreateBundle'
application/json:
schema:
$ref: '#/components/schemas/CreateBundle'
required: true
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"201":
description: The bundle is successfully created.
headers:
ETag:
description: The current version of the resource. Can be passed to the
corresponding PUT endpoint to enable conflict exposure (409 response).
style: simple
schema:
type: string
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/Bundle'
/api/bundles/{bundleId}:
get:
tags:
- Bundle
summary: Retrieve a bundle.
operationId: getBundle
parameters:
- name: bundleId
in: path
description: The ID of the bundle to retrieve
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"200":
description: The bundle is successfully retrieved.
headers:
ETag:
description: The current version of the resource. Can be passed to the
corresponding PUT endpoint to enable conflict exposure (409 response).
style: simple
schema:
type: string
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/Bundle'
/api/bundles/{bundleId}/termsOfUse:accept:
post:
tags:
- Bundle
summary: accept terms of use for a bundle
operationId: acceptTermsOfUseBundle
parameters:
- name: bundleId
in: path
description: The ID of the bundle where the terms of use are accepted of.
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"204":
description: The terms of use of the bundle is accepted
content:
application/vnd.illumina.v3+json: {}
/api/bundles/{bundleId}:release:
post:
tags:
- Bundle
summary: release a bundle
operationId: releaseBundle
parameters:
- name: bundleId
in: path
description: The ID of the bundle to release
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"204":
description: The bundle is successfully released
content:
application/vnd.illumina.v3+json: {}
/api/bundles/{bundleId}/termsOfUse:
get:
tags:
- Bundle
summary: Retrieve the last version of terms of use for a bundle.
operationId: getBundleTermsOfUse
parameters:
- name: bundleId
in: path
description: The ID of the bundle of the terms of use to retrieve
required: true
schema:
type: string
format: uuid
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"200":
description: Terms of use are successfully retrieved.
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/TermsOfUse'
/api/bundles/{bundleId}/termsOfUse/userAcceptance/currentUser:
get:
tags:
- Bundle
summary: Retrieve the acceptance record for a bundle for the current user.
operationId: getTermsOfUseAcceptance
parameters:
- name: bundleId
in: path
description: The ID of the bundle of the terms of use acceptance records.
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"200":
description: Terms of use acceptance is successfully retrieved.
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/TermsOfUseAcceptance'
/api/bundles/{bundleId}/termsOfUse:new:
post:
tags:
- Bundle
summary: Insert a new version of the terms of use for a bundle
operationId: insertBundleTermsOfUse
parameters:
- name: bundleId
in: path
description: The ID of the bundle to update
required: true
schema:
type: string
format: uuid
requestBody:
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/CreateTermsOfUse'
application/x-www-form-urlencoded:
schema:
$ref: '#/components/schemas/CreateTermsOfUse'
application/json:
schema:
$ref: '#/components/schemas/CreateTermsOfUse'
required: true
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"200":
description: A new version of the terms of use are successfully created.
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/TermsOfUse'
/api/bundles/{bundleId}:deprecate:
post:
tags:
- Bundle
summary: deprecate a bundle
operationId: deprecateBundle
parameters:
- name: bundleId
in: path
description: The ID of the bundle to deprecate.
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"204":
description: The bundle is successfully deprecated.
content:
application/vnd.illumina.v3+json: {}
/api/bundles/{bundleId}/data:
get:
tags:
- Bundle Data
summary: Retrieve the list of bundle data.
operationId: getBundleData
parameters:
- name: fullText
in: query
description: To search through multiple fields of data.
schema:
type: string
- name: id
in: query
description: The ids to filter on. This will always match exact.
schema:
type: string
- name: filename
in: query
description: The filenames to filter on. The filenameMatchMode-parameter determines
how the filtering is done.
schema:
type: string
- name: filenameMatchMode
in: query
description: How the filenames are filtered.
schema:
type: string
enum:
- EXACT
- EXCLUDE
- FUZZY
- name: filePath
in: query
description: The paths of the files to filter on.
schema:
type: string
- name: filePathMatchMode
in: query
description: "How the file paths are filtered: \n - STARTS_WITH_CASE_INSENSITIVE:\
\ Filters the file path to start with the value of the 'filePath' parameter,\
\ regardless of upper/lower casing. This allows e.g. listing all data in\
\ a folder and all it's sub-folders (recursively).\n - FULL_CASE_INSENSITIVE:\
\ Filters the file path to fully match the value of the 'filePath' parameter,\
\ regardless of upper/lower casing. Note that this can result in multiple\
\ results if e.g. two files exist with the same filename but different casing\
\ (abc.txt and ABC.txt)."
schema:
type: string
default: STARTS_WITH_CASE_INSENSITIVE
enum:
- STARTS_WITH_CASE_INSENSITIVE
- FULL_CASE_INSENSITIVE
- name: status
in: query
description: The statuses to filter on.
schema:
type: string
enum:
- PARTIAL
- AVAILABLE
- ARCHIVING
- ARCHIVED
- UNARCHIVING
- DELETING
- name: formatId
in: query
description: The IDs of the formats to filter on.
schema:
type: string
- name: formatCode
in: query
description: The codes of the formats to filter on.
schema:
type: string
- name: type
in: query
description: The type to filter on.
schema:
type: string
enum:
- FILE
- FOLDER
- name: parentFolderId
in: query
description: "The IDs of parents folders to filter on. Lists all files and\
\ folders within the folder for the given ID, non-recursively."
schema:
type: string
- name: parentFolderPath
in: query
description: "The full path of the parent folder. Should start and end with\
\ a '/'. Lists all files and folders within the folder for the given path,\
\ non-recursively. This can be used to browse through the hierarchical tree\
\ of folders, e.g. traversing one level up can be done by removing the last\
\ part of the path."
schema:
type: string
- name: creationDateAfter
in: query
description: "The date after which the data is created. Format: yyyy-MM-dd'T'HH:mm:ss'Z'\
\ eg: 2021-01-30T08:30:00Z"
schema:
type: string
- name: creationDateBefore
in: query
description: "The date before which the data is created. Format: yyyy-MM-dd'T'HH:mm:ss'Z'\
\ eg: 2021-01-30T08:30:00Z"
schema:
type: string
- name: statusDateAfter
in: query
description: "The date after which the status has been updated. Format: yyyy-MM-dd'T'HH:mm:ss'Z'\
\ eg: 2021-01-30T08:30:00Z"
schema:
type: string
- name: statusDateBefore
in: query
description: "The date before which the status has been updated Format: yyyy-MM-dd'T'HH:mm:ss'Z'\
\ eg: 2021-01-30T08:30:00Z"
schema:
type: string
- name: userTag
in: query
description: The usertags to filter on. The userTagMatchMode-parameter determines
how the filtering is done.
schema:
type: string
- name: userTagMatchMode
in: query
description: How the usertags are filtered.
schema:
type: string
enum:
- EXACT
- EXCLUDE
- FUZZY
- name: runInputTag
in: query
description: The runInputTags to filter on. The runInputTagMatchMode-parameter
determines how the filtering is done.
schema:
type: string
- name: runInputTagMatchMode
in: query
description: How the runInputTags are filtered.
schema:
type: string
enum:
- EXACT
- EXCLUDE
- FUZZY
- name: runOutputTag
in: query
description: The runOutputTags to filter on. The runOutputTagMatchMode-parameter
determines how the filtering is done.
schema:
type: string
- name: runOutputTagMatchMode
in: query
description: How the runOutputTags are filtered.
schema:
type: string
enum:
- EXACT
- EXCLUDE
- FUZZY
- name: connectorTag
in: query
description: The connectorTags to filter on. The connectorTagMatchMode-parameter
determines how the filtering is done.
schema:
type: string
- name: connectorTagMatchMode
in: query
description: How the connectorTags are filtered.
schema:
type: string
enum:
- EXACT
- EXCLUDE
- FUZZY
- name: technicalTag
in: query
description: The technicalTags to filter on. The techTagMatchMode-parameter
determines how the filtering is done.
schema:
type: string
- name: technicalTagMatchMode
in: query
description: How the technicalTags are filtered.
schema:
type: string
enum:
- EXACT
- EXCLUDE
- FUZZY
- name: notInRun
in: query
description: "When set to true, the data will be filtered on data which is\
\ not used in a run."
schema:
type: string
- name: notLinkedToSample
in: query
description: When set to true only date that is unlinked to a sample will
be returned. This filter implies a filter of type File.
schema:
type: string
- name: instrumentRunId
in: query
description: The instrument run IDs of the sequencing runs to filter on.
schema:
type: array
items:
type: string
- name: pageOffset
in: query
description: The amount of rows to skip in the result. Ideally this is a multiple
of the size parameter. Offset-based pagination has a result limit of 200K
rows and does not guarantee unique results across pages
schema:
type: string
- name: pageToken
in: query
description: The cursor to get subsequent results. The value to use is returned
in the result when using cursor-based pagination. Cursor-based pagination
guarantees complete and unique results across all pages.
schema:
type: string
- name: pageSize
in: query
description: The amount of rows to return. Use in combination with the offset
or cursor parameter to get subsequent results.
schema:
type: string
- name: sort
in: query
description: "Which field to order the results by. The default order is ascending,\
\ suffix with ' desc' to sort descending (suffix ' asc' also works for ascending).\
\ Multiple values should be separated with commas. An example: \"?sort=dateCreated,\
\ lastName desc\"\n\nThe attributes for which sorting is supported:\n- timeCreated\n\
- timeModified\n- name\n- path\n- fileSizeInBytes\n- status\n- format\n\
- dataType\n- willBeArchivedAt\n- willBeDeletedAt"
schema:
type: string
- name: bundleId
in: path
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"200":
description: The list of bundle data is successfully retrieved.
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/BundleDataPagedList'
/api/bundles/{bundleId}/data/{dataId}:
post:
tags:
- Bundle Data
summary: Link data to this bundle.
operationId: linkDataToBundle
parameters:
- name: bundleId
in: path
required: true
schema:
type: string
- name: dataId
in: path
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"204":
description: The data is successfully linked to this bundle.
content:
application/vnd.illumina.v3+json: {}
delete:
tags:
- Bundle Data
summary: Unlink data from this bundle.
operationId: unlinkDataFromBundle
parameters:
- name: bundleId
in: path
required: true
schema:
type: string
- name: dataId
in: path
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"204":
description: The data is successfully unlinked from this bundle.
content:
application/vnd.illumina.v3+json: {}
/api/bundles/{bundleId}/pipelines:
get:
tags:
- Bundle Pipeline
summary: Retrieve a list of bundle pipelines.
operationId: getBundlePipelines
parameters:
- name: bundleId
in: path
description: The ID of the bundle to retrieve pipelines for
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"200":
description: The list of bundle pipelines is successfully retrieved.
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/BundlePipelineList'
/api/bundles/{bundleId}/pipelines/{pipelineId}:
post:
tags:
- Bundle Pipeline
summary: Link a pipeline to a bundle.
operationId: linkPipelineToBundle
parameters:
- name: bundleId
in: path
description: The ID of the bundle
required: true
schema:
type: string
- name: pipelineId
in: path
description: The ID of the pipeline
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"204":
description: The pipeline is successfully linked to the bundle.
content:
application/vnd.illumina.v3+json: {}
delete:
tags:
- Bundle Pipeline
summary: Unlink a pipeline from a bundle.
operationId: unlinkPipelineFromBundle
parameters:
- name: bundleId
in: path
description: The ID of the bundle
required: true
schema:
type: string
- name: pipelineId
in: path
description: The ID of the pipeline
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"204":
description: The pipeline is successfully unlinked from the bundle.
content:
application/vnd.illumina.v3+json: {}
/api/bundles/{bundleId}/samples:
get:
tags:
- Bundle Sample
summary: Retrieve a list of bundle samples.
operationId: getBundleSamples
parameters:
- name: search
in: query
description: To search through multiple fields of data.
schema:
type: string
- name: userTags
in: query
description: The user tags to filter on.
schema:
type: string
- name: technicalTags
in: query
description: The technical tags to filter on.
schema:
type: string
- name: pageOffset
in: query
description: The amount of rows to skip in the result. Ideally this is a multiple
of the size parameter. Offset-based pagination has a result limit of 200K
rows and does not guarantee unique results across pages
schema:
type: string
- name: pageToken
in: query
description: The cursor to get subsequent results. The value to use is returned
in the result when using cursor-based pagination. Cursor-based pagination
guarantees complete and unique results across all pages.
schema:
type: string
- name: pageSize
in: query
description: The amount of rows to return. Use in combination with the offset
or cursor parameter to get subsequent results.
schema:
type: string
- name: sort
in: query
description: "Which field to order the results by. The default order is ascending,\
\ suffix with ' desc' to sort descending (suffix ' asc' also works for ascending).\
\ Multiple values should be separated with commas. An example: \"?sort=dateCreated,\
\ lastName desc\"\nThe attributes for which sorting is supported:\n- timeCreated\n\
- timeModified\n- name\n- description\n- metadataValid\n- status"
schema:
type: string
- name: bundleId
in: path
description: The ID of the bundle to get bundle samples from
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"200":
description: The list of bundle samples are successfully retrieved.
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/BundleSamplePagedList'
/api/bundles/{bundleId}/samples/{sampleId}:
post:
tags:
- Bundle Sample
summary: Link a sample to a bundle.
operationId: linkSampleToBundle
parameters:
- name: bundleId
in: path
required: true
schema:
type: string
- name: sampleId
in: path
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"204":
description: The sample is successfully linked to the bundle.
content:
application/vnd.illumina.v3+json: {}
delete:
tags:
- Bundle Sample
summary: Unlink a sample from a bundle.
operationId: unlinkSampleFromBundle
parameters:
- name: bundleId
in: path
required: true
schema:
type: string
- name: sampleId
in: path
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"204":
description: The sample is successfully unlinked from the bundle.
content:
application/vnd.illumina.v3+json: {}
/api/bundles/{bundleId}/tools:
get:
tags:
- Bundle Tool
summary: Retrieve a list of bundle tools.
operationId: getBundleTools
parameters:
- name: bundleId
in: path
description: The ID of the bundle to get tools from
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"200":
description: The list of bundle tools is successfully retrieved.
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/BundleToolsList'
/api/bundles/{bundleId}/tools/eligibleForLinking:
get:
tags:
- Bundle Tool
summary: Retrieve a list of tools eligible for linking to the bundle.
operationId: getToolsEligibleForLinkingToBundle
parameters:
- name: bundleId
in: path
description: The ID of the bundle to get the eligible tools for
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"200":
description: The list of tools is successfully retrieved.
content:
application/vnd.illumina.v3+json:
schema:
$ref: '#/components/schemas/CwlToolDefinitionList'
/api/bundles/{bundleId}/tools/{toolId}:
post:
tags:
- Bundle Tool
summary: Link a tool to a bundle
operationId: linkToolToBundle
parameters:
- name: bundleId
in: path
description: The ID of the bundle to link the tool to
required: true
schema:
type: string
- name: toolId
in: path
description: The ID of the tool to link
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"204":
description: The tool is successfully linked to the bundle.
content:
application/vnd.illumina.v3+json: {}
delete:
tags:
- Bundle Tool
summary: Unlink a tool from this bundle.
operationId: unlinkToolFromBundle
parameters:
- name: bundleId
in: path
required: true
schema:
type: string
- name: toolId
in: path
required: true
schema:
type: string
responses:
default:
description: A problem occurred.
content:
application/problem+json:
schema:
$ref: '#/components/schemas/Problem'
"204":
description: The tool is successfully unlinked from this bundle.
content:
application/vnd.illumina.v3+json: {}
/api/connectors:
get:
tags:
- Connector
summary: Retrieve a list of connectors.
operationId: getConnectors
parameters:
- name: activeOnly
in: query