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top-api.yml
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openapi: 3.0.0
info:
title: TOP API
version: 0.11.1
description: |-
API to manage phenotypes, repositories, ontologies, external terminologies and organisations and to execute phenotypic queries.
To interact with this API you need a JSON Web Token. You can request one as shown below with a curl example:
```sh
curl \
-d "client_id=top-frontend" \
-d "username=<USERNAME>" \
-d "password=<PASSWORD>" \
-d "grant_type=password" \
-X POST "https://top.imise.uni-leipzig.de/auth/realms/top-realm/protocol/openid-connect/token"
```
license:
name: MIT
url: 'https://github.com/Onto-Med/top-api/blob/main/LICENSE'
servers:
- url: 'https://top.imise.uni-leipzig.de/api'
description: Public demo server.
- url: 'http://localhost:8080'
description: Local development instance.
- url: 'http://host.docker.internal:8080'
description: In case the server is running on the Docker host.
paths:
/:
get:
operationId: ping
summary: Checks if the server is running and returns general description.
responses:
'200':
description: Server is up and running.
content:
application/json:
schema:
$ref: '#/components/schemas/AppDescription'
default:
$ref: '#/components/responses/UnexpectedError'
security:
- BearerAuth: []
/statistic:
summary: Get statistics about available content. Returned data may be cached.
get:
operationId: getStatistics
responses:
'200':
description: Object holding statistics.
content:
application/json:
schema:
$ref: '#/components/schemas/Statistic'
default:
$ref: '#/components/responses/UnexpectedError'
security:
- BearerAuth: []
/document:
get:
operationId: getDocuments
summary: Searches for documents.
parameters:
- $ref: '#/components/parameters/documentDataSource'
- name: name
in: query
description: Filter documents by name
schema:
type: string
- name: documentIds
in: query
description: Get only specific documents from a query
schema:
$ref: '#/components/schemas/StringArray'
- name: phraseIds
in: query
description: Filter documents by phrase ids that they are connected to
schema:
$ref: '#/components/schemas/StringArray'
- name: conceptClusterIds
in: query
description: Filter documents by the concept cluster ids to which they belong
schema:
$ref: '#/components/schemas/StringArray'
- name: phraseText
in: query
description: Filter documents by containing phrases (textual)
schema:
$ref: '#/components/schemas/StringArray'
- name: gatheringMode
in: query
description: 'Which gathering strategy for the documents regarding their concept cluster to employ (union, exclusive, intersection)'
schema:
$ref: '#/components/schemas/DocumentGatheringMode'
- name: exemplarOnly
in: query
description: Only gets documents if they contain phrases that are considered exemplary for the concept cluster
schema:
type: boolean
default: false
- $ref: '#/components/parameters/page'
- $ref: '#/components/parameters/include'
responses:
'200':
$ref: '#/components/responses/DocumentPageResponse'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- document
'/document/{documentId}':
summary: Represents a document
parameters:
- name: documentId
in: path
required: true
schema:
type: string
get:
operationId: getSingleDocumentById
summary: Returns a particular document
parameters:
- $ref: '#/components/parameters/documentDataSource'
- name: highlightConcepts
in: query
description: |
Highlights the terms that are connected to these concepts (given their id) in the resulting document.
A highlight color can be provided by prepending '$color::{COLORCODE; COLORSTRING}::color$'.
(e.g. [$color::#556b2f::color$21, $color::red::color$17])
schema:
$ref: '#/components/schemas/StringArray'
- $ref: '#/components/parameters/include'
responses:
'200':
$ref: '#/components/responses/Document'
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- document
'/document/query/{organisationId}/{repositoryId}/{queryId}':
get:
operationId: getDocumentsForQuery
summary: Get all document ids that were found in a query
parameters:
- $ref: '#/components/parameters/organisationId'
- $ref: '#/components/parameters/repositoryId'
- $ref: '#/components/parameters/queryId'
- $ref: '#/components/parameters/page'
responses:
'200':
$ref: '#/components/responses/DocumentPageResponse'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- document
/phrase:
get:
operationId: getPhrases
summary: Searches for phrases
parameters:
- $ref: '#/components/parameters/phraseText'
- name: conceptClusterId
in: query
description: Search phrase by a concept cluster id it is contained in
schema:
type: string
- $ref: '#/components/parameters/page'
responses:
'200':
$ref: '#/components/responses/PhrasePageResponse'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- phrase
'/phrase/{phraseId}':
summary: Represents a Phrase
parameters:
- name: phraseId
in: path
required: true
schema:
type: string
- $ref: '#/components/parameters/include'
get:
operationId: getPhraseById
summary: Returns a particular Phrase
responses:
'200':
$ref: '#/components/responses/Phrase'
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- phrase
'/phrase/document/{documentId}':
parameters:
- name: documentId
in: path
required: true
schema:
type: string
- $ref: '#/components/parameters/include'
get:
operationId: getPhrasesByDocumentId
summary: Searches for phrases that are contained in a specific document. Use the query parameters to filter the result.
parameters:
- $ref: '#/components/parameters/documentDataSource'
- $ref: '#/components/parameters/phraseText'
- $ref: '#/components/parameters/page'
responses:
'200':
$ref: '#/components/responses/PhrasePageResponse'
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- phrase
/conceptcluster:
get:
operationId: getConceptClusters
summary: Searches for specific concept clusters
parameters:
- name: labelsText
in: query
description: filter concept cluster by texts of its labels attribute
schema:
$ref: '#/components/schemas/StringArray'
- name: phraseId
in: query
description: filter concept cluster by ids of phrases it contains
schema:
$ref: '#/components/schemas/StringArray'
- name: recalculateCache
in: query
description: recalculate the cache of concept clusters (needed when new clusters were added due to some pipeline)
schema:
type: boolean
default: false
- $ref: '#/components/parameters/corpusId'
- $ref: '#/components/parameters/page'
- $ref: '#/components/parameters/include'
responses:
'200':
$ref: '#/components/responses/ConceptClusterPageResponse'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptcluster
/conceptcluster/corpora:
get:
operationId: getCorpusIds
summary: Get all corpus IDs.
responses:
'200':
description: Returns a distinct list of all the 'corpusIds' found in Concept Nodes.
content:
application/json:
schema:
$ref: '#/components/schemas/StringArray'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptcluster
'/conceptcluster/{conceptClusterId}':
summary: Represents a concept cluster
parameters:
- name: conceptClusterId
in: path
required: true
schema:
type: string
get:
operationId: getConceptClusterById
summary: Returns a particular concept cluster.
parameters:
- $ref: '#/components/parameters/corpusId'
- $ref: '#/components/parameters/include'
responses:
'200':
description: Details of the Concept cluster.
content:
application/json:
schema:
$ref: '#/components/schemas/ConceptCluster'
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptcluster
'/conceptcluster/document/{documentId}':
parameters:
- name: documentId
in: path
required: true
schema:
type: string
- $ref: '#/components/parameters/include'
get:
operationId: getConceptClusterByDocumentId
summary: Returns concept clusters for a specific document.
parameters:
- $ref: '#/components/parameters/documentDataSource'
- $ref: '#/components/parameters/page'
responses:
'200':
$ref: '#/components/responses/ConceptClusterPageResponse'
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptcluster
/concept_pipeline:
get:
operationId: getConceptGraphPipelines
summary: Returns all concept graph pipelines with some additional information.
responses:
'200':
description: An overview of all pipelines that are stored.
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/ConceptGraphPipeline'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptPipeline
post:
operationId: startConceptGraphPipeline
summary: |
Initialises a complete pipeline with all steps 'preprocessing', 'embedding', 'clustering' and 'graph creation'.
You can provide optional configuration files via the properties 'data', 'labels', 'dataConfig', 'embeddingConfig', 'clusteringConfig' and 'graphConfig'.
requestBody:
required: true
content:
multipart/form-data:
schema:
$ref: '#/components/schemas/ConceptPipelineRequest'
responses:
'200':
description: A short summary of the graphs created by this pipeline.
content:
application/json:
schema:
$ref: '#/components/schemas/PipelineResponse'
'202':
description: The POST request was accepted and a pipeline process started.
content:
application/json:
schema:
$ref: '#/components/schemas/PipelineResponse'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptPipeline
put:
operationId: startConceptGraphPipelineWithJson
summary: |
Initialises a complete pipeline with all steps 'preprocessing', 'embedding', 'clustering' and 'graph creation'.
Doesn't support file uploading; configuration is done via json body.
requestBody:
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/ConceptPipelineConfigRequest'
responses:
'200':
description: A short summary of the graphs created by this pipeline.
content:
application/json:
schema:
$ref: '#/components/schemas/PipelineResponse'
'202':
description: The PUT request was accepted and a pipeline process started.
content:
application/json:
schema:
$ref: '#/components/schemas/PipelineResponse'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptPipeline
'/concept_pipeline/{pipelineId}':
get:
operationId: getConceptGraphPipelineById
summary: Returns a pipeline description by its ID.
parameters:
- name: pipelineId
in: path
required: true
schema:
type: string
responses:
'200':
description: A description of the requested pipeline.
content:
application/json:
schema:
$ref: '#/components/schemas/ConceptGraphPipeline'
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptPipeline
delete:
operationId: deleteConceptPipelineById
summary: Deletes a whole concept pipeline and all concept clusters that resulted from it.
parameters:
- name: pipelineId
in: path
required: true
schema:
type: string
responses:
'202':
description: Pipeline has been deleted.
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptPipeline
/concept_pipeline/configuration:
get:
operationId: getConceptGraphPipelineConfiguration
summary: Returns either a default configuration or the configuration for a specific pipeline if an ID is given
parameters:
- name: pipelineId
in: query
required: false
schema:
type: string
- name: language
in: query
required: false
schema:
type: string
responses:
'200':
description: A configuration in JSON format
content:
application/json:
schema:
type: string
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptPipeline
'/concept_pipeline/{pipelineId}/stop':
get:
operationId: stopConceptGraphPipeline
summary: Stops the pipeline for this specific ID after the currently running step is finished
parameters:
- name: pipelineId
in: path
required: true
schema:
type: string
responses:
'202':
description: Pipeline will be stopped
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptPipeline
'/concept_pipeline/{pipelineId}/concept_cluster':
parameters:
- name: pipelineId
in: path
required: true
schema:
type: string
post:
operationId: createConceptClustersForPipelineId
summary: Create concept clusters from a pipeline that already built the concept graphs.
requestBody:
content:
application/json:
schema:
description: Only build concept clusters for the specified graphs.
type: array
items:
type: string
responses:
'200':
description: A short summary of the concept clusters created.
content:
application/json:
schema:
$ref: '#/components/schemas/PipelineResponse'
'202':
description: The request was accepted and a pipeline started to create the concept clusters.
content:
application/json:
schema:
$ref: '#/components/schemas/PipelineResponse'
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptcluster
delete:
operationId: deleteConceptClustersForPipelineId
summary: Delete all concept clusters that where derived from a concept pipeline.
responses:
'202':
description: Concept clusters where deleted.
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptcluster
'/concept_pipeline/{pipelineId}/concept_cluster/process':
get:
operationId: getConceptClusterProcess
summary: Checks the status of a specific Neo4j graph creation process
parameters:
- name: pipelineId
in: path
required: true
schema:
type: string
responses:
'200':
description: Returns a PipelineResponse object for the specified process
content:
application/json:
schema:
$ref: '#/components/schemas/PipelineResponse'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptcluster
'/concept_pipeline/{pipelineId}/concept_graph':
get:
operationId: getConceptGraphStatistics
summary: Returns an overview of the concept graphs for a pipeline.
parameters:
- name: pipelineId
in: path
required: true
schema:
type: string
responses:
'200':
description: A short summary of the graphs from a pipeline.
content:
application/json:
schema:
type: object
additionalProperties:
$ref: '#/components/schemas/ConceptGraphStat'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptPipeline
'/concept_pipeline/{pipelineId}/concept_graphs/{graphId}':
get:
operationId: getConceptGraph
summary: Get a specific Concept Graph for a pipeline by its ID.
parameters:
- name: pipelineId
in: path
required: true
schema:
type: string
- name: graphId
in: path
required: true
schema:
type: string
responses:
'200':
description: A graph object with node and adjacency information.
content:
application/json:
schema:
$ref: '#/components/schemas/ConceptGraph'
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- conceptPipeline
/organisation:
parameters:
- $ref: '#/components/parameters/include'
get:
operationId: getOrganisations
summary: Search for organisations. Use the query parameters to filter the result.
parameters:
- $ref: '#/components/parameters/nameFilter'
- $ref: '#/components/parameters/page'
responses:
'200':
$ref: '#/components/responses/OrganisationPageResponse'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- organisation
post:
operationId: createOrganisation
summary: Creates a new organisation.
requestBody:
description: Organisation details.
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/Organisation'
responses:
'201':
description: Created organisation.
content:
application/json:
schema:
$ref: '#/components/schemas/Organisation'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- organisation
/data_source:
get:
operationId: getDataSources
summary: Returns all available and accessible data sources. Only administrators should be able to perform this operation.
parameters:
- name: queryType
in: query
description: Filter by query type for which data sources can be used.
required: false
schema:
$ref: '#/components/schemas/QueryType'
responses:
'200':
description: List of data sources.
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/DataSource'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- query
post:
operationId: uploadDataSource
summary: |-
Reads the content of an uploaded file and loads contained data into a local data source of the framework.
If the specified data source already exists, data will be appended to that data source.
requestBody:
description: File to be loaded into the local data source.
required: true
content:
multipart/form-data:
schema:
type: object
properties:
file:
type: string
format: binary
fileType:
$ref: '#/components/schemas/DataSourceFileType'
dataSourceId:
description: ID of the local data source the data is to be loaded into.
type: string
config:
description: Additional configurations specific to the file type.
type: string
required:
- file
- fileType
- dataSourceId
responses:
'204':
description: Upload accepted.
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- query
'/data_source/{dataSourceId}':
delete:
operationId: deleteDataSource
summary: Delete an existing local data source.
parameters:
- name: dataSourceId
in: path
description: The ID of the local data source to be deleted.
required: true
schema:
type: string
responses:
'204':
description: Data source deleted.
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- query
'/{organisationId}':
summary: Represents an organisation.
parameters:
- $ref: '#/components/parameters/organisationId'
- $ref: '#/components/parameters/include'
get:
operationId: getOrganisationById
summary: Returns a particular organisation by ID.
responses:
'200':
description: Details of the organisation.
content:
application/json:
schema:
$ref: '#/components/schemas/Organisation'
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- organisation
patch:
operationId: updateOrganisationById
summary: Updates a particular organisation by ID and returns the result.
requestBody:
description: Organisation details to be applied.
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/Organisation'
responses:
'200':
description: Details about the updated organisation.
content:
application/json:
schema:
$ref: '#/components/schemas/Organisation'
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- organisation
delete:
operationId: deleteOrganisationById
summary: Deletes a particular organisation by ID.
responses:
'204':
description: The organisation was deleted successfully.
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- organisation
'/{organisationId}/data_source':
summary: Represents a data source available to a specific organisation.
parameters:
- $ref: '#/components/parameters/organisationId'
get:
operationId: getOrganisationDataSources
summary: Returns all available and accessible data sources for a specific organisation.
parameters:
- name: queryType
in: query
description: Filter by query type for which data sources can be used.
required: false
schema:
$ref: '#/components/schemas/QueryType'
responses:
'200':
description: List of data sources.
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/DataSource'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- query
post:
operationId: addOrganisationDataSource
summary: 'Add a new data source, available to a specific organisation. Only administrators should be able to perform this operation.'
requestBody:
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/DataSource'
responses:
'201':
description: Data source has been added to the set.
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- query
delete:
operationId: removeOrganisationDataSource
summary: Remove a data source from the set of available data sources of a specific organisation. Only administrators should be able to perform this operation.
requestBody:
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/DataSource'
responses:
'204':
description: Data source has been removed from the set.
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- query
/repository:
parameters:
- $ref: '#/components/parameters/include'
get:
operationId: getRepositories
summary: Search for repositories. Use the query parameters to filter the result.
parameters:
- $ref: '#/components/parameters/nameFilter'
- $ref: '#/components/parameters/primaryFilter'
- $ref: '#/components/parameters/repositoryTypeFilter'
- $ref: '#/components/parameters/page'
responses:
'200':
$ref: '#/components/responses/RepositoryPageResponse'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- repository
/entity:
parameters:
- $ref: '#/components/parameters/include'
get:
operationId: getEntities
summary: |
Search for entities (phenotypes, categories or concepts). Use the query parameters to filter the result.
Only entities in primary repositories are returned.
parameters:
- $ref: '#/components/parameters/nameFilter'
- $ref: '#/components/parameters/entityTypesFilter'
- $ref: '#/components/parameters/dataTypeFilter'
- $ref: '#/components/parameters/itemTypeFilter'
- $ref: '#/components/parameters/repositoryIdsFilter'
- name: includePrimary
in: query
description: |
Include all primary repositories in search. You can use this option in conjunction
with "repositoryIds" query parameter, which will add all primary repositories to the
list of searched repositories.
schema:
type: boolean
default: false
- $ref: '#/components/parameters/page'
responses:
'200':
$ref: '#/components/responses/EntityPageResponse'
'401':
$ref: '#/components/responses/Unauthorized'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- entity
'/{organisationId}/repository':
parameters:
- $ref: '#/components/parameters/organisationId'
- $ref: '#/components/parameters/include'
get:
operationId: getRepositoriesByOrganisationId
summary: Search for repositories in an organisation. Use the query parameters to filter the result.
parameters:
- $ref: '#/components/parameters/nameFilter'
- $ref: '#/components/parameters/repositoryTypeFilter'
- $ref: '#/components/parameters/page'
responses:
'200':
$ref: '#/components/responses/RepositoryPageResponse'
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- repository
post:
operationId: createRepository
summary: Creates new repository in organisation.
requestBody:
description: Repository details.
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/Repository'
responses:
'201':
description: Created repository.
content:
application/json:
schema:
$ref: '#/components/schemas/Repository'
'401':
$ref: '#/components/responses/Unauthorized'
'404':
$ref: '#/components/responses/NotFound'
default:
$ref: '#/components/responses/UnexpectedError'
tags:
- repository
'/{organisationId}/membership':
summary: Manage organisation memberships.
parameters:
- $ref: '#/components/parameters/organisationId'
get: