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ccf-api-spec.yaml
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openapi: "3.0.3"
info:
title: CCF-API
description: |
This API provides programmatic access to data registered to the CCF.
See the [HuBMAP CCF Portal](https://hubmapconsortium.github.io/ccf/) for details.
version: 1.0.0
servers:
- description: CCF-API
url: /v1
- description: Production Server (backup)
url: https://ccf-api.hubmapconsortium.org/v1
- description: Staging Server
url: https://r5i95k35v5.us-east-2.awsapprunner.com/v1
x-preprocessor:
description: |
For some openapi-generator-cli generators our custom preprocessor
has to be employed to "fix" this specification to circumvent
inconsistencies/bugs in the generated code.
The preprocessor uses `x-preprocessor-` properties to determine
which operation to apply and where to apply it.
operations:
delete: |
Delete one or more properties at the specified paths.
Will also delete the property from the `required` list if applicable.
paths:
/db-status:
get:
summary: Get current status of database
operationId: db-status
parameters:
- $ref: "#/components/parameters/Token"
responses:
"200": { $ref: "#/components/responses/DatabaseStatus" }
/sparql:
get:
summary: Run a SPARQL query
operationId: sparql
parameters:
- $ref: "#/components/parameters/Query"
- $ref: "#/components/parameters/Token"
- $ref: "#/components/parameters/Format"
responses:
"200": { $ref: "#/components/responses/SparqlResponse"}
post:
summary: Run a SPARQL query (POST)
operationId: sparql-post
requestBody: { $ref: "#/components/requestBodies/SparqlQuery" }
parameters:
- $ref: "#/components/parameters/Token"
- $ref: "#/components/parameters/Format"
responses:
"200": { $ref: "#/components/responses/SparqlResponse"}
/aggregate-results:
get:
summary: Get aggregate results / statistics
operationId: aggregate-results
parameters:
- $ref: "#/components/parameters/Age"
- $ref: "#/components/parameters/AgeRange"
- $ref: "#/components/parameters/Bmi"
- $ref: "#/components/parameters/BmiRange"
- $ref: "#/components/parameters/Cache"
- $ref: "#/components/parameters/OntologyTerms"
- $ref: "#/components/parameters/CellTypeTerms"
- $ref: "#/components/parameters/Providers"
- $ref: "#/components/parameters/Sex"
- $ref: "#/components/parameters/SpatialSearches"
- $ref: "#/components/parameters/Technologies"
- $ref: "#/components/parameters/Token"
responses:
"200": { $ref: "#/components/responses/AggregateResults" }
/get-spatial-placement:
post:
summary: Given a SpatialEntity already placed relative to a reference SpatialEntity, retrieve a new direct SpatialPlacement to the given SpatialEntity IRI
operationId: get-spatial-placement
requestBody: { $ref: "#/components/requestBodies/GetSpatialPlacement" }
responses:
"200": { $ref: "#/components/responses/SpatialPlacement" }
"404": { $ref: "#/components/responses/ErrorMessage" }
"500": { $ref: "#/components/responses/ErrorMessage" }
/hubmap/rui_locations.jsonld:
get:
summary: Get all hubmap rui locations (if enabled)
description: This option is only enabled if HUBMAP_ROUTES=true in the environment
operationId: hubmap-rui-locations
parameters:
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/Token'
responses:
"200":
description: Successful operation
content:
application/json:
schema:
type: object
"404":
description: Not found due to option being disabled
/ontology-term-occurences:
get:
summary: Get number of ontology term occurrences for a search
operationId: ontology-term-occurences
parameters:
- $ref: "#/components/parameters/Age"
- $ref: "#/components/parameters/AgeRange"
- $ref: "#/components/parameters/Bmi"
- $ref: "#/components/parameters/BmiRange"
- $ref: "#/components/parameters/Cache"
- $ref: "#/components/parameters/OntologyTerms"
- $ref: "#/components/parameters/CellTypeTerms"
- $ref: "#/components/parameters/Providers"
- $ref: "#/components/parameters/Sex"
- $ref: "#/components/parameters/SpatialSearches"
- $ref: "#/components/parameters/Technologies"
- $ref: "#/components/parameters/Token"
responses:
"200": { $ref: "#/components/responses/TermOccurences" }
/cell-type-term-occurences:
get:
summary: Get number of cell type term occurrences for a search
operationId: cell-type-term-occurences
parameters:
- $ref: "#/components/parameters/Age"
- $ref: "#/components/parameters/AgeRange"
- $ref: "#/components/parameters/Bmi"
- $ref: "#/components/parameters/BmiRange"
- $ref: "#/components/parameters/Cache"
- $ref: "#/components/parameters/OntologyTerms"
- $ref: "#/components/parameters/CellTypeTerms"
- $ref: "#/components/parameters/Providers"
- $ref: "#/components/parameters/Sex"
- $ref: "#/components/parameters/SpatialSearches"
- $ref: "#/components/parameters/Technologies"
- $ref: "#/components/parameters/Token"
responses:
"200": { $ref: "#/components/responses/TermOccurences" }
/ontology-tree-model:
get:
summary: Get ontology term tree nodes
operationId: ontology-tree-model
parameters:
- $ref: "#/components/parameters/Cache"
- $ref: "#/components/parameters/Token"
responses:
"200": { $ref: "#/components/responses/OntologyTree" }
/cell-type-tree-model:
get:
summary: Get cell type tree nodes
operationId: cell-type-tree-model
parameters:
- $ref: "#/components/parameters/Cache"
- $ref: "#/components/parameters/Token"
responses:
"200": { $ref: "#/components/responses/OntologyTree" }
/provider-names:
get:
summary: Get tissue provider names (for filtering)
operationId: provider-names
parameters:
- $ref: "#/components/parameters/Cache"
- $ref: "#/components/parameters/Token"
responses:
"200": { $ref: "#/components/responses/Strings" }
/reference-organs:
get:
summary: Get all reference organs
operationId: reference-organs
parameters:
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/Token'
responses:
"200": { $ref: "#/components/responses/SpatialEntities" }
/reference-organ-scene:
get:
summary: Get all nodes to form the 3D scene for an organ
operationId: reference-organ-scene
parameters:
- $ref: "#/components/parameters/Age"
- $ref: "#/components/parameters/AgeRange"
- $ref: "#/components/parameters/Bmi"
- $ref: "#/components/parameters/BmiRange"
- $ref: "#/components/parameters/Cache"
- $ref: "#/components/parameters/OntologyTerms"
- $ref: "#/components/parameters/CellTypeTerms"
- $ref: "#/components/parameters/OrganIri"
- $ref: "#/components/parameters/Providers"
- $ref: "#/components/parameters/Sex"
- $ref: "#/components/parameters/SpatialSearches"
- $ref: "#/components/parameters/Technologies"
- $ref: "#/components/parameters/Token"
responses:
"200": { $ref: "#/components/responses/SpatialSceneNodes" }
/scene:
get:
summary: Get all nodes to form the 3D scene of reference body, organs, and tissues
operationId: scene
parameters:
- $ref: "#/components/parameters/Age"
- $ref: "#/components/parameters/AgeRange"
- $ref: "#/components/parameters/Bmi"
- $ref: "#/components/parameters/BmiRange"
- $ref: "#/components/parameters/Cache"
- $ref: "#/components/parameters/OntologyTerms"
- $ref: "#/components/parameters/CellTypeTerms"
- $ref: "#/components/parameters/Providers"
- $ref: "#/components/parameters/Sex"
- $ref: "#/components/parameters/SpatialSearches"
- $ref: "#/components/parameters/Technologies"
- $ref: "#/components/parameters/Token"
responses:
"200": { $ref: "#/components/responses/SpatialSceneNodes" }
/technology-names:
get:
summary: Get technology names (for filtering)
operationId: technology-names
parameters:
- $ref: "#/components/parameters/Cache"
- $ref: "#/components/parameters/Token"
responses:
"200": { $ref: "#/components/responses/Strings" }
/tissue-blocks:
get:
summary: Get Tissue Block Results
operationId: tissue-blocks
parameters:
- $ref: "#/components/parameters/Age"
- $ref: "#/components/parameters/AgeRange"
- $ref: "#/components/parameters/Bmi"
- $ref: "#/components/parameters/BmiRange"
- $ref: "#/components/parameters/Cache"
- $ref: "#/components/parameters/OntologyTerms"
- $ref: "#/components/parameters/CellTypeTerms"
- $ref: "#/components/parameters/Providers"
- $ref: "#/components/parameters/Sex"
- $ref: "#/components/parameters/SpatialSearches"
- $ref: "#/components/parameters/Technologies"
- $ref: "#/components/parameters/Token"
responses:
"200": { $ref: "#/components/responses/TissueBlocks" }
/gtex/rui_locations.jsonld:
get:
summary: Get all GTEx rui locations (if enabled)
description: This option is only enabled if GTEX_ROUTES=true in the environment
operationId: gtex-rui-locations
parameters:
- $ref: "#/components/parameters/Cache"
responses:
"200":
description: Successful operation
content:
application/json:
schema:
type: object
components:
parameters:
Age:
name: age
description: Filter result by age.
in: query
required: false
schema: { $ref: "#/components/schemas/MinMax" }
AgeRange:
name: age-range
description: Filter result by age.
in: query
deprecated: true
required: false
schema:
type: string
example: 10,100
Bmi:
name: bmi
description: Filter result by bmi.
in: query
required: false
schema: { $ref: "#/components/schemas/MinMax" }
BmiRange:
name: bmi-range
description: Filter result by bmi.
in: query
deprecated: true
required: false
schema:
type: string
example: 0,40
SpatialSearches:
name: spatial
description: Filter result by spatial searches.
in: query
required: false
schema:
type: array
items:
{ $ref: "#/components/schemas/SpatialSearch" }
example:
- { x: 10, y: 10, z: 10, radius: 100, target: 'http://purl.org/ccf/latest/ccf.owl#VHMale' }
- { x: 11, y: 11, z: 11, radius: 101, target: 'http://purl.org/ccf/latest/ccf.owl#VHFemale' }
Cache:
name: cache
description: Hint to cache (or not) the response of this request
in: query
required: false
schema:
type: boolean
default: true
OntologyTerms:
name: ontology-terms
description: Filter result by ontology terms.
in: query
required: false
schema:
title: Terms
type: array
items:
type: string
CellTypeTerms:
name: cell-type-terms
description: Filter result by ontology terms.
in: query
required: false
schema:
title: Terms
type: array
items:
type: string
OrganIri:
name: organ-iri
description: Filter result by organ.
in: query
required: true
schema:
type: string
Providers:
name: providers
description: Filter result by providers.
in: query
required: false
schema:
title: Providers
type: array
items:
type: string
Sex:
name: sex
description: Filter result by sex.
in: query
required: false
schema:
type: string
enum:
- both
- female
- male
Technologies:
name: technologies
description: Filter result by technologies.
in: query
required: false
schema:
title: Technologies
type: array
items:
type: string
Query:
name: query
description: SPARQL query to use
in: query
required: true
schema:
type: string
example: "SELECT * WHERE { ?sub ?pred ?obj . } LIMIT 10"
Token:
name: token
description: Authentication token to use for authenticated searches
in: query
required: false
schema:
type: string
Format:
name: format
description: Override SPARQL response format (Note that not all formats are supported for all SPARQL query types)
in: query
required: false
schema:
type: string
enum: [
'application/json',
'application/ld+json',
'application/n-quads',
'application/n-triples',
'application/sparql-results+json',
'application/sparql-results+xml',
'application/trig',
'simple',
'stats',
'table',
'text/csv',
'text/n3',
'text/tab-separated-values',
'text/turtle',
'tree'
]
requestBodies:
GetSpatialPlacement:
description: Request format for requesting a spatial placement for a given spatial entity IRI and RUI location
required: true
content:
application/json:
schema: { $ref: "#/components/schemas/GetSpatialPlacementRequest" }
example:
target_iri: "http://purl.org/ccf/latest/ccf.owl#VHFemale"
rui_location: {
"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld",
"@id": "http://purl.org/ccf/1.5/f7130161-ad0a-4801-b5a4-f6297e0f1869",
"@type": "SpatialEntity",
"creator": "Bruce Herr",
"creator_first_name": "Bruce",
"creator_last_name": "Herr",
"creation_date": "2022-04-27",
"ccf_annotations": [
"http://purl.obolibrary.org/obo/UBERON_0002015",
"http://purl.obolibrary.org/obo/UBERON_0000362",
"http://purl.obolibrary.org/obo/UBERON_0004200",
"http://purl.obolibrary.org/obo/UBERON_0001225",
"http://purl.obolibrary.org/obo/UBERON_0001284",
"http://purl.obolibrary.org/obo/UBERON_0002189"
],
"x_dimension": 11,
"y_dimension": 12,
"z_dimension": 13,
"dimension_units": "millimeter",
"placement": {
"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld",
"@id": "http://purl.org/ccf/1.5/f7130161-ad0a-4801-b5a4-f6297e0f1869_placement",
"@type": "SpatialPlacement",
"target": "http://purl.org/ccf/latest/ccf.owl#VHFLeftKidneyV1.1",
"placement_date": "2022-04-27",
"x_scaling": 1,
"y_scaling": 1,
"z_scaling": 1,
"scaling_units": "ratio",
"x_rotation": -61,
"y_rotation": 50,
"z_rotation": -84,
"rotation_order": "XYZ",
"rotation_units": "degree",
"x_translation": 20.149,
"y_translation": 109.963,
"z_translation": 38.79,
"translation_units": "millimeter"
}
}
SparqlQuery:
description: Request format for a SPARQL query
required: true
content:
application/json:
schema: { $ref: "#/components/schemas/SparqlQueryRequest" }
example:
query: "SELECT * WHERE { ?sub ?pred ?obj . } LIMIT 10"
application/x-www-form-urlencoded:
schema: { $ref: "#/components/schemas/SparqlQueryRequest" }
responses:
AggregateResults:
description: Successful operation
content:
application/json:
schema:
type: array
items: { $ref: "#/components/schemas/AggregateCount" }
DatabaseStatus:
description: Successful operation
content:
application/json:
schema: { $ref: "#/components/schemas/DatabaseStatus" }
ErrorMessage:
description: Successful operation
content:
application/json:
schema: { $ref: "#/components/schemas/ErrorMessage" }
OntologyTree:
description: Successful operation
content:
application/json:
schema: { $ref: "#/components/schemas/OntologyTree" }
SparqlResponse:
description: Successful operation. SPARQL responses vary by format/content negotiation.
content:
application/json:
schema:
type: object
SpatialEntities:
description: Successful operation
content:
application/json:
schema:
type: array
items: { $ref: "#/components/schemas/SpatialEntity" }
SpatialSceneNodes:
description: Successful operation
content:
application/json:
schema:
type: array
items: { $ref: "#/components/schemas/SpatialSceneNode" }
SpatialPlacement:
description: Successful operation
content:
application/json:
schema: { $ref: "#/components/schemas/FlatSpatialPlacement" }
Strings:
description: Successful operation
content:
application/json:
schema:
type: array
items:
type: string
TermOccurences:
description: Successful operation
content:
application/json:
schema:
type: object
additionalProperties:
type: integer
TissueBlocks:
description: Successful operation
content:
application/json:
schema:
type: array
items: { $ref: "#/components/schemas/TissueBlock" }
schemas:
DatabaseStatus:
title: Database Status
type: object
required: [status]
properties:
status:
title: Current status of the database
enum: [ "Loading", "Ready", "Error" ]
x-preprocessor-delete: enum
checkback:
title: How long to wait (in milliseconds) before checking status again
type: integer
minimum: 0
loadTime:
title: The amount of time (in milliseconds) taken to load the database
type: integer
minimum: 0
message:
title: Human readable description of the current status
type: string
ErrorMessage:
title: Error Message
type: object
required: [error]
properties:
message:
title: Human readable description of the error
type: string
GetSpatialPlacementRequest:
title: get-spatial-placement request body
type: object
required: [target_iri, rui_location]
properties:
target_iri:
type: string
format: uri
rui_location: { $ref: "#/components/schemas/SpatialEntity" }
SparqlQueryRequest:
title: SPARQL query request body
type: object
required: [query]
properties:
query:
type: string
# Generic types
AggregateCount:
title: Aggregated Count \w Label
type: object
required: [label, count]
properties:
label:
title: Aggregate Name/Field
type: string
count:
title: Aggregated Count
nullable: false
oneOf:
- type: number
- type: string
x-preprocessor-delete: oneOf
JsonLdObject:
title: JSON-LD Object
description: Base object for all json-ld objects.
type: object
required: ["@id", "@type"]
additionalProperties: true
properties:
"@id":
title: Unique Identifier
type: string
format: uri
example: http://purl.obolibrary.org/obo/UBERON_0013702
"@type":
title: Object Type
description: Contains the name of object class/interface
type: string
example: Sample
x-preprocessor-delete: [properties/@id, properties/@type]
MinMax:
title: Number Range
description: |
Represents a range of numbers using a minimum and maximum.
Either end may be omitted to indicate an unlimited/infinite range in that direction.
`min` should be less than or equal to `max` but this is not strictly enforced.
type: object
properties:
min:
type: number
max:
type: number
SpatialSearch:
title: Probing Sphere
description: |
Specification for a Spatial Search via Probing Sphere
type: object
properties:
x:
title: X coordinate relative to target in millimeters
type: number
y:
title: Y coordinate relative to target in millimeters
type: number
z:
title: Z coordinate relative to target in millimeters
type: number
radius:
title: Size of the probing sphere in millimeters
type: number
target:
title: The target spatial entity IRI
type: string
Rgba:
title: RGBA Color Tuple
type: array
minItems: 4
maxItems: 4
items:
title: 8-Bit Value
type: number
minimum: 0
maximum: 255
# Tissue data formats
TissueCommon:
title: Common Tissue Data Properties
description: Properties available in all tissue data objects.
type: object
required: [label, description, link]
properties:
label:
type: string
description:
type: string
link:
title: Associated URL
type: string
format: uri
TissueSampleCommon:
title: Common Tissue Sample Properties
description: Properties available in all tissue sample objects.
type: object
required: ["@type", sampleType, datasets]
properties:
"@type":
type: string
enum: [Sample]
sampleType:
title: Object Type
type: string
datasets:
title: Associated Datasets
type: array
items: { $ref: "#/components/schemas/TissueDataset" }
x-preprocessor-delete: [properties/@type]
TissueDataset:
title: Tissue Dataset
description: Describes a single tissue dataset.
type: object
allOf:
- $ref: "#/components/schemas/JsonLdObject"
- $ref: "#/components/schemas/TissueCommon"
required: ["@type", technology, thumbnail]
properties:
"@type":
type: string
enum: [Dataset]
technology:
title: Technology Used
type: string
thumbnail:
title: Representative Thumbnail URL
type: string
format: uri
x-preprocessor-delete: [properties/@type]
TissueDonor:
title: Tissue Donor
description: Contains generic information about a tissue donor.
type: object
allOf:
- $ref: "#/components/schemas/JsonLdObject"
- $ref: "#/components/schemas/TissueCommon"
required: ["@type", providerName]
properties:
"@type":
type: string
enum: [Donor]
providerName:
title: Provider of Donor
type: string
x-preprocessor-delete: [properties/@type]
TissueSection:
title: Tissue Section
description: A single section sample.
type: object
allOf:
- $ref: "#/components/schemas/JsonLdObject"
- $ref: "#/components/schemas/TissueCommon"
- $ref: "#/components/schemas/TissueSampleCommon"
required: [sampleType, sectionNumber]
properties:
sampleType:
type: string
enum: ["Tissue Section", "Non-Standard"]
x-preprocessor-delete: enum
sectionNumber:
title: Section Index
description: Index of the section in the parent block.
type: integer
minimum: 0
TissueBlock:
title: Tissue Block
description: Information about a collection of tissue sections.
type: object
allOf:
- $ref: "#/components/schemas/JsonLdObject"
- $ref: "#/components/schemas/TissueCommon"
- $ref: "#/components/schemas/TissueSampleCommon"
required: [sampleType, spatialEntityId, donor, sectionCount, sectionSize, sectionUnits, sections]
properties:
sampleType:
type: string
enum: ["Tissue Block", "Non-Standard"]
x-preprocessor-delete: enum
spatialEntityId:
title: Associated Spatial Entity
description: The associated spatial entity (rui_location) for the block.
type: string
format: uri
donor: { $ref: "#/components/schemas/TissueDonor" }
sectionCount:
title: Number of Sections
description: Number of sections contained in the block.
type: integer
minimum: 0
sectionSize:
title: Section Size
description: Size of each section in the block.
type: number
minimum: 0
sectionUnits:
title: Section Size Unit
description: Length unit `sectionSize` is in (generally, millimeters)
type: string
default: millimeters
sections:
title: Contained Sections
description: All sections in the block.
type: array
items: { $ref: "#/components/schemas/TissueSection" }
# Ontology data format
OntologyTreeNode:
title: Ontology Node
description: A node in the ontology tree.
type: object
allOf:
- $ref: "#/components/schemas/JsonLdObject"
required: ["@type", id, label, synonymLabels, parent, children]
properties:
"@type":
type: string
enum: [OntologyTreeNode]
id:
title: Identifier
description: Unique identifier for the node.
type: string
format: uri
label:
title: Label
description: Main descriptive label for the node.
type: string
synonymLabels:
title: Synonym Labels
description: Additional label for the node.
type: array
items:
type: string
parent:
title: Parent Node Identifier
description: Reference to the parent node.
type: string
format: uri
children:
title: Child Node Identifiers
description: References to all child nodes.
type: array
items:
type: string
format: uri
x-preprocessor-delete: [properties/@type]
OntologyTree:
title: Ontology Tree
description: An ontology tree.
type: object
required: [root, nodes]
properties:
root:
title: Root Node
description: Reference to the root node.
type: string
format: url
nodes:
title: All Nodes
description: A mapping of identifiers to each node object.
additionalProperties: { $ref: "#/components/schemas/OntologyTreeNode" }
# Spatial data format
SpatialObjectReference:
title: Spatial Object Reference
description: "A Spatial Object Reference provides a reference to an external representation of a Spatial Entity."
type: object
allOf:
- $ref: "#/components/schemas/JsonLdObject"
required: ["@type", file, file_format]
properties:
"@type":
type: string
enum: [SpatialObjectReference]
file:
title: File
type: string
format: uri
file_format:
title: File Format
type: string
example: model/gltf-binary
file_subpath:
title: File Subpath
type: string
x-preprocessor-delete: [properties/@type]
SpatialEntityCommon:
title: Spatial Entity Common
description: Properties available in all spatial entity objects.
type: object
properties:
entityId:
title: Entity Identifier
description: Identifier of the entity the spatial object represents.
type: string
format: uri
ccf_annotations:
title: Annotations
description: Annotations attached to the entity.
type: array
items:
type: string
format: uri
representation_of:
title: Representation
description: Identifier for the item the spatial object represents.
type: string
format: uri
reference_organ:
title: Organ
description: Identifier for the organ the spatial object represents.
type: string
format: uri
SpatialEntityCreator:
title: Spatial Entity Creator
description: Describes by whom and when an entity object was created.
type: object
properties:
creator:
title: Full Name
type: string
creator_first_name:
title: First Name
type: string
creator_last_name:
title: Last Name
type: string
creator_orcid:
title: Creator's Identifier
type: string
creation_date:
title: Creation Date
type: string
format: date
SpatialEntityDimensions:
title: Spatial Entity Dimensions
description: The dimensions of a spatial entity.
type: object
required: [x_dimension, y_dimension, z_dimension, dimension_units]
properties:
x_dimension:
title: X-Dimension
type: number
y_dimension:
title: Y-Dimension
type: number
z_dimension:
title: Z-Dimension
type: number
dimension_units:
title: Dimension Units
description: Length units of dimensional values.
type: string
default: millimeters
SpatialEntity:
title: Spatial Entity
description: "A Spatial Entity defines a bounded cartesian space and the units it is measured in. It typically represents a real world thing, e.g., a human body, a human kidney, a tissue section, or an individual cell."