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openapi.yaml
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openapi: 3.0.1
info:
title: F-UJI
description: A Service for Evaluating Research Data Objects Based on <a href ='https://doi.org/10.5281/zenodo.3775793'>FAIRsFAIR Metrics</a>. <p> This work was supported by the <a href='https://www.fairsfair.eu/'>FAIRsFAIR</a> project (H2020-INFRAEOSC-2018-2020 Grant Agreement 831558).
contact:
email: anusuriya.devaraju@googlemail.com
x-additional-email: rhuber@marum.de
license:
name: MIT License
url: https://opensource.org/licenses/MIT
version: 3.0.1
externalDocs:
description: Find out more about F-UJI
url: https://github.com/pangaea-data-publisher/fuji
servers:
- url: http://localhost:1071/fuji/api/v1
description: Development Server
tags:
- name: FAIR object
description: FAIRness assessment of a data object
- name: FAIR metric
description: FAIRsFAIR assessment metrics
paths:
/evaluate:
post:
tags:
- FAIR object
security:
- basicAuth: []
description: Evaluate FAIRness of a data object based on its identifier
operationId: assess_by_id
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/body'
example:
object_identifier: https://doi.org/10.1594/PANGAEA.908011
test_debug: true
metadata_service_endpoint: http://ws.pangaea.de/oai/provider
metadata_service_type: oai_pmh
use_datacite: true
use_github: false
metric_version: metrics_v0.5
responses:
'200':
description: successful operation
content:
application/json:
schema:
$ref: '#/components/schemas/FAIRResults'
application/rdf+xml:
schema:
type: string
application/x-turtle:
schema:
type: string
text/turtle:
schema:
type: string
application/ld+json:
schema:
type: string
text/n3:
schema:
type: string
'400':
description: Invalid identifier supplied
'401':
description: Authentication information is missing or invalid
headers:
WWW_Authenticate:
style: simple
explode: false
schema:
type: string
'404':
description: Object not found
x-openapi-router-controller: fuji_server.controllers.fair_object_controller
/metrics/{version}:
get:
parameters:
- in: path
name: version
schema:
type: string
pattern: ^([0-9]+\.[0-9]+)(_[a-z]+)?$
required: true
tags:
- FAIR metric
summary: Return all metrics and their definitions
operationId: get_metrics
responses:
'200':
description: Metrics are successfully retrieved
content:
application/json:
schema:
$ref: '#/components/schemas/Metrics'
'400':
description: Invalid request supplied
'401':
description: Authentication information is missing or invalid
headers:
WWW_Authenticate:
style: simple
explode: false
schema:
type: string
'404':
description: Object not found
x-openapi-router-controller: fuji_server.controllers.fair_metric_controller
/metrics/{version}/{metric}:
get:
parameters:
- in: path
name: version
schema:
type: string
pattern: ^([0-9]+\.[0-9]+)(_[a-z]+)?$
required: true
- in: path
name: metric
schema:
type: string
required: true
tags:
- FAIR metric
summary: Return a single metric and it's definition
operationId: get_metric
responses:
'200':
description: Metrics are successfully retrieved
content:
application/json:
schema:
$ref: '#/components/schemas/Metric'
'400':
description: Invalid request supplied
'401':
description: Authentication information is missing or invalid
headers:
WWW_Authenticate:
style: simple
explode: false
schema:
type: string
'404':
description: Object not found
x-openapi-router-controller: fuji_server.controllers.fair_metric_controller
/harvest:
post:
tags:
- metadata
security:
- basicAuth: []
description: Harvest metadata of a data object based on its identifier
operationId: harvest_by_id
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/harvest'
example:
object_identifier: https://doi.org/10.1594/PANGAEA.908011
responses:
'200':
description: successful operation
content:
application/json:
schema:
$ref: '#/components/schemas/HarvestResults'
'400':
description: Invalid identifier supplied
'401':
description: Authentication information is missing or invalid
headers:
WWW_Authenticate:
style: simple
explode: false
schema:
type: string
'404':
description: Object not found
x-openapi-router-controller: fuji_server.controllers.harvest_controller
components:
securitySchemes:
basicAuth:
type: http
scheme: basic
x-basicInfoFunc: fuji_server.controllers.authorization_controller.checkUser
schemas:
HarvestResults:
type: object
properties:
target_uri:
type: string
metadata:
type: array
items:
type: object
properties:
method:
type: string
url:
type: string
format:
type: string
schema:
type: string
namespaces:
type: array
items:
type: string
metadata:
type: object
additionalProperties: true
FAIRResults:
type: object
properties:
test_id:
type: string
request:
type: object
additionalProperties: true
resolved_url:
type: string
start_timestamp:
type: string
format: date-time
end_timestamp:
type: string
format: date-time
expiry_timestamp:
type: string
format: date-time
metric_specification:
type: string
format: uri
metric_version:
type: string
software_version:
type: string
total_metrics:
type: integer
summary:
type: object
additionalProperties: true
results:
type: array
items:
anyOf:
- $ref: '#/components/schemas/Uniqueness'
- $ref: '#/components/schemas/Persistence'
- $ref: '#/components/schemas/CoreMetadata'
- $ref: '#/components/schemas/IdentifierIncluded'
- $ref: '#/components/schemas/Searchable'
- $ref: '#/components/schemas/DataAccessLevel'
- $ref: '#/components/schemas/FormalMetadata'
- $ref: '#/components/schemas/SemanticVocabulary'
- $ref: '#/components/schemas/RelatedResource'
- $ref: '#/components/schemas/DataContentMetadata'
- $ref: '#/components/schemas/License'
- $ref: '#/components/schemas/DataProvenance'
- $ref: '#/components/schemas/CommunityEndorsedStandard'
- $ref: '#/components/schemas/DataFileFormat'
- $ref: '#/components/schemas/MetadataPreserved'
- $ref: '#/components/schemas/CodeProvenance'
- $ref: '#/components/schemas/ComponentIdentifier'
- $ref: '#/components/schemas/TestCase'
- $ref: '#/components/schemas/UniquePersistentIdentifierSoftware'
- $ref: '#/components/schemas/VersionIdentifier'
- $ref: '#/components/schemas/API'
- $ref: '#/components/schemas/DevelopmentMetadata'
- $ref: '#/components/schemas/Requirements'
- $ref: '#/components/schemas/StandardisedProtocolData'
- $ref: '#/components/schemas/StandardisedProtocolMetadata'
FAIRResultCommon:
required:
- id
- metric_identifier
- metric_name
- score
- test_status
type: object
properties:
id:
type: integer
format: int32
metric_identifier:
type: string
metric_name:
type: string
metric_tests:
type: object
additionalProperties:
$ref: '#/components/schemas/FAIRResultEvaluationCriterium'
test_status:
type: string
default: fail
enum:
- pass
- fail
- indeterminate
score:
$ref: '#/components/schemas/FAIRResultCommon_score'
maturity:
type: integer
default: 0
Uniqueness:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/Uniqueness_output'
test_debug:
$ref: '#/components/schemas/Debug'
Persistence:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/Persistence_output'
test_debug:
$ref: '#/components/schemas/Debug'
CoreMetadata:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/CoreMetadata_output'
test_debug:
$ref: '#/components/schemas/Debug'
IdentifierIncluded:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/IdentifierIncluded_output'
test_debug:
$ref: '#/components/schemas/Debug'
Searchable:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/Searchable_output'
test_debug:
$ref: '#/components/schemas/Debug'
License:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/License_output'
test_debug:
$ref: '#/components/schemas/Debug'
DataAccessLevel:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/DataAccess_output'
test_debug:
$ref: '#/components/schemas/Debug'
RelatedResource:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/RelatedResource_output'
test_debug:
$ref: '#/components/schemas/Debug'
CommunityEndorsedStandard:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/CommunityEndorsedStandard_output'
test_debug:
$ref: '#/components/schemas/Debug'
DataFileFormat:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/DataFileFormat_output'
test_debug:
$ref: '#/components/schemas/Debug'
DataProvenance:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/DataProvenance_output'
test_debug:
$ref: '#/components/schemas/Debug'
DataContentMetadata:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/DataContentMetadata_output'
test_debug:
$ref: '#/components/schemas/Debug'
FormalMetadata:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/FormalMetadata_output'
test_debug:
$ref: '#/components/schemas/Debug'
SemanticVocabulary:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/SemanticVocabulary_output'
test_debug:
$ref: '#/components/schemas/Debug'
MetadataPreserved:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/MetadataPreserved_output'
test_debug:
$ref: '#/components/schemas/Debug'
CodeProvenance:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/CodeProvenance_output'
test_debug:
$ref: '#/components/schemas/Debug'
ComponentIdentifier:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/ComponentIdentifier_output'
test_debug:
$ref: '#/components/schemas/Debug'
TestCase:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/TestCase_output'
test_debug:
$ref: '#/components/schemas/Debug'
UniquePersistentIdentifierSoftware:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/UniquePersistentIdentifierSoftware_output'
test_debug:
$ref: '#/components/schemas/Debug'
VersionIdentifier:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/VersionIdentifier_output'
test_debug:
$ref: '#/components/schemas/Debug'
API:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/API_output'
test_debug:
$ref: '#/components/schemas/Debug'
DevelopmentMetadata:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/DevelopmentMetadata_output'
test_debug:
$ref: '#/components/schemas/Debug'
Requirements:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/Requirements_output'
test_debug:
$ref: '#/components/schemas/Debug'
StandardisedProtocolData:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/StandardisedProtocolData_output'
test_debug:
$ref: '#/components/schemas/Debug'
StandardisedProtocolMetadata:
allOf:
- $ref: '#/components/schemas/FAIRResultCommon'
- type: object
properties:
output:
$ref: '#/components/schemas/StandardisedProtocolMetadata_output'
test_debug:
$ref: '#/components/schemas/Debug'
FAIRResultEvaluationCriterium:
type: object
properties:
metric_test_name:
type: string
metric_test_requirements:
type: array
items:
type: object
additionalProperties: true
metric_test_score:
$ref: '#/components/schemas/FAIRResultCommon_score'
metric_test_maturity:
type: integer
nullable: true
metric_test_status:
type: string
default: fail
enum:
- pass
- fail
FAIRResultCommon_score:
type: object
properties:
earned:
type: number
default: 0
total:
type: number
default: 0
Uniqueness_output:
type: object
properties:
guid:
type: string
guid_scheme:
type: string
Persistence_output:
type: object
properties:
persistent_identifiers:
type: array
items:
$ref: '#/components/schemas/Persistence_output_inner'
Persistence_output_inner:
type: object
properties:
pid:
type: string
pid_scheme:
type: string
resolvable_status:
type: boolean
default: false
resolved_url:
type: string
output_core_metadata_found:
type: object
additionalProperties:
type: string
CoreMetadata_output:
type: object
properties:
core_metadata_status:
type: string
enum:
- insufficent metadata
- partial metadata
- all metadata
core_metadata_found:
$ref: '#/components/schemas/output_core_metadata_found'
core_metadata_source:
type: array
items:
type: string
IdentifierIncluded_output:
type: object
properties:
object_identifier_included:
type: string
object_content_identifier_included:
type: array
items:
$ref: '#/components/schemas/IdentifierIncluded_output_inner'
output_search_mechanisms:
type: object
properties:
mechanism:
type: string
enum:
- metadata registry
- structured data
mechanism_info:
type: array
items:
type: string
Searchable_output:
type: object
properties:
search_mechanisms:
type: array
items:
$ref: '#/components/schemas/output_search_mechanisms'
License_output:
type: array
items:
$ref: '#/components/schemas/License_output_inner'
DataAccess_output:
type: object
properties:
access_level:
type: string
enum:
- public
- embargoed
- restricted
- closed
- metadataonly
access_details:
type: object
RelatedResource_output:
type: array
items:
$ref: '#/components/schemas/RelatedResource_output_inner'
DataFileFormat_output:
type: array
items:
$ref: '#/components/schemas/DataFileFormat_output_inner'
CommunityEndorsedStandard_output:
type: array
items:
$ref: '#/components/schemas/CommunityEndorsedStandard_output_inner'
DataProvenance_output:
type: object
properties:
provenance_metadata_included:
$ref: '#/components/schemas/DataProvenance_output_inner'
structured_provenance_available:
$ref: '#/components/schemas/DataProvenance_output_inner'
DataContentMetadata_output:
type: object
properties:
object_type:
type: string
data_content_descriptor:
type: array
items:
$ref: '#/components/schemas/DataContentMetadata_output_inner'
FormalMetadata_output:
type: array
items:
$ref: '#/components/schemas/FormalMetadata_output_inner'
SemanticVocabulary_output:
type: array
items:
$ref: '#/components/schemas/SemanticVocabulary_output_inner'
MetadataPreserved_output:
type: object
properties:
metadata_preservation_method:
type: array
items:
type: string
enum:
- datacite
- tombstone
CodeProvenance_output:
type: object
ComponentIdentifier_output:
type: object
TestCase_output:
type: object
UniquePersistentIdentifierSoftware_output:
type: object
VersionIdentifier_output:
type: object
API_output:
type: object
DevelopmentMetadata_output:
type: object
Requirements_output:
type: object
Metrics:
type: object
properties:
total:
type: integer
metrics:
type: array
items:
$ref: '#/components/schemas/Metric'
example:
total: 0
metrics:
metric_identifier: FsF-F1-01D
metric_short_name: Globally Unique Identifier
metric_name: Data is assigned with a globally unique identifier.
description: A data object may be assigned with a globally unique identifier such that it can be referenced unambiguously by humans or machines. Globally unique means an identifier should be associated with only one resource at any time. Examples of unique identifiers of data are Internationalized Resource Identifier (IRI), Uniform Resource Identifier (URI) such as URL and URN, Digital Object Identifier (DOI), the Handle System, identifiers.org, w3id.org and Archival Resource Key (ARK). A data repository may assign a globally unique identifier to your data or metadata when you publish and make it available through their services.
fair_principle: F1
evaluation_mechanism: Identifier is considered unique if it is successfully validated through https://pythonhosted.org/IDUtils/. Supported schemes are ISBN10, ISBN13, ISSN, ISTC, DOI, Handle, EAN8, EAN13, ISNI ORCID, ARK, PURL, LSID, URN, Bibcode, arXiv, PubMed ID, PubMed Central ID, GND.
created_by: FAIRsFAIR
date_created: 2020-07-08
date_updated: 2020-07-08
version: 0.3
total_score: 1
Metric:
type: object
properties:
metric_identifier:
type: string
metric_name:
type: string
description:
type: string
fair_principle:
type: string
evaluation_mechanism:
type: string
date_created:
type: string
format: date
date_updated:
type: string
format: date
created_by:
type: string
version:
type: number
format: double
total_score:
type: integer
format: int32
Debug:
type: array
items:
type: string
body:
required:
- object_identifier
type: object
properties:
object_identifier:
type: string
description: The full identifier of data object that needs to be evaluated
test_debug:
type: boolean
description: Indicate if the detailed evaluation procedure of the metrics should to be included in the response
default: false
metadata_service_endpoint:
type: string
description: The URL of the catalogue endpoint (e.g. OAI-PMH data-provider)
metadata_service_type:
type: string
use_datacite:
type: boolean
description: Indicates if DataCite content negotiation (using the DOI) shall be used to collect metadata
use_github:
type: boolean
description: Indicates if the GitHub REST API shall be used to collect (meta)data
metric_version:
type: string
description: The FAIRsFAIR metric version be used fo rthe assessment
auth_token:
type: string
description: The authentication token for HTTP authentication
auth_token_type:
type: string
description: The authentication token type, 'Basic' or 'Bearer'
oaipmh_endpoint:
deprecated: true
type: string
description: (Deprecated) The URL of the OAI-PMH data-provider
harvest:
required:
- object_identifier
type: object
properties:
object_identifier:
type: string
description: The full identifier of data object that needs to be harvested
IdentifierIncluded_output_inner:
type: object
properties:
content_identifier_included:
type: string
License_output_inner:
type: object
properties:
license:
type: string
OSI_approved:
type: boolean
default: false
details_url:
type: string
RelatedResource_output_inner:
type: object
properties:
related_resource:
type: string
relation_type:
type: string
CommunityEndorsedStandard_output_inner:
type: object
properties:
metadata_standard:
type: string
url:
type: string
subject_areas:
type: array
items:
type: string
type:
type: string
source:
type: string
DataFileFormat_output_inner:
type: object
properties:
file_uri:
type: string
mime_type:
type: string
is_preferred_format:
type: boolean
default: false
preference_reason:
type: array
items:
type: string
subject_areas:
type: array
items:
type: string
DataProvenance_output_inner:
type: object
properties:
is_available:
type: boolean
default: true
provenance_metadata:
type: array
items:
type: object
additionalProperties:
type: string
DataContentMetadata_output_inner:
type: object
properties:
descriptor:
type: string
descriptor_value:
type: string
matches_content:
type: boolean
default: false
FormalMetadata_output_inner:
type: object
properties:
serialization_format:
type: string
source:
type: string
enum:
- typed_link
- content_negotiate
- structured_data
- sparql_endpoint
is_metadata_found:
type: boolean
default: false
SemanticVocabulary_output_inner:
type: object
properties:
namespace:
type: string
is_namespace_active:
type: boolean
default: false
StandardisedProtocolData_output:
type: object
properties:
standard_data_protocol:
type: string
StandardisedProtocolMetadata_output:
type: object
properties:
standard_metadata_protocol:
type: string
responses:
UnauthorizedError:
description: Authentication information is missing or invalid
headers:
WWW_Authenticate:
style: simple
explode: false
schema:
type: string