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ingest-api-spec.yaml
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openapi: 3.0.0
info:
description: |
A RESTful web service exposing calls needed for the SenNet Data Sharing Portal.
version: 1.7.2
title: SenNet Ingest API
contact:
name: SenNet Help Desk
email: [email protected]
license:
name: MIT License
url: 'https://github.com/sennetconsortium/ingest-api/blob/main/LICENSE'
servers:
- url: 'https://ingest.api.sennetconsortium.org'
security:
- BearerAuth: []
components:
securitySchemes:
BearerAuth:
type: http
scheme: bearer
description: Globus Bearer token to authorize requests
schemas:
file_info:
type: object
required:
- filename
- file_uuid
properties:
filename:
type: string
file_uuid:
type: string
file_uuid:
type: string
entity_uuid:
type: string
pattern: '^[a-f0-9]{32}$'
JobCreated:
type: object
properties:
job_id:
type: string
format: uuid
status:
type: string
Referrer:
type: object
description: The type of job and the URL path in the portal
properties:
type:
type: string
description: The type of job
path:
type: string
description: The URL path in the portal
Sources:
type: object
properties:
"1":
$ref: '#/components/schemas/Source'
"2":
$ref: '#/components/schemas/Source'
"3":
$ref: '#/components/schemas/Source'
Source:
type: object
properties:
created_timestamp:
type: integer
readOnly: true
description: The timestamp of when the node was created. The format is an integer representing milliseconds since midnight Jan 1, 1970
created_by_user_displayname:
type: string
readOnly: true
description: The name of the person or process authenticated when creating the object
created_by_user_email:
type: string
readOnly: true
description: The email address of the person or process authenticated when creating the object.
created_by_user_sub:
type: string
readOnly: true
description: The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object.
uuid:
type: string
readOnly: true
description: The SenNet unique identifier, intended for internal software use only. This is a 32 digit hexadecimal UUID e.g. 461bbfdc353a2673e381f632510b0f17
sennet_id:
type: string
readOnly: true
description: A SenNet Consortium wide unique identifier randomly generated in the format SNT###.ABCD.### for every Entity.
last_modified_timestamp:
type: integer
readOnly: true
description: The timestamp of when the object was last modified. The format is an integer representing milliseconds since midnight, Jan 1, 1970
last_modified_user_sub:
type: string
readOnly: true
description: The subject id of the user who last modified the Entity as provided by the authorization mechanism for the person or process authenticated when the object was modified.
last_modified_user_email:
type: string
readOnly: true
description: The email address of the person or process which authenticated when the object was last modified.
last_modified_user_displayname:
type: string
readOnly: true
description: The name of the person or process which authenticated when the object was last modified.
entity_type:
type: string
readOnly: true
description: 'Source'
description:
type: string
description: Free text description of the source
data_access_level:
type: string
readOnly: true
enum:
- consortium
- public
description: 'One of the values: public, consortium'
lab_source_id:
type: string
description: A lab specific identifier for the source.
group_uuid:
type: string
description: The UUID of globus group which the user who created this Entity is a member of. This is required on Create/POST if the user creating the Source is a member of more than one write group. This property cannot be set via PUT (only on Create/POST).
group_name:
readOnly: true
type: string
description: The displayname of globus group which the user who created this Entity is a member of
source_type:
type: string
enum:
- Human
- Human Organoid
- Mouse
- Mouse Organoid
description: "A high level description of where this source originates from. Valid values found in: [source types](https://ontology.api.hubmapconsortium.org/valueset?parent_sab=SENNET&parent_code=C050020&child_sabs=SENNET)"
Samples:
type: object
properties:
"1":
$ref: '#/components/schemas/Sample'
"2":
$ref: '#/components/schemas/Sample'
"3":
$ref: '#/components/schemas/Sample'
Sample:
type: object
properties:
created_timestamp:
type: integer
readOnly: true
description: The timestamp of when the node was created. The format is an integer representing milliseconds since midnight Jan 1, 1970
created_by_user_displayname:
type: string
readOnly: true
description: The name of the person or process authenticated when creating the object
created_by_user_email:
type: string
readOnly: true
description: The email address of the person or process authenticated when creating the object.
created_by_user_sub:
type: string
readOnly: true
description: The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object.
uuid:
type: string
readOnly: true
description: The SenNet unique identifier, intended for internal software use only. This is a 32 digit hexadecimal UUID e.g. 461bbfdc353a2673e381f632510b0f17
sennet_id:
type: string
readOnly: true
description: A SenNet Consortium wide unique identifier randomly generated in the format SNT###.ABCD.### for every Entity.
last_modified_timestamp:
type: integer
readOnly: true
description: The timestamp of when the object was last modified. The format is an integer representing milliseconds since midnight, Jan 1, 1970
last_modified_user_sub:
type: string
readOnly: true
description: The subject id of the user who last modified the Entity as provided by the authorization mechanism for the person or process authenticated when the object was modified.
last_modified_user_email:
type: string
readOnly: true
description: The email address of the person or process which authenticated when the object was last modified.
last_modified_user_displayname:
type: string
readOnly: true
description: The name of the person or process which authenticated when the object was last modified.
entity_type:
type: string
readOnly: true
description: 'Sample'
description:
type: string
description: Free text description of the source
data_access_level:
type: string
readOnly: true
enum:
- consortium
- public
description: 'One of the values: public, consortium'
lab_source_id:
type: string
description: A lab specific identifier for the source.
group_uuid:
type: string
description: The uuid of globus group which the user who created this Entity is a member of. This is required on Create/POST if the user creating the Source is a member of more than one write group. This property cannot be set via PUT (only on Create/POST).
group_name:
readOnly: true
type: string
description: The displayname of globus group which the user who created this Entity is a member of
sample_category:
type: string
enum:
- Block
- Organ
- Section
- Suspension
description: "The category of the sample. Valid values found in: [sample categories](https://ontology.api.hubmapconsortium.org/valueset?parent_sab=SENNET&parent_code=C020076&child_sabs=SENNET)"
organ:
type: string
enum:
- AD
- BD
- BM
- BR
- BS
- LK
- RK
- LI
- LV
- LL
- RL
- LN
- MU
- LO
- RO
- PA
- PL
- SK
description: "Organ code specifier, only set if `sample_category` is organ. Valid values found in: [organ types](https://ontology.api.hubmapconsortium.org/organs?application_context=sennet)"
Datasets:
type: object
properties:
"1":
$ref: '#/components/schemas/Dataset'
"2":
$ref: '#/components/schemas/Dataset'
"3":
$ref: '#/components/schemas/Dataset'
Dataset:
type: object
properties:
created_timestamp:
type: integer
readOnly: true
description: The timestamp of when the node was created. The format is an integer representing milliseconds since midnight Jan 1, 1970
created_by_user_displayname:
type: string
readOnly: true
description: The name of the person or process authenticated when creating the object
created_by_user_email:
type: string
readOnly: true
description: The email address of the person or process authenticated when creating the object.
created_by_user_sub:
type: string
readOnly: true
description: The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object.
uuid:
type: string
readOnly: true
description: The SenNet unique identifier, intended for internal software use only. This is a 32 digit hexadecimal UUID e.g. 461bbfdc353a2673e381f632510b0f17
sennet_id:
type: string
readOnly: true
description: A SenNet Consortium wide unique identifier randomly generated in the format SNT###.ABCD.### for every Entity.
last_modified_timestamp:
type: integer
readOnly: true
description: The timestamp of when the object was last modified. The format is an integer representing milliseconds since midnight, Jan 1, 1970
last_modified_user_sub:
type: string
readOnly: true
description: The subject id of the user who last modified the Entity as provided by the authorization mechanism for the person or process authenticated when the object was modified.
last_modified_user_email:
type: string
readOnly: true
description: The email address of the person or process which authenticated when the object was last modified.
last_modified_user_displayname:
type: string
readOnly: true
description: The name of the person or process which authenticated when the object was last modified.
entity_type:
type: string
readOnly: true
description: 'Dataset'
description:
type: string
description: Free text description of the dataset
data_access_level:
type: string
readOnly: true
enum:
- public
- consortium
description: 'One of the values: public, consortium.'
contains_human_genetic_sequences:
type: boolean
description: True if the data contains any human genetic sequence information. Can only be set at CREATE/POST time
status:
type: string
enum:
- New
- Processing
- QA
- Published
- Error
- Hold
- Invalid
description: 'One of: New|Processing|QA|Published|Error|Hold|Invalid'
dataset_type:
type: string
description: "The data or assay type contained in this dataset. Must be one of the values found in: [dataset types](https://ontology-api.dev.hubmapconsortium.org/valueset?parent_sab=SENNET&parent_code=C003041&child_sabs=SENNET)."
local_directory_rel_path:
type: string
readOnly: true
description: The path on the local HIVE file system, relative to the base data directory, where the data is stored.
group_uuid:
type: string
description: The UUID of globus group which the user who created this Entity is a member of. This is required on Create/POST if the user creating the Source is a member of more than one write group. This property cannot be set via PUT (only on Create/POST).
group_name:
type: string
readOnly: true
description: The displayname of globus group which the user who created this Entity is a member of
AssayTypeReturnDict:
type: object
properties:
name:
type: string
description:
type: string
primary:
type: boolean
vitessce-hints:
type: array
items:
type: string
Metadata:
type: object
paths:
/datasets:
post:
tags:
- datasets
summary: Creates a new SenNet Dataset.
operationId: addDataset
responses:
"201":
description: Successful created
"400":
description: Missing data that is required to create a new Dataset or a system error occurred
"401":
description: User is not authorized to create datasets or user's group information cannot be determined
requestBody:
content:
application/json:
schema:
$ref: "#/components/schemas/Dataset"
application/xml:
schema:
$ref: "#/components/schemas/Dataset"
description: Dataset object that needs to be created
required: true
/file-upload:
post:
tags:
- files
summary: "Upload a file to temporarily stage. On success the file will be staged and a temporary ID will be returned to reference the staged file. The temporary ID can be used in the `/file-commit` endpoint for Sources and Samples to commit the file permanantly and associate it with an Entity."
requestBody:
content:
multipart/form-data:
schema:
type: object
properties:
file:
type: string
format: binary
responses:
'200':
description: The file was successfully uploaded and staged, the temporary file ID is returned.
content:
application/json:
schema:
type: object
properties:
temp_file_id:
type: string
"400":
description: Missing file
"401":
description: The user's token has expired or the user did not supply a valid token
"403":
description: The user is not authorized to upload the file.
"500":
description: Internal error
/file-commit:
post:
tags:
- files
summary: "File commit triggered by the Entity API trigger method for Source/Sample/Dataset. Source: image files. Sample: image files and metadata files. Dataset: only the one thumbnail file. This call also creates the symbolic link from the file UUID directory under the uploads assets directory, so the uploaded files can be exposed via Globus's file assets service."
requestBody:
content:
application/json:
schema:
type: object
properties:
temp_file_id:
type: string
entity_uuid:
type: string
user_token:
type: string
responses:
"200":
description: The file was successfully commited, the file UUID is returned.
content:
application/json:
schema:
type: object
properties:
filename:
type: string
file_uuid:
type: string
"400":
description: Missing JSON input
"401":
description: The user's token has expired or the user did not supply a valid token
"500":
description: Internal error
/file-remove:
post:
tags:
- files
summary: "File removal triggered by Entity API trigger method for Source and Sample during Entity update. Source/Sample/Dataset. Source: image files. Sample: image files and metadata files. Dataset: only the one thumbnail file."
requestBody:
content:
application/json:
schema:
type: object
properties:
entity_uuid:
type: string
file_uuids:
type: array
items:
$ref: '#/components/schemas/file_uuid'
files_info_list:
type: array
items:
$ref: '#/components/schemas/file_info'
responses:
"200":
description: The file was successfully deleted.
"400":
description: Missing JSON input
"401":
description: The user's token has expired or the user did not supply a valid token
"500":
description: Internal error
/metadata/validate:
post:
tags:
- metadata
summary: Validate an uploaded metadata TSV file using the backend Job Queue.
requestBody:
required: true
content:
multipart/form-data:
schema:
type: object
properties:
entity_type:
type: string
enum:
- Source
- Sample
- Dataset
description: The type of Entity the metadata is for.
sub_type:
type: string
enum:
- Block
- Organ
- Section
- Suspension
description: The sub type of the Sample.
validate_uuids:
type: integer
description: Whether to validate UUIDs in the metadata, 0 or 1.
referrer:
type: string
description: 'The type of job and the URL path in the portal. Json formatted string {"type": "job_type", "path": "portal/url/path"}.'
metadata:
type: string
format: binary
description: The metadata TSV file.
responses:
"202":
description: The validation job was added to the queue and will be processed.
content:
application/json:
schema:
$ref: "#/components/schemas/JobCreated"
"400":
description: One or more required fields are missing or invalid.
content:
application/json:
schema:
properties:
error:
type: string
"401":
description: User's token is not valid or missing.
content:
application/json:
schema:
properties:
error:
type: string
"500":
description: An unexpected internal error occured.
content:
application/json:
schema:
properties:
error:
type: string
/metadata/register:
post:
tags:
- metadata
summary: Register metadata from a previously completed metadata validation job.
requestBody:
required: true
content:
application/json:
schema:
type: object
properties:
job_id:
type: string
description: The job_id of the completed validation job.
referrer:
$ref: "#/components/schemas/Referrer"
responses:
"202":
description: The registration job was added to the queue and will be processed.
content:
application/json:
schema:
$ref: "#/components/schemas/JobCreated"
"400":
description: One or more required fields are missing or invalid.
content:
application/json:
schema:
properties:
error:
type: string
"401":
description: User's token is not valid or missing.
content:
application/json:
schema:
properties:
error:
type: string
"500":
description: An unexpected internal error occured.
content:
application/json:
schema:
properties:
error:
type: string
/metadata/data-provider-groups:
get:
tags:
- metadata
summary: Returns an array of nested objects containing information pertaining to all Data Provider groups.
responses:
"200":
description: The JSON containing an array of data provider group information
"401":
description: User's token is not valid
"500":
description: An unexpected error occurred
/metadata/provenance-metadata/{identifier}:
get:
tags:
- metadata
summary: Returns the full provenance metadata for the provided dataset and all of its ancestors.
responses:
"200":
description: The JSON containing full provenance metadata
"401":
description: User's token is not valid
"500":
description: An unexpected error occurred
/sources/bulk/validate:
post:
tags:
- sources
summary: >
Validate an uploaded TSV file containing multiple Source records using the backend Job Queue.
requestBody:
content:
multipart/form-data:
schema:
type: object
properties:
file:
type: string
format: binary
description: The TSV file containing the Source records
group_uuid:
type: string
description: The UUID of the group the Sources should belong to
referrer:
type: string
description: 'The type of job and the URL path in the portal. Json formatted string {"type": "job_type", "path": "portal/url/path"}.'
responses:
"202":
description: File uploaded and validation job successfully created in the backend Job Queue
content:
application/json:
schema:
$ref: "#/components/schemas/JobCreated"
"400":
description: One or more required fields are missing or invalid.
content:
application/json:
schema:
properties:
error:
type: string
"401":
description: The user's token has expired or the user did not have authorization
"500":
description: Internal error
/sources/bulk/register:
post:
tags:
- sources
summary: Register the previously validated Source records using the backend Job Queue.
requestBody:
content:
application/json:
schema:
properties:
job_id:
type: string
description: The job ID of the previously created validation job
referrer:
$ref: "#/components/schemas/Referrer"
responses:
"202":
description: Registration job successfully created in the backend Job Queue
content:
application/json:
schema:
$ref: "#/components/schemas/JobCreated"
"400":
description: One or more required fields are missing or invalid.
content:
application/json:
schema:
properties:
error:
type: string
"401":
description: The user's token has expired or the user did not have authorization
"500":
description: Internal error
/samples/bulk/validate:
post:
tags:
- samples
summary: >
Validate an uploaded TSV file containing multiple Sample records using the backend Job Queue.
requestBody:
content:
multipart/form-data:
schema:
type: object
properties:
file:
type: string
format: binary
description: The TSV file containing the Sample records
group_uuid:
type: string
description: The UUID of the group the Samples should belong to
referrer:
type: string
description: 'The type of job and the URL path in the portal. Json formatted string {"type": "job_type", "path": "portal/url/path"}.'
responses:
"202":
description: File uploaded and validation job successfully created in the backend Job Queue
content:
application/json:
schema:
$ref: "#/components/schemas/JobCreated"
"400":
description: One or more required fields are missing or invalid.
content:
application/json:
schema:
properties:
error:
type: string
"401":
description: The user's token has expired or the user did not have authorization
"500":
description: Internal error
/samples/bulk/register:
post:
tags:
- samples
summary: Register the previously validated Sample records using the backend Job Queue.
requestBody:
content:
application/json:
schema:
properties:
job_id:
type: string
description: The job ID of the previously created validation job
referrer:
$ref: "#/components/schemas/Referrer"
responses:
"202":
description: Registration job successfully created in the backend Job Queue
content:
application/json:
schema:
$ref: "#/components/schemas/JobCreated"
"400":
description: One or more required fields are missing or invalid.
content:
application/json:
schema:
properties:
error:
type: string
"401":
description: The user's token has expired or the user did not have authorization
"500":
description: Internal error
/datasets/bulk/submit:
put:
tags:
- datasets
summary: "Submit a list of Datasets for processing. This requires SenNet Data-Admin privileges."
requestBody:
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/entity_uuid'
responses:
"202":
description: The Datasets were successfully submitted for processing
"401":
description: The user did not supply a valid token
"403":
description: The user does not have SenNet Data-Admin privileges
"404":
description: One or more supplied datasets do not exist
"500":
description: An unexpected error occured
/datasets/sankey_data:
get:
tags:
- datasets
summary: Retrieves the information needed to generate the sankey on software-docs as a json.
responses:
'200':
description: dataset_group_name, organ_type, dataset_data_types, and dataset_status for every primary dataset
content:
application/json:
schema:
type: object
properties:
dataset_group_name:
type: string
description: The display name of the Globus group which the user who created this entity is a member of
dataset_source_type:
type: string
description: The source type of the source associated with this dataset in the provenance chain
organ_type:
type: array
description: The organ type of the organ(s) associated with this dataset in the provenance chain
dataset_type_hierarchy:
type: string
description: The top level modality of the dataset type
dataset_type_description:
type: string
description: The description of the dataset type after being evaluated by the rule chain
dataset_status:
type: string
description: The status of the dataset New, QA, Published, etc ...
'500':
description: Internal error
/uploads/{identifier}/validate:
put:
tags:
- uploads
summary: Validate an upload.
operationId: validateUpload
parameters:
- name: identifier
in: path
description: The unique identifier of Upload. This identifier needs to be a valid SenNet ID.
required: true
schema:
type: string
responses:
"200":
description: Successful operation
"400":
description: There was a system error or an error in the data submitted
"401":
description: User's token is not valid
"500":
description: An unexpected error occured
/uploads/{identifier}/reorganize:
put:
tags:
- uploads
summary: Reorganize an upload. Creates Datasets from the Upload
operationId: reorganizeUpload
parameters:
- name: identifier
in: path
description: The unique identifier of Upload. This identifier needs to be a valid SenNet ID.
required: true
schema:
type: string
responses:
"200":
description: Successful operation
"400":
description: There was a system error or an error in the data submitted
"401":
description: User's token is not valid
"500":
description: An unexpected error occured
/vitessce/{identifier}:
get:
tags:
- vitessce
summary: Return a Vitessce configuration for a given Dataset UUID
parameters:
- name: identifier
in: path
description: The UUID of the Dataset.
required: true
schema:
type: string
responses:
"200":
description: The [Vitessce JSON configuration](http://vitessce.io/docs/view-config-json) for the given Dataset
"400":
description: Identifier is not a valid UUID
"401":
description: User's token is not valid
"500":
description: An unexpected error occurred
'/assaytype/{ds_uuid}':
get:
tags:
- assaytype
summary: Runs through the assay classifier with the provided Dataset to determine an assaytype
operationId: getAssayType
parameters:
- name: ds_uuid
in: path
description: The UUID of a Dataset
required: true
schema:
type: string
responses:
"200":
description: successful operation
content:
application/json:
schema:
$ref: '#/components/schemas/AssayTypeReturnDict'
"400":
description: The user sent a bad parameter (e.g. a nonexistent group name) or there was a system error
"401":
description: User's token is not valid
'/assaytype/metadata/{ds_uuid}':
get:
tags:
- assaytype
summary: Get the metadata for a specific Dataset
operationId: getMetadata
parameters:
- name: ds_uuid
in: path
description: The UUID of a Dataset
required: true
schema:
type: string
responses:
"200":
description: successful operation
content:
application/json:
schema:
$ref: '#/components/schemas/Metadata'
"400":
description: The user sent a bad parameter (e.g. a nonexistent group name) or there was a system error
"401":
description: User's token is not valid
'/assaytype':
post:
tags:
- assaytype
summary: Runs through the assay classifier with the provided metadata to determine an assaytype
operationId: getAssaytypeFromMetadata
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/Metadata'
responses:
"200":
description: successful operation
content:
application/json:
schema:
$ref: '#/components/schemas/AssayTypeReturnDict'
"400":
description: The user sent a bad parameter (e.g. a nonexistent group name) or there was a system error
"401":
description: User's token is not valid