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HuBMAP Entity API
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Schema
Checked 25m ago · Updated 1y ago
Details
Filter operations
get
Retrieve a provenance entity by id. Entity types of Donor, Sample and Datasets.
put
Update the properties of a given Donor, Sample, Dataset or Upload
get
Get a list of all the available entity types defined in the schema yaml
get
Get the ancestor list for an Entity. The ancestors are the nodes connected "upstream" from the current node. This list traverses all the levels in the graph.
get
Get the descendant list for an Entity. The descendants are the nodes "downstream" from the current node. This list traverses all the levels in the graph. Returns all descendants as an array of Entities.
get
Get the immediate parent list for an Entity. The parents are the nodes connected one level "upstream" from the current node. This list only goes to the next higher level in the graph.
get
Get the list of children directly connected to an Entity. The children are the nodes one level below the current node. This list only returns the items one level below in the graph.
get
Get the siblings list for an Entity. The siblings have the same direct ancestor. This list does not include all nodes whom have common ancestors, only the direct ancestor.
get
Get the tuplets list for an Entity. The tuplets have the same parent activity node.
get
Get the list of all collections the Entity belongs to.
get
Get the list of all uploads the Entity belongs to.
get
Get Provenance Data for Entity. This returns a PROV JSON compliant representation of the entity's provenance. Refer to this document for more information regarding [PROV JSON format](https://www.w3.org/Submission/2013/SUBM-prov-json-20130424/)
delete
Delete the cached data from Memcached for a given entity, HuBMAP-Read access is required in AWS API Gateway
get
Determines if the Entity with id is an instance of type
get
Determines if the Entity type type_a is an instance of type_b
get
Retrievea list of ancestor organ(s) of a given uuid
post
Create multiple samples from the same source entity. 'count' samples will be generated each with individual uuids, hubmap_ids and submission_ids.
get
Redirect a request from a doi service
get
Get the Globus URL to the given Dataset or Upload entity
get
Returns full provenance metadata for a Dataset, which can be used when publishing the Dataset.
get
Retrive the latest (newest) revision of a given Dataset. Public/Consortium access rules apply - if no token/consortium access then must be for a public dataset and the returned Dataset must be the latest public version. If the given dataset itself is the latest revision, meaning it has no next revisions, this dataset gets returned.
get
Retrive the calculated revision number of a Dataset. The calculated revision is number is based on the [:REVISION_OF] relationships to the oldest dataset in a revision chain. Where the oldest dataset = 1 and each newer version is incremented by one (1, 2, 3 ...). Public/Consortium access rules apply, if is for a non-public dataset and no token or a token without membership in HuBMAP-Read group is sent with the request then a 403 response should be returned.
get
From a given ID of a versioned dataset, retrieve a list of every dataset in the chain ordered from most recent to oldest. The revision number, as well as the dataset uuid will be included. An optional parameter ?include_dataset=true will include the full dataset for each revision as well. Public/Consortium access rules apply, if is for a non-public dataset and no token or a token without membership in HuBMAP-Read group is sent with the request then a 403 response should be returned. If the given id is published, but later revisions are not and the user is not in HuBMAP-Read group, only published revisions will be returned. The field next_revision_uuid will not be returned if the next revision is unpublished
get
Retrieve a list of all of the smples that are organs that are associated with the dataset id
get
Retrieve a list of all of the samples that are not organs that are associated with the dataset id
get
Retrieve a list of all of the donors that are associated with the dataset id
put
Retracts a dataset after it has been published. Requires a json body with a single field {retraction_reason: string}. The dataset for the given id is modified to include this new retraction_reason field and sets the dataset property sub_status to Retracted. The complete modified dataset is returned. Requires that the dataset being retracted has already been published (dataset.status == Published. Requires a user token with membership in the HuBMAP-Data-Admin group otherwise then a 403 will be returned.
get
returns aLL provenance information for a single dataset in a default table/tsv format or optionally a json format when an optional ?format=json parameter is provided
get
Retrieves the information needed to generate the sankey on software-docs as a json.
put
Bulk updating of entity type dataset. it's only limited to the fields:: assigned_to_group_name, ingest_task, status
put
Bulk updating of entity type upload. it's only limited to the fields:: assigned_to_group_name, ingest_task, status
get
returns information about all unpublished datasets in json or tsv format. Defaults to json
get
Retrieve uuids for associated dataset of given data_type which shares a sample ancestor of given dataset id
post
Create multiple component datasets from a single Multi-Assay ancestor
Bulk updating of entity type upload. it's only limited to the fields:: assigned_to_group_name, ingest_task, status
put
/uploads
Request body
object
required
Response
request is being processed
string[]
required
Changes