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entity-api-spec.yaml
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entity-api-spec.yaml
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openapi: 3.0.0
info:
description: 'The HuBMAP Entity API is a standard RESTful web service with create, update and read operations for the standard HuBMAP provenance graph entities.'
version: 2.0.21
title: HuBMAP Entity API
contact:
name: HuBMAP Help Desk
email: [email protected]
license:
name: MIT License
url: 'https://github.com/hubmapconsortium/entity-api/blob/main/license.txt'
servers:
- url: 'https://entity.api.hubmapconsortium.org'
components:
securitySchemes:
bearerAuth:
type: apiKey
name: Authorization
in: header
description: Globus bearer token to authorize requests. Have to use apiKey to pass AWS API Gateway import validation
schemas:
Person:
type: object
properties:
first_name:
type: string
description: "The full name of the person."
last_name:
type: string
description: The last name of the person.
middle_name_or_initial:
type: string
description: The middle name or initial of the person.
orcid_id:
type: string
description: The ORCID iD of the person.
affiliation:
type: string
description: The institution that the person is affiliated with.
Antibody:
type: object
properties:
antibody_name:
type: string
description: "The name of the antibody."
channel_id:
type: string
description: "The assay specific identifier for the channel corresponding to the antibody."
conjugated_cat_number:
type: string
description: "An antibody may be conjugated to a fluorescent tag or a metal tag for detection. Conjugated antibodies may be purchased from commercial providers. Blank if not applicable."
conjugated_tag:
type: string
description: "An antibody may be conjugated to a fluorescent tag or a metal tag for detection. Conjugated antibodies may be purchased from commercial providers. Blank if not applicable."
dilution:
type: string
description: "The dilition ratio, e.g. 1/200 for the antibody. Blank if not applicable."
lot_number:
type: string
description: "The antibody lot number from the vendor."
rr_id:
type: string
description: "The unique antibody identifier from the Antibody Registry (https://antibodyregistry.org). "
uniprot_accession_number:
type: string
description: "The unique identifier for the target protein in the UniProt database (https://www.uniprot.org)."
DonorMetadata:
type: object
properties:
code:
type: string
description: "This is a Code from a source vocabulary in the HuBMAP Knowledge Graph, currently limited to UMLS source vocabulary terms."
sab:
type: string
description: "This is the source vocabulary in the HuBMAP Knowledge Graph. Currently limited to UMLS source vocabularies."
concept_id:
type: string
description: "This is the Concept ID from the HuBMAP Knowledge Graph. Currently limited to UMLS concepts."
data_type:
type: string
enum:
- Nominal
- Numeric
description: "This is the data type of thw record. Numeric types will generally have non-null data_value. Nominal types will generally have null data_value."
data_value:
type: string
description: "The data value of the record."
numeric_operator:
type: string
enum:
- EQ
- GT
- LT
description: "This is the numeric operator for the data value .This enables inputing thresholds and ranges for data values by using greater than or less than."
units:
type: string
description: "This are the units for the data value."
preferred_term:
type: string
description: "This is the preferred display term for the item. It may or may not correspond to a term in UMLS for this concept."
grouping_concept:
type: string
description: "This is the Concept ID from the HuBMAP Knowledge Graph, currently limited to UMLS concetps, that is to be used for grouping the record."
grouping_concept_preferred_term:
type: string
description: "This is the preferred display term for the facet in which this record should be counted for faceted search in the portal. It may or may not correspond to a term in UMLS for the grouping concept."
grouping_code:
type: string
description: "This is a Code from a source vocabulary in the HuBMAP Knowledge Graph, currently limited to UMLS vocabulary codes. This code corresponds to the grouping_concept."
grouping_sab:
type: string
description: "This is a grouping for the source vocabulary in the HuBMAP Knowledge Graph, currently limited to UMLS source vocabularies.. This sab corresponds to the grouping_code."
graph_version:
type: string
description: "This is the version of the HuBMAP Knowledge Graph that the Concept appears in, currently the version of UMLS that is used."
start_datetime:
type: integer
description: "This is the approximate time difference in seconds between the procurement and the start of this event (this is to construct time series records of clinical data for event-level data not donor-level data). An empty or zero value designates missing data or that this field is not applicable for the concept."
end_datetime:
type: integer
description: "This is the approximate time difference in seconds between the procurement and the end of this event (this is to construct time series records of clinical data for event-level data not donor-level data). An epty of zero value designates missing data or that this field is not applicable for the concept"
SampleMetadata:
type: object
description: "The sample specific metadata derived from the uploaded sample_metadata.tsv file. Returned as a json object."
properties:
sample_id:
type: string
description: "The HuBMAP Identifier for the sample."
vital_state:
type: string
enum:
- living
- deceased
description: "The vital state of the donor who the tissue sample came from."
health_status:
type: string
enum:
- cancer
- "relatively healthy"
- "chronic illness"
description: "Donor from which the tissue sample came from's baseline physical condition prior to immediate event leading to organ/tissue acquisition. For example, if a relatively healthy patient suffers trauma, and as a result of reparative surgery, a tissue sample is collected, the subject will be deemed 'relatively healthy'. Likewise, a relatively healthy subject may have experienced trauma leading to brain death. As a result of organ donation, a sample is collected. In this scenario, the subject is deemed 'relatively healthy'."
organ_condition:
type: string
enum:
- healthy
- diseased
description: "Health status of the organ at the time of tissue sample recovery."
procedure_date:
type: string
description: "The date at which the organ from which the tissue sample came from was procurred, in the format YYYY-MM-DD"
perfusion_solution:
type: string
enum:
- UWS
- HTK
- Belzer MPS/KPS
- Formalin
- Unknown
- None
description: "Health status of the organ at the time of sample recovery."
pathologist_report:
type: string
description: "Further details on organ level QC checks."
warm_ischemia_time_value:
type: integer
description: "Time interval between cessation of blood flow and cooling to 4C. Blank if not applicable."
warm_ischemia_time_unit:
type: string
description: "Time units that the warm_ischemia_time_value is reported in. Blank if not applicable"
cold_ischemia_time_value:
type: integer
description: "Time interval on ice to the start of preservation protocol. Blank if not applicable."
cold_ischemia_time_unit:
type: string
description: "Time units that the cold_ischemia_time_value is reported in. Blank if not applicable."
specimen_preservation_temperature:
type: string
description: "The temperature of the medium during the preservation process. Reported as preservation method, temperature and units, e.g. Freezer (-80 Celsius)"
specimen_quality_criteria:
type: string
description: "RIN score. e.g. RIN: 8.7"
specimen_tumor_distance_value:
type: string
description: "If surgical sample from a tumor biopsy, how far from the tumor was the sample obtained from. Typically a number of centimeters. Blank if not applicable or unknown."
specimen_tumor_distance_unit:
type: string
description: ""
File:
type: object
properties:
filename:
type: string
description: "The name of the file."
description:
type: string
description: "A description of the file. The Dataset.thumbnail_file does not have this file description."
file_uuid:
type: string
description: "The HuBMAP unique identifier for the file."
Donor:
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 HuBMAP unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17"
hubmap_id:
type: string
readOnly: true
description: "A HuBMAP Consortium wide unique identifier randomly generated in the format HBM###.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: "One of the normalized entity types: Dataset, Collection, Sample, Donor, Upload"
registered_doi:
type: string
description: "The doi of a the registered entity. e.g. 10.35079/hbm289.pcbm.487. This is set during the publication process and currently available for certain Collections and Datasets."
doi_url:
type: string
readOnly: true
description: "The url from the doi registry for this entity. e.g. https://doi.org/10.35079/hbm289.pcbm.487"
creators:
type: array
items:
$ref: '#/components/schemas/Person'
description: "A list of the people who created the entity with full name, email, ORCID iD, institution, etc.. This is analogus to the author list on a publication."
contacts:
type: array
items:
$ref: '#/components/schemas/Person'
description: "A list of the people who are the main contacts to get information about the entity."
description:
type: string
description: "Free text description of the donor"
data_access_level:
type: string
readOnly: true
enum:
- consortium
- public
description: "One of the values: public, consortium"
image_files:
readOnly: true
type: array
items:
$ref: '#/components/schemas/File'
description: "List of uploaded image files and descriptions of the files. Stored in db as a stringfied json array."
image_files_to_add:
writeOnly: true
type: array
items:
type: string
format: temp_file_id
description: 'List of temporary file ids with an optional description. Provide as a json array with an temp_file_id and description attribute for each element like {"files": [{"temp_file_id":"dzevgd6xjs4d5grmcp4n","description":"This is image file one"},{"temp_file_id":"yrahjadfhadf","description":"This is image file two"}]}'
image_files_to_remove:
writeOnly: true
type: array
items:
type: string
format: file_uuid
description: 'List of image files previously uploaded to delete. Provide as a json array of the file_uuids of the file like: ["232934234234234234234270c0ea6c51d604a850558ef2247d0b4", "230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa"]'
metadata:
type: object
properties:
organ_donor_data:
type: array
description: "Information about the donor who's organ(s) was/were used. The organ was obtained via an organ donation program from a deceaced donor. Only living_donor_data or organ_donor_data, not both can be defined for a single donor."
items:
$ref: '#/components/schemas/DonorMetadata'
living_donor_data:
type: array
description: "Information about the donor who's tissue was used. The tissue was obtained during a procedure. Only living_donor_data or organ_donor_data, not both can be defined for a single donor."
items:
$ref: '#/components/schemas/DonorMetadata'
description: "Donor metadata as an array of UMLS codes and descriptions"
protocol_url:
type: string
description: "The protocols.io doi url pointing the protocol describing the donor selection, inclusion/exclusion criteria"
lab_donor_id:
type: string
description: "A lab specific identifier for the donor."
submission_id:
readOnly: true
type: string
description: "The hubmap internal id with embedded semantic information e.g.: VAN0003. This id is generated at creation time which tracks the lab, donor, organ and sample hierarchy per the following: https://docs.google.com/document/d/1DjHgmqWF1VA5-3mfzLFNfabbzmc8KLSG9xWx1DDLlzo/edit?usp=sharing"
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 Donor 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"
label:
type: string
description: "Lab provided, de-identified name for the donor"
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 HuBMAP unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17"
hubmap_id:
type: string
readOnly: true
description: "A HuBMAP Consortium wide unique identifier randomly generated in the format HBM###.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: "One of the normalized entity types: Dataset, Collection, Sample, Donor"
registered_doi:
type: string
description: "The doi of a the registered entity. e.g. 10.35079/hbm289.pcbm.487. This is set during the publication process and currently available for certain Collections and Datasets."
doi_url:
type: string
readOnly: true
description: "The url from the doi registry for this entity. e.g. https://doi.org/10.35079/hbm289.pcbm.487"
creators:
type: array
items:
$ref: '#/components/schemas/Person'
description: "A list of the people who created the entity with full name, email, ORCID iD, institution, etc.. This is analogus to the author list on a publication."
contacts:
type: array
items:
$ref: '#/components/schemas/Person'
description: "A list of the people who are the main contacts to get information about the entity."
description:
type: string
description: "Free text description of the sample"
data_access_level:
type: string
enum:
- consortium
- public
description: "One of the values: public, consortium."
sample_category:
type: string
enum:
- organ
- block
- section
- suspension
description: "A code representing the type of specimen. Must be an organ, block, section, or suspension"
protocol_url:
type: string
description: "The protocols.io doi url pointing the protocol under wich the sample was obtained and/or prepared."
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 Donor 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"
organ:
type: string
enum:
- AO
- BL
- BD
- BM
- BR
- LF
- RF
- HT
- LB
- LE
- LI
- LK
- LL
- LN
- LV
- LY
- LO
- RO
- OT
- PA
- PL
- RB
- RE
- RK
- RL
- RN
- SI
- SK
- SP
- ST
- TH
- TR
- UR
- UT
description: "Organ code specifier, only set if sample_category == organ. Valid values found in: [organ types](https://github.com/hubmapconsortium/search-api/blob/main/src/search-schema/data/definitions/enums/organ_types.yaml)"
organ_other:
type: string
description: The organ type provided by the user if "other" organ type is selected
direct_ancestor_uuid:
type: string
writeOnly: true
description: "The uuid of source entity from which this new entity is derived from. Used on creation or edit to create an action and relationship to the ancestor. The direct ancestor must be a Donor or Sample. If the direct ancestor is a Donor, the sample must be of type organ."
direct_ancestor:
readOnly: true
type: object
description: "The entitiy directly above this sample in the provenance graph (direct parent)."
submission_id:
type: string
description: "The hubmap internal id with embedded semantic information e.g.: VAN0003-LK-1-10. This id is generated at creation time which tracks the lab, donor, organ and sample hierarchy per the following: https://docs.google.com/document/d/1DjHgmqWF1VA5-3mfzLFNfabbzmc8KLSG9xWx1DDLlzo/edit?usp=sharing"
lab_tissue_sample_id:
type: string
description: "Lab specific id for the sample."
metadata:
$ref: '#/components/schemas/SampleMetadata'
rui_location:
type: object
description: "The sample location and orientation in the ancestor organ as specified in the RUI tool. Returned as a json object."
visit:
type: string
description: "The visit id for the donor/patient when the sample was obtained."
image_files:
readOnly: true
type: array
items:
$ref: '#/components/schemas/File'
description: "List of uploaded image files and descriptions of the files. Stored in db as a stringfied json array."
image_files_to_add:
writeOnly: true
type: array
items:
type: string
format: temp_file_id
description: 'List of temporary file ids with an optional description. Provide as a json array with an temp_file_id and description attribute for each element like {"files": [{"temp_file_id":"dzevgd6xjs4d5grmcp4n","description":"This is image file one"},{"temp_file_id":"yrahjadfhadf","description":"This is image file two"}]}'
image_files_to_remove:
writeOnly: true
type: array
items:
type: string
format: file_uuid
description: 'List of image files previously uploaded to delete. Provide as a json array of the file_uuids of the file like: ["232934234234234234234270c0ea6c51d604a850558ef2247d0b4", "230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa"]'
metadata_files:
readOnly: true
type: array
items:
$ref: '#/components/schemas/File'
description: "List of uploaded image files and descriptions of the files. Stored in db as a stringfied json array."
metadata_files_to_add:
type: array
items:
type: string
format: temp_file_id
description: 'List of temporary file ids with an optional description. Provide as a json array with an temp_file_id and description attribute for each element like {"files": [{"temp_file_id":"dzevgd6xjs4d5grmcp4n","description":"This is image file one"},{"temp_file_id":"yrahjadfhadf","description":"This is image file two"}]}'
metadata_files_to_remove:
type: array
items:
type: string
format: file_uuid
description: 'List of image files previously uploaded to delete. Provide as a json array of the file_uuids of the file like: ["232934234234234234234270c0ea6c51d604a850558ef2247d0b4", "230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa"]'
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 HuBMAP unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17"
hubmap_id:
type: string
readOnly: true
description: "A HuBMAP Consortium wide unique identifier randomly generated in the format HBM###.ABCD.### for every entity."
error_message:
type: string
readOnly: false
description: "An open text field that holds the last error message that arose from pipeline validation or analysis."
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: "One of the normalized entity types: Dataset, Collection, Sample, Donor"
registered_doi:
type: string
description: "The doi of a the registered entity. e.g. 10.35079/hbm289.pcbm.487. This is set during the publication process and currently available for certain Collections and Datasets."
doi_url:
type: string
readOnly: true
description: "The url from the doi registry for this entity. e.g. https://doi.org/10.35079/hbm289.pcbm.487"
creators:
type: array
items:
$ref: '#/components/schemas/Person'
description: "A list of the people who created the entity with full name, email, ORCID iD, institution, etc.. This is analogus to the author list on a publication."
contacts:
type: array
items:
$ref: '#/components/schemas/Person'
description: "A list of the people who are the main contacts to get information about the entity."
antibodies:
type: array
items:
$ref: '#/components/schemas/Antibody'
description: "A list of antibodies used in the assay that created the 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"
title:
type: string
description: "The dataset title."
data_types:
type: array
items:
type: string
enum:
- AF
- ATACseq-bulk
- bulk_atacseq
- cell-dive
- CODEX
- codex_cytokit
- DART-FISH
- image_pyramid
- IMC
- 3D-IMC
- lc-ms_label-free
- lc-ms_labeled
- lc-ms-ms_label-free
- lc-ms-ms_labeled
- LC-MS-untargeted
- Lightsheet
- MALDI-IMS-neg
- MALDI-IMS-pos
- MxIF
- PAS
- bulk-RNA
- salmon_rnaseq_bulk
- SNAREseq
- sc_atac_seq_snare_lab
- sc_atac_seq_snare
- scRNA-Seq-10x
- salmon_rnaseq_10x
- sc_rna_seq_snare_lab
- salmon_rnaseq_snareseq
- sciATACseq
- sc_atac_seq_sci
- sciRNAseq
- salmon_rnaseq_sciseq
- seqFish
- seqFish_lab_processed
- snATACseq
- sn_atac_seq
- snRNAseq
- salmon_sn_rnaseq_10x
- Slide-seq
- Targeted-Shotgun-LC-MS
- TMT-LC-MS
- WGS
description: "The data or assay types contained in this dataset as a json array of strings. Each is an assay code from [assay types](https://github.com/hubmapconsortium/search-api/blob/main/src/search-schema/data/definitions/enums/assay_types.yaml)."
collections:
readOnly: true
type: array
items:
$ref: '#/components/schemas/Collection'
description: "A list of collections that this dataset belongs to."
upload:
readOnly: true
type: array
items:
$ref: '#/components/schemas/Upload'
description: "The Data Upload that this dataset is associated with."
contributors:
readOnly: true
type: array
items:
$ref: '#/components/schemas/Person'
description: "A list of people who contributed to the creation of this dataset. Returned as an array of contributor where the structure of a contributor is"
direct_ancestors:
readOnly: true
type: array
items:
anyOf:
- $ref: '#/components/schemas/Sample'
- $ref: '#/components/schemas/Dataset'
description: "A list of direct parent ancensters (one level above) that the Dataset was derived from."
published_timestamp:
readOnly: true
type: integer
description: "The timestamp of when the dataset was published. The format is an integer representing milliseconds since midnight, Jan 1, 1970."
published_user_displayname:
readOnly: true
type: string
description: "The name of the authenticated user or process that published the data."
published_user_sub:
readOnly: true
type: string
description: "The subject id for the user who published the data as provided by the authorization mechanism for the person or process authenticated when the dataset was publised."
published_user_email:
readOnly: true
type: string
description: "The email address of the user who published the provided by the authorization mechanism for the person or process authenticated when published."
ingest_metadata:
type: object
description: "The metadata returned from the ingest pipeline processing at data submission time. Provided as json."
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 Donor 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"
previous_revision_uuid:
type: string
description: "The uuid of previous revision dataset. Can only be set at Create/POST time."
next_revision_uuid:
type: string
readOnly: true
description: "The uuid of next revision dataset"
previous_revision_uuids:
type: list
description: "The uuids of previous revision datasets. Can only be set at Create/POST time."
next_revision_uuids:
type: list
readOnly: true
description: "The uuids of next revision dataset"
thumbnail_file:
readOnly: true
description: 'The dataset thumbnail file detail. Stored in db as a stringfied json, e.g., {"filename": "thumbnail.jpg", "file_uuid": "c35002f9c3d49f8b77e1e2cd4a01803d"}'
thumbnail_file_to_add:
writeOnly: true
type: string
format: temp_file_id
description: 'Just a temporary file id. Provide as a json object with an temp_file_id like {"temp_file_id":"dzevgd6xjs4d5grmcp4n"}'
thumbnail_file_to_remove:
writeOnly: true
type: string
format: file_uuid
description: 'The thumbnail image file previously uploaded to delete. Provide as a string of the file_uuid like: "c35002f9c3d49f8b77e1e2cd4a01803d"'
sub_status:
type: string
description: 'A sub-status provided to further define the status. The only current allowable value is "Retracted"'
retraction_reason:
type: string
description: 'Information recorded about why a the dataset was retracted.'
dbgap_sra_experiment_url:
type: string
description: 'A URL linking the dataset to the associated uploaded data at dbGaP.'
dbgap_study_url:
type: string
description: 'A URL linking the dataset to the particular study on dbGap it belongs to'
creation_action:
type: string
description: 'The associated action that represents the creation of that dataset'
Upload:
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 HuBMAP unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17"
hubmap_id:
type: string
readOnly: true
description: "A HuBMAP Consortium wide unique identifier randomly generated in the format HBM###.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: "One of the normalized entity types: Dataset, Collection, Sample, Donor, Upload"
description:
type: string
description: "Free text description of the data being submitted."
title:
type: string
description: "Title of the datasets, a sentance or less"
status:
type: string
description: "One of: New|Valid|Invalid|Error|Submitted"
validation_message:
type: string
description: A message from the validataion tools describing what is invalid with the upload.
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 Donor 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"
dataset_uuids_to_link:
type: array
items:
type: string
writeOnly: true
description: 'List of datasets to add to the Upload. Provide as a json array of the dataset uuids like: ["232934234234234234234270c0ea6c51d604a850558ef2247d0b4", "230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa"]'
dataset_uuids_to_unlink:
type: array
items:
type: string
writeOnly: true
description: 'List of datasets to remove from a Upload. Provide as a json array of the dataset uuids like: ["232934234234234234234270c0ea6c51d604a850558ef2247d0b4", "230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa"]'
datasets:
type: array
items:
$ref: '#/components/schemas/Dataset'
readOnly: true
description: "The datasets that are contained in this Upload."
Collection:
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 HuBMAP unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17"
hubmap_id:
type: string
readOnly: true
description: "A HuBMAP Consortium wide unique identifier randomly generated in the format HBM###.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: "One of the normalized entity types: Dataset, Collection, Sample, Donor"
registered_doi:
type: string
description: "The doi of a the registered entity. e.g. 10.35079/hbm289.pcbm.487. This is set during the publication process and currently available for certain Collections and Datasets."
doi_url:
type: string
readOnly: true
description: "The url from the doi registry for this entity. e.g. https://doi.org/10.35079/hbm289.pcbm.487"
contributors:
type: array
items:
$ref: '#/components/schemas/Person'
description: "A list of the people who created the entity with full name, email, ORCID iD, institution, etc.. This is analogus to the author list on a publication."
contacts:
type: array
items:
$ref: '#/components/schemas/Person'
description: "A list of the people who are the main contacts to get information about the entity."
title:
type: string
description: "The title of the Collection"
datasets:
type: array
readOnly: true
items:
$ref: '#/components/schemas/Dataset'
description: "The datasets that are contained in the Collection."
Publication:
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 HuBMAP unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17"
error_message:
type: string
readOnly: false
description: "An open text field that holds the last error message that arose from pipeline validation or analysis."
hubmap_id:
type: string
readOnly: true
description: "A HuBMAP Consortium wide unique identifier randomly generated in the format HBM###.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: "One of the normalized entity types: Dataset, Collection, Sample, Donor"
registered_doi:
type: string
description: "The doi of a the registered entity. e.g. 10.35079/hbm289.pcbm.487. This is set during the publication process and currently available for certain Collections and Datasets."
doi_url:
type: string
readOnly: true
description: "The url from the doi registry for this entity. e.g. https://doi.org/10.35079/hbm289.pcbm.487"
creators:
type: array
items:
$ref: '#/components/schemas/Person'
description: "A list of the people who created the entity with full name, email, ORCID iD, institution, etc.. This is analogus to the author list on a publication."
contacts:
type: array
items:
$ref: '#/components/schemas/Person'
description: "A list of the people who are the main contacts to get information about the entity."
antibodies:
type: array
items:
$ref: '#/components/schemas/Antibody'
description: "A list of antibodies used in the assay that created the dataset"
description:
type: string
description: "Free text description of the dataset"
data_access_level: