diff --git a/entity-api-spec.yaml b/entity-api-spec.yaml index 647b4aed..ac1e09fe 100644 --- a/entity-api-spec.yaml +++ b/entity-api-spec.yaml @@ -1,7 +1,7 @@ openapi: 3.0.3 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: 2.4.6 + version: 2.5.3 title: HuBMAP Entity API contact: name: HuBMAP Help Desk @@ -693,7 +693,7 @@ components: - 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).' + description: 'The data or assay types contained in this dataset as a json array of strings.' collections: readOnly: true type: array @@ -1134,7 +1134,7 @@ components: - 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).' + description: 'The data or assay types contained in this dataset as a json array of strings.' collections: readOnly: true type: array diff --git a/src/schema/provenance_schema.yaml b/src/schema/provenance_schema.yaml index dbb3351b..aab5d801 100644 --- a/src/schema/provenance_schema.yaml +++ b/src/schema/provenance_schema.yaml @@ -201,6 +201,12 @@ ENTITIES: - lab_dataset_id - metadata: - lab_id + - acquisition_id + - library_id + - donor_id + - slide_id + - tissue_id + - parent_sample_id # Collection can not be derivation source but not target derivation: source: false @@ -316,6 +322,12 @@ ENTITIES: - lab_dataset_id - metadata: - lab_id + - acquisition_id + - library_id + - donor_id + - slide_id + - tissue_id + - parent_sample_id - direct_ancestors: # Sample ancestors of a Dataset must have these fields removed - lab_tissue_sample_id @@ -325,6 +337,12 @@ ENTITIES: # Both Sample and Dataset ancestors of a Dataset must have these fields removed - metadata: - lab_id + - acquisition_id + - library_id + - donor_id + - slide_id + - tissue_id + - parent_sample_id derivation: source: true target: true @@ -404,7 +422,7 @@ ENTITIES: type: list indexed: true required_on_create: false - 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)." + description: "The data or assay types contained in this dataset as a json array of strings." dataset_type: before_property_create_validators: - validate_recognized_dataset_type @@ -669,7 +687,23 @@ ENTITIES: before_entity_update_validator: # Halt modification of entities which are "locked", such as a Dataset with status == 'Published' - validate_entity_not_locked_before_update - # Publications can be either derivation source or target + # Dataset can be either derivation source or target + excluded_properties_from_public_response: + - direct_ancestors: + # Sample ancestors of a Publication must have these fields removed + - lab_tissue_sample_id + - submission_id + # Dataset ancestors of a Publication must have these fields removed + - lab_dataset_id + # Both Sample and Dataset ancestors of a Publication must have these fields removed + - metadata: + - lab_id + - acquisition_id + - library_id + - donor_id + - slide_id + - tissue_id + - parent_sample_id # Publications can be either derivation source or target derivation: source: true target: true @@ -972,7 +1006,7 @@ ENTITIES: type: string indexed: true immutable: true - description: "Organ code specifier, only set if sample_type == organ. Valid values found in: [organ types](https://github.com/hubmapconsortium/search-api/blob/main/src/search-schema/data/definitions/enums/organ_types.yaml)" + description: "Organ code specifier, only set if sample_category == organ" organ_other: type: string indexed: true @@ -1026,6 +1060,10 @@ ENTITIES: type: json_string indexed: true description: "The sample location and orientation in the ancestor organ as specified in the RUI tool." + rui_exemption: + type: boolean + indexed: true + description: "Identifies Sample Blocks that are exempt from spatial registration via RUI." visit: type: string indexed: true