From 716cd73f6bbd36e95089a97f693ecd8e1dd27195 Mon Sep 17 00:00:00 2001 From: Derek Furst Date: Thu, 13 Aug 2026 16:53:37 -0400 Subject: [PATCH] completely removed all uses of sample.other_organ --- entity-api-spec.yaml | 6 ------ src/schema/provenance_schema.yaml | 4 ---- .../api-template-test/entity-Template.yaml | 3 --- .../example-yaml-templates/entity-api-spec-TEMPLATE.yaml | 3 --- .../example-yaml-templates/sample-schema.yaml | 3 --- 5 files changed, 19 deletions(-) diff --git a/entity-api-spec.yaml b/entity-api-spec.yaml index b2f8b578..c2949cb5 100644 --- a/entity-api-spec.yaml +++ b/entity-api-spec.yaml @@ -483,9 +483,6 @@ components: - UR - UT description: 'Organ code specifier, only set if sample_category == organ. Valid values found in: [organ types](https://ontology.api.hubmapconsortium.org/organs/by-code?application_context=HUBMAP)' - 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 @@ -1407,7 +1404,6 @@ components: data_access_level: 'public' sample_category: 'organ' organ: 'AO' - organ_other: 'other' image_files: [image_files objects] image_files_to_add: [strings] image_files_to_remove: [strings] @@ -1729,7 +1725,6 @@ components: data_access_level: 'public' sample_category: 'organ' organ: 'AO' - organ_other: 'other' image_files: [image_files objects] image_files_to_add: [strings] image_files_to_remove: [strings] @@ -1763,7 +1758,6 @@ components: data_access_level: 'public' sample_category: 'organ' organ: 'AO' - organ_other: 'other' image_files: [image_files objects] image_files_to_add: [strings] image_files_to_remove: [strings] diff --git a/src/schema/provenance_schema.yaml b/src/schema/provenance_schema.yaml index b013570c..16aa5c00 100644 --- a/src/schema/provenance_schema.yaml +++ b/src/schema/provenance_schema.yaml @@ -1019,10 +1019,6 @@ ENTITIES: indexed: true immutable: true description: "Organ code specifier, only set if sample_category == organ" - organ_other: - type: string - indexed: true - description: The organ type provided by the user if "other" organ type is selected direct_ancestor_uuid: type: string required_on_create: true # Creating the hubmap ids via uuid-api requires `parent_ids` diff --git a/src/schema_templating/example-yaml-templates/api-template-test/entity-Template.yaml b/src/schema_templating/example-yaml-templates/api-template-test/entity-Template.yaml index 07bd4e1c..9af73a74 100644 --- a/src/schema_templating/example-yaml-templates/api-template-test/entity-Template.yaml +++ b/src/schema_templating/example-yaml-templates/api-template-test/entity-Template.yaml @@ -444,9 +444,6 @@ x-ref-components: - UR - UT 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)" - 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 diff --git a/src/schema_templating/example-yaml-templates/entity-api-spec-TEMPLATE.yaml b/src/schema_templating/example-yaml-templates/entity-api-spec-TEMPLATE.yaml index 6b06be25..a777dd78 100644 --- a/src/schema_templating/example-yaml-templates/entity-api-spec-TEMPLATE.yaml +++ b/src/schema_templating/example-yaml-templates/entity-api-spec-TEMPLATE.yaml @@ -423,9 +423,6 @@ components: X-replace-enum-list: enum-file-ref: https://raw.githubusercontent.com/hubmapconsortium/search-api/main/src/search-schema/data/definitions/enums/organ_types.yaml 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)" - 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 diff --git a/src/schema_templating/example-yaml-templates/sample-schema.yaml b/src/schema_templating/example-yaml-templates/sample-schema.yaml index 2b6f3f11..6daca5eb 100644 --- a/src/schema_templating/example-yaml-templates/sample-schema.yaml +++ b/src/schema_templating/example-yaml-templates/sample-schema.yaml @@ -88,9 +88,6 @@ Sample: X-replace-enum-list: enum-file-ref: https://raw.githubusercontent.com/hubmapconsortium/search-api/main/src/search-schema/data/definitions/enums/organ_types.yaml 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)" - 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