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completely removed all uses of sample.other_organ #1025

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Merged
yuanzhou merged 1 commit into from
Aug 14, 2026
Merged

completely removed all uses of sample.other_organ #1025

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6 changes: 0 additions & 6 deletions entity-api-spec.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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]
Expand Down
4 changes: 0 additions & 4 deletions src/schema/provenance_schema.yaml
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Expand Up @@ -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`
Expand Down
3 changes: 0 additions & 3 deletions src/schema_templating/example-yaml-templates/api-template-test/entity-Template.yaml
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Expand Up @@ -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
Expand Down
3 changes: 0 additions & 3 deletions src/schema_templating/example-yaml-templates/entity-api-spec-TEMPLATE.yaml
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Expand Up @@ -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
Expand Down
3 changes: 0 additions & 3 deletions src/schema_templating/example-yaml-templates/sample-schema.yaml
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Expand Up @@ -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
Expand Down
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