New fields to exclude from public responses

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

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