Derek furst/exclude results

VERSION

@@ -1 +1 @@
-2.3.21
+2.3.22

docker/docker-compose.deployment.yml

@@ -1,5 +1,3 @@
-version: "3.7"
-
 services:
 
   entity-api: 

docker/docker-compose.development.yml

@@ -1,5 +1,3 @@
-version: "3.7"
-
 services:
 
   entity-api:

docker/docker-compose.yml

@@ -1,6 +1,3 @@
-version: "3.7"
-
-# Will use the hostname when talking between services on the same network
 services:
 
   entity-api:

docker/docker-deployment.sh

@@ -56,11 +56,11 @@ else
     echo
 
     if [ "$1" = "start" ]; then
-        docker-compose -f docker-compose.yml -f docker-compose.deployment.yml -p entity-api up -d
+        docker compose -f docker-compose.yml -f docker-compose.deployment.yml -p entity-api up -d
     elif [ "$1" = "stop" ]; then
-        docker-compose -f docker-compose.yml -f docker-compose.deployment.yml -p entity-api stop
+        docker compose -f docker-compose.yml -f docker-compose.deployment.yml -p entity-api stop
     elif [ "$1" = "down" ]; then
-        docker-compose -f docker-compose.yml -f docker-compose.deployment.yml -p entity-api down
+        docker compose -f docker-compose.yml -f docker-compose.deployment.yml -p entity-api down
     fi
 fi
 

docker/docker-development.sh

@@ -106,13 +106,13 @@ else
         cp ../VERSION entity-api
         cp ../BUILD entity-api
 
-        docker-compose -f docker-compose.yml -f docker-compose.development.yml -p entity-api build
+	docker compose -f docker-compose.yml -f docker-compose.development.yml -p entity-api build
     elif [ "$1" = "start" ]; then
-        docker-compose -f docker-compose.yml -f docker-compose.development.yml -p entity-api up -d
+	docker compose -f docker-compose.yml -f docker-compose.development.yml -p entity-api up -d
     elif [ "$1" = "stop" ]; then
-        docker-compose -f docker-compose.yml -f docker-compose.development.yml -p entity-api stop
+        docker compose -f docker-compose.yml -f docker-compose.development.yml -p entity-api stop
     elif [ "$1" = "down" ]; then
-        docker-compose -f docker-compose.yml -f docker-compose.development.yml -p entity-api down
+        docker compose -f docker-compose.yml -f docker-compose.development.yml -p entity-api down
     fi
 fi
 

docker/entity-api/Dockerfile

@@ -1,5 +1,5 @@
 # Parent image
-FROM hubmap/api-base-image:1.0.0
+FROM hubmap/api-base-image:1.1.0
 
 LABEL description="HuBMAP Entity API Service"
 

docker/entity-api/entrypoint.sh

@@ -26,7 +26,7 @@ chown -R hive:hive /var/run/nginx.pid
 chown -R hive:hive /var/cache/nginx
 chown -R hive:hive /var/log/nginx
 
-# Lastly we use gosu to execute our process "$@" as that user
+# Lastly we use su-exec to execute our process "$@" as that user
 # Remember CMD from a Dockerfile of child image gets passed to the entrypoint.sh as command line arguments
 # "$@" is a shell variable that means "all the arguments"
-exec /usr/local/bin/gosu hive "$@"
+exec /usr/local/bin/su-exec hive "$@"

src/schema/provenance_schema.yaml

@@ -131,23 +131,14 @@ doi_properties: &doi_properties
     before_property_update_validators:
      - verify_DOI_pair
      - halt_update_if_DOI_exists
-  # Currently creators and contacts are only available for public Collections
-  creators:
+  contributors:
     type: list
     indexed: true
     description: "A list of the people who created the entity with full name, email, ORCID iD, institution, etc.. This is analogous to the author list on a publication."
   contacts:
     type: list
     indexed: true
     description: "A list of the people who are the main contacts to get information about the entity."
-  # To-DO
-  # creator_ids:
-  #   type: list
-  #   immutable: true
-  #   description: "A list of ids (will need to decide on uuid or orcid id) referencing the people who created the entity"
-  # contact_ids:
-  #   type: list
-  #   description: "A list of ids (will need to decide on uuid or orcid id) referencing the people who are the main contacts about this entity"
 
 shared_entity_properties: &shared_entity_properties 
   ###### Last Modified Properties #######
@@ -210,9 +201,7 @@ ENTITIES:
       <<: *shared_properties
       <<: *shared_entity_properties
       # Because Collection-specific validation is needed for some
-      # DOI fields, all validations from
-      # <<: *doi_properties
-      # are merged into this section
+      # DOI fields, we don't use the shared <<: *doi_properties here
       ###### DOI properties with entity-specific validations + copies of validations in doi_properties ######
       registered_doi:
         type: string
@@ -311,6 +300,11 @@ ENTITIES:
     # Only allowed applications can create new Dataset via POST
     before_entity_create_validator: validate_application_header_before_entity_create
     # Dataset can be either derivation source or target
+    excluded_properties_from_public_response:
+      - lab_dataset_id
+      - ingest_metadata:
+          metadata:
+            - lab_id
     derivation:
       source: true
       target: true
@@ -416,10 +410,6 @@ ENTITIES:
         description: "The Upload that this dataset is associated with. Will be returned in response"
         on_read_trigger: get_dataset_upload
         # No on_index_trigger to include upload in the OpenSearch document for a Dataset
-      contributors:
-        type: list
-        indexed: true
-        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_ancestor_uuids:
         required_on_create: true # Only required for create via POST, not update via PUT
         type: list
@@ -748,6 +738,9 @@ ENTITIES:
     derivation:
       source: false
       target: true
+    excluded_properties_from_public_response:
+      - lab_donor_id
+      - submission_id
     properties:
       <<: *shared_properties
       <<: *shared_entity_properties
@@ -866,6 +859,9 @@ ENTITIES:
     derivation:
       source: true
       target: true
+    excluded_properties_from_public_response:
+      - lab_tissue_sample_id
+      - submission_id
     properties:
       <<: *shared_properties
       <<: *shared_entity_properties
@@ -1205,4 +1201,4 @@ ENTITIES:
       source: false
       target: false
     properties:
-      <<: *shared_collection_properties
+      <<: *shared_collection_properties

src/schema/schema_manager.py

@@ -259,6 +259,43 @@ def entity_instanceof(entity_uuid: str, entity_class: str) -> bool:
     return entity_type_instanceof(entity_type, entity_class)
 
 
+def get_fields_to_exclude(normalized_class=None):
+    # Determine the schema section based on class
+    excluded_fields = []
+    if normalized_class == 'Activity':
+        schema_section = _schema['ACTIVITIES']
+    else:
+        schema_section = _schema['ENTITIES']
+    exclude_list = schema_section[normalized_class].get('excluded_properties_from_public_response')
+    if exclude_list:
+        excluded_fields.extend(exclude_list)
+    return excluded_fields
+
+
+def exclude_properties_from_response(excluded_fields, json_body):
+    output_json = json_body.copy()
+
+    def delete_nested_field(data, nested_path):
+        if isinstance(nested_path, dict):
+            for key, value in nested_path.items():
+                if key in data:
+                    if isinstance(value, list):
+                        for nested_field in value:
+                            if isinstance(nested_field, dict):
+                                delete_nested_field(data[key], nested_field)
+                            elif nested_field in data[key]:
+                                del data[key][nested_field]
+                    elif isinstance(value, dict):
+                        delete_nested_field(data[key], value)
+        elif nested_path in data:
+            del data[nested_path]
+
+    for field in excluded_fields:
+        delete_nested_field(output_json, field)
+
+    return output_json
+
+
 """
 Generating triggered data based on the target events and methods
 

src/schema/schema_triggers.py

@@ -1312,6 +1312,7 @@ def commit_thumbnail_file(property_key, normalized_type, user_token, existing_da
         raise
 
 
+
 """
 Trigger event method for removing the thumbnail file from a dataset during update