Merge pull request #578 from hubmapconsortium/Derek-Furst/add_previou…

…s_revision_uuids

Derek furst/add previous revision uuids

entity-api-spec.yaml

@@ -782,6 +782,13 @@ components:
           type: string
           readOnly: true
           description: "The uuid of next revision dataset"
+        previous_revision_uuids:
+          type: list
+          description: "The uuids of previous revision datasets. Can only be set at Create/POST time."
+        next_revision_uuids:
+          type: list
+          readOnly: true
+          description: "The uuids of next revision dataset"
         thumbnail_file:
           readOnly: true
           description: 'The dataset thumbnail file detail. Stored in db as a stringfied json, e.g., {"filename": "thumbnail.jpg", "file_uuid": "c35002f9c3d49f8b77e1e2cd4a01803d"}'

src/schema/provenance_schema.yaml

@@ -427,13 +427,27 @@ ENTITIES:
         description: "The uuid of previous revision dataset"
         after_create_trigger: link_to_previous_revision
         on_read_trigger: get_previous_revision_uuid
+      previous_revision_uuids:
+        type: list
+        generated: true
+        transient: true
+        immutable: true
+        description: "The list of the uuids of previous revision datasets"
+        on_read_trigger: get_previous_revision_uuids
       next_revision_uuid:
         type: string
         generated: true
         transient: true
         immutable: true
         description: "The uuid of next revision dataset"
         on_read_trigger: get_next_revision_uuid
+      next_revision_uuids:
+        type: list
+        generated: true
+        transient: true
+        immutable: true
+        description: "The list of the uuids of next revision datasets"
+        on_read_trigger: get_next_revision_uuids
       # No like image and metadata files handling for Donor/Sample
       # Dataset has only one thumbnail file
       thumbnail_file:
@@ -657,13 +671,27 @@ ENTITIES:
         description: "The uuid of previous revision dataset"
         after_create_trigger: link_to_previous_revision
         on_read_trigger: get_previous_revision_uuid
+      previous_revision_uuids:
+        type: list
+        generated: true
+        transient: true
+        immutable: true
+        description: "The list of the uuids of previous revision datasets"
+        on_read_trigger: get_previous_revision_uuids
       next_revision_uuid:
         type: string
         generated: true
         transient: true
         immutable: true
         description: "The uuid of next revision dataset"
         on_read_trigger: get_next_revision_uuid
+      next_revision_uuids:
+        type: list
+        generated: true
+        transient: true
+        immutable: true
+        description: "The list of the uuids of next revision datasets"
+        on_read_trigger: get_next_revision_uuids
       # No like image and metadata files handling for Donor/Sample
       # Dataset has only one thumbnail file
       thumbnail_file:

src/schema/schema_neo4j_queries.py

@@ -723,6 +723,44 @@ def get_previous_revision_uuid(neo4j_driver, uuid):
     return result
 
 
+"""
+Get the uuids of previous revision entities for a given entity
+
+Parameters
+----------
+neo4j_driver : neo4j.Driver object
+    The neo4j database connection pool
+uuid : str
+    The uuid of the entity 
+
+Returns
+-------
+list
+    The previous revision uuids
+"""
+def get_previous_revision_uuids(neo4j_driver, uuid):
+    result = []
+
+    # Don't use [r:REVISION_OF] because
+    # Binding a variable length relationship pattern to a variable ('r') is deprecated
+    query = (f"MATCH (e:Entity)-[:REVISION_OF]->(previous_revision:Entity) "
+             f"WHERE e.uuid='{uuid}' "
+             f"RETURN COLLECT(previous_revision.uuid) AS {record_field_name}")
+
+    logger.info("======get_previous_revision_uuids() query======")
+    logger.info(query)
+
+    with neo4j_driver.session() as session:
+        record = session.read_transaction(execute_readonly_tx, query)
+
+        if record and record[record_field_name]:
+            result = record[record_field_name]
+
+    return result
+
+
+
+
 """
 Get the uuid of next revision entity for a given entity
 
@@ -759,6 +797,42 @@ def get_next_revision_uuid(neo4j_driver, uuid):
     return result
 
 
+"""
+Get the uuids of next revision entities for a given entity
+
+Parameters
+----------
+neo4j_driver : neo4j.Driver object
+    The neo4j database connection pool
+uuid : str
+    The uuid of the entity 
+
+Returns
+-------
+list
+    The uuids of the next revision
+"""
+def get_next_revision_uuids(neo4j_driver, uuid):
+    result = []
+
+    # Don't use [r:REVISION_OF] because
+    # Binding a variable length relationship pattern to a variable ('r') is deprecated
+    query = (f"MATCH (e:Entity)<-[:REVISION_OF]-(next_revision:Entity) "
+             f"WHERE e.uuid='{uuid}' "
+             f"RETURN COLLECT(next_revision.uuid) AS {record_field_name}")
+
+    logger.info("======get_next_revision_uuids() query======")
+    logger.info(query)
+
+    with neo4j_driver.session() as session:
+        record = session.read_transaction(execute_readonly_tx, query)
+
+        if record and record[record_field_name]:
+            result = record[record_field_name]
+
+    return result
+
+
 """
 Get a list of associated Datasets and Publications (subclass of Dataset) uuids for a given collection
 

src/schema/schema_triggers.py

@@ -1117,6 +1117,42 @@ def get_previous_revision_uuid(property_key, normalized_type, user_token, existi
     return property_key, previous_revision_uuid
 
 
+"""
+Trigger event method of getting the uuids of the previous revision datasets if they exist
+
+Parameters
+----------
+property_key : str
+    The target property key
+normalized_type : str
+    One of the types defined in the schema yaml: Dataset
+user_token: str
+    The user's globus nexus token
+existing_data_dict : dict
+    A dictionary that contains all existing entity properties
+new_data_dict : dict
+    A merged dictionary that contains all possible input data to be used
+
+Returns
+-------
+str: The target property key
+str: A list of the uuid strings of previous revision entity or an empty list if not found
+"""
+
+
+def get_previous_revision_uuids(property_key, normalized_type, user_token, existing_data_dict, new_data_dict):
+    if 'uuid' not in existing_data_dict:
+        raise KeyError(
+            "Missing 'uuid' key in 'existing_data_dict' during calling 'get_previous_revision_uuid()' trigger method.")
+
+    logger.info(f"Executing 'get_previous_revision_uuids()' trigger method on uuid: {existing_data_dict['uuid']}")
+
+    previous_revision_uuids = schema_neo4j_queries.get_previous_revision_uuids(schema_manager.get_neo4j_driver_instance(),
+                                                                             existing_data_dict['uuid'])
+
+    return property_key, previous_revision_uuids
+
+
 """
 Trigger event method of getting the uuid of the next version dataset if exists
 
@@ -1163,6 +1199,42 @@ def get_creation_action_activity(property_key, normalized_type, user_token, exis
     return property_key, creation_action_activity
 
 
+"""
+Trigger event method of getting the uuids of the next version dataset if they exist
+
+Parameters
+----------
+property_key : str
+    The target property key
+normalized_type : str
+    One of the types defined in the schema yaml: Dataset
+user_token: str
+    The user's globus nexus token
+existing_data_dict : dict
+    A dictionary that contains all existing entity properties
+new_data_dict : dict
+    A merged dictionary that contains all possible input data to be used
+
+Returns
+-------
+str: The target property key
+str: The list of uuid strings of next version entity or empty string if not found
+"""
+
+
+def get_next_revision_uuids(property_key, normalized_type, user_token, existing_data_dict, new_data_dict):
+    if 'uuid' not in existing_data_dict:
+        raise KeyError(
+            "Missing 'uuid' key in 'existing_data_dict' during calling 'get_next_revision_uuid()' trigger method.")
+
+    logger.info(f"Executing 'get_next_revision_uuid()' trigger method on uuid: {existing_data_dict['uuid']}")
+
+    next_revision_uuids = schema_neo4j_queries.get_next_revision_uuids(schema_manager.get_neo4j_driver_instance(),
+                                                                     existing_data_dict['uuid'])
+
+    return property_key, next_revision_uuids
+
+
 """
 Trigger event method to commit thumbnail file saved that were previously uploaded via ingest-api