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modified omitted fields to not include metadata. Modified /ancestors … #785

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merged 3 commits into from
Jan 17, 2025
Merged

modified omitted fields to not include metadata. Modified /ancestors … #785

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09a9076
modified omitted fields to not include metadata. Modified /ancestors …
DerekFurstPitt Jan 14, 2025
a852db5
changed /ancestors /children /parents/ descendants queries to omit fi…
DerekFurstPitt Jan 16, 2025
4ae38a8
removed superfluous key removals in ancestor, parent, children, desce…
DerekFurstPitt Jan 16, 2025
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2 changes: 1 addition & 1 deletion src/schema/schema_constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ class SchemaConstants(object):

DOI_BASE_URL = 'https://doi.org/'

DATASETS_OMITTED_FIELDS = ['ingest_metadata', 'metadata', 'files']
OMITTED_FIELDS = ['ingest_metadata', 'files']

# Define an enumeration to classify an entity's visibility, which can be combined with
# authorization info when verify operations on a request.
Expand Down
24 changes: 12 additions & 12 deletions src/schema/schema_neo4j_queries.py
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Expand Up @@ -164,7 +164,7 @@ def filter_ancestors_by_type(neo4j_driver, direct_ancestor_uuids, entity_type):
"""
def get_children(neo4j_driver, uuid, property_key = None):
results = []

fields_to_omit = SchemaConstants.OMITTED_FIELDS
if property_key:
query = (f"MATCH (e:Entity)-[:ACTIVITY_INPUT]->(:Activity)-[:ACTIVITY_OUTPUT]->(child:Entity) "
# The target entity can't be a Lab
Expand All @@ -178,7 +178,7 @@ def get_children(neo4j_driver, uuid, property_key = None):
f"WHERE e.uuid='{uuid}' AND e.entity_type <> 'Lab' "
# COLLECT() returns a list
# apoc.coll.toSet() reruns a set containing unique nodes
f"RETURN apoc.coll.toSet(COLLECT(child)) AS {record_field_name}")
f"RETURN apoc.coll.toSet(COLLECT(apoc.create.vNode(labels(child), apoc.map.removeKeys(properties(child), {fields_to_omit})))) AS {record_field_name}")

logger.info("======get_children() query======")
logger.info(query)
Expand All @@ -193,7 +193,7 @@ def get_children(neo4j_driver, uuid, property_key = None):
else:
# Convert the list of nodes to a list of dicts
results = nodes_to_dicts(record[record_field_name])

return results


Expand All @@ -216,7 +216,7 @@ def get_children(neo4j_driver, uuid, property_key = None):
"""
def get_parents(neo4j_driver, uuid, property_key = None):
results = []

fields_to_omit = SchemaConstants.OMITTED_FIELDS
if property_key:
query = (f"MATCH (e:Entity)<-[:ACTIVITY_OUTPUT]-(:Activity)<-[:ACTIVITY_INPUT]-(parent:Entity) "
# Filter out the Lab entities
Expand All @@ -230,7 +230,7 @@ def get_parents(neo4j_driver, uuid, property_key = None):
f"WHERE e.uuid='{uuid}' AND parent.entity_type <> 'Lab' "
# COLLECT() returns a list
# apoc.coll.toSet() reruns a set containing unique nodes
f"RETURN apoc.coll.toSet(COLLECT(parent)) AS {record_field_name}")
f"RETURN apoc.coll.toSet(COLLECT(apoc.create.vNode(labels(parent), apoc.map.removeKeys(properties(parent), {fields_to_omit})))) AS {record_field_name}")

logger.info("======get_parents() query======")
logger.info(query)
Expand Down Expand Up @@ -380,7 +380,7 @@ def get_tuplets(neo4j_driver, uuid, property_key=None):
"""
def get_ancestors(neo4j_driver, uuid, property_key = None):
results = []

fields_to_omit = SchemaConstants.OMITTED_FIELDS
if property_key:
query = (f"MATCH (e:Entity)<-[:ACTIVITY_INPUT|ACTIVITY_OUTPUT*]-(ancestor:Entity) "
# Filter out the Lab entities
Expand All @@ -394,7 +394,7 @@ def get_ancestors(neo4j_driver, uuid, property_key = None):
f"WHERE e.uuid='{uuid}' AND ancestor.entity_type <> 'Lab' "
# COLLECT() returns a list
# apoc.coll.toSet() reruns a set containing unique nodes
f"RETURN apoc.coll.toSet(COLLECT(ancestor)) AS {record_field_name}")
f"RETURN apoc.coll.toSet(COLLECT(apoc.create.vNode(labels(ancestor), apoc.map.removeKeys(properties(ancestor), {fields_to_omit})))) AS {record_field_name}")

logger.info("======get_ancestors() query======")
logger.info(query)
Expand Down Expand Up @@ -431,7 +431,7 @@ def get_ancestors(neo4j_driver, uuid, property_key = None):
"""
def get_descendants(neo4j_driver, uuid, property_key = None):
results = []

fields_to_omit = SchemaConstants.OMITTED_FIELDS
if property_key:
query = (f"MATCH (e:Entity)-[:ACTIVITY_INPUT|ACTIVITY_OUTPUT*]->(descendant:Entity) "
# The target entity can't be a Lab
Expand All @@ -445,7 +445,7 @@ def get_descendants(neo4j_driver, uuid, property_key = None):
f"WHERE e.uuid='{uuid}' AND e.entity_type <> 'Lab' "
# COLLECT() returns a list
# apoc.coll.toSet() reruns a set containing unique nodes
f"RETURN apoc.coll.toSet(COLLECT(descendant)) AS {record_field_name}")
f"RETURN apoc.coll.toSet(COLLECT(apoc.create.vNode(labels(descendant), apoc.map.removeKeys(properties(descendant), {fields_to_omit})))) AS {record_field_name}")

logger.info("======get_descendants() query======")
logger.info(query)
Expand All @@ -460,7 +460,7 @@ def get_descendants(neo4j_driver, uuid, property_key = None):
else:
# Convert the list of nodes to a list of dicts
results = nodes_to_dicts(record[record_field_name])

return results


Expand Down Expand Up @@ -1185,7 +1185,7 @@ def get_dataset_upload(neo4j_driver, uuid):
def get_collection_datasets(neo4j_driver, uuid):
results = []

fields_to_omit = SchemaConstants.DATASETS_OMITTED_FIELDS
fields_to_omit = SchemaConstants.OMITTED_FIELDS
query = (f"MATCH (e:Dataset)-[:IN_COLLECTION]->(c:Collection) "
f"WHERE c.uuid = '{uuid}' "
f"RETURN COLLECT(apoc.create.vNode(labels(e), apoc.map.removeKeys(properties(e), {fields_to_omit}))) AS {record_field_name}")
Expand Down Expand Up @@ -1391,7 +1391,7 @@ def unlink_datasets_from_upload(neo4j_driver, upload_uuid, dataset_uuids_list):
"""
def get_upload_datasets(neo4j_driver, uuid, property_key = None):
results = []
fields_to_omit = SchemaConstants.DATASETS_OMITTED_FIELDS
fields_to_omit = SchemaConstants.OMITTED_FIELDS
if property_key:
query = (f"MATCH (e:Dataset)-[:IN_UPLOAD]->(s:Upload) "
f"WHERE s.uuid = '{uuid}' "
Expand Down
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