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Fix issue with Exploration tool #1588

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merged 1 commit into from
Jan 14, 2017
Merged

Fix issue with Exploration tool #1588

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21 changes: 12 additions & 9 deletions refinery/core/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,20 +56,21 @@ def update_data_set_index(data_set):


@skip
def add_data_set_to_neo4j(dataset_uuid, user_id):
def add_data_set_to_neo4j(dataset, user_id):

"""Add a node in Neo4J for a dataset and give the owner read access.
Note: Neo4J manages read access only.
"""

logger.info(
'Add dataset (uuid: %s) to Neo4J and give read access to user ' +
'(id: %s)', dataset_uuid, user_id
'(id: %s)', dataset.uuid, user_id
)

graph = py2neo.Graph(urljoin(settings.NEO4J_BASE_URL, 'db/data'))

# Get annotations of the data_set
annotations = get_data_set_annotations(dataset_uuid)
annotations = get_data_set_annotations(dataset.uuid)
annotations = normalize_annotation_ont_ids(annotations)

try:
Expand All @@ -80,13 +81,13 @@ def add_data_set_to_neo4j(dataset_uuid, user_id):

statement_name = (
"MATCH (term:Class {name:{ont_id}}) "
"MERGE (ds:DataSet {uuid:{ds_uuid}}) "
"MERGE (ds:DataSet {id:{ds_id},uuid:{ds_uuid}}) "
"MERGE ds-[:`annotated_with`]->term"
)

statement_uri = (
"MATCH (term:Class {uri:{uri}}) "
"MERGE (ds:DataSet {uuid:{ds_uuid}}) "
"MERGE (ds:DataSet {id:{ds_id},uuid:{ds_uuid}}) "
"MERGE ds-[:`annotated_with`]->term"
)

Expand All @@ -96,7 +97,8 @@ def add_data_set_to_neo4j(dataset_uuid, user_id):
statement_uri,
{
'uri': annotation['value_uri'],
'ds_uuid': annotation['data_set_uuid']
'ds_id': dataset.id,
'ds_uuid': dataset.uuid
}
)
else:
Expand All @@ -108,7 +110,8 @@ def add_data_set_to_neo4j(dataset_uuid, user_id):
':' +
annotation['value_accession']
),
'ds_uuid': annotation['data_set_uuid']
'ds_id': dataset.id,
'ds_uuid': dataset.uuid
}
)

Expand All @@ -129,7 +132,7 @@ def add_data_set_to_neo4j(dataset_uuid, user_id):
tx.append(
statement,
{
'ds_uuid': dataset_uuid,
'ds_uuid': dataset.uuid,
'user_id': user_id
}
)
Expand All @@ -142,7 +145,7 @@ def add_data_set_to_neo4j(dataset_uuid, user_id):
"""
logger.error(
'Failed to add read access to data set (uuid: %s) for user '
'(uuid: %s) to Neo4J. Exception: %s', dataset_uuid, user_id, e
'(uuid: %s) to Neo4J. Exception: %s', dataset.uuid, user_id, e
)


Expand Down
6 changes: 4 additions & 2 deletions refinery/data_set_manager/tasks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,8 @@
from django.core.management import call_command

from core.models import DataSet, FileStoreItem, ExtendedGroup
from core.utils import update_data_set_index, add_data_set_to_neo4j
from core.utils import update_data_set_index, add_data_set_to_neo4j, \
update_annotation_sets_neo4j
from file_store.models import FileExtension
from .isa_tab_parser import IsaTabParser
from .models import Investigation, Node, \
Expand Down Expand Up @@ -385,7 +386,8 @@ def create_dataset(investigation_uuid, username, identifier=None, title=None,
dataset.save()
# Finally index data set
update_data_set_index(dataset)
add_data_set_to_neo4j(dataset.uuid, user.id)
add_data_set_to_neo4j(dataset, user.id)
update_annotation_sets_neo4j()
return dataset.uuid
return None

Expand Down