From f11157eab21f82a9c74186b9f5b826e690fa5cc6 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 8 Jul 2022 17:00:14 +0200
Subject: [PATCH] small fixes and cleanup
---
drugstone/management/commands/cleanuptasks.py | 1 -
drugstone/util/nedrex.py | 8 --------
drugstone/views.py | 18 ++++++++----------
tasks/util/read_graph_tool_graph.py | 2 ++
4 files changed, 10 insertions(+), 19 deletions(-)
delete mode 100644 drugstone/util/nedrex.py
diff --git a/drugstone/management/commands/cleanuptasks.py b/drugstone/management/commands/cleanuptasks.py
index 470611a..ee6fe53 100755
--- a/drugstone/management/commands/cleanuptasks.py
+++ b/drugstone/management/commands/cleanuptasks.py
@@ -11,7 +11,6 @@ class Command(BaseCommand):
def handle(self, *args, **kwargs):
print('Task cleanup...')
- print()
print(f'Closing {Task.objects.filter(started_at__isnull=True).count()} queued tasks')
Task.objects.filter(started_at__isnull=True).update(started_at=timezone.now(), finished_at=timezone.now(),
diff --git a/drugstone/util/nedrex.py b/drugstone/util/nedrex.py
deleted file mode 100644
index d3f85eb..0000000
--- a/drugstone/util/nedrex.py
+++ /dev/null
@@ -1,8 +0,0 @@
-def fetch_nedrex_data():
- print('fetching')
- return
-
-
-def integrate_nedrex_data():
- print('integrating')
- return
diff --git a/drugstone/views.py b/drugstone/views.py
index c081718..fa5ea27 100755
--- a/drugstone/views.py
+++ b/drugstone/views.py
@@ -337,16 +337,8 @@ def result_view(request) -> Response:
for node_id in nodes:
is_seed[node_id] = node_id in seeds
node_type = node_types.get(node_id).lower()
- # if node_type == 'node':
- # # TODO remove this if after next make_graphs
- # node_type = 'protein'
pvd_entity = None
details_s = None
- # if not node_type:
- # # TODO can this be removed? should never be reached
- # print('we should not see this 2')
- # node_type, pvd_entity = infer_node_type_and_details(int(node_id[1:]))
- # else:
if node_type == 'protein':
pvd_entity = Protein.objects.get(id=int(node_id[1:]))
elif node_type == 'drug':
@@ -409,14 +401,20 @@ def result_view(request) -> Response:
nodes_mapped, id_key = query_proteins_by_identifier(edge_endpoint_ids, identifier)
# change data structure to dict in order to be quicker when merging
nodes_mapped_dict = {node[id_key]: node for node in nodes_mapped}
-
for edge in edges:
# change edge endpoints if they were matched with a protein in the database
edge['from'] = nodes_mapped_dict[edge['from']][node_name_attribute] if edge['from'] in nodes_mapped_dict else \
edge['from']
edge['to'] = nodes_mapped_dict[edge['to']][node_name_attribute] if edge['to'] in nodes_mapped_dict else edge[
'to']
-
+ if 'autofill_edges' in parameters['config'] and parameters['config']['autofill_edges']:
+ proteins = set(map(lambda n:n[node_name_attribute][1:],filter(lambda n: node_name_attribute in n,parameters['input_network']['nodes'])))
+ dataset = 'STRING' if 'interaction_protein_protein' not in parameters['config'] else parameters['config']['interaction_protein_protein']
+ dataset_object = models.PPIDataset.objects.filter(name__iexact=dataset).last()
+ interaction_objects = models.ProteinProteinInteraction.objects.filter(
+ Q(ppi_dataset=dataset_object) & Q(from_protein__in=proteins) & Q(to_protein__in=proteins))
+ auto_edges = list(map(lambda n: {"from": f'p{n.from_protein_id}', "to":f'p{n.to_protein_id}'} ,interaction_objects))
+ edges.extend(auto_edges)
result['network']['edges'].extend(edges)
if not view:
diff --git a/tasks/util/read_graph_tool_graph.py b/tasks/util/read_graph_tool_graph.py
index 94db075..1e9caf2 100755
--- a/tasks/util/read_graph_tool_graph.py
+++ b/tasks/util/read_graph_tool_graph.py
@@ -106,6 +106,8 @@ def read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs=Fals
deleted_edges.append(edge)
if indir_drug and int(edge.source()) in drug_ids:
drug_ids.remove(int(edge.source()))
+ else:
+ deleted_edges.append(edge)
g.set_fast_edge_removal(fast=True)
for edge in deleted_edges:
--
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