From dc5998e56ede26437654ff2b8b964ce6f391b0e5 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 29 Jul 2022 11:55:07 +0200
Subject: [PATCH] fixed ensg mode; fixed auto edges on results; fixed issue
with dataset pairs on network generation
---
drugstone/management/commands/make_graphs.py | 16 ++++++-----
drugstone/util/query_db.py | 2 ++
drugstone/views.py | 30 ++++----------------
3 files changed, 16 insertions(+), 32 deletions(-)
diff --git a/drugstone/management/commands/make_graphs.py b/drugstone/management/commands/make_graphs.py
index 8794f48..5a1f6ec 100755
--- a/drugstone/management/commands/make_graphs.py
+++ b/drugstone/management/commands/make_graphs.py
@@ -242,18 +242,20 @@ class Command(BaseCommand):
parameter_combinations = []
for protein_interaction_dataset in ppi_datasets:
for pdi_dataset in pdi_datasets:
- licenced = protein_interaction_dataset.licenced or pdi_dataset.licenced
+ ppi_ds = protein_interaction_dataset
+ pdi_ds = pdi_dataset
+ licenced = ppi_ds.licenced or pdi_ds.licenced
if licenced:
- protein_interaction_dataset = licenced_ppi_dataset[
- protein_interaction_dataset.name] if protein_interaction_dataset.name in licenced_ppi_dataset else protein_interaction_dataset
- pdi_dataset = licenced_pdi_dataset[
- pdi_dataset.name] if pdi_dataset.name in licenced_pdi_dataset else pdi_dataset
- hash = f'{protein_interaction_dataset.name}-{pdi_dataset.name}_{licenced}'
+ ppi_ds = licenced_ppi_dataset[
+ ppi_ds.name] if protein_interaction_dataset.name in licenced_ppi_dataset else ppi_ds
+ pdi_ds = licenced_pdi_dataset[
+ pdi_ds.name] if pdi_ds.name in licenced_pdi_dataset else pdi_ds
+ hash = f'{ppi_ds.name}-{pdi_ds.name}_{licenced}'
if hash in uniq_combis:
continue
uniq_combis.add(hash)
for identifier in ['ensg', 'symbol', 'ensembl', 'uniprot']:
- parameter_combinations.append([protein_interaction_dataset, pdi_dataset, identifier])
+ parameter_combinations.append([ppi_ds, pdi_ds, identifier])
# close all database connections so subprocesses will create their own connections
# this prevents the processes from running into problems because of using the same connection
db.connections.close_all()
diff --git a/drugstone/util/query_db.py b/drugstone/util/query_db.py
index ba26adb..0afd48d 100644
--- a/drugstone/util/query_db.py
+++ b/drugstone/util/query_db.py
@@ -24,6 +24,8 @@ def query_proteins_by_identifier(node_ids: Set[str], identifier: str) -> Tuple[L
Returns name of backend attribute of Protein table
"""
# query protein table
+ if(len(node_ids) == 0):
+ return list(), identifier
if identifier == 'symbol':
protein_attribute = 'symbol'
q_list = map(lambda n: Q(gene__iexact=n), node_ids)
diff --git a/drugstone/views.py b/drugstone/views.py
index b5e8183..a60a38c 100755
--- a/drugstone/views.py
+++ b/drugstone/views.py
@@ -377,27 +377,13 @@ 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
- print(nodes_mapped)
- # nodes_mapped_dict = {node[id_key][0]: node for node in nodes_mapped}
- # nodes_mapped_dict_reverse = {}
- # for id, node in nodes_mapped_dict.items():
- # for drugstone_id in node[node_name_attribute]:
- # nodes_mapped_dict_reverse[node[drugstone_id]] = id
-
- print(nodes)
- # 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']:
+ prots = list(filter(lambda n: n['drugstone_type'] == 'protein',
+ filter(lambda n: 'drugstone_type' in n and node_name_attribute in n, parameters['input_network']['nodes'])))
- if 'autofill_edges' in parameters['config'] and parameters['config']['autofill_edges']:
- proteins = {node_name[1:] for nodes in map(lambda n: 'drugstoneType' in n and n[node_name_attribute],
- filter(lambda n: n.drugstoneType == 'protein' ,filter(lambda n: 'drugstoneType' in n and node_name_attribute in n ,parameters['input_network']['nodes']))) for node_name in nodes}
+ proteins = {node_name[1:] for node in prots for node_name in node[node_name_attribute]}
dataset = DEFAULTS['ppi'] if 'interaction_protein_protein' not in parameters['config'] else \
parameters['config'][
'interaction_protein_protein']
@@ -407,18 +393,15 @@ def result_view(request) -> Response:
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)
- # TODO check what to do with edges with from and to id lists
-
result['network']['edges'].extend(edges)
uniq_edges = dict()
for edge in result['network']['edges']:
- print(edge)
hash = edge['from'] + edge['to']
uniq_edges[hash] = edge
result['network']['edges'] = list(uniq_edges.values())
- # result['network']['nodes'] = list(identifier_nodes)
+
if 'scores' in result['node_attributes']:
del result['node_attributes']['scores']
@@ -671,9 +654,6 @@ class TissueExpressionView(APIView):
for node in nodes + seeds:
node_type = node_types.get(node)
details = None
- # if not node_type:
- # print('we should not see this 3')
- # node_type, details = infer_node_type_and_details(node)
if node_type == 'protein':
if details:
proteins.append(details)
--
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