From f9dec58d7c40b99beaea4081a7b645ff9178a999 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 16 Dec 2022 16:49:10 +0100
Subject: [PATCH] security update
Former-commit-id: 0cd54e4066312dd0583707166825861779282807 [formerly 88f96a8152fddd1603d9ee3866394c25b66d461d]
Former-commit-id: 0447f2435a55a189ef4edf4dafb9d69582c0bd6f
---
Dockerfile | 2 +-
drugstone/views.py | 59 +++++++++++++++++++---------------------------
requirements.txt | 2 +-
3 files changed, 26 insertions(+), 37 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index 8e86861..924a5c6 100755
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM andimajore/miniconda3:latest
+FROM andimajore/miniconda3_kinetic
WORKDIR /usr/src/drugstone/
diff --git a/drugstone/views.py b/drugstone/views.py
index 8195873..5024bab 100755
--- a/drugstone/views.py
+++ b/drugstone/views.py
@@ -25,43 +25,31 @@ from drugstone.settings import DEFAULTS
def get_ppi_ds(source, licenced):
- try:
- ds = models.PPIDataset.objects.filter(name__iexact=source, licenced=licenced).last()
- return ds
- except:
- if licenced:
- return get_ppi_ds(source, False)
- return None
+ ds = models.PPIDataset.objects.filter(name__iexact=source, licenced=licenced).last()
+ if ds is None and licenced:
+ return get_ppi_ds(source, False)
+ return ds
def get_pdi_ds(source, licenced):
- try:
- ds = models.PDIDataset.objects.filter(name__iexact=source, licenced=licenced).last()
- return ds
- except:
- if licenced:
- return get_pdi_ds(source, False)
- return None
+ ds = models.PDIDataset.objects.filter(name__iexact=source, licenced=licenced).last()
+ if ds is None and licenced:
+ return get_pdi_ds(source, False)
+ return ds
def get_pdis_ds(source, licenced):
- try:
- ds = models.PDisDataset.objects.filter(name__iexact=source, licenced=licenced).last()
- return ds
- except:
- if licenced:
- return get_pdis_ds(source, False)
- return None
+ ds = models.PDisDataset.objects.filter(name__iexact=source, licenced=licenced).last()
+ if ds is None and licenced:
+ return get_pdis_ds(source, False)
+ return ds
def get_drdis_ds(source, licenced):
- try:
- ds = models.DrDiDataset.objects.filter(name__iexact=source, licenced=licenced).last()
- return ds
- except:
- if licenced:
- return get_drdis_ds(source, False)
- return None
+ ds = models.DrDiDataset.objects.filter(name__iexact=source, licenced=licenced).last()
+ if ds is None and licenced:
+ return get_drdis_ds(source, False)
+ return ds
class TaskView(APIView):
@@ -143,6 +131,7 @@ def fetch_edges(request) -> Response:
return Response(ProteinProteinInteractionSerializer(many=True).to_representation(interaction_objects))
+
@api_view(['POST'])
def convert_compact_ids(request) -> Response:
nodes = request.data.get('nodes', '[]')
@@ -150,6 +139,7 @@ def convert_compact_ids(request) -> Response:
cleaned = clean_proteins_from_compact_notation(nodes, identifier)
return Response(cleaned)
+
@api_view(['POST'])
def map_nodes(request) -> Response:
"""Maps user given input nodes to Proteins in the django database.
@@ -502,7 +492,6 @@ def graph_export(request) -> Response:
node_name = node['drugstone_id']
G.add_node(node_name, **node)
-
for e in edges:
# networkx does not support datatypes such as lists or dicts
for prop in remove_edge_properties:
@@ -528,13 +517,13 @@ def graph_export(request) -> Response:
del data['multigraph']
# for node in data['nodes']:
- # for prop in remove_node_properties:
- # if prop in node:
- # del node[prop]
+ # for prop in remove_node_properties:
+ # if prop in node:
+ # del node[prop]
# for edge in data['links']:
- # for prop in remove_edge_properties:
- # if prop in edge:
- # del edge[prop]
+ # for prop in remove_edge_properties:
+ # if prop in edge:
+ # del edge[prop]
data["edges"] = data.pop("links")
data = json.dumps(data)
data = data.replace('"{', '{').replace('}"', '}').replace('"[', '[').replace(']"', ']').replace('\\"', '"')
diff --git a/requirements.txt b/requirements.txt
index 394a8ab..e2ca8b1 100755
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
asgiref==3.5.2
celery==5.2.7
-certifi==2020.6.20
+certifi==2022.12.7
chardet==3.0.4
click==8.1.3
cryptography==38.0.3
--
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