From ce9c6c76e3299359867cb144f75c874407c21ed0 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Tue, 7 Mar 2023 19:51:31 +0100
Subject: [PATCH] security update
Former-commit-id: 048c38b4ca80556de1fcfa6c9b7372140dcdf523 [formerly 604844a0e97c5a3e3b919d4acee407d0e2e2ef1e]
Former-commit-id: 2ea9aeb732f834b8ca53a07414955bff13f205c5
---
Dockerfile | 10 ++++------
docker-compose.yml | 1 +
docker-django.env.dev | 2 +-
drugstone/management/commands/import_from_nedrex.py | 11 +++++++----
requirements.txt | 2 +-
5 files changed, 14 insertions(+), 12 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index 924a5c6..3af76b5 100755
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM andimajore/miniconda3_kinetic
+FROM andimajore/miniconda3_lunar
WORKDIR /usr/src/drugstone/
@@ -7,13 +7,11 @@ ENV PYTHONUNBUFFERED 1
ENV LC_ALL=C.UTF-8
ENV LANG=C.UTF-8
-RUN apt-get update
-RUN apt-get install -y supervisor nginx
-RUN apt-get install -y libgtk-3-dev
-RUN apt-get install wget
+RUN apt update && apt upgrade
+RUN apt install -y supervisor nginx libgtk-3-dev wget
RUN conda install -y conda python=3.8
-RUN conda install -c conda-forge -y graph-tool=2.45
+RUN conda install -c conda-forge -y graph-tool=2.46
RUN pip install gunicorn
diff --git a/docker-compose.yml b/docker-compose.yml
index dbb61b5..49ed48c 100755
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -11,6 +11,7 @@ services:
env_file:
- 'docker-django.env.dev'
restart: always
+ user: '0'
volumes:
- drugstone_db_schema_volume:/usr/src/drugstone/drugstone/migrations
- ./data:/usr/src/drugstone/data
diff --git a/docker-django.env.dev b/docker-django.env.dev
index 91d6c04..6f5a076 100644
--- a/docker-django.env.dev
+++ b/docker-django.env.dev
@@ -15,4 +15,4 @@ CELERY_BROKER_URL=redis://redis:6379/0
FLOWER_PORT=8888
FLOWER_BASIC_AUTH=drugstone:test
GT_THREADS=2
-DB_UPDATE_ON_START=0
\ No newline at end of file
+DB_UPDATE_ON_START=1
\ No newline at end of file
diff --git a/drugstone/management/commands/import_from_nedrex.py b/drugstone/management/commands/import_from_nedrex.py
index dd8a434..f13aeb2 100644
--- a/drugstone/management/commands/import_from_nedrex.py
+++ b/drugstone/management/commands/import_from_nedrex.py
@@ -116,10 +116,13 @@ class NedrexImporter:
proteins[id] = models.Protein(uniprot_code=id, protein_name=name, gene=gene)
def add_edges(edge):
- id = to_id(edge['sourceDomainId'])
- protein = proteins[id]
- protein.entrez = to_id(edge['targetDomainId'])
- gene_to_prots[protein.entrez].add(id)
+ try:
+ id = to_id(edge['sourceDomainId'])
+ protein = proteins[id]
+ protein.entrez = to_id(edge['targetDomainId'])
+ gene_to_prots[protein.entrez].add(id)
+ except:
+ print(f"Edge was not mapped: {edge['sourceDomainId']}-{edge['targetDomainId']}")
def add_genes(node):
id = to_id(node['primaryDomainId'])
diff --git a/requirements.txt b/requirements.txt
index 499918e..eafb7ef 100755
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,7 +5,7 @@ chardet==3.0.4
click==8.1.3
cryptography==39.0.1
decorator==4.4.2
-Django==3.2.17
+Django==3.2.18
django-cors-headers==3.4.0
django-redis==4.11.0
django-rq-dashboard==0.3.3
--
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