security update

Former-commit-id: 048c38b4ca80556de1fcfa6c9b7372140dcdf523 [formerly 604844a0e97c5a3e3b919d4acee407d0e2e2ef1e]
Former-commit-id: 2ea9aeb732f834b8ca53a07414955bff13f205c5

Dockerfile

-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
 

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

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

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):
+            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'])

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