security patch; fixing update issues

Former-commit-id: bc6d68252e9f71e99ffa7c5f9fcbcee9e069eae9 [formerly db4cfd0d69a4a31b86b68901e80c30f6233a189e]
Former-commit-id: 12cb75353e319d4f01f72e209ef395f0cbee3bbc

Dockerfile

-FROM andimajore/miniconda3_kinetic
+FROM andimajore/miniconda3_lunar
 
 WORKDIR /usr/src/drugstone/
 

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 could not be saved: {edge["sourceDomainId"]} - {edge["targetDomainId"]}')
 
         def add_genes(node):
             id = to_id(node['primaryDomainId'])

drugstone/management/commands/populate_db.py

@@ -118,6 +118,7 @@ def populate(kwargs):
     total_n = 0
     nedrex_update = False
 
+
     if 'all' in kwargs and kwargs['all']:
         kwargs['drugs'] = True
         kwargs['disorders'] = True

drugstone/management/includes/DataPopulator.py

@@ -22,6 +22,9 @@ class DataPopulator:
         bulk = set()
         uniq = set()
 
+        if update:
+            uniq = {hash(expr) for expr in models.ExpressionLevel.objects.all()}
+
         size = 0
         for _, row in df.iterrows():
             gene_name = row['Description']

drugstone/settings/celery_schedule.py

@@ -3,7 +3,7 @@ from celery.schedules import crontab
 CELERY_BEAT_SCHEDULE = {
     'update_db': {
         'task': 'drugstone.tasks.task_update_db_from_nedrex',
-        'schedule': crontab(day_of_week=2, hour=3, minute=0),
+        'schedule': crontab(day_of_week=1, hour=22, minute=0),
         # 'schedule': crontab(minute='*/1'),
     },
 }

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