From 13e3db3c060faa5c0d630a536b2daa4f94064b94 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Tue, 14 Mar 2023 16:33:43 +0100
Subject: [PATCH] security patch; fixing update issues
Former-commit-id: bc6d68252e9f71e99ffa7c5f9fcbcee9e069eae9 [formerly db4cfd0d69a4a31b86b68901e80c30f6233a189e]
Former-commit-id: 12cb75353e319d4f01f72e209ef395f0cbee3bbc
---
Dockerfile | 2 +-
drugstone/management/commands/import_from_nedrex.py | 11 +++++++----
drugstone/management/commands/populate_db.py | 1 +
drugstone/management/includes/DataPopulator.py | 3 +++
drugstone/settings/celery_schedule.py | 2 +-
requirements.txt | 2 +-
6 files changed, 14 insertions(+), 7 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index 924a5c6..e68733e 100755
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM andimajore/miniconda3_kinetic
+FROM andimajore/miniconda3_lunar
WORKDIR /usr/src/drugstone/
diff --git a/drugstone/management/commands/import_from_nedrex.py b/drugstone/management/commands/import_from_nedrex.py
index dd8a434..472bca8 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 could not be saved: {edge["sourceDomainId"]} - {edge["targetDomainId"]}')
def add_genes(node):
id = to_id(node['primaryDomainId'])
diff --git a/drugstone/management/commands/populate_db.py b/drugstone/management/commands/populate_db.py
index 5bc37ed..0c2ec75 100755
--- a/drugstone/management/commands/populate_db.py
+++ b/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
diff --git a/drugstone/management/includes/DataPopulator.py b/drugstone/management/includes/DataPopulator.py
index 01715b4..4a4a570 100755
--- a/drugstone/management/includes/DataPopulator.py
+++ b/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']
diff --git a/drugstone/settings/celery_schedule.py b/drugstone/settings/celery_schedule.py
index 6c06894..0e52106 100644
--- a/drugstone/settings/celery_schedule.py
+++ b/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'),
},
}
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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