diff --git a/.gitignore b/.gitignore
index eba7b164c2dfcb3290ff160e2ad49bead31fc2d2..af2b847af25782ddc7b99e033dee329464c2713a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,3 +14,4 @@ celerybeat-schedule.dat
celerybeat-schedule.dir
docker-django.env.prodnetworks.zip
data/Networks/
+docker-django.env
diff --git a/docker-compose.yml b/docker-compose.yml
index 49ed48cea30b998d40c494676b7e2073d00b1c51..364e1570b3162a59073c5046a63efbd22c143a3d 100755
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -9,7 +9,7 @@ services:
- "scripts/docker-entrypoint.sh"
build: .
env_file:
- - 'docker-django.env.dev'
+ - 'docker-django.env'
restart: always
user: '0'
volumes:
@@ -63,7 +63,7 @@ services:
volumes:
- ./data:/usr/src/drugstone/data
env_file:
- - './docker-django.env.dev'
+ - './docker-django.env'
depends_on:
- redis
- db
@@ -78,7 +78,7 @@ services:
container_name: drugstone_celery_beat
hostname: drugstone_celery_beat
env_file:
- - './docker-django.env.dev'
+ - './docker-django.env'
depends_on:
- redis
- db
diff --git a/docker-django.env b/docker-django.env
deleted file mode 100755
index defd3e70b9c0efba92870547a9b16ef0e84aecc5..0000000000000000000000000000000000000000
--- a/docker-django.env
+++ /dev/null
@@ -1,16 +0,0 @@
-DEBUG=1
-SECRET_KEY="0&y9v0@9%@c^woz8m+h2(^$#3gd^c@d82kmmq8tu*nesc_x9i+"
-SUPERUSER_NAME=admin
-SUPERUSER_PASS=Mb2R7CbqAPbpaKawKg7Z
-SQL_ENGINE=django.db.backends.postgresql
-SQL_DATABASE=drugstone
-SQL_USER=drugstone
-SQL_PASSWORD=t6278yczAH7rPKVMxaDD
-SQL_HOST=drugstone_postgres
-SQL_PORT=5432
-REDIS_HOST=redis
-REDIS_PORT=6379
-GT_THREADS=16
-DJANGO_SETTINGS_MODULE=drugstone.settings
-CELERY_BROKER_URL=redis://redis:6379/0
-DB_UPDATE_ON_START=0
\ No newline at end of file
diff --git a/drugstone/management/commands/createfixtures.py b/drugstone/management/commands/createfixtures.py
index 5fc990941bfce46b3f1571defb7a361c9c45a4eb..95a833027c988b6b4a32eb3b582bf2c4c43ba50d 100755
--- a/drugstone/management/commands/createfixtures.py
+++ b/drugstone/management/commands/createfixtures.py
@@ -22,6 +22,6 @@ class Command(BaseCommand):
user.is_superuser = True
user.is_staff = True
user.save()
-
+
if created:
print('created admin superuser')
diff --git a/drugstone/management/commands/import_from_nedrex.py b/drugstone/management/commands/import_from_nedrex.py
index f13aeb21226769539e2790dfe9b9686c77796dff..472bca8b1854f4e16d7d71d54e4088fbe7c1fdf3 100644
--- a/drugstone/management/commands/import_from_nedrex.py
+++ b/drugstone/management/commands/import_from_nedrex.py
@@ -122,7 +122,7 @@ class NedrexImporter:
protein.entrez = to_id(edge['targetDomainId'])
gene_to_prots[protein.entrez].add(id)
except:
- print(f"Edge was not mapped: {edge['sourceDomainId']}-{edge['targetDomainId']}")
+ 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 5bc37ed7e45baa944bfe1542aa0f9040c3fd4915..0c2ec7510bda16357ec082c0e15aa40d0bc82bdb 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 01715b4b7fd52ad7590de90f28e54e3f2ab44390..4a4a570b230ee4b7e1067dc1b7332049daec152d 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 6c068944fe4b6bf516a180d5677b32c2ff0d7250..0e52106d458a271b2a3c889f6c6ea3b86d632bec 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/drugstone/settings/settings.py b/drugstone/settings/settings.py
index e274b939ad22c3d39a64578ad62306b5f8d7d686..7ac243950d59e330e63ccf4a4f6d5125e3666499 100755
--- a/drugstone/settings/settings.py
+++ b/drugstone/settings/settings.py
@@ -166,6 +166,14 @@ CACHES = {
}
}
+EMAIL_HOST = "exchange.uni-hamburg.de"
+EMAIL_PORT = 587
+EMAIL_HOST_USER="taa0368"
+EMAIL_ADDRESS = "tools-cosybio.zbh@uni-hamburg.de"
+EMAIL_HOST_PASSWORD = os.environ.get('EMAIL_HOST_PASSWORD')
+EMAIL_USE_SSL = False
+EMAIL_USE_TLS = True
+
CELERY_BROKER_URL = os.environ.get('CELERY_BROKER_URL')
# timezones: https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
CELERY_TIMEZONE = 'Europe/Berlin'
diff --git a/drugstone/tasks.py b/drugstone/tasks.py
index fd09e65ef21c0a321294f85d0389042855df90ab..2a7181dd7e5bfc2b447918a380afdf5dfdb27d5d 100644
--- a/drugstone/tasks.py
+++ b/drugstone/tasks.py
@@ -6,7 +6,6 @@ from drugstone.management.commands.populate_db import populate
logger = get_task_logger(__name__)
-nedrex_api_url = "http://82.148.225.92:8123/"
data_dir = "/usr/src/drugstone/data"
diff --git a/drugstone/urls.py b/drugstone/urls.py
index 680f18bf922ca024b4b952e7ba883faef65f1c33..eb547c75c0b82fa759778cc5820f1924e261a9e0 100755
--- a/drugstone/urls.py
+++ b/drugstone/urls.py
@@ -19,7 +19,7 @@ from django.urls import path
from drugstone.views import map_nodes, tasks_view, result_view, \
graph_export, TissueView, TissueExpressionView, query_tissue_proteins, TaskView, \
adjacent_drugs, adjacent_disorders, fetch_edges, create_network, load_network, get_license, get_datasets, \
- get_max_tissue_expression, convert_compact_ids
+ get_max_tissue_expression, convert_compact_ids, get_default_params, send_bugreport, save_selection, get_view, get_view_infos
# cache time is 6 hours
urlpatterns = [
@@ -40,5 +40,10 @@ urlpatterns = [
path('admin/', admin.site.urls),
path('create_network', create_network),
path('load_network', load_network),
- path('get_license', get_license)
+ path('get_default_params', get_default_params),
+ path('get_license', get_license),
+ path('send_bugreport/', send_bugreport),
+ path('save_selection', save_selection),
+ path('view/', get_view),
+ path('view_infos', get_view_infos)
]
diff --git a/drugstone/util/mailer.py b/drugstone/util/mailer.py
new file mode 100644
index 0000000000000000000000000000000000000000..c48b15d8c183df9c0a191c262dba438df634bfb6
--- /dev/null
+++ b/drugstone/util/mailer.py
@@ -0,0 +1,15 @@
+from django.core.mail import send_mail
+from drugstone.settings import settings
+
+default_sender = settings.EMAIL_ADDRESS
+
+
+def bugreport(title, body, cc=None):
+ if cc is None:
+ send(title, body)
+ else:
+ send(title=title, body=body, recipient=['contact@drugst.one', cc])
+
+
+def send(title, body, sender=default_sender, recipient=['contact@drugst.one'], fail_silently=False):
+ send_mail(title, body, sender, recipient, fail_silently=fail_silently)
diff --git a/drugstone/views.py b/drugstone/views.py
index 45ff92405eaa2e2388aed9e92dfccbfc2d47d34b..e4cf1bb1a39f6546f4e7c50b13222db75f9a8fa7 100755
--- a/drugstone/views.py
+++ b/drugstone/views.py
@@ -12,9 +12,12 @@ import networkx as nx
from django.http import HttpResponse
from django.db.models import Q, Max
from django.db import IntegrityError
+from rest_framework import status
from rest_framework.decorators import api_view
from rest_framework.response import Response
from rest_framework.views import APIView
+
+from drugstone.util.mailer import bugreport
from drugstone.util.query_db import query_proteins_by_identifier, clean_proteins_from_compact_notation
from drugstone.models import *
@@ -59,7 +62,7 @@ class TaskView(APIView):
token_str = ''.join(random.choice(chars) for _ in range(32))
parameters = request.data['parameters']
licenced = parameters.get('licenced', False)
-
+ algorithm = request.data['algorithm']
# find databases based on parameter strings
parameters['ppi_dataset'] = PPIDatasetSerializer().to_representation(
@@ -68,9 +71,14 @@ class TaskView(APIView):
parameters['pdi_dataset'] = PDIDatasetSerializer().to_representation(
get_pdi_ds(parameters.get('pdi_dataset', DEFAULTS['pdi']), licenced))
+ # if algorithm in ['connect', 'connectSelected', 'quick', 'super']:
+ # parameters["num_trees"] = 5
+ # parameters["tolerance"] = 5
+ # parameters["hub_penalty"] = 0.5
+
task = Task.objects.create(token=token_str,
target=request.data['target'],
- algorithm=request.data['algorithm'],
+ algorithm=algorithm,
parameters=json.dumps(parameters))
start_task(task)
task.save()
@@ -100,6 +108,20 @@ def get_license(request) -> Response:
return Response({'license': import_license()})
+@api_view(['GET'])
+def get_default_params(request) -> Response:
+ algorithm = request.GET.get('algorithm')
+ connect = {'algorithm': 'multisteiner', 'numTrees': 5, 'tolerance': 5, 'hubPenalty': 0.5}
+ quick = {'algorithm': 'closeness', 'result_size': 50, 'hub_penalty': 0, 'include_non_approved_drugs': False,
+ 'include_indirect_drugs': False}
+ resp = {}
+ if algorithm in ['quick', 'super', 'connect', 'connectSelected']:
+ resp['protein'] = connect
+ if algorithm in ['quick', 'super']:
+ resp['drug'] = quick
+ return Response(resp)
+
+
@api_view(['POST'])
def fetch_edges(request) -> Response:
"""Retrieves interactions between nodes given as a list of drugstone IDs.
@@ -652,6 +674,58 @@ def query_proteins(request) -> Response:
})
+@api_view(['POST'])
+def send_bugreport(request) -> Response:
+ data = request.data
+ title = data.get("title")
+ body = data.get("body")
+ email = data.get("email", None)
+ if email and len(email) == 0:
+ email = None
+ if not title or not body:
+ return Response({"status": 400})
+
+ bugreport(title, body, email)
+ return Response({"status": 200})
+
+
+@api_view(['POST'])
+def save_selection(request) -> Response:
+ chars = string.ascii_lowercase + string.ascii_uppercase + string.digits
+ token_str = ''.join(random.choice(chars) for _ in range(32))
+
+ config = request.data.get("config")
+ network = request.data.get("network")
+
+ Network.objects.create(id=token_str, config=json.dumps(config), nodes=json.dumps(network["nodes"]), edges=json.dumps(network["edges"]))
+ return Response({
+ 'token': token_str,
+ })
+
+@api_view(['GET'])
+def get_view(request) -> Response:
+ token = request.query_params.get('token')
+ network = Network.objects.get(id=token)
+ return Response({
+ 'config': json.loads(network.config),
+ 'created_at': network.created_at,
+ 'network': {
+ 'nodes': json.loads(network.nodes),
+ 'edges': json.loads(network.edges),
+ }
+ })
+
+
+@api_view(['POST'])
+def get_view_infos(request) -> Response:
+ tokens = request.data.get('tokens')
+ networks = Network.objects.filter(id__in = tokens)
+ return Response([{
+ 'token': n.id,
+ 'created_at': n.created_at,
+ } for n in networks])
+
+
@api_view(['GET'])
def get_max_tissue_expression(request) -> Response:
tissue = Tissue.objects.get(id=request.query_params.get('tissue'))