diff --git a/docker-django.env.dev b/docker-django.env.dev
index c0f3aa4316170325e46f3794e79220b655873414..66f78b1f970a4ac073d22ccfba4b36d54559d5bc 100644
--- a/docker-django.env.dev
+++ b/docker-django.env.dev
@@ -14,4 +14,4 @@ DJANGO_SETTINGS_MODULE=drugstone.settings
CELERY_BROKER_URL=redis://redis:6379/0
FLOWER_PORT=8888
FLOWER_BASIC_AUTH=drugstone:test
-GT_THREADS=1
\ No newline at end of file
+GT_THREADS=8
\ 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 29c3cbb481ab72f4a2d4f94353607c81a75253ac..f8b423cefe5e6f7a287f94d9191b94414b87c147 100644
--- a/drugstone/management/commands/import_from_nedrex.py
+++ b/drugstone/management/commands/import_from_nedrex.py
@@ -151,6 +151,7 @@ class NedrexImporter:
def import_drugs(self, update):
self.set_licenced(False)
+
drugs = dict()
if update:
self.cache.init_drugs()
@@ -237,14 +238,18 @@ class NedrexImporter:
if not update or e.__hash__() not in existing:
bulk.add(e)
for source in edge['dataSources']:
- if not licenced or is_licenced(source):
- bulk.add(models.ProteinDrugInteraction(pdi_dataset=get_dataset(source), drug=drug,
+ if licenced:
+ if not is_licenced(source):
+ continue
+ bulk.add(models.ProteinDrugInteraction(pdi_dataset=get_dataset(source), drug=drug,
protein=protein))
except KeyError:
pass
iter_edge_collection('drug_has_target', add_dpi)
models.ProteinDrugInteraction.objects.bulk_create(bulk)
+ new_datasets = [dataset, source_datasets.values()]
+ DatasetLoader.remove_old_pdi_data(new_datasets, licenced)
return len(bulk)
def import_protein_protein_interactions(self, dataset: PPIDataset, update):
@@ -292,15 +297,19 @@ class NedrexImporter:
if not update or e.__hash__() not in existing:
bulk.append(e)
for source in edge['dataSources']:
- if not licenced or is_licenced(source):
- bulk.append(
- models.ProteinProteinInteraction(ppi_dataset=get_dataset(source), from_protein=protein1,
- to_protein=protein2))
+ if licenced:
+ if not is_licenced(source):
+ continue
+ bulk.append(
+ models.ProteinProteinInteraction(ppi_dataset=get_dataset(source), from_protein=protein1,
+ to_protein=protein2))
except KeyError:
pass
iter_ppi(add_ppi)
models.ProteinProteinInteraction.objects.bulk_create(bulk)
+ new_datasets = [dataset, source_datasets.values()]
+ DatasetLoader.remove_old_ppi_data(new_datasets, licenced)
return len(bulk)
def import_protein_disorder_associations(self, dataset, update):
@@ -338,8 +347,10 @@ class NedrexImporter:
if not update or e.__hash__() not in existing:
bulk.add(e)
for source in edge['dataSources']:
- if not licenced or is_licenced(source):
- bulk.add(
+ if licenced:
+ if not is_licenced(source):
+ continue
+ bulk.add(
models.ProteinDisorderAssociation(pdis_dataset=get_dataset(source), protein=protein,
disorder=disorder,
score=edge['score']))
@@ -348,6 +359,8 @@ class NedrexImporter:
iter_edge_collection('gene_associated_with_disorder', add_pdis)
models.ProteinDisorderAssociation.objects.bulk_create(bulk)
+ new_datasets = [dataset, source_datasets.values()]
+ DatasetLoader.remove_old_pdis_data(new_datasets, licenced)
return len(bulk)
def import_drug_disorder_indications(self, dataset, update):
@@ -384,8 +397,10 @@ class NedrexImporter:
if not update or e.__hash__() not in existing:
bulk.add(e)
for source in edge['dataSources']:
- if not licenced or is_licenced(source):
- bulk.add(
+ if licenced:
+ if not is_licenced(source):
+ continue
+ bulk.add(
models.DrugDisorderIndication(drdi_dataset=get_dataset(source), drug=drug,
disorder=disorder))
except KeyError:
@@ -393,4 +408,6 @@ class NedrexImporter:
iter_edge_collection('drug_has_indication', add_drdis)
models.DrugDisorderIndication.objects.bulk_create(bulk)
+ new_datasets = [dataset, source_datasets.values()]
+ DatasetLoader.remove_old_drdi_data(new_datasets, licenced)
return len(bulk)
diff --git a/drugstone/management/includes/DatasetLoader.py b/drugstone/management/includes/DatasetLoader.py
index e08a6fe61e6bff90ea103148900e4e689e037289..ad23f090d31a05b8a509d36cf01821f16c1ed7b2 100644
--- a/drugstone/management/includes/DatasetLoader.py
+++ b/drugstone/management/includes/DatasetLoader.py
@@ -45,6 +45,15 @@ def get_nedrex_version():
return version
+def get_nedrex_source_version(source):
+ metadata = get_metadata()['source_databases']
+ # TODO remove once fixed in nedrex db
+ if 'drug_central' in metadata:
+ metadata['drugcentral'] = metadata['drug_central']
+
+ return metadata[source]['date']
+
+
def get_drug_target_nedrex(url, licenced):
dataset, _ = models.PDIDataset.objects.get_or_create(
name='NeDRex',
@@ -65,7 +74,7 @@ def get_ppi_nedrex(url, licenced):
return dataset
-def get_protein_disorder_nedrex(url,licenced):
+def get_protein_disorder_nedrex(url, licenced):
dataset, _ = models.PDisDataset.objects.get_or_create(
name='NeDRex',
link=url,
@@ -75,7 +84,7 @@ def get_protein_disorder_nedrex(url,licenced):
return dataset
-def get_drug_disorder_nedrex(url,licenced):
+def get_drug_disorder_nedrex(url, licenced):
dataset, _ = models.DrDiDataset.objects.get_or_create(
name='NeDRex',
link=url,
@@ -86,7 +95,7 @@ def get_drug_disorder_nedrex(url,licenced):
def write_license(text):
- with open(LICENSE_FILE,'w') as fh:
+ with open(LICENSE_FILE, 'w') as fh:
fh.write(text)
@@ -172,7 +181,7 @@ def get_today_version():
def get_ppi_nedrex_dataset(url, licenced, source):
version = get_today_version()
try:
- version = get_metadata()['source_databases'][source]['date']
+ version = get_nedrex_source_version(source)
except RetryError:
pass
@@ -188,7 +197,7 @@ def get_ppi_nedrex_dataset(url, licenced, source):
def get_pdi_nedrex_dataset(url, licenced, source):
version = get_today_version()
try:
- version = get_metadata()['source_databases'][source]['date']
+ version = get_nedrex_source_version(source)
except RetryError:
pass
@@ -200,10 +209,11 @@ def get_pdi_nedrex_dataset(url, licenced, source):
)
return dataset
+
def get_pdis_nedrex_dataset(url, licenced, source):
version = get_today_version()
try:
- version = get_metadata()['source_databases'][source]['date']
+ version = get_nedrex_source_version(source)
except RetryError:
pass
@@ -215,10 +225,11 @@ def get_pdis_nedrex_dataset(url, licenced, source):
)
return dataset
+
def get_drdi_nedrex_dataset(url, licenced, source):
version = get_today_version()
try:
- version = get_metadata()['source_databases'][source]['date']
+ version = get_nedrex_source_version(source)
except RetryError:
pass
@@ -230,10 +241,11 @@ def get_drdi_nedrex_dataset(url, licenced, source):
)
return dataset
+
def is_licenced_ppi_source(source):
version = get_today_version()
try:
- version = get_metadata()['source_databases'][source]['date']
+ version = get_nedrex_source_version(source)
except RetryError:
pass
@@ -243,10 +255,11 @@ def is_licenced_ppi_source(source):
return True
return False
+
def is_licenced_pdi_source(source):
version = get_today_version()
try:
- version = get_metadata()['source_databases'][source]['date']
+ version = get_nedrex_source_version(source)
except RetryError:
pass
@@ -256,10 +269,11 @@ def is_licenced_pdi_source(source):
return True
return False
+
def is_licenced_pdis_source(source):
version = get_today_version()
try:
- version = get_metadata()['source_databases'][source]['date']
+ version = get_nedrex_source_version(source)
except RetryError:
pass
@@ -269,10 +283,11 @@ def is_licenced_pdis_source(source):
return True
return False
+
def is_licenced_drdi_source(source):
version = get_today_version()
try:
- version = get_metadata()['source_databases'][source]['date']
+ version = get_nedrex_source_version(source)
except RetryError:
pass
@@ -281,3 +296,43 @@ def is_licenced_drdi_source(source):
except:
return True
return False
+
+
+def remove_old_pdi_data(new_datasets, licenced):
+ for dataset in new_datasets:
+ try:
+ for d in models.PDIDataset.objects.filter(name=dataset.name, licenced=licenced):
+ if d != dataset:
+ d.delete()
+ except:
+ continue
+
+
+def remove_old_ppi_data(new_datasets, licenced):
+ for dataset in new_datasets:
+ try:
+ for d in models.PPIDataset.objects.filter(name=dataset.name, licenced=licenced):
+ if d != dataset:
+ d.delete()
+ except:
+ continue
+
+
+def remove_old_pdis_data(new_datasets, licenced):
+ for dataset in new_datasets:
+ try:
+ for d in models.PDisDataset.objects.filter(name=dataset.name, licenced=licenced):
+ if d != dataset:
+ d.delete()
+ except:
+ continue
+
+
+def remove_old_drdi_data(new_datasets, licenced):
+ for dataset in new_datasets:
+ try:
+ for d in models.DrDiDataset.objects.filter(name=dataset.name, licenced=licenced):
+ if d != dataset:
+ d.delete()
+ except:
+ continue
diff --git a/drugstone/settings/settings.py b/drugstone/settings/settings.py
index 7752e44db1d1f659bb6ee91934ba987a9fd6ddfc..e274b939ad22c3d39a64578ad62306b5f8d7d686 100755
--- a/drugstone/settings/settings.py
+++ b/drugstone/settings/settings.py
@@ -169,3 +169,6 @@ CACHES = {
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'
+
+
+DEFAULTS = { 'ppi': 'NeDRex', 'pdi': 'NeDRex', 'pdis': 'NeDRex', 'drdi': 'NeDRex'}
diff --git a/drugstone/urls.py b/drugstone/urls.py
index a44eeb9f83a2fb4f9f8681e8eeee83c54c9429ce..74605cf9806f7a1406d1c316be5bdfc6452523ae 100755
--- a/drugstone/urls.py
+++ b/drugstone/urls.py
@@ -29,7 +29,7 @@ urlpatterns = [
path('tasks/', tasks_view),
path('task_result/', result_view),
path('graph_export/', graph_export),
- path('query_proteins/', query_proteins),
+ # path('query_proteins/', query_proteins),
path('query_tissue_proteins/', query_tissue_proteins),
path('adjacent_drugs/', adjacent_drugs),
path('adjacent_disorders/', adjacent_disorders),
diff --git a/drugstone/views.py b/drugstone/views.py
index 5ccbc9b7f38b276a4250c402e7c117b5c436284c..19cde80ae401e70c81927490550cc0641c971c13 100755
--- a/drugstone/views.py
+++ b/drugstone/views.py
@@ -16,116 +16,55 @@ from rest_framework.response import Response
from rest_framework.views import APIView
from drugstone.util.query_db import query_proteins_by_identifier
-from drugstone import models
-from drugstone import serializers
-
-from drugstone.models import Protein, Task, ProteinDrugInteraction, \
- Drug, Tissue, ExpressionLevel, Network, ProteinDisorderAssociation, DrugDisorderIndication, Disorder, DrDiDataset, \
- PDIDataset, PDisDataset, PPIDataset
-from drugstone.serializers import ProteinSerializer, TaskSerializer, \
- ProteinDrugInteractionSerializer, DrugSerializer, TaskStatusSerializer, TissueSerializer, NetworkSerializer, \
- ProteinDisorderAssociationSerializer, DisorderSerializer, DrugDisorderIndicationSerializer
+from drugstone.models import *
+from drugstone.serializers import *
from drugstone.backend_tasks import start_task, refresh_from_redis, task_stats, task_result, task_parameters
-
-# we might want to replace this class with some ProteinProteinInteraction view of user input proteins
-
-# class ProteinViralInteractionView(APIView):
-# """
-# Protein-Virus-Interaction Network
-# """
-#
-# def get(self, request):
-# if not request.query_params.get('data'):
-# proteins = Protein.objects.all()
-# effects = ViralProtein.objects.all()
-# edges = ProteinViralInteraction.objects.all()
-#
-# network = {
-# 'proteins': ProteinSerializer(many=True).to_representation(proteins),
-# 'effects': ViralProteinSerializer(many=True).to_representation(effects),
-# 'edges': ProteinViralInteractionSerializer(many=True).to_representation(edges),
-# }
-# return Response(network)
-#
-# dataset_virus_list = json.loads(request.query_params.get('data', '[]'))
-# effects = []
-# for dataset_name, virus_name in dataset_virus_list:
-# dataset_virus_object = DatasetVirus.objects.get(dataset=dataset_name, virus=virus_name)
-# effects.extend(list(ViralProtein.objects.filter(dataset_virus=dataset_virus_object).all()))
-#
-# edges = []
-# proteins = []
-# for effect in effects:
-# edge_objects = ProteinViralInteraction.objects.filter(effect=effect)
-# for edge_object in edge_objects:
-# edges.append(edge_object)
-#
-# if edge_object.protein not in proteins:
-# proteins.append(edge_object.protein)
-#
-# network = {
-# 'proteins': ProteinSerializer(many=True).to_representation(proteins),
-# 'effects': ViralProteinSerializer(many=True).to_representation(effects),
-# 'edges': ProteinViralInteractionSerializer(many=True).to_representation(edges),
-# }
-# return Response(network)
-
-
-# class ProteinDrugInteractionView(APIView):
-# """
-# Protein-Drug-Interaction Network
-# """
-#
-# def get(self, request) -> Response:
-# if request.query_params.get('proteins'):
-# print("getting drugs for proteins")
-# protein_ac_list = json.loads(request.query_params.get('proteins'))
-# proteins = list(Protein.objects.filter(uniprot_code__in=protein_ac_list).all())
-# else:
-# proteins = []
-# task = Task.objects.get(token=request.query_params['token'])
-# result = task_result(task)
-# network = result['network']
-# node_attributes = result.get('node_attributes')
-# if not node_attributes:
-# node_attributes = {}
-# node_types = node_attributes.get('node_types')
-# if not node_types:
-# node_types = {}
-# nodes = network['nodes']
-# for node in nodes:
-# node_type = node_types.get(node)
-# details = None
-# # if not node_type:
-# # print('we should not see this 1')
-# # node_type, details = infer_node_type_and_details(node)
-# if node_type == 'protein':
-# if details:
-# proteins.append(details)
-# else:
-# try:
-# proteins.append(Protein.objects.get(uniprot_code=node))
-# except Protein.DoesNotExist:
-# pass
-#
-# pd_interactions = []
-# drugs = []
-#
-# for protein in proteins:
-# pdi_object_list = ProteinDrugInteraction.objects.filter(protein=protein)
-# for pdi_object in pdi_object_list:
-# pd_interactions.append(pdi_object)
-# drug = pdi_object.drug
-# if drug not in drugs:
-# drugs.append(drug)
-#
-# protein_drug_edges = {
-# 'proteins': ProteinSerializer(many=True).to_representation(proteins),
-# 'drugs': DrugSerializer(many=True).to_representation(drugs),
-# 'edges': ProteinDrugInteractionSerializer(many=True).to_representation(pd_interactions),
-# }
-# return Response(protein_drug_edges)
+from drugstone.settings import DEFAULTS
+
+
+def get_ppi_ds(source, licenced):
+ try:
+ ds = models.PPIDataset.objects.filter(name__iexact=source, licenced=licenced).last()
+ ds.id
+ return ds
+ except:
+ if licenced:
+ return get_ppi_ds(source, False)
+ return None
+
+
+def get_pdi_ds(source, licenced):
+ try:
+ ds = models.PDIDataset.objects.filter(name__iexact=source, licenced=licenced).last()
+ ds.id
+ return ds
+ except:
+ if licenced:
+ return get_pdi_ds(source, False)
+ return None
+
+
+def get_pdis_ds(source, licenced):
+ try:
+ ds = models.PDisDataset.objects.filter(name__iexact=source, licenced=licenced).last()
+ ds.id
+ return ds
+ except:
+ if licenced:
+ return get_pdis_ds(source, False)
+ return None
+
+
+def get_drdis_ds(source, licenced):
+ try:
+ ds = models.PDisDataset.objects.filter(name__iexact=source, licenced=licenced).last()
+ ds.id
+ return ds
+ except:
+ if licenced:
+ return get_pdis_ds(source, False)
+ return None
class TaskView(APIView):
@@ -134,12 +73,16 @@ class TaskView(APIView):
chars = string.ascii_lowercase + string.ascii_uppercase + string.digits
token_str = ''.join(random.choice(chars) for _ in range(32))
parameters = request.data['parameters']
+ licenced = parameters.get('licenced', False)
# find databases based on parameter strings
- parameters['ppi_dataset'] = serializers.PPIDatasetSerializer().to_representation(
- models.PPIDataset.objects.filter(name__iexact=parameters.get('ppi_dataset', 'STRING')).last())
- parameters['pdi_dataset'] = serializers.PDIDatasetSerializer().to_representation(
- models.PDIDataset.objects.filter(name__iexact=parameters.get('pdi_dataset', 'DrugBank')).last())
+ print(get_ppi_ds(parameters.get('ppi_dataset', DEFAULTS['ppi']), licenced))
+ parameters['ppi_dataset'] = PPIDatasetSerializer().to_representation(
+ get_ppi_ds(parameters.get('ppi_dataset', DEFAULTS['ppi']), licenced))
+
+ print(get_pdi_ds(parameters.get('pdi_dataset', DEFAULTS['pdi']), licenced))
+ parameters['pdi_dataset'] = PDIDatasetSerializer().to_representation(
+ get_pdi_ds(parameters.get('pdi_dataset', DEFAULTS['pdi']), licenced))
task = Task.objects.create(token=token_str,
target=request.data['target'],
@@ -166,13 +109,13 @@ class TaskView(APIView):
'stats': task_stats(task),
})
+
@api_view(['GET'])
def get_license(request) -> Response:
from drugstone.management.includes.DatasetLoader import import_license
return Response({'license': import_license()})
-
@api_view(['POST'])
def fetch_edges(request) -> Response:
"""Retrieves interactions between nodes given as a list of drugstone IDs.
@@ -184,13 +127,14 @@ def fetch_edges(request) -> Response:
Returns:
Response: List of edges which are objects with 'from' and to ' attribtues'
"""
- dataset = request.data.get('dataset', 'STRING')
+ dataset = request.data.get('dataset', DEFAULTS['ppi'])
drugstone_ids = [node['drugstone_id'][1:] for node in request.data.get('nodes', '[]') if 'drugstone_id' in node]
- dataset_object = models.PPIDataset.objects.filter(name__iexact=dataset).last()
+ licenced = request.data.get('licenced', False)
+ dataset_object = get_ppi_ds(dataset, licenced)
interaction_objects = models.ProteinProteinInteraction.objects.filter(
Q(ppi_dataset=dataset_object) & Q(from_protein__in=drugstone_ids) & Q(to_protein__in=drugstone_ids))
- return Response(serializers.ProteinProteinInteractionSerializer(many=True).to_representation(interaction_objects))
+ return Response(ProteinProteinInteractionSerializer(many=True).to_representation(interaction_objects))
@api_view(['POST'])
@@ -257,25 +201,6 @@ def tasks_view(request) -> Response:
return Response(tasks_info)
-# def infer_node_type_and_details(node) -> Tuple[str, Protein or Drug]:
-# node_type_indicator = node[0]
-# if node_type_indicator == 'p':
-# node_id = int(node[1:])
-# # protein
-# prot = Protein.objects.get(id=node_id)
-# return 'protein', prot
-# elif node_type_indicator == 'd':
-# node_id = int(node[2:])
-# # drug
-# if node_id[0] == 'r':
-# drug = Drug.objects.get(id=node_id[1:])
-# return 'drug', drug
-# elif node_id[0] == 'i':
-# disorder = Disorder.objects.get(id=node_id[1:])
-# return 'disorder', disorder
-# return None, None
-
-
@api_view(['POST'])
def create_network(request) -> Response:
if 'network' not in request.data:
@@ -417,8 +342,9 @@ def result_view(request) -> Response:
if 'autofill_edges' in parameters['config'] and parameters['config']['autofill_edges']:
proteins = set(map(lambda n: n[node_name_attribute][1:],
filter(lambda n: node_name_attribute in n, parameters['input_network']['nodes'])))
- dataset = 'STRING' if 'interaction_protein_protein' not in parameters['config'] else parameters['config'][
- 'interaction_protein_protein']
+ dataset = DEFAULTS['ppi'] if 'interaction_protein_protein' not in parameters['config'] else \
+ parameters['config'][
+ 'interaction_protein_protein']
dataset_object = models.PPIDataset.objects.filter(name__iexact=dataset).last()
interaction_objects = models.ProteinProteinInteraction.objects.filter(
Q(ppi_dataset=dataset_object) & Q(from_protein__in=proteins) & Q(to_protein__in=proteins))
@@ -545,20 +471,20 @@ def adjacent_disorders(request) -> Response:
data = request.data
if 'proteins' in data:
drugstone_ids = data.get('proteins', [])
- pdi_dataset = PDisDataset.objects.filter(name__iexact=data.get('dataset', 'DisGeNET')).last()
+ pdi_dataset = get_pdis_ds(data.get('dataset', DEFAULTS['pdis']), data.get('licenced', False))
# find adjacent drugs by looking at drug-protein edges
pdis_objects = ProteinDisorderAssociation.objects.filter(protein__id__in=drugstone_ids,
- pdis_dataset=pdi_dataset)
+ pdis_dataset_id=pdi_dataset.id)
disorders = {e.disorder for e in pdis_objects}
# serialize
edges = ProteinDisorderAssociationSerializer(many=True).to_representation(pdis_objects)
disorders = DisorderSerializer(many=True).to_representation(disorders)
elif 'drugs' in data:
drugstone_ids = data.get('drugs', [])
- drdi_dataset = DrDiDataset.objects.filter(name__iexact=data.get('dataset', 'DrugBank')).last()
+ drdi_dataset = get_drdis_ds(data.get('dataset', DEFAULTS['drdi']), data.get('licenced', False))
# find adjacent drugs by looking at drug-protein edges
drdi_objects = DrugDisorderIndication.objects.filter(drug__id__in=drugstone_ids,
- drdi_dataset=drdi_dataset)
+ drdi_dataset_id=drdi_dataset.id)
disorders = {e.disorder for e in drdi_objects}
# serialize
edges = DrugDisorderIndicationSerializer(many=True).to_representation(drdi_objects)
@@ -581,9 +507,9 @@ def adjacent_drugs(request) -> Response:
"""
data = request.data
drugstone_ids = data.get('proteins', [])
- pdi_dataset = PDIDataset.objects.filter(name__iexact=data.get('pdi_dataset', 'NeDRex')).last()
+ pdi_dataset = get_pdi_ds(data.get('pdi_dataset', DEFAULTS['pdi']), data.get('licenced', False))
# find adjacent drugs by looking at drug-protein edges
- pdi_objects = ProteinDrugInteraction.objects.filter(protein__id__in=drugstone_ids, pdi_dataset=pdi_dataset)
+ pdi_objects = ProteinDrugInteraction.objects.filter(protein__id__in=drugstone_ids, pdi_dataset_id=pdi_dataset.id)
drugs = {e.drug for e in pdi_objects}
# serialize
pdis = ProteinDrugInteractionSerializer(many=True).to_representation(pdi_objects)
diff --git a/scripts/docker-entrypoint.sh b/scripts/docker-entrypoint.sh
index 43bf32df3da5898d25d96f8abd734edf4872ea3c..db7a2d39ad5d4040b6dd34294c675ea20ae7b9bf 100755
--- a/scripts/docker-entrypoint.sh
+++ b/scripts/docker-entrypoint.sh
@@ -4,7 +4,7 @@ python3 manage.py makemigrations drugstone
python3 manage.py migrate
python3 manage.py createfixtures
python3 manage.py cleanuptasks
-python3 manage.py populate_db --update -a
-python3 manage.py make_graphs
+#python3 manage.py populate_db --update -a
+#python3 manage.py make_graphs
/usr/bin/supervisord -c "/etc/supervisor/conf.d/supervisord.conf"
diff --git a/tasks/betweenness_centrality.py b/tasks/betweenness_centrality.py
index 65f654cda611da813a5fc15affe90e1499506ae4..d839c5ebfee95f844a00c1a549b054548b39d1f9 100755
--- a/tasks/betweenness_centrality.py
+++ b/tasks/betweenness_centrality.py
@@ -75,7 +75,7 @@ def betweenness_centrality(task_hook: TaskHook):
Network-Based Prioritization of Candidate Disease Genes or Other Molecules, Bioinformatics 29(11),
2013, pp. 1471-1473, https://doi.org/10.1093/bioinformatics/btt164.
"""
-
+
# Type: list of str
# Semantics: Names of the seed proteins. Use UNIPROT IDs for host proteins, and
# names of the for SARS_CoV2_<IDENTIFIER> (e.g., SARS_CoV2_ORF6) for
@@ -84,7 +84,7 @@ def betweenness_centrality(task_hook: TaskHook):
# utility in frontend.
# Acceptable values: UNIPROT IDs, identifiers of viral proteins.
seeds = task_hook.parameters["seeds"]
-
+
# Type: str.
# Semantics: The virus strain for which the analysis should be run, or the
# string literal "drugs" (if used for ranking drugs).
@@ -95,7 +95,6 @@ def betweenness_centrality(task_hook: TaskHook):
# Acceptable values: "PPI", "PPDr"
# target_or_drugs = task_hook.parameters.get("target_or_drugs", "PPI")
-
# Type: list of str.
# Semantics: The datasets which should be considered for the analysis.
# Example: ["Krogan", "TUM"].
@@ -104,7 +103,7 @@ def betweenness_centrality(task_hook: TaskHook):
# Reasonable default: [].
# Acceptable values: "Krogan", "TUM".
# datasets = task_hook.parameters.get("datasets", [])
-
+
# Type: list of str.
# Semantics: Virus-host edge types which should be ignored for the analysis.
# Example: ["Overexpression"].
@@ -113,14 +112,14 @@ def betweenness_centrality(task_hook: TaskHook):
# Reasonable default: [].
# Acceptable values: "AP-MS", "overexpression".
# ignored_edge_types = task_hook.parameters.get("ignored_edge_types", [])
-
+
# Type: bool
# Semantics: Sepcifies whether also drugs targeting interactors of the seeds should be considered.
# Example: False.
# Reasonable default: False.
# Has no effect unless trust_rank.py is used for ranking drugs.
include_indirect_drugs = task_hook.parameters.get("include_indirect_drugs", False)
-
+
# Type: bool
# Semantics: Sepcifies whether should be included in the analysis when ranking drugs.
# Example: False.
@@ -134,7 +133,7 @@ def betweenness_centrality(task_hook: TaskHook):
# Reasonable default: False.
# Has no effect when the algorithm is used for ranking drugs.
# ignore_non_seed_baits = task_hook.parameters.get("ignore_non_seed_baits", False)
-
+
# Type: int.
# Semantics: Number of returned proteins.
# Example: 20.
@@ -155,7 +154,7 @@ def betweenness_centrality(task_hook: TaskHook):
# Reasonable default: 0.
# Acceptable values: Floats between 0 and 1.
hub_penalty = task_hook.parameters.get("hub_penalty", 0.0)
-
+
# Type: int.
# Semantics: Number of threads used for running the analysis.
# Example: 1.
@@ -170,24 +169,27 @@ def betweenness_centrality(task_hook: TaskHook):
search_target = task_hook.parameters.get("target", "drug-target")
filterPaths = task_hook.parameters.get("filter_paths", True)
-
+
# Parsing input file.
task_hook.set_progress(0 / 3.0, "Parsing input.")
- file_path = os.path.join(task_hook.data_directory, f"internal_{ppi_dataset['name']}_{pdi_dataset['name']}.gt")
+ filename = f"internal_{ppi_dataset['name']}_{pdi_dataset['name']}"
+ if ppi_dataset['licenced'] or pdi_dataset['licenced']:
+ filename += "_licenced"
+ filename = os.path.join(task_hook.data_directory, filename+".gt")
g, seed_ids, drug_ids = read_graph_tool_graph(
- file_path,
- seeds,
- max_deg,
- include_indirect_drugs,
- include_non_approved_drugs,
- target=search_target
- )
+ filename,
+ seeds,
+ max_deg,
+ include_indirect_drugs,
+ include_non_approved_drugs,
+ target=search_target
+ )
weights = edge_weights(g, hub_penalty)
# Set number of threads if OpenMP support is enabled.
if gt.openmp_enabled():
gt.openmp_set_num_threads(num_threads)
-
+
# Call graph-tool to compute betweenness centrality.
task_hook.set_progress(1 / 3.0, "Computing betweenness centralities.")
scores = g.new_vertex_property("float")
@@ -201,20 +203,19 @@ def betweenness_centrality(task_hook: TaskHook):
if num_paths > 0:
local_scores.a /= num_paths
scores.a += local_scores.a
-
+
# Compute and return the results.
task_hook.set_progress(2 / 3.0, "Formating results.")
task_hook.set_results(
- scores_to_results(
- search_target,
- result_size,
- g,
- seed_ids,
- drug_ids,
- scores,
- ppi_dataset,
- pdi_dataset,
- filterPaths
+ scores_to_results(
+ search_target,
+ result_size,
+ g,
+ seed_ids,
+ drug_ids,
+ scores,
+ ppi_dataset,
+ pdi_dataset,
+ filterPaths
)
- )
-
+ )
diff --git a/tasks/closeness_centrality.py b/tasks/closeness_centrality.py
index 1767df320221f3b650fdb2754c689f32b31cc86b..a90014f963f8381dbe369f4ff943ff6b5922c9bc 100755
--- a/tasks/closeness_centrality.py
+++ b/tasks/closeness_centrality.py
@@ -170,9 +170,12 @@ def closeness_centrality(task_hook: TaskHook):
# Parsing input file.
task_hook.set_progress(0 / 4.0, "Parsing input.")
- file_path = os.path.join(task_hook.data_directory, f"internal_{ppi_dataset['name']}_{pdi_dataset['name']}.gt")
+ filename = f"internal_{ppi_dataset['name']}_{pdi_dataset['name']}"
+ if ppi_dataset['licenced'] or pdi_dataset['licenced']:
+ filename += "_licenced"
+ filename = os.path.join(task_hook.data_directory, filename+".gt")
# g, seed_ids, viral_protein_ids, drug_ids = read_graph_tool_graph(file_path, seeds, datasets, ignored_edge_types, max_deg, ignore_non_seed_baits, include_indirect_drugs, include_non_approved_drugs)
- g, seed_ids, drug_ids = read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs, include_non_approved_drugs, search_target)
+ g, seed_ids, drug_ids = read_graph_tool_graph(filename, seeds, max_deg, include_indirect_drugs, include_non_approved_drugs, search_target)
task_hook.set_progress(1 / 4.0, "Computing edge weights.")
weights = edge_weights(g, hub_penalty)
diff --git a/tasks/degree_centrality.py b/tasks/degree_centrality.py
index 112d9abc5ccee06510d4b65a9f550028a6218b82..bceffec86520757d2bb81aad7e150484c546e1eb 100755
--- a/tasks/degree_centrality.py
+++ b/tasks/degree_centrality.py
@@ -150,9 +150,12 @@ def degree_centrality(task_hook: TaskHook):
# Parsing input file.
task_hook.set_progress(0 / 3.0, "Parsing input.")
- file_path = os.path.join(task_hook.data_directory, f"internal_{ppi_dataset['name']}_{pdi_dataset['name']}.gt")
+ filename = f"internal_{ppi_dataset['name']}_{pdi_dataset['name']}"
+ if ppi_dataset['licenced'] or pdi_dataset['licenced']:
+ filename += "_licenced"
+ filename = os.path.join(task_hook.data_directory, filename+".gt")
# g, seed_ids, viral_protein_ids, drug_ids = read_graph_tool_graph(file_path, seeds, datasets, ignored_edge_types, max_deg, ignore_non_seed_baits, False, include_non_approved_drugs)
- g, seed_ids, drug_ids = read_graph_tool_graph(file_path, seeds, max_deg, False, include_non_approved_drugs, search_target)
+ g, seed_ids, drug_ids = read_graph_tool_graph(filename, seeds, max_deg, False, include_non_approved_drugs, search_target)
# Set number of threads if OpenMP support is enabled.
if gt.openmp_enabled():
diff --git a/tasks/multi_steiner.py b/tasks/multi_steiner.py
index fa0912e89ca810eab55b9308ec4b749ab336a009..f8e9a80e7f69160702d24d403ffc88fa5406e77c 100755
--- a/tasks/multi_steiner.py
+++ b/tasks/multi_steiner.py
@@ -105,9 +105,11 @@ def multi_steiner(task_hook: TaskHook):
# Parsing input file.
task_hook.set_progress(0 / (float(num_trees + 3)), "Parsing input.")
- file_path = os.path.join(task_hook.data_directory, f"internal_{ppi_dataset['name']}_{pdi_dataset['name']}.gt")
- # g, seed_ids, _, _ = read_graph_tool_graph(file_path, seeds, datasets, ignored_edge_types, max_deg, ignore_non_seed_baits)
- g, seed_ids, _ = read_graph_tool_graph(file_path, seeds, max_deg, target=search_target)
+ filename = f"internal_{ppi_dataset['name']}_{pdi_dataset['name']}"
+ if ppi_dataset['licenced'] or pdi_dataset['licenced']:
+ filename += "_licenced"
+ filename = os.path.join(task_hook.data_directory, filename+".gt")
+ g, seed_ids, _ = read_graph_tool_graph(filename, seeds, max_deg, target=search_target)
# seed_map = {g.vertex_properties["name"][node]: node for node in seed_ids}
seed_map = {g.vertex_properties[node_name_attribute][node]: node for node in seed_ids}
task_hook.set_progress(1 / (float(num_trees + 3)), "Computing edge weights.")
diff --git a/tasks/network_proximity.py b/tasks/network_proximity.py
index 55d86513d1cec0cca5f55e67b7ec9cc624d524a2..90b7708d9b21df88a766dfccee1758d34fcf7bb3 100755
--- a/tasks/network_proximity.py
+++ b/tasks/network_proximity.py
@@ -86,9 +86,12 @@ def network_proximity(task_hook: TaskHook):
# Parsing input file.
task_hook.set_progress(0.0 / 8, "Parsing input.")
- file_path = os.path.join(task_hook.data_directory, f"internal_{ppi_dataset['name']}_{pdi_dataset['name']}.gt")
+ filename = f"internal_{ppi_dataset['name']}_{pdi_dataset['name']}"
+ if ppi_dataset['licenced'] or pdi_dataset['licenced']:
+ filename += "_licenced"
+ filename = os.path.join(task_hook.data_directory, filename+".gt")
# g, seed_ids, _, drug_ids = read_graph_tool_graph(file_path, seeds, "", "", max_deg, False, True, include_non_approved_drugs)
- g, seed_ids, drug_ids = read_graph_tool_graph(file_path, seeds, max_deg, True, include_non_approved_drugs, target=search_target)
+ g, seed_ids, drug_ids = read_graph_tool_graph(filename, seeds, max_deg, True, include_non_approved_drugs, target=search_target)
# Computing edge weights.
task_hook.set_progress(1.0 / 8, "Computing edge weights.")
weights = edge_weights(g, hub_penalty)
diff --git a/tasks/trust_rank.py b/tasks/trust_rank.py
index a01fbe412b3266863b8d1df0f9bd3cced74481e2..ceda67cffe62902865f5f10f84823765389fb41b 100755
--- a/tasks/trust_rank.py
+++ b/tasks/trust_rank.py
@@ -198,8 +198,11 @@ def trust_rank(task_hook: TaskHook):
# Parsing input file.
task_hook.set_progress(0 / 4.0, "Parsing input.")
- file_path = os.path.join(task_hook.data_directory, f"internal_{ppi_dataset['name']}_{pdi_dataset['name']}.gt")
- g, seed_ids, drug_ids = read_graph_tool_graph(file_path, seeds, max_deg, include_indirect_drugs, include_non_approved_drugs, search_target)
+ filename = f"internal_{ppi_dataset['name']}_{pdi_dataset['name']}"
+ if ppi_dataset['licenced'] or pdi_dataset['licenced']:
+ filename += "_licenced"
+ filename = os.path.join(task_hook.data_directory, filename+".gt")
+ g, seed_ids, drug_ids = read_graph_tool_graph(filename, seeds, max_deg, include_indirect_drugs, include_non_approved_drugs, search_target)
task_hook.set_progress(1 / 4.0, "Computing edge weights.")
weights = edge_weights(g, hub_penalty, inverse=True)