From d6e5c876ef52c8ad071bfbf68719beae3849a741 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Thu, 15 Dec 2022 14:25:55 +0100
Subject: [PATCH] added output to remove old datasets functions to identify
problem in next update
Former-commit-id: c1312b5c7023fc054103a248d8f44b5054c18578 [formerly 87ecf4f1124bfffb46d542fa810fb3ef9a6aa7c8]
Former-commit-id: 51e87ce37a6e7c1136766c4ffd28083a7d22d170
---
.../management/commands/import_from_nedrex.py | 2 +-
drugstone/management/commands/populate_db.py | 27 +++++++++++++-----
.../management/includes/DatasetLoader.py | 28 ++++++++++++++++---
3 files changed, 45 insertions(+), 12 deletions(-)
diff --git a/drugstone/management/commands/import_from_nedrex.py b/drugstone/management/commands/import_from_nedrex.py
index bded48d..bc09491 100644
--- a/drugstone/management/commands/import_from_nedrex.py
+++ b/drugstone/management/commands/import_from_nedrex.py
@@ -256,7 +256,7 @@ class NedrexImporter:
iter_edge_collection('drug_has_target', add_dpi)
models.ProteinDrugInteraction.objects.bulk_create(bulk)
- new_datasets = [dataset, source_datasets.values()]
+ new_datasets = [dataset].extend(source_datasets.values())
DatasetLoader.remove_old_pdi_data(new_datasets, licenced)
return len(bulk)
diff --git a/drugstone/management/commands/populate_db.py b/drugstone/management/commands/populate_db.py
index 690ec3b..4df7c6a 100755
--- a/drugstone/management/commands/populate_db.py
+++ b/drugstone/management/commands/populate_db.py
@@ -10,6 +10,8 @@ from drugstone.management.includes.DataPopulator import DataPopulator
from .import_from_nedrex import NedrexImporter
from drugstone.management.includes.NodeCache import NodeCache
from drugstone.management.includes import DatasetLoader
+from ..includes.DatasetLoader import remove_old_pdi_data, remove_old_ppi_data, remove_old_pdis_data, \
+ remove_old_drdi_data
class DatabasePopulator:
@@ -59,7 +61,6 @@ class DatabasePopulator:
class Command(BaseCommand):
def add_arguments(self, parser):
-
# dataset directory
parser.add_argument('-dd', '--data_dir', type=str, help='Dataset directory path')
parser.add_argument('-dm', '--delete_model', type=str, help='Delete model(s)')
@@ -80,19 +81,28 @@ class Command(BaseCommand):
parser.add_argument('-pdi', '--protein_disorder', action='store_true',
help='Populate Protein-Disorder Associations')
parser.add_argument('-ddi', '--drug_disorder', action='store_true', help='Populate Drug-Disorder Indications')
+ parser.add_argument('-t', '--test', action='store_true', help='Running some function on startup')
def handle(self, *args, **kwargs):
populate(kwargs)
-def populate(kwargs):
+def populate(kwargs):
nedrex_api_url_open = "https://api.nedrex.net/open"
nedrex_api_url_licensed = "https://api.nedrex.net/licensed"
data_dir = kwargs['data_dir']
db_populator = DatabasePopulator(data_dir=data_dir)
-
+ if 'test' in kwargs and kwargs['test']:
+ pass
+ # remove_old_ppi_data([PPIDataset.objects.filter(name='biogrid', licenced=False).last()], False)
+ # remove_old_ppi_data([PPIDataset.objects.filter(name='iid', licenced=False).last()], False)
+ # remove_old_ppi_data([PPIDataset.objects.filter(name='intact', licenced=False).last()], False)
+ # remove_old_pdis_data([PDisDataset.objects.filter(name='disgenet', licenced=False).last()], False)
+ # remove_old_pdis_data([PDisDataset.objects.filter(name='omim', licenced=True).last()], True)
+ # remove_old_drdi_data([DrDiDataset.objects.filter(name='ctd', licenced=False).last()], False)
+ # remove_old_drdi_data([DrDiDataset.objects.filter(name='drugcentral', licenced=False).last()], False)
if 'clear' in kwargs and kwargs['clear']:
db_populator.delete_all()
@@ -121,7 +131,7 @@ def populate(kwargs):
if kwargs['drugs']:
print('Populating Drugs...')
n = NedrexImporter.import_drugs(importer, update)
- total_n +=n
+ total_n += n
nedrex_update = True
print(f'Populated {n} Drugs.')
@@ -152,14 +162,16 @@ def populate(kwargs):
if kwargs['protein_drug']:
print('Importing PDIs from unlicensed NeDRexDB...')
n = NedrexImporter.import_drug_target_interactions(importer,
- DatasetLoader.get_drug_target_nedrex(nedrex_api_url_open, False),
+ DatasetLoader.get_drug_target_nedrex(nedrex_api_url_open,
+ False),
update)
total_n += n
print(f'Imported {n} PDIs from unlicensed NeDRexDB')
print('Importing PDIs from licensed NeDRexDB...')
n = NedrexImporter.import_drug_target_interactions(importer,
- DatasetLoader.get_drug_target_nedrex(nedrex_api_url_licensed, True),
+ DatasetLoader.get_drug_target_nedrex(nedrex_api_url_licensed,
+ True),
update)
total_n += n
nedrex_update = True
@@ -196,7 +208,8 @@ def populate(kwargs):
if kwargs['drug_disorder']:
print('Importing DrDis from unlicensed NeDRexDB...')
n = NedrexImporter.import_drug_disorder_indications(importer,
- DatasetLoader.get_drug_disorder_nedrex(nedrex_api_url_open, False),
+ DatasetLoader.get_drug_disorder_nedrex(nedrex_api_url_open,
+ False),
update)
total_n += n
print(f'Imported {n} DrDis from unlicensed NeDRexDB')
diff --git a/drugstone/management/includes/DatasetLoader.py b/drugstone/management/includes/DatasetLoader.py
index 4ec2538..859fc11 100644
--- a/drugstone/management/includes/DatasetLoader.py
+++ b/drugstone/management/includes/DatasetLoader.py
@@ -302,39 +302,59 @@ def is_licenced_drdi_source(source):
def remove_old_pdi_data(new_datasets, licenced):
for dataset in new_datasets:
+ print("Deleting all except "+str(dataset))
try:
for d in models.PDIDataset.objects.filter(name=dataset.name, licenced=licenced):
+ print("Testing: "+str(d))
if d != dataset:
+ print("Deleting: "+str(d))
d.delete()
- except:
+ except Exception as e:
+ print("Error when trying to delete old datasets")
+ print(e)
continue
def remove_old_ppi_data(new_datasets, licenced):
for dataset in new_datasets:
+ print("Deleting all except " + str(dataset))
try:
for d in models.PPIDataset.objects.filter(name=dataset.name, licenced=licenced):
+ print("Testing: " + str(d))
if d != dataset:
+ print("Deleting: " + str(d))
d.delete()
- except:
+ except Exception as e:
+ print("Error when trying to delete old datasets")
+ print(e)
continue
def remove_old_pdis_data(new_datasets, licenced):
for dataset in new_datasets:
+ print("Deleting all except " + str(dataset))
try:
for d in models.PDisDataset.objects.filter(name=dataset.name, licenced=licenced):
+ print("Testing: " + str(d))
if d != dataset:
+ print("Deleting: " + str(d))
d.delete()
- except:
+ except Exception as e:
+ print("Error when trying to delete old datasets")
+ print(e)
continue
def remove_old_drdi_data(new_datasets, licenced):
for dataset in new_datasets:
+ print("Deleting all except " + str(dataset))
try:
for d in models.DrDiDataset.objects.filter(name=dataset.name, licenced=licenced):
+ print("Testing: " + str(d))
if d != dataset:
+ print("Deleting: " + str(d))
d.delete()
- except:
+ except Exception as e:
+ print("Error when trying to delete old datasets")
+ print(e)
continue
--
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