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populate_db.py
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populate_db.py 10.97 KiB
from django.core.management.base import BaseCommand
from django.db import OperationalError
from drugstone.models import Protein, Drug, Tissue, ExpressionLevel, PPIDataset, PDIDataset, Disorder, PDisDataset, \
DrDiDataset, EnsemblGene
from drugstone.models import ProteinProteinInteraction, ProteinDrugInteraction, ProteinDisorderAssociation, \
DrugDisorderIndication
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
class DatabasePopulator:
def __init__(self, data_dir):
self.data_dir = data_dir
def delete_model(self, model):
from django.db import connection
cursor = connection.cursor()
try:
cursor.execute('TRUNCATE TABLE "{0}" CASCADE'.format(model._meta.db_table))
except OperationalError:
cursor.execute('DELETE FROM "{0}"'.format(model._meta.db_table))
def delete_all(self):
models = ['PPI', 'PDI', 'DrDi', 'Protein', 'Drug', 'Disorder', 'PDi', 'Expression', 'Tissue']
self.delete_models(models)
def delete_models(self, model_list):
for model_name in model_list:
print(f'Deleting {model_name} model ...')
if model_name == 'PPI':
self.delete_model(PPIDataset)
self.delete_model(ProteinProteinInteraction)
elif model_name == 'PDI':
self.delete_model(PDIDataset)
self.delete_model(ProteinDrugInteraction)
elif model_name == 'DrDi':
self.delete_model(DrDiDataset)
self.delete_model(DrugDisorderIndication)
elif model_name == 'Protein':
self.delete_model(Protein)
self.delete_model(EnsemblGene)
elif model_name == 'Drug':
self.delete_model(Drug)
elif model_name == 'Disorder':
self.delete_model(Disorder)
elif model_name == 'PDi':
self.delete_model(PDisDataset)
self.delete_model(ProteinDisorderAssociation)
elif model_name == 'Expression':
self.delete_model(ExpressionLevel)
elif model_name == 'Tissue':
self.delete_model(Tissue)
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)')
parser.add_argument('-c', '--clear', action='store_true', help='Delete all models')
parser.add_argument('-a', '--all', action='store_true', help='Populate all tables')
parser.add_argument('-u', '--update', action='store_true', help='Execute database update for selected tables')
parser.add_argument('-p', '--proteins', action='store_true', help='Populate Proteins')
parser.add_argument('-di', '--disorders', action='store_true', help='Populate Disorders')
parser.add_argument('-dr', '--drugs', action='store_true', help='Drug file name')
parser.add_argument('-exp', '--exp', action='store_true',
help='Tissue expression file (.gct without first 2 lines)')
parser.add_argument('-pp', '--protein_protein', action='store_true',
help='Populate Protein-Protein Interactions')
parser.add_argument('-pdr', '--protein_drug', action='store_true', help='Populate Protein-Drug Interactions')
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')
def handle(self, *args, **kwargs):
populate(kwargs)
def populate(kwargs):
nedrex_api_url_open= "https://api.nedrex.net/open"
nedrex_api_url_licenced = "https://nedrex-api-licenced.zbh.uni-hamburg.de/licensed"
data_dir = kwargs['data_dir']
db_populator = DatabasePopulator(data_dir=data_dir)
if 'clear' in kwargs and kwargs['clear']:
db_populator.delete_all()
if 'delete_model' in kwargs and kwargs['delete_model'] is not None:
model_list = kwargs['delete_model'].split(',')
db_populator.delete_models(model_list)
cache = NodeCache()
update = True if kwargs['update'] else False
importer = NedrexImporter(nedrex_api_url_licenced, nedrex_api_url_open, cache)
populator = DataPopulator(cache)
total_n = 0
nedrex_update = False
if 'all' in kwargs and kwargs['all']:
kwargs['drugs'] = True
kwargs['disorders'] = True
kwargs['proteins'] = True
kwargs['exp'] = True
kwargs['protein_protein'] = True
kwargs['protein_drug'] = True
kwargs['protein_disorder'] = True
kwargs['drug_disorder'] = True
if kwargs['drugs']:
print('Populating Drugs...')
n = NedrexImporter.import_drugs(importer, update)
total_n +=n
nedrex_update = True
print(f'Populated {n} Drugs.')
if kwargs['disorders']:
print('Populating Disorders...')
n = NedrexImporter.import_disorders(importer, update)
total_n += n
nedrex_update = True
print(f'Populated {n} Disorders.')
if kwargs['proteins']:
print('Populating Proteins...')
n = NedrexImporter.import_proteins(importer, update)
total_n += n
nedrex_update = True
print(f'Populated {n} Proteins.')
print('Populating ENSG IDs...')
n = DataPopulator.populate_ensg(populator, update)
total_n += n
print(f'Populated {n} ENSG IDs.')
if kwargs['exp']:
print('Populating Expressions...')
n = DataPopulator.populate_expressions(populator, update)
total_n += n
print(f'Populated {n} Expressions.')
if kwargs['protein_drug']:
print('Importing PDIs from unlicenced NeDRexDB...')
n = NedrexImporter.import_drug_target_interactions(importer,
DatasetLoader.get_drug_target_nedrex(nedrex_api_url_open, False),
update)
total_n += n
print(f'Imported {n} PDIs from unlicenced NeDRexDB')
print('Importing PDIs from licenced NeDRexDB...')
n = NedrexImporter.import_drug_target_interactions(importer,
DatasetLoader.get_drug_target_nedrex(nedrex_api_url_licenced, True),
update)
total_n += n
nedrex_update = True
print(f'Imported {n} PDIs from licenced NeDRexDB')
print('Populating PDIs from Chembl...')
n = DataPopulator.populate_pdi_chembl(populator, DatasetLoader.get_drug_target_chembl(), update)
total_n += n
print(f'Populated {n} PDIs from Chembl.')
print('Populating PDIs from DGIdb...')
n = DataPopulator.populate_pdi_dgidb(populator, DatasetLoader.get_drug_target_dgidb(), update)
total_n += n
print(f'Populated {n} PDIs from DGIdb.')
if kwargs['protein_disorder']:
print('Importing PDis from unlicenced NeDRexDB...')
n = NedrexImporter.import_protein_disorder_associations(importer,
DatasetLoader.get_protein_disorder_nedrex(
nedrex_api_url_open, False),
update)
total_n += n
print(f'Imported {n} PDis from unlicenced NeDRexDB')
print('Importing PDis from licenced NeDRexDB...')
n = NedrexImporter.import_protein_disorder_associations(importer,
DatasetLoader.get_protein_disorder_nedrex(
nedrex_api_url_licenced, True),
update)
total_n += n
nedrex_update = True
print(f'Imported {n} PDis from licenced NeDRexDB')
if kwargs['drug_disorder']:
print('Importing DrDis from unlicenced NeDRexDB...')
n = NedrexImporter.import_drug_disorder_indications(importer,
DatasetLoader.get_drug_disorder_nedrex(nedrex_api_url_open, False),
update)
total_n += n
print(f'Imported {n} DrDis from unlicenced NeDRexDB')
print('Importing DrDis from licenced NeDRexDB...')
n = NedrexImporter.import_drug_disorder_indications(importer,
DatasetLoader.get_drug_disorder_nedrex(
nedrex_api_url_licenced, True),
update)
total_n += n
nedrex_update = True
print(f'Imported {n} DrDis from licenced NeDRexDB')
print('Populating DrDi indications from DrugBank...')
n = DataPopulator.populate_drdis_drugbank(populator, DatasetLoader.get_drug_disorder_drugbank(), update)
total_n += n
print(f'Populated {n} DrDi associations from DrugBank.')
if kwargs['protein_protein']:
print('Importing PPIs from unlicenced NeDRexDB...')
n = NedrexImporter.import_protein_protein_interactions(importer,
DatasetLoader.get_ppi_nedrex(nedrex_api_url_open, False),
update)
total_n += n
print(f'Imported {n} PPIs from unlicended NeDRexDB')
print('Importing PPIs from licenced NeDRexDB...')
n = NedrexImporter.import_protein_protein_interactions(importer,
DatasetLoader.get_ppi_nedrex(nedrex_api_url_licenced,
True),
update)
total_n += n
nedrex_update = True
print(f'Imported {n} PPIs from licended NeDRexDB')
print('Populating PPIs from STRING...')
n = DataPopulator.populate_ppi_string(populator, DatasetLoader.get_ppi_string(), update)
total_n += n
print(f'Populated {n} PPIs from STRING.')
print('Populating PPIs from APID...')
n = DataPopulator.populate_ppi_apid(populator, DatasetLoader.get_ppi_apid(), update)
total_n += n
print(f'Populated {n} PPIs from APID.')
if nedrex_update:
from drugstone.management.includes.DatasetLoader import update_license
update_license()
cache.clear()
return total_n