def chembl_assay(chemblid):
global CHEMBL
if CHEMBL is None:
from bioservices import ChEMBLdb
CHEMBL = ChEMBLdb()
data = CHEMBL.get_assay_by_chemblId(str(chemblid))['assay']
return {FIELDS[key]: value for key, value in data.items()
if key in FIELDS}
def run(days=180):
"""Run as::
$ python manage.py runscript update_activities
By default, updates bioactivities of compounds that were never updated
or updates 180 days ago.
To force updating bioactivities for all compounds, give 0 days argument
as follows::
$ python manage.py runscript update_activities --script-args=0
"""
try:
days = int(days)
except ValueError:
days = 180
chembl = ChEMBLdb()
#for table, func in [
# (Compound, chembl.get_compounds_activities),
# (Target, chembl.get_target_bioactivities),
# (Assay, chembl.get_assay_bioactivities), ]:
count = skip = error = ncomp = 0
# will iterate over all compounds one-by-one
for compound in Compound.objects.all():
# if no updates were made, last_update is None
if (compound.last_update is None or
(datetime.date.today() - compound.last_update) >=
datetime.timedelta(days)):
ncomp += 1
try:
acts = chembl.get_compounds_activities(str(compound.chemblid))
except BioServicesError:
continue
for act in acts['bioactivities']:
act = {FIELDS[key]: value for key, value in act.items()
if key in FIELDS}
tid, aid, cid, pid = (act['target'], act['assay'],
act['compound'], act['parent_compound'])
try:
parent = Compound.objects.get(chemblid=pid)
except Compound.DoesNotExist:
try:
parent = Compound.objects.create(locked=True, **chembl_compound(pid))
except ValueError:
error += 1
continue
try:
target = Target.objects.get(chemblid=tid)
except Target.DoesNotExist:
try:
target = Target.objects.create(locked=True, **chembl_target(tid))
except ValueError:
error += 1
continue
try:
assay = Assay.objects.get(chemblid=aid)
except Assay.DoesNotExist:
try:
assay = Assay.objects.create(locked=True, **chembl_assay(aid))
except ValueError:
error += 1
continue
try:
activity = Bioactivity.objects.get(
target=target, assay=assay, compound=compound)
except Bioactivity.DoesNotExist:
(act['target'], act['assay'], act['compound'],
act['parent_compound']) = (
target, assay, compound, parent)
try:
ba = Bioactivity.objects.create(locked=True, **act)
except ValueError:
error += 1
except Exception as err:
for key, val in act.items():
if isinstance(val, str):
print('{}: ({}) {}'.format(key, len(val), val))
raise err
else:
count += 1
else:
skip += 1
compound.last_update = datetime.date.today()
compound.save()
print('{} bioactivities were added, {} were found in the database, and '
'{} failed due to value errors.'.format(count, skip, error))
