def on_Drugs(self, row):
if row[5] not in Drug.approvals:
# print 'not approved: %s' % '\t'.join(row)
return
drug=Drug(id=row[3], name=row[2], condition=row[4], approval=row[5], src='ttd')
drug.save()
self.stats['n_drugs']+=1
self.cur_target.drugs.add(drug)
def onbegin_dc(self, mo):
id=mo.group(1)
self.cur_drug=Drug(id=id, src='db')
# self.cur_drug.save()
self.cur_obj=self.cur_drug
self.cur_target=None
class DrugcardBuilderDjango(DrugcardBuilder):
attr_names={'Generic_Name':'name', # drugs
'Primary_Accession_No':'primary_acc', # drugs
'Drug_Type':'approval', # drugs
'ID':'id', # targets
'Name':'name', # targets
}
def __init__(self, **kwargs):
self.cur_obj=None
self.cur_drug=None
self.cur_target=None
self.attr_name=None
# clear tables if called for:
if 'clear_table' in kwargs and kwargs['clear_table']:
print 'clearing tables...'
for cls in [ Drug, DrugSynonym, DrugPathway, Target, TargetSynonym, TargetPathway]:
dao=dao_django(cls=cls)
query = {'src':'db'} if cls==Drug or cls==Target else {}
dao.remove(query)
self.stats={'n_drugs':0,
'n_targets':0,
'n_drug_syns':0,
'n_target_syns':0,
'n_drug_pathways':0,
'n_target_pathways':0,
}
self.ug=uniprot2gene(kwargs['uniprot_gene_fn'])
def onbegin_dc(self, mo):
id=mo.group(1)
self.cur_drug=Drug(id=id, src='db')
# self.cur_drug.save()
self.cur_obj=self.cur_drug
self.cur_target=None
def onattr_name(self, mo):
self.attr_name=mo.group(1)
def onvalue(self, mo):
value=mo.group(1)
if self.attr_name in self.attr_names:
real_attr_name=self.attr_names[self.attr_name]
setattr(self.cur_obj, real_attr_name, value)
# Synonyms
elif self.attr_name == 'Synonyms':
if self.cur_target:
syn=TargetSynonym(synonym=value, target=self.cur_target)
self.cur_target.syns.append(syn)
else:
syn=DrugSynonym(synonym=value, drug=self.cur_drug)
self.stats['n_drug_syns']+=1
self.cur_obj.drugsynonym_set.add(syn)
syn.save()
# Gene_Name
elif self.attr_name == 'Gene_Name':
self.cur_target.gene_sym=value
try:
self.cur_target.uniprot_id=','.join(self.ug.g2u[value])
except KeyError:
pass
'''
# (Drug) Pathways
elif self.attr_name == 'Pathways': # drug
pathway=DrugPathway(name=value, drug=self.cur_drug)
pathway.save()
self.stats['n_drug_pathways']+=1
# (Target) Pathway
elif self.attr_name == 'Pathway': # target
pathway=TargetPathway(name=value, target=self.cur_target)
pathway.save()
self.stats['n_target_pathways']+=1
'''
def onseq_desc(self, mo):
pass # not interested
def onseq(self, mo):
pass # not interested
def onend_dc(self, mo):
self.cur_drug.save()
self.stats['n_drugs']+=1
print 'drug %s saved' % self.cur_drug.id
if self.cur_target:
# self.cur_target.save()
self.save_target()
self.cur_target.drugs.add(self.cur_drug)
self.stats['n_targets']+=1
def ondtnan(self, mo):
dt_N=int(mo.group(1))
dt_attr_name=mo.group(2)
# Is this a new target?
if not self.cur_target or self.target_n != dt_N:
if self.cur_target:
# self.cur_target.save() # re-save, really
self.save_target()
self.cur_drug.save()
self.cur_target.drugs.add(self.cur_drug)
self.stats['n_targets']+=1
self.cur_target=Target(src='db')
self.cur_target.syns=[]
self.cur_obj=self.cur_target
self.target_n=dt_N
self.attr_name=dt_attr_name
def onleave_ext_seq(self):
pass
'''
def save_drug(self):
self.cur_drug.save()
for target in self.targets:
target.drugs.add(self.cur_drug)
target.save()
'''
def save_target(self):
if not hasattr(self.cur_target, 'id'):
raise Exception('target has no id: %s' % self.cur_target)
# self.cur_target.save()
# print '%s saved' % self.cur_target
for s in self.cur_target.syns:
syn=TargetSynonym(synonym=s, target=self.cur_target)
self.cur_target.targetsynonym_set.add(syn)
self.cur_target.save()
print '%s saved' % self.cur_target