def aggregate(self, experimentID, user):
"""
Aggregate the GFP scores and send report
"""
gfps = GFP.objects.filter(experiment_id=experimentID)
log.debug("RUNNING aggregate: initialize method")
algorithm = Algorithm()
algorithm = algorithm.getAlgorithm("NV")
algorithm.loadDataAggregate()
algorithm.aggregate(gfps, experimentID)
experiment = Experiment.objects.filter(id=experimentID)
log.debug("RUNNING aggregate: start report")
report = Report(experimentID)
filename = REPORT_DIR + "sapling_gfp_report_" + slugify(experiment[0].Name) + "_" + str(experimentID) + ".pdf"
report.generateReport(filename)
del report
subject = "SAPLING report: " + experiment[0].Name
body = "Dear " + user.first_name + " "+ user.last_name + ",\n\n"
body += "Please find attached a report of your experiment " + experiment[0].Name + ".\n\n"
body += "Regards,\n SAPLING"
email = EmailMessage(subject=subject, body=body, from_email="*****@*****.**", to=[user.email])
reportname = "sapling_gfp_report_" + slugify(experiment[0].Name) + "_" + str(experimentID) + ".pdf"
handle = open(filename, 'rb')
email.attach(reportname, handle.read(), "application/pdf")
enrichname = "Enrichment_GeneList_GO_" + str(experimentID) + ".csv"
filename = REPORT_DIR + "Enrichment_GeneList_GO_" + str(experimentID) + ".csv"
handle = open(filename, 'rb')
email.attach(enrichname, handle.read(), "text/csv")
email.send()
handle.close()
log.debug("DONE Aggregate")
def predict(self, gfpID, user):
"""
annotation: list of gene symbols
"""
log.debug("Start time: %s" % timezone.now().strftime('%d/%m/%Y %H:%M:%S'))
gfp = GFP.objects.filter(id=gfpID)
gfp = gfp[0]
log.debug("RUNNING: initialize method")
self.update_state(state='RUNNING', meta='Initialize method')
if not ProcessManagement.objects.filter(gfp_id=gfpID, experiment_id=gfp.experiment_id).exists():
ProcessManagement.objects.create(gfp_id=gfpID, experiment_id=gfp.experiment_id, \
State= "RUNNING: initialize method", Name=gfp.Network+"_"+gfp.Algorithm)
else:
ProcessManagement.objects.filter(gfp_id=gfpID, experiment_id=gfp.experiment_id).update(State= \
"RUNNING: initialize method")
algorithm = Algorithm()
algorithm = algorithm.getAlgorithm(gfp.Algorithm)
log.debug("RUNNING: load files")
self.update_state(state='RUNNING', meta='Load files')
ProcessManagement.objects.filter(gfp_id=gfpID, experiment_id=gfp.experiment_id).update(State= \
"RUNNING: load files")
algorithm.loadData(gfpID)
log.debug("RUNNING: run method")
self.update_state(state='RUNNING', meta='Run method')
ProcessManagement.objects.filter(gfp_id=gfpID, experiment_id=gfp.experiment_id).update(State= \
"RUNNING: run method")
algorithm.run()
log.debug("RUNNING: save predictions")
self.update_state(state='RUNNING', meta='Save predictions')
ProcessManagement.objects.filter(gfp_id=gfpID, experiment_id=gfp.experiment_id).update( \
State="RUNNING: save predictions")
algorithm.save(gfpID)
log.debug("RUNNING: enrichment")
algorithm.enrichment(gfp.experiment_id, gfpID)
ProcessManagement.objects.filter(gfp_id=gfpID, experiment_id=gfp.experiment_id).update( \
State="FINISHED")
log.debug("FINISHED")
gfps = GFP.objects.filter(experiment_id=gfp.experiment_id)
processes = ProcessManagement.objects.filter(experiment_id=gfp.experiment_id)
flag = True
if len(processes) != len(gfps):
flag = False
else:
for process in processes:
if process.State != "FINISHED":
flag = False
break
log.debug("Experiment flag: %s", str(flag))
## Create report and aggregate
if flag:
log.debug("REPORT EMAIL")
gfps = GFP.objects.filter(experiment_id=gfp.experiment_id)
# Aggregation of GFPs
algorithm.aggregate(gfps, gfp.experiment_id)
experiment = Experiment.objects.filter(id=gfp.experiment_id)
log.debug("RUNNING: start report")
report = Report(gfp.experiment_id)
filename = REPORT_DIR + "sapling_gfp_report_" + slugify(experiment[0].Name) + "_" \
+ str(gfp.experiment_id) + ".pdf"
log.debug("RUNNING: %s" % filename)
report.generateReport(filename)
del report
subject = "SAPLING report: " + experiment[0].Name
body = "Dear " + user.first_name + " "+ user.last_name + ",\n\n"
body += "Please find attached a report of your experiment " + experiment[0].Name + ".\n\n"
body += "Regards,\n SAPLING"
email = EmailMessage(subject=subject, body=body, from_email="*****@*****.**", to=[user.email])
reportname = "sapling_gfp_report_" + slugify(experiment[0].Name) + "_" + str(gfp.experiment_id) + ".pdf"
handle = open(filename, 'rb')
email.attach(reportname, handle.read(), "application/pdf")
enrichname = "Enrichment_GeneList_GO_" + str(gfp.experiment_id) + ".csv"
filename = REPORT_DIR + "Enrichment_GeneList_GO_" + str(gfp.experiment_id) + ".csv"
handle = open(filename, 'rb')
email.attach(enrichname, handle.read(), "text/csv")
email.send()
handle.close()
log.debug("DONE")
