def load_orphan_sample(rowdic):
print rowdic
sampleid = rowdic['sampleid']
newsampleobj = Sample()
if Sample.objects.filter(sampleid=sampleid).exists():
newsampleobj = Sample.objects.get(sampleid=sampleid)
newsampleobj.sampleid = sampleid
# Things not in spread sheet but essential
newsampleobj.sampletype = "RNA"
newsampleobj.growthphase = Growthphase.objects.get(growthphase="log")
newsampleobj.phenotype = Phenotype.objects.get(phenotype="wildtype")
newsampleobj.author_modified = User.objects.get(username="******")
newsampleobj.sourcename = Source.objects.get(pk=1)
# Things From spread sheet
#
parentsampleid = "None"
if sampleid[-1].isdigit():
parentsampleid = "None"
else:
parentsampleid = rowdic['sampleid'][:-1]
print parentsampleid
newsampleobj.parent_sampleid = parentsampleid;
#
label_ontube = rowdic['oncap']
if rowdic['ontube']:
label_ontube = rowdic['oncap'] + ' / ' + rowdic['ontube']
newsampleobj.label_ontube = label_ontube
#
newsampleobj.genotype = Genotype.objects.get(genotype=rowdic['genotype'])
newsampleobj.lifestage = Lifestage.objects.get(lifestage=rowdic['stage'])
print rowdic['genus']
print rowdic['species']
print rowdic['strain']
print rowdic['dateisolated']
newsampleobj.organism = Organism.objects.get(genus=rowdic['genus'], species=rowdic['species'], strain=rowdic['strain'])
if rowdic['dateisolated']:
newsampleobj.collected_on = rowdic['dateisolated']
newsampleobj.collected_by = rowdic['sender']
newsampleobj.collected_by_emailid = rowdic['senderemailid']
newsampleobj.isolation_method = rowdic['isolationmethod']
newsampleobj.sample_dilution = rowdic['dilution']
if rowdic['daterecieved']:
newsampleobj.date_received = rowdic['daterecieved']
newsampleobj.sample_concentration = rowdic['concentration']
newsampleobj.sample_volume = rowdic['volume']
newsampleobj.sample_quantity = rowdic['quantity']
newsampleobj.biological_replicate_of = rowdic['replicate']
newsampleobj.freezer_location = rowdic['freezerlocation']
#
newsampleobj.sample_notes = rowdic['notesfromsender']
print rowdic['pi']
newsampleobj.collaborator = Collaborator.objects.get(lastname=rowdic['pi'])
print newsampleobj
newsampleobj.save()
def load_orphan_sample(rowdic):
print rowdic
sampleid = rowdic['sampleid']
newsampleobj = Sample()
if Sample.objects.filter(sampleid=sampleid).exists():
newsampleobj = Sample.objects.get(sampleid=sampleid)
newsampleobj.sampleid = sampleid
# Things not in spread sheet but essential
newsampleobj.sampletype = "RNA"
newsampleobj.growthphase = Growthphase.objects.get(growthphase="log")
newsampleobj.phenotype = Phenotype.objects.get(phenotype="wildtype")
newsampleobj.author_modified = User.objects.get(username="******")
newsampleobj.sourcename = Source.objects.get(pk=1)
# Things From spread sheet
#
parentsampleid = "None"
if sampleid[-1].isdigit():
parentsampleid = "None"
else:
parentsampleid = rowdic['sampleid'][:-1]
print parentsampleid
newsampleobj.parent_sampleid = parentsampleid
#
label_ontube = rowdic['oncap']
if rowdic['ontube']:
label_ontube = rowdic['oncap'] + ' / ' + rowdic['ontube']
newsampleobj.label_ontube = label_ontube
#
newsampleobj.genotype = Genotype.objects.get(genotype=rowdic['genotype'])
newsampleobj.lifestage = Lifestage.objects.get(lifestage=rowdic['stage'])
print rowdic['genus']
print rowdic['species']
print rowdic['strain']
print rowdic['dateisolated']
newsampleobj.organism = Organism.objects.get(genus=rowdic['genus'],
species=rowdic['species'],
strain=rowdic['strain'])
if rowdic['dateisolated']:
newsampleobj.collected_on = rowdic['dateisolated']
newsampleobj.collected_by = rowdic['sender']
newsampleobj.collected_by_emailid = rowdic['senderemailid']
newsampleobj.isolation_method = rowdic['isolationmethod']
newsampleobj.sample_dilution = rowdic['dilution']
if rowdic['daterecieved']:
newsampleobj.date_received = rowdic['daterecieved']
newsampleobj.sample_concentration = rowdic['concentration']
newsampleobj.sample_volume = rowdic['volume']
newsampleobj.sample_quantity = rowdic['quantity']
newsampleobj.biological_replicate_of = rowdic['replicate']
newsampleobj.freezer_location = rowdic['freezerlocation']
#
newsampleobj.sample_notes = rowdic['notesfromsender']
print rowdic['pi']
newsampleobj.collaborator = Collaborator.objects.get(lastname=rowdic['pi'])
print newsampleobj
newsampleobj.save()
sampleobj.collaborator = libobj.collaborator
sampleobj.source = libobj.source
sampleobj.sourcename = Source.objects.get(pk=1)
sampleobj.treatment = libobj.treatment
sampleobj.collected_at = libobj.collected_at
# from spread sheet
if rowdic['dateisolated']:
sampleobj.collected_on = rowdic['dateisolated']
sampleobj.collected_by = rowdic['sender']
sampleobj.collected_by_emailid = rowdic['senderemailid']
sampleobj.isolation_method = rowdic['isolationmethod']
if rowdic['daterecieved']:
sampleobj.date_received = rowdic['daterecieved']
sampleobj.sample_concentration = rowdic['concentration']
sampleobj.sample_volume = rowdic['volume']
sampleobj.sample_quantity = rowdic['quantity']
sampleobj.sample_dilution = rowdic['dilution']
sampleobj.biological_replicate_of = rowdic['replicate']
sampleobj.freezer_location = rowdic['freezerlocation']
sampleobj.sample_notes = libobj.sample_notes + "\n" + rowdic['notesfromsender']
#
parentsampleid = "None"
if sampleid[-1].isdigit():
parentsampleid = "None"
else:
parentsampleid = rowdic['sampleid'][:-1]
print parentsampleid
sampleobj.parent_sampleid = parentsampleid
sampleobj.author_modified = User.objects.get(username="******")
sampleobj.collaborator = libobj.collaborator
sampleobj.source = libobj.source
sampleobj.sourcename = Source.objects.get(pk=1)
sampleobj.treatment = libobj.treatment
sampleobj.collected_at = libobj.collected_at
# from spread sheet
if rowdic['dateisolated']:
sampleobj.collected_on = rowdic['dateisolated']
sampleobj.collected_by = rowdic['sender']
sampleobj.collected_by_emailid = rowdic['senderemailid']
sampleobj.isolation_method = rowdic['isolationmethod']
if rowdic['daterecieved']:
sampleobj.date_received = rowdic['daterecieved']
sampleobj.sample_concentration = rowdic['concentration']
sampleobj.sample_volume = rowdic['volume']
sampleobj.sample_quantity = rowdic['quantity']
sampleobj.sample_dilution = rowdic['dilution']
sampleobj.biological_replicate_of = rowdic['replicate']
sampleobj.freezer_location = rowdic['freezerlocation']
sampleobj.sample_notes = libobj.sample_notes + "\n" + rowdic[
'notesfromsender']
#
parentsampleid = "None"
if sampleid[-1].isdigit():
parentsampleid = "None"
else:
parentsampleid = rowdic['sampleid'][:-1]
print parentsampleid
sampleobj.parent_sampleid = parentsampleid