def migrate_library2sample_ingoringSpreadsheet(lib):
# check if its been migrated already
if Sample.objects.filter(sampleid=lib.sample_name).exists():
print "Library ", lib.library_code, "has been migrated already, skipping."
else:
#create an new samples.sample object
newsampleobj = Sample(organism=lib.organism, lifestage=lib.lifestage, growthphase=lib.growthphase, phenotype=lib.phenotype, genotype=lib.genotype, source=lib.source, sourcename=Source.objects.get(pk=1), sample_concentration=0, sample_volume=0, sample_quantity=0, author_modified=User.objects.get(username="******"))
newsampleobj.sampleid = 's' + lib.library_code
if lib.sample_name:
newsampleobj.sampleid = lib.sample_name
newsampleobj.date_created = lib.date_created
if lib.sample_notes != 'NA':
newsampleobj.sample_notes = lib.sample_notes
if lib.experiment_notes != 'NA':
newsampleobj.sample_notes = newsampleobj.sample_notes + ' ' + lib.experiment_notes
newsampleobj.collected_on = lib.collected_on
newsampleobj.collected_at = lib.collected_at
newsampleobj.collected_by = lib.collected_by
newsampleobj.treatment = lib.treatment
newsampleobj.collaborator = lib.collaborator
newsampleobj.sampletype = 'RNA'
#now save it
newsampleobj.save()
# save back sampleid into library table
lib.sampleid = newsampleobj
lib.save()
def migrate_library2sample_ingoringSpreadsheet(lib):
# check if its been migrated already
if Sample.objects.filter(sampleid=lib.sample_name).exists():
print "Library ", lib.library_code, "has been migrated already, skipping."
else:
#create an new samples.sample object
newsampleobj = Sample(
organism=lib.organism,
lifestage=lib.lifestage,
growthphase=lib.growthphase,
phenotype=lib.phenotype,
genotype=lib.genotype,
source=lib.source,
sourcename=Source.objects.get(pk=1),
sample_concentration=0,
sample_volume=0,
sample_quantity=0,
author_modified=User.objects.get(username="******"))
newsampleobj.sampleid = 's' + lib.library_code
if lib.sample_name:
newsampleobj.sampleid = lib.sample_name
newsampleobj.date_created = lib.date_created
if lib.sample_notes != 'NA':
newsampleobj.sample_notes = lib.sample_notes
if lib.experiment_notes != 'NA':
newsampleobj.sample_notes = newsampleobj.sample_notes + ' ' + lib.experiment_notes
newsampleobj.collected_on = lib.collected_on
newsampleobj.collected_at = lib.collected_at
newsampleobj.collected_by = lib.collected_by
newsampleobj.treatment = lib.treatment
newsampleobj.collaborator = lib.collaborator
newsampleobj.sampletype = 'RNA'
#now save it
newsampleobj.save()
# save back sampleid into library table
lib.sampleid = newsampleobj
lib.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()
# from library object
sampleobj.organism = libobj.organism
sampleobj.lifestage = libobj.lifestage
sampleobj.growthphase = libobj.growthphase
sampleobj.phenotype = libobj.phenotype
sampleobj.genotype = libobj.genotype
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():
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()
# from library object
sampleobj.organism = libobj.organism
sampleobj.lifestage = libobj.lifestage
sampleobj.growthphase = libobj.growthphase
sampleobj.phenotype = libobj.phenotype
sampleobj.genotype = libobj.genotype
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"
