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()
label_ontube = rowdic['oncap']
if rowdic['ontube']:
label_ontube = rowdic['oncap'] + ' / ' + rowdic['ontube']
sampleobj.label_ontube = label_ontube
# 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']
label_ontube = rowdic['oncap']
if rowdic['ontube']:
label_ontube = rowdic['oncap'] + ' / ' + rowdic['ontube']
sampleobj.label_ontube = label_ontube
# 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']
