def _get_new_or_db_barcode(name, index):
if (name and index):
barcodes = dnaBarcode.objects.filter(name=name, index=index)
if barcodes:
print("db barcode FOUND for name=%s; index=%s" % (name, index))
return barcodes[0]
return dnaBarcode()
def add_or_update_dnaBarcode(fields):
name = fields.get("name")
sequence = fields.get("sequence")
if sequence == "ALL":
updateObjs = dnaBarcode.objects.filter(name=name)
if updateObjs.count() == 0:
raise Exception("Barcode set %s is not installed" % name)
else:
fields.pop("sequence")
updateObjs.update(**fields)
else:
try:
barcodeObj = dnaBarcode.objects.get(name=name, sequence=sequence)
except dnaBarcode.DoesNotExist:
barcodeObj = dnaBarcode()
for key, value in fields.items():
setattr(barcodeObj, key, value)
barcodeObj.save()
def add_or_update_dnaBarcode(fields):
name = fields.get("name")
sequence = fields.get("sequence")
if sequence == "ALL":
updateObjs = dnaBarcode.objects.filter(name=name)
if updateObjs.count() == 0:
raise Exception("Barcode set %s is not installed" % name)
else:
fields.pop("sequence")
updateObjs.update(**fields)
else:
try:
barcodeObj = dnaBarcode.objects.get(name=name, sequence=sequence)
except dnaBarcode.DoesNotExist:
barcodeObj = dnaBarcode()
for key, value in fields.items():
setattr(barcodeObj, key, value)
barcodeObj.save()
def add_or_update_barcode_set2(blist,btype,name,adapter, scoreMode, scoreCutoff, alt_barcode_prefix = None, skip_barcode_leading_zero = False):
print("add_or_update_barcode_set2... name=%s; alt_barcode_prefix=%s" %(name, alt_barcode_prefix))
# Attempt to read dnabarcode set named 'IonXpress' from dbase
dnabcs = models.dnaBarcode.objects.filter(name=name)
if len(dnabcs) > 0:
#print '%s dnaBarcode Set exists in database' % name
# make sure we have all the sequences we expect
for index,sequence in enumerate(blist,start=1):
# Search for this sequence in the list of barcode records
bc_found = dnabcs.filter(sequence=sequence)
if len(bc_found) > 1:
print "ERROR: More than one entry with sequence %s" % sequence
print "TODO: Fix this situation, Mr. Programmer!"
# Make sure id string has zero padded index field if skip_barcode_leading_zero is not true
if alt_barcode_prefix:
if skip_barcode_leading_zero:
barcode_name = '%s%d' % (alt_barcode_prefix,index)
else:
barcode_name = '%s%02d' % (alt_barcode_prefix,index)
else:
if skip_barcode_leading_zero:
barcode_name = '%s_%d' % (name,index)
else:
barcode_name = '%s_%02d' % (name,index)
if len(bc_found) == 1:
#print "%s dnaBarcode sequence %s already in the database" % (name, sequence)
# Make sure floworder field is not 'none'
if bc_found[0].floworder == 'none':
bc_found[0].floworder = ''
bc_found[0].id_str = barcode_name
# update type
bc_found[0].type = btype
# Save changes to database
bc_found[0].save()
else: # array length is zero
#print "Adding entry for %s" % sequence
kwargs = {
'name':name,
'id_str': barcode_name,
'sequence':sequence,
'type':btype,
'length':len(sequence),
'floworder':'',
'index':index,
'annotation':'',
'adapter':adapter,
'score_mode':scoreMode,
'score_cutoff':scoreCutoff,
}
ret = models.dnaBarcode(**kwargs)
ret.save()
else:
# Add the barcodes because they do not exist.
# NOTE: name for id_str
for index,sequence in enumerate(blist,start=1):
if alt_barcode_prefix:
if skip_barcode_leading_zero:
barcode_name = '%s%d' % (alt_barcode_prefix,index)
else:
barcode_name = '%s%02d' % (alt_barcode_prefix,index)
else:
if skip_barcode_leading_zero:
barcode_name = '%s_%d' % (name,index)
else:
barcode_name = '%s_%02d' % (name,index)
kwargs = {
'name':name,
'id_str': barcode_name,
'sequence':sequence,
'type':btype,
'length':len(sequence),
'floworder':'',
'index':index,
'annotation':'',
'adapter':adapter,
'score_mode':scoreMode,
'score_cutoff':scoreCutoff,
}
ret = models.dnaBarcode(**kwargs)
ret.save()
print '%s dnaBarcode Set added to database' % name
def add_or_update_barcode_set(blist,btype,name,adapter):
# Attempt to read dnabarcode set named 'IonXpress' from dbase
dnabcs = models.dnaBarcode.objects.filter(name=name)
if len(dnabcs) > 0:
#print '%s dnaBarcode Set exists in database' % name
# make sure we have all the sequences we expect
for index,sequence in enumerate(blist,start=1):
# Search for this sequence in the list of barcode records
bc_found = dnabcs.filter(sequence=sequence)
if len(bc_found) > 1:
print "ERROR: More than one entry with sequence %s" % sequence
print "TODO: Fix this situation, Mr. Programmer!"
if len(bc_found) == 1:
# Make sure floworder field is not 'none'
if bc_found[0].floworder == 'none':
bc_found[0].floworder = ''
# Make sure id string has zero padded index field
bc_found[0].id_str = '%s_%03d' % (name,index)
# update type
bc_found[0].type = btype
# Save changes to database
bc_found[0].save()
else: # array length is zero
#print "Adding entry for %s" % sequence
kwargs = {
'name':name,
'id_str':'%s_%03d' % (name,index),
'sequence':sequence,
'type':btype,
'length':len(sequence),
'floworder':'',
'index':index,
'annotation':'',
'adapter':adapter,
'score_mode':1,
'score_cutoff':2.0,
}
ret = models.dnaBarcode(**kwargs)
ret.save()
else:
# Add the barcodes because they do not exist.
# NOTE: name for id_str
for index,sequence in enumerate(blist,start=1):
kwargs = {
'name':name,
'id_str':'%s_%03d' % (name,index),
'sequence':sequence,
'type':btype,
'length':len(sequence),
'floworder':'',
'index':index,
'annotation':'',
'adapter':adapter,
'score_mode':1,
'score_cutoff':2.0,
}
ret = models.dnaBarcode(**kwargs)
ret.save()
print '%s dnaBarcode Set added to database' % name
def add_or_update_barcode_set2(blist, btype, name, adapter, scoreMode,
scoreCutoff):
# Attempt to read dnabarcode set named 'IonXpress' from dbase
dnabcs = models.dnaBarcode.objects.filter(name=name)
if len(dnabcs) > 0:
#print '%s dnaBarcode Set exists in database' % name
# make sure we have all the sequences we expect
for index, sequence in enumerate(blist, start=1):
# Search for this sequence in the list of barcode records
bc_found = dnabcs.filter(sequence=sequence)
if len(bc_found) > 1:
print "ERROR: More than one entry with sequence %s" % sequence
print "TODO: Fix this situation, Mr. Programmer!"
if len(bc_found) == 1:
#print "%s dnaBarcode sequence %s already in the database" % (name, sequence)
# Make sure floworder field is not 'none'
if bc_found[0].floworder == 'none':
bc_found[0].floworder = ''
# Make sure id string has zero padded index field
bc_found[0].id_str = '%s_%02d' % (name, index)
# update type
bc_found[0].type = btype
# Save changes to database
bc_found[0].save()
else: # array length is zero
#print "Adding entry for %s" % sequence
kwargs = {
'name': name,
'id_str': '%s_%02d' % (name, index),
'sequence': sequence,
'type': btype,
'length': len(sequence),
'floworder': '',
'index': index,
'annotation': '',
'adapter': adapter,
'score_mode': scoreMode,
'score_cutoff': scoreCutoff,
}
ret = models.dnaBarcode(**kwargs)
ret.save()
else:
# Add the barcodes because they do not exist.
# NOTE: name for id_str
for index, sequence in enumerate(blist, start=1):
kwargs = {
'name': name,
'id_str': '%s_%02d' % (name, index),
'sequence': sequence,
'type': btype,
'length': len(sequence),
'floworder': '',
'index': index,
'annotation': '',
'adapter': adapter,
'score_mode': scoreMode,
'score_cutoff': scoreCutoff,
}
ret = models.dnaBarcode(**kwargs)
ret.save()
print '%s dnaBarcode Set added to database' % name
def _add_barcode(request):
"""add the barcodes, with CSV validation"""
if request.method == 'POST':
name = request.POST.get('name', '')
postedfile = request.FILES['postedfile']
barCodeSet = dnaBarcode.objects.filter(name=name)
if barCodeSet:
return HttpResponse(json.dumps({"status": "Error: Barcode set with the same name already exists"}), mimetype="text/html")
expectedHeader = ["id_str", "type", "sequence", "floworder", "index", "annotation", "adapter"]
barCodes = []
failed = {}
nucs = ["sequence", "floworder", "adapter"] # fields that have to be uppercase
reader = csv.DictReader(postedfile.read().splitlines())
for index, row in enumerate(reader, start=1):
invalid = _validate_barcode(row)
if invalid: # don't make dna object or add it to the list
failed[index] = invalid
continue
newBarcode = dnaBarcode(name=name, index=index)
for key in expectedHeader: # set the values for the objects
value = row.get(key, None)
if value:
value = value.strip() # strip the strings
if key in nucs: # uppercase if a nuc
value = value.upper()
setattr(newBarcode, key, value)
if not newBarcode.id_str: # make a id_str if one is not provided
newBarcode.id_str = str(name) + "_" + str(index)
newBarcode.length = len(newBarcode.sequence) # now set a default
barCodes.append(newBarcode) # append to our list for later saving
if failed:
r = {"status": "Barcodes validation failed. The barcode set has not been saved.", "failed": failed}
return HttpResponse(json.dumps(r), mimetype="text/html")
if not barCodes:
return HttpResponse(json.dumps({"status": "Error: There must be at least one barcode! Please reload the page and try again with more barcodes."}), mimetype="text/html")
usedID = []
for barCode in barCodes:
if barCode.id_str not in usedID:
usedID.append(barCode.id_str)
else:
error = {"status": "Duplicate id_str for barcodes named: " + str(barCode.id_str) + "."}
return HttpResponse(json.dumps(error), mimetype="text/html")
usedIndex = []
for barCode in barCodes:
if barCode.index not in usedIndex:
usedIndex.append(barCode.index)
else:
error = {"status": "Duplicate index: " + barCode.index + "."}
return HttpResponse(json.dumps(error), mimetype="text/html")
#saving to db needs to be the last thing to happen
for barCode in barCodes:
try:
barCode.save()
except:
logger.exception("Error saving barcode to database")
return HttpResponse(json.dumps({"status": "Error saving barcode to database!"}), mimetype="text/html")
r = {"status": "Barcodes Uploaded! The barcode set will be listed on the references page.", "failed": failed, 'success': True}
return HttpResponse(json.dumps(r), mimetype="text/html")
def add_or_update_barcode_set2(blist,btype,name,adapter, scoreMode, scoreCutoff, alt_barcode_prefix = None, skip_barcode_leading_zero = False, barcode_num_digits = 2, start_id_str_value = 1, index = 0):
print("add_or_update_barcode_set2... name=%s; alt_barcode_prefix=%s" %(name, alt_barcode_prefix))
digitCount = str(barcode_num_digits)
# Attempt to read dnabarcode set named 'IonXpress' from dbase
dnabcs = models.dnaBarcode.objects.filter(name=name)
if len(dnabcs) > 0:
#print '%s dnaBarcode Set exists in database' % name
# make sure we have all the sequences we expect
for id_index,sequence in enumerate(blist,start= start_id_str_value):
# Search for this sequence in the list of barcode records
bc_found = dnabcs.filter(sequence=sequence)
if len(bc_found) > 1:
print "ERROR: More than one entry with sequence %s" % sequence
print "TODO: Fix this situation, Mr. Programmer!"
index += 1
# Make sure id string has zero padded index field if skip_barcode_leading_zero is not true
if alt_barcode_prefix:
if skip_barcode_leading_zero:
barcode_name = '%s%d' % (alt_barcode_prefix,id_index)
else:
format_string = '%s%0'+digitCount+ 'd'
barcode_name = format_string % (alt_barcode_prefix,id_index)
else:
if skip_barcode_leading_zero:
barcode_name = '%s_%d' % (name,id_index)
else:
format_string = '%s_%0'+digitCount+'d'
barcode_name = format_string % (name,id_index)
if len(bc_found) == 1:
#print "%s dnaBarcode sequence %s already in the database" % (name, sequence)
# Make sure floworder field is not 'none'
if bc_found[0].floworder == 'none':
bc_found[0].floworder = ''
bc_found[0].id_str = barcode_name
# update type
bc_found[0].type = btype
# update index
bc_found[0].index = index
# Save changes to database
bc_found[0].save()
else: # array length is zero
#print "Adding entry for %s" % sequence
kwargs = {
'name':name,
'id_str': barcode_name,
'sequence':sequence,
'type':btype,
'length':len(sequence),
'floworder':'',
'index':index,
'annotation':'',
'adapter':adapter,
'score_mode':scoreMode,
'score_cutoff':scoreCutoff,
}
ret = models.dnaBarcode(**kwargs)
ret.save()
else:
# Add the barcodes because they do not exist.
# NOTE: name for id_str
format_string = '%s%0'+digitCount+'d'
for id_index,sequence in enumerate(blist,start= start_id_str_value):
index += 1
if alt_barcode_prefix:
if skip_barcode_leading_zero:
barcode_name = '%s%d' % (alt_barcode_prefix,id_index)
else:
barcode_name = format_string % (alt_barcode_prefix,id_index)
else:
if skip_barcode_leading_zero:
barcode_name = '%s_%d' % (name,id_index)
else:
barcode_name = format_string % (name,id_index)
kwargs = {
'name':name,
'id_str': barcode_name,
'sequence':sequence,
'type':btype,
'length':len(sequence),
'floworder':'',
'index':index,
'annotation':'',
'adapter':adapter,
'score_mode':scoreMode,
'score_cutoff':scoreCutoff,
}
ret = models.dnaBarcode(**kwargs)
ret.save()
print '%s dnaBarcode Set added to database' % name
return index