def handle(self, **options):
input_file = options['input_file']
output_dir = options['output_dir']
# Create output directory, exiting if already exists
if os.path.exists(output_dir):
raise CommandError(
'Output directory {} already exists'.format(output_dir))
else:
os.makedirs(output_dir)
# Parse input
reader = csv.reader(input_file, delimiter=',')
for experiment_id, well in reader:
try:
experiment_id = int(experiment_id.strip())
except ValueError:
continue
well = well.strip()
if re.match('Tile0000\d\d\.bmp', well):
tile = well.split('.bmp')[0]
elif re.match('Tile0000\d\d', well):
tile = well
else:
try:
tile = well_to_tile(well)
except ValueError:
continue
input_image_url = '{}/{}/{}.bmp'.format(settings.BASE_URL_IMG,
experiment_id, tile)
output_image_path = '{}/{}_{}.bmp'.format(output_dir,
experiment_id, tile)
r = requests.get(input_image_url, stream=True)
if r.status_code != 200:
raise CommandError(
'non-ok GET status for {}'.format(input_image_url))
with open(output_image_path, 'wb') as f:
r.raw.decode_content = True
shutil.copyfileobj(r.raw, f)
self.stdout.write('{} written'.format(output_image_path))
def handle(self, **options):
input_file = options['input_file']
output_dir = options['output_dir']
# Create output directory, exiting if already exists
if os.path.exists(output_dir):
raise CommandError('Output directory {} already exists'
.format(output_dir))
else:
os.makedirs(output_dir)
# Parse input
reader = csv.reader(input_file, delimiter=',')
for experiment_id, well in reader:
try:
experiment_id = int(experiment_id.strip())
except ValueError:
continue
well = well.strip()
if re.match('Tile0000\d\d\.bmp', well):
tile = well.split('.bmp')[0]
elif re.match('Tile0000\d\d', well):
tile = well
else:
try:
tile = well_to_tile(well)
except ValueError:
continue
input_image_url = '{}/{}/{}.bmp'.format(
settings.BASE_URL_IMG, experiment_id, tile)
output_image_path = '{}/{}_{}.bmp'.format(
output_dir, experiment_id, tile)
r = requests.get(input_image_url, stream=True)
if r.status_code != 200:
raise CommandError('non-ok GET status for {}'
.format(input_image_url))
with open(output_image_path, 'wb') as f:
r.raw.decode_content = True
shutil.copyfileobj(r.raw, f)
self.stdout.write('{} written'.format(output_image_path))
def get_image_url(self, mode=None):
"""
Get the image url for this experiment.
Optionally supply mode='thumbnail' or mode='devstar'.
"""
tile = well_to_tile(self.well)
if mode == 'thumbnail':
url = '/'.join(
(settings.BASE_URL_THUMBNAIL, str(self.plate_id), tile))
url += '.jpg'
elif mode == 'devstar':
url = '/'.join(
(settings.BASE_URL_DEVSTAR, str(self.plate_id), tile))
url += 'res.png'
else:
url = '/'.join((settings.BASE_URL_IMG, str(self.plate_id), tile))
url += '.bmp'
return url
def get_image_url(self, mode=None):
"""
Get the image url for this experiment.
Optionally supply mode='thumbnail' or mode='devstar'.
"""
tile = well_to_tile(self.well)
if mode == 'thumbnail':
url = '/'.join((settings.BASE_URL_THUMBNAIL,
str(self.plate_id), tile))
url += '.jpg'
elif mode == 'devstar':
url = '/'.join((settings.BASE_URL_DEVSTAR,
str(self.plate_id), tile))
url += 'res.png'
else:
url = '/'.join((settings.BASE_URL_IMG,
str(self.plate_id), tile))
url += '.bmp'
return url
def handle(self, **options):
######################################################
# FIRST STAGE
#
# Connect to legacy database and create a dictionary to
# translate from new canonical clones names to legacy
# clone information.
#
######################################################
legacy_db = MySQLdb.connect(host=LEGACY_DATABASE['HOST'],
user=LEGACY_DATABASE['USER'],
passwd=LEGACY_DATABASE['PASSWORD'],
db=LEGACY_DATABASE['NAME'])
cursor = legacy_db.cursor()
cursor.execute('SELECT clone, node_primary_name, 384PlateID, '
'384Well FROM RNAiPlate '
'WHERE RNAiPlateID != "L4440"')
new_to_old = {}
for row in cursor.fetchall():
old_clone_name = row[0].strip()
node_primary_name = row[1]
if isinstance(node_primary_name, str):
node_primary_name = node_primary_name.strip()
plate_384 = row[2].strip()
well_384 = row[3].strip()
if plate_384[0:3] == 'GHR':
new_clone_name = plate_384 + '@' + well_384
else:
new_clone_name = old_clone_name
new_to_old[new_clone_name] = {
'old_clone_name': old_clone_name,
'node_primary_name': node_primary_name,
}
######################################################
# SECOND STAGE
#
# For each row in cherrypick_list, create a corresponding
# row for the legacy database, with fields:
# ('mutant', 'mutantAllele', 'RNAiPlateID', '96well',
# 'ImgName', 'clone', 'node_primary_name',
# 'seq_node_primary_name')
#
######################################################
cherrypick_list = options['cherrypick_list']
# Skip header row
next(cherrypick_list)
'''
# Uncomment this to add header row with fieldnames
legacy_fields = ('mutant', 'mutantAllele', 'RNAiPlateID',
'96well', 'ImgName', 'clone',
'node_primary_name', 'seq_node_primary_name')
self.stdout.write(','.join(legacy_fields))
'''
for line in cherrypick_list:
row = line.split(',')
source_plate_name = row[0].strip()
# Since legacy database did not represent empty wells
if not source_plate_name or source_plate_name == "None":
continue
source_well = row[1].strip()
destination_plate_name = row[2].strip()
destination_well = row[3].strip()
destination_tile = well_to_tile(destination_well) + '.bmp'
try:
source_plate = LibraryPlate.objects.get(
id=source_plate_name)
source_stock = LibraryStock.objects.get(
plate=source_plate, well=source_well)
except ObjectDoesNotExist:
raise CommandError('{} at {} not found'
.format(source_plate_name, source_well))
allele = destination_plate_name.split('-')[0]
if allele == 'universal':
# For universal plates, allele == gene == 'universal'
gene = 'universal'
else:
# Otherwise, gene can be retrieved from WormStrain
gene = WormStrain.objects.get(allele=allele).gene
# Account for legacy database using mispelled allele 'zc310'
if allele == 'zu310':
allele = 'zc310'
destination_plate_chars = list(destination_plate_name)
destination_plate_chars[1] = 'c'
destination_plate_name = ''.join(destination_plate_chars)
if source_stock.intended_clone:
new_clone_name = source_stock.intended_clone.id
old_clone_name = new_to_old[new_clone_name]['old_clone_name']
node_primary_name = (
new_to_old[new_clone_name]['node_primary_name'])
if node_primary_name == 'NULL':
node_primary_name = ''
else:
old_clone_name = ''
node_primary_name = ''
output = [
gene, allele,
destination_plate_name, destination_well, destination_tile,
old_clone_name, node_primary_name, 'X'
]
self.stdout.write(','.join([str(x) for x in output]))
def handle(self, **options):
######################################################
# FIRST STAGE
#
# Connect to legacy database and create a dictionary to
# translate from new canonical clones names to legacy
# clone information.
#
######################################################
# legacy_db = MySQLdb.connect(host=LEGACY_DATABASE['HOST'],
legacy_db = mysql.connector.connect(host=LEGACY_DATABASE['HOST'],
user=LEGACY_DATABASE['USER'],
passwd=LEGACY_DATABASE['PASSWORD'],
db=LEGACY_DATABASE['NAME'])
cursor = legacy_db.cursor()
cursor.execute('SELECT clone, node_primary_name, 384PlateID, '
'384Well FROM RNAiPlate '
'WHERE RNAiPlateID != "L4440"')
new_to_old = {}
for row in cursor.fetchall():
old_clone_name = row[0].strip()
node_primary_name = row[1]
if isinstance(node_primary_name, str):
node_primary_name = node_primary_name.strip()
plate_384 = row[2].strip()
well_384 = row[3].strip()
if plate_384[0:3] == 'GHR':
new_clone_name = plate_384 + '@' + well_384
else:
new_clone_name = old_clone_name
new_to_old[new_clone_name] = {
'old_clone_name': old_clone_name,
'node_primary_name': node_primary_name,
}
######################################################
# SECOND STAGE
#
# For each row in cherrypick_list, create a corresponding
# row for the legacy database, with fields:
# ('mutant', 'mutantAllele', 'RNAiPlateID', '96well',
# 'ImgName', 'clone', 'node_primary_name',
# 'seq_node_primary_name')
#
######################################################
cherrypick_list = options['cherrypick_list']
# Skip header row
next(cherrypick_list)
'''
# Uncomment this to add header row with fieldnames
legacy_fields = ('mutant', 'mutantAllele', 'RNAiPlateID',
'96well', 'ImgName', 'clone',
'node_primary_name', 'seq_node_primary_name')
self.stdout.write(','.join(legacy_fields))
'''
for line in cherrypick_list:
row = line.split(',')
source_plate_name = row[0].strip()
# Since legacy database did not represent empty wells
if not source_plate_name or source_plate_name == "None":
continue
source_well = row[1].strip()
destination_plate_name = row[2].strip()
destination_well = row[3].strip()
destination_tile = well_to_tile(destination_well) + '.bmp'
try:
source_plate = LibraryPlate.objects.get(id=source_plate_name)
source_stock = LibraryStock.objects.get(plate=source_plate,
well=source_well)
except ObjectDoesNotExist:
raise CommandError('{} at {} not found'.format(
source_plate_name, source_well))
allele = destination_plate_name.split('-')[0]
if allele == 'universal':
# For universal plates, allele == gene == 'universal'
gene = 'universal'
else:
# Otherwise, gene can be retrieved from WormStrain
gene = WormStrain.objects.get(allele=allele).gene
# Account for legacy database using mispelled allele 'zc310'
if allele == 'zu310':
allele = 'zc310'
destination_plate_chars = list(destination_plate_name)
destination_plate_chars[1] = 'c'
destination_plate_name = ''.join(destination_plate_chars)
if source_stock.intended_clone:
new_clone_name = source_stock.intended_clone.id
old_clone_name = new_to_old[new_clone_name]['old_clone_name']
node_primary_name = (
new_to_old[new_clone_name]['node_primary_name'])
if node_primary_name == 'NULL':
node_primary_name = ''
else:
old_clone_name = ''
node_primary_name = ''
output = [
gene, allele, destination_plate_name, destination_well,
destination_tile, old_clone_name, node_primary_name, 'X'
]
self.stdout.write(','.join([str(x) for x in output]))
def get_devstar_count_path(self):
tile = well_to_tile(self.well)
f = '/'.join((settings.BASE_DIR_DEVSTAR_OUTPUT,
str(self.plate_id), tile))
f += 'cnt.txt'
return f
def get_tile(self):
return well_to_tile(self.well)
def get_tile(self):
return well_to_tile(self.well)
def get_tile(well):
"""Get the tile, e.g. Tile000094, corresponding to well."""
return well_to_tile(well)
def test_well_to_tile(self):
for well, tile in self.well_tile_tuples:
self.assertEqual(well_to_tile(well), tile)
def get_devstar_count_path(self):
tile = well_to_tile(self.well)
f = '/'.join(
(settings.BASE_DIR_DEVSTAR_OUTPUT, str(self.plate_id), tile))
f += 'cnt.txt'
return f
