def start(config, debug):
# This will ensure config is loaded through-out
# the app.
Config.load_config(config)
# Start Tornado app.
app = create_app(debug)
app.listen(port=8888)
tornado.ioloop.IOLoop.current().start()
def start(config, debug):
# This will ensure config is loaded through-out
# the app.
Config.load_config(config)
# Start Tornado app.
app = create_app(debug)
app.listen(port=8888)
tornado.ioloop.IOLoop.current().start()
def create_config_from_request(self, runfolder, request_data):
"""
For the specified runfolder, will look it up from the place setup in the
configuration, and then parse additinoal data from the request_data object.
This can be used to override any default setting in the resulting Bcl2FastqConfig
instance.
:param runfolder: name of the runfolder we want to create a config for
:param request_data: dict containing additional configurations
:return: an instances of Bcl2FastqConfig
"""
# TODO Make sure to escape them for sec. reasons.
bcl2fastq_version = ""
runfolder_input = ""
output = ""
barcode_mismatches = ""
tiles = ""
use_base_mask = ""
additional_args = ""
runfolder_base_path = Config.load_config()["runfolder_path"]
runfolder_input = "{0}/{1}".format(runfolder_base_path, runfolder)
import os.path as p
if not p.isdir(runfolder_input):
raise RuntimeError("No such file: {0}".format(runfolder_input))
if "bcl2fastq_version" in request_data:
bcl2fastq_version = request_data["bcl2fastq_version"]
if "output" in request_data:
output = request_data["output"]
if "barcode_mismatches" in request_data:
barcode_mismatches = request_data["barcode_mismatches"]
if "tiles" in request_data:
tiles = request_data["tiles"]
if "use_base_mask" in request_data:
use_base_mask = request_data["use_base_mask"]
if "additional_args" in request_data:
additional_args = request_data["additional_args"]
config = Bcl2FastqConfig(
bcl2fastq_version,
runfolder_input,
output,
barcode_mismatches,
tiles,
use_base_mask,
additional_args)
return config
def create_config_from_request(self, runfolder, request_data):
"""
For the specified runfolder, will look it up from the place setup in the
configuration, and then parse additinoal data from the request_data object.
This can be used to override any default setting in the resulting Bcl2FastqConfig
instance.
:param runfolder: name of the runfolder we want to create a config for
:param request_data: dict containing additional configurations
:return: an instances of Bcl2FastqConfig
"""
# TODO Make sure to escape them for sec. reasons.
bcl2fastq_version = ""
runfolder_input = ""
output = ""
barcode_mismatches = ""
tiles = ""
use_base_mask = ""
additional_args = ""
runfolder_base_path = Config.load_config()["runfolder_path"]
runfolder_input = "{0}/{1}".format(runfolder_base_path, runfolder)
import os.path as p
if not p.isdir(runfolder_input):
raise RuntimeError("No such file: {0}".format(runfolder_input))
if "bcl2fastq_version" in request_data:
bcl2fastq_version = request_data["bcl2fastq_version"]
if "output" in request_data:
output = request_data["output"]
if "barcode_mismatches" in request_data:
barcode_mismatches = request_data["barcode_mismatches"]
if "tiles" in request_data:
tiles = request_data["tiles"]
if "use_base_mask" in request_data:
use_base_mask = request_data["use_base_mask"]
if "additional_args" in request_data:
additional_args = request_data["additional_args"]
config = Bcl2FastqConfig(bcl2fastq_version, runfolder_input, output,
barcode_mismatches, tiles, use_base_mask,
additional_args)
return config
def post(self, runfolder):
"""
Starts a bcl2fastq for a runfolder. The input data can contain extra
parameters for bcl2fastq. It should be a json encoded object and
can contain one or more of the following parameters:
- bcl2fastq_version
- output
- barcode_mismatches
- tiles
- use_base_mask
- additional_args
If these are not set defaults setup in Bcl2FastqConfig will be
used (and those should be good enough for most cases).
:param runfolder: name of the runfolder we want to start bcl2fastq for
"""
try:
runfolder_config = self.create_config_from_request(
runfolder, json.loads(self.request.body))
cmd = self.bcl2fastq_cmd_generation_service().\
create_bcl2fastq_runner(runfolder_config).\
construct_command()
general_config = Config.load_config()
log_base_path = general_config["bcl2fastq_logs_path"]
log_file = "{0}/{1}.log".format(log_base_path, runfolder)
job_id = self.runner_service().start(
cmd,
nbr_of_cores=runfolder_config.nbr_of_cores,
run_dir=runfolder_config.runfolder_input,
stdout=log_file,
stderr=log_file)
status_end_point = self.reverse_url("status", job_id)
response_data = {
"job_id": job_id,
"link": status_end_point,
"state": State.STARTED
}
self.set_status(202, reason="started processing")
self.write_json(response_data)
except RuntimeError as e:
self.send_error(status_code=500, reason=e.message)
def post(self, runfolder):
"""
Starts a bcl2fastq for a runfolder. The input data can contain extra
parameters for bcl2fastq. It should be a json encoded object and
can contain one or more of the following parameters:
- bcl2fastq_version
- output
- barcode_mismatches
- tiles
- use_base_mask
- additional_args
If these are not set defaults setup in Bcl2FastqConfig will be
used (and those should be good enough for most cases).
:param runfolder: name of the runfolder we want to start bcl2fastq for
"""
try:
#TODO Make sure this works even if body is not set! /JD 20150820
runfolder_config = self.create_config_from_request(runfolder, json.loads(self.request.body))
cmd = self.bcl2fastq_cmd_generation_service().\
create_bcl2fastq_runner(runfolder_config).\
construct_command()
general_config = Config.load_config()
log_base_path = general_config["bcl2fastq_logs_path"]
log_file = "{0}/{1}.log".format(log_base_path, runfolder)
job_id = self.runner_service().start(
cmd,
nbr_of_cores=runfolder_config.nbr_of_cores,
run_dir=runfolder_config.runfolder_input,
stdout=log_file,
stderr=log_file)
status_end_point = "{0}://{1}{2}".format(
self.request.protocol,
self.request.host,
self.reverse_url("status", job_id))
response_data = {"job_id": job_id, "link": status_end_point, "state": State.STARTED}
self.set_status(202, reason="started processing")
self.write_json(response_data)
except RuntimeError as e:
self.send_error(status_code=500, reason=e.message)
def get_bcl2fastq_version_from_run_parameters(runfolder, config=None):
"""
Guess which bcl2fastq version to use based on the machine type
specified in the runfolder meta data, and the corresponding
mappings in the config file.
:param runfolder: to get bcl2fastq version to use for
:param config: to use matching machine type to bcl2fastq versions (will be
loaded from default config if not set).
:return the version of bcl2fastq to use.
"""
meta_data = InteropMetadata(runfolder)
model = meta_data.model
current_config = config or Config.load_config()
version = current_config["machine_type"][model]["bcl2fastq_version"]
return version
def get_bcl2fastq_version_from_run_parameters(runfolder, config=None):
"""
Guess which bcl2fastq version to use based on the machine type
specified in the runfolder meta data, and the corresponding
mappings in the config file.
:param runfolder: to get bcl2fastq version to use for
:param config: to use matching machine type to bcl2fastq versions (will be
loaded from default config if not set).
:return the version of bcl2fastq to use.
"""
meta_data = InteropMetadata(runfolder)
model = meta_data.model
current_config = config or Config.load_config()
version = current_config["machine_type"][model]["bcl2fastq_version"]
return version
def __init__(self,
bcl2fastq_version,
runfolder_input,
output,
barcode_mismatches=None,
tiles=None,
use_base_mask=None,
additional_args=None,
nbr_of_cores=None):
self.runfolder_input = runfolder_input
self.samplesheet_file = runfolder_input + "/SampleSheet.csv"
self.base_calls_input = runfolder_input + "/Data/Intensities/BaseCalls"
if bcl2fastq_version:
self.bcl2fastq_version = bcl2fastq_version
else:
self.bcl2fastq_version = Bcl2FastqConfig.\
get_bcl2fastq_version_from_run_parameters(runfolder_input)
if output:
self.output = output
else:
output_base = Config.load_config()["default_output_path"]
runfolder_base_name = os.path.basename(runfolder_input)
self.output = "{0}/{1}".format(output_base, runfolder_base_name)
self.barcode_mismatches = barcode_mismatches
self.tiles = tiles
# TODO Ensure that this is included in any user facing documentation.
# Note that for the base mask the "--use-bases-mask" must be included in the
# commandline passed. E.g. "--use-bases-mask 1:y*,6i,6i, y* --use-bases-mask y*,6i,6i, y* "
self.use_base_mask = use_base_mask
self.additional_args = additional_args
# Nbr of cores to use will default to the number of cpus on the system.
if nbr_of_cores:
self.nbr_of_cores = nbr_of_cores
else:
import multiprocessing
self.nbr_of_cores = multiprocessing.cpu_count()
def __init__(self,
bcl2fastq_version,
runfolder_input,
output,
barcode_mismatches=None,
tiles=None,
use_base_mask=None,
additional_args=None,
nbr_of_cores=None):
self.runfolder_input = runfolder_input
self.samplesheet_file = runfolder_input + "/SampleSheet.csv"
self.base_calls_input = runfolder_input + "/Data/Intensities/BaseCalls"
if bcl2fastq_version:
self.bcl2fastq_version = bcl2fastq_version
else:
self.bcl2fastq_version = Bcl2FastqConfig.\
get_bcl2fastq_version_from_run_parameters(runfolder_input)
if output:
self.output = output
else:
output_base = Config.load_config()["default_output_path"]
runfolder_base_name = os.path.basename(runfolder_input)
self.output = "{0}/{1}".format(output_base, runfolder_base_name)
self.barcode_mismatches = barcode_mismatches
self.tiles = tiles
# TODO Ensure that this is included in any user facing documentation.
# Note that for the base mask the "--use-bases-mask" must be included in the
# commandline passed. E.g. "--use-bases-mask 1:y*,6i,6i, y* --use-bases-mask y*,6i,6i, y* "
self.use_base_mask = use_base_mask
self.additional_args = additional_args
# Nbr of cores to use will default to the number of cpus on the system.
if nbr_of_cores:
self.nbr_of_cores = nbr_of_cores
else:
import multiprocessing
self.nbr_of_cores = multiprocessing.cpu_count()
def get(self):
config = Config.load_config()
available_versions = config["bcl2fastq"]["versions"].keys()
self.write_object(available_versions)
def get(self):
config = Config.load_config()
available_versions = config["bcl2fastq"]["versions"].keys()
self.write_object(available_versions)
def __init__(self, config=None):
config = config or Config.load_config()
self.bcl2fastq_mappings = config["bcl2fastq"]["versions"]
def __init__(self, config=None):
config = config or Config.load_config()
self.bcl2fastq_mappings = config["bcl2fastq"]["versions"]
