def register_thermo_com_net(path):
'''Register a bundle of Thermo's RawFileReader library's DLLs. The `--path` option can
be used to specify additional search paths.
'''
if path is None:
path = []
try:
import clr
except ImportError:
click.secho("pythonnet not installed", fg='yellow')
raise click.ClickException(
"This feature requires the pythonnet library. Please install it.")
from ms_deisotope.data_source.thermo_raw_net import _register_dll, _RawFileReader
from ms_deisotope.data_source.thermo_raw_net import determine_if_available
if _RawFileReader:
click.secho("DLL Already Registered and Loaded")
return
result = _register_dll(path)
if result:
click.secho("DLL Registration Successful")
if determine_if_available():
click.secho("DLL Load Succesful", fg='cyan')
if path is not None:
config = get_config()
rest = sorted(set(path) - set(config['vendor_readers']['thermo-net']))
config['vendor_readers']['thermo-net'].extend(rest)
save_config(config)
else:
click.secho("DLL Load Unsuccessful", fg='red')
else:
click.secho("DLL Registration Unsuccessful")
def register_thermo_com(path=None):
'''Register an installed MSFileReader or XRawFile DLL. Searches the standard installation
paths, but the `--path` option can be used to specify additional search paths.
'''
if path is None:
path = []
try:
import comtypes
except ImportError:
click.secho("comtypes not installed", fg='yellow')
raise click.ClickException(
"This feature requires the comtypes library. Please install it.")
import logging
from ms_deisotope.data_source._vendor.MSFileReader import _register_dll, log, DLL_IS_LOADED
from ms_deisotope.data_source.thermo_raw import determine_if_available
if DLL_IS_LOADED:
click.secho("DLL Already Registered and Loaded")
return
if log is not None:
log.addHandler(logging.StreamHandler())
log.setLevel('DEBUG')
result = _register_dll(path)
if result:
click.secho("DLL Registration Successful")
if determine_if_available():
click.secho("DLL Load Succesful", fg='cyan')
if path is not None:
config = get_config()
config['vendor_readers']['thermo-com'].extend(path)
save_config(config)
else:
click.secho("DLL Load Unsuccessful", fg='red')
else:
click.secho("DLL Registration Unsuccessful")
if log is not None:
log.handlers = log.handlers[:-1]
import unittest
import platform
import numpy as np
from ms_deisotope.data_source.thermo_raw import (determine_if_available)
from ms_deisotope.test.common import datafile
from ms_deisotope.data_source import infer_type
not_windows = not platform.platform().lower().startswith("windows")
missing_reader_dll = not determine_if_available()
@unittest.skipIf(not_windows or missing_reader_dll, "Requires Windows COM")
class TestThermoRawLoaderScanBehavior(unittest.TestCase):
path = datafile("small.RAW")
reference_mzml = datafile("small.mzML")
reference_mgf = datafile("small.mgf")
@property
def reader(self):
return infer_type.MSFileLoader(self.path)
def test_iteration(self):
reader = self.reader
reader.start_from_scan('controllerType=0 controllerNumber=1 scan=10')
bunch = next(reader)
assert bunch.precursor.id == 'controllerType=0 controllerNumber=1 scan=9'
bunch = next(reader)
assert bunch.precursor.id == 'controllerType=0 controllerNumber=1 scan=15'
import unittest
import platform
import numpy as np
from ms_deisotope.data_source.thermo_raw import (
determine_if_available)
from ms_deisotope.data_source.thermo_raw_net import (
determine_if_available as determine_if_available_net)
from ms_deisotope.test.common import datafile
from ms_deisotope.data_source import infer_type
not_windows = not platform.platform().lower().startswith("windows")
missing_reader_dll = not determine_if_available()
missing_net_dll = not determine_if_available_net()
class ThermoRawLoaderScanBehaviorBase(object):
path = datafile("small.RAW")
reference_mzml = datafile("small.mzML")
reference_mgf = datafile("small.mgf")
@property
def reader(self):
# return infer_type.MSFileLoader(self.path)
raise NotImplementedError()
def test_iteration(self):
reader = self.reader
reader.start_from_scan('controllerType=0 controllerNumber=1 scan=10')