def show_config():
'''Load the config file and write it to STDOUT
'''
import json
click.echo(get_config_dir())
config = get_config()
click.echo(json.dumps(config, sort_keys=True, indent=2))
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_waters_masslynx(path):
if path is None:
path = []
from ms_deisotope.data_source._vendor.masslynx import libload
path = list(map(os.path.abspath, path))
result = libload._register_dll(path)
if result:
click.secho("DLL Registration Successful")
out = libload.determine_if_available()
if out:
click.secho("DLL Load Succesful", fg='cyan')
if path is not None:
config = get_config()
config.setdefault('vendor_readers', {})
config['vendor_readers'].setdefault("waters-masslynx", [])
rest = sorted(
set(path) - set(
config.get('vendor_readers', {}).get(
'waters-masslynx', [])))
config['vendor_readers']['waters-masslynx'].extend(rest)
save_config(config)
else:
click.secho("DLL Load Unsuccessful", fg='red')
else:
click.secho("DLL Registration Unsuccessful")
def _register_dll(search_paths=None):
'''Start the Common Language Runtime interop service by importing
the :mod:`clr` module from Pythonnet, and then populate the global
names referring to .NET entities, and finally attempt to locate the
ThermoRawFileReader DLLs by searching alogn ``search_paths``.
Parameters
----------
search_paths: list
The paths to check along for the ThermoRawFileReader DLL bundle.
Returns
-------
:class:`bool`:
Whether or not the .NET library successfully loaded
'''
from ms_deisotope.config import get_config
if search_paths is None:
search_paths = []
search_paths = list(search_paths)
search_paths.append(_DEFAULT_DLL_PATH)
# Take user-specified search paths first.
search_paths = get_config().get('vendor_readers', {}).get(
'thermo-net', []) + search_paths
global _RawFileReader, Business, clr, NullReferenceException # pylint: disable=global-statement
global Marshal, IntPtr, Int64 # pylint: disable=global-statement
if _test_dll_loaded():
return True
try:
import clr # pylint: disable=redefined-outer-name
from System import NullReferenceException # pylint: disable=redefined-outer-name
clr.AddReference("System.Runtime")
clr.AddReference("System.Runtime.InteropServices")
from System import IntPtr, Int64 # pylint: disable=redefined-outer-name
from System.Runtime.InteropServices import Marshal # pylint: disable=redefined-outer-name
except ImportError:
return False
for path in search_paths:
sys.path.append(path)
try:
clr.AddReference('ThermoFisher.CommonCore.RawFileReader')
clr.AddReference('ThermoFisher.CommonCore.Data')
except OSError:
continue
try:
import ThermoFisher.CommonCore.Data.Business as Business # pylint: disable=redefined-outer-name
import ThermoFisher.CommonCore.RawFileReader as _RawFileReader # pylint: disable=redefined-outer-name
except ImportError:
continue
return _test_dll_loaded()
def _register_dll(search_paths=None, override=True):
if search_paths is None:
search_paths = []
elif isinstance(search_paths, str):
search_paths = [search_paths]
from ms_deisotope.config import get_config
search_paths.extend(get_config().get('vendor_readers',
{}).get('waters-masslynx', []))
search_paths.append(find_library("MassLynx.dll"))
global dll
if dll is None or override:
for lib_path in search_paths:
try:
dll = _load_library(lib_path)
except (Exception) as err:
continue
if dll is not None:
break
return dll
def _register_dll_dir(search_paths=None):
from ms_deisotope.config import get_config
if search_paths is None:
search_paths = []
global DLL_IS_LOADED
if DLL_IS_LOADED:
return True
search_paths = list(search_paths)
search_paths.extend(_default_paths)
search_paths.extend(get_config().get('vendor_readers', {}).get('agilent-com', []))
for dll_dir in search_paths:
try:
GetModule(os.path.join(dll_dir, 'MassSpecDataReader.tlb'))
GetModule(os.path.join(dll_dir, 'BaseCommon.tlb'))
GetModule(os.path.join(dll_dir, 'BaseDataAccess.tlb'))
DLL_IS_LOADED = True
return True
except Exception:
continue
else:
return False
def _register_dll(search_paths=None, override=True):
if search_paths is None:
search_paths = []
elif isinstance(search_paths, str):
search_paths = [search_paths]
elif not isinstance(search_paths, list):
raise TypeError("Expected a list of paths or a single path string")
from ms_deisotope.config import get_config
search_paths = list(search_paths)
search_paths.extend(get_config().get('vendor_readers',
{}).get('waters-masslynx', []))
found = find_library("MassLynx.dll")
if found:
search_paths.append(found)
global dll
if dll is None or override:
for lib_path in search_paths:
try:
dll = _load_library(lib_path)
except (Exception) as err:
continue
if dll is not None:
break
return dll
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]