/usr/lib/python3/dist-packages/ngs/__init__.py is in python3-ngs 1.3.0-3.
This file is owned by root:root, with mode 0o644.
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#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
#
#
#import os
from ctypes import c_char_p, c_int, byref, create_string_buffer, string_at
from .LibManager import LibManager # TODO probably, LibManager should not be the part of ngs package and be specific to engine
PY_RES_OK = 0
class NGS:
lib_manager = LibManager()
@staticmethod
def setAppVersionString(app_version):
NGS.lib_manager.initialize_ngs_bindings()
ERROR_BUFFER_SIZE = 4096
str_err = create_string_buffer(ERROR_BUFFER_SIZE)
res = NGS.lib_manager.PY_NGS_Engine_SetAppVersionString(app_version.encode(), str_err, len(str_err))
if res != PY_RES_OK:
raise ErrorMsg(str_err.value)
@staticmethod
def getVersion_impl():
if NGS.lib_manager.PY_NGS_Engine_GetVersion is None:
return "0"
from .String import NGS_RawString
ret = c_char_p()
ERROR_BUFFER_SIZE = 4096
str_err = create_string_buffer(ERROR_BUFFER_SIZE)
res = NGS.lib_manager.PY_NGS_Engine_GetVersion(byref(ret), str_err, len(str_err))
if res != PY_RES_OK:
raise ErrorMsg(str_err.value)
s = string_at(ret.value).decode()
if isinstance(s, bytes):
s = s.decode(encoding='UTF-8')
return s
@staticmethod
def getVersion():
NGS.lib_manager.initialize_ngs_bindings()
return NGS.getVersion_impl()
@staticmethod
def getPackageVersion_impl():
from .Package import Package
return Package.getPackageVersion()
@staticmethod
def getPackageVersion():
NGS.lib_manager.initialize_ngs_bindings()
from .Package import Package
return Package.getPackageVersion()
@staticmethod
def isValid(spec):
from .String import NGS_RawString
NGS.lib_manager.initialize_ngs_bindings()
ret = c_int()
ERROR_BUFFER_SIZE = 4096
str_err = create_string_buffer(ERROR_BUFFER_SIZE)
res = NGS.lib_manager.PY_NGS_Engine_IsValid(spec.encode(), byref(ret), str_err, len(str_err))
if res != PY_RES_OK:
raise ErrorMsg(str_err.value)
return bool(ret.value)
@staticmethod
def openReadCollection(spec):
NGS.lib_manager.initialize_ngs_bindings()
from .ReadCollection import openReadCollection # entry point - adding name to ngs package global namespace
return openReadCollection(spec)
@staticmethod
def openReferenceSequence(spec):
NGS.lib_manager.initialize_ngs_bindings()
from .ReferenceSequence import openReferenceSequence # entry point - adding name to ngs package global namespace
return openReferenceSequence(spec)
@staticmethod
def checkLibVersions():
from . LibChecker import check_versions
return check_versions()
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