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MsvsSettings.GetCflagsCC
(self, config)
Returns the flags that need to be added to .cc compilations.
Returns the flags that need to be added to .cc compilations.
def GetCflagsCC(self, config): """Returns the flags that need to be added to .cc compilations.""" config = self._TargetConfig(config) return ["/TP"] + self._GetPchFlags(config, ".cc")
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[ 570, 4 ]
[ 573, 57 ]
python
en
['en', 'en', 'en']
True
MsvsSettings._GetAdditionalLibraryDirectories
(self, root, config, gyp_to_build_path)
Get and normalize the list of paths in AdditionalLibraryDirectories setting.
Get and normalize the list of paths in AdditionalLibraryDirectories setting.
def _GetAdditionalLibraryDirectories(self, root, config, gyp_to_build_path): """Get and normalize the list of paths in AdditionalLibraryDirectories setting.""" config = self._TargetConfig(config) libpaths = self._Setting( (root, "AdditionalLibraryDirectories"), config, default=[]...
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[ 575, 4 ]
[ 586, 57 ]
python
en
['en', 'en', 'en']
True
MsvsSettings.GetLibFlags
(self, config, gyp_to_build_path)
Returns the flags that need to be added to lib commands.
Returns the flags that need to be added to lib commands.
def GetLibFlags(self, config, gyp_to_build_path): """Returns the flags that need to be added to lib commands.""" config = self._TargetConfig(config) libflags = [] lib = self._GetWrapper( self, self.msvs_settings[config], "VCLibrarianTool", append=libflags ) li...
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[ 588, 4 ]
[ 607, 23 ]
python
en
['en', 'en', 'en']
True
MsvsSettings.GetDefFile
(self, gyp_to_build_path)
Returns the .def file from sources, if any. Otherwise returns None.
Returns the .def file from sources, if any. Otherwise returns None.
def GetDefFile(self, gyp_to_build_path): """Returns the .def file from sources, if any. Otherwise returns None.""" spec = self.spec if spec["type"] in ("shared_library", "loadable_module", "executable"): def_files = [ s for s in spec.get("sources", []) if s.lower().e...
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[ 609, 4 ]
[ 620, 19 ]
python
en
['en', 'en', 'en']
True
MsvsSettings._GetDefFileAsLdflags
(self, ldflags, gyp_to_build_path)
.def files get implicitly converted to a ModuleDefinitionFile for the linker in the VS generator. Emulate that behaviour here.
.def files get implicitly converted to a ModuleDefinitionFile for the linker in the VS generator. Emulate that behaviour here.
def _GetDefFileAsLdflags(self, ldflags, gyp_to_build_path): """.def files get implicitly converted to a ModuleDefinitionFile for the linker in the VS generator. Emulate that behaviour here.""" def_file = self.GetDefFile(gyp_to_build_path) if def_file: ldflags.append('/DEF:"%s"' %...
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[ 622, 4 ]
[ 627, 50 ]
python
en
['en', 'en', 'en']
True
MsvsSettings.GetPGDName
(self, config, expand_special)
Gets the explicitly overridden pgd name for a target or returns None if it's not overridden.
Gets the explicitly overridden pgd name for a target or returns None if it's not overridden.
def GetPGDName(self, config, expand_special): """Gets the explicitly overridden pgd name for a target or returns None if it's not overridden.""" config = self._TargetConfig(config) output_file = self._Setting(("VCLinkerTool", "ProfileGuidedDatabase"), config) if output_file: ...
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[ 629, 4 ]
[ 638, 26 ]
python
en
['en', 'en', 'en']
True
MsvsSettings.GetLdflags
( self, config, gyp_to_build_path, expand_special, manifest_base_name, output_name, is_executable, build_dir, )
Returns the flags that need to be added to link commands, and the manifest files.
Returns the flags that need to be added to link commands, and the manifest files.
def GetLdflags( self, config, gyp_to_build_path, expand_special, manifest_base_name, output_name, is_executable, build_dir, ): """Returns the flags that need to be added to link commands, and the manifest files.""" config = self._Ta...
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[ 640, 4 ]
[ 771, 61 ]
python
en
['en', 'en', 'en']
True
MsvsSettings._GetLdManifestFlags
( self, config, name, gyp_to_build_path, allow_isolation, build_dir )
Returns a 3-tuple: - the set of flags that need to be added to the link to generate a default manifest - the intermediate manifest that the linker will generate that should be used to assert it doesn't add anything to the merged one. - the list of all the manifest files to be merged by the manif...
Returns a 3-tuple: - the set of flags that need to be added to the link to generate a default manifest - the intermediate manifest that the linker will generate that should be used to assert it doesn't add anything to the merged one. - the list of all the manifest files to be merged by the manif...
def _GetLdManifestFlags( self, config, name, gyp_to_build_path, allow_isolation, build_dir ): """Returns a 3-tuple: - the set of flags that need to be added to the link to generate a default manifest - the intermediate manifest that the linker will generate that should be used to...
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[ 773, 4 ]
[ 865, 49 ]
python
en
['en', 'haw', 'en']
True
MsvsSettings._GetAdditionalManifestFiles
(self, config, gyp_to_build_path)
Gets additional manifest files that are added to the default one generated by the linker.
Gets additional manifest files that are added to the default one generated by the linker.
def _GetAdditionalManifestFiles(self, config, gyp_to_build_path): """Gets additional manifest files that are added to the default one generated by the linker.""" files = self._Setting( ("VCManifestTool", "AdditionalManifestFiles"), config, default=[] ) if isinstance(files...
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[ 867, 4 ]
[ 878, 9 ]
python
en
['en', 'en', 'en']
True
MsvsSettings.IsUseLibraryDependencyInputs
(self, config)
Returns whether the target should be linked via Use Library Dependency Inputs (using component .objs of a given .lib).
Returns whether the target should be linked via Use Library Dependency Inputs (using component .objs of a given .lib).
def IsUseLibraryDependencyInputs(self, config): """Returns whether the target should be linked via Use Library Dependency Inputs (using component .objs of a given .lib).""" config = self._TargetConfig(config) uldi = self._Setting(("VCLinkerTool", "UseLibraryDependencyInputs"), config) ...
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[ 880, 4 ]
[ 885, 29 ]
python
en
['en', 'en', 'en']
True
MsvsSettings.IsEmbedManifest
(self, config)
Returns whether manifest should be linked into binary.
Returns whether manifest should be linked into binary.
def IsEmbedManifest(self, config): """Returns whether manifest should be linked into binary.""" config = self._TargetConfig(config) embed = self._Setting( ("VCManifestTool", "EmbedManifest"), config, default="true" ) return embed == "true"
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[ 887, 4 ]
[ 893, 30 ]
python
en
['en', 'en', 'en']
True
MsvsSettings.IsLinkIncremental
(self, config)
Returns whether the target should be linked incrementally.
Returns whether the target should be linked incrementally.
def IsLinkIncremental(self, config): """Returns whether the target should be linked incrementally.""" config = self._TargetConfig(config) link_inc = self._Setting(("VCLinkerTool", "LinkIncremental"), config) return link_inc != "1"
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[ 895, 4 ]
[ 899, 30 ]
python
en
['en', 'en', 'en']
True
MsvsSettings.GetRcflags
(self, config, gyp_to_ninja_path)
Returns the flags that need to be added to invocations of the resource compiler.
Returns the flags that need to be added to invocations of the resource compiler.
def GetRcflags(self, config, gyp_to_ninja_path): """Returns the flags that need to be added to invocations of the resource compiler.""" config = self._TargetConfig(config) rcflags = [] rc = self._GetWrapper( self, self.msvs_settings[config], "VCResourceCompilerTool", appe...
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[ 901, 4 ]
[ 914, 22 ]
python
en
['en', 'en', 'en']
True
MsvsSettings.BuildCygwinBashCommandLine
(self, args, path_to_base)
Build a command line that runs args via cygwin bash. We assume that all incoming paths are in Windows normpath'd form, so they need to be converted to posix style for the part of the command line that's passed to bash. We also have to do some Visual Studio macro emulation here because various rules use ...
Build a command line that runs args via cygwin bash. We assume that all incoming paths are in Windows normpath'd form, so they need to be converted to posix style for the part of the command line that's passed to bash. We also have to do some Visual Studio macro emulation here because various rules use ...
def BuildCygwinBashCommandLine(self, args, path_to_base): """Build a command line that runs args via cygwin bash. We assume that all incoming paths are in Windows normpath'd form, so they need to be converted to posix style for the part of the command line that's passed to bash. We also have to do s...
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[ 916, 4 ]
[ 936, 18 ]
python
en
['en', 'en', 'en']
True
MsvsSettings.IsRuleRunUnderCygwin
(self, rule)
Determine if an action should be run under cygwin. If the variable is unset, or set to 1 we use cygwin.
Determine if an action should be run under cygwin. If the variable is unset, or set to 1 we use cygwin.
def IsRuleRunUnderCygwin(self, rule): """Determine if an action should be run under cygwin. If the variable is unset, or set to 1 we use cygwin.""" return ( int(rule.get("msvs_cygwin_shell", self.spec.get("msvs_cygwin_shell", 1))) != 0 )
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[ 938, 4 ]
[ 944, 9 ]
python
en
['en', 'en', 'en']
True
MsvsSettings._HasExplicitRuleForExtension
(self, spec, extension)
Determine if there's an explicit rule for a particular extension.
Determine if there's an explicit rule for a particular extension.
def _HasExplicitRuleForExtension(self, spec, extension): """Determine if there's an explicit rule for a particular extension.""" for rule in spec.get("rules", []): if rule["extension"] == extension: return True return False
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[ 946, 4 ]
[ 951, 20 ]
python
en
['en', 'en', 'en']
True
MsvsSettings._HasExplicitIdlActions
(self, spec)
Determine if an action should not run midl for .idl files.
Determine if an action should not run midl for .idl files.
def _HasExplicitIdlActions(self, spec): """Determine if an action should not run midl for .idl files.""" return any( [action.get("explicit_idl_action", 0) for action in spec.get("actions", [])] )
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[ 953, 4 ]
[ 957, 9 ]
python
en
['en', 'en', 'en']
True
MsvsSettings.HasExplicitIdlRulesOrActions
(self, spec)
Determine if there's an explicit rule or action for idl files. When there isn't we need to generate implicit rules to build MIDL .idl files.
Determine if there's an explicit rule or action for idl files. When there isn't we need to generate implicit rules to build MIDL .idl files.
def HasExplicitIdlRulesOrActions(self, spec): """Determine if there's an explicit rule or action for idl files. When there isn't we need to generate implicit rules to build MIDL .idl files.""" return self._HasExplicitRuleForExtension( spec, "idl" ) or self._HasExplicitIdlActions(...
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[ 959, 4 ]
[ 964, 46 ]
python
en
['en', 'en', 'en']
True
MsvsSettings.HasExplicitAsmRules
(self, spec)
Determine if there's an explicit rule for asm files. When there isn't we need to generate implicit rules to assemble .asm files.
Determine if there's an explicit rule for asm files. When there isn't we need to generate implicit rules to assemble .asm files.
def HasExplicitAsmRules(self, spec): """Determine if there's an explicit rule for asm files. When there isn't we need to generate implicit rules to assemble .asm files.""" return self._HasExplicitRuleForExtension(spec, "asm")
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[ 966, 4 ]
[ 969, 61 ]
python
en
['en', 'en', 'en']
True
MsvsSettings.GetIdlBuildData
(self, source, config)
Determine the implicit outputs for an idl file. Returns output directory, outputs, and variables and flags that are required.
Determine the implicit outputs for an idl file. Returns output directory, outputs, and variables and flags that are required.
def GetIdlBuildData(self, source, config): """Determine the implicit outputs for an idl file. Returns output directory, outputs, and variables and flags that are required.""" config = self._TargetConfig(config) midl_get = self._GetWrapper(self, self.msvs_settings[config], "VCMIDLTool") ...
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[ 971, 4 ]
[ 1001, 47 ]
python
en
['en', 'en', 'en']
True
PrecompiledHeader._PchHeader
(self)
Get the header that will appear in an #include line for all source files.
Get the header that will appear in an #include line for all source files.
def _PchHeader(self): """Get the header that will appear in an #include line for all source files.""" return self.settings.msvs_precompiled_header[self.config]
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[ 1027, 4 ]
[ 1030, 65 ]
python
en
['en', 'en', 'en']
True
PrecompiledHeader.GetObjDependencies
(self, sources, objs, arch)
Given a list of sources files and the corresponding object files, returns a list of the pch files that should be depended upon. The additional wrapping in the return value is for interface compatibility with make.py on Mac, and xcode_emulation.py.
Given a list of sources files and the corresponding object files, returns a list of the pch files that should be depended upon. The additional wrapping in the return value is for interface compatibility with make.py on Mac, and xcode_emulation.py.
def GetObjDependencies(self, sources, objs, arch): """Given a list of sources files and the corresponding object files, returns a list of the pch files that should be depended upon. The additional wrapping in the return value is for interface compatibility with make.py on Mac, and xcode_emulation.py...
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[ 1032, 4 ]
[ 1044, 17 ]
python
en
['en', 'en', 'en']
True
PrecompiledHeader.GetPchBuildCommands
(self, arch)
Not used on Windows as there are no additional build steps required (instead, existing steps are modified in GetFlagsModifications below).
Not used on Windows as there are no additional build steps required (instead, existing steps are modified in GetFlagsModifications below).
def GetPchBuildCommands(self, arch): """Not used on Windows as there are no additional build steps required (instead, existing steps are modified in GetFlagsModifications below).""" return []
[ "def", "GetPchBuildCommands", "(", "self", ",", "arch", ")", ":", "return", "[", "]" ]
[ 1046, 4 ]
[ 1049, 17 ]
python
en
['en', 'en', 'en']
True
PrecompiledHeader.GetFlagsModifications
( self, input, output, implicit, command, cflags_c, cflags_cc, expand_special )
Get the modified cflags and implicit dependencies that should be used for the pch compilation step.
Get the modified cflags and implicit dependencies that should be used for the pch compilation step.
def GetFlagsModifications( self, input, output, implicit, command, cflags_c, cflags_cc, expand_special ): """Get the modified cflags and implicit dependencies that should be used for the pch compilation step.""" if input == self.pch_source: pch_output = ["/Yc" + self._PchHead...
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[ 1051, 4 ]
[ 1070, 35 ]
python
en
['en', 'en', 'en']
True
get_band
(session, dataset, freq_eff, freq_bw, freq_bw_max=.0)
Returns the frequency band for the given frequency parameters. Will create a new frequency band entry in the database if no match is found. You can limit the bandwidth of the band association with the freq_bw_max. args: session (sqlalchemy.orm.session.Session): a SQLAlchemy session object ...
Returns the frequency band for the given frequency parameters. Will create a new frequency band entry in the database if no match is found. You can limit the bandwidth of the band association with the freq_bw_max.
def get_band(session, dataset, freq_eff, freq_bw, freq_bw_max=.0): """ Returns the frequency band for the given frequency parameters. Will create a new frequency band entry in the database if no match is found. You can limit the bandwidth of the band association with the freq_bw_max. args: sess...
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[ 9, 0 ]
[ 48, 15 ]
python
en
['en', 'error', 'th']
False
update_skyregion_members
(session, skyregion)
This function performs a simple distance-check against current members of the runningcatalog to find sources that should be visible in the given skyregion, and updates the assocskyrgn table accordingly. Any previous entries in assocskyrgn relating to this skyregion are deleted first. Note 1. ...
This function performs a simple distance-check against current members of the runningcatalog to find sources that should be visible in the given skyregion, and updates the assocskyrgn table accordingly.
def update_skyregion_members(session, skyregion): """ This function performs a simple distance-check against current members of the runningcatalog to find sources that should be visible in the given skyregion, and updates the assocskyrgn table accordingly. Any previous entries in assocskyrgn relati...
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[ 51, 0 ]
[ 98, 16 ]
python
en
['en', 'error', 'th']
False
get_skyregion
(session, dataset, centre_ra, centre_decl, xtr_radius)
gets an id for a skyregion, given a pair of central co-ordinates and a radius. If no matching skyregion is found, a new one is inserted. In this case we also trigger execution of `updateSkyRgnMembers` for the new skyregion - this performs a simple assocation with current members of the runningcata...
gets an id for a skyregion, given a pair of central co-ordinates and a radius.
def get_skyregion(session, dataset, centre_ra, centre_decl, xtr_radius): """ gets an id for a skyregion, given a pair of central co-ordinates and a radius. If no matching skyregion is found, a new one is inserted. In this case we also trigger execution of `updateSkyRgnMembers` for the new skyregion ...
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[ 101, 0 ]
[ 131, 20 ]
python
en
['en', 'error', 'th']
False
insert_image
(session, dataset, freq_eff, freq_bw, taustart_ts, tau_time, beam_smaj_pix, beam_smin_pix, beam_pa_rad, deltax, deltay, url, centre_ra, centre_decl, xtr_radius, rms_qc, freq_bw_max=0.0, rms_min=None, rms_max=None, detection_thresh=None, analysis_thresh=None)
Insert an image for a given dataset. Args: session (sqlalchemy.orm.session.Session): A SQLalchemy sessions dataset (int): ID of parent dataset. freq_eff: See :ref:`Image table definitions <schema-image>`. freq_bw: See :ref:`Image table definitions <schema-image>`. freq_...
Insert an image for a given dataset.
def insert_image(session, dataset, freq_eff, freq_bw, taustart_ts, tau_time, beam_smaj_pix, beam_smin_pix, beam_pa_rad, deltax, deltay, url, centre_ra, centre_decl, xtr_radius, rms_qc, freq_bw_max=0.0, rms_min=None, rms_max=None, detection_thresh=None, analysis_thresh=None): """ ...
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[ 179, 16 ]
python
en
['en', 'error', 'th']
False
do_cache
(parser, token)
This will cache the contents of a template fragment for a given amount of time. Usage:: {% load cache %} {% cache [expire_time] [fragment_name] %} .. some expensive processing .. {% endcache %} This tag also supports varying by a list of arguments:: {% lo...
This will cache the contents of a template fragment for a given amount of time.
def do_cache(parser, token): """ This will cache the contents of a template fragment for a given amount of time. Usage:: {% load cache %} {% cache [expire_time] [fragment_name] %} .. some expensive processing .. {% endcache %} This tag also supports varying by ...
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[ 53, 0 ]
[ 93, 5 ]
python
en
['en', 'error', 'th']
False
show_actual_vendor_versions
(vendor_txt_versions)
Log the actual version and print extra info if there is a conflict or if the actual version could not be imported.
Log the actual version and print extra info if there is a conflict or if the actual version could not be imported.
def show_actual_vendor_versions(vendor_txt_versions): # type: (Dict[str, str]) -> None """Log the actual version and print extra info if there is a conflict or if the actual version could not be imported. """ for module_name, expected_version in vendor_txt_versions.items(): extra_message = '...
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[ 103, 0 ]
[ 118, 75 ]
python
en
['en', 'en', 'en']
True
load_job_config
(pipe_config)
Locates the job_params.cfg in 'job_directory' and loads via ConfigParser.
Locates the job_params.cfg in 'job_directory' and loads via ConfigParser.
def load_job_config(pipe_config): """ Locates the job_params.cfg in 'job_directory' and loads via ConfigParser. """ job_directory = pipe_config['DEFAULT']['job_directory'] job_config = ConfigParser.SafeConfigParser() job_config.read(os.path.join(job_directory, 'job_params.cfg')) return parse...
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[ 22, 0 ]
[ 29, 36 ]
python
en
['en', 'error', 'th']
False
check_job_configs_match
(job_config_1, job_config_2)
Check if job configs match, except dataset_id which we expect to change.
Check if job configs match, except dataset_id which we expect to change.
def check_job_configs_match(job_config_1, job_config_2): """ Check if job configs match, except dataset_id which we expect to change. """ jc_from_file = job_config_1.copy() jc_from_db = job_config_2.copy() del jc_from_file['persistence']['dataset_id'] del jc_from_db['persistence']['dataset_i...
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[ 41, 0 ]
[ 49, 35 ]
python
en
['en', 'error', 'th']
False
setup_logging
(log_dir, debug, use_colorlog, basename='trap')
Sets up logging to stdout, + info/debug level logfiles in log_dir. Args: log_dir (string): log directory debug (bool): do we want debug level logging on stdout? basename (string): basename of the log file
Sets up logging to stdout, + info/debug level logfiles in log_dir.
def setup_logging(log_dir, debug, use_colorlog, basename='trap'): """ Sets up logging to stdout, + info/debug level logfiles in log_dir. Args: log_dir (string): log directory debug (bool): do we want debug level logging on stdout? basename (string): basename of the...
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[ 52, 0 ]
[ 121, 80 ]
python
en
['en', 'error', 'th']
False
group_per_timestep
(metadatas)
groups a list of TRAP images per time step. Per time step the images are order per frequency. We could add other ordering logic (per stoke) later on. Args: metadatas (tuple): list of ImageMetadataForSort Returns: tuple: List of tuples. The list is sorted by timestamp. ...
groups a list of TRAP images per time step.
def group_per_timestep(metadatas): """ groups a list of TRAP images per time step. Per time step the images are order per frequency. We could add other ordering logic (per stoke) later on. Args: metadatas (tuple): list of ImageMetadataForSort Returns: tuple: List of tuples. Th...
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[ 146, 0 ]
[ 176, 78 ]
python
en
['en', 'error', 'th']
False
BmpImageFile._bitmap
(self, header=0, offset=0)
Read relevant info about the BMP
Read relevant info about the BMP
def _bitmap(self, header=0, offset=0): """ Read relevant info about the BMP """ read, seek = self.fp.read, self.fp.seek if header: seek(header) file_info = {} # read bmp header size @offset 14 (this is part of the header size) file_info["header_size"] = i32(re...
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[ 72, 4 ]
[ 259, 9 ]
python
en
['en', 'en', 'en']
True
BmpImageFile._open
(self)
Open file, check magic number and read header
Open file, check magic number and read header
def _open(self): """ Open file, check magic number and read header """ # read 14 bytes: magic number, filesize, reserved, header final offset head_data = self.fp.read(14) # choke if the file does not have the required magic bytes if not _accept(head_data): raise Synta...
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[ 261, 4 ]
[ 271, 35 ]
python
en
['en', 'en', 'en']
True
EmulationManager.__init__
(self, client: CDPSession)
Make new emulation manager.
Make new emulation manager.
def __init__(self, client: CDPSession) -> None: """Make new emulation manager.""" self._client = client self._emulatingMobile = False self._hasTouch = False
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[ 12, 4 ]
[ 16, 30 ]
python
en
['en', 'da', 'en']
True
EmulationManager.emulateViewport
(self, viewport: dict)
Evaluate viewport.
Evaluate viewport.
async def emulateViewport(self, viewport: dict) -> bool: """Evaluate viewport.""" options = dict() mobile = viewport.get('isMobile', False) options['mobile'] = mobile if 'width' in viewport: options['width'] = helper.get_positive_int(viewport, 'width') if 'hei...
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[ 18, 4 ]
[ 48, 27 ]
python
en
['en', 'id', 'en']
False
Format.create_dataset
(self, in_stream)
Create dataset from given string.
Create dataset from given string.
def create_dataset(self, in_stream): """ Create dataset from given string. """ raise NotImplementedError()
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[ 35, 4 ]
[ 39, 35 ]
python
en
['en', 'error', 'th']
False
Format.export_data
(self, dataset, **kwargs)
Returns format representation for given dataset.
Returns format representation for given dataset.
def export_data(self, dataset, **kwargs): """ Returns format representation for given dataset. """ raise NotImplementedError()
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[ 41, 4 ]
[ 45, 35 ]
python
en
['en', 'error', 'th']
False
Format.is_binary
(self)
Returns if this format is binary.
Returns if this format is binary.
def is_binary(self): """ Returns if this format is binary. """ return True
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[ 47, 4 ]
[ 51, 19 ]
python
en
['en', 'error', 'th']
False
Format.get_read_mode
(self)
Returns mode for opening files.
Returns mode for opening files.
def get_read_mode(self): """ Returns mode for opening files. """ return 'rb'
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[ 53, 4 ]
[ 57, 19 ]
python
en
['en', 'error', 'th']
False
Format.get_extension
(self)
Returns extension for this format files.
Returns extension for this format files.
def get_extension(self): """ Returns extension for this format files. """ return ""
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[ 59, 4 ]
[ 63, 17 ]
python
en
['en', 'error', 'th']
False
TablibFormat.get_format
(self)
Import and returns tablib module.
Import and returns tablib module.
def get_format(self): """ Import and returns tablib module. """ try: # Available since tablib 1.0 from tablib.formats import registry except ImportError: return import_module(self.TABLIB_MODULE) else: key = self.TABLIB_MODUL...
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[ 85, 4 ]
[ 96, 43 ]
python
en
['en', 'error', 'th']
False
XLS.create_dataset
(self, in_stream)
Create dataset from first sheet.
Create dataset from first sheet.
def create_dataset(self, in_stream): """ Create dataset from first sheet. """ import xlrd xls_book = xlrd.open_workbook(file_contents=in_stream) dataset = tablib.Dataset() sheet = xls_book.sheets()[0] dataset.headers = sheet.row_values(0) for i in...
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[ 177, 4 ]
[ 189, 22 ]
python
en
['en', 'error', 'th']
False
XLSX.create_dataset
(self, in_stream)
Create dataset from first sheet.
Create dataset from first sheet.
def create_dataset(self, in_stream): """ Create dataset from first sheet. """ from io import BytesIO import openpyxl xlsx_book = openpyxl.load_workbook(BytesIO(in_stream), read_only=True) dataset = tablib.Dataset() sheet = xlsx_book.active # obt...
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[ 196, 4 ]
[ 215, 22 ]
python
en
['en', 'error', 'th']
False
cursor_iter
(cursor, sentinel, col_count)
Yields blocks of rows from a cursor and ensures the cursor is closed when done.
Yields blocks of rows from a cursor and ensures the cursor is closed when done.
def cursor_iter(cursor, sentinel, col_count): """ Yields blocks of rows from a cursor and ensures the cursor is closed when done. """ try: for rows in iter((lambda: cursor.fetchmany(GET_ITERATOR_CHUNK_SIZE)), sentinel): yield [r[0:col_count] for r in rows...
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python
en
['en', 'error', 'th']
False
SQLCompiler.pre_sql_setup
(self)
Does any necessary class setup immediately prior to producing SQL. This is for things that can't necessarily be done in __init__ because we might not have all the pieces in place at that time.
Does any necessary class setup immediately prior to producing SQL. This is for things that can't necessarily be done in __init__ because we might not have all the pieces in place at that time.
def pre_sql_setup(self): """ Does any necessary class setup immediately prior to producing SQL. This is for things that can't necessarily be done in __init__ because we might not have all the pieces in place at that time. """ self.setup_query() order_by = self.get...
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[ 39, 4 ]
[ 50, 47 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.get_group_by
(self, select, order_by)
Returns a list of 2-tuples of form (sql, params). The logic of what exactly the GROUP BY clause contains is hard to describe in other words than "if it passes the test suite, then it is correct".
Returns a list of 2-tuples of form (sql, params).
def get_group_by(self, select, order_by): """ Returns a list of 2-tuples of form (sql, params). The logic of what exactly the GROUP BY clause contains is hard to describe in other words than "if it passes the test suite, then it is correct". """ # Some examples: ...
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[ 52, 4 ]
[ 130, 21 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.get_select
(self)
Returns three values: - a list of 3-tuples of (expression, (sql, params), alias) - a klass_info structure, - a dictionary of annotations The (sql, params) is what the expression will produce, and alias is the "AS alias" for the column (possibly None). The klass...
Returns three values: - a list of 3-tuples of (expression, (sql, params), alias) - a klass_info structure, - a dictionary of annotations
def get_select(self): """ Returns three values: - a list of 3-tuples of (expression, (sql, params), alias) - a klass_info structure, - a dictionary of annotations The (sql, params) is what the expression will produce, and alias is the "AS alias" for the column (p...
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[ 164, 4 ]
[ 231, 43 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.get_order_by
(self)
Returns a list of 2-tuples of form (expr, (sql, params, is_ref)) for the ORDER BY clause. The order_by clause can alter the select clause (for example it can add aliases to clauses that do not yet have one, or it can add totally new select clauses).
Returns a list of 2-tuples of form (expr, (sql, params, is_ref)) for the ORDER BY clause.
def get_order_by(self): """ Returns a list of 2-tuples of form (expr, (sql, params, is_ref)) for the ORDER BY clause. The order_by clause can alter the select clause (for example it can add aliases to clauses that do not yet have one, or it can add totally new select cla...
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[ 233, 4 ]
[ 338, 21 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.quote_name_unless_alias
(self, name)
A wrapper around connection.ops.quote_name that doesn't quote aliases for table names. This avoids problems with some SQL dialects that treat quoted strings specially (e.g. PostgreSQL).
A wrapper around connection.ops.quote_name that doesn't quote aliases for table names. This avoids problems with some SQL dialects that treat quoted strings specially (e.g. PostgreSQL).
def quote_name_unless_alias(self, name): """ A wrapper around connection.ops.quote_name that doesn't quote aliases for table names. This avoids problems with some SQL dialects that treat quoted strings specially (e.g. PostgreSQL). """ if name in self.quote_cache: ...
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[ 350, 4 ]
[ 365, 16 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.as_sql
(self, with_limits=True, with_col_aliases=False)
Creates the SQL for this query. Returns the SQL string and list of parameters. If 'with_limits' is False, any limit/offset information is not included in the query.
Creates the SQL for this query. Returns the SQL string and list of parameters.
def as_sql(self, with_limits=True, with_col_aliases=False): """ Creates the SQL for this query. Returns the SQL string and list of parameters. If 'with_limits' is False, any limit/offset information is not included in the query. """ refcounts_before = self.query....
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[ 401, 4 ]
[ 512, 56 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.get_default_columns
(self, start_alias=None, opts=None, from_parent=None)
Computes the default columns for selecting every field in the base model. Will sometimes be called to pull in related models (e.g. via select_related), in which case "opts" and "start_alias" will be given to provide a starting point for the traversal. Returns a list of strings,...
Computes the default columns for selecting every field in the base model. Will sometimes be called to pull in related models (e.g. via select_related), in which case "opts" and "start_alias" will be given to provide a starting point for the traversal.
def get_default_columns(self, start_alias=None, opts=None, from_parent=None): """ Computes the default columns for selecting every field in the base model. Will sometimes be called to pull in related models (e.g. via select_related), in which case "opts" and "start_alias" will be given ...
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[ 514, 4 ]
[ 557, 21 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.get_distinct
(self)
Returns a quoted list of fields to use in DISTINCT ON part of the query. Note that this method can alter the tables in the query, and thus it must be called before get_from_clause().
Returns a quoted list of fields to use in DISTINCT ON part of the query.
def get_distinct(self): """ Returns a quoted list of fields to use in DISTINCT ON part of the query. Note that this method can alter the tables in the query, and thus it must be called before get_from_clause(). """ qn = self.quote_name_unless_alias qn2 = self.con...
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[ 559, 4 ]
[ 580, 21 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.find_ordering_name
(self, name, opts, alias=None, default_order='ASC', already_seen=None)
Returns the table alias (the name might be ambiguous, the alias will not be) and column name for ordering by the given 'name' parameter. The 'name' is of the form 'field1__field2__...__fieldN'.
Returns the table alias (the name might be ambiguous, the alias will not be) and column name for ordering by the given 'name' parameter. The 'name' is of the form 'field1__field2__...__fieldN'.
def find_ordering_name(self, name, opts, alias=None, default_order='ASC', already_seen=None): """ Returns the table alias (the name might be ambiguous, the alias will not be) and column name for ordering by the given 'name' parameter. The 'name' is of the form ...
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[ 582, 4 ]
[ 612, 91 ]
python
en
['en', 'error', 'th']
False
SQLCompiler._setup_joins
(self, pieces, opts, alias)
A helper method for get_order_by and get_distinct. Note that get_ordering and get_distinct must produce same target columns on same input, as the prefixes of get_ordering and get_distinct must match. Executing SQL where this is not true is an error.
A helper method for get_order_by and get_distinct.
def _setup_joins(self, pieces, opts, alias): """ A helper method for get_order_by and get_distinct. Note that get_ordering and get_distinct must produce same target columns on same input, as the prefixes of get_ordering and get_distinct must match. Executing SQL where this is no...
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[ 614, 4 ]
[ 627, 55 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.get_from_clause
(self)
Returns a list of strings that are joined together to go after the "FROM" part of the query, as well as a list any extra parameters that need to be included. Sub-classes, can override this to create a from-clause via a "select". This should only be called after any SQL construc...
Returns a list of strings that are joined together to go after the "FROM" part of the query, as well as a list any extra parameters that need to be included. Sub-classes, can override this to create a from-clause via a "select".
def get_from_clause(self): """ Returns a list of strings that are joined together to go after the "FROM" part of the query, as well as a list any extra parameters that need to be included. Sub-classes, can override this to create a from-clause via a "select". This should...
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[ 629, 4 ]
[ 661, 29 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.get_related_selections
(self, select, opts=None, root_alias=None, cur_depth=1, requested=None, restricted=None)
Fill in the information needed for a select_related query. The current depth is measured as the number of connections away from the root model (for example, cur_depth=1 means we are looking at models with direct connections to the root model).
Fill in the information needed for a select_related query. The current depth is measured as the number of connections away from the root model (for example, cur_depth=1 means we are looking at models with direct connections to the root model).
def get_related_selections(self, select, opts=None, root_alias=None, cur_depth=1, requested=None, restricted=None): """ Fill in the information needed for a select_related query. The current depth is measured as the number of connections away from the root model ...
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[ 663, 4 ]
[ 791, 34 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.deferred_to_columns
(self)
Converts the self.deferred_loading data structure to mapping of table names to sets of column names which are to be loaded. Returns the dictionary.
Converts the self.deferred_loading data structure to mapping of table names to sets of column names which are to be loaded. Returns the dictionary.
def deferred_to_columns(self): """ Converts the self.deferred_loading data structure to mapping of table names to sets of column names which are to be loaded. Returns the dictionary. """ columns = {} self.query.deferred_to_data(columns, self.query.get_loaded_field...
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[ 793, 4 ]
[ 801, 22 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.results_iter
(self, results=None)
Returns an iterator over the results from executing this query.
Returns an iterator over the results from executing this query.
def results_iter(self, results=None): """ Returns an iterator over the results from executing this query. """ if results is None: results = self.execute_sql(MULTI) fields = [s[0] for s in self.select[0:self.col_count]] converters = self.get_converters(fields) ...
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[ 822, 4 ]
[ 834, 25 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.has_results
(self)
Backends (e.g. NoSQL) can override this in order to use optimized versions of "query has any results."
Backends (e.g. NoSQL) can override this in order to use optimized versions of "query has any results."
def has_results(self): """ Backends (e.g. NoSQL) can override this in order to use optimized versions of "query has any results." """ # This is always executed on a query clone, so we can modify self.query self.query.add_extra({'a': 1}, None, None, None, None, None) ...
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[ 836, 4 ]
[ 844, 45 ]
python
en
['en', 'error', 'th']
False
SQLCompiler.execute_sql
(self, result_type=MULTI, chunked_fetch=False)
Run the query against the database and returns the result(s). The return value is a single data item if result_type is SINGLE, or an iterator over the results if the result_type is MULTI. result_type is either MULTI (use fetchmany() to retrieve all rows), SINGLE (only retrieve ...
Run the query against the database and returns the result(s). The return value is a single data item if result_type is SINGLE, or an iterator over the results if the result_type is MULTI.
def execute_sql(self, result_type=MULTI, chunked_fetch=False): """ Run the query against the database and returns the result(s). The return value is a single data item if result_type is SINGLE, or an iterator over the results if the result_type is MULTI. result_type is either MU...
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[ 846, 4 ]
[ 917, 21 ]
python
en
['en', 'error', 'th']
False
SQLInsertCompiler.field_as_sql
(self, field, val)
Take a field and a value intended to be saved on that field, and return placeholder SQL and accompanying params. Checks for raw values, expressions and fields with get_placeholder() defined in that order. When field is None, the value is considered raw and is used as the placeh...
Take a field and a value intended to be saved on that field, and return placeholder SQL and accompanying params. Checks for raw values, expressions and fields with get_placeholder() defined in that order.
def field_as_sql(self, field, val): """ Take a field and a value intended to be saved on that field, and return placeholder SQL and accompanying params. Checks for raw values, expressions and fields with get_placeholder() defined in that order. When field is None, the value is c...
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[ 939, 4 ]
[ 969, 26 ]
python
en
['en', 'error', 'th']
False
SQLInsertCompiler.prepare_value
(self, field, value)
Prepare a value to be used in a query by resolving it if it is an expression and otherwise calling the field's get_db_prep_save().
Prepare a value to be used in a query by resolving it if it is an expression and otherwise calling the field's get_db_prep_save().
def prepare_value(self, field, value): """ Prepare a value to be used in a query by resolving it if it is an expression and otherwise calling the field's get_db_prep_save(). """ if hasattr(value, 'resolve_expression'): value = value.resolve_expression(self.query, allo...
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[ 971, 4 ]
[ 990, 20 ]
python
en
['en', 'error', 'th']
False
SQLInsertCompiler.pre_save_val
(self, field, obj)
Get the given field's value off the given obj. pre_save() is used for things like auto_now on DateTimeField. Skip it if this is a raw query.
Get the given field's value off the given obj. pre_save() is used for things like auto_now on DateTimeField. Skip it if this is a raw query.
def pre_save_val(self, field, obj): """ Get the given field's value off the given obj. pre_save() is used for things like auto_now on DateTimeField. Skip it if this is a raw query. """ if self.query.raw: return getattr(obj, field.attname) return field.pre_save...
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[ 992, 4 ]
[ 999, 44 ]
python
en
['en', 'error', 'th']
False
SQLInsertCompiler.assemble_as_sql
(self, fields, value_rows)
Take a sequence of N fields and a sequence of M rows of values, generate placeholder SQL and parameters for each field and value, and return a pair containing: * a sequence of M rows of N SQL placeholder strings, and * a sequence of M rows of corresponding parameter values. ...
Take a sequence of N fields and a sequence of M rows of values, generate placeholder SQL and parameters for each field and value, and return a pair containing: * a sequence of M rows of N SQL placeholder strings, and * a sequence of M rows of corresponding parameter values.
def assemble_as_sql(self, fields, value_rows): """ Take a sequence of N fields and a sequence of M rows of values, generate placeholder SQL and parameters for each field and value, and return a pair containing: * a sequence of M rows of N SQL placeholder strings, and * ...
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[ 1001, 4 ]
[ 1034, 43 ]
python
en
['en', 'error', 'th']
False
SQLDeleteCompiler.as_sql
(self)
Creates the SQL for this query. Returns the SQL string and list of parameters.
Creates the SQL for this query. Returns the SQL string and list of parameters.
def as_sql(self): """ Creates the SQL for this query. Returns the SQL string and list of parameters. """ assert len([t for t in self.query.tables if self.query.alias_refcount[t] > 0]) == 1, \ "Can only delete from one table at a time." qn = self.quote_name_unl...
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[ 1112, 4 ]
[ 1124, 46 ]
python
en
['en', 'error', 'th']
False
SQLUpdateCompiler.as_sql
(self)
Creates the SQL for this query. Returns the SQL string and list of parameters.
Creates the SQL for this query. Returns the SQL string and list of parameters.
def as_sql(self): """ Creates the SQL for this query. Returns the SQL string and list of parameters. """ self.pre_sql_setup() if not self.query.values: return '', () qn = self.quote_name_unless_alias values, update_params = [], [] for f...
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[ 1128, 4 ]
[ 1181, 62 ]
python
en
['en', 'error', 'th']
False
SQLUpdateCompiler.execute_sql
(self, result_type)
Execute the specified update. Returns the number of rows affected by the primary update query. The "primary update query" is the first non-empty query that is executed. Row counts for any subsequent, related queries are not available.
Execute the specified update. Returns the number of rows affected by the primary update query. The "primary update query" is the first non-empty query that is executed. Row counts for any subsequent, related queries are not available.
def execute_sql(self, result_type): """ Execute the specified update. Returns the number of rows affected by the primary update query. The "primary update query" is the first non-empty query that is executed. Row counts for any subsequent, related queries are not available. ...
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[ 1183, 4 ]
[ 1202, 19 ]
python
en
['en', 'error', 'th']
False
SQLUpdateCompiler.pre_sql_setup
(self)
If the update depends on results from other tables, we need to do some munging of the "where" conditions to match the format required for (portable) SQL updates. That is done here. Further, if we are going to be running multiple updates, we pull out the id values to update at t...
If the update depends on results from other tables, we need to do some munging of the "where" conditions to match the format required for (portable) SQL updates. That is done here.
def pre_sql_setup(self): """ If the update depends on results from other tables, we need to do some munging of the "where" conditions to match the format required for (portable) SQL updates. That is done here. Further, if we are going to be running multiple updates, we pull out ...
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[ 1204, 4 ]
[ 1245, 52 ]
python
en
['en', 'error', 'th']
False
SQLAggregateCompiler.as_sql
(self)
Creates the SQL for this query. Returns the SQL string and list of parameters.
Creates the SQL for this query. Returns the SQL string and list of parameters.
def as_sql(self): """ Creates the SQL for this query. Returns the SQL string and list of parameters. """ sql, params = [], [] for annotation in self.query.annotation_select.values(): ann_sql, ann_params = self.compile(annotation, select_format=FORCE) ...
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[ 1249, 4 ]
[ 1265, 26 ]
python
en
['en', 'error', 'th']
False
TestPageCreation.test_create_multipart
(self)
Test checks if 'enctype="multipart/form-data"' is added and only to forms that require multipart encoding.
Test checks if 'enctype="multipart/form-data"' is added and only to forms that require multipart encoding.
def test_create_multipart(self): """ Test checks if 'enctype="multipart/form-data"' is added and only to forms that require multipart encoding. """ # check for SimplePage where is no file field response = self.client.get(reverse('wagtailadmin_pages:add', args=('tests', 'simplepag...
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[ 131, 4 ]
[ 144, 70 ]
python
en
['en', 'error', 'th']
False
TestPageCreation.test_create_page_without_promote_tab
(self)
Test that the Promote tab is not rendered for page classes that define it as empty
Test that the Promote tab is not rendered for page classes that define it as empty
def test_create_page_without_promote_tab(self): """ Test that the Promote tab is not rendered for page classes that define it as empty """ response = self.client.get( reverse('wagtailadmin_pages:add', args=('tests', 'standardindex', self.root_page.id)) ) self....
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[ 146, 4 ]
[ 155, 106 ]
python
en
['en', 'error', 'th']
False
TestPageCreation.test_create_page_with_custom_tabs
(self)
Test that custom edit handlers are rendered
Test that custom edit handlers are rendered
def test_create_page_with_custom_tabs(self): """ Test that custom edit handlers are rendered """ response = self.client.get( reverse('wagtailadmin_pages:add', args=('tests', 'standardchild', self.root_page.id)) ) self.assertEqual(response.status_code, 200) ...
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[ 157, 4 ]
[ 167, 109 ]
python
en
['en', 'error', 'th']
False
TestPageCreation.test_create_page_with_non_model_field
(self)
Test that additional fields defined on the form rather than the model are accepted and rendered
Test that additional fields defined on the form rather than the model are accepted and rendered
def test_create_page_with_non_model_field(self): """ Test that additional fields defined on the form rather than the model are accepted and rendered """ response = self.client.get(reverse('wagtailadmin_pages:add', args=('tests', 'formclassadditionalfieldpage', self.root_page.id))) ...
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[ 169, 4 ]
[ 176, 70 ]
python
en
['en', 'error', 'th']
False
TestPageCreation.test_display_moderation_button_by_default
(self)
Tests that by default the "Submit for Moderation" button is shown in the action menu.
Tests that by default the "Submit for Moderation" button is shown in the action menu.
def test_display_moderation_button_by_default(self): """ Tests that by default the "Submit for Moderation" button is shown in the action menu. """ response = self.client.get(reverse('wagtailadmin_pages:add', args=('tests', 'simplepage', self.root_page.id))) self.assertContains( ...
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[ 725, 4 ]
[ 735, 9 ]
python
en
['en', 'error', 'th']
False
TestPageCreation.test_hide_moderation_button
(self)
Tests that if WAGTAIL_MODERATION_ENABLED is set to False, the "Submit for Moderation" button is not shown.
Tests that if WAGTAIL_MODERATION_ENABLED is set to False, the "Submit for Moderation" button is not shown.
def test_hide_moderation_button(self): """ Tests that if WAGTAIL_MODERATION_ENABLED is set to False, the "Submit for Moderation" button is not shown. """ response = self.client.get(reverse('wagtailadmin_pages:add', args=('tests', 'simplepage', self.root_page.id))) self.assertNotC...
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[ 738, 4 ]
[ 743, 162 ]
python
en
['en', 'error', 'th']
False
TestPerRequestEditHandler.test_create_page_with_per_request_custom_edit_handlers
(self)
Test that per-request custom behaviour in edit handlers is honoured
Test that per-request custom behaviour in edit handlers is honoured
def test_create_page_with_per_request_custom_edit_handlers(self): """ Test that per-request custom behaviour in edit handlers is honoured """ # non-superusers should not see secret_data self.login(username='siteeditor', password='password') response = self.client.get( ...
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[ 771, 4 ]
[ 791, 54 ]
python
en
['en', 'error', 'th']
False
remove_choose_permission
(apps, _schema_editor)
Reverse the above additions of permissions.
Reverse the above additions of permissions.
def remove_choose_permission(apps, _schema_editor): """Reverse the above additions of permissions.""" ContentType = apps.get_model('contenttypes.ContentType') Permission = apps.get_model('auth.Permission') document_content_type = ContentType.objects.get( model='document', app_label='wagt...
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[ 30, 0 ]
[ 42, 14 ]
python
en
['en', 'en', 'en']
True
main
(args=None)
This is preserved for old console scripts that may still be referencing it. For additional details, see https://github.com/pypa/pip/issues/7498.
This is preserved for old console scripts that may still be referencing it.
def main(args=None): # type: (Optional[List[str]]) -> int """This is preserved for old console scripts that may still be referencing it. For additional details, see https://github.com/pypa/pip/issues/7498. """ from pip._internal.utils.entrypoints import _wrapper return _wrapper(args)
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[ 6, 0 ]
[ 15, 25 ]
python
en
['en', 'en', 'en']
True
remove_unused_versions_dir
(args: argparse.Namespace)
Deletes cache data from obsolete Yarn versions. Yarn does not provide an interface for removing obsolete data from ~/.cache/yarn for packages that you haven't installed in years; but one can always remove the cache entirely.
Deletes cache data from obsolete Yarn versions.
def remove_unused_versions_dir(args: argparse.Namespace) -> None: """Deletes cache data from obsolete Yarn versions. Yarn does not provide an interface for removing obsolete data from ~/.cache/yarn for packages that you haven't installed in years; but one can always remove the cache entirely. """ ...
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[ 14, 0 ]
[ 40, 5 ]
python
en
['en', 'en', 'en']
True
addScriptOptions
(parser, pos_args, kw_args)
add script-specific script options
add script-specific script options
def addScriptOptions(parser, pos_args, kw_args): """ add script-specific script options """ script_req_group = sp.get_std_req_group(parser) hlpstr = "Input bamfile" option_short_name = "b" option_name = "bamfile" script_req_group.add_argument('-%s' % option_short_name, ...
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[ 127, 0 ]
[ 339, 37 ]
python
en
['en', 'it', 'en']
True
charcterizeIntrons
(read_iterator, genome, annotation_splices=None, splicepad=0, min_intron_length=20, pwms=None, pwmscorethreshold=3.0, logger=None, LOG_EVERY_N=10000, pwm_species="")
Return a dictionary {readID:[(start, stop)...]} Listing the intronic sites for each read (identified by 'N' in the cigar strings). read_iterator can be the result of a .fetch(...) call. Or it can be a generator filtering such reads. Example samfile.find_introns((read for read in samf...
Return a dictionary {readID:[(start, stop)...]} Listing the intronic sites for each read (identified by 'N' in the cigar strings). read_iterator can be the result of a .fetch(...) call. Or it can be a generator filtering such reads. Example samfile.find_introns((read for read in samf...
def charcterizeIntrons(read_iterator, genome, annotation_splices=None, splicepad=0, min_intron_length=20, pwms=None, pwmscorethreshold=3.0, logger=None, LOG_EVERY_N=10000, pwm_species=""): """Return a dictionary {readID:[(start, stop)...]} Listing the intron...
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[ 419, 0 ]
[ 814, 64 ]
python
en
['en', 'en', 'en']
True
getAnnotationIntrons
(annot, genome, chr_synonym_dic={}, logger=None, LOG_EVERY_N=10000)
return a dictionary with all the introns in a given annotation
return a dictionary with all the introns in a given annotation
def getAnnotationIntrons(annot, genome, chr_synonym_dic={}, logger=None, LOG_EVERY_N=10000): """ return a dictionary with all the introns in a given annotation """ if logger is not None: logger.info("parsing transcript exon structures....") annot.clear_all() annot.set_feature("exo...
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[ 816, 0 ]
[ 893, 26 ]
python
en
['en', 'en', 'en']
True
writeBamFiles
(thisbam, splice_read_details, prefix, splits, pwms=None, logger=None)
write bam files separating out the reads into their categories
write bam files separating out the reads into their categories
def writeBamFiles(thisbam, splice_read_details, prefix, splits, pwms=None, logger=None): """ write bam files separating out the reads into their categories """ annot_opts = ["annotated","novel"] cann_opts = ["canonical","non_canonical"] pwm_opts=["unclassified"] if pwms is not None: ...
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[ 895, 0 ]
[ 977, 32 ]
python
en
['en', 'en', 'en']
True
mkAnnotPWMBoxPlots
(splice_details, plotfile, pointsize=4, title="", legend_fontsize=10, legendloc=(0.2,0.7), logger=None)
plot the results of the analysis as a set of cool box plots...
plot the results of the analysis as a set of cool box plots...
def mkAnnotPWMBoxPlots(splice_details, plotfile, pointsize=4, title="", legend_fontsize=10, legendloc=(0.2,0.7), logger=None): """ plot the results of the analysis as a set of cool box plots...""" if logger is not None: logger.info("Plotting classified annotated splicing...
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[ 989, 0 ]
[ 1142, 48 ]
python
en
['en', 'en', 'en']
True
mkPWMBoxPlots
(splice_details, plotfile, pointsize=4, title="", logger=None)
plot the results of the analysis as a set of cool box plots...
plot the results of the analysis as a set of cool box plots...
def mkPWMBoxPlots(splice_details, plotfile, pointsize=4, title="", logger=None): """ plot the results of the analysis as a set of cool box plots...""" if logger is not None: logger.info("Plotting classified splicing details boxplots...") splice_exprs_data = {} for splice in s...
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[ 1144, 0 ]
[ 1215, 48 ]
python
en
['en', 'en', 'en']
True
mkAnnotBoxPlots
(splice_details, plotfile, pointsize=4, title="", legend_fontsize=8, logger=None)
plot the results of the analysis as a set of cool box plots...
plot the results of the analysis as a set of cool box plots...
def mkAnnotBoxPlots(splice_details, plotfile, pointsize=4, title="", legend_fontsize=8, logger=None): """ plot the results of the analysis as a set of cool box plots...""" if logger is not None: logger.info("Plotting annotated splicing details boxplots...") splice_exprs_data={"annotat...
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[ 1217, 0 ]
[ 1331, 48 ]
python
en
['en', 'en', 'en']
True
mkBoxPlots
(splice_details, plotfile, pointsize=4, title="", logger=None)
plot the results of the analysis as a set of cool box plots...
plot the results of the analysis as a set of cool box plots...
def mkBoxPlots(splice_details, plotfile, pointsize=4, title="", logger=None): """ plot the results of the analysis as a set of cool box plots...""" if logger is not None: logger.info("Plotting basic splicing details boxplots...") splice_exprs_data = {"canonical":[], ...
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[ 1333, 0 ]
[ 1409, 48 ]
python
en
['en', 'en', 'en']
True
Connection.request
(self, relative_endpoint, method='get', json=None, data=None, query_parameters=None, headers=None)
Core requests.Session wrapper that returns requests.Response objects
Core requests.Session wrapper that returns requests.Response objects
def request(self, relative_endpoint, method='get', json=None, data=None, query_parameters=None, headers=None): """Core requests.Session wrapper that returns requests.Response objects""" session_request_method = getattr(self.session, method, None) if not session_request_method: raise ...
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[ 67, 4 ]
[ 98, 23 ]
python
en
['en', 'en', 'en']
True
validate_options
(options)
Validates options.
Validates options.
def validate_options(options): """Validates options.""" kwcase = options.get('keyword_case') if kwcase not in [None, 'upper', 'lower', 'capitalize']: raise SQLParseError('Invalid value for keyword_case: ' '{!r}'.format(kwcase)) idcase = options.get('identifier_case')...
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[ 13, 0 ]
[ 128, 18 ]
python
en
['en', 'et', 'en']
False
build_filter_stack
(stack, options)
Setup and return a filter stack. Args: stack: :class:`~sqlparse.filters.FilterStack` instance options: Dictionary with options validated by validate_options.
Setup and return a filter stack.
def build_filter_stack(stack, options): """Setup and return a filter stack. Args: stack: :class:`~sqlparse.filters.FilterStack` instance options: Dictionary with options validated by validate_options. """ # Token filter if options.get('keyword_case'): stack.preprocess.append( ...
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[ 131, 0 ]
[ 197, 16 ]
python
en
['en', 'da', 'en']
True
decorate_urlpatterns
(urlpatterns, decorator)
Decorate all the views in the passed urlpatterns list with the given decorator
Decorate all the views in the passed urlpatterns list with the given decorator
def decorate_urlpatterns(urlpatterns, decorator): """Decorate all the views in the passed urlpatterns list with the given decorator""" for pattern in urlpatterns: if hasattr(pattern, 'url_patterns'): # this is an included RegexURLResolver; recursively decorate the views # contain...
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[ 3, 0 ]
[ 14, 22 ]
python
en
['en', 'en', 'en']
True
filter_empty_cols
(c)
Remove columns for bases which are not represented in the data
Remove columns for bases which are not represented in the data
def filter_empty_cols(c): '''Remove columns for bases which are not represented in the data''' c_t = c.T c_t = c_t[c_t.any(1)] return c_t.T
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[ 18, 0 ]
[ 22, 16 ]
python
en
['en', 'en', 'en']
True
test_significant_der_sites
(counts, fdr_threshold, fasta)
Conduct G-test on counts to identify sites with differential error profiles
Conduct G-test on counts to identify sites with differential error profiles
def test_significant_der_sites(counts, fdr_threshold, fasta): '''Conduct G-test on counts to identify sites with differential error profiles''' res = [] mismatch_counts = [] kd_has_replicates = len(counts['kd'].columns.levels[0]) > 1 cntrl_has_replicates = len(counts['cntrl'].columns.levels[0]) > ...
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[ 25, 0 ]
[ 79, 31 ]
python
en
['en', 'en', 'en']
True
RoutablePageMixin.reverse_subpage
(self, name, args=None, kwargs=None)
This method takes a route name/arguments and returns a URL path.
This method takes a route name/arguments and returns a URL path.
def reverse_subpage(self, name, args=None, kwargs=None): """ This method takes a route name/arguments and returns a URL path. """ args = args or [] kwargs = kwargs or {} return self.get_resolver().reverse(name, *args, **kwargs)
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[ 76, 4 ]
[ 83, 65 ]
python
en
['en', 'error', 'th']
False
RoutablePageMixin.resolve_subpage
(self, path)
This method takes a URL path and finds the view to call.
This method takes a URL path and finds the view to call.
def resolve_subpage(self, path): """ This method takes a URL path and finds the view to call. """ view, args, kwargs = self.get_resolver().resolve(path) # Bind the method view = view.__get__(self, type(self)) return view, args, kwargs
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[ 85, 4 ]
[ 94, 33 ]
python
en
['en', 'error', 'th']
False
RoutablePageMixin.route
(self, request, path_components)
This hooks the subpage URLs into Wagtail's routing.
This hooks the subpage URLs into Wagtail's routing.
def route(self, request, path_components): """ This hooks the subpage URLs into Wagtail's routing. """ if self.live: try: path = '/' if path_components: path += '/'.join(path_components) + '/' view, args, kw...
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[ 96, 4 ]
[ 111, 54 ]
python
en
['en', 'error', 'th']
False
RoutablePageMixin.render
(self, request, *args, template=None, context_overrides=None, **kwargs)
.. versionadded:: 2.11 This method replicates what ``Page.serve()`` usually does when ``RoutablePageMixin`` is not used. By default, ``Page.get_template()`` is called to derive the template to use for rendering, and ``Page.get_context()`` is always called to gather the data to ...
.. versionadded:: 2.11
def render(self, request, *args, template=None, context_overrides=None, **kwargs): """ .. versionadded:: 2.11 This method replicates what ``Page.serve()`` usually does when ``RoutablePageMixin`` is not used. By default, ``Page.get_template()`` is called to derive the template to...
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[ 122, 4 ]
[ 163, 59 ]
python
en
['en', 'error', 'th']
False