Python Bunch.file_type方法代码示例

# 需要导入模块: from galaxy.util.bunch import Bunch [as 别名]
# 或者: from galaxy.util.bunch.Bunch import file_type [as 别名]
 def get_uploaded_datasets( self, trans, context, override_name = None, override_info = None ):
     def get_data_file_filename( data_file, override_name = None, override_info = None ):
         dataset_name = override_name
         dataset_info = override_info
         def get_file_name( file_name ):
             file_name = file_name.split( '\\' )[-1]
             file_name = file_name.split( '/' )[-1]
             return file_name
         try:
             # Use the existing file
             if not dataset_name and 'filename' in data_file:
                 dataset_name = get_file_name( data_file['filename'] )
             if not dataset_info:
                 dataset_info = 'uploaded file'
             return Bunch( type='file', path=data_file['local_filename'], name=get_file_name( data_file['filename'] ) )
             #return 'file', data_file['local_filename'], get_file_name( data_file.filename ), dataset_name, dataset_info
         except:
             # The uploaded file should've been persisted by the upload tool action
             return Bunch( type=None, path=None, name=None )
             #return None, None, None, None, None
     def get_url_paste_urls_or_filename( group_incoming, override_name = None, override_info = None ):
         filenames = []
         url_paste_file = group_incoming.get( 'url_paste', None )
         if url_paste_file is not None:
             url_paste = open( url_paste_file, 'r' ).read( 1024 )
             if url_paste.lstrip().lower().startswith( 'http://' ) or url_paste.lstrip().lower().startswith( 'ftp://' ):
                 url_paste = url_paste.replace( '\r', '' ).split( '\n' )
                 for line in url_paste:
                     line = line.strip()
                     if line:
                         if not line.lower().startswith( 'http://' ) and not line.lower().startswith( 'ftp://' ):
                             continue # non-url line, ignore
                         precreated_name = line
                         dataset_name = override_name
                         if not dataset_name:
                             dataset_name = line
                         dataset_info = override_info
                         if not dataset_info:
                             dataset_info = 'uploaded url'
                         yield Bunch( type='url', path=line, name=precreated_name )
                         #yield ( 'url', line, precreated_name, dataset_name, dataset_info )
             else:
                 dataset_name = dataset_info = precreated_name = 'Pasted Entry' #we need to differentiate between various url pastes here
                 if override_name:
                     dataset_name = override_name
                 if override_info:
                     dataset_info = override_info
                 yield Bunch( type='file', path=url_paste_file, name=precreated_name )
                 #yield ( 'file', url_paste_file, precreated_name, dataset_name, dataset_info )
     def get_one_filename( context ):
         data_file = context['file_data']
         url_paste = context['url_paste']
         name = context.get( 'NAME', None )
         info = context.get( 'INFO', None )
         warnings = []
         space_to_tab = False 
         if context.get( 'space_to_tab', None ) not in ["None", None]:
             space_to_tab = True
         file_bunch = get_data_file_filename( data_file, override_name = name, override_info = info )
         if file_bunch.path and url_paste:
             if url_paste.strip():
                 warnings.append( "All file contents specified in the paste box were ignored." )
         else: #we need to use url_paste
             for file_bunch in get_url_paste_urls_or_filename( context, override_name = name, override_info = info ):
                 if file_bunch.path:
                     break
         return file_bunch, warnings
     def get_filenames( context ):
         rval = []
         data_file = context['file_data']
         url_paste = context['url_paste']
         name = context.get( 'NAME', None )
         info = context.get( 'INFO', None )
         space_to_tab = False
         if context.get( 'space_to_tab', None ) not in ["None", None]:
             space_to_tab = True
         warnings = []
         file_bunch = get_data_file_filename( data_file, override_name = name, override_info = info )
         if file_bunch.path:
             file_bunch.space_to_tab = space_to_tab
             rval.append( file_bunch )
         for file_bunch in get_url_paste_urls_or_filename( context, override_name = name, override_info = info ):
             if file_bunch.path:
                 file_bunch.space_to_tab = space_to_tab
                 rval.append( file_bunch )
         return rval
     file_type = self.get_file_type( context )
     d_type = self.get_datatype( trans, context )
     dbkey = context.get( 'dbkey', None )
     writable_files = d_type.writable_files
     writable_files_offset = 0
     groups_incoming = [ None for filename in writable_files ]
     for group_incoming in context.get( self.name, [] ):
         i = int( group_incoming['__index__'] )
         groups_incoming[ i ] = group_incoming
     if d_type.composite_type is not None:
         #handle uploading of composite datatypes
         #Only one Dataset can be created
         dataset = Bunch()
         dataset.type = 'composite'
#.........这里部分代码省略.........

# 需要导入模块: from galaxy.util.bunch import Bunch [as 别名]
# 或者: from galaxy.util.bunch.Bunch import file_type [as 别名]

#.........这里部分代码省略.........
                # This allows for comparison when the filesystem uses a different encoding than the browser.
                ftp_files = [unicodedata.normalize('NFC', f) for f in ftp_files if isinstance(f, unicode)]
                if trans.user is None:
                    log.warning( 'Anonymous user passed values in ftp_files: %s' % ftp_files )
                    ftp_files = []
                    # TODO: warning to the user (could happen if session has become invalid)
                else:
                    user_ftp_dir = trans.user_ftp_dir
                    for ( dirpath, dirnames, filenames ) in os.walk( user_ftp_dir ):
                        for filename in filenames:
                            path = relpath( os.path.join( dirpath, filename ), user_ftp_dir )
                            if not os.path.islink( os.path.join( dirpath, filename ) ):
                                # Normalize filesystem paths
                                if isinstance(path, unicode):
                                    valid_files.append(unicodedata.normalize('NFC', path ))
                                else:
                                    valid_files.append(path)

            else:
                ftp_files = []
            for ftp_file in ftp_files:
                if ftp_file not in valid_files:
                    log.warning( 'User passed an invalid file path in ftp_files: %s' % ftp_file )
                    continue
                    # TODO: warning to the user (could happen if file is already imported)
                ftp_data_file = { 'local_filename' : os.path.abspath( os.path.join( user_ftp_dir, ftp_file ) ),
                                  'filename' : os.path.basename( ftp_file ) }
                file_bunch = get_data_file_filename( ftp_data_file, override_name=name, override_info=info )
                if file_bunch.path:
                    file_bunch.to_posix_lines = to_posix_lines
                    file_bunch.space_to_tab = space_to_tab
                    rval.append( file_bunch )
            return rval
        file_type = self.get_file_type( context )
        d_type = self.get_datatype( trans, context )
        dbkey = context.get( 'dbkey', None )
        writable_files = d_type.writable_files
        writable_files_offset = 0
        groups_incoming = [ None for _ in writable_files ]
        for group_incoming in context.get( self.name, [] ):
            i = int( group_incoming['__index__'] )
            groups_incoming[ i ] = group_incoming
        if d_type.composite_type is not None:
            # handle uploading of composite datatypes
            # Only one Dataset can be created
            dataset = Bunch()
            dataset.type = 'composite'
            dataset.file_type = file_type
            dataset.dbkey = dbkey
            dataset.datatype = d_type
            dataset.warnings = []
            dataset.metadata = {}
            dataset.composite_files = {}
            dataset.uuid = None
            # load metadata
            files_metadata = context.get( self.metadata_ref, {} )
            metadata_name_substition_default_dict = dict( [ ( composite_file.substitute_name_with_metadata, d_type.metadata_spec[ composite_file.substitute_name_with_metadata ].default ) for composite_file in d_type.composite_files.values() if composite_file.substitute_name_with_metadata ] )
            for meta_name, meta_spec in d_type.metadata_spec.iteritems():
                if meta_spec.set_in_upload:
                    if meta_name in files_metadata:
                        meta_value = files_metadata[ meta_name ]
                        if meta_name in metadata_name_substition_default_dict:
                            meta_value = sanitize_for_filename( meta_value, default=metadata_name_substition_default_dict[ meta_name ] )
                        dataset.metadata[ meta_name ] = meta_value
            dataset.precreated_name = dataset.name = self.get_composite_dataset_name( context )
            if dataset.datatype.composite_type == 'auto_primary_file':

# 需要导入模块: from galaxy.util.bunch import Bunch [as 别名]
# 或者: from galaxy.util.bunch.Bunch import file_type [as 别名]
    def get_uploaded_datasets(self, trans, context, override_name=None, override_info=None):
        def get_data_file_filename(data_file, override_name=None, override_info=None, purge=True):
            dataset_name = override_name

            def get_file_name(file_name):
                file_name = file_name.split('\\')[-1]
                file_name = file_name.split('/')[-1]
                return file_name
            try:
                # Use the existing file
                if not dataset_name and 'filename' in data_file:
                    dataset_name = get_file_name(data_file['filename'])
                return Bunch(type='file', path=data_file['local_filename'], name=dataset_name, purge_source=purge)
            except Exception:
                # The uploaded file should've been persisted by the upload tool action
                return Bunch(type=None, path=None, name=None)

        def get_url_paste_urls_or_filename(group_incoming, override_name=None, override_info=None):
            url_paste_file = group_incoming.get('url_paste', None)
            if url_paste_file is not None:
                url_paste = open(url_paste_file, 'r').read()

                def start_of_url(content):
                    start_of_url_paste = content.lstrip()[0:8].lower()
                    looks_like_url = False
                    for url_prefix in ["http://", "https://", "ftp://", "file://"]:
                        if start_of_url_paste.startswith(url_prefix):
                            looks_like_url = True
                            break

                    return looks_like_url

                if start_of_url(url_paste):
                    url_paste = url_paste.replace('\r', '').split('\n')
                    for line in url_paste:
                        line = line.strip()
                        if line:
                            if not start_of_url(line):
                                continue  # non-url line, ignore

                            if "file://" in line:
                                if not trans.user_is_admin:
                                    raise AdminRequiredException()
                                elif not trans.app.config.allow_path_paste:
                                    raise ConfigDoesNotAllowException()
                                upload_path = line[len("file://"):]
                                dataset_name = os.path.basename(upload_path)
                            else:
                                dataset_name = line

                            if override_name:
                                dataset_name = override_name
                            yield Bunch(type='url', path=line, name=dataset_name)
                else:
                    dataset_name = 'Pasted Entry'  # we need to differentiate between various url pastes here
                    if override_name:
                        dataset_name = override_name
                    yield Bunch(type='file', path=url_paste_file, name=dataset_name)

        def get_one_filename(context):
            data_file = context['file_data']
            url_paste = context['url_paste']
            ftp_files = context['ftp_files']
            name = context.get('NAME', None)
            info = context.get('INFO', None)
            uuid = context.get('uuid', None) or None  # Turn '' to None
            file_type = context.get('file_type', None)
            dbkey = self.get_dbkey(context)
            warnings = []
            to_posix_lines = False
            if context.get('to_posix_lines', None) not in ["None", None, False]:
                to_posix_lines = True
            auto_decompress = False
            if context.get('auto_decompress', None) not in ["None", None, False]:
                auto_decompress = True
            space_to_tab = False
            if context.get('space_to_tab', None) not in ["None", None, False]:
                space_to_tab = True
            file_bunch = get_data_file_filename(data_file, override_name=name, override_info=info)
            if file_bunch.path:
                if url_paste is not None and url_paste.strip():
                    warnings.append("All file contents specified in the paste box were ignored.")
                if ftp_files:
                    warnings.append("All FTP uploaded file selections were ignored.")
            elif url_paste is not None and url_paste.strip():  # we need to use url_paste
                for file_bunch in get_url_paste_urls_or_filename(context, override_name=name, override_info=info):
                    if file_bunch.path:
                        break
                if file_bunch.path and ftp_files is not None:
                    warnings.append("All FTP uploaded file selections were ignored.")
            elif ftp_files is not None and trans.user is not None:  # look for files uploaded via FTP
                user_ftp_dir = trans.user_ftp_dir
                assert not os.path.islink(user_ftp_dir), "User FTP directory cannot be a symbolic link"
                for (dirpath, dirnames, filenames) in os.walk(user_ftp_dir):
                    for filename in filenames:
                        for ftp_filename in ftp_files:
                            if ftp_filename == filename:
                                path = relpath(os.path.join(dirpath, filename), user_ftp_dir)
                                if not os.path.islink(os.path.join(dirpath, filename)):
                                    ftp_data_file = {'local_filename' : os.path.abspath(os.path.join(user_ftp_dir, path)),
#.........这里部分代码省略.........