Python Bunch.auto_decompress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 auto_decompress [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:
                # 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(1024)

                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
            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)),
                                                     'filename' : os.path.basename(path)}
                                    purge = getattr(trans.app.config, 'ftp_upload_purge', True)
#.........这里部分代码省略.........