Source code for filesystem

# Copyright 2011-2014 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.

This module contains the FileSystem plugin for fastr

import os
import shutil
import urllib.parse
import fastr
from fastr import exceptions
from fastr.core.ioplugin import IOPlugin

class FileSystem(IOPlugin):
    The FileSystem plugin is create to handle ``file://`` type or URLs. This is
    generally not a good practice, as this is not portable over between
    machines. However, for test purposes it might be useful.

    The URL scheme is rather simple: ``file://host/path``
    (see `wikipedia <>`_ for details)

    We do not make use of the ``host`` part and at the moment only support
    localhost (just leave the host empty) leading to ``file:///`` URLs.

    .. warning:: This plugin ignores the hostname in the URL and does only
                 accept driver letters on Windows in the form ``c:/``
    scheme = 'file'

[docs] def __init__(self): # initialize the instance and register the scheme super(FileSystem, self).__init__()
[docs] def url_to_path(self, url): """ Get the path to a file from a url. Currently supports the file:// scheme Examples: .. code-block:: python >>> 'file:///d:/data/project/file.ext' 'd:\\data\\project\\file.ext' .. warning:: file:// will not function cross platform and is mainly for testing """ parsed_url = up.urlparse(str(url)) # Translate properly depending on the scheme being used if parsed_url.scheme == self.scheme: if == 'nt': path = parsed_url.path.lstrip('/') else: path = parsed_url.path return self._correct_separators(path) # return o.path else: raise exceptions.FastrValueError('This parses the {} scheme and not the {} scheme!'.format(self.scheme, parsed_url.scheme))
[docs] def path_to_url(self, path, mountpoint=None): """ Construct an url from a given mount point and a relative path to the mount point. """ return "{scheme}:///{path}".format(scheme=self.scheme, path=path)
[docs] def fetch_url(self, inurl, outpath): """ Fetch the files from the file. :param inurl: url to the item in the data store, starts with ``file://`` :param outpath: path where to store the fetch data locally """ inpath = self.url_to_path(inurl) # Clear away present data if os.path.exists(outpath):'Removing currently exists data at {}'.format(outpath)) if os.path.islink(outpath): os.remove(outpath) elif os.path.isdir(outpath): shutil.rmtree(outpath) else: os.remove(outpath) try: os.symlink(inpath, outpath) fastr.log.debug('Symlink successful') except OSError: fastr.log.debug('Cannot symlink, fallback to copy') if os.path.isdir(inpath): shutil.copytree(inpath, outpath) else: shutil.copy2(inpath, outpath) return outpath
[docs] def fetch_value(self, inurl): """ Fetch a value from an external file file. :param inurl: url of the value to read :return: the fetched value """ path = self.url_to_path(inurl) with open(path, 'r') as file_handle: data = return data
[docs] def put_url(self, inpath, outurl): """ Put the files to the external data store. :param inpath: path of the local data :param outurl: url to where to store the data, starts with ``file://`` """ outpath = self.url_to_path(outurl) fastr.vfs.copy_file_dir(inpath, outpath) return os.path.exists(outpath)
[docs] def put_value(self, value, outurl): """ Put the value in the external data store. :param value: value to store :param outurl: url to where to store the data, starts with ``file://`` """ outpath = self.url_to_path(outurl) with open(outpath, 'w') as file_handle: file_handle.write(str(value)) return os.path.exists(outpath)