Source code for xnatstorage

# 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 XNATStorage plugin for fastr

import fnmatch

import netrc
import os
import re
import time
import tempfile
import urllib.parse
from collections import OrderedDict

import requests
from requests.exceptions import RequestException
import xnat
import xnat.exceptions

import fastr
from fastr import exceptions
from fastr.core.ioplugin import IOPlugin

class XNATStorage(IOPlugin):

    .. warning::

        As this IOPlugin is under development, it has not been thoroughly

    The XNATStorage plugin is an IOPlugin that can download data from and
    upload data to an XNAT server. It uses its own ``xnat://`` URL scheme.
    This is a scheme specific for this plugin and though it looks somewhat
    like the XNAT rest interface, a different type or URL.

    Data resources can be access directly by a data url::


    In the second URL you can see a wildcard being used. This is possible at
    long as it resolves to exactly one item.

    The ``id`` query element will change the field from the default experiment to
    subject and the ``label`` query element sets the use of the label as the
    fastr id (instead of the XNAT id) to ``True`` (the default is ``False``)

    To disable ``https`` transport and use ``http`` instead the query string
    can be modified to add ``insecure=true``. This will make the plugin send
    requests over ``http``::


    For sinks it is import to know where to save the data. Sometimes you want
    to save data in a new assessor/resource and it needs to be created. To
    allow the Fastr sink to create an object in XNAT, you have to supply the
    type as a query parameter::


    Valid options are: subject_type, experiment_type, assessor_type, scan_type,
    and resource_type.

    If you want to do a search where
    multiple resources are returned, it is possible to use a search url::


    This will return all DICOMs for the T1 scans for experiments that end with _BRAIN that belong to a
    subjectXXX where XXX is a 3 digit number. By default the ID for the samples
    will be the experiment XNAT ID (e.g. XNAT_E00123). The wildcards that can
    be the used are the same UNIX shell-style wildcards as provided by the
    module :py:mod:`fnmatch`.

    It is possible to change the id to a different fields id or label. Valid
    fields are project, subject, experiment, scan, and resource::


    The following variables can be set in the search query:

    ============= ============== =============================================================================================
    variable      default        usage
    ============= ============== =============================================================================================
    projects      ``*``          The project(s) to select, can contain wildcards (see :py:mod:`fnmatch`)
    subjects      ``*``          The subject(s) to select, can contain wildcards (see :py:mod:`fnmatch`)
    experiments   ``*``          The experiment(s) to select, can contain wildcards (see :py:mod:`fnmatch`)
    scans         ``*``          The scan(s) to select, can contain wildcards (see :py:mod:`fnmatch`)
    resources     ``*``          The resource(s) to select, can contain wildcards (see :py:mod:`fnmatch`)
    id            ``experiment`` What field to use a the id, can be: project, subject, experiment, scan, or resource
    label         ``false``      Indicate the XNAT label should be used as fastr id, options ``true`` or ``false``
    insecure      ``false``      Change the url scheme to be used to http instead of https
    verify        ``true``       (Dis)able the verification of SSL certificates
    regex         ``false``      Change search to use regex :py:func:`re.match` instead of fnmatch for matching
    overwrite     ``false``      Tell XNAT to overwrite existing files if a file with the name is already present
    ============= ============== =============================================================================================

    For storing credentials the ``.netrc`` file can be used. This is a common
    way to store credentials on UNIX systems. It is required that the file is
    only accessible by the owner only or a ``NetrcParseError`` will be raised.
    A netrc file is really easy to create, as its entries look like::

                login username
                password secret123

    See the :py:mod:`netrc module <netrc>` or the
    `GNU inet utils website <>`_
    for more information about the ``.netrc`` file.

    .. note::

        On windows the location of the netrc file is assumed to be
        ``os.path.expanduser('~/_netrc')``. The leading underscore is
        because windows does not like filename starting with a dot.

    .. note::

        For scan the label will be the scan type (this is initially
        the same as the series description, but can be updated manually
        or the XNAT scan type cleanup).

    .. warning::

        labels in XNAT are not guaranteed to be unique, so be careful
        when using them as the sample ID.

    For background on XNAT, see the
    for the REST API of XNAT.
    scheme = ('xnat', 'xnat+http', 'xnat+https')

[docs] def __init__(self): # initialize the instance and register the scheme super(XNATStorage, self).__init__() self._xnat = (None, None)
[docs] def cleanup(self): if self.xnat is not None:'Attempting to cleanly disconnecting XNAT.') self.xnat.disconnect()
@property def server(self): return self._xnat[0] @property def xnat(self): return self._xnat[1]
[docs] def connect(self, server, path='', insecure=False, verify=True): if self.server != server: # Try to neatly clean previous connection if self.xnat is not None: self.xnat.disconnect() try: netrc_file = os.path.join('~', '_netrc' if == 'nt' else '.netrc') netrc_file = os.path.expanduser(netrc_file) user, _, password = netrc.netrc(netrc_file).authenticators(server) except TypeError: raise exceptions.FastrValueError('Could not retrieve login info for "{}" from the .netrc file!'.format(server)) # Create the URL for the XNAT connection schema = 'http' if insecure else 'https' session = xnat.connect(urllib.parse.urlunparse([schema, server, path, '', '', '']), user=user, password=password, debug=fastr.config.debug, verify=verify) # Time-out a request when no bytes are received for 120 seconds session.request_timeout = 120 self._xnat = (server, session)
@staticmethod def _path_to_dict(path):'Converting {} to dict...'.format(path)) if not path.startswith('/data/archive/'): # prefix, path = path.split('/data/archive') raise ValueError('Resources to be located should have a path starting with /data/ (found {})'.format(path)) # Break path apart parts = path.lstrip('/').split('/', 13) # Ignore first two parts and build a dict from /key/value/key/value pattern path_iterator = parts[2:].__iter__() location = OrderedDict() for key, value in zip(path_iterator, path_iterator): if key == 'files': filepath = [value] + list(path_iterator) value = '/'.join(filepath) location[key] = value'Found {}'.format(location)) return location def _locate_resource(self, url, create=False, use_regex=False): resources = self._find_objects(url=url, create=create, use_regex=use_regex) if len(resources) == 0: raise ValueError('Could not find data object at {}'.format(url)) elif len(resources) > 1: raise ValueError('Data item does not point to a unique resource! Matches found: {}'.format([x.fulluri for x in resources])) resource = resources[0] # Make sure the return value is actually a resource resource_cls = self.xnat.XNAT_CLASS_LOOKUP['xnat:abstractResource'] if not isinstance(resource, resource_cls): raise TypeError('The resource should be an instance of {}'.format(resource_cls)) return resource
[docs] def parse_uri(self, url): url = urllib.parse.urlparse(url) if url.scheme not in self.scheme: raise exceptions.FastrValueError('URL scheme {} not of supported type {}!'.format(url.scheme, self.scheme)) query = urllib.parse.parse_qs(url.query) path_prefix = url.path[:url.path.find('/data/')] # Strip the prefix of the url path url = url._replace(path=url.path[len(path_prefix):]) if not url.path.startswith('/data/archive/') and url.path.startswith('/data/'):'Patching archive into url path starting with data') url = url._replace(path=url.path[:6] + 'archive/' + url.path[6:]) url_str = urllib.parse.urlunparse(url)'New URL: {}'.format(url_str)) if not url.path.startswith('/data/archive'): raise exceptions.FastrValueError('Can only fetch urls with the /data/archive path') if url.scheme == 'xnat+http': insecure = True elif url.scheme == 'xnat+https': insecure = False else: fastr.log.warning('Using old-style insecure lookup, please use a xnat+http://' ' or xnat+https:// url scheme instead!') insecure = query.get('insecure', ['0'])[0] in ['true', '1'] verify = query.get('verify', ['1'])[0] in ['true', '1'] use_regex = query.get('regex', ['0'])[0] in ['true', '1'] return url, path_prefix, insecure, verify, use_regex, query
[docs] def fetch_url(self, inurl, outpath): """ Get the file(s) or values from XNAT. :param inurl: url to the item in the data store :param outpath: path where to store the fetch data locally """ url, path_prefix, insecure, verify, use_regex, query = self.parse_uri(inurl) # Create a session for this retrieval self.connect(url.netloc, path=path_prefix, insecure=insecure, verify=verify) # Find the filepath within the resource location = self._path_to_dict(url.path) filepath = location.get('files', '') # Find the resource resource = self._locate_resource(inurl, use_regex=use_regex) # Download the Resource workdir = outpath if not os.path.isdir(workdir): directory, filename = os.path.split(workdir) workdir = os.path.join(directory, filename.replace('.', '_')) os.makedirs(workdir) # Create uniquer dir to download in workdir = tempfile.mkdtemp(prefix='fastr_xnat_{}_tmp'.format(, dir=workdir) # Retry downloading in case of connection reset max_tries = tries = 3 success = False while tries > 0 and not success: try:'Download attempt {} of {}'.format(max_tries - tries + 1, max_tries)) tries -= 1 resource.download_dir(workdir, verbose=False) success = True except requests.exceptions.ChunkedEncodingError: if tries <= 0: raise else: # Sleep 10 seconds times the amount of tries time.sleep((max_tries - tries) * 10) # Find the file in the proper path resource_label = resource.label.replace(' ', '_') if filepath == '': filepath = file_name = 'files' target = 'resources/{}'.format(resource_label) else: file_directory, file_name = os.path.split(filepath) target = 'resources/{}/files/{}'.format(resource_label, file_directory).rstrip('/') for root, dirs, files in os.walk(workdir): if root.endswith(target) and (file_name in files or file_name in dirs): data_path = os.path.join(root, filepath)'Found data in {}'.format(data_path)) break else: message = "Could not find {} file in downloaded resource!".format(filepath) fastr.log.error(message) raise exceptions.FastrValueError(message) return data_path
[docs] def put_url(self, inpath, outurl): """ Upload the files to the XNAT storage :param inpath: path to the local data :param outurl: url to where to store the data in the external data store. """ # Create a session for this retrieval url, path_prefix, insecure, verify, use_regex, query = self.parse_uri(outurl) self.connect(url.netloc, path=path_prefix, insecure=insecure, verify=verify) # Determine the resource to upload to resource = self._locate_resource(outurl, create=True, use_regex=use_regex) # Determine the file within xnat parsed_url = urllib.parse.urlparse(outurl) location = self._path_to_dict(parsed_url.path) # Upload the file'Uploading to: {}'.format(resource.fulluri))'Uploading to path: {}'.format(location['files'])) try: overwrite = urllib.parse.parse_qs(url.query).get('overwrite', ['0'])[0] in ['true', '1'] self.upload(resource, inpath, location['files'], overwrite=overwrite) return True except xnat.exceptions.XNATUploadError as exception: fastr.log.error('Encountered error when uploading data: {}'.format(exception)) return False
[docs] @staticmethod def upload(resource, in_path, location, retries=3, overwrite=False): # Initial upload success = False tries = retries file_size = os.path.getsize(in_path) # Open the file once for streaming uploades with open(in_path, 'rb') as in_file_handle: while not success and tries > 0: tries -= 1 try: resource.upload(in_file_handle, location, overwrite=overwrite) success = True except (xnat.exceptions.XNATError, RequestException) as exception: fastr.log.warning('Encountered XNAT error during upload: {}'.format(exception)) if tries > 0: fastr.log.warning('Retrying {} times'.format(tries)) # Something went wrong, now forcefully try again max_retries = retries # Try multiple times to upload and try to avoid XNAT hiccups etc resource.clearcache() resource.files.clearcache() while location not in resource.files and retries > 0: resource.clearcache() resource.files.clearcache() retries -= 1 try: resource.upload(in_file_handle, location, overwrite=True) except xnat.exceptions.XNATError: # Allow exceptions to be raised again, just wait 10 seconds per try and retry delay = 10 * (max_retries - retries) fastr.log.warning('Got exception during upload, sleep {} seconds and retry'.format( delay )) time.sleep(delay) # Check if upload is successful resource.clearcache() resource.files.clearcache() if location not in resource.files: raise xnat.exceptions.XNATUploadError("Problem with uploading to XNAT " "(file not found, persisted after retries)") xnat_size = int(resource.files[location].size) if xnat_size != file_size: raise xnat.exceptions.XNATUploadError( "Problem with uploading to XNAT (file size differs uploaded {}, expected {})".format( xnat_size, file_size ) ) else:'It appears the file is uploaded to {} with a file size of {}'.format( resource.files[location].fulluri, xnat_size ))
def _find_objects(self, url, create=False, use_regex=False):'Locating {}'.format(url)) # Parse url parsed_url = urllib.parse.urlparse(url) path = parsed_url.path query = urllib.parse.parse_qs(parsed_url.query) if not path.startswith('/data/archive'): raise ValueError('Resources to be located should have a path starting with /data/archive') # Create a search uri location = self._path_to_dict(path) if 'resources' not in location: raise ValueError('All files should be located inside a resource, did not' ' find resources level in {}'.format(location)) # Sort xsi type directives neatly types = { 'resources': 'xnat:resourceCatalog' } for key in location.keys(): option1 = (key.rstrip('s') + '_type') option2 = (key + '_type') if option1 in query: types[key] = query[option1][0] if option2 in query: types[key] = query[option2][0] items = None # Parse location part by part for object_type, object_key in location.items(): # We don't want to go into files, those are put but not created # and they get via the resources if object_type == 'files': break'Locating {} / {} in {}'.format(object_type, object_key, items)) new_items = self._resolve_url_part(object_type, object_key, use_regex=use_regex, parents=items) if len(new_items) == 0: if not create: raise ValueError('Could not find data parent_object at {} (No values at level {})'.format(url, object_type)) elif items is not None and len(items) == 1: fastr.log.debug('Items: {}'.format(items)) parent_object = items[0] # Get the required xsitype if object_type in types: xsi_type = types[object_type] else: raise ValueError('Could not find the correct xsi:type for {} (available hints: {})'.format(object_type, types)) if '*' in object_key or '?' in object_key or '[' in object_key or ']' in object_key: raise ValueError('Illegal characters found in name of object_key' ' to create! (characters ?*[] or illegal!), found: {}'.format(object_key))'Creating new object under {} with type {}'.format(parent_object.uri, xsi_type)) # Create the object with the correct secondary lookup cls = self.xnat.XNAT_CLASS_LOOKUP[xsi_type] kwargs = {cls.SECONDARY_LOOKUP_FIELD: object_key} try: cls(parent=parent_object, **kwargs) except xnat.exceptions.XNATResponseError: fastr.log.warning(('Got a response error when creating the object {} (parent {}),' ' continuing to check if creating was in a race' ' condition and another processed created it').format( object_key, parent_object, )) new_items = self._resolve_url_part(object_type, object_key, use_regex=use_regex, parents=items) if len(new_items) != 1: raise ValueError('There appears to be a problem creating the object_key!') else: raise ValueError('To create an object, the path should point to a unique parent' ' object! Found {} matching items: {}'.format(len(items), items)) # Accept the new items for the new level scan items = new_items return items def _resolve_url_part(self, level, query=None, use_regex=False, parents=None): """ Get all matching projects :param dict query: the query to find projects to match for :return: """ # If there are no parents, work directly on the session if parents is None: parents = [self.xnat] if query is None: query = '.*' if use_regex else '*''Find {}: {} (parents: {})'.format(level, query, parents)) # Get all objects objects = [] for parent in parents: extra_options = getattr(parent, level) if use_regex: objects.extend(x for x in extra_options.values() if re.match(query, getattr(x, extra_options.secondary_lookup_field)) or == query) elif all(x not in query for x in '*?[]'): if query in extra_options: objects.append(extra_options[query]) else: objects.extend(x for x in extra_options.values() if fnmatch.fnmatchcase(getattr(x, extra_options.secondary_lookup_field), query) or == query)'Found: {}'.format(objects)) return objects
[docs] def expand_url(self, url): # Check if there is a wildcard in the URL: parsed_url = urllib.parse.urlparse(url) if parsed_url.path == '/search': # Parse the query query = urllib.parse.parse_qs(parsed_url.query) # Check if all fields given are valid fieldnames valid_fields = ("projects", "subjects", "experiments", "scans", "resources", "id", "label", "insecure", "verify", "regex") valid_query = True for key in query.keys(): if key not in valid_fields: fastr.log.error('Using invalid query field {} options are {}!'.format(key, valid_fields)) valid_query = False if not valid_query: raise ValueError('The query was malformed, see the error log for details.') id_field = query.get('id', ['experiment'])[0] id_use_label = query.get('label', ['0'])[0].lower() in ['1', 'true'] use_regex = query.get('regex', ['0'])[0].lower() in ['1', 'true'] insecure = query.get('insecure', ['0'])[0] in ['true', '1'] verify = query.get('verify', ['1'])[0] in ['true', '1'] # Make sure we are connect to the correct server self.connect(parsed_url.netloc, insecure=insecure, verify=verify) if id_field not in ['project', 'subject', 'experiment', 'scan', 'resource']: raise exceptions.FastrValueError('Requested id field ({}) is not a valid option!'.format(id_field)) # Create the url version for the search default = ['.*'] if use_regex else ['*'] search_path = '/data/archive/projects/{p}/subjects/{s}/experiments/{e}/scans/{sc}/resources/{r}'.format( p=query.get('projects', default)[0], s=query.get('subjects', default)[0], e=query.get('experiments', default)[0], sc=query.get('scans', default)[0], r=query.get('resources', default)[0] ) # Find all matching resources resources = self._find_objects(search_path, use_regex=use_regex) # Format the new expanded urls urls = [] for resource in resources: match = re.match(r'/data/experiments/(?P<experiment>[a-zA-Z0-9_\-]+)/scans/(?P<scan>[a-zA-Z0-9_\-]+)/resources/(?P<resource>[a-zA-Z0-9_\-]+)', resource.uri) experiment = self.xnat.experiments['experiment')] project = self.xnat.projects[experiment.project] subject = self.xnat.subjects[experiment.subject_id] scan = experiment.scans['scan')] # TODO: Just use resource.fulluri + '/files/filename' ? newpath = '/data/archive/projects/{}/subjects/{}/experiments/{}/scans/{}/resources/{}/files/{}'.format(,,,,, query.get('files', [''])[0] ) newurl = urllib.parse.urlunparse(('xnat', parsed_url.netloc, newpath, parsed_url.params, '', '')) # Determine the ID of the sample if id_field == 'resource': id_obj = resource elif id_field == 'scan': id_obj = scan elif id_field == 'experiment': id_obj = experiment elif id_field == 'subject': id_obj = subject else: # Must be project id_obj = project if id_use_label: id_ = id_obj.label else: id_ = urls.append((id_, newurl)) return tuple(urls) else: return url