Added the cachedir configuration for XNATSource and XNATSink

Author: Yannick Schwartz

nipype/interfaces/io.py

@@ -21,6 +21,7 @@
 import glob
 import os
 import shutil
+import hashlib
 from warnings import warn
 
 from enthought.traits.trait_errors import TraitError
@@ -493,9 +494,11 @@ class XNATSourceInputSpec(DynamicTraitedSpec): #InterfaceInputSpec):
  value=dict(outfiles=[]), usedefault=True,
  desc='Information to plug into template')
 
- xnat_server = traits.Str(mandatory=True, desc='XNAT server URL')
- xnat_user = traits.Str(mandatory=True, desc='XNAT user')
- xnat_pwd = traits.Password(mandatory=True, desc='XNAT password')
+ xnat_server = traits.Str(mandatory=True, requires=['xnat_user', 'xnat_pwd'], xor=['xnat_config'])
+ xnat_user = traits.Str()
+ xnat_pwd = traits.Password()
+ xnat_config = File(mandatory=True, xor=['xnat_server'])
+
  cache_dir = Directory(desc='Cache directory')
  cache_size = traits.Str(desc='Optional cache max size')
 
@@ -582,7 +585,13 @@ def _list_outputs(self):
  # infields are mandatory, however I could not figure out how to set 'mandatory' flag dynamically
  # hence manual check
 
- xnat = pyxnat.Interface(self.inputs.xnat_server,self.inputs.xnat_user, self.inputs.xnat_pwd)
+ cache_dir = self.cache_dir or tempfile.gettempdir()
+
+ if self.inputs.xnat_server:
+ xnat = pyxnat.Interface(self.inputs.xnat_server,self.inputs.xnat_user, self.inputs.xnat_pwd, cache_dir)
+ else:
+ xnat = pyxnat.Interface(self.inputs.xnat_config)
+
 # xnat.set_offline_mode()
 
  if self._infields:
@@ -646,17 +655,12 @@ def _list_outputs(self):
 
 class XNATSinkInputSpec(DynamicTraitedSpec):
 
-# base_directory = Directory( 
-# desc='Path to the base directory consisting of subject data.')
-# container = traits.Str(desc = 'Folder within basedirectory in which to store output')
-# parameterization = traits.Bool(True, usedefault=True,
-# desc='store output in parameterized structure')
-# strip_dir = Directory(desc='path to strip out of filename')
  _outputs = traits.Dict(traits.Str, value={}, usedefault=True)
 
- xnat_server = traits.Str(mandatory=True)
- xnat_user = traits.Str(mandatory=True)
- xnat_pwd = traits.Password(mandatory=True)
+ xnat_server = traits.Str(mandatory=True, requires=['xnat_user', 'xnat_pwd'], xor=['xnat_config'])
+ xnat_user = traits.Str()
+ xnat_pwd = traits.Password()
+ xnat_config = File(mandatory=True, xor=['xnat_server'])
  cache_dir = Directory(desc='')
  cache_size = traits.Str()
 
@@ -669,6 +673,7 @@ def __setattr__(self, key, value):
  self._outputs[key] = value
  else:
  super(XNATSinkInputSpec, self).__setattr__(key, value)
+
 
 class XNATSink(IOBase):
  """ Generic datasink module that takes a directory containing a
@@ -681,12 +686,19 @@ def _list_outputs(self):
  """Execute this module.
  """
 
- xnat = pyxnat.Interface(self.inputs.xnat_server,self.inputs.xnat_user, self.inputs.xnat_pwd)
+ cache_dir = self.cache_dir or tempfile.gettempdir()
+
+ if self.inputs.xnat_server:
+ xnat = pyxnat.Interface(self.inputs.xnat_server,self.inputs.xnat_user, self.inputs.xnat_pwd, cache_dir)
+ else:
+ xnat = pyxnat.Interface(self.inputs.xnat_config)
 
  uri_template_args = {'project_id':self.inputs.project_id,
  'subject_id':self.inputs.subject_id,
- 'experiment_id':str(hash(self.inputs.subject_id)) + \
- '_' + self.inputs.experiment_id,
+ 'experiment_id': '%s_%s' % \
+ (hashlib.md5(self.inputs.subject_id).hexdigest(),
+ self.inputs.experiment_id
+ )
  }
 
  for key,files in self.inputs._outputs.items():
@@ -714,18 +726,19 @@ def write_file_to_XNAT(xnat, name, key, uri_template_args):
  if str(self.inputs.subject_id) not in val:
  recon_label.extend([key, val])
 
+ uri_template_args['recon_label'] = \
+ hashlib.md5(uri_template_args['experiment_id']).hexdigest()
+
  if recon_label:
- uri_template_args['recon_label'] = str(hash(uri_template_args['experiment_id'])) + \
- '_' + '_'.join(recon_label)
- else:
- uri_template_args['recon_label'] = str(hash(uri_template_args['experiment_id']))
+ uri_template_args['recon_label'] += '_'.join(recon_label)
 
- uri_template_args['resource_label'] = str(hash(uri_template_args['recon_label'])) + \
- '_' + key.split('.')[0]
+ uri_template_args['resource_label'] = '%s_%s' % \
+ (hashlib.md5(uri_template_args['recon_label']).hexdigest(),
+ key.split('.')[0]
+ )
 
  uri_template_args['file_name'] = os.path.split(os.path.abspath(name))[1]
 
-
  uri_template = ('/project/%(project_id)s/subject/%(subject_id)s'
  '/experiment/%(experiment_id)s/reconstruction/%(recon_label)s'
  '/out/resource/%(resource_label)s/file/%(file_name)s')