Use default base_dir.

ohsu-qin · Jun 14, 2017 · 18a3375 · 18a3375
1 parent 9883e20
commit 18a3375
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Showing 4 changed files with 12 additions and 26 deletions.
diff --git a/qipipe/pipeline/modeling.py b/qipipe/pipeline/modeling.py
@@ -308,7 +308,7 @@ def _create_workflow(self, **opts):
         self.logger.debug("Building the modeling workflow...")
 
         # The supervisory workflow.
-        mdl_wf = pe.Workflow(name='modeling', base_dir=self.base_dir)
+        workflow = pe.Workflow(name='modeling', base_dir=self.base_dir)
 
         # The default modeling technique is the OHSU proprietary modeling
         # workflow.
@@ -455,7 +455,8 @@ def _create_airc_workflow(self, **opts):
         :param opts: the PK modeling parameters
         :return: the Nipype Workflow
         """
-        workflow = pe.Workflow(name='airc', base_dir=self.base_dir)
+        base_dir = "%s/%s" % (self.base_dir, 'airc')
+        workflow = pe.Workflow(name='airc', base_dir=base_dir)
 
         # The modeling profile configuration sections.
         self.profile_sections = OHSU_CONF_SECTIONS
@@ -634,7 +635,8 @@ def _create_mock_workflow(self, **opts):
         :param opts: the PK modeling parameters
         :return: the Nipype Workflow
         """
-        workflow = pe.Workflow(name='mock', base_dir=self.base_dir)
+        base_dir = "%s/%s" % (self.base_dir, 'mock')
+        workflow = pe.Workflow(name='mock', base_dir=base_dir)
 
         # The modeling profile configuration sections.
         self.profile_sections = []

diff --git a/qipipe/pipeline/registration.py b/qipipe/pipeline/registration.py
@@ -259,7 +259,7 @@ def _create_execution_workflow(self, reference, dest, recursive=False):
 
         # The execution workflow.
         exec_wf = pe.Workflow(
-            name='registration', base_dir=self.workflow.base_dir
+            name='registration', base_dir=self.base_dir
         )
 
         # The registration workflow input.
@@ -386,17 +386,15 @@ def _create_realignment_workflow(self, **opts):
         - Upload the realign outputs to XNAT
 
         :param opts: the following workflow options:
-        :keyword base_dir: the workflow directory
-            (default a new temp directory)
         :keyword initialize: flag indicating whether to create an
             initial affine transform (ANTs only, default false)
         :return: the Workflow object
         """
         self.logger.debug('Creating the registration realignment workflow...')
 
         # The workflow.
-        base_dir = opts.get('base_dir', tempfile.mkdtemp(prefix='qipipe_'))
-        realign_wf = pe.Workflow(name=self.technique, base_dir=self.base_dir)
+        base_dir = "%s/%s" % (self.base_dir, self.technique)
+        realign_wf = pe.Workflow(name=self.technique, base_dir=base_dir)
 
         # The workflow input.
         in_fields = ['subject', 'session', 'scan', 'in_file',

diff --git a/qipipe/pipeline/staging.py b/qipipe/pipeline/staging.py
@@ -170,7 +170,7 @@ def _create_workflow(self):
         self.logger.debug('Creating the scan staging workflow...')
 
         # The Nipype workflow object.
-        workflow = pe.Workflow(name='stage_scan')
+        workflow = pe.Workflow(name='stage_scan', base_dir=self.base_dir)
 
         # The workflow input.
         hierarchy_fields = ['subject', 'session', 'scan']
@@ -190,14 +190,12 @@ def _create_workflow(self):
 
         # The volume staging node wraps the stage_volume function.
         stg_inputs = (
-            in_fields + iter_fields + ['collection', 'base_dir', 'opts']
+            in_fields + iter_fields + ['collection', 'opts']
         )
         stg_xfc = Function(input_names=stg_inputs, output_names=['out_dir'],
                            function=stage_volume)
         stg_node = pe.Node(stg_xfc, name='stage')
         child_opts = self._child_options()
-        base_dir = child_opts.pop('base_dir')
-        stg_node.inputs.base_dir = base_dir
         stg_node.inputs.opts = child_opts
         for fld in in_fields:
             workflow.connect(input_spec, fld, stg_node, fld)
@@ -386,7 +384,8 @@ def _create_workflow(self):
         self.logger.debug('Creating the DICOM processing workflow...')
 
         # The Nipype workflow object.
-        workflow = pe.Workflow(name='staging', base_dir=self.base_dir)
+        base_dir = "%s/%s" % (self.base_dir, 'stage_volume')
+        workflow = pe.Workflow(name='stage_volume', base_dir=base_dir)
 
         # The workflow input.
         in_fields = ['collection', 'subject', 'session', 'scan',

diff --git a/qipipe/pipeline/workflow_base.py b/qipipe/pipeline/workflow_base.py
@@ -183,27 +183,14 @@ def _child_options(self, name=None):
         """
         Collects the following options for creating a child workflow:
         * project
-        * base_dir
         * config_dir
         * dry_run
         * distributable
 
-        If the *name* option is set, then the child *base_dir* is
-        the subdirectory *base_dir*\ /\ *name*, where *base_dir*
-        is this parent workflow's *base_dir*. Otherwise the child
-        *base_dir* is this parent workflow's *base_dir*.
-
-        :param name: the optional child workflow name
         :return: the options sufficient to create a child workflow
         """
-        if name:
-            base_dir = "%s/%s" % (self.base_dir, name)
-        else:
-            base_dir = self.base_dir
-
         return dict(
             project=self.project,
-            base_dir=base_dir,
             config_dir=self.config_dir,
             dry_run=self.dry_run,
             distributable=self.is_distributable