BUG: Need to propogate FS failures from sub-scripts.

matsuij · Jan 24, 2013 · 87f2953 · 87f2953
1 parent 794e9f7
commit 87f2953
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Showing 5 changed files with 56 additions and 75 deletions.
diff --git a/AutoWorkup/ShortWorkupT1T2.py b/AutoWorkup/ShortWorkupT1T2.py
@@ -290,6 +290,7 @@ def AccumulateLikeTissuePosteriors(posteriorImages):
 
 
 def ShortWorkupT1T2(subjectid, mountPrefix, ExperimentBaseDirectoryCache, ExperimentBaseDirectoryResults, ExperimentDatabase, atlas_fname_wpath, BCD_model_path,
+                    GLOBAL_DATA_SINK_REWRITE,
                     InterpolationMode="Linear", Mode=10, DwiList=[], WORKFLOW_COMPONENTS=[], CLUSTER_QUEUE='', CLUSTER_QUEUE_LONG=''):
     """
     Run autoworkup on all subjects data defined in the ExperimentDatabase

diff --git a/AutoWorkup/WorkupT1T2.py b/AutoWorkup/WorkupT1T2.py
@@ -300,7 +300,7 @@ def MakeNewAtlasTemplate(t1_image, deformed_list,
 ###########################################################################
 ###########################################################################
 def WorkupT1T2(subjectid, mountPrefix, ExperimentBaseDirectoryCache, ExperimentBaseDirectoryResults, ExperimentDatabase, atlas_fname_wpath, BCD_model_path,
-               InterpolationMode="Linear", Mode=10, DwiList=[], WORKFLOW_COMPONENTS=[], CLUSTER_QUEUE='', CLUSTER_QUEUE_LONG='', SGE_JOB_SCRIPT='#!/bin/bash'):
+               GLOBAL_DATA_SINK_REWRITE, InterpolationMode="Linear", Mode=10, DwiList=[], WORKFLOW_COMPONENTS=[], CLUSTER_QUEUE='', CLUSTER_QUEUE_LONG='', SGE_JOB_SCRIPT='#!/bin/bash'):
     """
     Run autoworkup on all subjects data defined in the ExperimentDatabase
 
@@ -1079,9 +1079,10 @@ def WorkupT1T2(subjectid, mountPrefix, ExperimentBaseDirectoryCache, ExperimentB
                         FS_DS[sessionid].inputs.regexp_substitutions = [
                             ('/_uid_(?P<myuid>[^/]*)', r'/\g<myuid>')
                             ]
-                        baw200.connect(myLocalFSWF[sessionid], 'outputspec.FreeSurferOutputDirectory', FS_DS[sessionid], 'FREESURFER_SUBJ.@FreeSurferOutputDirectory')
+                        baw200.connect(myLocalFSWF[sessionid], 'outputspec.FreeSurferOutputDirectory', FS_DS[sessionid], 'FREESURFER52_SUBJECTS.@FreeSurferOutputDirectory')
                     ### Now define where the final organized outputs should go.
-                    FSPREP_DataSink[sessionid] = pe.Node(nio.DataSink(), name="FREESURFER_PREP_" + str(subjectid) + "_" + str(sessionid))
+                    FSPREP_DataSink[sessionid] = pe.Node(nio.DataSink(), name="FREESURFER_PREP_DS_" + str(subjectid) + "_" + str(sessionid))
+                    FSPREP_DataSink[sessionid].overwrite = GLOBAL_DATA_SINK_REWRITE
                     FSPREP_DataSink[sessionid].inputs.base_directory = ExperimentBaseDirectoryResults
                     FREESURFER_PREP_PATTERNS = GenerateOutputPattern(projectid, subjectid, sessionid, 'FREESURFER_PREP')
                     FSPREP_DataSink[sessionid].inputs.regexp_substitutions = FREESURFER_PREP_PATTERNS
@@ -1095,7 +1096,8 @@ def WorkupT1T2(subjectid, mountPrefix, ExperimentBaseDirectoryCache, ExperimentB
                     baw200.connect(myLocalFSWF[sessionid], 'outputspec.cnr_optimal_image', FSPREP_DataSink[sessionid], 'FREESURFER_PREP.@cnr_optimal_image')
 
                 #} end of "for sessionid in allSessions:"
-                #{  Do longitudinal
+                #{  Do template building
+                """
                 ##HACK : Move later
                 FS_TEMPLATE_oneSubjWorkflow = CreateFreeSurferSubjectTemplate(projectid,
                                                                                subjectid,
@@ -1115,12 +1117,12 @@ def WorkupT1T2(subjectid, mountPrefix, ExperimentBaseDirectoryCache, ExperimentB
                 baw200.connect(FreeSurferSessionID_MergeNode[subjectid],'out', FS_TEMPLATE_oneSubjWorkflow, 'inputspec.FreeSurferSession_IDs')
 
                 FSTEMP_DataSink[subjectid] = pe.Node(nio.DataSink(), name='FREESURFER_TEMP_' + str(subjectid))
+                FSTEMP_DataSink[subjectid].overwrite = GLOBAL_DATA_SINK_REWRITE
                 FREESURFER_TEMP_PATTERNS = GenerateOutputPattern(projectid, subjectid, 'FREESURFER_TEMP', '')
                 FSTEMP_DataSink[subjectid].inputs.regexp_substitutions = FREESURFER_TEMP_PATTERNS
-                FSTEMP_DataSink[subjectid].overwrite = GLOBAL_DATA_SINK_REWRITE
-                baw200.connect(FS_TEMPLATE_oneSubjWorkflow, 'outputspec.FreeSurferTemplateDir', FSTEMP_DataSink[subjectid], 'FREESURFER_SUBJ.@FreeSurferTemplateDir')
+                baw200.connect(FS_TEMPLATE_oneSubjWorkflow, 'outputspec.FreeSurferTemplateDir', FSTEMP_DataSink[subjectid], 'FREESURFER52_SUBJECTS.@FreeSurferTemplateDir')
                 #}
-                #{
+                #{ Do longitudinal analysis
                 FSLONG_DataSink = dict()
                 FS_LONG_oneSubjWorkflow = dict()
                 for sessionid in allSessions:
@@ -1136,14 +1138,15 @@ def WorkupT1T2(subjectid, mountPrefix, ExperimentBaseDirectoryCache, ExperimentB
                     baw200.connect(FS_TEMPLATE_oneSubjWorkflow, 'outputspec.FreeSurferTemplateDir', FS_LONG_oneSubjWorkflow[sessionid], 'inputspec.SingleSubject_ID')
                     # baw200.connect(FREESURFER_SUBJ_ID, 'subjectTemplate_id', FS_LONG_oneSubjWorkflow[sessionid], 'inputspec.SingleSubject_ID')
                     FSLONG_DataSink[sessionid] = pe.Node(nio.DataSink(), name='_'.join(['FREESURFER_LONG', str(subjectid), str(sessionid)]))
+                    FSLONG_DataSink[sessionid].overwrite = GLOBAL_DATA_SINK_REWRITE
                     FSLONG_DataSink[sessionid].inputs.base_directory = ExperimentBaseDirectoryResults
                     FREESURFER_LONG_PATTERNS = GenerateOutputPattern(projectid, subjectid, sessionid, 'FREESURFER_LONG')
                     FSLONG_DataSink[sessionid].inputs.regexp_substitutions = FREESURFER_LONG_PATTERNS
-                    FSLONG_DataSink[sessionid].overwrite = GLOBAL_DATA_SINK_REWRITE
 
-                    baw200.connect(FS_LONG_oneSubjWorkflow[sessionid], 'outputspec.FreeSurferLongitudinalDir', FSLONG_DataSink[sessionid], 'FREESURFER_SUBJ.@longitudinalDirs')
+                    baw200.connect(FS_LONG_oneSubjWorkflow[sessionid], 'outputspec.FreeSurferLongitudinalDir', FSLONG_DataSink[sessionid], 'FREESURFER52_SUBJECTS.@longitudinalDirs')
 
                 #} end of "for sessionid in allSessions:"
+                """
             else:
                 print "Skipping freesurfer"
     return baw200
diff --git a/AutoWorkup/WorkupT1T2FreeSurfer_custom.py b/AutoWorkup/WorkupT1T2FreeSurfer_custom.py
@@ -68,7 +68,7 @@ def CreateFreeSurferWorkflow_custom(projectid, subjectid, sessionid, WFname, CLU
     freesurfer_sge_options_dictionary = {'qsub_args': '-S /bin/bash -pe smp1 1 -l h_vmem=18G,mem_free=8G -o /dev/null -e /dev/null ' + CLUSTER_QUEUE, 'overwrite': True}
     if RunAllFSComponents == True:
         print("""Run FreeSurfer ReconAll at""")
-        fs_reconall = pe.Node(interface=fswrap.FSScript(), name="FS52_custom")
+        fs_reconall = pe.Node(interface=fswrap.FSScript(), name="FS52_cross_"+str(sessionid))
         fs_reconall.plugin_args = freesurfer_sge_options_dictionary
         fs_reconall.inputs.subcommand = 'autorecon'
         # fs_reconall.inputs.directive = 'all'
@@ -108,7 +108,7 @@ def CreateFreeSurferSubjectTemplate(projectid, subjectid, session_ids, WFname, C
     os.environ['SUBJECTS_DIR'] = constructed_FS_SUBJECTS_DIR
     inputsSpec.inputs.subjects_dir = constructed_FS_SUBJECTS_DIR  # HACK
     print("""Run FreeSurfer Within Subject Template at""")
-    fs_template = pe.Node(interface=fswrap.FSScript(), name="FS55_template_build_"+str(subjectid))
+    fs_template = pe.Node(interface=fswrap.FSScript(), name="FS52_base_"+str(subjectid))
     fs_template.plugin_args = freesurfer_sge_options_dictionary
     fs_template.inputs.session_ids = session_ids
     fs_template.inputs.subcommand = 'template'
@@ -133,7 +133,7 @@ def CreateFreeSurferLongitudinalWorkflow(projectid, sessionid, subjectid, WFname
     os.environ['SUBJECTS_DIR'] = constructed_FS_SUBJECTS_DIR
     inputsSpec.inputs.subjects_dir = constructed_FS_SUBJECTS_DIR  # HACK
 
-    fs_longitudinal = pe.Node(interface=fswrap.FSScript(), name="FS55_longitudinal_"+str(sessionid))
+    fs_longitudinal = pe.Node(interface=fswrap.FSScript(), name="FS52_long_"+str(sessionid))
     fs_longitudinal.plugin_args = freesurfer_sge_options_dictionary
     fs_longitudinal.inputs.subcommand = 'longitudinal'
     fs_longitudinal.inputs.session_id = sessionid

diff --git a/AutoWorkup/baw_exp.py b/AutoWorkup/baw_exp.py
@@ -15,8 +15,6 @@
 import sys
 
 ##############################################################################
-GLOBAL_DATA_SINK_REWRITE = True
-
 
 def get_global_sge_script(pythonPathsList, binPathsList, customEnvironment={}):
     """This is a wrapper script for running commands on an SGE cluster
@@ -96,17 +94,18 @@ def setGlobalDatasinkRewrite(cli, cfg):
     :param cfg: configuration file value
     :type cfg: bool
 
-    Sets the global variable `GLOBAL_DATA_SINK_REWRITE` constant flag used in :mod:`WorkupT1T2()`
+    Sets the variable `GLOBAL_DATA_SINK_REWRITE` constant flag used in :mod:`WorkupT1T2()`
 
     """
     assert isinstance(cli, bool) and isinstance(cfg, bool), \
       "Inputs are not boolean: {0}, {1}".format(cli, cfg)
-    global GLOBAL_DATA_SINK_REWRITE
+    GLOBAL_DATA_SINK_REWRITE=False
     if cli or cfg:
         print "*** Ignoring datasinks for pipeline rewriting ***" # TODO: Use logging
         GLOBAL_DATA_SINK_REWRITE = False
     else:
         GLOBAL_DATA_SINK_REWRITE = True
+    return GLOBAL_DATA_SINK_REWRITE
 
 
 def main(argv=None):
@@ -140,8 +139,8 @@ def main(argv=None):
     expConfig.read(input_arguments.ExperimentConfig)
 
     # Pipeline-specific information
-    ignore_datasinks = expConfig.getboolean('PIPELINE', 'IGNORE_DATASINKS')
-    setGlobalDatasinkRewrite(input_arguments.ignore_datasinks, ignore_datasinks)
+    ignore_datasinks = expConfig.getboolean('PIPELINE', 'GLOBAL_DATA_SINK_REWRITE')
+    GLOBAL_DATA_SINK_REWRITE=setGlobalDatasinkRewrite(input_arguments.ignore_datasinks, ignore_datasinks)
 
     # Experiment specific information
     subject_data_file = expConfig.get('EXPERIMENT_DATA', 'SESSION_DB')
@@ -303,14 +302,18 @@ def main(argv=None):
                                                      ExperimentBaseDirectoryResults,
                                                      ExperimentDatabase,
                                                      CACHE_ATLASPATH,
-                                                     CACHE_BCDMODELPATH, WORKFLOW_COMPONENTS=WORKFLOW_COMPONENTS, CLUSTER_QUEUE=CLUSTER_QUEUE, CLUSTER_QUEUE_LONG=CLUSTER_QUEUE_LONG)
+                                                     CACHE_BCDMODELPATH,
+                                                     GLOBAL_DATA_SINK_REWRITE,
+                                                     WORKFLOW_COMPONENTS=WORKFLOW_COMPONENTS, CLUSTER_QUEUE=CLUSTER_QUEUE, CLUSTER_QUEUE_LONG=CLUSTER_QUEUE_LONG)
         else:
             baw200 = WorkupT1T2.WorkupT1T2(subjectid, mountPrefix,
                                            os.path.join(ExperimentBaseDirectoryCache, str(subjectid)),
                                            ExperimentBaseDirectoryResults,
                                            ExperimentDatabase,
                                            CACHE_ATLASPATH,
-                                           CACHE_BCDMODELPATH, WORKFLOW_COMPONENTS=WORKFLOW_COMPONENTS, CLUSTER_QUEUE=CLUSTER_QUEUE, CLUSTER_QUEUE_LONG=CLUSTER_QUEUE_LONG, SGE_JOB_SCRIPT=JOB_SCRIPT)
+                                           CACHE_BCDMODELPATH,
+                                           GLOBAL_DATA_SINK_REWRITE,
+                                           WORKFLOW_COMPONENTS=WORKFLOW_COMPONENTS, CLUSTER_QUEUE=CLUSTER_QUEUE, CLUSTER_QUEUE_LONG=CLUSTER_QUEUE_LONG, SGE_JOB_SCRIPT=JOB_SCRIPT)
         print "Start Processing"
 
         SGEFlavor = 'SGE'