fix: cleaned up file removal to pay attention to related files such as img/hdr/mat, BRIK/HEAD

Author: satra

CHANGES

@@ -48,6 +48,8 @@ Next release
 * FIX: FILMGLS compatibility with FSL 5.0.5
 * FIX: Freesurfer recon-all resume now avoids setting inputs
 
+* FIX: File removal from node respects file associations img/hdr/mat, BRIK/HEAD
+
 Release 0.8.0 (May 8, 2013)
 ===========================
 

doc/users/install.rst

@@ -127,6 +127,8 @@ SciPy_ 0.7 - 0.12
 
 Enthought_ Traits_ 4.0.0 - 4.3.0
 
+Dateutil 1.5 -
+
 .. note::
 
     Full distributions such as pythonxy_ or EPD_ provide the above packages,

nipype/pipeline/tests/test_utils.py

@@ -7,14 +7,12 @@
 from tempfile import mkdtemp
 from shutil import rmtree
 
-from ...testing import (assert_equal, assert_true,
-                            assert_false)
+from ...testing import (assert_equal, assert_true, assert_false)
 import nipype.pipeline.engine as pe
 import nipype.interfaces.base as nib
 import nipype.interfaces.utility as niu
 from ... import config
-from ..utils import merge_dict
-
+from ..utils import merge_dict, clean_working_directory
 
 def test_identitynode_removal():
 
@@ -46,6 +44,48 @@ def test_function(arg1, arg2, arg3):
     yield assert_equal, len(eg.nodes()), 8
 
 
+def test_clean_working_directory():
+    class OutputSpec(nib.TraitedSpec):
+        files = nib.traits.List(nib.File)
+        others = nib.File()
+    class InputSpec(nib.TraitedSpec):
+        infile = nib.File()
+    outputs = OutputSpec()
+    inputs = InputSpec()
+
+    wd = mkdtemp()
+    filenames = ['file.hdr', 'file.img', 'file.BRIK', 'file.HEAD',
+                 '_0x1234.json', 'foo.txt']
+    outfiles = []
+    for filename in filenames:
+        outfile = os.path.join(wd, filename)
+        with open(outfile, 'wt') as fp:
+            fp.writelines('dummy')
+        outfiles.append(outfile)
+    outputs.files = outfiles[:4:2]
+    outputs.others = outfiles[5]
+    inputs.infile = outfiles[-1]
+    needed_outputs = ['files']
+    config.set_default_config()
+    yield assert_true, os.path.exists(outfiles[5])
+    config.set_default_config()
+    config.set('execution', 'remove_unnecessary_outputs', False)
+    out = clean_working_directory(outputs, wd, inputs, needed_outputs,
+                                  deepcopy(config._sections))
+    yield assert_true, os.path.exists(outfiles[5])
+    yield assert_equal, out.others, outfiles[5]
+    config.set('execution', 'remove_unnecessary_outputs', True)
+    out = clean_working_directory(outputs, wd, inputs, needed_outputs,
+                                  deepcopy(config._sections))
+    yield assert_true, os.path.exists(outfiles[1])
+    yield assert_true, os.path.exists(outfiles[3])
+    yield assert_true, os.path.exists(outfiles[4])
+    yield assert_false, os.path.exists(outfiles[5])
+    yield assert_equal, out.others, nib.Undefined
+    yield assert_equal, len(out.files), 2
+    config.set_default_config()
+    rmtree(wd)
+
 def test_outputs_removal():
 
     def test_function(arg1):
@@ -140,19 +180,12 @@ def test_function(arg1):
         file1 = os.path.join(os.getcwd(), 'file1.txt')
         file2 = os.path.join(os.getcwd(), 'file2.txt')
         file3 = os.path.join(os.getcwd(), 'file3.txt')
-        fp = open(file1, 'wt')
-        fp.write('%d' % arg1)
-        fp.close()
-        fp = open(file2, 'wt')
-        fp.write('%d' % arg1)
-        fp.close()
-        fp = open(file3, 'wt')
-        fp.write('%d' % arg1)
-        fp.close()
+        file4 = os.path.join(os.getcwd(), 'subdir', 'file1.txt')
+        files = [file1, file2, file3, file4]
         os.mkdir("subdir")
-        fp = open("subdir/file1.txt", 'wt')
-        fp.write('%d' % arg1)
-        fp.close()
+        for filename in files:
+            with open(filename, 'wt') as fp:
+                fp.write('%d' % arg1)
         return file1, file2, os.path.join(os.getcwd(),"subdir")
 
     def test_function2(in_file, arg):
@@ -161,15 +194,10 @@ def test_function2(in_file, arg):
         file1 = os.path.join(os.getcwd(), 'file1.txt')
         file2 = os.path.join(os.getcwd(), 'file2.txt')
         file3 = os.path.join(os.getcwd(), 'file3.txt')
-        fp = open(file1, 'wt')
-        fp.write('%d' % arg + in_arg)
-        fp.close()
-        fp = open(file2, 'wt')
-        fp.write('%d' % arg + in_arg)
-        fp.close()
-        fp = open(file3, 'wt')
-        fp.write('%d' % arg + in_arg)
-        fp.close()
+        files = [file1, file2, file3]
+        for filename in files:
+            with open(filename, 'wt') as fp:
+                fp.write('%d' % arg + in_arg)
         return file1, file2, 1
 
     def test_function3(arg):

nipype/pipeline/utils.py

@@ -20,7 +20,7 @@
 import networkx as nx
 
 from ..utils.filemanip import (fname_presuffix, FileNotFoundError,
-                               filename_to_list)
+                               filename_to_list, get_related_files)
 from ..utils.misc import create_function_from_source, str2bool
 from ..interfaces.base import (CommandLine, isdefined, Undefined, Bunch,
                                InterfaceResult)
@@ -1006,6 +1006,10 @@ def clean_working_directory(outputs, cwd, inputs, needed_outputs, config,
         needed_dirs.extend(filename_to_list(dirs2keep))
     for extra in ['_nipype', '_report']:
         needed_dirs.extend(glob(os.path.join(cwd, extra)))
+    temp = []
+    for filename in needed_files:
+        temp.extend(get_related_files(filename))
+    needed_files = temp
     logger.debug('Needed files: %s' % (';'.join(needed_files)))
     logger.debug('Needed dirs: %s' % (';'.join(needed_dirs)))
     files2remove = []