Long working directory names

[Fred Loney]

I have a node that simply creates a destination directory name. The workflow fails on this node because the NiPy working directory is too long (see below). Is there a way to nudge NiPy to generate shorter working directories? A SHA-1 hash temp working directory name would be nice.

Thanks,

Fred

File: /Users/loneyf/workspace/qipipe/test/results/pipelines/qipipeline/crash-20130319-191209-loneyf-ctp_dir.a076.npz

Node: qipipeline.ctp_dir.a076

Working directory: /var/folders/tt/cws2x3ms2j13xwdyrmyf5shr0000gn/T/tmp7pSqDN/qipipeline/_dcm_files_..Users..loneyf..workspace..qipipe..test..fixtures..staging..group_dicom..sarcoma..Subj_2..S2V1..dce_concat..110909DCE_1_0003...Users..loneyf..workspace..qipipe..test..fixtures..staging..group_dicom..sarcoma..Subj_2..S2V1..dce_concat..110909DCE_1_0004_series_10_session_Sarcoma01_Session01_subject_Sarcoma01/ctp_dir

Node inputs:

dest = /Users/loneyf/workspace/qipipe/test/results/pipelines/qipipeline/sarcoma

function_str = S'def ctp_series_directory(self, dest, subject, session, series):\n    """\n    @return: the dest/subject/session/series directory path\n    """\n    import os\n    return os.path.join(dest, subject, session, series)\n'

.

ignore_exception = False

series = 10

session = Sarcoma01_Session01

subject = Sarcoma01

Traceback: 

Traceback (most recent call last):

  File "/usr/local/src/nipype/nipype/pipeline/plugins/linear.py", line 37, in run

    node.run(updatehash=updatehash)

  File "/usr/local/src/nipype/nipype/pipeline/engine.py", line 1121, in run

    outdir = make_output_dir(outdir)

  File "/usr/local/src/nipype/nipype/pipeline/utils.py", line 610, in make_output_dir

    os.makedirs(outdir)

  File "/usr/local/Cellar/python/2.7.3/lib/python2.7/os.py", line 150, in makedirs

    makedirs(head, mode)

  File "/usr/local/Cellar/python/2.7.3/lib/python2.7/os.py", line 157, in makedirs

    mkdir(name, mode)

OSError: [Errno 63] File name too long: '/var/folders/tt/cws2x3ms2j13xwdyrmyf5shr0000gn/T/tmp7pSqDN/qipipeline/_dcm_files_..Users..loneyf..workspace..qipipe..test..fixtures..staging..group_dicom..sarcoma..Subj_2..S2V1..dce_concat..110909DCE_1_0003...Users..loneyf..workspace..qipipe..test..fixtures..staging..group_dicom..sarcoma..Subj_2..S2V1..dce_concat..110909DCE_1_0004_series_10_session_Sarcoma01_Session01_subject_Sarcoma01'

[Fred Loney]

I submitted the following pull request that fixes the problem:

SHA-1 parameterization working directory name

Fred

[Juliane]

I have the same problem. Is this solution included in the newest development version?

[Chris Filo Gorgolewski]

Still working on it (see https://github.com/nipy/nipype/pull/535) will be there soon!

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