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  • BIRCH: Comprehensive bioinfo. system - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1112 ] bioLegato fails to clean up temporary files
    02/18/11 17:53
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    bioLegato fails to clean up temporary files
    Original submission:
    There are numerous functions in various biolegato instances that fail to clean up temporary files. The worst culprit is FEATURES, but there are others. Obviously, a 2 step approach is needed:

    1. Identify these functions.
    2. Review the clean up functions. Are there some that might have been inadvertantly commented out?
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    Comment Date By
    This bug will be closed because the specified .item files have been fixed.

    It is likely to be a problem that will crop up, from time to time, because it is up to the programmer to make sure that each .item and script run by bioLegato cleans up after itself.
    03/13/11 19:18 B_Fristensky
    Fixed cleanup issues in the following item files:

    bldna - blrevcomp.item

    bldna - FASTADNA.item still leaves a bioxxxxx.tmp file. Oddly, FASTXY.item, with the same rm command, does not. This seems bizarre, and will require more work.
    02/22/11 18:04 B_Fristensky
    Fixed tcoffee.item in bldna and blprotein so that .aln and .fsa temporary files get cleaned up. 02/22/11 15:43 B_Fristensky
    The menu items for dialign-tx in bldna and blprotein failed to remove the .fsa and .dialign temporary files. This has been fixed.

    I will check whether the TCOFFEE .item files have a similar problem.
    02/21/11 18:23 B_Fristensky

    It is not clear to me what you are describing, but I think its a different problem than I am referring to. I am talking about places where either a biolegato .item, or the script it runs, fails to remove temporary files.

    I wonder if what you're describing is a different thing. It would be best to submit a separate bug with an example. Are you talking about files not being removed, say, with Getbirch?
    02/21/11 17:42 B_Fristensky
    features failed to remove files matching temp.$jobid.fea. This was added to the remove list, so this one is fixed.

    That seems to be the only problem related to the FEATURES program, but there is at least one more class of errors in which bioxxxxxxxxxxx.something files are not removed. That will require further investigation.
    02/21/11 17:39 B_Fristensky
    I am running into a similar problem with temporary files. I notice it varies from system to system, leading me to believe it related to metadata. I am already working python api to handle metadata, so we might be able to fix this in python. Luckily, jython works two ways, so it is possible for java to make calls to python libraries.

    How are files normally removed in Java? How does bioLegato do it? Is there an easy builtin? I looked into what birchconfig does to move files, and i've found that the python library works much more reliably. This might be as easy as just swapping out the java API call to a python API call in one spot by introducing python remove into the root namespace, overridding all subclassing functions. (ie, give a sub-attribute to object, something like this).

    @Graham, can you point me to some of the code, so that I can take a look at it?
    02/19/11 22:32 umhameld
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    Ticket change history
    Field Old value Date By
    status_id Open 03/13/11 19:18 B_Fristensky
    resolution_id Unset 03/13/11 19:18 B_Fristensky
    close_date 12/31/69 19:00 03/13/11 19:18 B_Fristensky
    priority 5 02/21/11 17:06 B_Fristensky
    status_id Pending 02/18/11 17:54 B_Fristensky
    assigned_to unset 02/18/11 17:54 B_Fristensky


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