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  • BIRCH: Comprehensive bioinfo. system - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1163 ] bioLegato - Long filenames in file chooser
    Date:
    11/29/11 12:17
    Submitted by:
    B_Fristensky
    Assigned to:
    Alvare
    Category:
    bioLegato
    Priority:
    4
    Ticket group:
    Bug
    Resolution:
    Not Resolved
    Summary:
    bioLegato - Long filenames in file chooser
    Original submission:
    When reading in a User-defined tree with DNAML,
    files with long names apparently give a File not found error
    in the terminal window, and blank output windows pop up.
    This seems to be caused by an error in creating the tmp
    file name. If the file name is something like LONGFILENAME,
    then the tmp file will be something like

    bio4857347LONGFILENAME88774.tmp

    (The above is from memory - I have to check exactly
    what it looks like.)

    For now the workaround is to use shorter names for your treefiles.

    This needs a bit more experimentation to find out what
    will break the file chooser, and what
    Please log in to add comments and receive followups via email.
    Followups
    Comment Date By
    Graham discovered that because of the way bioLegato0.7.7a parses file names, any filename containing the string 'in1' would have a random number added to the name, resulting in the file not found error.

    This problem only affects bioLegato 0.7.7a, and not later versions, which use the PCD parsing scheme.

    A fix would be a lot of work right now, and since the PCD version will be used in the next release, we will mark this as a "documented bug". It will not be fixed.
    03/31/12 09:45 B_Fristensky
    Sample files illustrating the problem can be found in
    /home/psgendb/BIRCHDEV/temp/as3-biolegato-error.

    Test: bldna
    File --> Open gamglobin1-350.fsa
    Phylogeny --> DNAML
    Evaluate User-defined Tree: gamglobin1_350_dnapars_boot.treefile
    Output windows are empty

    Rerun using
    Evaluate User-defined Tree: pars.treefile

    This is the same file with a different name.
    Now, dnaml runns correctly.


    Probably best to worry about this after we have made the transition to PCD.
    12/28/11 16:00 B_Fristensky
    No results for "Dependent on ticket"
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    No other tickets are dependent on this ticket
    Ticket change history
    Field Old value Date By
    status_id Open 03/31/12 09:45 B_Fristensky
    assigned_to unset 03/31/12 09:45 B_Fristensky
    close_date 12/31/69 19:00 03/31/12 09:45 B_Fristensky
    status_id Pending 11/29/11 12:17 B_Fristensky
    priority 5 11/29/11 12:17 B_Fristensky
    resolution_id Unset 11/29/11 12:17 B_Fristensky

     

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