[University of Birmingham]
Not logged in
  • Log in
    Membership (42900+) Group hosting [?] Wiki
    Franklin Award

    About bioinformatics
    Bioinformatics jobs

    All information groups
    Online databases Online analysis tools Online education tools More tools

    All software groups
    FTP repository
    SVN & CVS repositories [?]
    Mailing lists

    News & Commentary
  • Submit
  • Archives
  • Subscribe

  • Jobs Forum
    (Career Center)
  • Submit
  • Archives
  • Subscribe
  • BIRCH: Comprehensive bioinfo. system - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1197 ] temp files deleted before can open them
    11/30/14 12:24
    Submitted by:
    Assigned to:
    Ticket group:
    temp files deleted before can open them
    Original submission: is a wrapper for deciding file type by its extension and calling the right application to view the file.
    When called by BioLegato, the call to is almost always followed by a rm command to delete the temporary file. In many cases, the rm command seems to run before the application can read in the file, so we get a file not found error.

    One hack that works is to just put a sleep 5 command between the chooseviewer call and the rm call.

    We need to fix so that this problem can be solved in a more deterministic way.

    Right now, when runs commands using Popen,
    the p.wait() commands have been commented out. It might
    be best to try uncommenting them and see if that fixes the

    Please log in to add comments and receive followups via email.
    Comment Date By
    The solution was to make sleep for 2 seconds after calling the appropriate wrapper using Popen. This delay allows the wrapper to make a temporary copy of the file that it can then open. p.wait() wasn't the answer, because that means that the calling processes (eg. BioLegato, ACEDB) couldn't do anything until the wrapper and had terminated. This lets the wrapper run in the background, even if you terminat the calling program.
    03/06/15 18:58 B_Fristensky
    No results for "Dependent on ticket"
    No results for "Dependent on Task"
    No other tickets are dependent on this ticket
    Ticket change history
    Field Old value Date By
    status_id Open 03/06/15 18:58 B_Fristensky
    resolution_id Unset 03/06/15 18:58 B_Fristensky
    close_date 12/31/69 19:00 03/06/15 18:58 B_Fristensky
    status_id Pending 11/30/14 12:24 B_Fristensky
    priority 5 11/30/14 12:24 B_Fristensky
    assigned_to unset 11/30/14 12:24 B_Fristensky


    Copyright © 2021 Scilico, LLC · Privacy Policy