Bioinformatics.org
[Regeneron]
Not logged in
  • Log in
  • Bioinformatics.org
    Membership (41338+) Group hosting [?] Wiki
    Franklin Award
    Sponsorships

    Careers
    About bioinformatics
    Bioinformatics training
    Bioinformatics jobs

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

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

    Forums
    News & Commentary
  • Submit
  • Archives
  • Subscribe

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

    Submit | Open tickets | Closed tickets

    [ Ticket #1150 ] newuser inconsistency
    Date:
    08/19/11 00:44
    Submitted by:
    umhameld
    Assigned to:
    umhameld
    Category:
    Winbirch
    Priority:
    1
    Ticket group:
    Getbirch
    Resolution:
    Not Resolved
    Summary:
    newuser inconsistency
    Original submission:
    Steps to reproduce:
    Confirmed: install on my user account on albacore virtual machine. Untested for other users, but this has come up in an issue in the past (it is a clear regression, indicating more that a cohesive method is needed). It has in practice not been an issue on any other system, but it may be an issue on end-user systems if I am noticing it. This may or may not be in same way because of the virtual machine, as it has never happened on actual hardware.
    Testing required on other systems, including actual hardware.

    Issue:
    newuser is having issue detecting the home directory on all systems, but appears to work on most (only one account in the virtual machine has this issue; it baffles me as to why).

    Reason:
    newuser puts the scripts in the windows homedir instead of the cygwin homedir; the wrong environment. This is because of a namespace collision using global variables.

    Solution:
    Isolate the correct namespace.

    Implementation:
    Options:
    1. Infer it based on the current user's name - not safe on all systems
    2. Use getbirch to manually write to the cygwin rc files, deprecating the newuser script and integrating it as a python module
    3. Use a birch shell to gain control of our own namespaces - this solution could be applied to all sytems. The implementation would be simple: a client server architecture with a scrolling text pane sending the output, and a text box taking input (less than 100 lines of code for the java GUI frontend). The code used by getbirch's console could serve as a framework. This would be a good time to experiment with this idea, and transfer over the jython libraries to merge them with with Graham's python scripts.
    Please log in to add comments and receive followups via email.
    No followups have been posted
    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
    priority 8 03/16/15 17:56 B_Fristensky
    status_id Pending 08/19/11 00:44 umhameld
    priority 5 08/19/11 00:44 umhameld
    assigned_to unset 08/19/11 00:44 umhameld
    resolution_id Unset 08/19/11 00:44 umhameld

     

    Copyright © 2019 · Scilico, LLC