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  • BIRCH: Comprehensive bioinfo. system - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1134 ] $BIRCH terminates with a '/'
    Date:
    03/12/11 14:08
    Submitted by:
    B_Fristensky
    Assigned to:
    umhameld
    Category:
    Getbirch
    Priority:
    5
    Ticket group:
    Bug
    Resolution:
    Resolved
    Summary:
    $BIRCH terminates with a '/'
    Original submission:
    Looks like an old bug is back. I did several installs with getbirch-2fb3c32. On solaris-x86_64, osx-x86_64 and linux-intel the '/' character ends up as part of the $BIRCH environment variable.


    {merak:/usr/local/tmp/frist}echo $BIRCH
    /usr/local/tmp/frist/BIRCH/

    {canolaoil.plants.umanitoba.ca:/home/frist}echo $birch
    /home/frist/temp/BIRCH/


    {albacore.cs.umanitoba.ca:/Users/birch}echo $birch
    /Users/birch/BIRCH/
    Please log in to add comments and receive followups via email.
    Followups
    Comment Date By
    Fixed both issues, although I am wondering if the value in labace/wspec/passwd.wrm should not also be changed. I seem to remember you giving a reason for only changing it in the one in public_html... 03/31/11 18:09 umhameld
    As for the log, i am aware of that already and can explain why if you'd like. I can fix it if you think it is worth it.

    As for the database thing, the fix you suggested should work.
    03/30/11 14:43 umhameld
    One more problem: birchhome.py is not changing 'psgendb' to the installer's userid in the wspec/password.wrm files.

    If you look at birchhome.sh, you'll see that the string that is being changed is 'psgendb', not 'frist'. So probably the change that needs to be made in in main, where

    set_db_id(home,"frist")

    should be changed to

    set_db_id(home,"psgendb")


    Also, notice the message from the log file has two slashes after the word BIRCH.

    Setting values for acedb
    getbirch.py: Replacing lines in file/home/other/staff/frist/birch/BIRCH//public_html/birchdb/wspec/passwd.wrm

    I think this is only a cosmetic thing in the log message, but take a look at it.
    03/30/11 14:27 B_Fristensky
    Issue resolved with commit sha fcae0b41849c21819f35aee271386aefd260cbaa 03/26/11 14:47 umhameld
    birchhome.py needs to be rewritten, plain and simple. I wrote it last summer when I was working on winbirch and it contains too many deprecated winbirch hacks to touch. Every change i make breaks something else, and puts me in a death spiral of wasting time. I will have to reimplement this. 03/15/11 23:30 umhameld
    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 04/03/11 18:19 B_Fristensky
    resolution_id Not Resolved 04/03/11 18:19 B_Fristensky
    close_date 03/26/11 14:47 04/03/11 18:19 B_Fristensky
    status_id Closed 03/30/11 14:27 B_Fristensky
    resolution_id Resolved 03/30/11 14:27 B_Fristensky
    status_id Open 03/26/11 14:47 umhameld
    close_date 12/31/69 19:00 03/26/11 14:47 umhameld
    priority 9 03/26/11 14:47 umhameld
    resolution_id Not Resolved 03/26/11 14:47 umhameld
    priority 7 03/15/11 23:30 umhameld
    status_id Pending 03/12/11 14:09 B_Fristensky
    priority 5 03/12/11 14:09 B_Fristensky
    assigned_to unset 03/12/11 14:09 B_Fristensky
    resolution_id Unset 03/12/11 14:09 B_Fristensky

     

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