Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Galaxy Tool Development: Reading user id before the execution of the tool

    I have posted this twice on Galaxy Dev list, however, I did not receive any response, therefore, I am posting this here in a hope that here might be the guy who could stop me pulling my few left hairs.

    My tool meant to load up (in a dropdown) some custom data from a non-galaxy database for the user to select and submit a job. I am using dynamic_options for loading such dynamic values, however to restrict data for a logged-in user I need to know the user id.

    So far I have tried many things including setting dynamic_options="load_dynamic_values($__user_id__) in the xml wrapper but it did not work. I know $__user_id__ can be passed to the tool as a command line arguments, however, my issue is to read user id even before the execution of main tool.


    I have also tried following code in a hope to grab the webapp session.

    ini_file = '/galaxy-dist/universe_wsgi.ini'

    conf_parser = ConfigParser.ConfigParser( {'here's.getcwd()} )

    conf_parser.read( ini_file )

    configuration = {}

    for key, value in conf_parser.items( "app:main" ):

    configuration[key] = value

    global_conf = { '__file__' : ini_file }

    app = galaxy.app.UniverseApplication(**configuration )



    But this generates following error.

    UnboundExecutionError: Parent instance <History at 0x581cdd0> is not bound to a Session; lazy load operation of attribute 'active_datasets' cannot proceed.

    Thanks for your help guys.

  • #2
    Originally posted by chipseq View Post
    I have posted this twice on Galaxy Dev list, however, I did not receive any response, therefore, I am posting this here in a hope that here might be the guy who could stop me pulling my few left hairs.
    I think the Galaxy dev list is the best place to ask, even if some folk do read both that and SEQanswers.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    66 views
    0 likes
    Last Post seqadmin  
    Working...
    X