Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:

      Description

      This issue calls for improving the Galaxy-to-IGB bridge javascript code galaxy.js.

      The Galaxy-to-IGB workflow works like this:

      1. User visits usegalaxy.org and uses the site to create some files, which get added to their History.
      2. User clicks a file in their History and sees a link to view the file in IGB
      3. Users clicks the link, which goes to the Galaxy-to-IGB bridge page on Bioviz.org
      4. The page contains some javascript code that detects whether or not IGB is running by hitting an IGB REST endpoint on localhost
      5. If IGB is running, the javascript code then hits another REST endpoint in IGB, passing it the location of the file stored on Galaxy that the user wants to load
      6. IGB then accesses the file and creates a new track for it
      7. User can then load data by clicking the Load Data button in IGB

      Once number 5 (above) happens, the javascript code displays a poorly worded message: "Data loading takes a while. If it doesn't load in a minute then, Please go back to galaxy and try again!"

      Change this message to:

      "Your data will appear in IGB as a new (empty) track. When you see the new track, zoom in and click Load Data."

      Note: "Load Data" should be in bold font.

      Also note:

      To do this task, you will need to deploy a local copy of BioViz.org on your machine or onto a cloud VM, such as EC2. Code and instructions on how to deploy the BioViz Web site code are here: https://bitbucket.org/lorainelab/bioviz

      Use the same workflow for developing BioViz.org as you use for developing IGB itself: make a fork, clone your fork, make a branch, develop on your branch, push to your fork, etc

      Once you have deployed bioviz on EC2 or on your local host, you will need to test with Galaxy itself. The links coming from Galaxy all go to the production server at http://bioviz.org, not your local computer or EC2 instances. However, you can "trick" your computer into think your local machine or your EC2 instance is actually Bioviz.org by editing some local configuration files. The files you edit will depend on your OS. If you set this up correctly, then you can click links in Galaxy and they will go to your own development site and not the main production site.

      See:

        Attachments

          Activity

            People

            • Assignee:
              pbole Pawan Bole (Inactive)
              Reporter:
              ann.loraine Ann Loraine
            • Votes:
              0 Vote for this issue
              Watchers:
              Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: