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  1. IGB
  2. IGBF-1496

Determine why gene sets are not loaded after switching to backup Quickload site

    Details

    • Story Points:
      3
    • Sprint:
      Winter 2018 Sprint 3

      Description

      IGB has several Quickload sites loaded by default. Most of these have backup Quickload sites that IGB uses if the main sites are not available.

      The main Quickload and their corresponding backup sites are configured in file igb_preferences.json, which is packaged with IGB and read upon startup.

      The backup sites are supposed to be identical to the main site, and so when IGB switches to using a backup site, it should have all the same datasets. In addition, the datasets which have load_hint "load_hint="Whole Sequence" ought to be automatically loaded, just like with the main site. However, sometimes this automatic loading does not happen.

      From the user's perspective, what happens is that when a user visits a genome, the gene models fail to load.

      For this task, try to reproduce the bug. Then, also find out when this change or flaw (if you find it) was introduced. Investigate the root cause of the bug and try to find which commit introduced it. Once that is done, create a new Jira story where the task is: implement a fix.

      Some tips:

      1) To simulate a quickload site becoming unavailable, modify your /etc/hosts (or Windows equivalent) to point the quickload site domain to an incorrect address, e.g., google or some other site.
      2) Datasets are configured as using annots.xml files residing in genome directories. An example: http://igbquickload.org/quickload/A_thaliana_Jun_2009/annots.xml
      3) In the IGB UI, a dataset with load_hint "Whole Sequence" should have a "load mode" equal to "Genome" when listed in the loaded data sets table. (This just reflects differences between code and user-facing text.)
      4) This is a complex task. Search for Quickload-related issues in Jira to gain background knowledge. Also, read documentation in the User's Guide to better understand how Quickload sites function.
      5) You can tell that a backup site is being used by opening the Preferences window. Click the "Data Sources" tab. If a site name in the table has a yellow background, it means the backup site is being used. If the site name has a red background, it means that the main site and the backup site are both unavailable for some reason. However, the UI won't display the address of the backup site. (Side note: it might be good to add a feature that would let a user find out what the backup site address is.)

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          srishteeM Srishtee Marotkar (Inactive) added a comment -

          Result: Not reproducing issue of not loading gene sets after switching to backup Quickload site. Investigated on IGB master repository and released version. I followed below steps and monitored behavior of IGB over a period of 2 days by keep on switching between main and backup Quickload site, still it was not reproduced. I suspect that it could be intermittent issue and if occurred next time it can then immediately investigating that issue can help to understand cause.
          Check attached IGBF_1496_Observation.doc

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          srishteeM Srishtee Marotkar (Inactive) added a comment - Result: Not reproducing issue of not loading gene sets after switching to backup Quickload site. Investigated on IGB master repository and released version. I followed below steps and monitored behavior of IGB over a period of 2 days by keep on switching between main and backup Quickload site, still it was not reproduced. I suspect that it could be intermittent issue and if occurred next time it can then immediately investigating that issue can help to understand cause. Check attached IGBF_1496_Observation.doc

            People

            • Assignee:
              srishteeM Srishtee Marotkar (Inactive)
              Reporter:
              ann.loraine Ann Loraine
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              Dates

              • Created:
                Updated:
                Resolved: