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    • Sprint:
      Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14

      Description

      Situation: The igbDefaultPrefs.json is missing a commit (here) that updated the primary and mirror repositories for default quickloads. It appears that there were several commits that were merged to release-9.1.6 that have not been merged to master.

      Task: Update the igbDefaultPrefs.json file to include proper quickloads and mirrors.

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          aloraine Ann Loraine added a comment - - edited

          Please test using new master branch installers.

          To test thoroughly, you need to check the behavior following installation onto a system that already has 9.1.6, as follows:

          • Reset preferences to defaults (to erase any previously added quickloads)
          • Install and run 9.1.6 from bioviz.org Web site
          • Install and run 9.1.8 release candidate from bitbucket

          Then check that:

          • soyseq quickload is disabled (this is new with 9.1.8)
          • rna-seq, chip-seq, dna-seq, genome in a bottle, and ucsc DAS data sources are enabled
          • genome in a bottle is served from bioviz.org/quickload/genome-in-a-bottle
          Show
          aloraine Ann Loraine added a comment - - edited Please test using new master branch installers. To test thoroughly, you need to check the behavior following installation onto a system that already has 9.1.6, as follows: Reset preferences to defaults (to erase any previously added quickloads) Install and run 9.1.6 from bioviz.org Web site Install and run 9.1.8 release candidate from bitbucket Then check that: soyseq quickload is disabled (this is new with 9.1.8) rna-seq, chip-seq, dna-seq, genome in a bottle, and ucsc DAS data sources are enabled genome in a bottle is served from bioviz.org/quickload/genome-in-a-bottle
          Hide
          nfreese Nowlan Freese added a comment -

          Tested on Mac:

          Reset preference to default.
          Opened 9.1.6, (SoySeq enabled, no UCSC DAS), closed 9.1.6
          Opened 9.1.8.
          SoySeq enabled, UCSC DAS enabled.

          Reset preference to default.
          Opened 9.1.4, (SoySeq enabled, UCSC DAS disabled), closed 9.1.4
          Opened 9.1.8.
          SoySeq disabled, UCSC DAS disabled.

          Default preferences for IGB 9.1.8 should be SoySeq disabled and UCSC DAS enabled. I am unclear what the IGB logic is for enabling/disabling Quickloads. It seems like IGB sometimes uses the existing user preferences for which Quickloads are enabled/disabled and other times it uses the default preferences.

          Testing in 9.1.8 after resetting preferences to default:

          SoySeq is disabled
          rna-seq, chip-seq, dna-seq, genome in a bottle, and ucsc DAS data sources are enabled
          genome in a bottle is served from bioviz.org/quickload/genome-in-a-bottle with a mirror on Bitbucket, data load from both sources.

          All Quickloads have mirrors.

          Show
          nfreese Nowlan Freese added a comment - Tested on Mac: Reset preference to default. Opened 9.1.6, (SoySeq enabled, no UCSC DAS), closed 9.1.6 Opened 9.1.8. SoySeq enabled, UCSC DAS enabled. Reset preference to default. Opened 9.1.4, (SoySeq enabled, UCSC DAS disabled), closed 9.1.4 Opened 9.1.8. SoySeq disabled, UCSC DAS disabled. Default preferences for IGB 9.1.8 should be SoySeq disabled and UCSC DAS enabled. I am unclear what the IGB logic is for enabling/disabling Quickloads. It seems like IGB sometimes uses the existing user preferences for which Quickloads are enabled/disabled and other times it uses the default preferences. Testing in 9.1.8 after resetting preferences to default: SoySeq is disabled rna-seq, chip-seq, dna-seq, genome in a bottle, and ucsc DAS data sources are enabled genome in a bottle is served from bioviz.org/quickload/genome-in-a-bottle with a mirror on Bitbucket, data load from both sources. All Quickloads have mirrors.
          Hide
          nfreese Nowlan Freese added a comment -

          Dr. Ann Loraine - I am unclear whether this issue should be closed. The igbdefaultprefs.json appears to be correct, so the issue with SoySeq still being enabled when upgrading from 9.1.6 to 9.1.8 would need further exploring and would most likely be beyond the scope of this ticket.

          Show
          nfreese Nowlan Freese added a comment - Dr. Ann Loraine - I am unclear whether this issue should be closed. The igbdefaultprefs.json appears to be correct, so the issue with SoySeq still being enabled when upgrading from 9.1.6 to 9.1.8 would need further exploring and would most likely be beyond the scope of this ticket.

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            • Assignee:
              aloraine Ann Loraine
              Reporter:
              nfreese Nowlan Freese
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                Resolved:

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