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  1. IGB
  2. IGBF-1398

Fix zooming in BAR to IGB bridge bar.js

        Details

        • Type: Bug
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          1
        • Sprint:
          Fall 2018 Sprint 2

          Attachments

            Issue Links

            relates to

            Bug - A problem which impairs or prevents the functions of the product. IGBF-1402 Error while loading data from eFP-Seq Browser (Show: Alignments in IGB) when using Firefox

            • Major - Major loss of function.
            • Closed

              Activity

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              ann.loraine Ann Loraine created issue -
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              ann.loraine Ann Loraine added a comment -

              Parameter should be "seqid" not "seq_id"

              http://localhost:7085/IGBControl?server_url=http://lorainelab-quickload.scidas.org/bar/&version=A_thaliana_Jun_2009&feature_url_0=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/dark/SRR477076/accepted_hits.bam&query_url=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/dark/SRR477076/accepted_hits.bam&start=8997369&end=9001185&seqid=Chr3&loadresidues=True

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              ann.loraine Ann Loraine added a comment - Parameter should be "seqid" not "seq_id" http://localhost:7085/IGBControl?server_url=http://lorainelab-quickload.scidas.org/bar/&version=A_thaliana_Jun_2009&feature_url_0=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/dark/SRR477076/accepted_hits.bam&query_url=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/dark/SRR477076/accepted_hits.bam&start=8997369&end=9001185&seqid=Chr3&loadresidues=True
              ann.loraine Ann Loraine made changes -
              Status Open [ 1 ] Needs Testing [ 10002 ]
              ann.loraine Ann Loraine made changes -
              Sprint Fall 2018 Sprint 2 [ 52 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Summary Fix bookmark in 9.0.1 Fix zooming in BAR to IGB bridge bar.js
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              ann.loraine Ann Loraine added a comment - - edited

              Fixed with https://bitbucket.org/lorainelab/bioviz/commits/b1939e9981eb34f8083218528ea993827de3594a

              Deployed fix to main bioviz.org site.

              To test:

              • visit https://bar.utoronto.ca/eFP-Seq_Browser/
              • search for genes on each chromosome
              • click link labeled "Show: Alignments in IGB"
              • IGB should zoom to region with gene (showing 500 bases on left and right side)
              • RNA-Seq read alignments and sequence data should load
              • Data set should be shown as selected (checked) in Available Data Sets under BAR Quickload site in Data Access Panel
              Show
              ann.loraine Ann Loraine added a comment - - edited Fixed with https://bitbucket.org/lorainelab/bioviz/commits/b1939e9981eb34f8083218528ea993827de3594a Deployed fix to main bioviz.org site. To test: visit https://bar.utoronto.ca/eFP-Seq_Browser/ search for genes on each chromosome click link labeled "Show: Alignments in IGB" IGB should zoom to region with gene (showing 500 bases on left and right side) RNA-Seq read alignments and sequence data should load Data set should be shown as selected (checked) in Available Data Sets under BAR Quickload site in Data Access Panel
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ]
              mason Mason Meyer (Inactive) made changes -
              Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
              mason Mason Meyer (Inactive) made changes -
              Assignee Mason Meyer [ mason ]
              stiwari8 Srishti Tiwari (Inactive) made changes -
              Status Testing In Progress [ 10003 ] Needs Testing [ 10002 ]
              stiwari8 Srishti Tiwari (Inactive) made changes -
              Assignee Mason Meyer [ mason ] Srishti Tiwari [ stiwari8 ]
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              stiwari8 Srishti Tiwari (Inactive) added a comment -

              Javascript code under version control - https://bitbucket.org/lorainelab/bioviz

              Show
              stiwari8 Srishti Tiwari (Inactive) added a comment - Javascript code under version control - https://bitbucket.org/lorainelab/bioviz
              stiwari8 Srishti Tiwari (Inactive) made changes -
              Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
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              stiwari8 Srishti Tiwari (Inactive) added a comment -

              The changes made in the Jira are working correctly.

              I debugged the JavaScript code, it was working fine for Chrome, but was throwing an error in Firefox.
              Chrome allows localhost invocation whereas Firefox browser prevents it, considering http://127.0.0.1 as mixed content. Once I added an exception for that URL in Firefox, it worked as expected.

              Show
              stiwari8 Srishti Tiwari (Inactive) added a comment - The changes made in the Jira are working correctly. I debugged the JavaScript code, it was working fine for Chrome, but was throwing an error in Firefox. Chrome allows localhost invocation whereas Firefox browser prevents it, considering http://127.0.0.1 as mixed content. Once I added an exception for that URL in Firefox, it worked as expected.
              stiwari8 Srishti Tiwari (Inactive) made changes -
              Resolution Done [ 10000 ]
              Status Testing In Progress [ 10003 ] Closed [ 6 ]
              stiwari8 Srishti Tiwari (Inactive) made changes -
              Link This issue relates to IGBF-1402 [ IGBF-1402 ]
              ann.loraine Ann Loraine made changes -
              Workflow Loraine Lab Workflow [ 18102 ] Fall 2019 Workflow Update [ 19940 ]
              ann.loraine Ann Loraine made changes -
              Workflow Fall 2019 Workflow Update [ 19940 ] Revised Fall 2019 Workflow Update [ 22060 ]

                People

                • Assignee:
                  stiwari8 Srishti Tiwari (Inactive)
                  Reporter:
                  ann.loraine Ann Loraine
                • Votes:
                  0 Vote for this issue
                  Watchers:
                  2 Start watching this issue

                  Dates

                  • Created:
                    Updated:
                    Resolved: