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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

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            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 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
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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
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              stiwari8 Srishti Tiwari (Inactive) added a comment -

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

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              stiwari8 Srishti Tiwari (Inactive) added a comment - Javascript code under version control - https://bitbucket.org/lorainelab/bioviz
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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.

                People

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

                  Dates

                  • Created:
                    Updated:
                    Resolved: