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  1. IGB
  2. IGBF-1367

Modify bar.js to handle new query params

        Details

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

          Attachments

            Issue Links

            relates to

            Improvement - An improvement or enhancement to an existing feature or task. IGBF-1364 Turn off "zoom in and click load data" message if using position bookmark

            • Major - Major loss of function.
            • Closed

            Bug - A problem which impairs or prevents the functions of the product. IGBF-1353 Optimize IGB Javascript bridge code

            • Major - Major loss of function.
            • Closed

              Activity

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              ann.loraine Ann Loraine added a comment - - edited

              Sample link to activate IGB on localhost:

              http://localhost:7085/IGBControl?version=A_thaliana_Jun_2009&seq_id=Chr1&start=2257408&end=2260187&server_url=http://lorainelab-quickload.scidas.org/bar&loadresidues=True&feature_url_0=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&query_url=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam

              Note: query_url is the same as feature_url_0, feature_url_1, etc. For every feature_url_n, include an identical query_url. For example, if you have feature_url_0=foo&feature_url_1=bar, then include query_url=foo&query_url=bar

              This is just how IGB 9.0.1 and below wants it. We will investigate why this is necessary later.

              Show
              ann.loraine Ann Loraine added a comment - - edited Sample link to activate IGB on localhost: http://localhost:7085/IGBControl?version=A_thaliana_Jun_2009&seq_id=Chr1&start=2257408&end=2260187&server_url=http://lorainelab-quickload.scidas.org/bar&loadresidues=True&feature_url_0=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&query_url=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam Note: query_url is the same as feature_url_0, feature_url_1, etc. For every feature_url_n, include an identical query_url. For example, if you have feature_url_0=foo&feature_url_1=bar, then include query_url=foo&query_url=bar This is just how IGB 9.0.1 and below wants it. We will investigate why this is necessary later.
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              ann.loraine Ann Loraine added a comment - - edited

              Residues are getting loaded after data from feature_url_0 are getting loaded. Appears to be a thread-related issue.

              Workaround:

              In the Javascript (bar.js) first make this call:

              http://localhost:7085/IGBControl?version=A_thaliana_Jun_2009&seq_id=Chr1&start=2257408&end=2260187&server_url=http://lorainelab-quickload.scidas.org/bar&loadresidues=True

              Wait a moment, then make this call:

              http://localhost:7085/IGBControl?version=A_thaliana_Jun_2009&seq_id=Chr1&start=2257408&end=2260187&server_url=http://lorainelab-quickload.scidas.org/bar&feature_url_0=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&query_url=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam

              This ensures that when IGB accesses the data set (feature_url_0), the reference sequence will already have been loaded.

              Show
              ann.loraine Ann Loraine added a comment - - edited Residues are getting loaded after data from feature_url_0 are getting loaded. Appears to be a thread-related issue. Workaround: In the Javascript (bar.js) first make this call: http://localhost:7085/IGBControl?version=A_thaliana_Jun_2009&seq_id=Chr1&start=2257408&end=2260187&server_url=http://lorainelab-quickload.scidas.org/bar&loadresidues=True Wait a moment, then make this call: http://localhost:7085/IGBControl?version=A_thaliana_Jun_2009&seq_id=Chr1&start=2257408&end=2260187&server_url=http://lorainelab-quickload.scidas.org/bar&feature_url_0=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&query_url=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam This ensures that when IGB accesses the data set (feature_url_0), the reference sequence will already have been loaded.
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              ann.loraine Ann Loraine added a comment -

              http://bioviz.org/cgi-bin/geneIdLookup.py?gene_id=AT1G07350 returns JSON with gene coordinates

              Show
              ann.loraine Ann Loraine added a comment - http://bioviz.org/cgi-bin/geneIdLookup.py?gene_id=AT1G07350 returns JSON with gene coordinates
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              ann.loraine Ann Loraine added a comment -

              BAR code that forms links: https://github.com/asully/eFP-Seq-Browser/blob/master/cgi-bin/core/custom.js

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              ann.loraine Ann Loraine added a comment - BAR code that forms links: https://github.com/asully/eFP-Seq-Browser/blob/master/cgi-bin/core/custom.js
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              sneha Sneha Ramesh Watharkar (Inactive) added a comment -

              You can find work on Branch: https://bitbucket.org/swathark/bioviz/branch/IGBF-1367#diff

              Show
              sneha Sneha Ramesh Watharkar (Inactive) added a comment - You can find work on Branch: https://bitbucket.org/swathark/bioviz/branch/IGBF-1367#diff
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              sneha Sneha Ramesh Watharkar (Inactive) added a comment -

              PR submitted.

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              sneha Sneha Ramesh Watharkar (Inactive) added a comment - PR submitted.
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              ann.loraine Ann Loraine added a comment -

              PR merged. Testing on https://ann.bioviz.org

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              ann.loraine Ann Loraine added a comment - PR merged. Testing on https://ann.bioviz.org
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              ann.loraine Ann Loraine added a comment - - edited

              Fix bar.html to show footer correctly.

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              ann.loraine Ann Loraine added a comment - - edited Fix bar.html to show footer correctly.
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              sneha Sneha Ramesh Watharkar (Inactive) added a comment -

              Prof [~aloraine] : Fixed footer of bar.html
              Branch : https://bitbucket.org/swathark/bioviz/branch/IGBF-1367-barjsFooterFix#diff

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              sneha Sneha Ramesh Watharkar (Inactive) added a comment - Prof [~aloraine] : Fixed footer of bar.html Branch : https://bitbucket.org/swathark/bioviz/branch/IGBF-1367-barjsFooterFix#diff
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              ann.loraine Ann Loraine added a comment -

              Merged to master.

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              ann.loraine Ann Loraine added a comment - Merged to master.

                People

                • Assignee:
                  sneha Sneha Ramesh Watharkar (Inactive)
                  Reporter:
                  sneha Sneha Ramesh Watharkar (Inactive)
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                  Dates

                  • Created:
                    Updated:
                    Resolved: