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  1. IGB
  2. IGBF-3755

Enable bioviz.org/bar.html to handle multiple files in one URL

        Details

        • Type: Improvement
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Situation: Dr. Provart would like to be able to submit multiple samples to be loaded in IGB through one URL. This is possible through IGB Bookmarks, but when we receive a request from the eFP-Seq browser the server_url parameter is not duplicated as needed, leading to no data loading in IGB.

          Task: When a URL from https://bar.utoronto.ca/eFP-Seq_Browser/ to bioviz.org/bar.html is received, bioviz.org needs to be able to handle multiple files in the same URL. The URL will need to include feature_url_# for each file, as well as query_url for each file (doesn't seem to need a number), as well as server_url for each file (also does not need a number). Update the logic on bioviz.org/bar.html that is converting the server_url from bar to http://lorainelab-quickload.scidas.org/bar/ so that it can handle two server_url in the URL (see email discussion for additional details).

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              nfreese Nowlan Freese added a comment - - edited

              Question from Dr. Provart

              On Fri, May 24, 2024 at 11:23AM Nicholas Provart <nicholas.provart@utoronto.ca> wrote:
              [Caution: Email from External Sender. Do not click or open links or attachments unless you know this sender.]

              Hi Ann,

              Hope you're enjoying the end of term. Question: we generate links for IGB in the eFP-Seq Browser that look like this:

              https://bioviz.org/bar.html?version=A_thaliana_Jun_2009&gene_id=AT2G24270&feature_url_0=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&genome=A_thaliana_Jun_2009&annotation_set=Araport11&query_url=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&server_url=bar

              Is it possible to have multiple files be opened in IGB by including additional parameters in the URL? We were thinking it would be nice to have the BED file from your FindJunction program be opened along with its corresponding BAM file. I tried adding a "&feature_url_1=" parameter with a different BAM file as a test, to open 2 BAM files at once, but that didn't seem to work - neither BAM file was displayed in IGB.

              Thanks!

              Nick

              Response from Nowlan

              The URL will need to include feature_url_# for each file, as well as query_url for each file (doesn't seem to need a number), as well as server_url for each file (also does not need a number).

              The link below is what I think the URL you would create should look like:
              https://bioviz.org/bar.html?version=A_thaliana_Jun_2009&gene_id=AT2G24270&feature_url_0=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&feature_url_1=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/carpel/SRR1207194/accepted_hits.bam&server_url=bar&genome=A_thaliana_Jun_2009&annotation_set=Araport11&query_url=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&query_url=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/carpel/SRR1207194/accepted_hits.bam&server_url=bar

              However, we have some logic on bioviz.org/bar.html that is converting the server_url from bar to http://lorainelab-quickload.scidas.org/bar/ and it does not seem to like it when there are two server_url in the URL, so I think we will need to make a small change on the bioviz.org logic.

              What should then get passed to IGB is:
              http://127.0.0.1:7085/IGBControl?server_url=http://lorainelab-quickload.scidas.org/bar/&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/aerial/ERR274310/accepted_hits.bam&query_url=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&feature_url_1=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/carpel/SRR1207194/accepted_hits.bam&query_url=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/carpel/SRR1207194/accepted_hits.bam&start=10326417&end=10330548&seqid=Chr2&loadresidues=True

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              nfreese Nowlan Freese added a comment - - edited Question from Dr. Provart On Fri, May 24, 2024 at 11:23AM Nicholas Provart <nicholas.provart@utoronto.ca> wrote: [Caution: Email from External Sender. Do not click or open links or attachments unless you know this sender.] Hi Ann, Hope you're enjoying the end of term. Question: we generate links for IGB in the eFP-Seq Browser that look like this: https://bioviz.org/bar.html?version=A_thaliana_Jun_2009&gene_id=AT2G24270&feature_url_0=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&genome=A_thaliana_Jun_2009&annotation_set=Araport11&query_url=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&server_url=bar Is it possible to have multiple files be opened in IGB by including additional parameters in the URL? We were thinking it would be nice to have the BED file from your FindJunction program be opened along with its corresponding BAM file. I tried adding a "&feature_url_1=" parameter with a different BAM file as a test, to open 2 BAM files at once, but that didn't seem to work - neither BAM file was displayed in IGB. Thanks! Nick Response from Nowlan The URL will need to include feature_url_# for each file, as well as query_url for each file (doesn't seem to need a number), as well as server_url for each file (also does not need a number). The link below is what I think the URL you would create should look like: https://bioviz.org/bar.html?version=A_thaliana_Jun_2009&gene_id=AT2G24270&feature_url_0=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&feature_url_1=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/carpel/SRR1207194/accepted_hits.bam&server_url=bar&genome=A_thaliana_Jun_2009&annotation_set=Araport11&query_url=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&query_url=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/carpel/SRR1207194/accepted_hits.bam&server_url=bar However, we have some logic on bioviz.org/bar.html that is converting the server_url from bar to http://lorainelab-quickload.scidas.org/bar/ and it does not seem to like it when there are two server_url in the URL, so I think we will need to make a small change on the bioviz.org logic. What should then get passed to IGB is: http://127.0.0.1:7085/IGBControl?server_url=http://lorainelab-quickload.scidas.org/bar/&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/aerial/ERR274310/accepted_hits.bam&query_url=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&feature_url_1=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/carpel/SRR1207194/accepted_hits.bam&query_url=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/carpel/SRR1207194/accepted_hits.bam&start=10326417&end=10330548&seqid=Chr2&loadresidues=True

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                • Assignee:
                  Unassigned
                  Reporter:
                  nfreese Nowlan Freese
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                    Updated: