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  1. IGB
  2. IGBF-2457

Fix View in IGB on usegalaxy.org

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Blocker
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Situation: When a user clicks View in IGB for data at usegalaxy.org a url is created and the user is directed to bioviz where javascript alters the url allowing data to be streamed to IGB. Currently, when clicking View in IGB at usegalaxy.org the page responds with "This site can't be reached".

          Example data: https://usegalaxy.org/u/nfreese/h/visualization-of-whole-genome-dna-methylation-data-in-igb-focus-on-a-feature

          Task: Determine the problem and implement a solution so that data are sent to IGB.

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              ann.loraine Ann Loraine added a comment -

              Creating a new Jira issue to investigate building testing using ansible.

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              ann.loraine Ann Loraine added a comment - Creating a new Jira issue to investigate building testing using ansible.
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              ann.loraine Ann Loraine added a comment -

              Investigate "test" infrastructure in ansible.

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              ann.loraine Ann Loraine added a comment - Investigate "test" infrastructure in ansible.
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              ann.loraine Ann Loraine added a comment -

              Somehow we have to build some automated testing on live bioviz test sites.

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              ann.loraine Ann Loraine added a comment - Somehow we have to build some automated testing on live bioviz test sites.
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              ann.loraine Ann Loraine added a comment -

              Notes on testing:

              Nowlan Freese noted:
              Hitting this URL:
              https://usegalaxy.org/display_application/bbd44e69cb8906b52300b547db6d5d14/igb_bam/View

              Causes Galaxy to redirect to this URL:
              http://www.bioviz.org/galaxy.html?version=Arabidopsis_thaliana_TAIR10&feature_url_0=https://usegalaxy.org/display_application/bbd44e69cb8906b52300b547db6d5d14/igb_bam/View/89cd57707cd25ba9/data/BS_seq_Chr1_KO.bam&sym_name_0=BS_seq_Chr1_KO&sym_method_0=https://usegalaxy.org/display_application/bbd44e69cb8906b52300b547db6d5d14/igb_bam/View/89cd57707cd25ba9/data/BS_seq_Chr1_KO.bam&query_url=https://usegalaxy.org/display_application/bbd44e69cb8906b52300b547db6d5d14/igb_bam/View/89cd57707cd25ba9/dat

              When this goes to Bioviz.org, BioViz.org substitutes https for http and redirects again.

              Next, BioViz modifies the URL a bit and substitutes domain localhost.

              We need something that tests each part of this sequence.

              Show
              ann.loraine Ann Loraine added a comment - Notes on testing: Nowlan Freese noted: Hitting this URL: https://usegalaxy.org/display_application/bbd44e69cb8906b52300b547db6d5d14/igb_bam/View Causes Galaxy to redirect to this URL: http://www.bioviz.org/galaxy.html?version=Arabidopsis_thaliana_TAIR10&feature_url_0=https://usegalaxy.org/display_application/bbd44e69cb8906b52300b547db6d5d14/igb_bam/View/89cd57707cd25ba9/data/BS_seq_Chr1_KO.bam&sym_name_0=BS_seq_Chr1_KO&sym_method_0=https://usegalaxy.org/display_application/bbd44e69cb8906b52300b547db6d5d14/igb_bam/View/89cd57707cd25ba9/data/BS_seq_Chr1_KO.bam&query_url=https://usegalaxy.org/display_application/bbd44e69cb8906b52300b547db6d5d14/igb_bam/View/89cd57707cd25ba9/dat When this goes to Bioviz.org, BioViz.org substitutes https for http and redirects again. Next, BioViz modifies the URL a bit and substitutes domain localhost. We need something that tests each part of this sequence.
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              ann.loraine Ann Loraine added a comment -

              Problem was with redirect configuration in httpd.conf.

              For fix: See commit 21b8eb3 in lorainelab/bioviz-playbooks.git.

              We need to automate testing of BioViz Web site deployment – AL (me) forgot to check Galaxy connectivity.

              Show
              ann.loraine Ann Loraine added a comment - Problem was with redirect configuration in httpd.conf. For fix: See commit 21b8eb3 in lorainelab/bioviz-playbooks.git. We need to automate testing of BioViz Web site deployment – AL (me) forgot to check Galaxy connectivity.
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              ann.loraine Ann Loraine added a comment -

              https://github.com/galaxyproject/galaxy - Galaxy code base

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              ann.loraine Ann Loraine added a comment - https://github.com/galaxyproject/galaxy - Galaxy code base
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              nfreese Nowlan Freese added a comment - - edited

              May be an issue with a misplaced forward slash.

              This is the URL that I am currently getting that is broken:

              https://www.bioviz.orggalaxy.html/?version=Arabidopsis_thaliana_TAIR10&feature_url_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&sym_name_0=RNA_seq_Chr1_KO&sym_method_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&query_url=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&server_url=galaxy

              Note that there is no forward slash between org and galaxy.html, but there is a forward slash between html and ?

              Moving the forward slash to the correct position seems to fix the url.

              https://www.bioviz.org/galaxy.html?version=Arabidopsis_thaliana_TAIR10&feature_url_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&sym_name_0=RNA_seq_Chr1_KO&sym_method_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&query_url=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&server_url=galaxy

              Show
              nfreese Nowlan Freese added a comment - - edited May be an issue with a misplaced forward slash. This is the URL that I am currently getting that is broken: https://www.bioviz.orggalaxy.html/?version=Arabidopsis_thaliana_TAIR10&feature_url_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&sym_name_0=RNA_seq_Chr1_KO&sym_method_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&query_url=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&server_url=galaxy Note that there is no forward slash between org and galaxy.html, but there is a forward slash between html and ? Moving the forward slash to the correct position seems to fix the url. https://www.bioviz.org/galaxy.html?version=Arabidopsis_thaliana_TAIR10&feature_url_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&sym_name_0=RNA_seq_Chr1_KO&sym_method_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&query_url=https://usegalaxy.org/display_application/bbd44e69cb8906b51371325f402dce0f/igb_bam/View/f7d0b06217bfdb8a/data/RNA_seq_Chr1_KO.bam&server_url=galaxy

                People

                • Assignee:
                  Unassigned
                  Reporter:
                  nfreese Nowlan Freese
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                  Dates

                  • Created:
                    Updated:
                    Resolved: