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  1. IGB
  2. IGBF-3807

Create link outs for UCSC REST data sets / files

    Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: 10.1.0
    • Labels:
      None

      Description

      There is a way to link to UCSC track descriptions using this link pattern:

      Where "g" is a string identifying a track.

      You can also add a "db" parameter to specify the genome version of interest. With this new parameter, the URL pattern is:

      For example:

      opens a page at the UCSC genome browser with a page describing track "dbSnp155Composite" in the context of the hg18 genome version.

      This page is even an entry-point for the UCSC genome browser interface. The page has a "submit" button. When you click this "submit" button, a new page opens showing a genomic scene for the requested genome version, with the track shown, as well. It's hard to interpret this page if you are not already familiar with the browser, but it provides an entrée for a user to start comparing how the track data look in its native UCSC Genome Browser context with how it looks in IGB.

      It would be fantastic if we could provide link-outs going from the IGB UCSC REST data sets shown in IGB's Data Access panel.

      Doing this shouldn't be too difficult, and the goal of this task is to determine if it is feasible. If yes, we can include implementation in this ticket as well, as the developer sees fit.

      The code would construct the "link out" URLs using this pattern:

      or, even better:

      Let's call this "option 1" also known as (aka) "direct link into UCSC Web site."

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          Issue Links

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            ann.loraine Ann Loraine created issue -
            ann.loraine Ann Loraine made changes -
            Field Original Value New Value
            Epic Link IGBF-3129 [ 21675 ]
            ann.loraine Ann Loraine made changes -
            Sprint Summer 3 [ 197 ] Summer 3, Summer 4 [ 197, 198 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Assignee Nowlan Freese [ nfreese ] Jaya Sravani Sirigineedi [ jsirigin ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            ann.loraine Ann Loraine made changes -
            Description There is a way to link to UCSC track descriptions using this link pattern:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)

            Where "g" is a string identifying a track.

            You can also add a "db" parameter to specify the genome version of interest. With this new parameter, the URL pattern is:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)&db=(ucsc genome version name)

            For example:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=dbSnp155Composite&db=hg18

            opens a page at the UCSC genome browser with a page describing track "dbSnp155Composite" in the context of the hg18 genome version.

            This page is even an entry-point for the UCSC genome browser interface. The page has a "submit" button. When you click this "submit" button, a new page opens showing a genomic scene for the requested genome version, with the track shown, as well. It's hard to interpret this page if you are not already familiar with the browser, but it provides an entrée for a user to start comparing how the track data look in its native UCSC Genome Browser context with how it looks in IGB.

            It would be fantastic if we could provide link-outs going from the IGB UCSC REST data sets shown in IGB's Data Access panel.

            Doing this shouldn't be too difficult, and the goal of this task is to determine if it is feasible. If yes, we can include implementation in this ticket as well, as the developer sees fit.

            The code would construct the "link out" URLs using this pattern:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)

            or, even better:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)&db=(ucsc genome name)

            There is a way to link to UCSC track descriptions using this link pattern:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)

            Where "g" is a string identifying a track.

            You can also add a "db" parameter to specify the genome version of interest. With this new parameter, the URL pattern is:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)&db=(ucsc genome version name)

            For example:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=dbSnp155Composite&db=hg18

            opens a page at the UCSC genome browser with a page describing track "dbSnp155Composite" in the context of the hg18 genome version.

            This page is even an entry-point for the UCSC genome browser interface. The page has a "submit" button. When you click this "submit" button, a new page opens showing a genomic scene for the requested genome version, with the track shown, as well. It's hard to interpret this page if you are not already familiar with the browser, but it provides an entrée for a user to start comparing how the track data look in its native UCSC Genome Browser context with how it looks in IGB.

            It would be fantastic if we could provide link-outs going from the IGB UCSC REST data sets shown in IGB's Data Access panel.

            Doing this shouldn't be too difficult, and the goal of this task is to determine if it is feasible. If yes, we can include implementation in this ticket as well, as the developer sees fit.

            The code would construct the "link out" URLs using this pattern:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)

            or, even better:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)&db=(ucsc genome name)

            Let's call this "option 1" or "direct link into UCSC Web site."

            ann.loraine Ann Loraine made changes -
            Description There is a way to link to UCSC track descriptions using this link pattern:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)

            Where "g" is a string identifying a track.

            You can also add a "db" parameter to specify the genome version of interest. With this new parameter, the URL pattern is:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)&db=(ucsc genome version name)

            For example:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=dbSnp155Composite&db=hg18

            opens a page at the UCSC genome browser with a page describing track "dbSnp155Composite" in the context of the hg18 genome version.

            This page is even an entry-point for the UCSC genome browser interface. The page has a "submit" button. When you click this "submit" button, a new page opens showing a genomic scene for the requested genome version, with the track shown, as well. It's hard to interpret this page if you are not already familiar with the browser, but it provides an entrée for a user to start comparing how the track data look in its native UCSC Genome Browser context with how it looks in IGB.

            It would be fantastic if we could provide link-outs going from the IGB UCSC REST data sets shown in IGB's Data Access panel.

            Doing this shouldn't be too difficult, and the goal of this task is to determine if it is feasible. If yes, we can include implementation in this ticket as well, as the developer sees fit.

            The code would construct the "link out" URLs using this pattern:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)

            or, even better:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)&db=(ucsc genome name)

            Let's call this "option 1" or "direct link into UCSC Web site."

            There is a way to link to UCSC track descriptions using this link pattern:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)

            Where "g" is a string identifying a track.

            You can also add a "db" parameter to specify the genome version of interest. With this new parameter, the URL pattern is:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)&db=(ucsc genome version name)

            For example:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=dbSnp155Composite&db=hg18

            opens a page at the UCSC genome browser with a page describing track "dbSnp155Composite" in the context of the hg18 genome version.

            This page is even an entry-point for the UCSC genome browser interface. The page has a "submit" button. When you click this "submit" button, a new page opens showing a genomic scene for the requested genome version, with the track shown, as well. It's hard to interpret this page if you are not already familiar with the browser, but it provides an entrée for a user to start comparing how the track data look in its native UCSC Genome Browser context with how it looks in IGB.

            It would be fantastic if we could provide link-outs going from the IGB UCSC REST data sets shown in IGB's Data Access panel.

            Doing this shouldn't be too difficult, and the goal of this task is to determine if it is feasible. If yes, we can include implementation in this ticket as well, as the developer sees fit.

            The code would construct the "link out" URLs using this pattern:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)

            or, even better:

            * https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=(track name)&db=(ucsc genome name)

            Let's call this "option 1" also known as (aka) "direct link into UCSC Web site."

            jsirigin Jaya Sravani Sirigineedi made changes -
            Story Points 0.25 1
            nfreese Nowlan Freese made changes -
            Summary Investigate: Can we create link outs for UCSC REST data sets / files ? Create link outs for UCSC REST data sets / files ?
            Story Points 1 2
            nfreese Nowlan Freese made changes -
            Summary Create link outs for UCSC REST data sets / files ? Create link outs for UCSC REST data sets / files
            jsirigin Jaya Sravani Sirigineedi made changes -
            Link This issue relates to IGBF-3813 [ IGBF-3813 ]
            nfreese Nowlan Freese made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            nfreese Nowlan Freese made changes -
            Assignee Jaya Sravani Sirigineedi [ jsirigin ] Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ] Jaya Sravani Sirigineedi [ jsirigin ]
            nfreese Nowlan Freese made changes -
            Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Sprint Summer 3, Summer 4 [ 197, 198 ] Summer 3, Summer 4, Summer 5 [ 197, 198, 199 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            jsirigin Jaya Sravani Sirigineedi made changes -
            Assignee Jaya Sravani Sirigineedi [ jsirigin ] Nowlan Freese [ nfreese ]
            ann.loraine Ann Loraine made changes -
            Sprint Summer 3, Summer 4, Summer 5 [ 197, 198, 199 ] Summer 3, Summer 4, Summer 5, Summer 6 [ 197, 198, 199, 200 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Sprint Summer 3, Summer 4, Summer 5, Summer 6 [ 197, 198, 199, 200 ] Summer 3, Summer 4, Summer 5, Summer 6, Summer 7 [ 197, 198, 199, 200, 201 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            ann.loraine Ann Loraine made changes -
            Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
            ann.loraine Ann Loraine made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            ann.loraine Ann Loraine made changes -
            Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
            ann.loraine Ann Loraine made changes -
            Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
            ann.loraine Ann Loraine made changes -
            Assignee Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ] Jaya Sravani Sirigineedi [ jsirigin ]
            nfreese Nowlan Freese made changes -
            Resolution Done [ 10000 ]
            Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
            nfreese Nowlan Freese made changes -
            Fix Version/s 10.1.0 [ 11000 ]

              People

              • Assignee:
                jsirigin Jaya Sravani Sirigineedi
                Reporter:
                ann.loraine Ann Loraine
              • Votes:
                0 Vote for this issue
                Watchers:
                3 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: