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  1. IGB
  2. IGBF-32

Don't replace spaces with underscore characters when viewing files from Galaxy.

    Details

    • Type: Improvement
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
    • Story Points:
      4
    • Sprint:
      Summer 2019 Sprint 11, Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct

      Description

      Kick this up to 8.2 if not feasible to do safely for 8.1 release.

      It would be nice if the name of tracks imported from Galaxy would EXACTLY match the name of the data set as shown in the Galaxy interface. Currently, names that contain spaces are being replaced by underscore characters. It would be better if the names were identical.

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            Hide
            nfreese Nowlan Freese added a comment - - edited

            Testing on early access IGB as of September 25, 2019 and usegalaxy.bioviz.org.

            All file formats except for bigbed are shown correctly with spaces.

            Bigbed is displaying spaces correctly before the data are loaded. Once Load Data is clicked spaces are replaced with "%20".

            Show
            nfreese Nowlan Freese added a comment - - edited Testing on early access IGB as of September 25, 2019 and usegalaxy.bioviz.org. All file formats except for bigbed are shown correctly with spaces. Bigbed is displaying spaces correctly before the data are loaded. Once Load Data is clicked spaces are replaced with "%20".
            Hide
            noor91zahara Noor Zahara (Inactive) added a comment - - edited

            The above mentioned bug has been fixed.
            Code changes can be viewed - https://bitbucket.org/noorzahara/integrated-genome-browser-local1/branch/IGBF-32#diff

            Note from Dr. Loraine (added Nov 2019): Branch is merged into IGB 9.1

            Show
            noor91zahara Noor Zahara (Inactive) added a comment - - edited The above mentioned bug has been fixed. Code changes can be viewed - https://bitbucket.org/noorzahara/integrated-genome-browser-local1/branch/IGBF-32#diff Note from Dr. Loraine (added Nov 2019): Branch is merged into IGB 9.1
            Hide
            nfreese Nowlan Freese added a comment - - edited

            The spaces are now showing correctly in bigbed, but when I click Load Data the file extension is removed from the name.

            Edited:
            After talking with Noor, the bigbed file extension issue does not seem to be related to her changes. The release version of IGB also has the behavior of removing bigbed file extensions. I'm not sure why this is the case, as this is not consistent to how other file types are treated.

            Show
            nfreese Nowlan Freese added a comment - - edited The spaces are now showing correctly in bigbed, but when I click Load Data the file extension is removed from the name. Edited: After talking with Noor, the bigbed file extension issue does not seem to be related to her changes. The release version of IGB also has the behavior of removing bigbed file extensions. I'm not sure why this is the case, as this is not consistent to how other file types are treated.
            Hide
            noor91zahara Noor Zahara (Inactive) added a comment - - edited

            I investigated on how to support backward compatibility to older version of IGB.

            I tried to replace spaces/ non-alphabetic characters in the file name with "" in bioviz before sending it to the older version of IGB ( replicating the functionality of galaxy before my changes). But the issue here is that IGB tries to validate the url (modified url via bioviz) and figures out that it is invalid since that file name does not exist in galaxy. (In galaxy the filename is stored without "" .)

            Show
            noor91zahara Noor Zahara (Inactive) added a comment - - edited I investigated on how to support backward compatibility to older version of IGB. I tried to replace spaces/ non-alphabetic characters in the file name with " " in bioviz before sending it to the older version of IGB ( replicating the functionality of galaxy before my changes). But the issue here is that IGB tries to validate the url (modified url via bioviz) and figures out that it is invalid since that file name does not exist in galaxy. (In galaxy the filename is stored without " " .)
            Hide
            noor91zahara Noor Zahara (Inactive) added a comment -

            Closing this ticket and creating a new one to investigate about the IGB backward compatibility with these changes of galaxy.

            Show
            noor91zahara Noor Zahara (Inactive) added a comment - Closing this ticket and creating a new one to investigate about the IGB backward compatibility with these changes of galaxy.

              People

              • Assignee:
                noor91zahara Noor Zahara (Inactive)
                Reporter:
                ann.loraine Ann Loraine
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                Dates

                • Created:
                  Updated:
                  Resolved: