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  1. IGB
  2. IGBF-3164

Improve Public TrackHub toasts messages

        Details

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

          Description

          Situation: The toast messages that appear when clicking "Add Hub to IGB" or "Open in IGB" on bioviz.org/public-trackhubs.html could be improved.

          Task: Improve the Bioviz.org track hub toast messages.

            Attachments

              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-3169 Investigate IGB 9.1.10 opening genomes slowly

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3147 Add data source button to Track Hub webpages

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-2831 [ 19524 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3147 [ IGBF-3147 ]
                nfreese Nowlan Freese made changes -
                Description Situation:

                Task: Improve the Bioviz.org track hub toast messages.                 		Situation: The toast messages that appear when clicking "Add Hub to IGB" or "Open in IGB" on bioviz.org/public-trackhubs.html could be improved.

                Task: Improve the Bioviz.org track hub toast messages.
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                nfreese Nowlan Freese added a comment - - edited

                Here are the current messages as tested with the following versions of IGB:

                IGB is not running:
                Add Hub to IGB - "Could not add to IGB \n Please restart IGB and try again"
                Open in IGB - "IGB is not running: \n Start IGB to open this genome version in IGB."

                Running IGB 9.1.4 (IGB status check does not return version (version added in 9.1.6), no add data source endpoint)
                Add Hub to IGB - "Could not add to IGB \n Please restart IGB and try again"
                Open in IGB - "Opening in IGB \n Establishing connection to IGB..."

                Running IGB 9.1.8 (IGB status check returns version, no add data source endpoint)
                Add Hub to IGB - "Could not add to IGB \n Please restart IGB and try again"
                Open in IGB - "Opening in IGB \n Establishing connection to IGB..."

                Running IGB 9.1.10 (IGB status check returns version, add data source endpoint is available)
                Add Hub to IGB - "Success \n genome is loading in IGB"
                Open in IGB - "Opening in IGB \n Establishing connection to IGB..."

                Show
                nfreese Nowlan Freese added a comment - - edited Here are the current messages as tested with the following versions of IGB: IGB is not running: Add Hub to IGB - "Could not add to IGB \n Please restart IGB and try again" Open in IGB - "IGB is not running: \n Start IGB to open this genome version in IGB." Running IGB 9.1.4 (IGB status check does not return version (version added in 9.1.6), no add data source endpoint) Add Hub to IGB - "Could not add to IGB \n Please restart IGB and try again" Open in IGB - "Opening in IGB \n Establishing connection to IGB..." Running IGB 9.1.8 (IGB status check returns version, no add data source endpoint) Add Hub to IGB - "Could not add to IGB \n Please restart IGB and try again" Open in IGB - "Opening in IGB \n Establishing connection to IGB..." Running IGB 9.1.10 (IGB status check returns version, add data source endpoint is available) Add Hub to IGB - "Success \n genome is loading in IGB" Open in IGB - "Opening in IGB \n Establishing connection to IGB..."
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                nfreese Nowlan Freese added a comment -

                Alternatives:

                IGB is not running:
                Add Hub to IGB - "IGB is not running \n Please start IGB"
                Open in IGB - "IGB is not running \n Please start IGB"

                Running IGB 9.1.4 (IGB status check does not return version (version added in 9.1.6), no add data source endpoint)
                Add Hub to IGB - "Could not add to IGB \n Please update IGB to latest version"
                Open in IGB - "Success \n Opening genome in IGB"

                Running IGB 9.1.8 (IGB status check returns version, no add data source endpoint)
                Add Hub to IGB - "Could not add to IGB \n Please update IGB to latest version"
                Open in IGB - "Success \n Opening genome in IGB"

                Running IGB 9.1.10 (IGB status check returns version, add data source endpoint is available)
                Add Hub to IGB - "Success \n Adding data source to IGB"
                Open in IGB - "Success \n Opening genome in IGB"

                1. Check the version returned from igbStatusCheck, if no version, assume less than 9.1.10.
                2. How much work would it add to insert the genome name clicked into the toast?
                Show
                nfreese Nowlan Freese added a comment - Alternatives: IGB is not running: Add Hub to IGB - "IGB is not running \n Please start IGB" Open in IGB - "IGB is not running \n Please start IGB" Running IGB 9.1.4 (IGB status check does not return version (version added in 9.1.6), no add data source endpoint) Add Hub to IGB - "Could not add to IGB \n Please update IGB to latest version" Open in IGB - "Success \n Opening genome in IGB" Running IGB 9.1.8 (IGB status check returns version, no add data source endpoint) Add Hub to IGB - "Could not add to IGB \n Please update IGB to latest version" Open in IGB - "Success \n Opening genome in IGB" Running IGB 9.1.10 (IGB status check returns version, add data source endpoint is available) Add Hub to IGB - "Success \n Adding data source to IGB" Open in IGB - "Success \n Opening genome in IGB" Check the version returned from igbStatusCheck, if no version, assume less than 9.1.10. How much work would it add to insert the genome name clicked into the toast?
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                nfreese Nowlan Freese added a comment - - edited

                Please also change the Quickload URI button to provide the trackhub quickload uri without the igbDataSource endpoint.

                For example:
                Replace: http://127.0.0.1:7085/igbDataSource?quickloadurl=https://translate.bioviz.org/api/?hubUrl=https://raw.githubusercontent.com/Kraus-Lab/publichubs/master/breast_cancer_lncrna_pmid_26236012/hub.txt%26filePath=/&quickloadname=Breast%20Cancer%20lncRNA

                With this: https://translate.bioviz.org/api/?hubUrl=https://raw.githubusercontent.com/Kraus-Lab/publichubs/master/breast_cancer_lncrna_pmid_26236012/hub.txt&filePath=/

                Show
                nfreese Nowlan Freese added a comment - - edited Please also change the Quickload URI button to provide the trackhub quickload uri without the igbDataSource endpoint. For example: Replace: http://127.0.0.1:7085/igbDataSource?quickloadurl=https://translate.bioviz.org/api/?hubUrl=https://raw.githubusercontent.com/Kraus-Lab/publichubs/master/breast_cancer_lncrna_pmid_26236012/hub.txt%26filePath=/&quickloadname=Breast%20Cancer%20lncRNA With this: https://translate.bioviz.org/api/?hubUrl=https://raw.githubusercontent.com/Kraus-Lab/publichubs/master/breast_cancer_lncrna_pmid_26236012/hub.txt&filePath=/
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Story Points 0.5 1
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                karthik Karthik Raveendran added a comment -

                Changes mentioned above has been implemented. See Commit

                Show
                karthik Karthik Raveendran added a comment - Changes mentioned above has been implemented. See Commit
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                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 ]
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                nfreese Nowlan Freese added a comment -

                Messages after commit:

                IGB is not running:
                Add Hub to IGB - "IGB is not running. \n Please start IGB"
                Open in IGB - "IGB is not running: \n Start IGB to open this genome version in IGB."

                Running IGB 9.1.4 (IGB status check does not return version (version added in 9.1.6), no add data source endpoint)
                Add Hub to IGB - "Could not add to IGB \n Please update IGB to latest version"
                Open in IGB - "Opening in IGB \n Establishing connection with IGB..."

                Running IGB 9.1.8 (IGB status check returns version, no add data source endpoint)
                Add Hub to IGB - "Could not add to IGB \n Please update IGB to latest version"
                Open in IGB - "Opening in IGB \n Establishing connection with IGB..."

                Running IGB 9.1.10 (IGB status check returns version, add data source endpoint is available)
                Add Hub to IGB - "Success! \n Adding data source to IGB"
                Open in IGB - "Opening in IGB \n Establishing connection with IGB..."

                Note: To test locally, need to set the BACKEND_DOMAIN to https://translate.bioviz.org in util.js.

                export const BACKEND_DOMAIN = "https://translate.bioviz.org";

                Ready for pull request.

                Show
                nfreese Nowlan Freese added a comment - Messages after commit: IGB is not running: Add Hub to IGB - "IGB is not running. \n Please start IGB" Open in IGB - "IGB is not running: \n Start IGB to open this genome version in IGB." Running IGB 9.1.4 (IGB status check does not return version (version added in 9.1.6), no add data source endpoint) Add Hub to IGB - "Could not add to IGB \n Please update IGB to latest version" Open in IGB - "Opening in IGB \n Establishing connection with IGB..." Running IGB 9.1.8 (IGB status check returns version, no add data source endpoint) Add Hub to IGB - "Could not add to IGB \n Please update IGB to latest version" Open in IGB - "Opening in IGB \n Establishing connection with IGB..." Running IGB 9.1.10 (IGB status check returns version, add data source endpoint is available) Add Hub to IGB - "Success! \n Adding data source to IGB" Open in IGB - "Opening in IGB \n Establishing connection with IGB..." Note: To test locally, need to set the BACKEND_DOMAIN to https://translate.bioviz.org in util.js. export const BACKEND_DOMAIN = "https: //translate.bioviz.org" ; Ready for pull request.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Karthik Raveendran [ karthik ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
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                karthik Karthik Raveendran added a comment -

                PR Submitted: https://bitbucket.org/lorainelab/bioviz/pull-requests/103/igbf-3164-fix-toast-message-to-be-precise

                Show
                karthik Karthik Raveendran added a comment - PR Submitted: https://bitbucket.org/lorainelab/bioviz/pull-requests/103/igbf-3164-fix-toast-message-to-be-precise
                nfreese Nowlan Freese made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                nfreese Nowlan Freese made changes -
                Assignee Karthik Raveendran [ karthik ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                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 ]
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                ann.loraine Ann Loraine added a comment - - edited

                Merged. Deployed to BioViz main and ready for testing at bioviz.org.

                Show
                ann.loraine Ann Loraine added a comment - - edited Merged. Deployed to BioViz main and ready for testing at bioviz.org.
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Assignee Ann Loraine [ aloraine ] Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3169 [ IGBF-3169 ]
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                nfreese Nowlan Freese added a comment -

                Tested on Firefox 103.0.2 on macOS 12.5.1 using latest IGB master.
                Reset preferences to default and removed the .igb folder.

                Toasts appear correctly and the Quickload URI copied button copies the expected URI.

                Note: While testing the Open in IGB link between various versions of IGB, it appears that the latest IGB master opens genomes much slower than previous versions of IGB, such as 9.1.8 release. I have created IGBF-3169 to investigate this discrepancy.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Tested on Firefox 103.0.2 on macOS 12.5.1 using latest IGB master. Reset preferences to default and removed the .igb folder. Toasts appear correctly and the Quickload URI copied button copies the expected URI. Note: While testing the Open in IGB link between various versions of IGB, it appears that the latest IGB master opens genomes much slower than previous versions of IGB, such as 9.1.8 release. I have created IGBF-3169 to investigate this discrepancy. Closing ticket.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Karthik Raveendran [ karthik ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    karthik Karthik Raveendran
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: