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  1. IGB
  2. IGBF-3370

Add link to advanced search info to IGB interface

    Details

    • Story Points:
      3
    • Sprint:
      Summer 5 2023 July 10, Summer 6 2023 July 24, Summer 7 2023 Aug 7

      Description

      Situation: As part of IGBF-3236 we are adding additional meta characters to the Advanced Search residues logic (R = A or G). This information should be made easily available to IGB users.

      Task: Add an info icon button to the Advanced Search tab that explains this and the other "advanced searches" a user can do.

      Additional task: update the advanced search wiki page with the additional meta character information.

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          Issue Links

            Activity

            nfreese Nowlan Freese created issue -
            nfreese Nowlan Freese made changes -
            Field Original Value New Value
            Epic Link IGBF-1765 [ 17855 ]
            nfreese Nowlan Freese made changes -
            Link This issue relates to IGBF-3236 [ IGBF-3236 ]
            nfreese Nowlan Freese made changes -
            Sprint Summer 5 2023 July 10 [ 174 ]
            ann.loraine Ann Loraine made changes -
            Description Situation: As part of IGBF-3236 we are adding additional meta characters to the Advanced Search residues logic (R = A or G). This information should be made easily available to IGB users.

            Task: Add an info icon button to the Advanced Search tab that appears or is only clickable for residue searches. Clicking the button will either open a window/tooltip with the list of meta characters and wildcards, or will link to a webpage with the meta characters and wildcards.

            Additional task: update the [advanced search wiki page|https://wiki.bioviz.org/confluence/display/igbman/Advanced+Search] with the additional meta character information.
            Situation: As part of IGBF-3236 we are adding additional meta characters to the Advanced Search residues logic (R = A or G). This information should be made easily available to IGB users.

            Task: Add an info icon button to the Advanced Search tab that explains this and the other "advanced searches" a user can do.

            Additional task: update the [advanced search wiki page|https://wiki.bioviz.org/confluence/display/igbman/Advanced+Search] with the additional meta character information.
            ann.loraine Ann Loraine made changes -
            Summary Add residue search info (regex/metacharacters) to IGB interface Add link to advanced search info to IGB interface
            ann.loraine Ann Loraine made changes -
            Sprint Summer 5 2023 July 10 [ 174 ] Summer 5 2023 July 10, Summer 6 2023 July 24 [ 174, 175 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            kgopu Kaushik Gopu made changes -
            Assignee Kaushik Gopu [ kgopu ]
            nfreese Nowlan Freese made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            kgopu Kaushik Gopu made changes -
            Attachment Advanced Search Design.pdf [ 17919 ]
            kgopu Kaushik Gopu made changes -
            Comment [ * I am attaching the document, which contains designs of the use case, for reference. [^Advanced Search Design.pdf] ]
            Hide
            ann.loraine Ann Loraine added a comment -

            Regarding the target of the proposed informational link for "design one":

            • Instead of sending the user to a page on wiki.bioviz.org, let's send the user to a new page on BioViz.org: "https://bioviz.org/advancedsearch.html"

            The benefit of sending users to a page on bioviz.org is that it's now very easy to modify and update bioviz.org pages. From there, we can link to the Advanced Search documentation on wiki.bioviz.org. We could also configure the server with a redirect rule that would automatically send the user there. There are many options, all very easy to implement.

            Linking directly to a pages on wiki.bioviz.org, which hosts wiki software Confluence, is problematic because the addresses of pages on wiki.bioviz.org frequently change. such as when we edit page titles.

            Show
            ann.loraine Ann Loraine added a comment - Regarding the target of the proposed informational link for "design one": Instead of sending the user to a page on wiki.bioviz.org, let's send the user to a new page on BioViz.org: "https://bioviz.org/advancedsearch.html" The benefit of sending users to a page on bioviz.org is that it's now very easy to modify and update bioviz.org pages. From there, we can link to the Advanced Search documentation on wiki.bioviz.org. We could also configure the server with a redirect rule that would automatically send the user there. There are many options, all very easy to implement. Linking directly to a pages on wiki.bioviz.org, which hosts wiki software Confluence, is problematic because the addresses of pages on wiki.bioviz.org frequently change. such as when we edit page titles.
            ann.loraine Ann Loraine made changes -
            Link This issue relates to IGBF-3396 [ IGBF-3396 ]
            nfreese Nowlan Freese made changes -
            Status In Progress [ 3 ] To-Do [ 10305 ]
            Hide
            kgopu Kaushik Gopu added a comment - - edited

            added info button which takes user to advancedsearch page.

            • commit
            • branch
            • There is a info button that appears right next to clear button and if it gets clicked, a html page, which is broken currently, will appear in default browser.
            • moving to first level review.
            Show
            kgopu Kaushik Gopu added a comment - - edited added info button which takes user to advancedsearch page. commit branch There is a info button that appears right next to clear button and if it gets clicked, a html page, which is broken currently, will appear in default browser. moving to first level review.
            kgopu Kaushik Gopu made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            kgopu Kaushik Gopu made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            nfreese Nowlan Freese made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            nfreese Nowlan Freese made changes -
            Assignee Kaushik Gopu [ kgopu ] Nowlan Freese [ nfreese ]
            Hide
            nfreese Nowlan Freese added a comment - - edited

            Tested Kaushik's branch on Mac:

            1. Loaded the Arabidopsis genome.
            2. Under the Advanced Search tab the i info button appears for all four of the search dropdown options.
            3. Clicking the button opens a web browser and navigates to https://bioviz.org/advancedsearch.html
            4. Hovering over the button shows a tooltip with "About Advance Search"

            My only comment would be to change the tooltip to "About Advanced Search". That way it matches the tab (Advanced Search). i.e. Advance -> Advanced

            Everything else is working correctly.

            Show
            nfreese Nowlan Freese added a comment - - edited Tested Kaushik's branch on Mac: Loaded the Arabidopsis genome. Under the Advanced Search tab the i info button appears for all four of the search dropdown options. Clicking the button opens a web browser and navigates to https://bioviz.org/advancedsearch.html Hovering over the button shows a tooltip with "About Advance Search" My only comment would be to change the tooltip to "About Advanced Search". That way it matches the tab (Advanced Search). i.e. Advance -> Advanced Everything else is working correctly.
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ] Kaushik Gopu [ kgopu ]
            nfreese Nowlan Freese made changes -
            Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
            Hide
            kgopu Kaushik Gopu added a comment - - edited
            • renamed tooltip text from advance to advanced.
            • pull request submitted.
            Show
            kgopu Kaushik Gopu added a comment - - edited renamed tooltip text from advance to advanced. pull request submitted.
            kgopu Kaushik Gopu made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            kgopu Kaushik Gopu made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            kgopu Kaushik Gopu made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            kgopu Kaushik Gopu made changes -
            Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
            nfreese Nowlan Freese made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            nfreese Nowlan Freese made changes -
            Assignee Kaushik Gopu [ kgopu ] Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
            nfreese Nowlan Freese made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ]
            ann.loraine Ann Loraine made changes -
            Sprint Summer 5 2023 July 10, Summer 6 2023 July 24 [ 174, 175 ] Summer 5 2023 July 10, Summer 6 2023 July 24, Summer 7 2023 Aug 7 [ 174, 175, 176 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            nfreese Nowlan Freese made changes -
            Assignee Ann Loraine [ aloraine ]
            Hide
            ann.loraine Ann Loraine added a comment -

            Since we have time to make some improvements, I would like to request the following:

            • Modify the code itself so that methods, variables, and class names use the prefix "advancedSearch" instead of "advanceSearch". This is because "advanced" is an adjective modifying "Search", where "Search" is acting as a noun. The word "Advance" can be a verb or a noun, but never an adjective, so far as I know. The code will be a little more comprehensible to English speakers if we better adhere to the grammar conventions people are familiar with. But obviously, this change does not affect the functionality. It is a code aesthetics change only.
            Show
            ann.loraine Ann Loraine added a comment - Since we have time to make some improvements, I would like to request the following: Modify the code itself so that methods, variables, and class names use the prefix "advancedSearch" instead of "advanceSearch". This is because "advanced" is an adjective modifying "Search", where "Search" is acting as a noun. The word "Advance" can be a verb or a noun, but never an adjective, so far as I know. The code will be a little more comprehensible to English speakers if we better adhere to the grammar conventions people are familiar with. But obviously, this change does not affect the functionality. It is a code aesthetics change only.
            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 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ] Kaushik Gopu [ kgopu ]
            Hide
            kgopu Kaushik Gopu added a comment - - edited
            • Modified the branch so that methods, variables, and class names use *advanced" as prefix instead of advance.
            • If everything looks fine, will squash the commits and submit the pull request.
            Show
            kgopu Kaushik Gopu added a comment - - edited Modified the branch so that methods, variables, and class names use *advanced" as prefix instead of advance. If everything looks fine, will squash the commits and submit the pull request.
            kgopu Kaushik Gopu made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            kgopu Kaushik Gopu made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            nfreese Nowlan Freese made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            nfreese Nowlan Freese made changes -
            Assignee Kaushik Gopu [ kgopu ] Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
            Hide
            nfreese Nowlan Freese added a comment - - edited

            All instances of advance have been changed to advanced.

            Ready for pull request.

            Show
            nfreese Nowlan Freese added a comment - - edited All instances of advance have been changed to advanced. Ready for pull request.
            nfreese Nowlan Freese made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            nfreese Nowlan Freese made changes -
            Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
            nfreese Nowlan Freese made changes -
            Status Reviewing Pull Request [ 10303 ] To-Do [ 10305 ]
            nfreese Nowlan Freese made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            nfreese Nowlan Freese made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            nfreese Nowlan Freese made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            nfreese Nowlan Freese made changes -
            Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ] Kaushik Gopu [ kgopu ]
            Hide
            kgopu Kaushik Gopu added a comment -

            pull request submitted.

            Show
            kgopu Kaushik Gopu added a comment - pull request submitted.
            kgopu Kaushik Gopu made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            nfreese Nowlan Freese made changes -
            Assignee Kaushik Gopu [ kgopu ] Ann Loraine [ aloraine ]
            ann.loraine Ann Loraine made changes -
            Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            Thanks for making the changes Kaushik Gopu. PR is now merged. Built development branch installers and ran bioviz-playbook "setup.yml" to copy the installers over to the "early access" section of BioViz.org Web site.

            Read for testing.

            To test:

            • Download and install "early access" IGB from the BioViz.org web site; run the new IGB version
            • Choose File > Preferences > Other > Reset Preferences to defaults (to ensure a "fresh" run of IGB)
            • Restart this new version of IGB
            • Choose Help > About IGB to confirm the latest commit is from this ticket
            • Select Advanced Search Tab
            • You should observe a "i" icon on the interface. Click the icon and confirm that a Web page opens in your default Web browser and that the page being shown is the https://bioviz.org/advancedsearch.html
            • Choose the "log" tab. You should see no errors or warnings. If you see any errors or warnings, repeat the above steps using IGB version 9.1.10 to determine if the errors or warnings are new.

            If testing reveals any problems, report them here and move the ticket to "To-Do" for further investigation. Or, if the problems exist in previous version of IGB, consult with the team to determine if a new ticket needs to be created.

            Show
            ann.loraine Ann Loraine added a comment - - edited Thanks for making the changes Kaushik Gopu . PR is now merged. Built development branch installers and ran bioviz-playbook "setup.yml" to copy the installers over to the "early access" section of BioViz.org Web site. Read for testing. To test: Download and install "early access" IGB from the BioViz.org web site; run the new IGB version Choose File > Preferences > Other > Reset Preferences to defaults (to ensure a "fresh" run of IGB) Restart this new version of IGB Choose Help > About IGB to confirm the latest commit is from this ticket Select Advanced Search Tab You should observe a "i" icon on the interface. Click the icon and confirm that a Web page opens in your default Web browser and that the page being shown is the https://bioviz.org/advancedsearch.html Choose the "log" tab. You should see no errors or warnings. If you see any errors or warnings, repeat the above steps using IGB version 9.1.10 to determine if the errors or warnings are new. If testing reveals any problems, report them here and move the ticket to "To-Do" for further investigation. Or, if the problems exist in previous version of IGB, consult with the team to determine if a new ticket needs to be created.
            ann.loraine Ann Loraine made changes -
            Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            ann.loraine Ann Loraine made changes -
            Assignee Molly Davis [ molly ]
            nfreese Nowlan Freese made changes -
            Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
            nfreese Nowlan Freese made changes -
            Assignee Molly Davis [ molly ] Nowlan Freese [ nfreese ]
            Hide
            nfreese Nowlan Freese added a comment -

            Followed testing outlined above on Mac.

            Everything working correctly, no issues found in log.

            Closing ticket.

            Show
            nfreese Nowlan Freese added a comment - Followed testing outlined above on Mac. Everything working correctly, no issues found in log. Closing ticket.
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ] Kaushik Gopu [ kgopu ]
            nfreese Nowlan Freese made changes -
            Resolution Done [ 10000 ]
            Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
            pkulzer Paige Kulzer made changes -
            Fix Version/s 10.0.0 Major Release [ 10900 ]

              People

              • Assignee:
                kgopu Kaushik Gopu
                Reporter:
                nfreese Nowlan Freese
              • Votes:
                0 Vote for this issue
                Watchers:
                3 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: