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  1. IGB
  2. IGBF-1149

default file extension for graph tracks

    Details

    • Sprint:
      Fall 2017

      Description

      When saving a graph track there are two file type options: .gr or .bedgraph.

      You select one from a pull down menu.

      When the save track window comes up, one of them is already selected (the default).

      But which one? its seems to be a random pick every time.
      Its not consistently the same one I most recently used (which would be ideal)
      And its not consistently the recommend one (which would be unideal but acceptable).

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            ieclabau Ivory Blakley (Inactive) created issue -
            ieclabau Ivory Blakley (Inactive) made changes -
            Field Original Value New Value
            Link This issue relates to IGBF-1090 [ IGBF-1090 ]
            ieclabau Ivory Blakley (Inactive) made changes -
            Link This issue relates to IGBF-1128 [ IGBF-1128 ]
            ieclabau Ivory Blakley (Inactive) made changes -
            Rank Ranked higher
            ieclabau Ivory Blakley (Inactive) made changes -
            Sprint Spring 2017 [ 47 ]
            ieclabau Ivory Blakley (Inactive) made changes -
            Rank Ranked lower
            ieclabau Ivory Blakley (Inactive) made changes -
            Assignee Ann Loraine [ aloraine ] Ivory Clabaugh [ ieclabau ]
            ieclabau Ivory Blakley (Inactive) made changes -
            Status Open [ 1 ] In Progress [ 3 ]
            Hide
            ieclabau Ivory Blakley (Inactive) added a comment -

            The graph file extension options are .gr and .bedgraph.
            The value when the pop up window opens is randomly picked between those.

            Likewise, in saving annotation files,
            The annotation file options are bed (.bed) or bed detail (.bed).
            The value when the pop up window opens is randomly picked between those.

            Show
            ieclabau Ivory Blakley (Inactive) added a comment - The graph file extension options are .gr and .bedgraph. The value when the pop up window opens is randomly picked between those. Likewise, in saving annotation files, The annotation file options are bed (.bed) or bed detail (.bed). The value when the pop up window opens is randomly picked between those.
            ieclabau Ivory Blakley (Inactive) made changes -
            Assignee Ivory Clabaugh [ ieclabau ]
            Hide
            ieclabau Ivory Blakley (Inactive) added a comment - - edited

            I never did get mvn clean install to work, it keeps failing tests.

            But the same tests fail from master, so I really don't think the changes in this issue are causing any problems, but it would be best if the first level reviewer could get the tests to run (at least the ones that don't fail on the master branch).

            I have implemented and tested a solution on a branch called IGBF-1149.
            I'm moving this to get first level review.

            In the current IGB, click Save Track As... several times, notice that the default file type is randomly picked from the two options.
            You can do this very quickly by selecting a track and using control+S, and click cancel, and repeat.

            With this fix, the graph tracks consistently get the "bedgraph" default and annotation tracks get the "bed" default. This is not based on the most recent selection or the recommendation, but it is consistent. And it so happens that the first type when you sort this way is the option I would recommend for each case.

            Show
            ieclabau Ivory Blakley (Inactive) added a comment - - edited I never did get mvn clean install to work, it keeps failing tests. But the same tests fail from master, so I really don't think the changes in this issue are causing any problems, but it would be best if the first level reviewer could get the tests to run (at least the ones that don't fail on the master branch). I have implemented and tested a solution on a branch called IGBF-1149 . I'm moving this to get first level review. In the current IGB, click Save Track As... several times, notice that the default file type is randomly picked from the two options. You can do this very quickly by selecting a track and using control+S, and click cancel, and repeat. With this fix, the graph tracks consistently get the "bedgraph" default and annotation tracks get the "bed" default. This is not based on the most recent selection or the recommendation, but it is consistent. And it so happens that the first type when you sort this way is the option I would recommend for each case.
            ieclabau Ivory Blakley (Inactive) made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            ieclabau Ivory Blakley (Inactive) made changes -
            Assignee Mason Meyer [ mason ]
            Hide
            ieclabau Ivory Blakley (Inactive) added a comment -

            I'm assigning to Mason for first level review.

            Show
            ieclabau Ivory Blakley (Inactive) added a comment - I'm assigning to Mason for first level review.
            Show
            ieclabau Ivory Blakley (Inactive) added a comment - My branch for this issue is called IGBF-1149 . https://bitbucket.org/IvoryBlak/integrated-genome-browser/branch/IGBF-1149
            sneha Sneha Ramesh Watharkar (Inactive) made changes -
            Assignee Mason Meyer [ mason ] Jennifer Daly [ jdaly ]
            sneha Sneha Ramesh Watharkar (Inactive) made changes -
            Status Needs 1st Level Review [ 10005 ] Reviewing [ 10301 ]
            Hide
            sneha Sneha Ramesh Watharkar (Inactive) added a comment -

            1st Level Testing:

            • Does not fail any additional tests
            • Save As... file extension drop down menu showed 'BED (bed)' first when saving an annotation, and 'Graph (bedgraph)' first when saving a graph, as expected.
            • All four choices saved files successfully ( BED (bed), bed detail (bed), Graph (bedgraph), Graph (gr) )
            • Documentation comments in AbstractExportFileAction.java is clear enough that someone adding a new file extension will know that they will be sorted alphabetically.
            Show
            sneha Sneha Ramesh Watharkar (Inactive) added a comment - 1st Level Testing: Does not fail any additional tests Save As... file extension drop down menu showed 'BED (bed)' first when saving an annotation, and 'Graph (bedgraph)' first when saving a graph, as expected. All four choices saved files successfully ( BED (bed), bed detail (bed), Graph (bedgraph), Graph (gr) ) Documentation comments in AbstractExportFileAction.java is clear enough that someone adding a new file extension will know that they will be sorted alphabetically.
            sneha Sneha Ramesh Watharkar (Inactive) made changes -
            Status Reviewing [ 10301 ] Ready for Pull Request [ 10304 ]
            sneha Sneha Ramesh Watharkar (Inactive) made changes -
            Assignee Jennifer Daly [ jdaly ] Ivory Clabaugh [ ieclabau ]
            Hide
            ieclabau Ivory Blakley (Inactive) added a comment -

            I rebased from main master and created a pull request.

            Show
            ieclabau Ivory Blakley (Inactive) added a comment - I rebased from main master and created a pull request.
            ieclabau Ivory Blakley (Inactive) made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            Hide
            ieclabau Ivory Blakley (Inactive) added a comment -

            I'm reassigned this issue to Ann so she can look at the pull request.

            Show
            ieclabau Ivory Blakley (Inactive) added a comment - I'm reassigned this issue to Ann so she can look at the pull request.
            ieclabau Ivory Blakley (Inactive) made changes -
            Assignee Ivory Clabaugh [ ieclabau ] 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 ] Pull Request Submitted [ 10101 ]
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            ann.loraine Ann Loraine made changes -
            Status Pull Request Submitted [ 10101 ] Needs Testing [ 10002 ]
            mason Mason Meyer (Inactive) made changes -
            Assignee Mason Meyer [ mason ]
            mason Mason Meyer (Inactive) made changes -
            Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
            Hide
            mason Mason Meyer (Inactive) added a comment -

            @Ivory:

            I started testing this issue by trying to reproduce the original problem on IGB 9.0.0, however, I was not able to do so. I tried several different files and used the method of hitting Ctrl "S" to quickly bring up the save menu and then selecting cancel but I always saw "BED" come up for annotations and "BEDGRAPH" come up for graphs; I never saw "BED_Detail" or "Gr" come up first. The issue is functioning as expected, but I feel uncomfortable closing an issue when I was not able to reproduce the original problem. Any idea on why I am not able to do this? I tested on Windows and Mac, by the way. Please let me know if you have any advice on this.

            Show
            mason Mason Meyer (Inactive) added a comment - @Ivory: I started testing this issue by trying to reproduce the original problem on IGB 9.0.0, however, I was not able to do so. I tried several different files and used the method of hitting Ctrl "S" to quickly bring up the save menu and then selecting cancel but I always saw "BED" come up for annotations and "BEDGRAPH" come up for graphs; I never saw "BED_Detail" or "Gr" come up first. The issue is functioning as expected, but I feel uncomfortable closing an issue when I was not able to reproduce the original problem. Any idea on why I am not able to do this? I tested on Windows and Mac, by the way. Please let me know if you have any advice on this.
            mason Mason Meyer (Inactive) made changes -
            Status Testing In Progress [ 10003 ] Needs Testing [ 10002 ]
            Hide
            ieclabau Ivory Blakley (Inactive) added a comment -

            That is odd. Perhaps try a fresh install of IGB 9.0.0, just to be sure that you are testing it on the live bioviz.org IGB, and not the main master IGB (both of which show version 9.0.0).

            Not mind-blowing or anything, but that's all I can think of. I've seen the random-choice on every machine I've looked at (my mac, my windows, Jenn's linux).

            Show
            ieclabau Ivory Blakley (Inactive) added a comment - That is odd. Perhaps try a fresh install of IGB 9.0.0, just to be sure that you are testing it on the live bioviz.org IGB, and not the main master IGB (both of which show version 9.0.0). Not mind-blowing or anything, but that's all I can think of. I've seen the random-choice on every machine I've looked at (my mac, my windows, Jenn's linux).
            Hide
            mason Mason Meyer (Inactive) added a comment -

            After testing this issue it appears that the story is resolved:

            *Save As... file extension drop down menu showed 'BED (bed)' first when saving an annotation, and 'Graph (bedgraph)' first when saving a graph, as expected.
            *All four choices saved files successfully ( BED (bed), bed detail (bed), Graph (bedgraph), Graph (gr) )

            • There is no missing data or additional artifacts seen when opening the saved files.
              *There seems to be no additional behavior caused by this code change.

            Since the issue is resolved, it will now be closed.

            Show
            mason Mason Meyer (Inactive) added a comment - After testing this issue it appears that the story is resolved: *Save As... file extension drop down menu showed 'BED (bed)' first when saving an annotation, and 'Graph (bedgraph)' first when saving a graph, as expected. *All four choices saved files successfully ( BED (bed), bed detail (bed), Graph (bedgraph), Graph (gr) ) There is no missing data or additional artifacts seen when opening the saved files. *There seems to be no additional behavior caused by this code change. Since the issue is resolved, it will now be closed.
            mason Mason Meyer (Inactive) made changes -
            Resolution Done [ 10000 ]
            Status Needs Testing [ 10002 ] Closed [ 6 ]
            mason Mason Meyer (Inactive) made changes -
            Fix Version/s 9.0.1 Minor Release [ 10500 ]
            ann.loraine Ann Loraine made changes -
            Workflow Loraine Lab Workflow [ 17791 ] Fall 2019 Workflow Update [ 19796 ]
            ann.loraine Ann Loraine made changes -
            Workflow Fall 2019 Workflow Update [ 19796 ] Revised Fall 2019 Workflow Update [ 21915 ]

              People

              • Assignee:
                mason Mason Meyer (Inactive)
                Reporter:
                ieclabau Ivory Blakley (Inactive)
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                Dates

                • Created:
                  Updated:
                  Resolved: