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  1. IGB
  2. IGBF-2253

Implement TwentyThreeAndMeVariationSym using test-first programming

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          1.5
        • Epic Link:
        • Sprint:
          Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun

          Description

          Implement methods in genotyping TwentyThreeAndMeSeqSymmetry class.
          Write javadoc comments and check format by compiling javadocs.

          First:

          • Create unit tests for methods (may require some re-factoring)
          • Add new stub methods as required (in case existing methods should call other methods)

          Next:

          • Implement methods
          • Re-factor class as needed.

          Note: You may need to mock other classes used by TwentyThreeAndMeSeqSymmetry.

            Attachments

              Issue Links

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              Task - A task that needs to be done. IGBF-2252 Implement TwentyThreeAndMeSymLoader using test-first programming

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-2246 [ 18393 ]
                ann.loraine Ann Loraine made changes -
                Link This issue blocks IGBF-2252 [ IGBF-2252 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Summary Implement TwentyThreeAndMeSeqSymmetry using test-first programming Implement TwentyThreeAndMeVariationSym using test-first programming
                nfreese Nowlan Freese made changes -
                Sprint Spring 3 : 17 Feb to 28 Feb [ 87 ] Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 87, 89 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Sprint Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 87, 89 ] Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 87, 89, 90 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 87, 89, 90 ] Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 87, 89, 90, 91 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                stiwari8 Srishti Tiwari (Inactive) added a comment -

                Hi Dr. Loraine,

                Please review my changes for visualizing 23andme file format:

                https://bitbucket.org/srishtitiwari/integrated-genome-browser/commits/36a86308d9f7e21036a2a50b42383f7538e54a52

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - Hi Dr. Loraine, Please review my changes for visualizing 23andme file format: https://bitbucket.org/srishtitiwari/integrated-genome-browser/commits/36a86308d9f7e21036a2a50b42383f7538e54a52
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Thanks! Please see comments on the PR.

                cc: Srishti Tiwari

                Show
                ann.loraine Ann Loraine added a comment - Thanks! Please see comments on the PR. cc: Srishti Tiwari
                Hide
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                stiwari8 Srishti Tiwari (Inactive) added a comment -

                Hi Dr. [~aloraine],

                I have made the changes as mentioned in the comments and raised a Pull request. Please review the same:

                https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/781/igbf-2253-igbf-2252-implement/diff

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - Hi Dr. [~aloraine] , I have made the changes as mentioned in the comments and raised a Pull request. Please review the same: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/781/igbf-2253-igbf-2252-implement/diff
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Sorry, I should asked about this yesterday:

                There are some lines being deleted - <include>*/.properties</include>

                I have a doubt as to why this required.

                cc: Srishti Tiwari

                Show
                ann.loraine Ann Loraine added a comment - Sorry, I should asked about this yesterday: There are some lines being deleted - <include>* / .properties</include> I have a doubt as to why this required. cc: Srishti Tiwari
                Hide
                Permalink
                stiwari8 Srishti Tiwari (Inactive) added a comment - - edited

                Hi Professor,

                I was seeing this error message in my pom that element <includes> is not allowed here.
                It was also not able to resolve the <include> tag.
                It still shows the same error message.

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - - edited Hi Professor, I was seeing this error message in my pom that element <includes> is not allowed here. It was also not able to resolve the <include> tag. It still shows the same error message.
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Attachment the includes tag error message.png [ 14689 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Ok thanks for the explanation!
                PR is merged.

                cc: Noor Zahara and Srishti Tiwari

                Show
                ann.loraine Ann Loraine added a comment - Ok thanks for the explanation! PR is merged. cc: Noor Zahara and Srishti Tiwari
                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 -
                Sprint Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 87, 89, 90, 91 ] Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr [ 87, 89, 90, 91, 92 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr [ 87, 89, 90, 91, 92 ] Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 87, 89, 90, 91, 92, 93 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 87, 89, 90, 91, 92, 93 ] Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 87, 89, 90, 91, 92, 93, 94 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 87, 89, 90, 91, 92, 93, 94 ] Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun [ 87, 89, 90, 91, 92, 93, 94, 95 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment - - edited

                Note: Not yet fully tested. Testing and validation will be first part of next development push.

                Show
                ann.loraine Ann Loraine added a comment - - edited Note: Not yet fully tested. Testing and validation will be first part of next development push.

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: