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  1. IGB
  2. IGBF-1371

Remove obsolete dependency statements from pom.xml

        Details

        • Story Points:
          0.5
        • Sprint:
          Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2

          Description

          net.sf.samtools packages have been replaced by htsjkd.samtools packages.

          References to the obsolete net.sf.samtools packages need to be removed from child POM files.

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              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1366 Fix App Manager failure to load bundles when running in Development mode

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                kkorey Kiran Korey (Inactive) made changes -
                Field Original Value New Value
                Status Open [ 1 ] In Progress [ 3 ]
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                kkorey Kiran Korey (Inactive) added a comment -

                Removed net.sf.samtools library, the changes are in the branch mentioned below.
                https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1098-sam-so

                Ready for first level review.

                Show
                kkorey Kiran Korey (Inactive) added a comment - Removed net.sf.samtools library, the changes are in the branch mentioned below. https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1098-sam-so Ready for first level review.
                kkorey Kiran Korey (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-1366 [ IGBF-1366 ]
                ann.loraine Ann Loraine made changes -
                Story Points 1 0.5
                Labels Intermediate
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2018 Part 3 [ 50 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                ieclabau Ivory Blakley (Inactive) added a comment - - edited

                The branch mentioned above (https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1098-sam-so) has been replaced by this branch:
                https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1371-library
                _________________________

                My comments:

                The commit for removing the net.sf.samtools is clearly just that.
                And the formatting fixes are very simple and clearly just that.
                So the code-review and the git review are good. : )

                These changes are minor and only affect the pom file. We have already removed all of the import statements for the samtools library.
                To make sure IGB is able to build without the net.sf.sam-exec library, I removed it from my .m2, and I cleared IGB's bundle directory, and I ran $mvn clean install.
                IGB was able to build with tests, without errors, and run. The net.sf.sam-exec was not re-downloaded to .m2, so it looks like IGB is completely free of the dependency.
                That's the only functional review I can think of for this, and it looks good. : )

                I'm reassigning this to Kiran and moving it to ready for pull request.

                ----Because this changes the same files as the IGBF-1366 fix, you may want to put all changes on one branch. Otherwise you will need to do a rebase between the pull requests (maybe ask Ann).

                Show
                ieclabau Ivory Blakley (Inactive) added a comment - - edited The branch mentioned above ( https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1098-sam-so ) has been replaced by this branch: https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1371-library _________________________ My comments: The commit for removing the net.sf.samtools is clearly just that. And the formatting fixes are very simple and clearly just that. So the code-review and the git review are good. : ) These changes are minor and only affect the pom file. We have already removed all of the import statements for the samtools library. To make sure IGB is able to build without the net.sf.sam-exec library, I removed it from my .m2, and I cleared IGB's bundle directory, and I ran $mvn clean install. IGB was able to build with tests, without errors, and run. The net.sf.sam-exec was not re-downloaded to .m2, so it looks like IGB is completely free of the dependency. That's the only functional review I can think of for this, and it looks good. : ) I'm reassigning this to Kiran and moving it to ready for pull request. ----Because this changes the same files as the IGBF-1366 fix, you may want to put all changes on one branch. Otherwise you will need to do a rebase between the pull requests (maybe ask Ann).
                ieclabau Ivory Blakley (Inactive) made changes -
                Status Needs 1st Level Review [ 10005 ] Ready for Pull Request [ 10304 ]
                ieclabau Ivory Blakley (Inactive) made changes -
                Assignee Kiran Korey [ kkorey ] Ivory Blakley [ ieclabau ]
                ieclabau Ivory Blakley (Inactive) made changes -
                Assignee Ivory Blakley [ ieclabau ] Kiran Korey [ kkorey ]
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                kkorey Kiran Korey (Inactive) added a comment -

                I have made all the changes for 1366 and 1371 in a single branch.

                https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1371-library

                Please do take a look at it once.

                Show
                kkorey Kiran Korey (Inactive) added a comment - I have made all the changes for 1366 and 1371 in a single branch. https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1371-library Please do take a look at it once.
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                ieclabau Ivory Blakley (Inactive) added a comment -

                This looks good.
                comments are in issue IGBF-1366

                Show
                ieclabau Ivory Blakley (Inactive) added a comment - This looks good. comments are in issue IGBF-1366
                ieclabau Ivory Blakley (Inactive) made changes -
                Status Ready for Pull Request [ 10304 ] Ready for Pull Request [ 10304 ]
                kkorey Kiran Korey (Inactive) made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
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                kkorey Kiran Korey (Inactive) added a comment -

                Moving this issue to pull request submitted.
                Will close IGBF-1366 once the case study document is ready.

                Show
                kkorey Kiran Korey (Inactive) added a comment - Moving this issue to pull request submitted. Will close IGBF-1366 once the case study document is ready.
                ann.loraine Ann Loraine made changes -
                Summary Remove obsolete dependency statements from POM.xml Remove obsolete dependency statements from pom.xml
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Assignee Kiran Korey [ kkorey ] Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment -

                Possible problem:

                • sam-ext library references are gone, but samVersion is still defined in parent POM (top-level pom.xml)

                Check to see if samVersion variable is still needed now that sam-ext library is purged. If not, remove it from parent POM and instances of it being used in child POMs.

                Show
                ann.loraine Ann Loraine added a comment - Possible problem: sam-ext library references are gone, but samVersion is still defined in parent POM (top-level pom.xml) Check to see if samVersion variable is still needed now that sam-ext library is purged. If not, remove it from parent POM and instances of it being used in child POMs.
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Kiran Korey [ kkorey ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Open [ 1 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                kkorey Kiran Korey (Inactive) added a comment -

                I have changed the sam-ext version to htsjdkVersion.
                Also, there is a newer version of the library which is available, do you want me to change the version to the newer version.

                Show
                kkorey Kiran Korey (Inactive) added a comment - I have changed the sam-ext version to htsjdkVersion. Also, there is a newer version of the library which is available, do you want me to change the version to the newer version.
                kkorey Kiran Korey (Inactive) made changes -
                Status Open [ 1 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Assignee Kiran Korey [ kkorey ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2018 Part 3 [ 50 ] Summer 2018 Part 3, Fall 2018 1 [ 50, 51 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked lower
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2018 Part 3, Fall 2018 1 [ 50, 51 ] Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2 [ 50, 51, 52 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked lower
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                sneha Sneha Ramesh Watharkar (Inactive) added a comment -

                Tested on master for the functional testing case mentioned by Ivory.
                Works fine!
                Moving it to done column!

                Show
                sneha Sneha Ramesh Watharkar (Inactive) added a comment - Tested on master for the functional testing case mentioned by Ivory. Works fine! Moving it to done column!
                sneha Sneha Ramesh Watharkar (Inactive) made changes -
                Assignee Sneha Ramesh Watharkar [ jdaly ]
                sneha Sneha Ramesh Watharkar (Inactive) made changes -
                Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
                sneha Sneha Ramesh Watharkar (Inactive) made changes -
                Resolution Done [ 10000 ]
                Status Testing In Progress [ 10003 ] Closed [ 6 ]
                sneha Sneha Ramesh Watharkar (Inactive) made changes -
                Assignee Sneha Ramesh Watharkar [ jdaly ] Kiran Korey [ kkorey ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18071 ] Fall 2019 Workflow Update [ 19929 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 19929 ] Revised Fall 2019 Workflow Update [ 22049 ]

                  People

                  • Assignee:
                    kkorey Kiran Korey (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
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                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: