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  1. IGB
  2. IGBF-1977

Remove unneeded logging and println statements from tests

        Details

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

          Description

          Many of IGB's test cases are printing unnecessary stuff to console.

          This is unnecessary. If a test fails, we will notice. If it passes, we don't want to hear about it.

          Here is an example of gratuitous printing of stuff to the console:

          -------------------------------------------------------
          T E S T S
          -------------------------------------------------------
          Running apollo.analysis.RemoteBlastNCBITest
          GAAGTTTCCTTATCATCATTAATCATGCCTATGAAAACCCTAACCGGCCT
          https://blast.ncbi.nlm.nih.gov/Blast.cgi?RID=NJHUT165015&CMD=Get
          RID=NJHUT165015
          GAAGTTTCCTTATCATCATTAATCATGCCTATGAAAACCCTAACCGGCCTACATATTTGCAGTCTCTTTTAGGTCAGGAATCTAATGAGAATGAATTATTTTATTTTATTTAACAATAATTGGAGCATGTCATTAATTCTCTTTATTCTTCTTACACAACTAATCATTTAGATGTGTTACAATATTATTTCCTTTAGTCATTTTCATAATTTTAATACCTCCGTACTTTTCACTAATACCTCCCCTTTTAATTTTCATTATTTCTTCTTTTCTATCAGTCTATGCATGCATTCTTTTGAATATTAAAATGCATTTTATATTCTTTTGACAACTATGCACAAGCCTTTTGAGACACATCTACACAATATAATAGCACAAGCCTTTATGAGACATATCTACACAATATCATTGCTACTTGTAGACTATTTGGAATACGTATTTACATATTCCATTGTATCATCCCTTTGCAAATGTTTTATACATATAACTAACATATACATTATTCGTAACTTTGTTCCCCTATATCGAAAAATGTGGGCTACACATATAACTAACATATATATATATATGTATGTTTATATGATATAGTCTCCATGTCTATATATCTTATATATTACATGTTTCATGTTTACGGTCAAGGGAGTATTTTTATACGCATACACAATCATACACACTTAACCCTACTTATAATGATGTAGGTTCATATATTTATCTTATTTTAGGATCATTCGATCACAAATTATACGGACCCTCATACTCTCTAAAGATATACAAAATCCGCTATGTCATATCCGATCCGAATTAGCAGCTAAAGAAAAACAAACACATGCATCTACTGAAGATTTGAGTCTCGAGTGCTTAGTTACATGAACTATCACAAAGGATATGGATAATATAAGGTGTACTGAAGTATGTCTATGCAATGGGAGGGAAATACATTCTGTTAAATGACTTGTCGATTTGATCTTTCATGCCAAAGATTAAAAATTTAACACTTAATTAACGCAATCTTACCATATATTCATGGACTACATGCAGAATAGTAATTCTCCCAACCTTTCTAGTTATTTACCTGAATGTGTTTATGTACATGGACCGGTAACCTCATGTATATATGCACATACTGACAATCTGACATACATATATATAGTAGATATGACAACAACAACAAAAAAAAAAAAAATTCCTTGTTCGTGAAGCATGATCTGAGAGTTCCTAGTTAGCATGTTGTGTGGGATCATACTTTTAATATGCTGCAAGTACCAGTCAATTTTAGTATGGGAAACTATAAACATGTATAATCAACCAATGAACACGTCAATAACCTATTGAACAGCTTAGGGTGAAAATTATGATCCGTAGAGACAGCATTTAAAAGTTCCTTACGTCCACGTAAAATAATATATCAATTTATACATATACATGTGTAAACTGTGTATATATAGGGTAGGTATATGTGTATATATATAGTAATTGACAAATGATTTAGGTTCTAACATATATTCTAAAAGTACTCATGAGTTTGTGAGATCTACACAAGATACCTGATTTGATAAAAATGGCTTCAACTTGCAATCCAAACCAAACCAAACAAAGTTAATAACCAAGGGTTAATAACAAAAACAAGAATCTAGAATTAGTAAAAAAATGAGAAATTAATGAACCTGTGATCATAAAAAAAGTCAAACAATGTGAAAACATATCATACCTTTTGTTCTTTTTAATATAATAATTGAATTACTAAATGGATGGATCAGTCCTTCTTCCATAGCTAGCTTCTCTTTATTTTCTCTGCCCATAACCTGCAGAAAATCTCTTTAACCGAGCAAAATTACAAGAGTAACCAAACAAACAAAATAGGACCATCAGAGAGAGAGAAAAGAGTGCCTTTTTTTGGACCTGCCCATTAGCTTAGAATGTACCATGAAACACTTTGTCAGTGTAGGGAGATAGGCACAGAGAGTACAATTCATGAAATTTATAAGCTTTTTTCCCACTCATCAATT
          https://blast.ncbi.nlm.nih.gov/Blast.cgi?RID=NJHUWRD7015&CMD=Get
          RID=NJHUWRD7015
          Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.481 sec - in apollo.analysis.RemoteBlastNCBITest

          For this task, please inspect the testing code and remove println and logging statements.

            Attachments

              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1981 Investigate and fix test errors in BookMarkTest.java (BookMark Plugin)

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-1765 [ 17855 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                svallapu Sai Charan Reddy Vallapureddy (Inactive) made changes -
                Assignee Sai Charan Reddy Vallapureddy [ svallapu ]
                svallapu Sai Charan Reddy Vallapureddy (Inactive) made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                Hide
                Permalink
                svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment -

                Branch: https://bitbucket.org/svallapu/charan_igb/branch/IGBF-1977

                Checked all projects test files. Removed unnecessary print and logger statements.

                Did not touch:
                1. Necessary log statements
                2. ignored part of the code (using "ignored" annotation)
                3. commented print and log statements.

                Note: While going through the projects, I found that BookMarkTest.java (BookMark Plugin) dependencies are not resolved. I will fix this in another ticket.

                Show
                svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment - Branch: https://bitbucket.org/svallapu/charan_igb/branch/IGBF-1977 Checked all projects test files. Removed unnecessary print and logger statements. Did not touch: 1. Necessary log statements 2. ignored part of the code (using "ignored" annotation) 3. commented print and log statements. Note: While going through the projects, I found that BookMarkTest.java (BookMark Plugin) dependencies are not resolved. I will fix this in another ticket.
                svallapu Sai Charan Reddy Vallapureddy (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                svallapu Sai Charan Reddy Vallapureddy (Inactive) made changes -
                Assignee Sai Charan Reddy Vallapureddy [ svallapu ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Please create new issue for the BookMarkTest.java issue and link it to IGBF-1977 (this Jira ticket.)
                Once that is done, please submit pull request and move this ticket forward on the board.

                Show
                ann.loraine Ann Loraine added a comment - Please create new issue for the BookMarkTest.java issue and link it to IGBF-1977 (this Jira ticket.) Once that is done, please submit pull request and move this ticket forward on the board.
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] Open [ 1 ]
                ann.loraine Ann Loraine made changes -
                Assignee Sai Charan Reddy Vallapureddy [ svallapu ]
                svallapu Sai Charan Reddy Vallapureddy (Inactive) made changes -
                Link This issue relates to IGBF-1981 [ IGBF-1981 ]
                Hide
                Permalink
                svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment -

                Created new ticket for bookmarktest.java(IGBF-1981) and linked to this ticket.

                Pull Request Submitted

                Show
                svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment - Created new ticket for bookmarktest.java( IGBF-1981 ) and linked to this ticket. Pull Request Submitted
                svallapu Sai Charan Reddy Vallapureddy (Inactive) made changes -
                Status Open [ 1 ] Pull Request Submitted [ 10101 ]
                svallapu Sai Charan Reddy Vallapureddy (Inactive) made changes -
                Assignee Sai Charan Reddy Vallapureddy [ svallapu ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18701 ] Fall 2019 Workflow Update [ 19057 ]
                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 ]
                noor91zahara Noor Zahara (Inactive) made changes -
                Assignee Noor Zahara [ noor91zahara ]
                noor91zahara Noor Zahara (Inactive) made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                Hide
                Permalink
                noor91zahara Noor Zahara (Inactive) added a comment -

                Logs have been removed.

                Show
                noor91zahara Noor Zahara (Inactive) added a comment - Logs have been removed.
                noor91zahara Noor Zahara (Inactive) made changes -
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                noor91zahara Noor Zahara (Inactive) made changes -
                Assignee Noor Zahara [ noor91zahara ] Sai Charan Reddy Vallapureddy [ svallapu ]
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-1765 [ 17855 ] IGBF-1531 [ 17617 ]
                ann.loraine Ann Loraine made changes -
                Summary Remove loggin and println statements from tests Remove unneeded logging and println statements from tests
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 19057 ] Revised Fall 2019 Workflow Update [ 22488 ]
                ann.loraine Ann Loraine made changes -
                Status Closed [ 6 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Assignee Sai Charan Reddy Vallapureddy [ svallapu ] Ann Loraine [ aloraine ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Looks there are still some unnecessary things being printed during build. Looking into this a bit more.

                Show
                ann.loraine Ann Loraine added a comment - Looks there are still some unnecessary things being printed during build. Looking into this a bit more.
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Tests are exposing places where tested code prints to stdout instead of using the logging system.
                For example: core/genometry/src/main/java/com/affymetrix/genometry/parsers/graph/BgrParser.java.

                Show
                ann.loraine Ann Loraine added a comment - Tests are exposing places where tested code prints to stdout instead of using the logging system. For example: core/genometry/src/main/java/com/affymetrix/genometry/parsers/graph/BgrParser.java.
                ann.loraine Ann Loraine made changes -
                Comment [ Merged to master. ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Some notes:

                • Tests in core/das package declaration did not match directory structure. Fixed.

                Pushed new IGBF-1977 branch to my fork and merged with lorainelab/master.

                Show
                ann.loraine Ann Loraine added a comment - Some notes: Tests in core/das package declaration did not match directory structure. Fixed. Pushed new IGBF-1977 branch to my fork and merged with lorainelab/master.
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Fix Version/s 9.1.0 Major Release [ 10601 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                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 -
                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 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: