Details
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Type:
Improvement
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:1
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Epic Link:
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Sprint:Fall 2019 Sprint 1
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:
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T E S T S
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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
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IGBF-1981 Investigate and fix test errors in BookMarkTest.java (BookMark Plugin)
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- Closed
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Activity
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.
Created new ticket for bookmarktest.java(IGBF-1981) and linked to this ticket.
Pull Request Submitted
Logs have been removed.
Looks there are still some unnecessary things being printed during build. Looking into this a bit more.
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.
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.
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.