making gatk --version print the version #5537

lbergelson · 2018-12-19T19:16:39Z

lbergelson · 2018-12-19T19:20:27Z

./gatk --version
Using GATK wrapper script /Users/louisb/Workspace/gatk/build/install/gatk/bin/gatk
Running:
    /Users/louisb/Workspace/gatk/build/install/gatk/bin/gatk --version
The Genome Analysis Toolkit (GATK) v4.0.12.0-1-g10aa8c7-SNAPSHOT

This is different than the output of the tool --version...

Using GATK wrapper script /Users/louisb/Workspace/gatk/build/install/gatk/bin/gatk
Running:
    /Users/louisb/Workspace/gatk/build/install/gatk/bin/gatk PrintReads --version
Version:4.0.12.0-1-g10aa8c7-SNAPSHOT
Tool returned:
0

I can change this to be that version, or we can change barclay to do it differently and provide more info. It might be useful to print the library versions with both commands as well.. that's printed during the normal run...

14:19:57.172 INFO  PrintReads - HTSJDK Version: 2.18.1
14:19:57.173 INFO  PrintReads - Picard Version: 2.18.16

@cmnbroad What do you think?

cmnbroad · 2018-12-19T21:51:04Z

src/main/java/org/broadinstitute/hellbender/Main.java

+                    System.out.println(String.format("%s v%s", getToolkitName(), getVersion()));
+                    return 0;
+                }
+            }.doWork();


It would be nice to find a solution that worked for downstream toolkits - I think this would only work if they repackaged GATK classes in their own jar ? I'm not sure I see an obvious solution that doesn't involve a lot more work though.

Either way, what do you think about adding a couple of methods to RuntimeUtils or somewhere that get the toolkit name and version number from the manifest, and then call those from here and from the corresponding CommandLineProgram methods ? It still wouldn't completely solve the downstream toolkit issue, but at least we wouldn't have to spin up a dummy CLP. Longer term I really want to fix the special argument handling and delegation in Barclay.

BTW, by "from the manifest" I meant "they way they do now", ie., getClass().getPackage().getImplementationVersion().

sooheelee · 2018-12-20T03:35:00Z

This is great. For what it's worth, I would love for the Picard and HTSJDK versions to print also with gatk --version.

lbergelson · 2018-12-21T18:17:16Z

@cmnbroad I extracted a bunch of methods to RunTimeUtils and made it cleaner. I fixed a todo in CommandLineProgram that was related as well. It's hard to test these things because the tests sometimes but don't always the jar with a manifest so I didn't test most of the new methods. I can try to do something more clever if you think it's necessary though...

cmnbroad

Looks great when test pass - thx for doing all that.

codecov-io · 2019-01-02T20:26:06Z

Codecov Report

Merging #5537 into master will decrease coverage by 0.009%.
The diff coverage is 72.917%.

@@               Coverage Diff               @@
##              master     #5537       +/-   ##
===============================================
- Coverage     87.085%   87.075%   -0.009%     
- Complexity     31222     31227        +5     
===============================================
  Files           1915      1915               
  Lines         144079    144097       +18     
  Branches       15891     15899        +8     
===============================================
+ Hits          125471    125473        +2     
- Misses         12837     12841        +4     
- Partials        5771      5783       +12

Impacted Files	Coverage Δ	Complexity Δ
...ls/runtime/StreamingProcessControllerUnitTest.java	`91% <ø> (-2.694%)`	`16 <0> (-2)`
...t/java/org/broadinstitute/hellbender/MainTest.java	`82.927% <100%> (+0.876%)`	`6 <1> (+1)`	⬆️
...stitute/hellbender/utils/runtime/RuntimeUtils.java	`70.588% <66.667%> (-3.096%)`	`10 <4> (+4)`
...hellbender/utils/runtime/RuntimeUtilsUnitTest.java	`87.5% <66.667%> (-12.5%)`	`4 <1> (+1)`
.../main/java/org/broadinstitute/hellbender/Main.java	`72.43% <69.231%> (-0.207%)`	`51 <1> (+3)`
...stitute/hellbender/cmdline/CommandLineProgram.java	`85.333% <80%> (+2.216%)`	`44 <6> (+1)`	⬆️
...nder/utils/runtime/StreamingProcessController.java	`67.299% <0%> (-4.265%)`	`33% <0%> (-4%)`
...lotypecaller/readthreading/ReadThreadingGraph.java	`88.861% <0%> (+0.253%)`	`145% <0%> (+1%)`	⬆️

* extracting methods from CommandLineProgram -> RuntimeUtils for getting version and manifest attributes * fixing a todo in CommandLineProgram * opportunistically changing an instance of map.entryset().stream().foreach() -> map.foreach()

I was told that it is a flakey test that tests something that is no longer necessary.

lbergelson · 2019-01-02T22:09:04Z

resolving merge conflicts...

lbergelson · 2019-01-02T22:09:35Z

@cmnbroad You're ok with this test being removed? Just wanted to double check before merging.

cmnbroad · 2019-01-02T23:55:45Z

@lbergelson Yes - this test is a leftover artifact of the original implementation, but we're no longer dependent on the features tested it so its fine to remove.

lbergelson requested a review from cmnbroad December 19, 2018 19:16

lbergelson assigned cmnbroad Dec 19, 2018

cmnbroad reviewed Dec 19, 2018

View reviewed changes

lbergelson force-pushed the lb_version branch 2 times, most recently from ce58ba3 to 54cb2be Compare December 21, 2018 18:15

cmnbroad approved these changes Dec 21, 2018

View reviewed changes

lbergelson force-pushed the lb_version branch from 386ce03 to 97f096a Compare January 2, 2019 19:54

lbergelson added 4 commits January 2, 2019 17:05

making gatk --version print the version

7be06d7

responding to comments

64b774f

* extracting methods from CommandLineProgram -> RuntimeUtils for getting version and manifest attributes * fixing a todo in CommandLineProgram * opportunistically changing an instance of map.entryset().stream().foreach() -> map.foreach()

fix NPE

5f66d40

removing failing test

c254442

I was told that it is a flakey test that tests something that is no longer necessary.

lbergelson force-pushed the lb_version branch from 97f096a to c254442 Compare January 2, 2019 22:08

lbergelson merged commit 9562a48 into master Jan 3, 2019

lbergelson deleted the lb_version branch January 3, 2019 03:33

lbergelson mentioned this pull request Feb 1, 2019

Add --version #5627

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making gatk --version print the version #5537

making gatk --version print the version #5537

lbergelson commented Dec 19, 2018

lbergelson commented Dec 19, 2018

cmnbroad Dec 19, 2018

cmnbroad Dec 19, 2018

sooheelee commented Dec 20, 2018

lbergelson commented Dec 21, 2018

cmnbroad left a comment

codecov-io commented Jan 2, 2019 •

edited

lbergelson commented Jan 2, 2019

lbergelson commented Jan 2, 2019

cmnbroad commented Jan 2, 2019

making gatk --version print the version #5537

making gatk --version print the version #5537

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lbergelson commented Dec 19, 2018

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codecov-io commented Jan 2, 2019 • edited

Codecov Report

lbergelson commented Jan 2, 2019

lbergelson commented Jan 2, 2019

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codecov-io commented Jan 2, 2019 •

edited