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Funcotation Engine Refactoring #5134

Merged
merged 4 commits into from
Sep 19, 2018
Merged

Funcotation Engine Refactoring #5134

merged 4 commits into from
Sep 19, 2018

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LeeTL1220
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  • Added a FuncotationEngine class. This is meant to decouple the CLI from the funcotation generation.
  • Moved the querying of datasources into the funcotation factories. This means that the funcotation factory generates the funcotations using a feature context, instead of a map of feature inputs.
  • Funcotation factories now encapsulate the feature input of the source file. Non-locatable funcotation factories will have a null for this attribute.

@droazen droazen self-requested a review August 24, 2018 19:07
@droazen droazen self-assigned this Aug 24, 2018
@droazen droazen changed the title Funcotation Enginer Refactoring Funcotation Engine Refactoring Aug 24, 2018
@jonn-smith
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@LeeTL1220 can you fix broken build prior to review?

@LeeTL1220
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@jonn-smith @droazen I forgot to run the tests on my laptop before PR. Anyway, should be okay now. If not, I'll fix (again).

@LeeTL1220
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@jonn-smith @droazen Had to make two very small changes. Should be ready for review if tests pass.

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codecov-io commented Aug 28, 2018 •
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Codecov Report

Merging #5134 into master will increase coverage by 65.599%.
The diff coverage is 90.181%.

@@               Coverage Diff                @@
##              master     #5134        +/-   ##
================================================
+ Coverage     21.259%   86.858%   +65.599%     
- Complexity      4663     30392     +25729     
================================================
  Files           1110      1833       +723     
  Lines          65822    139740     +73918     
  Branches       10536     15841      +5305     
================================================
+ Hits           13993    121375    +107382     
+ Misses         49755     12826     -36929     
- Partials        2074      5539      +3465
Impacted Files Coverage Δ Complexity Δ
...broadinstitute/hellbender/engine/FeatureInput.java 94.366% <ø> (+21.127%) 18 <0> (+6) ⬆️
...org/broadinstitute/hellbender/engine/GATKTool.java 91.589% <ø> (+21.356%) 100 <0> (+28) ⬆️
...uncotator/mafOutput/MafOutputRendererUnitTest.java 98.535% <ø> (ø) 16 <0> (?)
...decs/xsvLocatableTable/XsvLocatableTableCodec.java 82.716% <ø> (+74.074%) 60 <0> (+54) ⬆️
...te/hellbender/tools/funcotator/FuncotationMap.java 84.211% <ø> (+84.211%) 28 <0> (+28) ⬆️
...ataSources/xsv/SimpleKeyXsvFuncotationFactory.java 87.097% <ø> (+87.097%) 27 <0> (+27) ⬆️
...tools/funcotator/FuncotatorArgumentCollection.java 100% <100%> (ø) 1 <1> (?)
...tools/funcotator/DataSourceFuncotationFactory.java 86.364% <100%> (+69.697%) 16 <5> (+12) ⬆️
...oadinstitute/hellbender/engine/FeatureContext.java 78.571% <100%> (+67.761%) 28 <1> (+27) ⬆️
...cotator/dataSources/vcf/VcfFuncotationFactory.java 86.897% <100%> (+86.897%) 47 <0> (+47) ⬆️
... and 1699 more

jonn-smith
jonn-smith requested changes Aug 29, 2018
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Some minor comments and questions. In general it looks good.

I'm wondering if there is a way to restrict the access to some of the exposed methods that are used only in testing. My guess is no, but there could be some Java wizardry that can make it happen (aside from reflection, which would work but be really nasty).

Maybe @droazen or @lbergelson have an idea.

src/main/java/org/broadinstitute/hellbender/engine/FeatureManager.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/DataSourceUtils.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/DataSourceFuncotationFactory.java Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/DataSourceUtils.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/engine/FuncotationEngine.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/engine/FuncotationEngine.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/engine/FuncotationEngine.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/engine/FuncotationEngine.java Outdated Show resolved Hide resolved
...st/java/org/broadinstitute/hellbender/tools/funcotator/engine/FuncotationEngineUnitTest.java Outdated Show resolved Hide resolved
droazen
droazen requested changes Aug 29, 2018
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Added my comments @LeeTL1220. I've proposed a simple refactoring surrounding the creation of the FeatureInputs that should allow you to further reduce the amount of code left in Functotator itself.

src/main/java/org/broadinstitute/hellbender/engine/FeatureManager.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/Funcotator.java Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/engine/FuncotationEngine.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/DataSourceFuncotationFactory.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/DataSourceUtils.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/engine/FuncotationEngine.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/engine/FuncotationEngine.java Outdated Show resolved Hide resolved
@droazen droazen assigned LeeTL1220 and unassigned droazen and jonn-smith Aug 30, 2018
@jonn-smith jonn-smith assigned jonn-smith and unassigned LeeTL1220 Sep 12, 2018
LeeTL1220 and others added 2 commits September 13, 2018 15:32
@LeeTL1220 @jonn-smith
Extraced a FuncotatorEngine from Funcotator.java
b822fc5 
A large refactoring of the architecture of Funcotator to make the
creation of annotations separate from the command line interface.

This will enable better testing of the annotation functionality by
allowing for unit tests that can test the created funcotations directly
(as opposed to requiring integration tests for the same purpose).
@jonn-smith
Fixing a small error made in the rebasing onto master.
5a3b039
@jonn-smith jonn-smith assigned droazen and unassigned jonn-smith Sep 13, 2018
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@droazen back to you for a final look-over.

droazen
droazen requested changes Sep 18, 2018
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Final review complete, back to @jonn-smith for some last changes. Merge after addressing this round of comments.

Summary: I think we can push a bit more code out of Funcotator and into the FuncotatorEngine, and I also would like to try to eliminate some parallel test-only codepaths.

src/main/java/org/broadinstitute/hellbender/engine/FeatureContext.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/engine/FeatureManager.java Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/DataSourceFuncotationFactory.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/DataSourceFuncotationFactory.java Outdated Show resolved Hide resolved
...va/org/broadinstitute/hellbender/tools/funcotator/dataSources/vcf/VcfFuncotationFactory.java Outdated Show resolved Hide resolved
...oadinstitute/hellbender/tools/funcotator/dataSources/xsv/LocatableXsvFuncotationFactory.java Outdated Show resolved Hide resolved
...oadinstitute/hellbender/tools/funcotator/dataSources/xsv/LocatableXsvFuncotationFactory.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/engine/FeatureContext.java Outdated Show resolved Hide resolved
src/main/java/org/broadinstitute/hellbender/engine/GATKTool.java Outdated Show resolved Hide resolved
@droazen droazen assigned jonn-smith and unassigned droazen Sep 18, 2018
@jonn-smith jonn-smith merged commit 6391a47 into master Sep 19, 2018
@jonn-smith jonn-smith deleted the ll_funcotation_engine_refactor branch September 19, 2018 18:44
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