Update pom file.

[ypriverol]

New version of jmzIdentML. 1.2.10 PR.

[ypriverol]

Release has been done: https://github.com/PRIDE-Utilities/jmzIdentML/issues/7

[codecov-io]

Codecov Report

Merging #138 into master will decrease coverage by 0.3%. The diff coverage is 36.99%.

@@             Coverage Diff             @@
##             master    #138      +/-   ##
===========================================
- Coverage      52.8%   52.5%   -0.31%     
- Complexity     2316    2331      +15     
===========================================
  Files           174     174              
  Lines         17488   17432      -56     
  Branches       2879    2941      +62     
===========================================
- Hits           9235    9153      -82     
+ Misses         7290    7279      -11     
- Partials        963    1000      +37

Impacted Files	Coverage Δ	Complexity Δ
.../protein/inference/SpectrumExtractorInference.java	84.61% <ø> (-0.05%)	65 <0> (ø)
...c/pia/modeller/protein/ProteinExecuteCommands.java	0% <ø> (ø)	0 <0> (ø)	:arrow_down:
.../de/mpc/pia/tools/openms/jaxb/DigestionEnzyme.java	44% <ø> (+1.69%)	3 <0> (ø)	:arrow_down:
...ler/protein/inference/OccamsRazorWorkerThread.java	0% <0%> (ø)	0 <0> (ø)	:arrow_down:
...mpc/pia/modeller/report/filter/AbstractFilter.java	28.39% <0%> (ø)	28 <0> (ø)	:arrow_down:
...ava/de/mpc/pia/modeller/peptide/ReportPeptide.java	57.25% <0%> (ø)	69 <0> (ø)	:arrow_down:
.../java/de/mpc/pia/intermediate/piaxml/ScoreXML.java	78.57% <0%> (ø)	8 <0> (ø)	:arrow_down:
...c/pia/modeller/report/filter/FilterComparator.java	21.12% <0%> (ø)	1 <0> (ø)	:arrow_down:
...c/pia/intermediate/compiler/PIACachedCompiler.java	71.15% <0%> (ø)	28 <0> (ø)	:arrow_down:
...java/de/mpc/pia/tools/matomo/PIAMatomoTracker.java	0% <0%> (ø)	0 <0> (ø)	:arrow_down:
... and 46 more

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[julianu]

The release of jmzidentml does unfortunately not really help. The original version in the PR https://github.com/PRIDE-Utilities/jmzIdentML/pull/3 did massively improve jmzidentml performance, but the current release 1.2.10 does unfortunately not. Running the test MzIdentMLExportAndImportTest takes 18s with release 1.2.5 and 240s with >=1.2.6 (including 1.2.10).

I did not have time to check why, but will try to have a look later. For now, I have build issues with this part of the jmzidentml pom, when trying to build the GitHub code directly:

<parent>
    <groupId>uk.ac.ebi.pride.architectural</groupId>
    <artifactId>pride-core</artifactId>
    <version>1.0.1</version>
</parent>

Basically, I cannot find the dependency. Is it available somewhere?

[ypriverol]

I have the feeling is the writing process. I have check some of the tests and they are really slow writing.

[julianu]

The test stucks mainly during the reading of the mzIdentML file. I will dig into this later and come back. If you could help me with building the jmzidentml local, would be great.

[ypriverol]

Here the pride-core project. You can build it locally. BTW, I will go back to the previous version of jmzIdentML.

[ypriverol]

New changes have been implemented to the way we generate the hashCode on every important object without needs to generate an object inside the hashCode. See this discussion about the performance of https://stackoverflow.com/questions/5038204/apache-commons-equals-hashcode-builder

[ypriverol]

@julianu This has been fixed locally in my machine and I will commit a new version soon. We need to release first all the dependencies.