Issue with Spectrum Reader
Closed this issue · 7 comments
Good morning,
I’ve made a few modifications to the ms-data-core-api (2.0.8-SNAPSHOT version). I, then, ran "mvn install" to get it on my local machine and added this version to my pom file, which is working with the 2.0.8-SNAPSHOT version.
I do, however, get some weird behavior when using 2.0.8-SNAPSHOT instead of the 2.0.5 fat jar from github’s release. Weird behavior include:
When debugging my application, I get the following errors during initial setup:
java.io.FileNotFoundException: /home/.m2/repository/edu/ucar/netcdf4/4.5.5/jcl-over-slf4j-1.7.7.jar
java.io.FileNotFoundException: /home/.m2/repository/edu/ucar/netcdf4/4.5.5/ehcache-core-2.6.2.jar
Whenever I use uk.ac.ebi.pride.utilities.data.controller.impl.ControllerImpl.MzXmlControllerImpl.getSpectrumById(Comparable id), the id value gets outputted to stdout, which doesn’t occur on 2.0.5. This can’t be ignored because it slows down considerably the program. I traced this to here.
I do get a lot of logback warnings that I don’t get using 2.0.5
Is there something that I’m missing here, regarding the warnings and the file not found exception? Should I be making a fat jar to use locally as well? I didn’t think that’d be necessary. Maybe I’m not building the lib correctly?
Thank you very much for your assistance
The sysout that outputs the Spectrum ID value can be located here, which I understand is out of scope for ms-data-core-api.
Also, can you build the source code from release 2.0.5? For me maven informs that it fails under two tests:
Failed tests:
MzIdentMLIgnoreProteinInferenceTest.testGetIdentificationIDs:126 The id of the first identification should be PDH_psu|NC_LIV_020800_0 expected:<DBSeq_1_[psu|NC_LIV_10274]0> but was:<DBSeq_1_[Rnd1psu|NC_LIV_14506]0>
MzTabControllerImplTest.testProteinIdentification:72 The first protein has
Tests run: 98, Failures: 2, Errors: 0, Skipped: 0
I updated that in the current version. Can you check the current version. I also update the some of the dependencies including jmzTab. I don't think I can go back to version 2.0.5. But I will be more that happy to support you and help you the deploy this version 2.0.8.
I can’t look into it right now but I’ll check the updated version as soon as I get some time. Thank you so much for your support, I’ll keep you updated if anything goes wrong!
Natan Streppel
On Aug 3, 2016, at 12:03 PM, Yasset Perez-Riverol notifications@github.com wrote:
I updated that in the current version. Can you check the current version. I also update the some of the dependencies including jmzTab. I don't think I can go back to version 2.0.5. But I will be more that happy to support you and help you the deploy this version 2.0.8.
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Please do it. I will leave open this issue until you have a look.!!!
Also, feel free to contribute, just make a pull-request and I will integrate your changes.
I'm sorry it took so long to reply. You can close the bug now!
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