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Release 0.9.9 of jmztab-m
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@nilshoffmann nilshoffmann released this 18 Jul 17:11
· 207 commits to master since this release
release-0.9.9
30ce8f2

This is release 0.9.9 of the jmztab-m libraries that was published to Maven Central.
It implements the draft of mzTab-m 2.0 at https://github.com/HUPO-PSI/mzTab.

This release fixes issues with the default mapping file in the previous release.

To access the release artefacts, please go to Maven Central:

https://search.maven.org/#search%7Cga%7C1%7Cde.isas.mztab

For everyone who is working off any generated code, please update to the latest version:

R: https://search.maven.org/remotecontent?filepath=de/isas/mztab/jmztabm-api/0.9.9/jmztabm-api-0.9.9-r.zip,

Python: https://search.maven.org/remotecontent?filepath=de/isas/mztab/jmztabm-api/0.9.9/jmztabm-api-0.9.9-python.zip

The CLI package bundles parser and semantic validator and contains sample files and the latest mapping file:

https://search.maven.org/remotecontent?filepath=de/isas/mztab/jmztabm-cli/0.9.9/jmztabm-cli-0.9.9-bin.zip

Running

java -jar jmztabm-cli-0.9.9.jar

on your command line will show you the possible arguments (staying close to the old jmztab).

Run a basic parse and validation on Error level:

java -jar jmztabm-cli-0.9.9.jar -check inFile=examples/MTBLS263.mztab

Run a basic parse and validation followed by applying a provided mapping file on Error level:

java -jar jmztabm-cli-0.9.9.jar -check inFile=examples/MTBLS263.mztab -checkSemantic mappingFile=cv-mapping/mzTab-M-mapping.xml

Running the same on Info level yields additional messages (for optional parameters):

java -jar jmztabm-cli-0.9.9.jar -check inFile=examples/MTBLS263.mztab -checkSemantic mappingFile=cv-mapping/mzTab-M-mapping.xml -level Info

To use the IO libraries (reading, writing and structural and logical validation) in your own Maven projects, use the following dependency:

<dependency>
    <groupId>de.isas.mztab</groupId>
    <artifactId>jmztabm-io</artifactId>
    <version>0.9.9</version>
</dependency>

To use the semantic validation with the mapping file in your own Maven project, use the following dependency:

<dependency>
    <groupId>de.isas.mztab</groupId>
    <artifactId>jmztabm-validation</artifactId>
    <version>0.9.9</version>
</dependency>

The semantic validation requires access to EBI's Ontology Lookup Service to resolve child terms in the mzTab file against their potential parents in the mapping file.

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