Skip to content

Release 1.0.1 of jmztab-m
Compare
Choose a tag to compare
@nilshoffmann nilshoffmann released this 30 Aug 15:58
· 196 commits to master since this release
release-1.0.1
695629b

This is release 1.0.1 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.

Please note that release 1.0.0 was incompletely deployed to Maven Central.
Release 1.0.1 is virtually identical to 1.0.0 and replaces it.

This release fixes issues with the validation of cv and user parameters.

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/1.0.1/jmztabm-api-1.0.1-r.zip,

Python: https://search.maven.org/remotecontent?filepath=de/isas/mztab/jmztabm-api/1.0.1/jmztabm-api-1.0.1-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/1.0.1/jmztabm-cli-1.0.1-bin.zip

Running

java -jar jmztabm-cli-1.0.1.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-1.0.1.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-1.0.1.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-1.0.1.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>1.0.1</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>1.0.1</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.

Assets 2
Loading