Releases: lifs-tools/jmzTab-m
Release 1.0.6 of jmztab-m
This is release 1.0.6 of the jmztab-m libraries that was published to Maven Central.
It implements the mzTab-m 2.0 specification for metabolomics at https://github.com/HUPO-PSI/mzTab.
Major Changes:
- This release requires at least Java 11 to run.
Minor Changes:
- The internal data model was changed to simplify generation of OpenAPI clients in R and Python concerning the
IndexedElementclass. This change should not affect users of the JAVA version, unless you are using mzTab-M JSON data generated before version 1.0.6. You can convert the data by serializing it to mzTab-M format first and then saving it to JSON with the 1.0.6 version library (e.g. using the command line interface).
Features:
- Added MzTabAccess to simplify accessing objects by id.
Bug Fixes:
Release 1.0.6 should be backwards compatible to 1.0.5, 1.0.4, 1.0.3 and 1.0.2.
However, due to a stricter validation of the ms scan id referencing, files that have validated before may now fail to validate. Please contact us if you need help fixing your files.
This release also includes any amendments that were made as a result of the publication reviewers' feedback and the feedback from the PSI document review process. We have substantially updated the API documentation and have added examples from the specification document and have increased the unit test coverage.
To access the release artefacts, please go to Maven Central:
https://search.maven.org/#search%7Cga%7C1%7Cde.isas.mztab
To access the latest JavaDoc, please to the project's Maven page:
https://lifs-tools.github.io/jmzTab-m/
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/1.0.6/jmztabm-api-1.0.6-r.zip,
The reference implementation for R is now being developed here: https://github.com/lifs-tools/rmzTab-m
Python: https://search.maven.org/remotecontent?filepath=de/isas/mztab/jmztabm-api/1.0.6/jmztabm-api-1.0.6-python.zip
The reference implementation for Python 3 is now being developed here: https://github.com/lifs-tools/pymzTab-m
The CLI package bundles parser and semantic validator and contains sample files and the latest mapping file:
Running
java -jar jmztabm-cli-1.0.6.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-1.0.6.jar -c examples/MTBLS263.mztab
Run a basic parse and validation followed by applying the default mapping file on Error level for semantic validation:
java -jar jmztabm-cli-1.0.6.jar -c examples/MTBLS263.mztab -s
Run a basic parse and validation followed by applying a provided mapping file on Error level for semantic validation:
java -jar jmztabm-cli-1.0.6.jar -c examples/MTBLS263.mztab -s cv-mapping/mzTab-M-mapping.xml
Running the same on Info level yields additional messages (for optional parameters):
java -jar jmztabm-cli-1.0.6.jar -c examples/MTBLS263.mztab -s 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>1.0.6</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>1.0.6</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.
Release 1.0.5 of jmztab-m
This is release 1.0.5 of the jmztab-m libraries that was published to Maven Central.
It implements the mzTab-m 2.0 specification for metabolomics at https://github.com/HUPO-PSI/mzTab.
This release comes with an updated Maven site and JavaDoc and fixes issue #26.
Release 1.0.5 should be backwards compatible to 1.0.4, 1.0.3 and 1.0.2.
However, due to a stricter validation of the ms scan id referencing, files that have validated before may now fail to validate. Please contact us if you need help fixing your files.
This release also includes any amendments that were made as a result of the publication reviewers' feedback and the feedback from the PSI document review process. We have substantially updated the API documentation and have added examples from the specification document and have increased the unit test coverage.
To access the release artefacts, please go to Maven Central:
https://search.maven.org/#search%7Cga%7C1%7Cde.isas.mztab
To access the latest JavaDoc, please to the project's Maven page:
https://lifs-tools.github.io/jmzTab-m/
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/1.0.5/jmztabm-api-1.0.5-r.zip,
The reference implementation for R is now being developed here: https://github.com/lifs-tools/rmzTab-m
Python: https://search.maven.org/remotecontent?filepath=de/isas/mztab/jmztabm-api/1.0.5/jmztabm-api-1.0.5-python.zip
The reference implementation for Python 3 is now being developed here: https://github.com/lifs-tools/pymzTab-m
The CLI package bundles parser and semantic validator and contains sample files and the latest mapping file:
Running
java -jar jmztabm-cli-1.0.5.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-1.0.5.jar -c examples/MTBLS263.mztab
Run a basic parse and validation followed by applying the default mapping file on Error level for semantic validation:
java -jar jmztabm-cli-1.0.5.jar -c examples/MTBLS263.mztab -s
Run a basic parse and validation followed by applying a provided mapping file on Error level for semantic validation:
java -jar jmztabm-cli-1.0.5.jar -c examples/MTBLS263.mztab -s cv-mapping/mzTab-M-mapping.xml
Running the same on Info level yields additional messages (for optional parameters):
java -jar jmztabm-cli-1.0.5.jar -c examples/MTBLS263.mztab -s 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>1.0.5</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>1.0.5</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.
Release 1.0.4 of jmztab-m
This is release 1.0.4 of the jmztab-m libraries that was published to Maven Central.
It implements the mzTab-m 2.0 specification for metabolomics at https://github.com/HUPO-PSI/mzTab.
This release comes with an updated README and a POSIX compatible command line interface. Please note: the old command line examples will no longer work. Please check the updated examples below or on the main project page for the new syntax.
Release 1.0.4 should be backwards compatible to 1.0.3 and 1.0.2. However, for implementors, the refine validation within the io package's MTDLineParser has been refactored into separate validator implementations into the de.isas.mztab2.io.validators package.
This release also includes any amendments that were made as a result of the publication reviewers' feedback and the feedback from the PSI document review process. We have substantially updated the API documentation and have added examples from the specification document and have increased the unit test coverage.
To access the release artefacts, please go to Maven Central:
https://search.maven.org/#search%7Cga%7C1%7Cde.isas.mztab
To access the latest JavaDoc, please to the project's Maven page:
https://lifs-tools.github.io/jmzTab-m/
For everyone who is working off any generated code, please update to the latest version:
Please note that these packages do not include parser or writer code yet. However, the JSON created can be converted to proper mzTab using the Java CLI.
The CLI package bundles parser and semantic validator and contains sample files and the latest mapping file:
Running
java -jar jmztabm-cli-1.0.4.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-1.0.4.jar -c examples/MTBLS263.mztab
Run a basic parse and validation followed by applying the default mapping file on Error level for semantic validation:
java -jar jmztabm-cli-1.0.4.jar -c examples/MTBLS263.mztab -s
Run a basic parse and validation followed by applying a provided mapping file on Error level for semantic validation:
java -jar jmztabm-cli-1.0.4.jar -c examples/MTBLS263.mztab -s cv-mapping/mzTab-M-mapping.xml
Running the same on Info level yields additional messages (for optional parameters):
java -jar jmztabm-cli-1.0.4.jar -c examples/MTBLS263.mztab -s 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>1.0.4</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>1.0.4</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.
Release 1.0.3 of jmztab-m
This is release 1.0.3 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 comes with an updated, POSIX compatible command line interface. Please note: the old command line examples will no longer work. Please check the updated examples below or on the main project page for the new syntax.
Release 1.0.3 should be backwards compatible to 1.0.2. However, for implementors, the refine validation within the io package's MTDLineParser has been refactored into separate validator implementations into the de.isas.mztab2.io.validators package.
This release also includes any amendments that were made as a result of the publication reviewers' feedback and the feedback from the PSI document review process. We have substantially updated the API documentation and have added examples from the specification document and have increased the unit test coverage.
To access the release artefacts, please go to Maven Central:
https://search.maven.org/#search%7Cga%7C1%7Cde.isas.mztab
To access the latest JavaDoc, please to the project's Maven page:
https://lifs-tools.github.io/jmzTab-m/
For everyone who is working off any generated code, please update to the latest version:
Please note that these packages do not include parser or writer code yet. However, the JSON created can be converted to proper mzTab using the Java CLI.
The CLI package bundles parser and semantic validator and contains sample files and the latest mapping file:
Running
java -jar jmztabm-cli-1.0.3.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-1.0.3.jar -c examples/MTBLS263.mztab
Run a basic parse and validation followed by applying the default mapping file on Error level for semantic validation:
java -jar jmztabm-cli-1.0.3.jar -c examples/MTBLS263.mztab -s
Run a basic parse and validation followed by applying a provided mapping file on Error level for semantic validation:
java -jar jmztabm-cli-1.0.3.jar -c examples/MTBLS263.mztab -s cv-mapping/mzTab-M-mapping.xml
Running the same on Info level yields additional messages (for optional parameters):
java -jar jmztabm-cli-1.0.3.jar -c examples/MTBLS263.mztab -s 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>1.0.3</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>1.0.3</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.
Release 1.0.2 of jmztab-m
This is release 1.0.2 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 also includes any amendments that were made as a result of the publication reviewers' feedback and the feedback from the PSI document review process. We have substantially updated the API documentation and have added examples from the specification document.
Release 1.0.2 should be backwards compatible to 1.0.1. However, due to fixes in the handling of optional columns using CV parameters, files written with the old version may need to be updated to follow the optional column specification for CV parameters, namely only the value for the affected row MUST be reported in the table. The column header name must follow the opt_global_cv_MS_MS:12189_parameter_name pattern or the opt_assay[1]_cv_MS_MS:12189_parameter_name pattern (please change the values accordingly).
Also, the MZTabFileParser class has been renamed to MzTabFileParser and was moved from the uk.ac.ebi.pride.jmztab2.utils package to the de.isas.mztab2.io package.
The mapping file has been updated to use the https://www.ebi.ac.uk/ols/ontologies/msio[Metabolomics Standards Society MSIO ontology] for sample processing related terms and the https://www.ebi.ac.uk/ols/ontologies/chebi[CHEBI ontology] for derivatization groups to replace the SEP and XLMOD ontologies. Semantic validation should in this case report a warning to alert you to these changes. Please update your files and implementations accordingly.
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:
Please note that these packages do not include parser or writer code yet. However, the JSON created can be converted to proper mzTab using the Java CLI.
The CLI package bundles parser and semantic validator and contains sample files and the latest mapping file:
Running
java -jar jmztabm-cli-1.0.2.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-1.0.2.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-1.0.2.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-1.0.2.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>1.0.2</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>1.0.2</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.
Release 1.0.1 of jmztab-m
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:
The CLI package bundles parser and semantic validator and contains sample files and the latest mapping file:
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.
Release 0.9.9 of jmztab-m
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:
The CLI package bundles parser and semantic validator and contains sample files and the latest mapping file:
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.
Release 0.9.8 of jmztab-m
This is release 0.9.8 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 arefacts, 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:
The CLI package bundles parser and semantic validator and contains sample files and the latest mapping file:
Running
java -jar jmztabm-cli-0.9.8.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-0.9.8.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-0.9.8.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-0.9.8.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>0.9.8</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>0.9.8</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.
Release 0.9.7 of jmztab-m
This is release 0.9.7 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 arefacts, 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:
The CLI package bundles parser and semantic validator and contains sample files and the latest mapping file:
Running
java -jar jmztabm-cli-0.9.7.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-0.9.7.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-0.9.7.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-0.9.7.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>0.9.7</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>0.9.7</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.
Release 0.9.6 of jmztab-m
This is release 0.9.6 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.
To access the release arefacts, 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:
The CLI package bundles parser and semantic validator and contains sample files and the latest mapping file:
Running
java -jar jmztabm-cli-0.9.6.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-0.9.6.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-0.9.6.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-0.9.6.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>0.9.6</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>0.9.6</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.