mzidentml-validator

mzidentml validator ui and command line tool allows developers of the mzIdentML standard to validate their implementation using the following tools.

The latest version of the tool can be also found in the following folder: bin/

Disclaimer

This validator is not part of the formal document process and is still under development. At this stage, the validation is neither complete nor has been thoroughly tested for correctness. The current version should be regarded as a prototype and proof of concept implementation not as final version!

mzidentml-validator-{version}-gui.jar

The GUI version is a desktop tool that enable users to configure among others the level of errors (WARNING, ERROR, FAILS), the ontologies to be used to validate semantically the files, etc. The jar can be executed as:

jar -jar mzidentml-validator-{version}-gui.jar

When the validation finished a report like this is created:

Final report created by the validator

mzidentml-validator-{version}-cmd.jar

The commandline tool enables to validate the mzidentml using the commandline. When the tool get executed the following message defines the parameters needed by the tool:

java -jar mzidentml-validator-1.4.35-SNAPSHOT-cmd.jar

usage: mzidentml-validator [-e] -f <arg> [-l <arg>] [-m <arg>] [-o <arg>]
       [-r <arg>] [-s] [-t <arg>] [-w <arg>] [-x <arg>]
mzidentml-validator version 1.4.35

 -e,--full_validation
 -f,--mzidentml_file_to_validate <arg>   mzidentml file to be validated
 -l,--error_level <arg>                  The error level of the validation
                                         process
 -m,--cv_mapping_config_file <arg>       The CV mapping configuration file
 -o,--ontology_config_file <arg>         Ontology configuration file
 -r,--coded_rules_config_file <arg>      Coded rules configuration file
 -s,--semantic_validation
 -t,--xml_file_filter_file <arg>         The filter definition file
 -w,--schema_file <arg>
 -x,--schema_version <arg>               Schema version, supported values
                                         1.1.0, 1.1.1, 1.2.0

schema validation

java -jar mzidentml-validator-1.4.35-SNAPSHOT-cmd.jar -s -x 1.1.0 -f file.mzid

-f (--mzidentml_file_to_validate): The file input is defined by the parameter -f which is the mzIdentML to be validated. -x (--schema_version): The schema version that will be used to validate the mzidentml file. Currently, te validator supports versions 1.1.0, 1.1.1, 1.2.0.

These options are mutually exclusive, if the -x option is provided the tool uses one of the mzIdentML default schemas in the following repo (https://github.com/HUPO-PSI/mzIdentML/tree/master/schema).

semantic (full) validation

java -jar mzidentml-validator-1.4.35-SNAPSHOT-cmd.jar -e -f file.mzid

-e (--full_validation): perform semantic and schema validation.

The following files are needed fot the tool:

ontology_config_file: An example can be found the default configuration file here https://raw.githubusercontent.com/ypriverol/mzidentml-validator/main/src/main/resources/ontologies.xml
cv_mapping_config_file: An example can be found the default configuration file here https://raw.githubusercontent.com/ypriverol/mzidentml-validator/main/src/main/resources/mzIdentML-mapping_1.1.0.xml
coded_rules_config_file: An example can be found the default configuration file here https://raw.githubusercontent.com/ypriverol/mzidentml-validator/main/src/main/resources/ObjectRulesMIAPE.1.1.0.xml
xml_file_filter_file: An example can be found the default configuration file here https://raw.githubusercontent.com/ypriverol/mzidentml-validator/main/src/main/resources/ruleFilter_MIAPEMSI.xml
mzml_file_to_validate: The mzidentml that will be validated
message_level: One of the following values: DEBUG, INFO, WARN, ERROR, FATAL

Contributing

Please feel free to contribute with the following project.

HUPO-PSI / mzidentml-validator

readme