lifs-tools / jmztab-m Goto Github PK

Hi,
On newer Java's (here. openjdk 10.0.1) I get a java.lang.NoClassDefFoundError: javax/xml/bind/ValidationException. This is because newer java (since 1.9) have removed them from
the ClassPath [1]. Hence, a new dependency has to be added explicitly.

PR coming.
Yours,
Steffen

[1] https://stackoverflow.com/questions/43574426/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-j

Hi, does the validator capture if e.g. in the SML we have four ambiguous smiles A|B|C|D but there are three ambiguous InChIs X|Y|Z ?

For now this is just a question, but if the answer is no, it is an issue ;-)

The stock templates used by swagger-codegen currently have some shortcomings. We should add testcases to validate and improve the JSON serialization and deserialization in R.

Hi, the web app is uber-cool, but I want a command-line validator.
I am sure it is simple to java -jar ... myfile.mzTab somehow,
but it would save my soul if README.adoc has a cut&past'able example.
Yours, Steffen

A name for each study variable (experimental condition or factor), to serve as a list of the study variables that MUST be reported in the following tables. For software that does not capture study variables, a single study variable MUST be reported, linking to all assays. This single study variable MUST have the identifier “undefined“.

Right now, the mzTabWriter implementation will skip any missing values, so it may be possible to write
an mzTab file, that is not valid according to the specification.

The current validator runs off of the parser, which requires a written file / string in the first place.
As a first step, one could serialize the file to String, the run the parser on it and cancel writing if any issues are reported (printing the errors or alternatively, returning the error list).

The Bean validation is currently not fully up to the task, apart from performing checks for null values and also not linked into the error reporting system of the parser.

retention time fields have been extended to hold the unit (seconds) in their name. HUPO-PSI/mzTab#77
This requires adaptation of the

• Swagger model
• the example files,
• the parser and
• validator

In CCMS-UCSD/GNPS_Workflows#85 it is reported that the mzTab-M example files use index instead of scan to reference the original ms scans from the linked mzML files.

This needs to be fixed in the example files, but also, the validator should check these formats. This is not always possible if the scan_id type is not defined. We might need to define a default for that in the standard, unless "scan" is already the default fallback as it seems from those examples. If a cv term for the format is given, the validator should check that references follow this format.

However, without access to the original mzML files, the validator can not actually cross-check that these scan ids (apart from scan number, which should work always with TPP style mzMLs) actually exist and are accessible. The latter is currently out of scope for the validator but could be added in the future to simplify creating a complete submission.

The SEP ontology in OLS uses term id's with a lower-case prefix of sep: ...
Initially, that seemed to be the culprit for term resolution, but it turned out that actually, the default semantic mapping file does not know of SEP. If added, the validation succeeds. See the second comment on why SEP should non-the-less be left out of the mapping file.

As seen during the hangout, in some cases the file upload "Durchsuchen" is not visible,
and/or not responding to user clicks. Yours, Steffen

Some of the array types in the current class diagram https://lifs-tools.github.io/jmzTab-m/1.0.5/apidocs/resources/apidocs/mzTab-M-object-model-small.png are incorrect.

A new one needs to be prepared to reflect the correct member types.

Pull request HUPO-PSI/mzTab#76

There needs to be a test to check, that reading and writing a file produces the sample result, as the original input file.
We may have to exclude the following, though: Comments, order of elements, unless specified in the standard. Encoding of optional columns (numeric vs string).

Hi, with

openjdk version "10.0.2" 2018-07-17
OpenJDK Runtime Environment (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.1)
OpenJDK 64-Bit Server VM (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.1, mixed mode)

I get a

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.20.1:test (default-test) on project jmztabm-api: Execution default-test of goal org.apache.maven.plugins:maven-surefire-plugin:2.20.1:test failed.: NullPointerException -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.20.1:test (default-test) on project jmztabm-api: Execution default-test of goal org.apache.maven.plugins:maven-surefire-plugin:2.20.1:test failed.
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:213)
...
Caused by: java.lang.NullPointerException
    at org.apache.maven.surefire.shade.org.apache.commons.lang3.SystemUtils.isJavaVersionAtLeast (SystemUtils.java:1626)
    at org.apache.maven.plugin.surefire.AbstractSurefireMojo.getEffectiveJvm (AbstractSurefireMojo.java:2107)
...

This is reported in https://issues.apache.org/jira/browse/SUREFIRE-1439
and fixed in https://blog.soebes.de/blog/2018/03/06/apache-maven-surefire-plugin-version-2-dot-21-released/.

PR coming.
Yours, Steffen

This seems to be
projectlombok/lombok#1572
So updating to 1.16.22 helps. PR coming ...
Yours, Steffen

I think m.matches() here should be replaced with m.find() because a possible value for identifier is assay[1]_peak_mz or as given in this example, it could be assay[1]_my_value for which m.matches() will give false

The content of README.md is currently not available from within the Maven site at https://lifs-tools.github.io/jmzTab-m

It should be included as "Overview".

This could output versions for different components,
git commit hash etc. Yours, Steffen

Column order should be fixed, as in the column definitions.
Validator should output an error if column order is not as expected.

study_variables[1-n]-assay_refs is supposed to be bar separated, but currently a comma separated values are parsed correctly instead.

Hi, I am getting

Begin check mztab file: /vol/R/BioC/devel/xcms/R/faahKO.mzTab
There exist errors in the metadata section or protein/peptide/small_molecule/small_molecule_feature/small_molecule_evidence header section! Validation will stop, and ignore data table check!
No errors in file:/vol/R/BioC/devel/xcms/R/faahKO.mzTab file!
There were errors while processing your file, please check the output for details!
Finish!

Only if I -level Warn then I see
[Warn-2041] line 88: The metadata section does not contain a small_molecule-identification_reliability parameter definition.. Note that https://github.com/HUPO-PSI/mzTab/blob/master/specification_document/1_1_draft_specs/mzTab_format_specification_1_1-M_draft.adoc#6252-small_molecule-identification_reliability says mandatory=False.
Yours, Steffen

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HUPO-PSI/mzTab#51