webin-cli-validator

Contains common classes which acts as an interface between webin-cli and the context specific validators.

Key concepts

Context

The context uniquely identifies the manifest parser, the validator and the submission objects that have to be used. Currently supported contexts are:

1. reads: raw reads (BAM, CRAM, Fastq) context (validation is part of readtools project)
2. genome: genome assembly validation context (validation is part of sequencetools project)
3. transcriptome: transcriptome assembly validation context (validation is part of sequencetools project)
4. template: annotated sequence (cvs, flatfile) validation context (validation is part of sequencetools project)

Manifest

A manifest provides all the meta and file information required to validate a submission. The manifest fields are specific to each context and the webin-cli-validator contains a specific manifest object for each of the contexts. A Manifest object is created by the Webin-CLI from the submitter provided manifest files.

An extract of a genome context manifest file:

NAME assembly1
MINGAPLENGTH 100
FLATFILE	test_wgs.embl.gz
AGP	test_chromosome.agp.gz
CHROMOSOME_LIST	test_chromosome.txt.gz

Manifest implementation

Please provide us with the desired manifest file fields for your specific context. A context specific Manifest class will be created Webin-CLI maintainers after an agreement on the manifest fields with the validator implementors.

The context specific Manifest class will extend the uk.ac.ebi.ena.webin.cli.validator.manifest.Manifest abstract class. Manifest fields defined in the abstract class that are available to all contexts include:

• description
• authors
• address
• sample
• study
• run
• analysis
• files
• ignoreErrors

Validator

A validator accepts a context specific manifest object, writes any errors into report files, and returns the validation result as a ValidationResponse object.

Validator implementation

• All validators must implement the uk.ac.ebi.ena.webin.cli.validator.api.Validator interface.
• The Validator interface has a single method validate that accepts a context specific manifest object and returns a uk.ac.ebi.ena.webin.cli.validator.api.ValidationResponse object.
• Webin-CLI will take care of reading and contructing the manifest object and invoking the validator.
• The ValidationResponse contains the validation status that is either is either VALIDATION_SUCCESS or VALIDATION_ERROR.
• If the validate method throws any exception then this is considered a system error by Webin-CLI.

Validator implementation example

public class YourSubmissionValidator implements Validator {
   @Override
   public ValidationResponse validate(Manifest manifest) {
       if (isYourValidationSuccessful(manifest)) {
           return new ValidationResponse(ValidationResponse.status.VALIDATION_SUCCESS);
       }
       else {
           return new ValidationResponse(ValidationResponse.status.VALIDATION_ERROR);
       }
    }
 }

More complex implementation example can be found in https://github.com/enasequence/sequencetools/blob/master/src/main/java/uk/ac/ebi/embl/api/validation/submission/SubmissionValidator.java

Validator report files

The ValidationResponse only contains the VALIDATION_SUCCESS or VALIDATION_ERROR state. The validators are expected to write all messages intended for submitters, including error messages and exception stack traces, into report files. The report file locations and names are set by the Webin-CLI and provided to the validators using the Manifest object.

Input file specific report files

Whenever possible, messages should be written into input file specific report files. These report files are defined in the uk.ac.ebi.ena.webin.cli.validator.file.SubmissionFile.reportFile field. They point to '<output directory>/<context>/<name>/validate/<file>.report' files where <file> corresponds to the input file name that is being validated. The input file is defined in the uk.ac.ebi.ena.webin.cli.validator.file.SubmissionFile.file field.

Submission specific report files

Messages which can’t be attributed to specific input files should be written into the submission specific report file. This report file is defined in the uk.ac.ebi.ena.webin.cli.validator.file.Manifest.reportFile field and point to the '<output directory>/<context>/<name>/validate/webin-cli.report' file.

Validator temporary files

Any temporary files should be written into the uk.ac.ebi.ena.webin.cli.validator.file.Manifest.processDir directory.

Adding the validator to Webin-CLI

• Make your validator available in a public maven repository as a fat JAR containing all required dependencies.
• Send the artifact details to the Webin-CLI maintainers.
• Webin-CLI maintainers will add your JAR dependency into Webin-CLI and implement a manifest reader as well as xml creation and submission functionality for your context.

Webin-CLI maintainers

• Rasko Leinonen: [email protected]
• Senthilnathan Vijayaraja: [email protected]