BioValidator

BioValidator is a schema validator that validates biological file format like Fasta, GFF, etc. Currently, it only supports Fasta file format

Usage

The most simple way to validate supported file types is to use ValidatorHelper provided by library.
Example: Arguments in the below validate method

filename: absolute file path
validator-type: type of validator
isStrict: whether to validate in strict mode or permissive

ValidationResult validationResult = ValidatorHelper.validate("filepath", ValidatorType.FASTA, true);
OR
ValidationResult validationResult = ValidatorHelper.validate("filepath", "fasta-dna", true);
OR
ValidationResult validationResult = ValidatorHelper.validateFasta("filepath");

Check whether file is valid or not:

assertTrue(validationResult.isValid());

If file contain errors or warnings:

if (!validationResult.isValid()) {
    validationResult.getErrorMessages().forEach(System.out::println);
    validationResult.getWarningMessages().forEach(System.out::println);
}

Validation Result Customization

Validator's behaviour and result and can be easily customize, ValidatorBuilder can be used to customize behaviour and result of the validator.
Example: To validate a file by disabling warnings and continue validation even if error occurred

Validator validator = ValidatorBuilder.withFile("path", "fasta-protein")
        .disableWarnings()
        .enableErrors()
        .disableStopAtFirstError()
        .build();

assertTrue(validator.validate().isValid());
OR
validator.validate(result -> {
    assertTrue(result.isValid());
})

Construct a raw validator:

String dnaSequence = "> seqId | header name\nACTGACTGACTG";

InputStreamReader isr = new InputStreamReader(new ByteArrayInputStream(dnaSequence.getBytes()));
Validator validator = new FastaValidator(isr, SequenceType.DNA);
ValidationResult result = validator.validate();

assertTrue(result.isValid());

Using biovalidator in your application

Maven dependency

<dependency>
  <groupId>org.intermine</groupId>
  <artifactId>biovalidator</artifactId>
  <version>0.1.2</version>
  <type>pom</type>
</dependency>

Gradle dependency

compile 'org.intermine:biovalidator:0.1.2'

Using biovalidator as a command line utility

Step 1: Get biovalidator Fat-Jar(either build from source or dirctly download from bintray

Build from source : $ ./gradlew createFatJar
- this will generate a jar named 'biovalidator-fat-x.x.x.jar' in 'build/libs' directory
Or Download fat-jar version of biovalidator from bintray

Setp 2: run as an executable jar file

java -jar biovalidator-fat-0.1.2.jar --help

BioValidator Documentation

Documentation about BioValidator uses and validation rules: https://github.com/intermine/biovalidator/wiki

deepakkumar96 / biovalidator