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Ran 26 Jan 2018 03:25PM UTC

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Build # 271

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travis-ci

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Commit Message

Merge pull request #45 from pabarcgar/javaClinvarXmlParser

EVA-866 new Java clinvar XML to json parser

New Java parser that transform a Clinvar XML file into Json using three main components, each of those running in a separate thread:
- XmlClinVarReader: class that (helped by an auxiliar class XmlClinvarSetIterator) returns each "PublicSet" XML element found in a XML file, not being necessary parse the whole XML file in memory
- ClinvarSetTransformer: class that (helped by auxiliar class PublicSetParser) transform each "ClinvarSet" XML string into a PublicSet object. The unmarshalling is made in a Jaxb Context, so the schema is validated while parsing
- ClinvarJsonSerializer: class that serialize PublicSet objects into Json records (tipically in a gzip file, but the output stream is injected)

There is a main App class that create those components, submitting them to separate threads for obtaining a better performance. The objects are passed between those components using ArrayBlockingQueues.

There is also a python script that downloads the XSD file for a given clinvar XML file and generates the JAXB binding classes into the java source directory.

Work to do: code cleaning, licenses, javadoc, wiki with the steps necessary for transforming a new clinvar XML file

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ID	Job ID	Ran	Files	Coverage
1	271.1	26 Jan 2018 03:25PM UTC	0	75.04	Travis Job 271.1

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