EBIvariation / eva-cttv-pipeline

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• 2017.12
• 2016.10
• 2016.11
• 2017.02
• 2018.06
• bugfix-none-iteration
• clinvar-schema-1-55
• clinvar2018-05
• dependabot/maven/clinvar-xml-parser/com.fasterxml.jackson.core-jackson-databind-2.10.0.pr1
• dependabot/maven/clinvar-xml-parser/com.fasterxml.jackson.core-jackson-databind-2.9.10.3
• dependabot/maven/clinvar-xml-parser/com.fasterxml.jackson.core-jackson-databind-2.9.10.4
• eva-1445-mondo
• eva-1446-incremental-evidence-strings
• eva-1469-clinvar-schema
• eva-1471-iteration-bugfix
• eva-1472-curation-postprocess
• eva-1473-evidence-strings
• eva-1483-vulnerabilities
• eva-1774-schema-1-59
• feature/add-variant-id
• feature/batch-18.02
• feature/update-json_schema-1.2.8
• feature/update-xml-parser-2018-02
• hotfix/oxo-500
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• javaClinvarXmlParser
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Build # 294

Build Type

push

travis-ci

Committed by web-flow

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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