1
79%
master: 79%

Ran 26 Jan 2018 03:25PM UTC

Files 26

Run time 1s

Badge

Embed ▾

Committed 26 Jan 2018 03:24PM UTC coverage: 75.037% (+0.6%) from 74.477%

Job # 271.1

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

Run Details

1019 of 1358 relevant lines covered (75.04%)

0.75 hits per line

EBIvariation / eva-cttv-pipeline / 271 / 1
79%
master: 79%

README BADGES
x

Markdown

Textile

RDoc

HTML

Rst

Source Files on job 271.1

EBIvariation / eva-cttv-pipeline / 271 / 1 79% master: 79%

README BADGES x

Markdown

Textile

RDoc

HTML

Rst

Source Files on job 271.1

EBIvariation / eva-cttv-pipeline / 271 / 1
79%
master: 79%

README BADGES
x