PankratzLab / PankratzLab/DonorCheck
Add support for LinkSeq XML
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@kaitlinrenee is already working on this.
Since Jun 24, 2019.
- Dominant language
- Java
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- 2
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- 0
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Description
Referenced here.
XML Sections to parse
It looks like the XML has an labAssignmentSection block at the top which includes the assigned typings. These can be read and passed to a ValidationModelBuilder to populate the core typing data.
For haplotype information, there is a testResultsSection that has all the possible alleles for each locus, which will be used to populate haplotype information.
Implementation Notes
- You can use the Score6 XML parser as a reference for how to read the desired XML sections.
- For reference, the XML parsing is done with JSoup. You're given the
Document, so building the parser is all about finding the appropriate XMLElements, getting their text contents, and passing them appropriately to the builder.
Goals
- Assigned typing parsing works
- Haplotype parsing works
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Assessment
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