giuseppetotaro / isatabparser

Tika parsers for ISA-Tab data formats

ISATabParser

This is a preliminary work to add to Tika the ability to parse the ISA-Tab data formats. ISA-Tab files are related to ISA Tools.

This work aims at providing the following features:

• Detection based on glob patterns and pattern matching on header values.
• One Tika Parser for each ISA-Tab filetype (three parsers: Investigation, Study, Assay)
• The Investigation parser gets only metadata. Since ISA-Tab files are organized Top-Down, I am working on extending it in order to parse related files (study and assay files) starting from investigation.
• Study and Assay parsers rely on Apache Commons CSV to perform parsing, because both study and assay files are organized in a per-row basis and they essentially are CSV files using the tab character as delimiter.

What’s the next

The most important improvement is to refine these three parsers and combine them in order to parse a ISArchive as well as possible. Another improvement is better mapping of study and assay data on XHTML structures.

TIKA-1580

An issue has been created on the Tika Issue Tracker system: TIKA-1580. Please refer to that issue for comments and feedback.