[TIKA-1580] ISA-Tab parsers

• Type: New Feature
• Status: Resolved
• Priority: Minor
• Resolution: Fixed
• Fix Version/s: 1.8
• Component/s: parser
• Labels: new-parser
• Assignee: Chris A. Mattmann
• Reporter: Giuseppe Totaro
• Created: 20/Mar/15 01:15
• Updated: 23/Apr/15 17:47
• Resolved: 28/Mar/15 21:51

Description

We are going to add parsers for ISA-Tab data formats.
ISA-Tab files are related to ISA Tools which help to manage an increasingly diverse set of life science, environmental and biomedical experiments that employing one or a combination of technologies.
The ISA tools are built upon Investigation, Study, and Assay tabular format. Therefore, ISA-Tab data format includes three types of file: Investigation file (a_xxxx.txt), Study file (s_xxxx.txt), Assay file (a_xxxx.txt). These files are organized as top-down hierarchy: An Investigation file includes one or more Study files: each Study files includes one or more Assay files.
Essentially, the Investigation files contains high-level information about the related study, so it provides only metadata about ISA-Tab files.
More details on file format specification are available online.

The patch in attachment provides a preliminary version of ISA-Tab parsers (there are three parsers; one parser for each ISA-Tab filetype):

• ISATabInvestigationParser.java: parses Investigation files. It extracts only metadata.
• ISATabStudyParser.java: parses Study files.
• ISATabAssayParser.java: parses Assay files.

The most important improvements are:

• Combine these three parsers in order to parse an ISArchive
• Provide a better mapping of both study and assay data on XHML. Currently, ISATabStudyParser and ISATabAssayParser provide a naive mapping function relying on Apache Commons CSV.

Thanks for supporting me on this work chrismattmann.