TextFileImport

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About this document

This is an official Request for Comment (RFC) for General text file import framework.

For details on RFCs in general, check out the Wikipedia Entry: Request for Comments (RFCs)

Status

10/11/2006 Still under construction.

How to Comment

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Proposal

This RFC is for the new import framework for general text files.

Biological Questions / Use Cases

Most of biological data files are available in text or Microsoft Excel file format. By implementing this function, users can import following files:

• Tab/comma/space delimited text tables
• Excel files

General Notes

Requirements

This project contains two main components:

• File readers
  • for text files
  • for Excel (xsl) files
• Swing GUI

To provide maximm flexibility for users, the GUI should accept the following:

• Selectable mapping keys. Users can map text

Deferred Items

Open Issues

The following is a prototype GUI for the file importer:

http://chianti.ucsd.edu/kono/images/fileImport1.png

Features requested in the Hackason (first 2 days of Cytoscape retreat 2006) were the following:

• Direct import from Excel files (.xsl) This can be done using open source library POI.

• Support for multiple delimiters.

• Network file import. This is related to RFC 16 (text table network import).

• Inteligent file type checker. If the input file data looks like existing data file format, apply a template.

Backward Compatibility

Expected growth and plan for growth

References

Implementation Plan

Prototype readers and GUI is done.

Comments

I think it should be useful if the text table import could be done via pasting (clipboard). I imagine a menu item Edit->Paste As..-> attributes table. I expect it is just a matter of parsing a stream of space or tab delimited chars...