Opened 17 years ago

Closed 17 years ago

Last modified 17 years ago

#101 closed task (fixed)

Import plug-in for SNP raw data

Reported by: Nicklas Nordborg Owned by: Martin Svensson
Priority: critical Milestone: Illumina package v1.0
Component: net.sf.basedb.illumina Keywords:
Cc:

Description (last modified by Martin Svensson)

SNP data comes from BeadStudio with one file that contains several data sets. This plug-in should be similar to the BASE core plug-in that imports Illumina data. It should:

  • Create one raw bioassay for each data set
  • Split the original data file into smaller files containing a single data set. The new files should get the extension '.split'
  • Both the original data file and the split file should be linked to the raw bioassays
  • The plug-in should set the number of data values with RawBioAssay.setNumFileSpots().

The plug-in should be started from either the raw bioassays list page or from an experiment that is of the correct type (Illumina SNP variant). If started from an experiment the new raw bioassays should be linked with that experiment.

Change History (10)

comment:1 by Nicklas Nordborg, 17 years ago

Priority: major → critical

comment:2 by Nicklas Nordborg, 17 years ago

Milestone: Illumina package v1.x → Illumina package v1.0

comment:3 by Martin Svensson, 17 years ago

Description: modified (diff)

comment:4 by Martin Svensson, 17 years ago

Owner: changed from Johan Enell to Martin Svensson
Status: new → assigned

comment:5 by Martin Svensson, 17 years ago

(In [592]) References #101. Started on the plugin. A commit for the weekend.

comment:6 by Martin Svensson, 17 years ago

(In [617]) References #101. Creating RawBioAssays and split up files. The data have to also be split up.

comment:7 by Martin Svensson, 17 years ago

(In [618]) References #101. The import is now done. Code needs to be cleaned up before this ticket is finished.

comment:8 by Martin Svensson, 17 years ago

Resolution: → fixed
Status: assigned → closed

(In [619]) Fixes #101. The plug-in tested both from raw bioassay-listview and experiment-singel_itemview. Code has been cleaned up and documentation added.

comment:9 by Nicklas Nordborg, 17 years ago

I think the import should set the following properties on the split files:

  • Write protected, so the files are not deleted by accident
  • MIME type = text/plain
  • Compress the files

comment:10 by Martin Svensson, 17 years ago

(In [622]) References #101comment:9 - fixes the listed items in the comment.

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