Opened 3 months ago

Last modified 3 months ago

#987 assigned task

Cohort exporter plugin

Reported by: nicklas Owned by: nicklas
Priority: major Milestone: Relax v1.1
Component: net.sf.basedb.relax Keywords:


We should implement a plug-in that can export cohort data into tab-separated file. The basic functionality is similar to the original release exporter in reggie (see #887).

The plug-in should use an item list as input.

A project must be active since that will decide which annotations that are exported.

It should be possible to start with a list of any type of item (eg. rawbioassay, derived bioassay or biomaterial).

The exporter should only move upwards to parent items. For example, if the start list contains a library items, the exporter should create files for the libraries, rna, specimen and biosources.

It is assumed that all root items are of the same type. We can check this and give an error message if not. It is also expected that moving up along the parent item path we will pass through the same type of parents for all items. This might be possible to check or we could ignore it (but then we will end up with different number of items in some of the files).

The first column in each file should be the name of the "root" item. The second column should be the name of the current item. After that annotations that are relevant for the current item type are following.

Do we need columns for paths to files?

Expression values will not be exported in the first version.

Change History (3)

comment:1 Changed 3 months ago by nicklas

  • Owner set to nicklas
  • Status changed from new to assigned

comment:2 Changed 3 months ago by nicklas

(In [4553]) References #987: Cohort exporter plugin

Added the "Cohort exporter" plug-in. It seems to work and produce files as expected.

comment:3 Changed 3 months ago by nicklas

(In [4554]) References #987: Cohort exporter plugin

Added checks for an active project.

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