Opened 14 years ago

Closed 14 years ago

#771 closed enhancement (fixed)

Make annotations for Bioassays available in bioassay table within a BioassaySet

Reported by: Johan Vallon-Christersson Owned by: Nicklas Nordborg
Priority: minor Milestone: BASE 2.6
Component: web Version:
Keywords: Cc:

Description

When viewing the bioassay table in a Bioassayset, allow the user to display columns for annotations. This will facilitate selection of Bioassays when creating filters for sub selections of Bioassays.
This functionality is implemented as plugins in BASE1.

Change History (9)

comment:1 Changed 14 years ago by Nicklas Nordborg

Resolution: worksforme
Status: newclosed

This has already been implemented.

comment:2 Changed 14 years ago by Jari Häkkinen

In which version?

comment:3 in reply to:  2 Changed 14 years ago by Johan Vallon-Christersson

Working on the onk installation BASE 2.4.1 (build #3722; schema #40) I cannot display annotations for Bioassays in the Bioassay table as described above. The Bioassays have annotations inherited from Samples. When I view individual Bioassays I can see the annotations but not when I view the table.

comment:4 Changed 14 years ago by Nicklas Nordborg

Inherited annotations can't be viewed in the list views, only annotations that are directly assigned to the item type in the list view (ie. Bioassay:s).

It would be impractical to allow inherited annotations to be viewed in the list view. It would require that a column definition for all annotation types on the server is added and for each item checking if it has an annotation of that type. Given that the number of annotation types can be high this will result in a lot of database queries.

It would be possible to display the experimental factors in a similar way as in the experiment explorer.

comment:5 in reply to:  4 Changed 14 years ago by Johan Vallon-Christersson

Resolution: worksforme
Status: closedreopened

To display the experimental factors in a similar way as in the experiment explorer would suffice and be very useful. An enhancement to that would be if the column displaying the experimental factor can be sorted on and filtered on using a filter bar (this goes for the experiment explorers as well).
Of course, having the option to display more than one experimental factor at the time would be most useful. This would allow for an straightforward and easy selection of Bioassay in one step instead of multiple.

comment:6 Changed 14 years ago by Nicklas Nordborg

Component: corepluginsweb
Milestone: BASE 2.x+BASE 2.6
Priority: majorminor

I'll fix this so that experimental factor annotations can be displayed in the bioassay list. This will show up just as other annotation types that are already supported. Filtering is supported. Sorting will never be supported, since it is not possible to query annotations in the same time as anything else. The annotation values can only be retrieved individually after (for display) or before (for filtering) the bioassays are queried.

comment:7 Changed 14 years ago by Nicklas Nordborg

Owner: changed from everyone to Nicklas Nordborg
Status: reopenednew

comment:8 Changed 14 years ago by Nicklas Nordborg

Status: newassigned

comment:9 Changed 14 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [4057]) Fixes #771: Make annotations for Bioassays available in bioassay table within a BioassaySet?

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