Opened 14 years ago

Closed 12 years ago

#742 closed enhancement (fixed)

Refactor BioAssaySetExporter

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: minor Milestone: BASE 2.12
Component: coreplugins Version:
Keywords: Cc:

Description

There has been requests on the mailing list to be able to subclass the BioAssaySetExporter? for different purposes. It is currently a problem since most of the methods are private and can't be called/overridden from a subclass.

For more information see: http://www.mail-archive.com/basedb-devel@lists.sourceforge.net/msg00038.html and ticket #741.

Change History (11)

comment:1 Changed 14 years ago by Jari Häkkinen

Milestone: BASE 2.6

comment:2 Changed 14 years ago by Johan Enell

Milestone: BASE 2.6BASE 2.x+

comment:3 Changed 12 years ago by Nicklas Nordborg

Milestone: BASE 2.x+BASE 2.12
Owner: changed from everyone to Nicklas Nordborg
Status: newassigned

There is now a new use case in http://baseplugins.thep.lu.se/ticket/212. At the same time I think we should move the MeV TDMS export into the MeV extension. To avoid backwards compatibility issues I think we should deprecate the entire BioAssaySetExporter class and start fresh with a new structure.

comment:4 Changed 12 years ago by Nicklas Nordborg

(In [4925]) References #742: Refactor BioAssaySetExporter?

The new exporter structure is in place. The old export and plug-in has not been touched yet.

comment:5 Changed 12 years ago by Nicklas Nordborg

(In [4926]) References #742: Refactor BioAssaySetExporter?

Added some more support functionality into superclasses.

comment:6 in reply to:  3 Changed 12 years ago by Jari Häkkinen

Replying to nicklas:

There is now a new use case in http://baseplugins.thep.lu.se/ticket/212. At the same time I think we should move the MeV TDMS export into the MeV extension. To avoid backwards compatibility issues I think we should deprecate the entire BioAssaySetExporter class and start fresh with a new structure.

I concur, deprecate BioAssaySetExporter.

comment:7 Changed 12 years ago by Nicklas Nordborg

(In [4928]) References #742: Refactor BioAssaySetExporter?

The new BASEfile exporter plug-in is in place. The BioAssaySetExporter? has been deprecated but no changes have yet been made to code that uses it. The installation will unshare the BioAssaySetExporter? if upgrading and doesn't install it as a plug-in in a new installation. Also fixed DynamicPositionQuery? so that it handles extra values properly (=support for automatic joins to the needed tables).

comment:8 Changed 12 years ago by Nicklas Nordborg

(In [4930]) References #742: Refactor BioAssaySetExporter?

Base1PluginExecuter now uses the new exporter code.

comment:9 Changed 12 years ago by Nicklas Nordborg

(In [4931]) References #742: Refactor BioAssaySetExporter?

This fixes the web services by depracating the on-the-fly export and adding new methods for downloading pre-generated BASE files.

comment:10 Changed 12 years ago by Nicklas Nordborg

(In [4932]) References #742: Refactor BioAssaySetExporter?

Removed references in the documentation to BioAssaySetExporter?.

comment:11 Changed 12 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

This seems to work fine now. Both MeV exporters are in place and working.

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