Biomaterial LIMS

[Johan Vallon-Christersson]

Enhancing biomaterial management in BASE by adding Biomaterial LIMS (BioLIMS) functionality. Shortly, the BioLIMS functionality would comprise the capability to organize biomaterial items into plates, broadly corresponding to how reporters can be organized in plates under Array LIMS.

Main features:

• Create BioPlates with wells that can hold Biomaterial items.
  
• BioPlates have a Geometry (re-use from Array LIMS).
  
• Organize Biomaterials in BioPlates by moving/removing them to/from a well of a BioPlate, i.e., a biomaterial item can exist outside of a well or in a well. NOTE: in the regular table views of biomaterials all items should be viewable (both those in and outside of BioPlate wells). BioPlate and BioPlateWell could be columns in the view tables.
  
• Create new biomaterial directly into a BioPlate well. For example, from an existing biomaterial, pointing to a BioPlate well can create a child biomaterial in that well. Thus, a user has the option to move a biomaterial into a well or to create a child biomaterial in a well.
  

Creating plates:
From a BioLIMS menu one would access functionality to create BioPlates that can hold biomaterials. Essentially, for these functions one would have the same interface as for ArrayLIMS with the exception that users should be able to create individual plates by clicking a “New…” button (for Array LIMS plates are always uploaded from file).

Managing BioPlates:
Table views for BioPlates should be available and can basically have the same layout as table view for ArrayLIMS plates. BioPlate view table can be available from the BioLIMS menu or from the regular view menu. Single BioPlate view could share layout with single ArrayLIMS plate view with tabs for properties, annotations, and wells. Additional action button (BioPlateAct) to remove/add biomaterials would be needed. Importantly, in the regular table views of biomaterials all items should be viewable (both those in and outside of BioPlate wells). BioPlate and BioPlateWell could be columns in the view tables.

UML Diagram
Added BioPlate and BioWell to the existing biomaterials diagram: source:trunk/doc/src/docbook/figures/uml/datalayer.biomaterials.png​

[Nicklas Nordborg]

(In [4658]) References #979: Biomaterial LIMS

Added BioLIMS to UML diagram.

[Martin Svensson]

(In [4670]) References #979 Added data- and item classes needed by BioMaterial? LIMS. Also created a test-class to test BioPlate? functionallity.

[Martin Svensson]

(In [4671]) References #979 Added keyword to svn-properties

[Martin Svensson]

(In [4672]) References #979 Missed some files in the last commit.

[Martin Svensson]

(In [4677]) References #979 Updated schema_version, implemented the last methods to the classes and re-arranged in BioPlate?. Tests and documentation will be written next.

[Martin Svensson]

(In [4678]) References #979 Removed compling error in test-class

[Martin Svensson]

(In [4685]) References #979 Added some more comments for javadoc and finished the test.

[Martin Svensson]

(In [4704]) References #979 First commit of bioplates-support in the webbinterface.

[Martin Svensson]

(In [4729]) References #979 Removed edit and view pages for biowells because they are not needed. Added support to view/edit a sample's bioplate/biowell

[Martin Svensson]

(In [4730]) References #979 A labeledextract's or extract's bioplate/biowell are now available in the webclient. The pages has gone through some testings but can still have some bugs.

[Martin Svensson]

(In [4731]) References #979 The implementation of bioplates/biowells in the webclient is now done.

[Martin Svensson]

(In [4732]) Fixes #979 Biomaterial LIMS

[Martin Svensson]

(In [4734]) References #979 A biowell's coordinates are split into two columns on biomaterial list-pages.

[Martin Svensson]

(In [4735]) References #979 Images for the documentation about biomaterial LIMS

[Nicklas Nordborg]

(In [4781]) References #979: Biomaterial LIMS

Made 'ok' and 'cancel' buttons fixed on page so we don't have to scroll every time.