Add possiblitiy for direct file - sample links

[Fredrik Levander]

It should be possible to set direct links between samples (biomaterials) and files in a two-way many-to-many association. This can be used for annotation or for linking search results, spectrum files etc directly with samples. There should be a separate table that handles these links. The sample and extract forms should show associated files, and provide possibilities to add new links. When clicking on files, associated biomaterials could be shown too.

[Fredrik Levander]

(In [2145]) Refs #283. Added biomaterial-file association table. Added possiblitiy to use files to annotate samples as extension.

When viewing files the annotated biomaterials are listed

When viewing samples the associated files are listed under the annotations tab

Removed warnings and comma from item class

[Fredrik Levander]

(In [2153]) Refs #283. Added possibility to add file annotations to active sample

[Fredrik Levander]

The functionality has been added to the database and to the sample form.

[olle]

(In [2422]) Refs #283. Class/file action/file/ViewActiveFile.java in client/servlet/ updated in public method void runMe() by only showing BioMaterials? table if the file has a link to any biomaterial.

[Fredrik Levander]

(In [4431]) Refs #283. Fixed display of file type when not set.

[olle]

(In [4456]) Refs #283. Refs #339. Classes/files action/sample/AddSampleFile.java, action/extract/AddExtractFile.java, and action/extract/AddLabeledExtractFile.java in client/servlet/ updated to not crash if no active project has been selected.

[olle]

(In [4457]) Refs #283. Refs #339. Classes/files action/sample/CreateSampleFile.java, action/extract/CreateExtractFile.java, and action/extract/CreateLabeledExtractFile.java in client/servlet/ updated to check if file list equals null before calling its isEmpty() method.

[olle]

(In [4458]) Refs #803. Refs #283. Biomaterial - file associations can now be defined by selecting biomaterials to be associated with a file, instead of the other way around:

1. Class/file action/file/ViewActiveFile.java in client/servlet/ updated to always show the association table. The table tool-bar is updated with a new button "Add BioMaterials" coupled to action link to new class/file action/file/AddFileBioMaterial.java in client/servlet/.
2. New class/file action/file/AddFileBioMaterial.java in client/servlet/ added. It uses class ViewItemTable to display a table of available biomaterials to select from, after which action is forwarded to new class CreateFileBioMaterial.
3. Class/file action/ViewItemTable.java in client/servlet/ is based on class/file action/directory/ViewActiveDirectory.java in client/servlet/, but without the extra complexity added by the directory table. ViewItemTable is intended to be used for item classes of type Class<? extends BasicItem>. If session attribute VBoolean ViewItemTable.VSELECT is null or true, select mode will be used. The list of integer id values for selected items is available in valid parameter FormFactory.VID.
4. New class/file action/file/CreateFileBioMaterial.java in client/servlet/ added. It obtains a list of biomaterial id values from valid parameter FormFactory.VID and adds the items to the file.
5. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.
6. Default icon settings file icons/default in client/servlet/ updated with icon assignments for new string keys.