Enable annotations for extracts

[Fredrik Levander]

It should be possible to view and add annotations for extracts, as is currently possible for samples.

[olle]

Ticket accepted.

[olle]

Severity changed to 2, as changes needed for Extract.class and LabeledExtract.class in order to add annotations can be based on corresponding code for Sample.class. Similarly, new needed classes can be based on corresponding classes used for adding annotations to Sample items.

[olle]

(In [2477]) Refs #339. Class/file action/write/AddAnnotation.java in client/servlet/ updated in public method void runMe():

1. An ItemFactory instance is obtained by calling getItemFactory(dc), instead of always creating a new ItemFactory instance.

2. A BasicItem item with known id 'id' is obtained by calling factory.getById(Item.valueOf(itemType).getItemClass(), id) instead of Item.valueOf(itemType).getById(dc, id). This removes the need for the core class for the item to have a getById(...) method.

[olle]

(In [2479]) Refs #339. Update to allow annotation support for extracts and labeled extracts.

1. Classes/files action/extract/ViewActiveExtract.java and action/extract/ViewActiveLabeledExtract.java in client/servlet/ updated in protected method void runMe() by adding an annotation form analogously to action/sample/ViewActiveSample.java in client/servlet/.

2. New classes/files action/extract/AddExtractFile.java and action/extract/AddLabeledExtractFile.java in client/servlet/ based on class/file action/sample/AddSampleFile.java in client/servlet/.

3. New classes/files action/extract/CreateExtractFile.java and action/extract/CreateLabeledExtractFile.java in client/servlet/ based on class/file action/sample/CreateSampleFile.java in client/servlet/.

[Gregory Vincic]

(In [2487]) Refs #339. Fixed bug when saving existing annotations.

[olle]

(In [4158]) Refs #741. Refs #339. Annotation management for biomaterials, i.e. samples, extracts, and labeled extracts, updated with view action for an annotation, that allows the value to be edited, and support for deleting an annotation:

1. Class/file action/annotation/SaveAnnotation.java in client/servlet/ updated to obtain an action link id from valid parameter VString ForwardField.VPARAM, and forward action to this when it is finished.

2. Class/file action/annotation/ViewAnnotation.java in client/servlet/ updated to obtain an action link id from valid parameter VString ForwardField.VPARAM, and transfer the value to SaveAnnotation, if the latter action is called.

3. Class/file action/file/ViewActiveFile.java in client/servlet/ updated to set value of valid parameter VString ForwardField.VPARAM to that of the class itself (in this case ViewActiveFile), when action ViewAction is called.

4. Class/file action/sample/ViewActiveSample.java in client/servlet/ updated in private method Table createAnnotationsTable(TableFactory tableFactory, ItemQuery<Annotation> annotationQuery) to set view action for annotation value to ViewAnnotation and add tool bar with button coupled to action link to DeleteAnnotations.

5. Class/file action/extract/ViewActiveExtract.java in client/servlet/ updated to create annotation table using same private method Table createAnnotationsTable(TableFactory tableFactory, ItemQuery<Annotation> annotationQuery) as was used for ViewActiveSample.

6. Class/file action/extract/ViewActiveLabeledExtract.java in client/servlet/ updated to create annotation table using same private method Table createAnnotationsTable(TableFactory tableFactory, ItemQuery<Annotation> annotationQuery) as was used for ViewActiveSample.

[olle]

(In [4159]) Refs #741. Refs #339. View action defined for items when listing labeled extracts:

1. Class/file action/ActionFactory.java in client/servlet/ updated in public synchronized method ActionLink getViewActionLink(AttributeDefinition ad) to set view action for labeled extract items to ViewLabeledExtract.

[olle]

(In [4161]) Refs #741. Refs #339. Annotation management for biomaterials, i.e. samples, extracts, and labeled extracts, updated with links for associated file items, that leads to the properties form for the file:

1. Class/file action/sample/ViewActiveSample.java in client/servlet/ updated in private method Table createFileTable(Sample sample) with action link for associated file items. The action link is coupled to action ViewFile, and the file id value is added to valid parameter VInteger FormFactory.VID.

2. Class/file action/extract/ViewActiveExtract.java in client/servlet/ updated in protected method void runMe() with action link for associated file items. The action link is coupled to action ViewFile, and the file id value is added to valid parameter VInteger FormFactory.VID.

3. Class/file action/extract/ViewActiveLabeledExtract.java in client/servlet/ updated in protected method void runMe() with action link for associated file items. The action link is coupled to action ViewFile, and the file id value is added to valid parameter VInteger FormFactory.VID.

[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.