Generic tree-like item overview

[Nicklas Nordborg]

Implement a function that is similar to the "Experiment overview" that can be rooted at any kind of item from biosource down to experiment. Eg.

• Biosource
• Sample
• Extract
• Labeled extract
• Hybridization
• Scan
• Raw bioassay
• Experiment

As it is now the experiment overview functionality is very static and it is not trivial to re-use code from it for this purpose. One part of this ticket should be to investigate if and how we can re-design the experiment overview so that we don't have to duplicate a lot of code. Other things that needs to discussed:

• Lazy loading. Eg. do not load sub-tree until it is clicked on in the web interface.
• Validation. Do we only need it when rooted at an experiment? The original use case was to be able to validate and experiment before exporting data to a Tab2Mage. This use case doesn't hold when rooted at other items. Validation also affects lazy loading since we need to load the entire tree before it is possible to validate.

[Nicklas Nordborg]

(In [4740]) Refernces #1193: Generic tree-like item overview

Initial checkin of a lot of classes. This is by no way completed, but should be enough to start prototyping a web interface so we can really test the functionality.

[Nicklas Nordborg]

(In [4743]) References #1193: Generic tree-like item overview

Added validation of annotation.

[Nicklas Nordborg]

In [4745]: References #1193: Generic tree-like item overview

Web interface has been added to Hybridization view

[Nicklas Nordborg]

(In [4746]) References #1193: Generic tree-like item overview

Web interface has been added to the other items.

[Nicklas Nordborg]

(In [4747]) References #1193: Generic tree-like item overview

Verified that AnnotationValidator can find all expected problems.

[Nicklas Nordborg]

(In [4748]) References #1193: Generic tree-like item overview

Verified that ProtocolValidator and HardwareValidator can find all expected problems.

[Nicklas Nordborg]

(In [4749]) References #1193: Generic tree-like item overview

Verified that software and protocol parameters are loaded and validated correctly.

[Nicklas Nordborg]

(In [4750]) References #1193: Generic tree-like item overview

Verified that data files are loaded and validated correctly.

[Nicklas Nordborg]

(In [4752]) References #1193: Generic tree-like item overview

Found another validation issue with inherited annotations and made some old validation rules visible in the "Validation options" function.

[Nicklas Nordborg]

(In [4753]) References #1193: Generic tree-like item overview

Verified that samples are loaded and validated correctly.

[Nicklas Nordborg]

(In [4754]) References #1193: Generic tree-like item overview

Adding some more icons for the overview.

[Nicklas Nordborg]

(In [4755]) References #1193: Generic tree-like item overview

Verified that extracts are loaded and validated correctly.

[Nicklas Nordborg]

(In [4756]) References #1193: Generic tree-like item overview

Verified that labeled extracts are loaded and validated correctly.

[Nicklas Nordborg]

(In [4757]) References #1193: Generic tree-like item overview

Annotation errors are now attached to the annotation nodes instead of the parent node. Fixes some display issues with null and PermissionDeniedException

[Nicklas Nordborg]

(In [4758]) References #1193: Generic tree-like item overview

Verified that hybridizations are loaded and validated correctly.

[Nicklas Nordborg]

(In [4759]) References #1193: Generic tree-like item overview

Verified that raw bioassays are loaded and validated correctly.

[Nicklas Nordborg]

(In [4760]) References #1193: Generic tree-like item overview

Verified loading and validation of array designs/batches/slides.

[Nicklas Nordborg]

(In [4761]) References #1193: Generic tree-like item overview

Added check for missing experimental factor values.

[Nicklas Nordborg]

(In [4762]) References #1193: Generic tree-like item overview

Added check for experiments using multiple array designs.

[Nicklas Nordborg]

(In [4763]) References #1193: Generic tree-like item overview

Fixes NPE.

[Nicklas Nordborg]

(In [4764]) References #1193: Generic tree-like item overview

Added check for items that doesn't have a unique name.

[Nicklas Nordborg]

(In [4765]) References #1193: Generic tree-like item overview

Fixes some IE-related issues and a nicer display of failures.

[Nicklas Nordborg]

(In [4766]) References #1193: Generic tree-like item overview

Fixes a problem with caching items that can be loaded in more than one section or direction within the tree.

[Nicklas Nordborg]

(In [4767]) References #1193: Generic tree-like item overview

Marked old ExperimentOverivew as deprecated and removed old jsp files related to this.

[Nicklas Nordborg]

(In [4768]) References #1193: Generic tree-like item overview

Cleaned up and documented remaining code. This ticket is now nearly finished. Performance-related things, for example lazy loading, will have to wait for BASE 2.11.

[Nicklas Nordborg]

(In [4770]) References #1193: Generic tree-like item overview

Do not cache protocols due to validation issues with protocol parameters.

[Nicklas Nordborg]

(In [4771]) Fixes #1193: Generic tree-like item overview

Documentation has been updated.

[Nicklas Nordborg]

(In [4772]) References #1193: Generic tree-like item overview

Changed some old references to "Experiment overview" to "Item overview"

[Nicklas Nordborg]

(In [4779]) References #1193: Generic tree-like item overview

Fixed a problem with data file validation and disabled caching/cloning of nodes since it causes incorrect numbers of errors/warnings to be reported.

[Nicklas Nordborg]

(In [4786]) References #1193: Generic tree-like item overview

Fixed javadoc that referenced deprecated classes.

[Nicklas Nordborg]

This belong to #1993!!!

(In [7108]) Fixes #1193: Display error messages from startup problems in web client

StartStopServlet must not throw an exception. This is what causes Tomcat to send a 404 error message.

Turned out that quite a few places expected BASE to be started. This included the error handling pages. Added checks in those places to avoid secondary problems (eg. NullPointerException) from masking the real issue.