Opened 13 years ago

Closed 13 years ago

Last modified 6 years ago

#1193 closed task (fixed)

Generic tree-like item overview

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: BASE 2.10
Component: web Version:
Keywords: Cc:

Description

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.

Change History (32)

comment:1 Changed 13 years ago by Nicklas Nordborg

Owner: changed from everyone to Nicklas Nordborg
Status: newassigned

comment:2 Changed 13 years ago by 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.

comment:3 Changed 13 years ago by Nicklas Nordborg

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

Added validation of annotation.

comment:4 Changed 13 years ago by Nicklas Nordborg

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

Web interface has been added to Hybridization view

comment:5 Changed 13 years ago by Nicklas Nordborg

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

Web interface has been added to the other items.

comment:6 Changed 13 years ago by Nicklas Nordborg

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

Verified that AnnotationValidator? can find all expected problems.

comment:7 Changed 13 years ago by Nicklas Nordborg

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

Verified that ProtocolValidator? and HardwareValidator? can find all expected problems.

comment:8 Changed 13 years ago by Nicklas Nordborg

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

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

comment:9 Changed 13 years ago by Nicklas Nordborg

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

Verified that data files are loaded and validated correctly.

comment:10 Changed 13 years ago by 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.

comment:11 Changed 13 years ago by Nicklas Nordborg

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

Verified that samples are loaded and validated correctly.

comment:12 Changed 13 years ago by Nicklas Nordborg

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

Adding some more icons for the overview.

comment:13 Changed 13 years ago by Nicklas Nordborg

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

Verified that extracts are loaded and validated correctly.

comment:14 Changed 13 years ago by Nicklas Nordborg

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

Verified that labeled extracts are loaded and validated correctly.

comment:15 Changed 13 years ago by 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?

comment:16 Changed 13 years ago by Nicklas Nordborg

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

Verified that hybridizations are loaded and validated correctly.

comment:17 Changed 13 years ago by Nicklas Nordborg

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

Verified that raw bioassays are loaded and validated correctly.

comment:18 Changed 13 years ago by Nicklas Nordborg

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

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

comment:19 Changed 13 years ago by Nicklas Nordborg

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

Added check for missing experimental factor values.

comment:20 Changed 13 years ago by Nicklas Nordborg

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

Added check for experiments using multiple array designs.

comment:21 Changed 13 years ago by Nicklas Nordborg

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

Fixes NPE.

comment:22 Changed 13 years ago by Nicklas Nordborg

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

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

comment:23 Changed 13 years ago by Nicklas Nordborg

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

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

comment:24 Changed 13 years ago by 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.

comment:25 Changed 13 years ago by Nicklas Nordborg

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

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

comment:26 Changed 13 years ago by 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.

comment:27 Changed 13 years ago by Nicklas Nordborg

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

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

comment:28 Changed 13 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

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

Documentation has been updated.

comment:29 Changed 13 years ago by Nicklas Nordborg

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

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

comment:30 Changed 13 years ago by 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.

comment:31 Changed 13 years ago by Nicklas Nordborg

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

Fixed javadoc that referenced deprecated classes.

comment:32 Changed 6 years ago by 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.

Last edited 6 years ago by Nicklas Nordborg (previous) (diff)
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