source: trunk/doc/development/drafts/experiment_overview.txt @ 3024

Experiment overview/validation
==============================

See tickets:
262: Overview of an experiment (http://base.thep.lu.se/ticket/262)
340: Experiment validation tool (http://base.thep.lu.se/ticket/340)


The experiment overview/validation tool can display a tree-structure of
all up-stream items (ie. not the analysis) in an experiment and validate
that everything makes sense. The tree stops at biosource and array 
design. Ie. plates are not included in the overview.

Before the overview is generated the user has to select options for
the validation. This could include:
 
 - checking against project defaults if a project is active
 - checking for missing values/references
 - checking for correct number of labeled extracts
 - and a lot more (see below)

For each type of validation the user can select if it should be ignored,
generate a warning or generate an error.

The overview is generated and stored as some kind of object structure. This
structure always include the validation results. When the HTML is generated the 
validation options are checked to decide which warnings/errors that should be 
displayed and which ones that should be ignored. This makes it possible to 
select different validation options without having to re-generate to the overview.

The validation options can be saved as presets. A pre-configured preset
for validation according to MAGE rules will be included in the installation.

The tree starts with the experiment as the top node. Each subnode is either
a folder node (for one/many-to-many relations) or an item node (for 
many/one-to-one relations).

Warnings/error are indicated for each node by a different icon. Warnings on child
nodes are propagated to parent nodes. There are four cases (with possibly eight 
different icons):
 - no warnings/errors on the node or any of the child nodes
 - warnings/errors on the child nodes
 - warnings/errors on the node but not on any of the child nodes
 - warnings/errors on both the node and the child nodes


Below follows an overview of the different nodes, their subnodes and possible 
warnings for each node. 

If an item can't be reached due to a PermissionDeniedException, it should be 
displayed as a question mark icon for the item that is linking to it.


Experiment
==========
Folder subnodes:
 - Experimental factors
 - Raw bioassays
 
Item subnodes: none
 
Warnings:
 - the raw data type is not the same as the project default raw data type
 - the raw bioassays has different array designs
 - if there is more than one item of the same type and name
   (checked against all items in the project)

 
Experimental factor
===================
Folder subnodes: none
Item subnodes: none
Warnings: none


Raw bioassay
============
Folder subnodes:
 - Annotations

Item subnodes:
 - Array design
 - Scan
 - Software
 - Protocol
 
Warnnings:
 - the raw data type is not the same as the project default raw data type
 - missing array design
 - missing value for experimental factor
 - array design is different from array design via hybridization
 - missing scan
 - missing protocol
 - missing software


Array design
============
Subnodes: none
Warnings:
 - not same as the project default 

 
Protocol
========
Folder subnodes:
 - Parameters

Item subnodes: none

Warnings:
 - not same as the project default
 - incorrect protocol type
 - missing value for a parameter

Note! Protocols are always validated together with the item they are attached to

Annotation
==========
Subnodes: none

Warnings:
 - invalid annotation value according to annotation type
 - inheriting value from non-parent
 - annotation type is a protocol parameter
 - annotation type is not valid for the current item type

Note! Annotations are always validated together with the item they are attached to

Software
========
Subnodes: none
Warnings:
 - incorrect software type
 
Hardware
========
Subnodes: none
Warnings:
 - incorrect hardware type
 
Scan
====
Folder subnodes:
 - Annotations
 - Images
 
Item subnodes:
 - Scanner
 - Protocol
 - Hybridization

Warnings:
 - missing scanner
 - missing protocol
 - missing hybridization

Hybridization
=============
Folder subnodes:
 - Annotations
 - Labeled extracts

Item subnodes:
 - Hybridization station
 - Protocol
 - Array slide

Warnings:
 - missing hybridization station
 - missing protocol
 - missing array slide
 - wrong number of labeled extracts (checked against experiment raw data type)
 - the labeled extracts doesn't have unique labels
 
Array slide
===========
Folder subnodes:
 - Annotations

Item subnodes:
 - Array batch

Warnings: none

Array batch
===========
Folder subnodes:
 - Annotations

Item subnodes:
 - Array design
 - Print robot
 - Protocol

Warnings:
 - missing print robot
 - missing protocol
 

Labeled extract (non-pooled)
============================
Folder subnodes:
 - Annotations

Item subnodes:
 - Extract
 - Protocol
 
Warnings:
 - missing protocol
 - missing extract
 
Labeled extract (pooled)
========================
Folder subnodes:
 - Annotations
 - Parents
 
Item subnodes:
 - Protocol
 
Warnings:
 - parents use different label
 - missing parents
 - circular reference
 
Extract (non-pooled)
====================
Folder subnodes:
 - Annotations
 
Item subnodes:
 - Sample
 - Protocol
 
Warnings:
 - missing protocol
 - missing sample
 
Extract (pooled)
================
Folder subnodes: 
 - Annotations
 - Parents

Item subnodes:
 - Protocol
 
Warnings:
 - missing protocol
 - circular reference
 
Sample (non-pooled)
===================
Folder subnodes:
 - Annotations
 
Item subnodes:
 - Biosource
 - Protocol
 
Warnings:
 - missing protocol
 - missing biosource

Sample (pooled)
===============
Folder subnodes: 
 - Annotations
 - Parents

Item subnodes:
 - Protocol
 
Warnings:
 - missing protocol
 - circular reference
 
Biosource
=========
Folder subnodes:
 - Annotations
 
Item subnodes: none

Warnings: none