source: trunk/doc/development/drafts/experiment_overview.txt @ 3033

Last change on this file since 3033 was 3033, checked in by Nicklas Nordborg, 15 years ago

References #262, #340: First prototype for experiment overview. Reads most of an
experiment. Limited validation. No presets. No detailed information about an error/warning.

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1
2Experiment overview/validation
3==============================
4
5See tickets:
6262: Overview of an experiment (http://base.thep.lu.se/ticket/262)
7340: Experiment validation tool (http://base.thep.lu.se/ticket/340)
8
9
10The experiment overview/validation tool can display a tree-structure of
11all up-stream items (ie. not the analysis) in an experiment and validate
12that everything makes sense. The tree stops at biosource and array
13design. Ie. plates are not included in the overview.
14
15Before the overview is generated the user has to select options for
16the validation. This could include:
17 
18 - checking against project defaults if a project is active
19 - checking for missing values/references
20 - checking for correct number of labeled extracts
21 - and a lot more (see below)
22
23For each type of validation the user can select if it should be ignored,
24generate a warning or generate an error.
25
26The overview is generated and stored as some kind of object structure. This
27structure always include the validation results. When the HTML is generated the
28validation options are checked to decide which warnings/errors that should be
29displayed and which ones that should be ignored. This makes it possible to
30select different validation options without having to re-generate to the overview.
31
32The validation options can be saved as presets. A pre-configured preset
33for validation according to MAGE rules will be included in the installation.
34
35The tree starts with the experiment as the top node. Each subnode is either
36a folder node (for one/many-to-many relations) or an item node (for
37many/one-to-one relations).
38
39Warnings/error are indicated for each node by a different icon. Warnings on child
40nodes are propagated to parent nodes. There are four cases (with possibly eight
41different icons):
42 - no warnings/errors on the node or any of the child nodes
43 - warnings/errors on the child nodes
44 - warnings/errors on the node but not on any of the child nodes
45 - warnings/errors on both the node and the child nodes
46
47
48Below follows an overview of the different nodes, their subnodes and possible
49warnings for each node.
50
51If an item can't be reached due to a PermissionDeniedException, it should be
52displayed as a question mark icon for the item that is linking to it.
53
54
55Experiment
56==========
57Folder subnodes:
58 - Experimental factors
59 - Raw bioassays
60 
61Item subnodes: none
62 
63Warnings:
64 - the raw data type is not the same as the project default raw data type
65 - the raw bioassays has different array designs
66 - if there is more than one item of the same type and name
67   (checked against all items in the project)
68
69 
70Experimental factor
71===================
72Folder subnodes: none
73Item subnodes: none
74Warnings: none
75
76
77Raw bioassay
78============
79Folder subnodes:
80 - Annotations
81
82Item subnodes:
83 - Array design
84 - Scan
85 - Software
86 - Protocol
87 
88Warnnings:
89 - the raw data type is not the same as the project default raw data type
90 - missing array design
91 - missing value for experimental factor
92 - array design is different from array design via hybridization
93 - missing scan
94 - missing protocol
95 - missing software
96
97
98Array design
99============
100Subnodes: none
101Warnings:
102 - not same as the project default
103
104 
105Protocol
106========
107Folder subnodes:
108 - Parameters
109
110Item subnodes: none
111
112Warnings:
113 - not same as the project default
114 - incorrect protocol type
115 - missing value for a parameter
116
117Note! Protocols are always validated together with the item they are attached to
118
119Annotation
120==========
121Subnodes: none
122
123Warnings:
124 - invalid annotation value according to annotation type
125 - inheriting value from non-parent
126 - inheriting multiple annotation of the same type (from different parents)
127 - annotation type is a protocol parameter
128 - annotation type is not valid for the current item type
129 - missing value for a "Required by MIAME" annotation type (on folder node)
130
131Note! Annotations are always validated together with the item they are attached to
132
133Software
134========
135Subnodes: none
136Warnings:
137 - incorrect software type
138 
139Hardware
140========
141Subnodes: none
142Warnings:
143 - incorrect hardware type
144 
145Scan
146====
147Folder subnodes:
148 - Annotations
149 - Images
150 
151Item subnodes:
152 - Scanner
153 - Protocol
154 - Hybridization
155
156Warnings:
157 - missing scanner
158 - missing protocol
159 - missing hybridization
160
161Hybridization
162=============
163Folder subnodes:
164 - Annotations
165 - Labeled extracts
166
167Item subnodes:
168 - Hybridization station
169 - Protocol
170 - Array slide
171
172Warnings:
173 - missing hybridization station
174 - missing protocol
175 - missing array slide
176 - wrong number of labeled extracts (checked against experiment raw data type)
177 - the labeled extracts doesn't have unique labels
178 
179Array slide
180===========
181Folder subnodes:
182 - Annotations
183
184Item subnodes:
185 - Array batch
186
187Warnings: none
188
189Array batch
190===========
191Folder subnodes:
192 - Annotations
193
194Item subnodes:
195 - Array design
196 - Print robot
197 - Protocol
198
199Warnings:
200 - missing print robot
201 - missing protocol
202 
203
204Labeled extract (non-pooled)
205============================
206Folder subnodes:
207 - Annotations
208
209Item subnodes:
210 - Extract
211 - Protocol
212 
213Warnings:
214 - missing protocol
215 - missing extract
216 
217Labeled extract (pooled)
218========================
219Folder subnodes:
220 - Annotations
221 - Parents
222 
223Item subnodes:
224 - Protocol
225 
226Warnings:
227 - parents use different label
228 - missing parents
229 - circular reference
230 
231Extract (non-pooled)
232====================
233Folder subnodes:
234 - Annotations
235 
236Item subnodes:
237 - Sample
238 - Protocol
239 
240Warnings:
241 - missing protocol
242 - missing sample
243 
244Extract (pooled)
245================
246Folder subnodes:
247 - Annotations
248 - Parents
249
250Item subnodes:
251 - Protocol
252 
253Warnings:
254 - missing protocol
255 - circular reference
256 
257Sample (non-pooled)
258===================
259Folder subnodes:
260 - Annotations
261 
262Item subnodes:
263 - Biosource
264 - Protocol
265 
266Warnings:
267 - missing protocol
268 - missing biosource
269
270Sample (pooled)
271===============
272Folder subnodes:
273 - Annotations
274 - Parents
275
276Item subnodes:
277 - Protocol
278 
279Warnings:
280 - missing protocol
281 - circular reference
282 
283Biosource
284=========
285Folder subnodes:
286 - Annotations
287 
288Item subnodes: none
289
290Warnings: none
291
292
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