source: trunk/doc/development/drafts/experiment_overview.txt @ 3045

Last change on this file since 3045 was 3045, checked in by Nicklas Nordborg, 15 years ago

References #262 and #340. The overview and validation is now complete.
Still missing possibility to save validation options as presets.

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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
51After the first prototype we have found that warnings should be attached to
52the nodes that has the possibility to correct the warning/error. In most cases
53this means that the warnings should be attached to: rawbioassay, scan, hybridization,
54labeled extract, extract, sample, biosource, array slide, array batch and array
55design. One exception is 'Access denied' warnings that can't be corrected by the
56logged in user anyway.
57
58We will also try to add a list of possible "fixes" to a warning. A fix consists
59of an explaining text and an item that should be edited.
60
61If an item can't be reached due to a PermissionDeniedException, it should be
62displayed as a question mark icon for the item that is linking to it.
63
64
65Experiment
66==========
67Folder subnodes:
68 - Experimental factors
69 - Raw bioassays
70 
71Item subnodes: none
72 
73Warnings:
74 - the raw data type is not the same as the project default raw data type
75   (possible fix: change project default)
76   (done)
77 - the raw bioassays has different array designs
78   (no fix)
79   (done)
80 - if there is more than one item of the same type and name
81   (checked against all items in the project)
82   (possible fix: rename the item)
83   (done)
84
85 
86Experimental factor
87===================
88Folder subnodes: none
89Item subnodes: none
90Warnings: none
91
92
93Raw bioassay
94============
95Folder subnodes:
96 - Annotations
97
98Item subnodes:
99 - Array design
100 - Scan
101 - Software
102 - Protocol
103 
104Warnings:
105 - the raw data type is not the same as the project default raw data type
106   (possible fix: change project default)
107   (done)
108 - missing array design
109   (no fix)
110   (done)
111 - missing value for experimental factor
112   (possible fix: add value or inherit from parent item)
113   (done)
114 - array design is different from array design via hybridization
115   (possible fix: change array slide of hyb)
116   (done)
117 - missing scan
118   (possible fix: add scan)
119   (done)
120 - missing protocol
121   (possible fix: add protocol)
122   (done)
123 - missing software
124   (possible fix: add software)
125   (done)
126
127
128Array design
129============
130Subnodes: none
131Warnings:
132 - not same as the project default (warning is added to parent item)
133   (possible fix: change project default)
134   (done)
135
136Protocol
137========
138Folder subnodes:
139 - Parameters
140
141Item subnodes: none
142
143Warnings:
144 - not same as the project default
145   (possible fix: change protocol, change project default)
146   (done)
147 - incorrect protocol type
148   (possible fix: change protocol, change protocol type)
149   (done)
150 - missing value for a parameter
151   (possible fix: add parameter value)
152   (done)
153
154Note! Protocols are always validated together with the item they are attached
155to and are added to the parent item
156
157Annotation
158==========
159Subnodes: none
160
161Warnings:
162 - invalid annotation value according to annotation type
163   (possible fix: change annotation value)
164   (done)
165 - inheriting value from non-parent
166   (possible fix: change inherited annotations)
167   (done)
168 - inheriting multiple annotation of the same type (from different parents)
169   (possible fix: change inherited annotations)
170   (done)
171 - annotation type is a protocol parameter
172   (possible fix: remove annotation value, remove 'parameter' flag from annotation type)
173   (done)
174 - annotation type is not valid for the current item type
175   (possible fix: remove annotation value, add item type to annotation type)
176   (done)
177 - missing value for a "Required by MIAME" annotation type (on folder node)
178   (possible fix: add annotation value, uncheck the 'Required by MIAME' flag)
179   (done)
180
181Note! Annotations are always validated together with the item they are attached
182to and the warnnings are added to that item
183
184Software
185========
186Subnodes: none
187Warnings (added to parent item):
188 - incorrect software type
189   (possible fix: change software, change software type)
190   (done)
191 - not same as project default
192   (possible fix: change software, change project default)
193   (done)
194 
195Hardware
196========
197Subnodes: none
198Warnings (added to parent item):
199 - incorrect hardware type
200   (possible fix: change hardware, change hardware type)
201   (done)
202 - not same as project default
203   (possible fix: change software, change project default)
204   (done)
205 
206Scan
207====
208Folder subnodes:
209 - Annotations
210 - Images
211 
212Item subnodes:
213 - Scanner
214 - Protocol
215 - Hybridization
216
217Warnings:
218 - missing scanner
219   (possible fix: add scanner)
220   (done)
221 - missing protocol
222   (possible fix: add protocol)
223   (done)
224 - missing hybridization
225   (possible fix: add hybridization)
226   (done)
227
228Hybridization
229=============
230Folder subnodes:
231 - Annotations
232 - Labeled extracts
233
234Item subnodes:
235 - Hybridization station
236 - Protocol
237 - Array slide
238
239Warnings:
240 - missing hybridization station
241   (possible fix: add hyb station)
242   (done)
243 - missing protocol
244   (possible fix: add protocol)
245   (done)
246 - missing array slide
247   (possible fix: add array slide)
248   (done)
249 - wrong number of labeled extracts (checked against experiment raw data type)
250   (possible fix: add/remove labeled extracts)
251   (done)
252 - the labeled extracts doesn't have unique labels
253   (possible fix: add/remove labeled extracts, change label of labeled extract)
254   (done)
255 
256Array slide
257===========
258Folder subnodes:
259 - Annotations
260
261Item subnodes:
262 - Array batch
263
264Warnings: none
265
266Array batch
267===========
268Folder subnodes:
269 - Annotations
270
271Item subnodes:
272 - Array design
273 - Print robot
274 - Protocol
275
276Warnings:
277 - missing print robot
278   (possible fix: add print robot)
279   (done)
280 - missing protocol
281   (possible fix: add protocol)
282   (done)
283
284Labeled extract (non-pooled)
285============================
286Folder subnodes:
287 - Annotations
288
289Item subnodes:
290 - Extract
291 - Protocol
292 
293Warnings:
294 - missing protocol
295   (possible fix: add protocol)
296   (done)
297 - missing extract
298   (possible fix: add extract)
299   (done)
300 
301Labeled extract (pooled)
302========================
303Folder subnodes:
304 - Annotations
305 - Parents
306 
307Item subnodes:
308 - Protocol
309 
310Warnings:
311 - parents use different label
312   (possible fix: add/remove parents, change label of parents)
313   (done)
314 - missing parents
315   (possible fix: add parents)
316   (done)
317 - circular reference
318   (possible fix: add/remove parents)
319   (done)
320 
321Extract (non-pooled)
322====================
323Folder subnodes:
324 - Annotations
325 
326Item subnodes:
327 - Sample
328 - Protocol
329 
330Warnings:
331 - missing protocol
332   (possible fix: add protocol)
333   (done)
334 - missing sample
335   (possible fix: add sample)
336   (done)
337 
338Extract (pooled)
339================
340Folder subnodes:
341 - Annotations
342 - Parents
343
344Item subnodes:
345 - Protocol
346 
347Warnings:
348 - missing protocol
349   (possible fix: add protocol)
350   (done)
351 - missing parents
352   (possible fix: add parents)
353   (done)
354 - circular reference
355   (possible fix: add/remove parents)
356   (done)
357 
358Sample (non-pooled)
359===================
360Folder subnodes:
361 - Annotations
362 
363Item subnodes:
364 - Biosource
365 - Protocol
366 
367Warnings:
368 - missing protocol
369   (possible fix: add protocol)
370   (done)
371 - missing biosource
372   (possible fix: add biosource)
373   (done)
374
375Sample (pooled)
376===============
377Folder subnodes:
378 - Annotations
379 - Parents
380
381Item subnodes:
382 - Protocol
383 
384Warnings:
385 - missing protocol
386   (possible fix: add protocol)
387   (done)
388 - missing parents
389   (possible fix: add parents)
390   (done)
391 - circular reference
392   (possible fix: add/remove parents)
393   (done)
394 
395Biosource
396=========
397Folder subnodes:
398 - Annotations
399 
400Item subnodes: none
401
402Warnings: none
403
404
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