source: trunk/doc/historical/specifications/webclient/webguispecs.html @ 4394

Last change on this file since 4394 was 190, checked in by Jari Häkkinen, 19 years ago

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1<html>
2
3<head>
4  <title>Web GUI 31 October specifications</title>
5</head>
6
7<body bgcolor=white>
8
9  <h2>
10    Web GUI 31 October specifications.
11  </h2>
12
13  <p>
14  $Id: webguispecs.html 190 2005-03-17 15:06:01Z jari $
15  </p>
16
17  <p>
18  <b><u>Bold Underlined</u></b> items are not implemented.
19  </p>
20
21  <h3><font color=#aaaa00>
22      Biomaterial functionality (in somewhat chronological implementation
23      order).</font></h3>
24
25  <p>
26  NOTE1: When a Biomaterial is created from an existing Biomaterial
27  (i.e. a parent exists in the database), the default name of the child
28  should be the name of the parent followed by suffix ".yX" (where X is
29  a number, 1 for the first child created, 2 for the second and so on,
30  and y is a character denoting the type of the child where s=sample,
31  e=extract, and l=labeled extract). The default name should be editable
32  in the "New Biomaterial" dialogue window before saving.
33  </p>
34
35  <p>
36  NOTE2: All measured biomaterials (i.e. not BioSource) should have a
37  protocol (connected to the BiomaterialEvent). For october 31 release
38  this does not need to be implemented BUT the dropdown menu (empty)
39  should preferably be available in the Biomaterial creation dialogue
40  for demonstration purposes.
41  </p>
42
43  <p>
44  NOTE3: When the parent of a new Biomaterial (i.e. during creation of
45  the new Biomaterial through the dialogue window) has a measured
46  quantity this value should be displayed (getRemainingQuantity) along
47  with original quantity (getOriginalQuantity), and the user should be
48  able to specify amount used (of parent). For example: "23 ug available
49  (out of original 100 ug)" is displayed and the user can fill in amount
50  used.
51  </p>
52
53
54  <ol>
55
56    <li><p>List items for main menu "Biomaterials"</p>
57    <ol>
58      <li type=a>Submenu "Biosources", "Samples", "Extracts", "Labeled
59      extracts", "Labels" (already implemented).
60      </li>
61    </ol>
62    </li>
63
64    <li><p>ShareableItem Permissions <br> All ShareableItems
65        should in their edit-window (or something similar) have
66        sharing settings to give permissions to Users,Groups and
67        <b><u>Projects.</u></b></p>
68    </li>
69
70    <li><p>List items for sub menu "Hybridizations"</p>
71
72    <ol>
73
74      <li type=a><p>Create new "Hybridization" (using button
75      "" in the table header).</p>
76      <ol>
77        <li type=i>
78        <p>Through web interface (W) assign a name, description,
79        Labeled extract(s) through dropdown(s), and so on.  Dropdowns
80        for Labeled extracts could default to one. Below the dropdown
81        a button named "Additional Labeled extract" could be placed.
82        If clicked, an additional dropdown appears (sort of like when
83        filter criterions are added one after the other).</p>
84        </li>
85      </ol>
86      </li>
87
88      <li type=a><p>Add column "Labeled extracts" in the Hybridization
89      table. In this column Labeled extracts associated with the
90      corresponding Hybridization are displayed. Labeled
91      extracts in this column are links to the Labeled
92      extracts. Next to the name of the Labeled extracts the
93      name of the label should be displayed, e.g., for labeled
94      extract "ABC.e1.l1" labeled with label "Cy3" the column
95      should hold "ABC.e1.l1 (Cy3)".</p>
96      </li>
97
98      <li type=a>Hybridizations/Hybridizations SUMMARY columns:
99      <ul>
100        <li>Row number</li>
101        <li>Check boxes</li>
102        <li>Name</li>
103        <li>Labeled extracts</li>
104        <li>Description</li>
105        <li>Owner</li>
106        <li>Shared</li>
107        <li>Hyb date</li>
108        <li>Array slide</li>
109        <li>[newSc]</li>
110        <li>Scans</li>
111        <li>Images</li>
112        <li>Results files</li>
113      </ul>
114      </li>
115
116    </ol>
117
118    <li><p>Biosource (Biomaterial/Biosources):</p>
119
120    <ol>
121      <li type=a><p>Create new "Biosource" (using button "" in the
122      table header).</p>
123      <ol>
124        <li type=i><p>Through web interface (W) assign a name,
125        description and so on.</p>
126        </li>
127      </ol>
128      </li>
129
130      <li type=a><p>Create new "Sample" from "Biosource". Add a
131      function column in the Biosource table with a link
132      "[newS]". When clicked, a "sample" is created from the
133      corresponding "Biosource".</p>
134      </li>
135
136      <li type=a><p>Add column "Samples" in the Biosource table. In this
137      column child Samples from the corresponding Biosource are
138      displayed. Samples in this column are links to the
139      samples.</p>
140      </li>
141    </ol>
142    </li>
143
144    <li><p>Sample (Biomaterial/Samples):</p>
145
146    <ol>
147      <li type=a><p>Create new "Sample" (using button "" in the table
148      header). In this way a "New Sample" dialogue window, without
149      selected parent, is created. </p>
150      <ol>
151        <li type=i>
152        <p>
153        Through web interface (W) assign a parent (optional and
154        accessed through a dropdown list of available parents, <b><u>
155          Q: one dropdown for Biosources and one for Samples?)
156        </u></b>, name, description, event date (i.e.  Sample date),
157        original Quantity and so on.
158        </p>
159        </li>
160      </ol>
161      </li>
162
163      <li type=a><p>Create new <b><u>"Sample" from "Sample"</u></b>,
164      and new "Extract" from "Sample". Add 2 function columns in
165      the Sample table with a link <b><u>"[newS]"</u></b>, and
166      "[newE]" respectively. When clicked, a "Sample" or "Extract"
167      is created from the corresponding "Sample".</p>
168
169      <p><b><u>NOTE: an update will be required here (at some point
170          when there is time). By selecting multiple "Samples",
171          using the check boxes, and then using button "" in the
172          table header a pooled sample is created.</u></b></p>
173      </li>
174
175      <li type=a><p>Add column "Extracts" in the Sample table. In this
176      column child Extracts from the corresponding Sample are
177      displayed. Extracts in this column are links to the
178      extracts.</p>
179      </li>
180
181      <li type=a><p><b><u>Add column "Hybridizations" in the Sample
182          table. In this column child Hybridizations from the
183          corresponding Sample are displayed. Hybridizations in
184          this column are links to the hybridizations.</u></b></p>
185      </li>
186    </ol>
187
188    <li><p>Extracts (Biomaterial/Extracts):</p>
189
190    <ol>
191      <li type=a><p>Create new "Extract" (using button "" in the table
192      header). In this way a "New Extract" dialogue window,
193      without selected parent, is created. </p>
194      <ol>
195        <li type=i><p>Through web interface (W) assign a parent
196        (optional and accessed through a dropdown list of
197        available parents, <b><u>Q: one dropdown for Samples and
198            one for Extracts?)</u></b>, name, description, event
199        date (i.e. Extract date) and so on.</p>
200        </li>
201      </ol>
202
203      <li type=a><p>Create new <b><u>"Extract" from
204          "Extract"</u></b>, and new "Labeled extract" from
205      "Extract". Add 2 function columns in the Sample table
206      with a link <b><u>"[newE]"</u></b>, and "[newL]"
207      respectively. When clicked, an "Extract" or "Labeled
208      extract" is created from the corresponding
209      "Extract".</p>
210      <p><b><u>NOTE: an update will be required here (at some point
211          when there is time). By selecting multiple "Extract",
212          using the check boxes, and then using button "" in the
213          table header a pooled Extract is created. </u></b></p>
214      </li>
215
216      <li type=a><p>Add column "Labeled extracts" in the Extract
217      table. In this column child Labeled extracts from the
218      corresponding Extract are displayed. Labeled extracts in
219      this column are links to the Labeled extracts.</p>
220      </li>
221
222      <li type=a><p><b><u>Add column "Hybridizations" in the Extract
223          table. In this column child Hybridizations from the
224          corresponding Extract are displayed. Hybridizations in
225          this column are links to the hybridizations.</u></b></p>
226      </li>
227    </ol>
228    </li>
229
230    <li><p>Labeledextracts (Biomaterial/Labeled extracts):</p>
231
232    <ol>
233      <li type=a><p>Create new "Labeled extract" (using button "" in
234      the table header). In this way a "New Labeled extract"
235      dialogue window, without selected parent, is created. </p>
236      <ol>
237        <li type=i><p>Through web interface (W) assign a parent
238        (optional and accessed through a dropdown list of
239        available parents, <b><u>Q: one dropdown for Extracts
240            and one for Labeled extracts?</u></b>, name,
241        description, event date (i.e. Labeled extract date) and
242        so on.</p>
243        </li>
244      </ol>
245      </li>
246
247      <li type=a><p>Create new <b><u>"Labeled extract" from "Labeled
248          extract"</u></b>, and new "Hybridization" from "Labeled
249      extract". Add 2 function columns in the Labeled extract
250      table with a link <b><u>"[newL]"</u></b>, and "[newH]"
251      respectively. When clicked, a "Labeled extract" or
252      "Hybridization" is created from the corresponding
253      "Extract".</p>
254      <p><b><u>NOTE: By selecting multiple "Labeled extract", using
255          the check boxes, and then using the link "[newH]" a
256          Hybridization is created using the selected Labeled
257          extracts.</u></b></p>
258      </li>
259
260      <li type=a><p><b><u>Add column "Hybridizations" in the Labeled
261          extract table. In this column child Hybridizations from
262          the corresponding Labeled extract are
263          displayed. Hybridizations in this column are links to
264          the hybridizations.</u></b></p>
265      <p><b><u>NOTE: an update will be required here (at some point
266          when there is time). By selecting multiple "Labeled
267          extract", using the check boxes, and then using button
268          "" in the table header a pooled Labeled extract is
269          created.</u></b></p>
270      </li>
271    </ol>
272    </li>
273
274    <li><p>Protocols (Biomaterial/Protocols)</p>
275
276    <dd>NOTE: When you select the "Protocols" tab under the
277    Biomaterial main menu you should list protocols in the current
278    context. You should not jump to the "Administrate/Protocol"
279    page. It is perfectly fine to have only 1 protocol page (i.e.,
280    in the background) but when accessed through the "Biomaterial"
281    menu it should be shown in the context of the other
282    "Biomaterial" tabs, and when accessed through the
283    "Administrate" menu it should be shown in the context of the
284    "Administrate" tabs.</dd>
285    </li>
286
287
288
289
290    <h3><font color=#aaaa00><b><u>Hybridization functionality (in somewhat chronological
291            implementation order)</u></b></font></h3>
292
293
294
295
296    <li><p><b><u>Submenu "Hybridizations/Hybridizations"</u></b></p>
297
298    <ol>
299      <li type=a><p>(Same as 3.a. above) Create new
300      "Hybridization" (using button "" in the table
301      header).</p>
302      <ol>
303        <li type=i>
304        <p> (Same as 3.a.i. above) Through web interface (W) assign a
305        name, description, Labeled extract(s) through dropdown(s), and
306        so on.  Dropdowns for Labeled extracts could default to one.
307        Below the dropdown a button named "Additional Labeled extract"
308        could be placed. If clicked, an additional dropdown appears
309        (sort of like when filter criterions are added one after the
310        other).  </p>
311        </li>
312      </ol>
313      </li>
314
315      <li type=a>
316      <p>(Same as 3.b. above) Add column "Labeled extracts" in the
317      Hybridization table. In this column Labeled extracts associated
318      with the corresponding Hybridization are displayed. Labeled
319      extracts in this column are links to the Labeled extracts. Next to
320      the name of the Labeled extracts the name of the label should be
321      displayed, e.g., for labeled extract "ABC.e1.l1" labeled with
322      label "Cy3"the column should hold "ABC.e1.l1 (Cy3)".</p>
323      </li>
324
325      <li type=a><p>Add column "Scans", "Images", and "Results files"
326      in the Hybridization table. In this column items associated
327      with the corresponding Hybridization are displayed (when
328      implemented). Add column "Array slide".</p>
329      </li>
330
331      <li type=a><p>Create new "Scan" from "Hybridization". Add
332      function column in the Hybridization table with a link
333      "[newSc]". When clicked, a "Scan" is created from the
334      corresponding "Hybridization"(similar to section 8.a.,
335          but with a parent-hybridization already
336          selected. Default name for the "Scan" should be the Name
337          of the parent-hybridization and suffix " scan X", where
338          X is a number indicating the number of scans created for
339          the corresponding hybridization. E.g.,
340          "HybridizationABC scan 1".).</p>
341      </li>
342    </ol>
343    </li>
344
345    <li><p><b><u>Submenu "Hybridizations/Scans"</u></b></p>
346
347    <ol>
348      <li type=a><p>Create new "Scan" (using button "" in the
349          table header). In this way a "New Scan" dialogue window,
350          without selected parent-hybridization, is created. </p>
351      <ol>
352        <li type=i><p>Through web interface assign a
353        hybridization (<b><u>optional</u></b> and accessed through a
354        dropdown list of available hybridizations), name,
355        description,<b><u> event date (i.e. Scan date)</u></b>, Scanner
356            (dropdown), and so on.</p>
357        </li>
358      </ol>
359      </li>
360
361      <li type=a>
362      <p>Add column "Hybridization" in the Scans table. In this column
363      parent-hybridization for the corresponding Scan is displayed.
364      Hybridizations in this column are links to the hybridization.</p>
365      </li>
366
367      <li type=a>
368      <p>Add column "Raw data sets" in the Scans table. In this column
369      child-raw data sets for the corresponding Scan is displayed.<b><u>
370          Raw data sets in this column are links to the raw data
371          sets.</u></b></p>
372      </li>
373
374      <li type=a><p>Add column "Scanner" in the Scans table. In
375      this column Scanner for the corresponding Scan is
376      displayed.</p>
377      </li>
378    </ol>
379    </li>
380
381    <li><p>Submenu "Hybridizations/Scanners"</p>
382
383    <ol>
384
385      <li type=a><p>By using button "" in the table header a
386      "New Scanner" dialogue window is opened. Through the web
387      interface, assign a name, description, and so
388      on.</p>
389      <p>NOTE1: Scanner is a Hardware type (analogue to
390      Protocol and Protocol type). Under main menu
391      "Administrate", add sub-menu options "Hardware", and
392      "Software". Implement it as done for protocols. As
393      stated, in the current BASE2 we only support one
394      Hardware type and one Software type, i.e., Scanner, and
395      Feature extraction software respectively. In the future
396      this could possibly be changed. </p>
397      <p>NOTE2: When you select the "Scanners" tab under the
398      Hybridization main menu you should list protocols in the
399      current context. You should not jump to the
400      "Administrate/Hardware" page. It is perfectly fine to
401      have only 1 hardware page but when accessed through the
402      "Hybridization" menu it should be shown in the context
403      of the other "Hybridization" tabs. This is analogue to
404      the description of "Biomaterial/Protocols" (section 7
405      above).</p>
406      </li>
407    </ol>
408    </li>
409
410    <li><p>Submenu "Hybridizations/Image processors"</p>
411
412    <ol>
413      <li type=a><p>By using button "" in the table header a
414      "New Image processor" dialogue window is opened. Through
415      the web interface, assign a name, description, and so
416      on.</p>
417      <p>NOTE: Image processor is a Software type (analogue to
418      Protocol and Protocol type). See the two NOTEs under Sub
419      menu "Hybridizations/Scanners" (section 10
420      above).</p>
421      </li>
422    </ol>
423    </li>
424
425    <li><p>Sub menu "Hybridizations/Result file
426    formats"</p>
427
428    <p>NOTE: This does only list items of the PluginConfiguration class.
429    As of yet there is no way of telling whether a PluginConfiguration item is
430    a result file format or not.</p>
431    <p><u><b>NOTE: We will have to wait and see how importing raw data
432        is implemented. I imagine that, if import is implemented
433        through a plugin, this page will list various configurations
434        of the import plugin. However, if import is implemented as a
435        www client thingy something else will reside here (hopefully
436        we"ll go for the plugin approach). </u></b></p>
437    </li>
438
439    <li><p><b><u>Submenu "Hybridizations/Raw data types"</u></b></p>
440
441    <ol>
442      <li type=a><p>Start by implementing listing of "Raw data
443          types"</p>
444      </li>
445
446      <li type=a><p>Add columns; Name, Description, Nmbr of
447          Channels, and Nmbr of fields (i.e., the number of
448          RawDataPropertys <b><u>(NOTE: we should discuss
449          this)). </u></b></p>
450      </li>
451
452      <li type=a><p><b><u>Wait with this until we discussed
453          it </u></b><u><b>\rightarrow</b></u><b><u> [View
454          Raw data type. I.e., when a Raw data type is selected
455          (clicked) a window displaying information about the Raw
456          data type is opened. This should include; Name,
457          Description, Nmbr of Channels, and Nmbr of fields. In
458          addition, it should list all RawDataPropertys in a table
459          including; Name, Description, Length, and
460          Type.] </u></b></p>
461      </li>
462    </ol>
463    </li>
464
465    <li><p>Submenu "Hybridizations/Protocols"</p></li>
466
467    <h3><font color=#aaaa00><b><u>Array LIMS lists (in somewhat chronological implementation
468            order)</u></b></font></h3>
469
470    <li><p>Submenu "Plate Types"</p>
471    <ol>
472      <li type="a">Only basic listing.</li>
473      <li type="a"><b><u>Needs edit/save/delete functionality.</u></b></li>
474    </ol>
475    </li>
476
477    <li><p>Submenu "Plates"</p>
478    <ol>
479      <li type="a">Only basic listing.</li>
480      <li type="a"><b><u>Needs edit/save/delete functionality.</u></b></li>
481    </ol>
482    </li>
483
484    <li><p><b><u>Submenu "Reporter/Plate search"</u></b></p></li>
485
486    <li><p>Submenu "Array Designs"</p>
487    <ol>
488      <li type="a">Only basic listing.</li>
489      <li type="a"><b><u>Needs edit/save/delete functionality.</u></b></li>
490    </ol>
491    </li>
492
493    <li><p><b><u>Submenu "Array batches"</u></b></p></li>
494
495    <li><p><b><u>Submenu "Array slides"</u></b></p></li>
496
497    <li><p><b><u>Submenu "Reporter/Array search"</u></b></p></li>
498
499    <h3><font color=#aaaa00><b><u>Analyze data functionality (in somewhat chronological
500            implementation order)</u></b></font></h3>
501
502    <li><p>Submenu "Raw Data Sets"</p>
503    <ol>
504      <li type="a">List table and edit dialogue. Simple and incomplete.</li>
505      <li type="a"><b><u>Should be possible to utilize Analyze/Plugin pages to do new RawDataSets</u></b></li>
506    </ol>
507    </li>
508
509    <li><p>Submenu "Experiments"</p>
510    <ol>
511      <li type="a">Only basic listing.</li>
512      <li type="a"><b><u>Needs edit/save/delete functionality.</u></b></li>
513    </ol>
514    </li>
515
516    <li><p><b><u>Submenu "Jobs"</u></b></p></li>
517
518    <li><p>Submenu "Plug-in definitions"</p></li>
519    <ol>
520      <li type="a">List PluginDefinitions.</li>
521      <li type="a">No edit functionality. PluginDefinitions defined externally.</li>
522    </ol>
523
524    <li><p>Submenu "Plug-ins"</p></li>
525    <ol>
526      <li type="a">List PluginConfigurations.</li>
527      <li type="a">Configuration iteration loop.</li>
528      <li type="a">Column with buttons to run plugins.</li>
529      <li type="a">Plugins executable.</li>
530    </ol>
531
532    <h3><font color=#aaaa00><b><u>Reporter functionality (in somewhat chronological
533            implementation order)</u></b></font></h3>
534
535    <li><p><b><u>Submenu "Reporters"</u></b></p></li>
536
537    <h3><font color=#aaaa00>My BASE functionality (in somewhat chronological implementation
538        order)</font></h3>
539
540    <li><p>Submenu "Home"</p></li>
541
542    <li><p>Submenu "Contact information"</p></li>
543
544    <li><p>Submenu "Change password"</p></li>
545
546    <li><p>Submenu "Other settings"</p></li>
547
548    <li><p>Submenu "Preferences"</p></li>
549
550    <li><p>Submenu "Files"</p></li>
551
552    <li><p>Submenu "Logout"</p></li>
553
554    <ol>
555      <li type=a><p>GUI</p>
556      </li>
557    </ol>
558    </li>
559
560    <h3><font color=#aaaa00><b><u>Project functionality (in somewhat chronological
561            implementation order)</u></b></font></h3>
562
563    <b><u>dialogue for setting permissions for each user in the
564        project.</u></b>
565
566    <li><p><b><u>Submenu "List"</u></b></p>
567    <p><b><u>Project feeling. Display current project clearly. Different
568        stylesheets for projects? Different project colors? </u></b></p>
569    </li>
570
571    <h3><font color=#aaaa00><b><u>Help functionality (in somewhat chronological
572            implementation order)</u></b></font></h3>
573
574    <li><p><b><u>Submenu "Help"</u></b></p></li>
575
576    <li><p><b><u>Submenu "About"</u></b></p></li>
577
578    <li><p>Submenu "Base project site"</p></li>
579
580    <h3><font color=#aaaa00><b><u>Administrate (in somewhat chronological implementation
581            order)</u></b></font></h3>
582
583    <li><p>Submenu 'Users'</p></li>
584
585    <li><p>Submenu 'Groups'</p></li>
586
587    <li><p>Submenu 'Roles'</p></li>
588
589    <li><p>Submenu 'Quotas'</p></li>
590
591    <li><p>Submenu "Protocols"</p></li>
592    <ol>
593      <li type="a">List and create Protocols.</li>
594      <li type="a"><b><u>Attach file to Protocol.</u></b></li>
595    </ol>
596
597    <li><p>Submenu 'Hardware'</p></li>
598
599    <li><p>Submenu 'Software'</p></li>
600
601    <li><p>Submenu 'Global settings for client'</p></li>
602
603    <li><p>Submenu 'News'</p></li>
604
605  </ol>
606
607</body>
608
609</html>
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