Project

General

Profile

FirstDeveloperMeetingMinutes » History » Version 24

Andreas Müller, 09/11/2007 02:06 PM

1 17 Markus Döring
{{>toc}}
2
3
4
5 1 Pepe Ciardelli
6 2 Pepe Ciardelli
# EDIT WP5: First EDIT Developer Meeting - BGBM Berlin September 6-7, 2007
7
8
9
## Meeting minutes
10
11
_Note: areas requiring further discussion are in italics._
12
13
14
15 5 Pepe Ciardelli
16
17 2 Pepe Ciardelli
## Day 1 - Developer Presentations
18
19
The first part of the meeting consisted of 10 Minute Developer Presentations (listed below). Any relevant discussion/decisions or suggestions have also been recorded.
20
21 1 Pepe Ciardelli
22 5 Pepe Ciardelli
1. **Malte Ebach (BGBM) – BDTracker** 
23 2 Pepe Ciardelli
24
25
Please start using the Tracker, we would like to establish this as something that exists well beyond EDIT’s 2011 end date.
26 1 Pepe Ciardelli
27 2 Pepe Ciardelli
28 5 Pepe Ciardelli
2. **Lutz Suhrbier (FUB) - Shibboleth SSO** 
29 2 Pepe Ciardelli
30
31 1 Pepe Ciardelli
OpenID or Shibboleth debate must take place soon, in light of the substantial consequences for client developers, service providers.
32 2 Pepe Ciardelli
33 22 Markus Döring
* use SHARPE to define policies and user metadata
34 1 Pepe Ciardelli
35 5 Pepe Ciardelli
3. **Andreas Kohlbecker (BGBM) - Experts database & Dataportal for WP6** 
36 2 Pepe Ciardelli
37 22 Markus Döring
* managing user data in several places is not manageable. ExpertsDB and SHARPE tool for IdP must work on the same dataset. Modify LDAP in Drupal is a possible way to go.
38 2 Pepe Ciardelli
39 5 Pepe Ciardelli
4. **Simon Rycroft (NHML) - Community Websites with Scratchpads** 
40 2 Pepe Ciardelli
41
42
Scratchpads represent a bottom-up approach, with the philosophy that to have semi-structured data online now is better than nothing – the hope is to “meet in the middle” with EDIT’S top-down approach; 
43 1 Pepe Ciardelli
44 2 Pepe Ciardelli
45
Markus: aren't Scratchpads better suited to community building, EDIT for real taxonomic work?
46
47
48 5 Pepe Ciardelli
5. **Julius Welby (NHML) - Virtual library** 
49 2 Pepe Ciardelli
50
51
ViTaL scheduled to go live month 30
52
53 1 Pepe Ciardelli
54 9 Pepe Ciardelli
Use CDM community store as metadata repository?
55 1 Pepe Ciardelli
56 9 Pepe Ciardelli
57 5 Pepe Ciardelli
6. **Marc Geoffroy (BGBM) - Common Data Model in UML** 
58 2 Pepe Ciardelli
59
60
Unfortunately not as easy as hoped to work collaboratively with Enterprise Architect (or more precisely the SQL*Server it runs on top of).
61 1 Pepe Ciardelli
62 2 Pepe Ciardelli
63 5 Pepe Ciardelli
7. **Andreas Müller (BGBM) - Common Data Model java library + sync store** 
64 2 Pepe Ciardelli
65
66 1 Pepe Ciardelli
_Discussion: Hibernate consequences, how easily can it be hidden? Is CATE’s temporal state solution - "snapshots" of an object at a point in time - the best way to update objects and guarantee their validity?_
67 2 Pepe Ciardelli
68
69 5 Pepe Ciardelli
8. **Pepe Ciardelli (BGBM) - Taxonomic editor** 
70 2 Pepe Ciardelli
71
72
Good example of Eclipse Rich Client Platform used for a biological application: Bioclipse http://bioclipse.net
73
74 1 Pepe Ciardelli
75 5 Pepe Ciardelli
9. **Dave Taylor (RBGK) - Use cases & workflow modeling outcomes** 
76 1 Pepe Ciardelli
77 2 Pepe Ciardelli
78 1 Pepe Ciardelli
Results of questionnaires on revisionary taxonomy models at http://dev.e-taxonomy.eu/trac/wiki/RevisionaryModels
79 2 Pepe Ciardelli
80
81
Gregor: are there areas other than revisionary taxonomy for which the platform will / should be used?
82 1 Pepe Ciardelli
83
84
10. **Dilan Latif (SMNS) - ATBI platform w/ field recorder & site database** 
85
86 9 Pepe Ciardelli
87
Use CDM community store as central observation repository for an ATBI site?
88 2 Pepe Ciardelli
89 8 Markus Döring
90 5 Pepe Ciardelli
11. **Magda Zymtoska (MIZPAN) - Geo services**   
91 2 Pepe Ciardelli
92 23 Pepe Ciardelli
93
94
95 5 Pepe Ciardelli
12. **Pere Roca (MINCN) - Spatial completeness analysis & Taxonomic data visualisation** 
96 2 Pepe Ciardelli
97
98
99 5 Pepe Ciardelli
100
101 2 Pepe Ciardelli
## Day 2 - Developer Tools
102
103
 **The EDIT wiki** 
104
105
* http://dev.e-taxonomy.eu/trac/wiki/
106
107
* All users have permission to edit all sections - go nuts!
108
109
* Note from Malta: we should try to establish as many collaborative activities as possible by the next development meeting in February, because our lack of integrative work was criticized by the Scientific Advisory Committee
110
111
 **SVN** 
112
113
* All code should be checked in to http://dev.e-taxonomy.eu/svn
114
115
* Try to get all source code to date checked in by **September 21** 
116
117
 **Trac** 
118
119
* Ticket overview at http://dev.e-taxonomy.eu/trac/report
120
121 1 Pepe Ciardelli
* Tickets don't have due dates, but they are associated with milestones, which do
122
123 2 Pepe Ciardelli
* MyLyn
124
125
  * Trac plugin for Eclipse, comes standard with 3.3
126
127
  * Tickets associated with source code files in which appropriate changes were made
128
129
  * Eclipse settings: http://dev.e-taxonomy.eu/trac, "XML-RPC"
130
131 4 Pepe Ciardelli
132 2 Pepe Ciardelli
133 5 Pepe Ciardelli
134
135 2 Pepe Ciardelli
## Day 2 - Common Data Model
136
137
 **EDIT developers' access to the CDM** 
138
139 7 Pepe Ciardelli
* Unfortunately no access available from outside BGBM-Berlin
140 2 Pepe Ciardelli
141 7 Pepe Ciardelli
* Send proposed changes to CDM mailing list (dev-edit@mnhn.fr)
142 2 Pepe Ciardelli
143 7 Pepe Ciardelli
* Latest Enterprise Architect file (*.eap) available at http://dev.e-taxonomy.eu/trac/wiki/CommonDataModel
144 2 Pepe Ciardelli
145
 **Platform Independent Model (PIM)** 
146
147 7 Pepe Ciardelli
* Used to generate model in Java Model using Enterprise Architect's transformation functionality
148 2 Pepe Ciardelli
149 7 Pepe Ciardelli
* The source for the CDM view at http://wp5.e-taxonomy.eu/cdm 
150 2 Pepe Ciardelli
151
 **eu.etaxonomy.cdm.model.description** 
152
153 7 Pepe Ciardelli
* For taxa, specimens, observations
154 2 Pepe Ciardelli
155 7 Pepe Ciardelli
* Still largely empty, copied almost directly from SDD
156 2 Pepe Ciardelli
157 19 Markus Döring
* Linked to Occurrence or Taxon class
158
159 2 Pepe Ciardelli
 **eu.etaxonomy.cdm.model.name** 
160
161
* Gregor proposed changing **name** to **scientificname** 
162
163 6 Pepe Ciardelli
* Different subclasses created for different nomenclatural codes, i.e. "!BacterialName", "!ZoologicalName", etc. Initially skeptical of too many class hierarchies / subclasses, but it proved helpful for things like the name subclasses.
164 2 Pepe Ciardelli
165 6 Pepe Ciardelli
* _Discussion: in class "!NonViralName", is "isAtomised" the best way to express whether a full name has been parsed? Alternative naming suggestions in the attribute notes._
166 2 Pepe Ciardelli
167
 **eu.etaxonomy.cdm.model.publication** 
168 1 Pepe Ciardelli
169 19 Markus Döring
* Modelled on the blend of BibTex, EndNote and some custom extensions found in the Berlin Model.
170 1 Pepe Ciardelli
171 19 Markus Döring
* Should we strictly follow BibTex which has a great deal of open source software available, e.g converters to/from mayn different formats incl EndNote & MARC ?
172
173 2 Pepe Ciardelli
* Native speakers agreed **reference** is more accurate than **publication** 
174
175
* _Discussion: publication year properly belongs in **publication** not *name*, even if this requires creating a dummy publication for a nomenclatural reference (similarly, basionyms will require the creation of an incomplete author object for basionym authors)_
176
177
 **eu.etaxonomy.cdm.model.location** 
178 7 Pepe Ciardelli
179 1 Pepe Ciardelli
* This package and **eu.etaxonomy.cdm.model.specimen** should be extended for ATBI
180 6 Pepe Ciardelli
181 19 Markus Döring
* Gregor: change "Region" to "!NamedArea", get rid of "Locality" class and make it a free-text attribute of the Occurrence class
182 1 Pepe Ciardelli
183 2 Pepe Ciardelli
* Magda: add "accuracy" and "reference system" (a.k.a. "datum") to main class; the latter is necessary because coordinates can vary from system to system
184
185 19 Markus Döring
* Markus: how could shape definitions / polygons be stored for regions? Add binary shape file atttribute rather than GML?
186 1 Pepe Ciardelli
187
* Regions also have language implications
188
189 19 Markus Döring
* validInTime also applies to regions
190 1 Pepe Ciardelli
191 19 Markus Döring
* Pere: distinguish between natural, political, etc. regions. Add NamedAreaType (controlled) and NamedAreaLevel (free)
192
193
* add acronym to region
194
195
* Change "Country" to "!WaterbodyOrCountry" and merge waterboy entries into country table
196 2 Pepe Ciardelli
197 21 Markus Döring
 **Versioning** 
198
199
* tbd
200
201 5 Pepe Ciardelli
 **Miscellaneous** 
202 2 Pepe Ciardelli
203
* Abstract class names in Enterprise Architect are in italics
204
205
* Logic behind design decisions are written in the notes fields attached to the entity in question – high priority to get these populated!
206
207
* _Discussion: for boolean fields, should there be the possibility of a 3rd state, i.e. NULL? DB implications – how does hibernate handle NULLs?_
208 8 Markus Döring
209
210
211
## Breakout Sessions
212
213
214
215
### Common Data Model
216
217 14 Markus Döring
The first day session focussed on multilingual controlled vocabularies. See wiki:FirstDeveloperMeetingMinutes#Day2-CommonDataModel for outcomes.
218 8 Markus Döring
219
220
221
### CDM Library
222
223 14 Markus Döring
Attendees: 
224 8 Markus Döring
225 14 Markus Döring
* Andreas Müller
226 8 Markus Döring
227 14 Markus Döring
* Ben Clark
228 1 Pepe Ciardelli
229 14 Markus Döring
230 24 Andreas Müller
The main topic of the discussion were technological aspects of which technologies to use. Some major issues were, which project management and building tool to use (ant, maven), the security framework 'asegi', how to use the framework 'Spring' in a rich-client-platform(RCP) environment, aspect oriented programming and testing with Spring, integration tests with dbUnit, etc.
231
232
Also Ben gave a introduction to the structure and to implementational aspects of the CATE project.
233
234
Questions of how to make both projects compatible and how to use synergetic effects were also under discussion with the result that the EDIT cdmLibrary could use CATE's technological knowledge gained over the last 2 years whereas CATE could use medium-term the EDIT cdmLibrary with it's broader data model and more general approach.
235
236
In a longer discussion detailed aspects of versioning (technology, data model, performance, alternatives) were looked at.
237
238
239 14 Markus Döring
240 1 Pepe Ciardelli
### Geoservices + ATBI
241
242 14 Markus Döring
Attendees: 
243
244
* Pere Roca
245
246 16 Markus Döring
* Magda Zytomska 
247 14 Markus Döring
248 1 Pepe Ciardelli
* Markus Döring
249 16 Markus Döring
250
251 20 Markus Döring
The centre of discussion was the visualisation geo-services needed for other applications within the platform. The current webapplication demo is great for visualising multiple species to a human which would be exactly what is needed for ATBI sites and their point occurrence data on a limited survey site. But for taxonomic data two other simple map generation services are needed to visualise occurrence data (points) and distribution data (presence/absence) respectively. The services should be machine services, as far as possible simple URLs to be called, that do not need any human interaction. WMS services provide most of this functionality alread, but the data itself must be present as a layer already. We came to the conclusion that an intermediate service would be needed that translates a simple URL call into a proper WMS call, potentially creating a usable layer on the fly, and returning the requested image. See tickets  #64, #55, #56, #57, #58, #59 for details.
252 8 Markus Döring
253
254
255
### Tax Editor Requirements
256
257 13 Pepe Ciardelli
Attendees: 
258
259
* Pepe Ciardelli
260
261
* Dave Taylor
262
263
* Eckhard Raab-Straube
264
265
	
266 15 Pepe Ciardelli
The main topic of discussion was how to integrate the use case work done by Dave and his colleague at Kew Soraya Villalba into the design  of the Taxonomic Editor user interface. Dave's work for EDIT Deliverable 5.2.1.1 gathered descriptions of the work processes used by revisionary taxonomists throughout the EU to produced integrated use cases. Soraya's use cases (UseCasePalmMonography) (also detailed in proposals for Palm Web sent a few months ago to Eckhard) - detail the initial publication of a monograph and the attendant peer review process. 
267 13 Pepe Ciardelli
268
269
To date, Pepe's work on the UI design has been based largely on duplicating the functionality (EditorRequirements) of the Berlin Model Web Editor, which was built mainly to edit imported checklists; the work done by Kew will help extend the new Editor's functionality to a wider range of users. Known bottlenecks in the Web Editor - such as frequently used functions requiring a maddening number of clicks - will be relevant during UI design. In addition, the group of taxonomists working at BGBM-Berlin has a range of technical sophistication, and the UI development team in Berlin hopes to enlist as many of them as possible for usability tests and the like. Dave will likely join Pepe in the actual coding of the UI.
270
271
272
Dave and Pepe will be at the TDWG conference in Bratislava next week, and will continue the discussion there. 
273 8 Markus Döring
274
275
276
### Drupal
277
278 1 Pepe Ciardelli
279 10 Andreas Kohlbecker
Attendees: 
280
281
* Andreas Kohlbecker
282
283
  *	Lutz Suhrbier
284
285
  *	Simon Rycroft
286
287
  *	Julius Welby
288
289
	
290
The breakout group discussed on how the development and integration of Community Web Tools (mainly based on Drupal) can be improved and facilitated.
291
292 11 Andreas Kohlbecker
As an outcome to this, a [[DrupalModules|page on Drupal modules]] has been introduced into the developer Wiki by which experiences and EDIT specific modules are to be shared. This page will initially cover all modules used by bdTracker, by the EDIT WP5 Wiki and by the Scratchpads. By this we ensure a better harmonization between development made at the BGBM and at the NHM. 
293 10 Andreas Kohlbecker
294
There has been furthermore a intense discussion on finding the best way to incorporate data exchange between the modules which are used in the Scratchpads and the CDM (Common Data Model) Store. 
295
296
297
Another conversation was on Sibboleth, which has been chosen as authentication framework for the EDIT platform for cyber taxonomy. 
298
299 12 Markus Döring
Once the Shibboleth module for Drupal is finished, it will be installed into the Scratchpads to also allow federated login into this CommunityWebtools Compilation.