CHANGELOG 14.1 KB
Newer Older
Piotr Gawron's avatar
Piotr Gawron committed
1
2
3
4
5
minerva (12.0.0~beta.2) unstable; urgency=medium
  * Bug fix: issues that appeared in 12.0.0~beta.1

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 9 Apr 2018 13:00:00 +0200

6
7
8
9
minerva (12.0.0~beta.1) unstable; urgency=medium
  * Bug fix: issues that appeared in 12.0.0~beta.0

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 9 Apr 2018 13:00:00 +0200
10

Piotr Gawron's avatar
Piotr Gawron committed
11
minerva (12.0.0~beta.0) unstable; urgency=medium
12
  * Feature: searching for elements in submap gives marker on top map
Piotr Gawron's avatar
Piotr Gawron committed
13
14
15
16
17
    indicating the submap connection
  * Feature: similar search results are merged
  * Feature: visualization of protein structures by MolStart
  * Small improvement: JS plugin API allows to store data on server side
  * Small improvement: submap reference in publication list
18
  * Small improvement: size of connection to database reduced to 90 (so default
Piotr Gawron's avatar
Piotr Gawron committed
19
    connection pool to postgres is not completely filled with minerva)
20
  * Small improvement: visualization of sbml function improved (lambda
Piotr Gawron's avatar
Piotr Gawron committed
21
22
23
    expression removed from the definition)
  * Small improvement: handling of additional miriam types from BiGG ontology
  * Small improvement: configuration options are grouped in categories
24
25
  * Bug fix: searching with two queries sometimes resulted in one complex
    instead of two queries
Piotr Gawron's avatar
Piotr Gawron committed
26
  * Bug fix: uploaded submaps didn't have hierarchical masking
27
  * Bug fix: other bugs that appeared in 12.0.0~alpha
Piotr Gawron's avatar
Piotr Gawron committed
28
29
30

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 23 Mar 2018 15:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
31
32
33
34
35
36
minerva (12.0.0~alpha.1) unstable; urgency=medium
  * Feature: reordering of data overlays is supported
  * Bug fix: db script fixed

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 12 Mar 2018 15:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
37
minerva (12.0.0~alpha.0) unstable; urgency=medium
38
  * Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA  annotators
Piotr Gawron's avatar
Piotr Gawron committed
39
40
41
42
43
44
45
  * Feature: annotations contain info about source (there is difference
    between manual and automatically added annotations)
  * Feature: default permission for new projects are configurable
  * Feature: SBML support (with and without layout extension)
  * Feature: kinetics support
  * Feature: plugin API
  * Feature: all functionalities are provided via REST API
Piotr Gawron's avatar
Piotr Gawron committed
46
47
  * Feature: visualization of two (or more) overlaying results (like drug
    target, mirna target) is highlighted with different icon
Piotr Gawron's avatar
Piotr Gawron committed
48
49
50
51
52
53
54
55
56
57
  * Small improvement: email for account request contain configurable text
  * Small improvement: transparency level for data overlays is configurable
  * Small improvement: CellDesigner reactions of Modifier type are acceptable
  * Small improvement: performance improved for overlays identified by
    annotation identifiers
  * Small improvement: Legend is always on top
  * Small improvement: When email content is too big it's compressed
  * Small improvement: Description of chemical panel refers to the disease
    connected to the map
  * Small improvement: Confirm button when removing data overlay
Piotr Gawron's avatar
Piotr Gawron committed
58
59
  * Small improvement: Clicking on data overlayed element behaves in the same
    way as clicking on not overlayed element
Piotr Gawron's avatar
Piotr Gawron committed
60
61
62
  * Small improvement: Title of list of submaps doesn't contain UNKNOWN tag
  * Small improvement: DOI is supported as miriam type
  * Small improvement: When loading data in search tab there is "LOADING" icon
Piotr Gawron's avatar
Piotr Gawron committed
63
64
  * Small improvement: Data overlays can use source element identifiers for
    filtering
Piotr Gawron's avatar
Piotr Gawron committed
65
66
67
  * Small improvement: Data overlays can submap column to differentiate between
    maps
  * Small improvement: search by chemical names is possible
Piotr Gawron's avatar
Piotr Gawron committed
68
  * Small improvement: auto complete functionality for drugs, mirnas and
Piotr Gawron's avatar
Piotr Gawron committed
69
    chemicals
Piotr Gawron's avatar
Piotr Gawron committed
70
  * Small improvement: columns value and type are not mutually exclusive in
Piotr Gawron's avatar
Piotr Gawron committed
71
72
73
74
    data overlays
  * Small improvement: column type is case insensitive in data overlays
  * Small improvement: every submap contains default center position and zoom
    level to customize default view when entering map for the first time
Piotr Gawron's avatar
Piotr Gawron committed
75
  * Small improvement: data overlays color scale contains configurable default
Piotr Gawron's avatar
Piotr Gawron committed
76
77
78
    middle color (for 0 values)
  * Small improvement: opening data overlay switch to empty background
  * Bug fix: uploading of zip files created by mac doesn't crash due to
Piotr Gawron's avatar
Piotr Gawron committed
79
80
    .DS_Store folder
  * Bug fix: auto complete is case insensitive
Piotr Gawron's avatar
Piotr Gawron committed
81
  * Bug fix: google maps API 404 errors for non existing tiles are removed
Piotr Gawron's avatar
Piotr Gawron committed
82

Piotr Gawron's avatar
Piotr Gawron committed
83
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 12:00:00 +0200
84

85
86
minerva (11.0.10) stable; urgency=medium
  * Bug fix: link from overview image to search result was broken
87

88
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Apr 2018 15:00:00 +0200
89
90


Piotr Gawron's avatar
Piotr Gawron committed
91
92
93
minerva (11.0.9) stable; urgency=medium
  * Bug fix: some comment couldn't be loaded
  * Bug fix: when adding comment it didn't appear on map immediately
Piotr Gawron's avatar
Piotr Gawron committed
94

Piotr Gawron's avatar
Piotr Gawron committed
95
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
96

Piotr Gawron's avatar
Piotr Gawron committed
97
98
99
100
101
102
103
104
105
106
107
108
minerva (11.0.8) stable; urgency=medium
  * Bug fix: XSS vulnerability
  * Bug fix: "java.lang.IllegalStateException: getWriter()" exceptions
    in logs
  * Bug fix: crash for uploading and caching chemical data
  * Bug fix: disappearing tiles in submodels
  * Bug fix: max number of results is properly taken from configuration
  * Bug fix: overlay cannot be hidden before process of fetching data
    during opening is finished
  * Bug fix: redirection to login page when session expired and access to
    export page is requested
  * Bug fix: sometimes overlays couldn't be hidden in submaps
Piotr Gawron's avatar
Piotr Gawron committed
109
  * Bug fix: comments on submaps are visualized properly
Piotr Gawron's avatar
Piotr Gawron committed
110

Piotr Gawron's avatar
Piotr Gawron committed
111
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 05 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
112

Piotr Gawron's avatar
Piotr Gawron committed
113
114
115
116
117
118
119
120
121
122
minerva (11.0.7) stable; urgency=medium
  * Bug fix: redirection added when anonymous tries to access secured map
  * Bug fix: loading time of custom overlays is reduced
  * Bug fix: there should be no problem with symlink when upgrading debian
    package
  * Bug fix: number of services changed API address to https: pmceurope
    (pubmed), uniprot, ensembl, hgnc, recon, ctd database

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 18 Jan 2018 16:00:00 +0200

123
minerva (11.0.6) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
124
125
  * Bug fix: fix a bug when entering invalid mirna id

126
127
128
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 14 Dec 2017 16:00:00 +0200
 
minerva (11.0.5) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
129
  * Bug fix: fix on connection to drugbank database
130
131
  * Bug fix: posttranslational modification data was sometimes unavailable
    in search results panel
Piotr Gawron's avatar
Piotr Gawron committed
132

133
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 30 Nov 2017 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
134

135
minerva (11.0.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
136
  * Bug fix: fix on connection to taxonomy database
137
138
  * Bug fix: color coding for reactions (wrong color was chosen)
  * Bug fix: overlays with many reactions did not work properly
Piotr Gawron's avatar
Piotr Gawron committed
139

140
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 09 Nov 2017 14:50:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
141

142
minerva (11.0.3) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
143
  * Bug fix: removing empty project removed images from all projects
144
145
146
147
148
149
150
151
152
  * Bug fix: clicking on map when left panel was hidden threw error
  * Bug fix: links to invalid annotations were opening invalid web page
  * Bug fix: service resolving miriam resources doesn't work over http
    anymore
  * Bug fix: chebi annotator doesn't work over http anymore

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 19 Oct 2017 13:50:00 +0200

minerva (11.0.2) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
153
  * Bug fix: login issues when default page is in secure area
154
155
156
157

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 25 Sep 2017 12:00:00 +0200

minerva (11.0.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
158
  * Bug fix: logout caused issues with session data
159
160
161
162
163

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 08 Sep 2017 12:00:00 +0200

minerva (11.0.0) stable; urgency=medium

Piotr Gawron's avatar
Piotr Gawron committed
164
165
  * Bug fix: security issue - access to specific map can be restricted
    by the user login
166
167
  * Bug fix: sbgn import
  * Bug fix: mesh connector
Piotr Gawron's avatar
Piotr Gawron committed
168
  * Rest API (documentation can be found here:
169
170
    https://git-r3lab.uni.lu/piotr.gawron/minerva/blob/master/README.md)
  * Selecting an element on the map shows info about it in the bottom left
Piotr Gawron's avatar
Piotr Gawron committed
171
    corner (when Search tab is not open)
172
173
  * Upload of data overlays allows to upload just names of the proteins
    (or other elements), it can be done via file or just by typing in the
Piotr Gawron's avatar
Piotr Gawron committed
174
175
    proper text box
  * Layout changes: the main one is that there are only 3 tab panels
176
177
178
179
180
181
182
183
184
    (search, overlay, info), so it should be easier to navigate

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Aug 2017 12:00:00 +0200

minerva (10.0.5) stable; urgency=medium

  * Bug fix: interacting drugs can be found for RNAs
  * Bug fix: error handling improved on map upload
  * Bug fix: taxonomy ncbi server switched to https
Piotr Gawron's avatar
Piotr Gawron committed
185
186
  * Overlay presents description field if possible

187
188

 -- Piotr Gawron <piotr.gawron@uni.lu>  Sat, 04 Mar 2017 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
189

190
191
192
193
194
195
196
197
198
199
200
minerva (10.0.4) stable; urgency=medium

  * Bug fix: overlays colors are centered in white (not black)
  * Bug fix: export to CellDesigner fixed
  * Bug fix: DrugBank connector updated due to change in DrugBank website

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 29 Dec 2016 17:01:16 +0200

minerva (10.0.3) stable; urgency=medium

  * Bug fix: login cannot contain whitespace
Piotr Gawron's avatar
Piotr Gawron committed
201
  * Bug fix: search for multiple drugs will not return more drugs than
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
    queried for
  * Bug fix: drug list for some proteins (like RHOA) hung webpage
  * Bug fix: comments on submaps issue
  * Bug fix: link to submap from comment panel
  * Overlay coloring can be defined in Configuration

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 15 Dec 2016 15:01:16 +0200

minerva (10.0.2) stable; urgency=medium

  * Bug fix: markers for mirna targets visibility

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 29 Sep 2016 10:01:16 +0200

minerva (10.0.1) stable; urgency=medium

  * Bug fix: export to image
Piotr Gawron's avatar
Piotr Gawron committed
219
220
  * Bug fix: trigger reaction and physical stimulation reactions are no
    longer allowed (CellDesigner data model issue)
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
  * Bug fix: clicking on reactions in submaps

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 21 Sep 2016 13:01:16 +0200

minerva (10) stable; urgency=medium

  * Project info tab available for users
  * Management of overlays in admin panel
  * Bug fix: Visualization of text mining
  * Bug fix: Exception when accessing non-existing project
  * Bug fix: Zooming issue when searching for results on submaps
  * Bug fix: Out of memory when caching a lot of data
  * Bug fix: Corrupted drug names
  * Bug fix: Unexpected errors when uploading layouts
  * Bug fix: Coordinates in url
  * Bug fix: Hiding left panel
  * Bug fix: CellDesigner font size is processed properly
  * Bug fix: Search by reaction id is not case sensitive

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Aug 2016 13:01:16 +0200

minerva (9) stable; urgency=medium

  * Fix on install script of version 8 that crashed some new installations

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 29 Jun 2016 09:58:34 +0200

minerva (8) stable; urgency=medium

  * Micro RNA interface
  * Toxic chemicals interface
  * Data sets (layouts) visualized dynamically in the browser
  * Reverse query for drugs, chemicals, micro RNAs interfaces
  * Small bug fixes

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 14 Apr 2016 13:03:55 +0200

minerva (7) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
260
261
262
263
264
265
  * Uploaded datasets are available for download
  * Entrez annotator
  * Ensembl annotator
  * Valid/required annotations and used annotations saved in user profile
  * Export to pdf/png/jpg/svg
  * New web interface
266
267
268
269
270

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 3 Dec 2015 22:00:00 +0200

minerva (6) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
271
272
273
274
275
  * Searching by annotations
  * Errors from parsing data forwarded to client
  * Notification email system added
  * Warnings are downloadable
  * Complex map (composed from many small maps)
276
  * Visualization of Recon specific annotations
Piotr Gawron's avatar
Piotr Gawron committed
277
278
279
280
281
282
283
  * Versioning system
  * Galaxy connector
  * Miriam types report
  * Advanced annotation options
  * Uniprot annotation module
  * Customized validation of miriam annotations
  * Recon annotation service
284
  * Bug fix: Data autofill problem in user management
Piotr Gawron's avatar
Piotr Gawron committed
285
286
  * Bug fix: User privileges for adding project
  * Bug fix: Problem with some miriam entries in RDF format
287
  * Bug fix: Reporting of drawing problems
Piotr Gawron's avatar
Piotr Gawron committed
288
289
  * Bug fix: Visualization of posttranslationa modification
  * Bug fix: Drugbank problem after update of Drugbank interface
290
  * Bug fix: Session scope fixed (browsing many maps at the same time)
Piotr Gawron's avatar
Piotr Gawron committed
291
292
293
294
295
  * Bug fix: Asynchronous removing/adding maps
  * Bug fix: Export to CellDesigner rarely produced corrupted CellDesigner file
  * Bug fix: Recon annotations of reactions
  * Bug fix: Login problem when browsing not default map
  * Bug fix: Multimers are available for every element
296
297

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 21 Jul 2015 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
298

299
300
minerva (5) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
301
  * Additional checkboxes in upload model: annotate automatically, cache data, verify annotations
302
  * Popup window in admin panel that list warnings
Piotr Gawron's avatar
Piotr Gawron committed
303
304
  * Information about build
  * Parsing and annotation warnings for models in admin panel
305
  * Custom reaction visualization in upload overlay
Piotr Gawron's avatar
Piotr Gawron committed
306
307
308
309
310
  * Bug fix: Problem with touch interface on Windows 8.1
  * Bug fix: Google Maps API problem with floating bubbles
  * Bug fix: Error handling in admin panel
  * Bug fix: Reaction color in CellDesigner file
  * Bug fix: Reaction line width
311
312

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 18 Dec 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
313

314
315
316
minerva (4) stable; urgency=low

  * Export of the part of the map into CellDesigner file
Piotr Gawron's avatar
Piotr Gawron committed
317
318
  * Logo files managable via config webpage
  * Import data from GO
319
320
321
  * Custom overlay upload
  * Additional structural information imported from annotation service
  * Bug fix: Fonts and lines in hierarchical view
Piotr Gawron's avatar
Piotr Gawron committed
322
323
324
325
326
  * Bug fix: Visualization of residues in rna, antisense rna, proteins
  * Bug fix: Problem with touching bubbles on touch interface
  * Bug fix: Problem with special UTF-8 characters in CellDesigner file
  * Bug fix: Problem with users and session expire
  * Bug fix: Export problem
327
328

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 11 Sep 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
329

330
331
332
minerva (3) stable; urgency=low

  * Drug targeting interface
Piotr Gawron's avatar
Piotr Gawron committed
333
334
335
  * Export to CellDesigner
  * Status page of all dependent services
  * Configuration page
336
337

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 5 Jun 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
338

339
340
341
minerva (2) stable; urgency=low

  * Upload of the CellDesigner map
Piotr Gawron's avatar
Piotr Gawron committed
342
343
  * Bug fix: Problem with touch interface after update of browsers engine
  * Bug fix: Problem in Safari when searching for elements
344
345

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 2 Apr 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
346

347
348
minerva (1) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
349
  * Initial release
350
351

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 4 Dec 2013 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
352