CHANGELOG 36.8 KB
Newer Older
Piotr Gawron's avatar
Piotr Gawron committed
1
2
minerva (14.0.0~alpha.0) unstable; urgency=low
  * Feature: log4j is replaced with log4j2 logging mechanism (#291)
Piotr Gawron's avatar
Piotr Gawron committed
3
4
  * Feature: database installed via debian package is done via dbconfig-commons 
    (#469)
Piotr Gawron's avatar
Piotr Gawron committed
5
6
  * Feature removal: BioCompendium annotator removed (#32)

7
8
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 16 May 2019 15:00:00 +0200

9
minerva (13.1.0~alpha.0) unstable; urgency=low
Piotr Gawron's avatar
Piotr Gawron committed
10
  * Feature: annotators are more flexible - you can define set of input and
11
    outputs used by annotator (#617)
Piotr Gawron's avatar
Piotr Gawron committed
12
13
  * Feature: changes in admin panel doesn't require saving - they are saved
    automatically (#676)
Piotr Gawron's avatar
Piotr Gawron committed
14
15
16
  * Feature: elements can have custom glyphs used for visualization (#487)
  * Small improvement: all bio entities have z-index associated with them 
    (#487)
Piotr Gawron's avatar
Piotr Gawron committed
17
18
  * Small improvement: validation of the organism and disease id on map upload
    added (#618)
Piotr Gawron's avatar
Piotr Gawron committed
19
  * Small improvement: added current username next to logout button in admin
20
    panel (#660)
Piotr Gawron's avatar
Piotr Gawron committed
21
  * Small improvement: New comment dialog does not contain content of previous
22
    comment dialog (#680)
Piotr Gawron's avatar
Piotr Gawron committed
23
  * Small improvement: Left logo is configurable (#731)
24
  * Small improvement: list of element types in choose annotator dialog is
Piotr Gawron's avatar
Piotr Gawron committed
25
    sorted (#758)
26
27
  * Small improvement: Plugin API provides list of overview images (#702)
  * Small improvement: Plugin API allows to show/hide overview images (#702)
28
  * Small improvement: Plugin API allows to trigger search on the map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
29
  * Small improvement: Plugin API allows to clear search results on map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
30
  * Small improvement: edit/remove project button is disabled until project is
31
    uploaded (#683)
Piotr Gawron's avatar
Piotr Gawron committed
32
  * Small improvement: warning about capslock is visible on login page when
33
    necessary (#658)
Piotr Gawron's avatar
Piotr Gawron committed
34
  * Small improvement: names of columns in data overlay are unified: no
Piotr Gawron's avatar
Piotr Gawron committed
35
    whitespace, "_" used as separator (#596)
36
37
  * Small improvement: list of references in drug panel contains PUBMED prefix
    (#666)
Piotr Gawron's avatar
Piotr Gawron committed
38
  * Small improvement: list of projects is auto refreshed every 5 seconds if at
39
    least one of the project is uploading/removing (#610)
Piotr Gawron's avatar
Piotr Gawron committed
40
  * Small improvement: passwords to email account and ldap are not sent over
Piotr Gawron's avatar
Piotr Gawron committed
41
    API (#732)
Piotr Gawron's avatar
Piotr Gawron committed
42
  * Small improvement: reactant/product/modifier specific colors are parsed
Piotr Gawron's avatar
Piotr Gawron committed
43
    properly from CellDesigner file (#597)
Piotr Gawron's avatar
Piotr Gawron committed
44
  * Small improvement: Info tab contains information about disease and
45
    organism when info is provided
Piotr Gawron's avatar
Piotr Gawron committed
46
47
48
  * Small improvement: Info tab provides information about model annotations
    and submap tabs provide information about submaps annotations if applicable
    (#591)
49
50
  * Small improvement: uploading sbml file should automatically discover a file
    type (#784)
51
  * Small improvement: when plugin listeners crash the system notifies user
52
    about problem with a plugin (#767)
53
  * Small improvement: when exporting reaction and elements there is
Piotr Gawron's avatar
Piotr Gawron committed
54
    possibility to filter by (sub)map (#615)
55
  * Small improvement: during first opening of a map, the zoom level is
Piotr Gawron's avatar
Piotr Gawron committed
56
    automatically computed if no default information is provided (#776)
57
  * Small improvement: when adding new project columns "Root map", "Mapping
Piotr Gawron's avatar
Piotr Gawron committed
58
    file" and "Map type" are merged (#700)
Piotr Gawron's avatar
Piotr Gawron committed
59
  * Small improvement: allow admin to disable CORS check (#802)
60
  * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
61
    SemanticZoomLevelTransparency (#801)
62
63
  * Small improvement: export/import from SBML support z-index in LAYOUT 
    extension
Piotr Gawron's avatar
Piotr Gawron committed
64
  * Bug fix: progress bar of gene genome mapping upload is refreshing properly
65
    (#728)
Piotr Gawron's avatar
Piotr Gawron committed
66
  * Bug fix: when editing project Disease and Organism could not be removed
Piotr Gawron's avatar
Piotr Gawron committed
67
    (#616)
Piotr Gawron's avatar
Piotr Gawron committed
68
69
70
  * Bug fix: dashed line partially wasn't dashed in "Unknown Catalysis" and
    "Unknown Inhibition" reactions (#664)
  * Bug fix: "Unknown Catalysis" and "Unknown Inhibition" reaction end is
71
    slightly separated from target phenotype (#664)
72
  * Bug fix: order of genomes in admin panel doesn't change after refreshing
73
    list of genomes (#761)
74
  * Bug fix: fixing situation when Molart started with variation overlay not
Piotr Gawron's avatar
Piotr Gawron committed
75
    having the aa change information
76
  * Bug fix: plugin contect element width is adjusted when link to tabs are
77
    wrapped in more than one line (#758)
Piotr Gawron's avatar
Piotr Gawron committed
78
  * Bug fix: export to CellDesigner preserve font size (#803)
Piotr Gawron's avatar
Piotr Gawron committed
79
80
  * Bug fix: layout data was ignored for some reactions when improting from 
    SBML (#812)
81

82
83
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 7 May 2019 15:00:00 +0200

84
minerva (13.0.0) stable; urgency=medium
85
86
  * Bug fix: Since Oracle Java cannot be installed as debian dependency we use
    openjdk-8. Due to this dependency minerva can be no longer installed on
87
88
89
90
    Ubuntu-14 (#223)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 6 May 2019 18:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
91
92
minerva (12.2.3) stable; urgency=medium
  * Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790)
93
  * Bug fix: searching of chemicals stopped working due to expired SSL
Piotr Gawron's avatar
Piotr Gawron committed
94
    certificate on https://ctdbase.org/
95
  * Bug fix: remove button is disabled after starting removing of the data
96
    overlay (#791)
97
  * Bug fix: search autocomplete hint could be initially hidden (#793)
98
  * Bug fix: updating terms of use could crash when list of users was removed
99
    in separate tab or by another user (#797)
Piotr Gawron's avatar
Piotr Gawron committed
100
  * Bug fix: name of the checkbox in ADD PROJECT window adjusted (#799)
101
102
  * Bug fix: when user didn't have privileges to remove comments the button was
    active on pages other than page 1 (#792)
Piotr Gawron's avatar
Piotr Gawron committed
103
104
  * Bug fix: export of reaction to SBML didn't work when lines on the map were
    too short (#805)
Piotr Gawron's avatar
Piotr Gawron committed
105
106
107

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 24 Apr 2019 17:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
108
minerva (12.2.2) stable; urgency=medium
109
  * Bug fix: downloading overlays didn't work from admin panel when project
Piotr Gawron's avatar
Piotr Gawron committed
110
    with different id than default map was accessed
111
  * Bug fix: change of owner of the data overlay in admin panel incorrectly
Piotr Gawron's avatar
Piotr Gawron committed
112
    ordered overlays (#777)
113
  * Bug fix: chemical search didn't use updated disease identifier, original
114
    disease id from project upload was used instead (#779)
115
  * Bug fix: user login with special characters (like '@')  could cause
Piotr Gawron's avatar
Piotr Gawron committed
116
    problems in admin panel (#780)
117
118
  * Bug fix: removing project without full control in the system (but with
    enough privileges to remove project) caused "Not enough privileges" error
119
    (#778)
120
  * Bug fix: export of custom properties (like synonyms) are properly encoded
Piotr Gawron's avatar
Piotr Gawron committed
121
    in CellDesigner xml (#785)
122
123
124
  * Bug fix: notification about not supported version in IE 11 fixed (#783)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 9 Apr 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
125

Piotr Gawron's avatar
Piotr Gawron committed
126
127
minerva (12.2.1) stable; urgency=medium
  * Bug fix: export of reaction colorsi in SBML is properly encoded (COPASI can
Piotr Gawron's avatar
Piotr Gawron committed
128
129
    read colors properly) (#744)
  * Bug fix: removing active plugin didn't switch plugin tab to the next loaded
130
    plugin (#757)
Piotr Gawron's avatar
Piotr Gawron committed
131
132
  * Bug fix: closed submap will not be reopened after page refresh (#763)
  * Bug fix: comment remove button is disabled for users without proper
133
    privileges (#766)
Piotr Gawron's avatar
Piotr Gawron committed
134
  * Bug fix: invalid pubmed identifier could break clicking on element
135
    containing it (#764, #765, #769)
Piotr Gawron's avatar
Piotr Gawron committed
136
  * Bug fix: cache for API queries is explicitly disabled - some queries could
137
    be mistakenly cached and the system behaviour might get unstable (#771)
Piotr Gawron's avatar
Piotr Gawron committed
138
139
140

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 1 Apr 2019 17:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
141
minerva (12.2.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
142
  * Feature: bug report utility
Piotr Gawron's avatar
Piotr Gawron committed
143
144
  * Feature: url GET parameters support all kind of search and selected overlays
    highlight
145
  * Feature: user can create custom logging configuration in file
Piotr Gawron's avatar
Piotr Gawron committed
146
147
148
149
    /etc/minerva/log4j.properties
  * Feature: plugin panel in admin allows to configure set of available plugins
  * Feature: import export from SBML supports RENDER package
  * Feature: import export from SBML supports MULTI package
150
  * Feature: API tool providing possibility to transform different types of
Piotr Gawron's avatar
Piotr Gawron committed
151
    file formats
152
  * Feature: current state of the browsed map is reflected in the url (position,
Piotr Gawron's avatar
Piotr Gawron committed
153
    zoom, overlays, search queries, etc.)
Piotr Gawron's avatar
Piotr Gawron committed
154
155
156
157
158
  * Small improvement: highlighting table rows in admin panel uses better
    contrast color (#706)
  * Small improvement: list of publication can be filtered by submap (#614)
  * Small improvement: size of add overlay window adjusted to show more data
    without scrollbars (#657)
Piotr Gawron's avatar
Piotr Gawron committed
159
  * Small improvement: all popup dialogs in the application have dialog
Piotr Gawron's avatar
Piotr Gawron committed
160
161
162
    specific css class names (#665)
  * Small improvement: JS plugin can create listener that is triggered on
    search results focus change
Piotr Gawron's avatar
Piotr Gawron committed
163
164
  * Small improvement: export to SBML includes unit factors
  * Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
165
  * Small improvement: genetics information allows to provide information about
Piotr Gawron's avatar
Piotr Gawron committed
166
    modification on peptide level that could be visualized in MolArt
167
  * Small improvement: allow to control the background and font color of areas
Piotr Gawron's avatar
Piotr Gawron committed
168
    drawn from text areas in CellDesigner "layers"
169
  * Small improvement: config logo location is relative to the root minerva
Piotr Gawron's avatar
Piotr Gawron committed
170
171
    deployment directory
  * Small improvement: there is branding minerva logo in the left panel
172
173
174
175
176
177
178
179
180
181
182
183
  * Small improvement: there is possibility to download part of the map limited
    to set of reactions/elements
  * Small improvement: allow admin to configure parameters displayed in the
    left panel
  * Small improvement: arrows for Transcription Starting Sites looks more like
    in CellDesigner
  * Small improvement: popup window appear with info about exceeding max number
    of search results when necessary
  * Small improvement: plugins can define default width of the container tab
  * Small improvement: new miriam type is handled: ClinicalTrials.gov
  * Small improvement: click on the border of compartment select the
    compartment
Piotr Gawron's avatar
Piotr Gawron committed
184
185
  * Small improvement: there is max size of the map in configuration panel that
    disables upload of too big files
186
  * Small improvement: hitting enter on login page logs in the user (no need to
Piotr Gawron's avatar
Piotr Gawron committed
187
    click on the login button)
188
  * Small improvement: refresh button in overlays panel (useful when data
Piotr Gawron's avatar
Piotr Gawron committed
189
190
191
    overlays are uploaded separately in using API calls)
  * Small improvement: list of publications is downloadable
  * Small improvement: export of reactions support filtering by reaction type
192
  * Small improvement: 'BACK TO MAP' link is available only when guest account
Piotr Gawron's avatar
Piotr Gawron committed
193
194
    has proper access level
  * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
195
196
    email account is provided
  * Small improvement: Plugin API allows to show/hide data overlays
Piotr Gawron's avatar
Piotr Gawron committed
197
  * Bug fix: Icons were sometimes not properly loaded on Safari (#661)
Piotr Gawron's avatar
Piotr Gawron committed
198
  * Bug fix: migration scripts are compatibile with postgres 9.3 version that
Piotr Gawron's avatar
Piotr Gawron committed
199
    is default on Ubuntu 14 (#762)
Piotr Gawron's avatar
Piotr Gawron committed
200
  * Bug fix: update/remove button is disabled when user has no privileges for
Piotr Gawron's avatar
Piotr Gawron committed
201
    managing overlays (#742)
Piotr Gawron's avatar
Piotr Gawron committed
202
  * Bug fix: when user cannot manage users information in overlays and users
Piotr Gawron's avatar
Piotr Gawron committed
203
    tab in edit project dialog is provided instead of hiding tabs (#756)
Piotr Gawron's avatar
Piotr Gawron committed
204
205
  * Bug fix: removing comments in a project asked for confirmation twice after
    edit project dialog for specific project was opened; closed and opened
Piotr Gawron's avatar
Piotr Gawron committed
206
207
    again (#697)
  * Bug fix: editing/removing project requires Map Management privilege (#681)
Piotr Gawron's avatar
Piotr Gawron committed
208
  * Bug fix: when removeAllListeners is called list of registered listeners is
Piotr Gawron's avatar
Piotr Gawron committed
209
    cleaned (#687)
Piotr Gawron's avatar
Piotr Gawron committed
210
  * Bug fix: when plugin is removed the html elements associated with it are
Piotr Gawron's avatar
Piotr Gawron committed
211
212
    removed as well (#686)
  * Bug fix: when creating new user default privileges are set properly (#692)
Piotr Gawron's avatar
Piotr Gawron committed
213
  * Bug fix: plugin can be added after plugin has been removed in admin plugin
Piotr Gawron's avatar
Piotr Gawron committed
214
    panel (#686)
Piotr Gawron's avatar
Piotr Gawron committed
215
  * Bug fix: too many annotations (>=100) caused misaligning in the left panel
Piotr Gawron's avatar
Piotr Gawron committed
216
    (#708)
Piotr Gawron's avatar
Piotr Gawron committed
217
218
219
  * Bug fix: export to svg contains viewBox info (#716)
  * Bug fix: overlays added via API couldn't be visualized after refresh (#718)
  * Bug fix: Safari sometimes cached server responses and used wrong data, for
Piotr Gawron's avatar
Piotr Gawron committed
220
221
    example in admin panel configuration tab (#719)
  * Bug fix: description of transcription site is centered (#720)
Piotr Gawron's avatar
Piotr Gawron committed
222
  * Bug fix: selecting too few parameters in export doesn't throw reportable
Piotr Gawron's avatar
Piotr Gawron committed
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
    error (#721)
  * Bug fix: providing invalid overlay id in url could break minerva (#726)
  * Bug fix: removing project that doesn't exist doesn't cause 500 error (#723)
  * Bug fix: opening map with invalid id shows proper error message (#724)
  * Bug fix: Fixing an issue where search panel was not properly resized on
    expansion (#682)
  * Bug fix: loading icon is not overlapping input in the search panel (#404)
  * Bug fix: position of transcription sites in genes are computed properly
    (#553)
  * Bug fix: REQUEST AN ACCOUNT was enabled when associated email was invalid
    (#626)
  * Bug fix: working with too many maps within the single session could crash
    connection to server (#651)
  * Bug fix: drawing corrupted heterodimer association in CellDesigner could
    crash map upload (#673)
Piotr Gawron's avatar
Piotr Gawron committed
238
  * Bug fix: export to CellDesigner align inhibition reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
239
  * Bug fix: export/import to/from SBML handles Heterodimer Association
Piotr Gawron's avatar
Piotr Gawron committed
240
    reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
241
  * Bug fix: logo doesn't need to be square
242
  * Bug fix: when clicking on a search link (in overview window), input in the
Piotr Gawron's avatar
Piotr Gawron committed
243
    left tab was not modified
244
  * Bug fix: in admin panel changing of genome version is blocking interface
Piotr Gawron's avatar
Piotr Gawron committed
245
    until data about url is retrieved
246
247
  * Bug fix: export of species inside complex into CellDesigner was causing
    problems when reading the file in CellDesigner
Piotr Gawron's avatar
Piotr Gawron committed
248
249
  * Bug fix: export to SBGN did not export compartments
  * Bug fix: export of complex states to SBGN did not work
250
  * Bug fix: type of the data overlay can be defined in the file content
Piotr Gawron's avatar
Piotr Gawron committed
251
252
    (useful when uploading genetic variants)
  * Bug fix: CLEAR button clears comment checkbox if necessary
Piotr Gawron's avatar
Piotr Gawron committed
253
  * Bug fix: minerva install problem on ubuntu 18 fixed
Piotr Gawron's avatar
Piotr Gawron committed
254

Piotr Gawron's avatar
Piotr Gawron committed
255
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 25 Mar 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
256

Sascha Herzinger's avatar
Sascha Herzinger committed
257
minerva (12.1.8) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
258
  * Bug fix: add a project reset users custom overlays limit to default (#679)
259
  * Bug fix: edit/remove project button was disabled based on Configuration
Piotr Gawron's avatar
Piotr Gawron committed
260
    Manage Privilege, but should be based on Project Manage Privilege (#681)
261
  * Bug fix: another minor problem with updating privileges introduced in
Piotr Gawron's avatar
Piotr Gawron committed
262
    12.1.6 fixed (#659)
Sascha Herzinger's avatar
Sascha Herzinger committed
263

Piotr Gawron's avatar
Piotr Gawron committed
264
265
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 8 Feb 2019 15:30:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
266
267
268
269
270
minerva (12.1.7) stable; urgency=medium
  * Bug fix: problems with updating privileges introduced in 12.1.6 fixed

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 6 Feb 2019 15:30:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
271
272
minerva (12.1.6) stable; urgency=medium
  * Bug fix: logo on login page was broken with image link being full url
Piotr Gawron's avatar
Piotr Gawron committed
273
274
  * Bug fix: plugin API had sometimes problems with fetching reactions
    properly
Piotr Gawron's avatar
Piotr Gawron committed
275
276
  * Bug fix: upload of data overlays without privileges triggers proper
    error message also in situation when user cannot create projects
Piotr Gawron's avatar
Piotr Gawron committed
277
278
  * Bug fix: first login on website when there is Term of use to accept
    raised error for regular users
Piotr Gawron's avatar
Piotr Gawron committed
279
  * Bug fix: fetching some drugs via API could cause 500
Piotr Gawron's avatar
Piotr Gawron committed
280

Piotr Gawron's avatar
Piotr Gawron committed
281
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Jan 2019 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
282

Piotr Gawron's avatar
Piotr Gawron committed
283
284
285
286
287
minerva (12.1.5) stable; urgency=medium
  * Bug fix: Drugbank changed output format which crashed drug connector
  * Bug fix: word wrapping fixed in overlay table for long overlay names
    in Firefox browser

Piotr Gawron's avatar
Piotr Gawron committed
288
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 10 Jan 2019 14:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
289

290
minerva (12.1.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
291
  * Bug fix: no check for limit on custom data overlays fixed
292
  * Bug fix: error message improved when there is privilege problem during
Piotr Gawron's avatar
Piotr Gawron committed
293
    data overlay upload
Piotr Gawron's avatar
Piotr Gawron committed
294
  * Bug fix: upload of data overlay from admin panel didn't work
295
  * Bug fix: add project button is disabled when user doesn't have proper
Piotr Gawron's avatar
Piotr Gawron committed
296
    privileges ("Add project" privilege)
297
  * Bug fix: there are no more extra markers due to map wrapping
298
299
  * Bug fix: upload of the project failed when another project was removed
    during upload
Piotr Gawron's avatar
Piotr Gawron committed
300
  * Bug fix:  word wrapping fixed in overlay table for long overlay names
301
302
303

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 28 Dec 2018 14:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
304
305
306
minerva (12.1.3) stable; urgency=medium
  * Bug fix: add project button is disabled when user has no privileges
  * Bug fix: projectId was missing in the edit window
Piotr Gawron's avatar
Piotr Gawron committed
307
308
309
310
  * Bug fix: user could provide invalid mesh ID that caused errors when
    browsing map
  * Bug fix: user created from LDAP connection doesn't have a password
    stored in the database
Piotr Gawron's avatar
Piotr Gawron committed
311
312
313

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 14 Dec 2018 14:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
314
315
316
minerva (12.1.2) stable; urgency=medium
  * Bug fix: vmh annotations should be properly matching id entered in the input
  * Bug fix: opacity was not working when highliting objects in plugins
Piotr Gawron's avatar
Piotr Gawron committed
317
  * Bug fix: integer configurtion options (like SMTP_PORT) are properly
Piotr Gawron's avatar
Piotr Gawron committed
318
319
    validated before saving
  * Bug fix: inside of reaction box wasn't properly aligned
Piotr Gawron's avatar
Piotr Gawron committed
320
  * Bug fix: too long data overlay name disturbed size of the map div and
Piotr Gawron's avatar
Piotr Gawron committed
321
322
323
324
325
    interaction with the map
  * Bug fix: search for some drugs resulted in internal server error
  * Bug fix: LDAP login is case insensitive
  * Bug fix: adding user could end up with error in the frontend

Piotr Gawron's avatar
Piotr Gawron committed
326
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Dec 2018 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
327

Piotr Gawron's avatar
Piotr Gawron committed
328
minerva (12.1.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
329
330
331
332
333
334
335
336
337
  * Bug fix: lineWidth in data overlays was ignored
  * Bug fix: legend was blinking after using controls
  * Bug fix: comment header was missing
  * Bug fix: click on drug target zooms to the results
  * Bug fix: export columns return proper value types
  * Bug fix: partial zooming is disabled

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 2 Nov 2018 13:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
338
minerva (12.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
339
340
341
342
  * Small improvement: default privilege value for 'Custom overlays' added
  * Small improvement: explicit logging of successful and unsuccessful logins
  * Small improvement: clicking on search result icon (on the map) change tab to 
    the corresponding search results
343
  * Small improvement: option to remove additional overlays generated by custom
Piotr Gawron's avatar
Piotr Gawron committed
344
    semantic zoom
345
  * Small improvement: 'Reduced modulation' edge was displayed differently in
Piotr Gawron's avatar
Piotr Gawron committed
346
347
348
    CellDesigner and Minerva
  * Small improvement: user-friendly documentation for plugin URL field
  * Small improvement: plugins have to access information about active submap
349
350
351
352
  * Feature: genome browser with gene variants
  * Feature: support of all CellDesigner element modifications
  * Feature: ldap authentication
  * Feature: multicolored anchors for data overlays
Piotr Gawron's avatar
Piotr Gawron committed
353
  * Feature: minerva is distributed using rpm packages
354
  * Small improvement: annotations from RHEA are handled
Piotr Gawron's avatar
Piotr Gawron committed
355
356
  * Small improvement: changing of Terms of Service url allows admin to reset
    the status of ToS acceptance for all users
357
358
  * Small improvement: description of a grouped results in improved
  * Small improvement: selection of required annotation on map upload improved
Piotr Gawron's avatar
Piotr Gawron committed
359
360
361
362
363
364
365
366
  * Bug fix: annotations for elements with mutation in name (like "BID (p15)")
    weren't provided properly
  * Bug fix: passwords in the configuration tab are hidden with '*'
  * Bug fix: user has access to transparency level when creating custom semantic
    view (without this parametere functionality was very difficult to use)
  * Bug fix: loading invalid plugin doesn't render empty div anymore
  * Bug fix: sorting of custom overlays was broken when description of overlay
    was present
367
  * Bug fix: when there is a problem with adjusting font in complexes (because
Piotr Gawron's avatar
Piotr Gawron committed
368
369
370
371
372
    the font should be smaller than 1pt) description is not drawn anymore
  * Bug fix: going to export page and back was breaking a map
  * Bug fix: coordinates of selected area wasn't processed properly when they
    exceeded canvas
  * Bug fix: postgres migration script fixed to work with new docker compose
373
  * Bug fix: double click on user add button disabled
Piotr Gawron's avatar
Piotr Gawron committed
374
375
  * Bug fix: privileges are mirrored correctly across different popups
  * Bug fix: plugin tab css fixed
376
  * Bug fix: uploading sbml file with no ids in glyphs returned error that
Piotr Gawron's avatar
Piotr Gawron committed
377
378
379
    could not be easily understand
  * Bug fix: ds_store files in subfolders crashed zip upload
  * Bug fix: when creating new user default privileges were not filled
380

Piotr Gawron's avatar
Piotr Gawron committed
381
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Oct 2018 13:00:00 +0200
382

Piotr Gawron's avatar
Piotr Gawron committed
383
minerva (12.0.4) stable; urgency=medium
384
  * Bug fix: CellDesigner modifications that are drawn as reaction are handled
Piotr Gawron's avatar
Piotr Gawron committed
385
386
387
    properly (like catalysis)
  * Bug fix: Removing of guest (anonymous) account is forbidden - system is
    unstable after removing such user
Piotr Gawron's avatar
Piotr Gawron committed
388
  * Bug fix: Tair database moved to https
389
  * Bug fix: Taxnomy database changed html output that resulted in problems
Piotr Gawron's avatar
Piotr Gawron committed
390
    with resolving species name to the id
391

Piotr Gawron's avatar
Piotr Gawron committed
392
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Sep 2018 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
393

Piotr Gawron's avatar
Piotr Gawron committed
394
395
396
397
398
399
minerva (12.0.3) stable; urgency=medium
  * Bug fix: SBML model annotations caused errors on upload
  * Bug fix: Export of some models to SBML didn't work properly
  * Bug fix: zip files weren't processed properly
  * Bug fix: required annotations were always required for some types
  * Bug fix: user cannot remove default map anymore
Piotr Gawron's avatar
Piotr Gawron committed
400

Piotr Gawron's avatar
Piotr Gawron committed
401
402
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Aug 2018 11:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
403
404
405
minerva (12.0.2) stable; urgency=medium
  * Bug fix: data overlay by annotation type fixed
  * Bug fix: [plugin] getting reactions with set of id larger than 100 elements
Piotr Gawron's avatar
Piotr Gawron committed
406
    works properly
Piotr Gawron's avatar
Piotr Gawron committed
407
408
409
410
  * Bug fix: name of commented protein was remembered for the new comment
  * Bug fix: setting zoom level wasn't ranged and validated
  * Bug fix: when uploading data overlay there is a warning regarding mixed new
    line characters when necessary
Piotr Gawron's avatar
Piotr Gawron committed
411
  * Performance: tomcat inside docker image by default can use 3G of memory
Piotr Gawron's avatar
Piotr Gawron committed
412

413
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 31 Jul 2018 13:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
414

Piotr Gawron's avatar
Piotr Gawron committed
415
416
417
418
419
minerva (12.0.1) stable; urgency=medium
  * Bug fix: setting default zoom level on submap
  * Bug fix: opened submap had different background then current selection
  * Bug fix: clicking on comments was difficult in OpenLayers
  * Bug fix: general map comment didn't display coordinates properly
Piotr Gawron's avatar
Piotr Gawron committed
420
  * Bug fix: opening map could crash when CellDesigner file contained duplicate
Piotr Gawron's avatar
Piotr Gawron committed
421
    reaction id
Piotr Gawron's avatar
Piotr Gawron committed
422
423
  * Bug fix: map is repositioned when info window is outside of current view in
    OpenLayers library
424

425
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 24 Jul 2018 10:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
426

Piotr Gawron's avatar
Piotr Gawron committed
427
428
minerva (12.0.0) stable; urgency=medium
  * Feature: There is alternative OpenLayers map engine available
Piotr Gawron's avatar
Piotr Gawron committed
429
  * Feature: database connection configuration (login, password, host, etc)
Piotr Gawron's avatar
Piotr Gawron committed
430
    can be modified using /etc/minerva/db.properties file
431
  * Feature: searching for elements in submap gives marker on top map
Piotr Gawron's avatar
Piotr Gawron committed
432
433
    indicating the submap connection
  * Feature: similar search results are merged
Piotr Gawron's avatar
Piotr Gawron committed
434
  * Feature: visualization of protein structures by MolArt
Piotr Gawron's avatar
Piotr Gawron committed
435
  * Feature: reordering of data overlays is supported
436
  * Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA  annotators
Piotr Gawron's avatar
Piotr Gawron committed
437
438
439
440
441
442
443
  * 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
444
445
  * 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
446
447
448
449
450
451
452
453
454
455
  * 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
456
457
  * 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
458
459
460
  * 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
461
462
  * Small improvement: Data overlays can use source element identifiers for
    filtering
Piotr Gawron's avatar
Piotr Gawron committed
463
464
465
  * 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
466
  * Small improvement: auto complete functionality for drugs, mirnas and
Piotr Gawron's avatar
Piotr Gawron committed
467
    chemicals
Piotr Gawron's avatar
Piotr Gawron committed
468
  * Small improvement: columns value and type are not mutually exclusive in
Piotr Gawron's avatar
Piotr Gawron committed
469
470
471
472
    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
473
  * Small improvement: data overlays color scale contains configurable default
Piotr Gawron's avatar
Piotr Gawron committed
474
475
    middle color (for 0 values)
  * Small improvement: opening data overlay switch to empty background
Piotr Gawron's avatar
Piotr Gawron committed
476
477
478
479
480
481
482
483
484
485
486
487
488
  * Small improvement: multiple x-frame domains are allowed
  * Small improvement: No duration of the text notification in overlay tab
  * Small improvement: JS plugin API allows to store data on server side
  * Small improvement: submap reference in publication list
  * Small improvement: size of connection to database reduced to 90 (so default
    connection pool to postgres is not completely filled with minerva)
  * Small improvement: visualization of sbml function improved (lambda
    expression removed from the definition)
  * Small improvement: handling of additional miriam types from BiGG ontology
  * Small improvement: configuration options are grouped in categories
  * Bug fix: searching with two queries sometimes resulted in one complex
    instead of two queries
  * Bug fix: uploaded submaps didn't have hierarchical masking
Piotr Gawron's avatar
Piotr Gawron committed
489
  * Bug fix: uploading of zip files created by mac doesn't crash due to
Piotr Gawron's avatar
Piotr Gawron committed
490
491
    .DS_Store folder
  * Bug fix: auto complete is case insensitive
Piotr Gawron's avatar
Piotr Gawron committed
492
  * Bug fix: google maps API 404 errors for non existing tiles are removed
Piotr Gawron's avatar
Piotr Gawron committed
493

Piotr Gawron's avatar
Piotr Gawron committed
494
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Jul 2018 12:00:00 +0200
495

496
497
498
499
500
501
minerva (11.1.3) stable; urgency=medium
  * Bug fix RPM: remove directory with contents of unpacked war file
    when uninstalling
  * Bug fix: don't append Google API key to Google maps javascript URL
    when it is not set

Piotr Gawron's avatar
Piotr Gawron committed
502
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 23 Jul 2018 12:00:00 +0200
503

Piotr Gawron's avatar
Piotr Gawron committed
504
minerva (11.1.2) stable; urgency=medium
505
506
  * Bug fix: Searching for chemicals with invalid mesh ID crashed
  * Bug fix: opening map that was removed and re-uploaded could crash
Piotr Gawron's avatar
Piotr Gawron committed
507
508
509
510
  * warning message due to lack of google consent improved

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 04 Jul 2018 16:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
511
512
513
514
515
516
517
518
519
520
minerva (11.1.1) stable; urgency=medium
  * Bug fix: Updating privileges takes much less time
  * Bug fix: Concurent update on privileges shouldn't crash anymore
  * Bug fix: Search by element id crashed when submaps were available
  * Bug fix: GO connector uses new API, because the old one was turned off
    and stopped working


 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 27 Jun 2018 15:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
521
522
523
minerva (11.1.0) stable; urgency=high
  * User can provide Google Maps API key that must be registered in google
    cloud account
524
525
  * User data overlays must be Google Maps API terms of use compliant
  * Terms of Use added
526

527
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 05 Jun 2018 9:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
528
  
529
530
minerva (11.0.10) stable; urgency=medium
  * Bug fix: link from overview image to search result was broken
531

532
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Apr 2018 15:00:00 +0200
533

Piotr Gawron's avatar
Piotr Gawron committed
534
535
536
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
537

Piotr Gawron's avatar
Piotr Gawron committed
538
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
539

Piotr Gawron's avatar
Piotr Gawron committed
540
541
542
543
544
545
546
547
548
549
550
551
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
552
  * Bug fix: comments on submaps are visualized properly
Piotr Gawron's avatar
Piotr Gawron committed
553

Piotr Gawron's avatar
Piotr Gawron committed
554
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 05 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
555

Piotr Gawron's avatar
Piotr Gawron committed
556
557
558
559
560
561
562
563
564
565
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

566
minerva (11.0.6) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
567
568
  * Bug fix: fix a bug when entering invalid mirna id

569
570
571
 -- 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
572
  * Bug fix: fix on connection to drugbank database
573
574
  * Bug fix: posttranslational modification data was sometimes unavailable
    in search results panel
Piotr Gawron's avatar
Piotr Gawron committed
575

576
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 30 Nov 2017 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
577

578
minerva (11.0.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
579
  * Bug fix: fix on connection to taxonomy database
580
581
  * 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
582

583
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 09 Nov 2017 14:50:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
584

585
minerva (11.0.3) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
586
  * Bug fix: removing empty project removed images from all projects
587
588
589
590
591
592
593
594
595
  * 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
596
  * Bug fix: login issues when default page is in secure area
597
598
599
600

 -- 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
601
  * Bug fix: logout caused issues with session data
602
603
604
605
606

 -- 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
607
608
  * Bug fix: security issue - access to specific map can be restricted
    by the user login
609
610
  * Bug fix: sbgn import
  * Bug fix: mesh connector
Piotr Gawron's avatar
Piotr Gawron committed
611
  * Rest API (documentation can be found here:
612
613
    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
614
    corner (when Search tab is not open)
615
616
  * 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
617
618
    proper text box
  * Layout changes: the main one is that there are only 3 tab panels
619
620
621
622
623
624
625
626
627
    (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
628
629
  * Overlay presents description field if possible

630
631

 -- Piotr Gawron <piotr.gawron@uni.lu>  Sat, 04 Mar 2017 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
632

633
634
635
636
637
638
639
640
641
642
643
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
644
  * Bug fix: search for multiple drugs will not return more drugs than
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
    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
662
663
  * Bug fix: trigger reaction and physical stimulation reactions are no
    longer allowed (CellDesigner data model issue)
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
  * 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
703
704
705
706
707
708
  * 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
709
710
711
712
713

 -- 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
714
715
716
717
718
  * Searching by annotations
  * Errors from parsing data forwarded to client
  * Notification email system added
  * Warnings are downloadable
  * Complex map (composed from many small maps)
719
  * Visualization of Recon specific annotations
Piotr Gawron's avatar
Piotr Gawron committed
720
721
722
723
724
725
726
  * Versioning system
  * Galaxy connector
  * Miriam types report
  * Advanced annotation options
  * Uniprot annotation module
  * Customized validation of miriam annotations
  * Recon annotation service
727
  * Bug fix: Data autofill problem in user management
Piotr Gawron's avatar
Piotr Gawron committed
728
729
  * Bug fix: User privileges for adding project
  * Bug fix: Problem with some miriam entries in RDF format
730
  * Bug fix: Reporting of drawing problems
Piotr Gawron's avatar
Piotr Gawron committed
731
732
  * Bug fix: Visualization of posttranslationa modification
  * Bug fix: Drugbank problem after update of Drugbank interface
733
  * Bug fix: Session scope fixed (browsing many maps at the same time)
Piotr Gawron's avatar
Piotr Gawron committed
734
735
736
737
738
  * 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
739
740

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 21 Jul 2015 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
741

742
743
minerva (5) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
744
  * Additional checkboxes in upload model: annotate automatically, cache data, verify annotations
745
  * Popup window in admin panel that list warnings
Piotr Gawron's avatar
Piotr Gawron committed
746
747
  * Information about build
  * Parsing and annotation warnings for models in admin panel
748
  * Custom reaction visualization in upload overlay
Piotr Gawron's avatar
Piotr Gawron committed
749
750
751
752
753
  * 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
754
755

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 18 Dec 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
756

757
758
759
minerva (4) stable; urgency=low

  * Export of the part of the map into CellDesigner file
Piotr Gawron's avatar
Piotr Gawron committed
760
761
  * Logo files managable via config webpage
  * Import data from GO
762
763
764
  * 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
765
766
767
768
769
  * 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
770
771

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 11 Sep 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
772

773
774
775
minerva (3) stable; urgency=low

  * Drug targeting interface
Piotr Gawron's avatar
Piotr Gawron committed
776
777
778
  * Export to CellDesigner
  * Status page of all dependent services
  * Configuration page
779
780

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 5 Jun 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
781

782
783
784
minerva (2) stable; urgency=low

  * Upload of the CellDesigner map
Piotr Gawron's avatar
Piotr Gawron committed
785
786
  * Bug fix: Problem with touch interface after update of browsers engine
  * Bug fix: Problem in Safari when searching for elements
787
788

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 2 Apr 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
789

790
791
minerva (1) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
792
  * Initial release
793
794

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 4 Dec 2013 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
795