CHANGELOG 30.9 KB
Newer Older
Piotr Gawron's avatar
Piotr Gawron committed
1
minerva (12.2.0~beta.2) unstable; urgency=medium
2
3
  * Bug fix: parent compartment/pathway use proper type name in left panel 
   (#324)
4
  * Bug fix: editing/removing project requires Map Management privilege (#681)
5
6
  * Bug fix: when removeAllListeners is called list of registered listeners is 
    cleaned (#687)
7
8
  * Bug fix: when plugin is removed the html elements associated with it are 
    removed as well (#686)
Piotr Gawron's avatar
Piotr Gawron committed
9
  * Bug fix: when creating new user default privileges are set properly (#692)
10
11
  * Bug fix: import from SBML issue - reaction with product and modifier being
    the same element caused exception (#703)
12
13
  * Bug fix: plugin can be added after plugin has been removed in admin plugin 
    panel (#686)
14
15
  * Bug fix: too many annotations (>=100) caused misaligning in the left panel 
    (#708)
Piotr Gawron's avatar
Piotr Gawron committed
16
  * Bug fix: text was outside the popup window (#711)
17
18
  * Bug fix: custom semantic zooming contains multiple overlays checkbox was 
    disabled (#715) 
19
  * Bug fix: export to svg contains viewBox info (#716) 
20
21
  * Bug fix: import from sbml with layout could crash when two elements 
    occupied the exact same position (#717) 
22
  * Bug fix: overlays added via API couldn't be visualized after refresh (#718) 
Piotr Gawron's avatar
Piotr Gawron committed
23
24
  * Bug fix: Safari sometimes cached server responses and used wrong data, for 
    example in admin panel configuration tab (#719)
25
  * Bug fix: description of transcription site is centered (#720)
26
27
  * Bug fix: selecting too few parameters in export doesn't throw reportable 
    error (#721)
Piotr Gawron's avatar
Piotr Gawron committed
28
  * Bug fix: changes in selected checkbox in add project dialog block UI (#722)
Piotr Gawron's avatar
Piotr Gawron committed
29
  * Bug fix: providing invalid overlay id in url could break minerva (#726)
Piotr Gawron's avatar
Piotr Gawron committed
30
  * Bug fix: removing project that doesn't exist doesn't cause 500 error (#723)
Piotr Gawron's avatar
Piotr Gawron committed
31
32
  * Bug fix: Editing project with images and submaps could cause a problem 
    (#725)
Piotr Gawron's avatar
Piotr Gawron committed
33
  * Bug fix: opening map with invalid id shows proper error message (#724)
Piotr Gawron's avatar
Piotr Gawron committed
34
35
  * Bug fix: Fixing an issue where search panel was not properly resized on
    expansion (#682)
Piotr Gawron's avatar
Piotr Gawron committed
36
37
  * Small improvement: highlighting table rows in admin panel uses better
    contrast color (#706)
Piotr Gawron's avatar
Piotr Gawron committed
38
39
40

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 20 Feb 2019 14:00:00 +0200

Piotr Gawron's avatar
typo    
Piotr Gawron committed
41
minerva (12.2.0~beta.1) unstable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
42
  * Small improvement: list of publication can be filtered by submap (#614)
43
  * Small improvement: report bug utility shows confirmation dialog on success
Piotr Gawron's avatar
Piotr Gawron committed
44
45
    (#648)
  * Small improvement: size of add overlay window adjusted to show more data
46
47
    without scrollbars (#657)
  * Small improvement: all popup dialogs in the app have dialog specific css
Piotr Gawron's avatar
Piotr Gawron committed
48
49
    class names (#665)
  * Bug fix: loading icon is not overlapping input in the search panel (#404)
50
  * Bug fix: position of transcription sites in genes are computed properly
Piotr Gawron's avatar
Piotr Gawron committed
51
    (#553)
52
  * Bug fix: REQUEST AN ACCOUNT was enabled when associated email was invalid
Piotr Gawron's avatar
Piotr Gawron committed
53
    (#626)
54
  * Bug fix: layout exported to SBML can be properly visualized by COPASI
Piotr Gawron's avatar
Piotr Gawron committed
55
    (#654)
56
  * Bug fix: working with too many maps within the single session could crash
Piotr Gawron's avatar
Piotr Gawron committed
57
    connection to server (#651)
58
  * Bug fix: invalid pubmed id could crash listing/downloading publications
Piotr Gawron's avatar
Piotr Gawron committed
59
60
    (#656)
  * Bug fix: icons in safari sometimes disappear (#661)
61
  * Bug fix: downloading reference genome for the second time resulted in an
Piotr Gawron's avatar
Piotr Gawron committed
62
    error (#670)
63
  * Bug fix: plugin validation in admin panel improved to catch more problems
Piotr Gawron's avatar
Piotr Gawron committed
64
    (#672)
65
  * Bug fix: drawing corrupted heterodimer association in CellDesigner could
Piotr Gawron's avatar
Piotr Gawron committed
66
    crash map upload (#673)
67
  * Bug fix: custom semantic zooming didn't work with pathways imported from
Piotr Gawron's avatar
Piotr Gawron committed
68
69
70
71
    CellDesigner layers (#678)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 7 Feb 2019 14:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
72
73
minerva (12.2.0~beta.0) unstable; urgency=medium
  * Feature: bug report utility
74
  * Small improvement: JS plugin can create listener that is triggered on
Piotr Gawron's avatar
Piotr Gawron committed
75
76
    search results focus change

Piotr Gawron's avatar
Piotr Gawron committed
77
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 23 Jan 2019 15:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
78

Piotr Gawron's avatar
Piotr Gawron committed
79
80
81
82
83
84
85
minerva (12.2.0~alpha.1) unstable; urgency=medium
  * Bug fix: problems with SBML-CellDesigner translation fixed
  * Bug fix: gitlab CI tests fixed

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 17 Jan 2019 15:00:00 +0200

minerva (12.2.0~alpha.0) unstable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
86
87
  * Feature: url GET parameters support all kind of search and selected overlays
    highlight
88
  * Feature: user can create custom logging configuration in file
Piotr Gawron's avatar
Piotr Gawron committed
89
90
91
92
    /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
93
  * Feature: API tool providing possibility to transform different types of
Piotr Gawron's avatar
Piotr Gawron committed
94
    file formats
95
  * Feature: current state of the browsed map is reflected in the url (position,
Piotr Gawron's avatar
Piotr Gawron committed
96
97
98
    zoom, overlays, search queries, etc.)
  * Small improvement: export to SBML includes unit factors
  * Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
99
  * Small improvement: genetics information allows to provide information about
Piotr Gawron's avatar
Piotr Gawron committed
100
    modification on peptide level that could be visualized in MolArt
101
  * Small improvement: allow to control the background and font color of areas
Piotr Gawron's avatar
Piotr Gawron committed
102
    drawn from text areas in CellDesigner "layers"
103
  * Small improvement: config logo location is relative to the root minerva
Piotr Gawron's avatar
Piotr Gawron committed
104
105
    deployment directory
  * Small improvement: there is branding minerva logo in the left panel
106
107
108
109
110
111
112
113
114
115
116
117
  * 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
118
119
  * Small improvement: there is max size of the map in configuration panel that
    disables upload of too big files
120
  * Small improvement: hitting enter on login page logs in the user (no need to
Piotr Gawron's avatar
Piotr Gawron committed
121
    click on the login button)
122
  * Small improvement: refresh button in overlays panel (useful when data
Piotr Gawron's avatar
Piotr Gawron committed
123
124
125
    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
126
  * Small improvement: 'BACK TO MAP' link is available only when guest account
Piotr Gawron's avatar
Piotr Gawron committed
127
128
    has proper access level
  * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
129
130
    email account is provided
  * Small improvement: Plugin API allows to show/hide data overlays
Piotr Gawron's avatar
Piotr Gawron committed
131
  * Bug fix: export to CellDesigner align inhibition reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
132
  * Bug fix: export/import to/from SBML handles Heterodimer Association
Piotr Gawron's avatar
Piotr Gawron committed
133
    reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
134
  * Bug fix: logo doesn't need to be square
135
  * Bug fix: when clicking on a search link (in overview window), input in the
Piotr Gawron's avatar
Piotr Gawron committed
136
    left tab was not modified
137
  * Bug fix: in admin panel changing of genome version is blocking interface
Piotr Gawron's avatar
Piotr Gawron committed
138
    until data about url is retrieved
139
140
  * 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
141
142
  * Bug fix: export to SBGN did not export compartments
  * Bug fix: export of complex states to SBGN did not work
143
  * Bug fix: type of the data overlay can be defined in the file content
Piotr Gawron's avatar
Piotr Gawron committed
144
145
    (useful when uploading genetic variants)
  * Bug fix: CLEAR button clears comment checkbox if necessary
Piotr Gawron's avatar
Piotr Gawron committed
146
  * Bug fix: minerva install problem on ubuntu 16 fixed
Piotr Gawron's avatar
Piotr Gawron committed
147

Piotr Gawron's avatar
Piotr Gawron committed
148
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 11 Jan 2019 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
149

Sascha Herzinger's avatar
Sascha Herzinger committed
150
minerva (12.1.8) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
151
  * Bug fix: add a project reset users custom overlays limit to default (#679)
152
  * Bug fix: edit/remove project button was disabled based on Configuration
Piotr Gawron's avatar
Piotr Gawron committed
153
    Manage Privilege, but should be based on Project Manage Privilege (#681)
154
  * Bug fix: another minor problem with updating privileges introduced in
Piotr Gawron's avatar
Piotr Gawron committed
155
    12.1.6 fixed (#659)
Sascha Herzinger's avatar
Sascha Herzinger committed
156

Piotr Gawron's avatar
Piotr Gawron committed
157
158
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 8 Feb 2019 15:30:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
159
160
161
162
163
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
164
165
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
166
167
  * Bug fix: plugin API had sometimes problems with fetching reactions
    properly
Piotr Gawron's avatar
Piotr Gawron committed
168
169
  * 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
170
171
  * 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
172
  * Bug fix: fetching some drugs via API could cause 500
Piotr Gawron's avatar
Piotr Gawron committed
173

Piotr Gawron's avatar
Piotr Gawron committed
174
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Jan 2019 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
175

Piotr Gawron's avatar
Piotr Gawron committed
176
177
178
179
180
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
181
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 10 Jan 2019 14:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
182

183
minerva (12.1.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
184
  * Bug fix: no check for limit on custom data overlays fixed
185
  * Bug fix: error message improved when there is privilege problem during
Piotr Gawron's avatar
Piotr Gawron committed
186
    data overlay upload
Piotr Gawron's avatar
Piotr Gawron committed
187
  * Bug fix: upload of data overlay from admin panel didn't work
188
  * Bug fix: add project button is disabled when user doesn't have proper
Piotr Gawron's avatar
Piotr Gawron committed
189
    privileges ("Add project" privilege)
190
  * Bug fix: there are no more extra markers due to map wrapping
191
192
  * Bug fix: upload of the project failed when another project was removed
    during upload
Piotr Gawron's avatar
Piotr Gawron committed
193
  * Bug fix:  word wrapping fixed in overlay table for long overlay names
194
195
196

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

Piotr Gawron's avatar
Piotr Gawron committed
197
198
199
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
200
201
202
203
  * 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
204
205
206

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

Piotr Gawron's avatar
Piotr Gawron committed
207
208
209
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
210
  * Bug fix: integer configurtion options (like SMTP_PORT) are properly
Piotr Gawron's avatar
Piotr Gawron committed
211
212
    validated before saving
  * Bug fix: inside of reaction box wasn't properly aligned
Piotr Gawron's avatar
Piotr Gawron committed
213
  * Bug fix: too long data overlay name disturbed size of the map div and
Piotr Gawron's avatar
Piotr Gawron committed
214
215
216
217
218
    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
219
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Dec 2018 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
220

Piotr Gawron's avatar
Piotr Gawron committed
221
minerva (12.1.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
222
223
224
225
226
227
228
229
230
  * 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
231
minerva (12.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
232
233
234
235
  * 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
236
  * Small improvement: option to remove additional overlays generated by custom
Piotr Gawron's avatar
Piotr Gawron committed
237
    semantic zoom
238
  * Small improvement: 'Reduced modulation' edge was displayed differently in
Piotr Gawron's avatar
Piotr Gawron committed
239
240
241
    CellDesigner and Minerva
  * Small improvement: user-friendly documentation for plugin URL field
  * Small improvement: plugins have to access information about active submap
242
243
244
245
  * 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
246
  * Feature: minerva is distributed using rpm packages
247
  * Small improvement: annotations from RHEA are handled
Piotr Gawron's avatar
Piotr Gawron committed
248
249
  * Small improvement: changing of Terms of Service url allows admin to reset
    the status of ToS acceptance for all users
250
251
  * 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
252
253
254
255
256
257
258
259
  * 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
260
  * Bug fix: when there is a problem with adjusting font in complexes (because
Piotr Gawron's avatar
Piotr Gawron committed
261
262
263
264
265
    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
266
  * Bug fix: double click on user add button disabled
Piotr Gawron's avatar
Piotr Gawron committed
267
268
  * Bug fix: privileges are mirrored correctly across different popups
  * Bug fix: plugin tab css fixed
269
  * Bug fix: uploading sbml file with no ids in glyphs returned error that
Piotr Gawron's avatar
Piotr Gawron committed
270
271
272
    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
273

Piotr Gawron's avatar
Piotr Gawron committed
274
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Oct 2018 13:00:00 +0200
275

Piotr Gawron's avatar
Piotr Gawron committed
276
minerva (12.0.4) stable; urgency=medium
277
  * Bug fix: CellDesigner modifications that are drawn as reaction are handled
Piotr Gawron's avatar
Piotr Gawron committed
278
279
280
    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
281
  * Bug fix: Tair database moved to https
282
  * Bug fix: Taxnomy database changed html output that resulted in problems
Piotr Gawron's avatar
Piotr Gawron committed
283
    with resolving species name to the id
284

Piotr Gawron's avatar
Piotr Gawron committed
285
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Sep 2018 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
286

Piotr Gawron's avatar
Piotr Gawron committed
287
288
289
290
291
292
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
293

Piotr Gawron's avatar
Piotr Gawron committed
294
295
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Aug 2018 11:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
296
297
298
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
299
    works properly
Piotr Gawron's avatar
Piotr Gawron committed
300
301
302
303
  * 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
304
  * Performance: tomcat inside docker image by default can use 3G of memory
Piotr Gawron's avatar
Piotr Gawron committed
305

306
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 31 Jul 2018 13:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
307

Piotr Gawron's avatar
Piotr Gawron committed
308
309
310
311
312
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
313
  * Bug fix: opening map could crash when CellDesigner file contained duplicate
Piotr Gawron's avatar
Piotr Gawron committed
314
    reaction id
Piotr Gawron's avatar
Piotr Gawron committed
315
316
  * Bug fix: map is repositioned when info window is outside of current view in
    OpenLayers library
317

318
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 24 Jul 2018 10:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
319

Piotr Gawron's avatar
Piotr Gawron committed
320
321
minerva (12.0.0) stable; urgency=medium
  * Feature: There is alternative OpenLayers map engine available
Piotr Gawron's avatar
Piotr Gawron committed
322
  * Feature: database connection configuration (login, password, host, etc)
Piotr Gawron's avatar
Piotr Gawron committed
323
    can be modified using /etc/minerva/db.properties file
324
  * Feature: searching for elements in submap gives marker on top map
Piotr Gawron's avatar
Piotr Gawron committed
325
326
    indicating the submap connection
  * Feature: similar search results are merged
Piotr Gawron's avatar
Piotr Gawron committed
327
  * Feature: visualization of protein structures by MolArt
Piotr Gawron's avatar
Piotr Gawron committed
328
  * Feature: reordering of data overlays is supported
329
  * Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA  annotators
Piotr Gawron's avatar
Piotr Gawron committed
330
331
332
333
334
335
336
  * 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
337
338
  * 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
339
340
341
342
343
344
345
346
347
348
  * 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
349
350
  * 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
351
352
353
  * 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
354
355
  * Small improvement: Data overlays can use source element identifiers for
    filtering
Piotr Gawron's avatar
Piotr Gawron committed
356
357
358
  * 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
359
  * Small improvement: auto complete functionality for drugs, mirnas and
Piotr Gawron's avatar
Piotr Gawron committed
360
    chemicals
Piotr Gawron's avatar
Piotr Gawron committed
361
  * Small improvement: columns value and type are not mutually exclusive in
Piotr Gawron's avatar
Piotr Gawron committed
362
363
364
365
    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
366
  * Small improvement: data overlays color scale contains configurable default
Piotr Gawron's avatar
Piotr Gawron committed
367
368
    middle color (for 0 values)
  * Small improvement: opening data overlay switch to empty background
Piotr Gawron's avatar
Piotr Gawron committed
369
370
371
372
373
374
375
376
377
378
379
380
381
  * 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
382
  * Bug fix: uploading of zip files created by mac doesn't crash due to
Piotr Gawron's avatar
Piotr Gawron committed
383
384
    .DS_Store folder
  * Bug fix: auto complete is case insensitive
Piotr Gawron's avatar
Piotr Gawron committed
385
  * Bug fix: google maps API 404 errors for non existing tiles are removed
Piotr Gawron's avatar
Piotr Gawron committed
386

Piotr Gawron's avatar
Piotr Gawron committed
387
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Jul 2018 12:00:00 +0200
388

389
390
391
392
393
394
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
395
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 23 Jul 2018 12:00:00 +0200
396

Piotr Gawron's avatar
Piotr Gawron committed
397
minerva (11.1.2) stable; urgency=medium
398
399
  * 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
400
401
402
403
  * 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
404
405
406
407
408
409
410
411
412
413
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
414
415
416
minerva (11.1.0) stable; urgency=high
  * User can provide Google Maps API key that must be registered in google
    cloud account
417
418
  * User data overlays must be Google Maps API terms of use compliant
  * Terms of Use added
419

420
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 05 Jun 2018 9:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
421
  
422
423
minerva (11.0.10) stable; urgency=medium
  * Bug fix: link from overview image to search result was broken
424

425
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Apr 2018 15:00:00 +0200
426

Piotr Gawron's avatar
Piotr Gawron committed
427
428
429
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
430

Piotr Gawron's avatar
Piotr Gawron committed
431
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
432

Piotr Gawron's avatar
Piotr Gawron committed
433
434
435
436
437
438
439
440
441
442
443
444
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
445
  * Bug fix: comments on submaps are visualized properly
Piotr Gawron's avatar
Piotr Gawron committed
446

Piotr Gawron's avatar
Piotr Gawron committed
447
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 05 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
448

Piotr Gawron's avatar
Piotr Gawron committed
449
450
451
452
453
454
455
456
457
458
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

459
minerva (11.0.6) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
460
461
  * Bug fix: fix a bug when entering invalid mirna id

462
463
464
 -- 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
465
  * Bug fix: fix on connection to drugbank database
466
467
  * Bug fix: posttranslational modification data was sometimes unavailable
    in search results panel
Piotr Gawron's avatar
Piotr Gawron committed
468

469
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 30 Nov 2017 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
470

471
minerva (11.0.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
472
  * Bug fix: fix on connection to taxonomy database
473
474
  * 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
475

476
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 09 Nov 2017 14:50:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
477

478
minerva (11.0.3) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
479
  * Bug fix: removing empty project removed images from all projects
480
481
482
483
484
485
486
487
488
  * 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
489
  * Bug fix: login issues when default page is in secure area
490
491
492
493

 -- 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
494
  * Bug fix: logout caused issues with session data
495
496
497
498
499

 -- 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
500
501
  * Bug fix: security issue - access to specific map can be restricted
    by the user login
502
503
  * Bug fix: sbgn import
  * Bug fix: mesh connector
Piotr Gawron's avatar
Piotr Gawron committed
504
  * Rest API (documentation can be found here:
505
506
    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
507
    corner (when Search tab is not open)
508
509
  * 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
510
511
    proper text box
  * Layout changes: the main one is that there are only 3 tab panels
512
513
514
515
516
517
518
519
520
    (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
521
522
  * Overlay presents description field if possible

523
524

 -- Piotr Gawron <piotr.gawron@uni.lu>  Sat, 04 Mar 2017 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
525

526
527
528
529
530
531
532
533
534
535
536
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
537
  * Bug fix: search for multiple drugs will not return more drugs than
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
    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
555
556
  * Bug fix: trigger reaction and physical stimulation reactions are no
    longer allowed (CellDesigner data model issue)
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
  * 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
596
597
598
599
600
601
  * 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
602
603
604
605
606

 -- 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
607
608
609
610
611
  * Searching by annotations
  * Errors from parsing data forwarded to client
  * Notification email system added
  * Warnings are downloadable
  * Complex map (composed from many small maps)
612
  * Visualization of Recon specific annotations
Piotr Gawron's avatar
Piotr Gawron committed
613
614
615
616
617
618
619
  * Versioning system
  * Galaxy connector
  * Miriam types report
  * Advanced annotation options
  * Uniprot annotation module
  * Customized validation of miriam annotations
  * Recon annotation service
620
  * Bug fix: Data autofill problem in user management
Piotr Gawron's avatar
Piotr Gawron committed
621
622
  * Bug fix: User privileges for adding project
  * Bug fix: Problem with some miriam entries in RDF format
623
  * Bug fix: Reporting of drawing problems
Piotr Gawron's avatar
Piotr Gawron committed
624
625
  * Bug fix: Visualization of posttranslationa modification
  * Bug fix: Drugbank problem after update of Drugbank interface
626
  * Bug fix: Session scope fixed (browsing many maps at the same time)
Piotr Gawron's avatar
Piotr Gawron committed
627
628
629
630
631
  * 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
632
633

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 21 Jul 2015 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
634

635
636
minerva (5) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
637
  * Additional checkboxes in upload model: annotate automatically, cache data, verify annotations
638
  * Popup window in admin panel that list warnings
Piotr Gawron's avatar
Piotr Gawron committed
639
640
  * Information about build
  * Parsing and annotation warnings for models in admin panel
641
  * Custom reaction visualization in upload overlay
Piotr Gawron's avatar
Piotr Gawron committed
642
643
644
645
646
  * 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
647
648

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 18 Dec 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
649

650
651
652
minerva (4) stable; urgency=low

  * Export of the part of the map into CellDesigner file
Piotr Gawron's avatar
Piotr Gawron committed
653
654
  * Logo files managable via config webpage
  * Import data from GO
655
656
657
  * 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
658
659
660
661
662
  * 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
663
664

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 11 Sep 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
665

666
667
668
minerva (3) stable; urgency=low

  * Drug targeting interface
Piotr Gawron's avatar
Piotr Gawron committed
669
670
671
  * Export to CellDesigner
  * Status page of all dependent services
  * Configuration page
672
673

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 5 Jun 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
674

675
676
677
minerva (2) stable; urgency=low

  * Upload of the CellDesigner map
Piotr Gawron's avatar
Piotr Gawron committed
678
679
  * Bug fix: Problem with touch interface after update of browsers engine
  * Bug fix: Problem in Safari when searching for elements
680
681

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 2 Apr 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
682

683
684
minerva (1) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
685
  * Initial release
686
687

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 4 Dec 2013 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
688