CHANGELOG 30.7 KB
Newer Older
Piotr Gawron's avatar
Piotr Gawron committed
1
minerva (12.2.0~beta.2) unstable; urgency=medium
2
3
  * Bug fix: when plugin is removed the html elements associated with it are 
    removed as well (#686)
Piotr Gawron's avatar
Piotr Gawron committed
4
  * Bug fix: when creating new user default privileges are set properly (#692)
5
6
  * Bug fix: import from SBML issue - reaction with product and modifier being
    the same element caused exception (#703)
7
8
  * Bug fix: plugin can be added after plugin has been removed in admin plugin 
    panel (#686)
9
10
  * Bug fix: too many annotations (>=100) caused misaligning in the left panel 
    (#708)
Piotr Gawron's avatar
Piotr Gawron committed
11
  * Bug fix: text was outside the popup window (#711)
12
13
  * Bug fix: custom semantic zooming contains multiple overlays checkbox was 
    disabled (#715) 
14
  * Bug fix: export to svg contains viewBox info (#716) 
15
16
  * Bug fix: import from sbml with layout could crash when two elements 
    occupied the exact same position (#717) 
17
  * Bug fix: overlays added via API couldn't be visualized after refresh (#718) 
Piotr Gawron's avatar
Piotr Gawron committed
18
19
  * Bug fix: Safari sometimes cached server responses and used wrong data, for 
    example in admin panel configuration tab (#719)
20
  * Bug fix: description of transcription site is centered (#720)
21
22
  * Bug fix: selecting too few parameters in export doesn't throw reportable 
    error (#721)
Piotr Gawron's avatar
Piotr Gawron committed
23
  * Bug fix: changes in selected checkbox in add project dialog block UI (#722)
Piotr Gawron's avatar
Piotr Gawron committed
24
  * Bug fix: providing invalid overlay id in url could break minerva (#726)
Piotr Gawron's avatar
Piotr Gawron committed
25
  * Bug fix: removing project that doesn't exist doesn't cause 500 error (#723)
Piotr Gawron's avatar
Piotr Gawron committed
26
27
  * Bug fix: Editing project with images and submaps could cause a problem 
    (#725)
Piotr Gawron's avatar
Piotr Gawron committed
28
  * Bug fix: opening map with invalid id shows proper error message (#724)
Piotr Gawron's avatar
Piotr Gawron committed
29
30
  * Bug fix: Fixing an issue where search panel was not properly resized on
    expansion (#682)
Piotr Gawron's avatar
Piotr Gawron committed
31
32
  * Small improvement: highlighting table rows in admin panel uses better
    contrast color (#706)
Piotr Gawron's avatar
Piotr Gawron committed
33
34
35

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

Piotr Gawron's avatar
typo    
Piotr Gawron committed
36
minerva (12.2.0~beta.1) unstable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
37
  * Small improvement: list of publication can be filtered by submap (#614)
38
  * Small improvement: report bug utility shows confirmation dialog on success
Piotr Gawron's avatar
Piotr Gawron committed
39
40
    (#648)
  * Small improvement: size of add overlay window adjusted to show more data
41
42
    without scrollbars (#657)
  * Small improvement: all popup dialogs in the app have dialog specific css
Piotr Gawron's avatar
Piotr Gawron committed
43
44
    class names (#665)
  * Bug fix: loading icon is not overlapping input in the search panel (#404)
45
  * Bug fix: position of transcription sites in genes are computed properly
Piotr Gawron's avatar
Piotr Gawron committed
46
    (#553)
47
  * Bug fix: REQUEST AN ACCOUNT was enabled when associated email was invalid
Piotr Gawron's avatar
Piotr Gawron committed
48
    (#626)
49
  * Bug fix: layout exported to SBML can be properly visualized by COPASI
Piotr Gawron's avatar
Piotr Gawron committed
50
    (#654)
51
  * Bug fix: working with too many maps within the single session could crash
Piotr Gawron's avatar
Piotr Gawron committed
52
    connection to server (#651)
53
  * Bug fix: invalid pubmed id could crash listing/downloading publications
Piotr Gawron's avatar
Piotr Gawron committed
54
55
    (#656)
  * Bug fix: icons in safari sometimes disappear (#661)
56
  * Bug fix: downloading reference genome for the second time resulted in an
Piotr Gawron's avatar
Piotr Gawron committed
57
    error (#670)
58
  * Bug fix: plugin validation in admin panel improved to catch more problems
Piotr Gawron's avatar
Piotr Gawron committed
59
    (#672)
60
  * Bug fix: drawing corrupted heterodimer association in CellDesigner could
Piotr Gawron's avatar
Piotr Gawron committed
61
    crash map upload (#673)
62
  * Bug fix: custom semantic zooming didn't work with pathways imported from
Piotr Gawron's avatar
Piotr Gawron committed
63
64
65
66
    CellDesigner layers (#678)

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

Piotr Gawron's avatar
Piotr Gawron committed
67
68
minerva (12.2.0~beta.0) unstable; urgency=medium
  * Feature: bug report utility
69
  * Small improvement: JS plugin can create listener that is triggered on
Piotr Gawron's avatar
Piotr Gawron committed
70
71
    search results focus change

Piotr Gawron's avatar
Piotr Gawron committed
72
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 23 Jan 2019 15:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
73

Piotr Gawron's avatar
Piotr Gawron committed
74
75
76
77
78
79
80
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
81
82
  * Feature: url GET parameters support all kind of search and selected overlays
    highlight
83
  * Feature: user can create custom logging configuration in file
Piotr Gawron's avatar
Piotr Gawron committed
84
85
86
87
    /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
88
  * Feature: API tool providing possibility to transform different types of
Piotr Gawron's avatar
Piotr Gawron committed
89
    file formats
90
  * Feature: current state of the browsed map is reflected in the url (position,
Piotr Gawron's avatar
Piotr Gawron committed
91
92
93
    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
94
  * Small improvement: genetics information allows to provide information about
Piotr Gawron's avatar
Piotr Gawron committed
95
    modification on peptide level that could be visualized in MolArt
96
  * Small improvement: allow to control the background and font color of areas
Piotr Gawron's avatar
Piotr Gawron committed
97
    drawn from text areas in CellDesigner "layers"
98
  * Small improvement: config logo location is relative to the root minerva
Piotr Gawron's avatar
Piotr Gawron committed
99
100
    deployment directory
  * Small improvement: there is branding minerva logo in the left panel
101
102
103
104
105
106
107
108
109
110
111
112
  * 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
113
114
  * Small improvement: there is max size of the map in configuration panel that
    disables upload of too big files
115
  * Small improvement: hitting enter on login page logs in the user (no need to
Piotr Gawron's avatar
Piotr Gawron committed
116
    click on the login button)
117
  * Small improvement: refresh button in overlays panel (useful when data
Piotr Gawron's avatar
Piotr Gawron committed
118
119
120
    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
121
  * Small improvement: 'BACK TO MAP' link is available only when guest account
Piotr Gawron's avatar
Piotr Gawron committed
122
123
    has proper access level
  * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
124
125
    email account is provided
  * Small improvement: Plugin API allows to show/hide data overlays
Piotr Gawron's avatar
Piotr Gawron committed
126
  * Bug fix: export to CellDesigner align inhibition reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
127
  * Bug fix: export/import to/from SBML handles Heterodimer Association
Piotr Gawron's avatar
Piotr Gawron committed
128
    reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
129
  * Bug fix: logo doesn't need to be square
130
  * Bug fix: when clicking on a search link (in overview window), input in the
Piotr Gawron's avatar
Piotr Gawron committed
131
    left tab was not modified
132
  * Bug fix: in admin panel changing of genome version is blocking interface
Piotr Gawron's avatar
Piotr Gawron committed
133
    until data about url is retrieved
134
135
  * 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
136
137
  * Bug fix: export to SBGN did not export compartments
  * Bug fix: export of complex states to SBGN did not work
138
  * Bug fix: type of the data overlay can be defined in the file content
Piotr Gawron's avatar
Piotr Gawron committed
139
140
    (useful when uploading genetic variants)
  * Bug fix: CLEAR button clears comment checkbox if necessary
Piotr Gawron's avatar
Piotr Gawron committed
141
  * Bug fix: minerva install problem on ubuntu 16 fixed
Piotr Gawron's avatar
Piotr Gawron committed
142

Piotr Gawron's avatar
Piotr Gawron committed
143
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 11 Jan 2019 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
144

Sascha Herzinger's avatar
Sascha Herzinger committed
145
minerva (12.1.8) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
146
  * Bug fix: add a project reset users custom overlays limit to default (#679)
147
  * Bug fix: edit/remove project button was disabled based on Configuration
Piotr Gawron's avatar
Piotr Gawron committed
148
    Manage Privilege, but should be based on Project Manage Privilege (#681)
149
  * Bug fix: another minor problem with updating privileges introduced in
Piotr Gawron's avatar
Piotr Gawron committed
150
    12.1.6 fixed (#659)
Sascha Herzinger's avatar
Sascha Herzinger committed
151

Piotr Gawron's avatar
Piotr Gawron committed
152
153
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 8 Feb 2019 15:30:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
154
155
156
157
158
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
159
160
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
161
162
  * Bug fix: plugin API had sometimes problems with fetching reactions
    properly
Piotr Gawron's avatar
Piotr Gawron committed
163
164
  * 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
165
166
  * 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
167
  * Bug fix: fetching some drugs via API could cause 500
Piotr Gawron's avatar
Piotr Gawron committed
168

Piotr Gawron's avatar
Piotr Gawron committed
169
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Jan 2019 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
170

Piotr Gawron's avatar
Piotr Gawron committed
171
172
173
174
175
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
176
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 10 Jan 2019 14:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
177

178
minerva (12.1.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
179
  * Bug fix: no check for limit on custom data overlays fixed
180
  * Bug fix: error message improved when there is privilege problem during
Piotr Gawron's avatar
Piotr Gawron committed
181
    data overlay upload
Piotr Gawron's avatar
Piotr Gawron committed
182
  * Bug fix: upload of data overlay from admin panel didn't work
183
  * Bug fix: add project button is disabled when user doesn't have proper
Piotr Gawron's avatar
Piotr Gawron committed
184
    privileges ("Add project" privilege)
185
  * Bug fix: there are no more extra markers due to map wrapping
186
187
  * Bug fix: upload of the project failed when another project was removed
    during upload
Piotr Gawron's avatar
Piotr Gawron committed
188
  * Bug fix:  word wrapping fixed in overlay table for long overlay names
189
190
191

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

Piotr Gawron's avatar
Piotr Gawron committed
192
193
194
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
195
196
197
198
  * 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
199
200
201

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

Piotr Gawron's avatar
Piotr Gawron committed
202
203
204
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
205
  * Bug fix: integer configurtion options (like SMTP_PORT) are properly
Piotr Gawron's avatar
Piotr Gawron committed
206
207
    validated before saving
  * Bug fix: inside of reaction box wasn't properly aligned
Piotr Gawron's avatar
Piotr Gawron committed
208
  * Bug fix: too long data overlay name disturbed size of the map div and
Piotr Gawron's avatar
Piotr Gawron committed
209
210
211
212
213
    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
214
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Dec 2018 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
215

Piotr Gawron's avatar
Piotr Gawron committed
216
minerva (12.1.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
217
218
219
220
221
222
223
224
225
  * 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
226
minerva (12.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
227
228
229
230
  * 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
231
  * Small improvement: option to remove additional overlays generated by custom
Piotr Gawron's avatar
Piotr Gawron committed
232
    semantic zoom
233
  * Small improvement: 'Reduced modulation' edge was displayed differently in
Piotr Gawron's avatar
Piotr Gawron committed
234
235
236
    CellDesigner and Minerva
  * Small improvement: user-friendly documentation for plugin URL field
  * Small improvement: plugins have to access information about active submap
237
238
239
240
  * 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
241
  * Feature: minerva is distributed using rpm packages
242
  * Small improvement: annotations from RHEA are handled
Piotr Gawron's avatar
Piotr Gawron committed
243
244
  * Small improvement: changing of Terms of Service url allows admin to reset
    the status of ToS acceptance for all users
245
246
  * 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
247
248
249
250
251
252
253
254
  * 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
255
  * Bug fix: when there is a problem with adjusting font in complexes (because
Piotr Gawron's avatar
Piotr Gawron committed
256
257
258
259
260
    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
261
  * Bug fix: double click on user add button disabled
Piotr Gawron's avatar
Piotr Gawron committed
262
263
  * Bug fix: privileges are mirrored correctly across different popups
  * Bug fix: plugin tab css fixed
264
  * Bug fix: uploading sbml file with no ids in glyphs returned error that
Piotr Gawron's avatar
Piotr Gawron committed
265
266
267
    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
268

Piotr Gawron's avatar
Piotr Gawron committed
269
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Oct 2018 13:00:00 +0200
270

Piotr Gawron's avatar
Piotr Gawron committed
271
minerva (12.0.4) stable; urgency=medium
272
  * Bug fix: CellDesigner modifications that are drawn as reaction are handled
Piotr Gawron's avatar
Piotr Gawron committed
273
274
275
    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
276
  * Bug fix: Tair database moved to https
277
  * Bug fix: Taxnomy database changed html output that resulted in problems
Piotr Gawron's avatar
Piotr Gawron committed
278
    with resolving species name to the id
279

Piotr Gawron's avatar
Piotr Gawron committed
280
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Sep 2018 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
281

Piotr Gawron's avatar
Piotr Gawron committed
282
283
284
285
286
287
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
288

Piotr Gawron's avatar
Piotr Gawron committed
289
290
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Aug 2018 11:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
291
292
293
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
294
    works properly
Piotr Gawron's avatar
Piotr Gawron committed
295
296
297
298
  * 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
299
  * Performance: tomcat inside docker image by default can use 3G of memory
Piotr Gawron's avatar
Piotr Gawron committed
300

301
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 31 Jul 2018 13:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
302

Piotr Gawron's avatar
Piotr Gawron committed
303
304
305
306
307
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
308
  * Bug fix: opening map could crash when CellDesigner file contained duplicate
Piotr Gawron's avatar
Piotr Gawron committed
309
    reaction id
Piotr Gawron's avatar
Piotr Gawron committed
310
311
  * Bug fix: map is repositioned when info window is outside of current view in
    OpenLayers library
312

313
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 24 Jul 2018 10:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
314

Piotr Gawron's avatar
Piotr Gawron committed
315
316
minerva (12.0.0) stable; urgency=medium
  * Feature: There is alternative OpenLayers map engine available
Piotr Gawron's avatar
Piotr Gawron committed
317
  * Feature: database connection configuration (login, password, host, etc)
Piotr Gawron's avatar
Piotr Gawron committed
318
    can be modified using /etc/minerva/db.properties file
319
  * Feature: searching for elements in submap gives marker on top map
Piotr Gawron's avatar
Piotr Gawron committed
320
321
    indicating the submap connection
  * Feature: similar search results are merged
Piotr Gawron's avatar
Piotr Gawron committed
322
  * Feature: visualization of protein structures by MolArt
Piotr Gawron's avatar
Piotr Gawron committed
323
  * Feature: reordering of data overlays is supported
324
  * Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA  annotators
Piotr Gawron's avatar
Piotr Gawron committed
325
326
327
328
329
330
331
  * 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
332
333
  * 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
334
335
336
337
338
339
340
341
342
343
  * 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
344
345
  * 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
346
347
348
  * 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
349
350
  * Small improvement: Data overlays can use source element identifiers for
    filtering
Piotr Gawron's avatar
Piotr Gawron committed
351
352
353
  * 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
354
  * Small improvement: auto complete functionality for drugs, mirnas and
Piotr Gawron's avatar
Piotr Gawron committed
355
    chemicals
Piotr Gawron's avatar
Piotr Gawron committed
356
  * Small improvement: columns value and type are not mutually exclusive in
Piotr Gawron's avatar
Piotr Gawron committed
357
358
359
360
    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
361
  * Small improvement: data overlays color scale contains configurable default
Piotr Gawron's avatar
Piotr Gawron committed
362
363
    middle color (for 0 values)
  * Small improvement: opening data overlay switch to empty background
Piotr Gawron's avatar
Piotr Gawron committed
364
365
366
367
368
369
370
371
372
373
374
375
376
  * 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
377
  * Bug fix: uploading of zip files created by mac doesn't crash due to
Piotr Gawron's avatar
Piotr Gawron committed
378
379
    .DS_Store folder
  * Bug fix: auto complete is case insensitive
Piotr Gawron's avatar
Piotr Gawron committed
380
  * Bug fix: google maps API 404 errors for non existing tiles are removed
Piotr Gawron's avatar
Piotr Gawron committed
381

Piotr Gawron's avatar
Piotr Gawron committed
382
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Jul 2018 12:00:00 +0200
383

384
385
386
387
388
389
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
390
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 23 Jul 2018 12:00:00 +0200
391

Piotr Gawron's avatar
Piotr Gawron committed
392
minerva (11.1.2) stable; urgency=medium
393
394
  * 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
395
396
397
398
  * 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
399
400
401
402
403
404
405
406
407
408
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
409
410
411
minerva (11.1.0) stable; urgency=high
  * User can provide Google Maps API key that must be registered in google
    cloud account
412
413
  * User data overlays must be Google Maps API terms of use compliant
  * Terms of Use added
414

415
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 05 Jun 2018 9:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
416
  
417
418
minerva (11.0.10) stable; urgency=medium
  * Bug fix: link from overview image to search result was broken
419

420
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Apr 2018 15:00:00 +0200
421

Piotr Gawron's avatar
Piotr Gawron committed
422
423
424
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
425

Piotr Gawron's avatar
Piotr Gawron committed
426
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
427

Piotr Gawron's avatar
Piotr Gawron committed
428
429
430
431
432
433
434
435
436
437
438
439
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
440
  * Bug fix: comments on submaps are visualized properly
Piotr Gawron's avatar
Piotr Gawron committed
441

Piotr Gawron's avatar
Piotr Gawron committed
442
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 05 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
443

Piotr Gawron's avatar
Piotr Gawron committed
444
445
446
447
448
449
450
451
452
453
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

454
minerva (11.0.6) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
455
456
  * Bug fix: fix a bug when entering invalid mirna id

457
458
459
 -- 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
460
  * Bug fix: fix on connection to drugbank database
461
462
  * Bug fix: posttranslational modification data was sometimes unavailable
    in search results panel
Piotr Gawron's avatar
Piotr Gawron committed
463

464
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 30 Nov 2017 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
465

466
minerva (11.0.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
467
  * Bug fix: fix on connection to taxonomy database
468
469
  * 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
470

471
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 09 Nov 2017 14:50:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
472

473
minerva (11.0.3) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
474
  * Bug fix: removing empty project removed images from all projects
475
476
477
478
479
480
481
482
483
  * 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
484
  * Bug fix: login issues when default page is in secure area
485
486
487
488

 -- 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
489
  * Bug fix: logout caused issues with session data
490
491
492
493
494

 -- 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
495
496
  * Bug fix: security issue - access to specific map can be restricted
    by the user login
497
498
  * Bug fix: sbgn import
  * Bug fix: mesh connector
Piotr Gawron's avatar
Piotr Gawron committed
499
  * Rest API (documentation can be found here:
500
501
    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
502
    corner (when Search tab is not open)
503
504
  * 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
505
506
    proper text box
  * Layout changes: the main one is that there are only 3 tab panels
507
508
509
510
511
512
513
514
515
    (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
516
517
  * Overlay presents description field if possible

518
519

 -- Piotr Gawron <piotr.gawron@uni.lu>  Sat, 04 Mar 2017 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
520

521
522
523
524
525
526
527
528
529
530
531
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
532
  * Bug fix: search for multiple drugs will not return more drugs than
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
    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
550
551
  * Bug fix: trigger reaction and physical stimulation reactions are no
    longer allowed (CellDesigner data model issue)
552
553
554
555
556
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
  * 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
591
592
593
594
595
596
  * 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
597
598
599
600
601

 -- 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
602
603
604
605
606
  * Searching by annotations
  * Errors from parsing data forwarded to client
  * Notification email system added
  * Warnings are downloadable
  * Complex map (composed from many small maps)
607
  * Visualization of Recon specific annotations
Piotr Gawron's avatar
Piotr Gawron committed
608
609
610
611
612
613
614
  * Versioning system
  * Galaxy connector
  * Miriam types report
  * Advanced annotation options
  * Uniprot annotation module
  * Customized validation of miriam annotations
  * Recon annotation service
615
  * Bug fix: Data autofill problem in user management
Piotr Gawron's avatar
Piotr Gawron committed
616
617
  * Bug fix: User privileges for adding project
  * Bug fix: Problem with some miriam entries in RDF format
618
  * Bug fix: Reporting of drawing problems
Piotr Gawron's avatar
Piotr Gawron committed
619
620
  * Bug fix: Visualization of posttranslationa modification
  * Bug fix: Drugbank problem after update of Drugbank interface
621
  * Bug fix: Session scope fixed (browsing many maps at the same time)
Piotr Gawron's avatar
Piotr Gawron committed
622
623
624
625
626
  * 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
627
628

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 21 Jul 2015 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
629

630
631
minerva (5) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
632
  * Additional checkboxes in upload model: annotate automatically, cache data, verify annotations
633
  * Popup window in admin panel that list warnings
Piotr Gawron's avatar
Piotr Gawron committed
634
635
  * Information about build
  * Parsing and annotation warnings for models in admin panel
636
  * Custom reaction visualization in upload overlay
Piotr Gawron's avatar
Piotr Gawron committed
637
638
639
640
641
  * 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
642
643

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 18 Dec 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
644

645
646
647
minerva (4) stable; urgency=low

  * Export of the part of the map into CellDesigner file
Piotr Gawron's avatar
Piotr Gawron committed
648
649
  * Logo files managable via config webpage
  * Import data from GO
650
651
652
  * 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
653
654
655
656
657
  * 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
658
659

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 11 Sep 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
660

661
662
663
minerva (3) stable; urgency=low

  * Drug targeting interface
Piotr Gawron's avatar
Piotr Gawron committed
664
665
666
  * Export to CellDesigner
  * Status page of all dependent services
  * Configuration page
667
668

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 5 Jun 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
669

670
671
672
minerva (2) stable; urgency=low

  * Upload of the CellDesigner map
Piotr Gawron's avatar
Piotr Gawron committed
673
674
  * Bug fix: Problem with touch interface after update of browsers engine
  * Bug fix: Problem in Safari when searching for elements
675
676

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 2 Apr 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
677

678
679
minerva (1) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
680
  * Initial release
681
682

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 4 Dec 2013 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
683