CHANGELOG 31.5 KB
Newer Older
Piotr Gawron's avatar
Piotr Gawron committed
1
minerva (12.2.0~beta.2) unstable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
2
3
  * Bug fix: order of the overlays is defined explicitly also for general 
    overlays (#684)
Piotr Gawron's avatar
Piotr Gawron committed
4
  * Bug fix: files are saved in proper folder (#694, #670)
5
6
7
  * Bug fix: removing comments in a project asked for confirmation twice after 
    edit project dialog for specific project was opened; closed and opened 
    again (#697)
8
9
  * Bug fix: clicking on compartment border inside pathway should return 
    compartment, not a pathway (#324)
10
11
  * Bug fix: clicking outside of the element sometimes resulted with the 
    invalid element highlighted  (#324)
12
  * Bug fix: parent compartment/pathway use proper type name in left panel 
13
    (#324)
14
  * Bug fix: editing/removing project requires Map Management privilege (#681)
15
16
  * Bug fix: when removeAllListeners is called list of registered listeners is 
    cleaned (#687)
17
18
  * Bug fix: when plugin is removed the html elements associated with it are 
    removed as well (#686)
Piotr Gawron's avatar
Piotr Gawron committed
19
  * Bug fix: when creating new user default privileges are set properly (#692)
20
21
  * Bug fix: import from SBML issue - reaction with product and modifier being
    the same element caused exception (#703)
22
23
  * Bug fix: plugin can be added after plugin has been removed in admin plugin 
    panel (#686)
24
25
  * Bug fix: too many annotations (>=100) caused misaligning in the left panel 
    (#708)
Piotr Gawron's avatar
Piotr Gawron committed
26
  * Bug fix: text was outside the popup window (#711)
27
28
  * Bug fix: custom semantic zooming contains multiple overlays checkbox was 
    disabled (#715) 
29
  * Bug fix: export to svg contains viewBox info (#716) 
30
31
  * Bug fix: import from sbml with layout could crash when two elements 
    occupied the exact same position (#717) 
32
  * Bug fix: overlays added via API couldn't be visualized after refresh (#718) 
Piotr Gawron's avatar
Piotr Gawron committed
33
34
  * Bug fix: Safari sometimes cached server responses and used wrong data, for 
    example in admin panel configuration tab (#719)
35
  * Bug fix: description of transcription site is centered (#720)
36
37
  * Bug fix: selecting too few parameters in export doesn't throw reportable 
    error (#721)
Piotr Gawron's avatar
Piotr Gawron committed
38
  * Bug fix: changes in selected checkbox in add project dialog block UI (#722)
Piotr Gawron's avatar
Piotr Gawron committed
39
  * Bug fix: providing invalid overlay id in url could break minerva (#726)
Piotr Gawron's avatar
Piotr Gawron committed
40
  * Bug fix: removing project that doesn't exist doesn't cause 500 error (#723)
Piotr Gawron's avatar
Piotr Gawron committed
41
42
  * Bug fix: Editing project with images and submaps could cause a problem 
    (#725)
Piotr Gawron's avatar
Piotr Gawron committed
43
  * Bug fix: opening map with invalid id shows proper error message (#724)
Piotr Gawron's avatar
Piotr Gawron committed
44
45
  * Bug fix: Fixing an issue where search panel was not properly resized on
    expansion (#682)
Piotr Gawron's avatar
Piotr Gawron committed
46
47
  * Small improvement: highlighting table rows in admin panel uses better
    contrast color (#706)
Piotr Gawron's avatar
Piotr Gawron committed
48
49
50

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

Piotr Gawron's avatar
typo    
Piotr Gawron committed
51
minerva (12.2.0~beta.1) unstable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
52
  * Small improvement: list of publication can be filtered by submap (#614)
53
  * Small improvement: report bug utility shows confirmation dialog on success
Piotr Gawron's avatar
Piotr Gawron committed
54
55
    (#648)
  * Small improvement: size of add overlay window adjusted to show more data
56
57
    without scrollbars (#657)
  * Small improvement: all popup dialogs in the app have dialog specific css
Piotr Gawron's avatar
Piotr Gawron committed
58
59
    class names (#665)
  * Bug fix: loading icon is not overlapping input in the search panel (#404)
60
  * Bug fix: position of transcription sites in genes are computed properly
Piotr Gawron's avatar
Piotr Gawron committed
61
    (#553)
62
  * Bug fix: REQUEST AN ACCOUNT was enabled when associated email was invalid
Piotr Gawron's avatar
Piotr Gawron committed
63
    (#626)
64
  * Bug fix: layout exported to SBML can be properly visualized by COPASI
Piotr Gawron's avatar
Piotr Gawron committed
65
    (#654)
66
  * Bug fix: working with too many maps within the single session could crash
Piotr Gawron's avatar
Piotr Gawron committed
67
    connection to server (#651)
68
  * Bug fix: invalid pubmed id could crash listing/downloading publications
Piotr Gawron's avatar
Piotr Gawron committed
69
70
    (#656)
  * Bug fix: icons in safari sometimes disappear (#661)
71
  * Bug fix: downloading reference genome for the second time resulted in an
Piotr Gawron's avatar
Piotr Gawron committed
72
    error (#670)
73
  * Bug fix: plugin validation in admin panel improved to catch more problems
Piotr Gawron's avatar
Piotr Gawron committed
74
    (#672)
75
  * Bug fix: drawing corrupted heterodimer association in CellDesigner could
Piotr Gawron's avatar
Piotr Gawron committed
76
    crash map upload (#673)
77
  * Bug fix: custom semantic zooming didn't work with pathways imported from
Piotr Gawron's avatar
Piotr Gawron committed
78
79
80
81
    CellDesigner layers (#678)

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

Piotr Gawron's avatar
Piotr Gawron committed
82
83
minerva (12.2.0~beta.0) unstable; urgency=medium
  * Feature: bug report utility
84
  * Small improvement: JS plugin can create listener that is triggered on
Piotr Gawron's avatar
Piotr Gawron committed
85
86
    search results focus change

Piotr Gawron's avatar
Piotr Gawron committed
87
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 23 Jan 2019 15:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
88

Piotr Gawron's avatar
Piotr Gawron committed
89
90
91
92
93
94
95
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
96
97
  * Feature: url GET parameters support all kind of search and selected overlays
    highlight
98
  * Feature: user can create custom logging configuration in file
Piotr Gawron's avatar
Piotr Gawron committed
99
100
101
102
    /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
103
  * Feature: API tool providing possibility to transform different types of
Piotr Gawron's avatar
Piotr Gawron committed
104
    file formats
105
  * Feature: current state of the browsed map is reflected in the url (position,
Piotr Gawron's avatar
Piotr Gawron committed
106
107
108
    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
109
  * Small improvement: genetics information allows to provide information about
Piotr Gawron's avatar
Piotr Gawron committed
110
    modification on peptide level that could be visualized in MolArt
111
  * Small improvement: allow to control the background and font color of areas
Piotr Gawron's avatar
Piotr Gawron committed
112
    drawn from text areas in CellDesigner "layers"
113
  * Small improvement: config logo location is relative to the root minerva
Piotr Gawron's avatar
Piotr Gawron committed
114
115
    deployment directory
  * Small improvement: there is branding minerva logo in the left panel
116
117
118
119
120
121
122
123
124
125
126
127
  * 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
128
129
  * Small improvement: there is max size of the map in configuration panel that
    disables upload of too big files
130
  * Small improvement: hitting enter on login page logs in the user (no need to
Piotr Gawron's avatar
Piotr Gawron committed
131
    click on the login button)
132
  * Small improvement: refresh button in overlays panel (useful when data
Piotr Gawron's avatar
Piotr Gawron committed
133
134
135
    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
136
  * Small improvement: 'BACK TO MAP' link is available only when guest account
Piotr Gawron's avatar
Piotr Gawron committed
137
138
    has proper access level
  * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
139
140
    email account is provided
  * Small improvement: Plugin API allows to show/hide data overlays
Piotr Gawron's avatar
Piotr Gawron committed
141
  * Bug fix: export to CellDesigner align inhibition reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
142
  * Bug fix: export/import to/from SBML handles Heterodimer Association
Piotr Gawron's avatar
Piotr Gawron committed
143
    reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
144
  * Bug fix: logo doesn't need to be square
145
  * Bug fix: when clicking on a search link (in overview window), input in the
Piotr Gawron's avatar
Piotr Gawron committed
146
    left tab was not modified
147
  * Bug fix: in admin panel changing of genome version is blocking interface
Piotr Gawron's avatar
Piotr Gawron committed
148
    until data about url is retrieved
149
150
  * 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
151
152
  * Bug fix: export to SBGN did not export compartments
  * Bug fix: export of complex states to SBGN did not work
153
  * Bug fix: type of the data overlay can be defined in the file content
Piotr Gawron's avatar
Piotr Gawron committed
154
155
    (useful when uploading genetic variants)
  * Bug fix: CLEAR button clears comment checkbox if necessary
Piotr Gawron's avatar
Piotr Gawron committed
156
  * Bug fix: minerva install problem on ubuntu 16 fixed
Piotr Gawron's avatar
Piotr Gawron committed
157

Piotr Gawron's avatar
Piotr Gawron committed
158
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 11 Jan 2019 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
159

Sascha Herzinger's avatar
Sascha Herzinger committed
160
minerva (12.1.8) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
161
  * Bug fix: add a project reset users custom overlays limit to default (#679)
162
  * Bug fix: edit/remove project button was disabled based on Configuration
Piotr Gawron's avatar
Piotr Gawron committed
163
    Manage Privilege, but should be based on Project Manage Privilege (#681)
164
  * Bug fix: another minor problem with updating privileges introduced in
Piotr Gawron's avatar
Piotr Gawron committed
165
    12.1.6 fixed (#659)
Sascha Herzinger's avatar
Sascha Herzinger committed
166

Piotr Gawron's avatar
Piotr Gawron committed
167
168
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 8 Feb 2019 15:30:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
169
170
171
172
173
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
174
175
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
176
177
  * Bug fix: plugin API had sometimes problems with fetching reactions
    properly
Piotr Gawron's avatar
Piotr Gawron committed
178
179
  * 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
180
181
  * 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
182
  * Bug fix: fetching some drugs via API could cause 500
Piotr Gawron's avatar
Piotr Gawron committed
183

Piotr Gawron's avatar
Piotr Gawron committed
184
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Jan 2019 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
185

Piotr Gawron's avatar
Piotr Gawron committed
186
187
188
189
190
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
191
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 10 Jan 2019 14:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
192

193
minerva (12.1.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
194
  * Bug fix: no check for limit on custom data overlays fixed
195
  * Bug fix: error message improved when there is privilege problem during
Piotr Gawron's avatar
Piotr Gawron committed
196
    data overlay upload
Piotr Gawron's avatar
Piotr Gawron committed
197
  * Bug fix: upload of data overlay from admin panel didn't work
198
  * Bug fix: add project button is disabled when user doesn't have proper
Piotr Gawron's avatar
Piotr Gawron committed
199
    privileges ("Add project" privilege)
200
  * Bug fix: there are no more extra markers due to map wrapping
201
202
  * Bug fix: upload of the project failed when another project was removed
    during upload
Piotr Gawron's avatar
Piotr Gawron committed
203
  * Bug fix:  word wrapping fixed in overlay table for long overlay names
204
205
206

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

Piotr Gawron's avatar
Piotr Gawron committed
207
208
209
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
210
211
212
213
  * 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
214
215
216

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

Piotr Gawron's avatar
Piotr Gawron committed
217
218
219
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
220
  * Bug fix: integer configurtion options (like SMTP_PORT) are properly
Piotr Gawron's avatar
Piotr Gawron committed
221
222
    validated before saving
  * Bug fix: inside of reaction box wasn't properly aligned
Piotr Gawron's avatar
Piotr Gawron committed
223
  * Bug fix: too long data overlay name disturbed size of the map div and
Piotr Gawron's avatar
Piotr Gawron committed
224
225
226
227
228
    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
229
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Dec 2018 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
230

Piotr Gawron's avatar
Piotr Gawron committed
231
minerva (12.1.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
232
233
234
235
236
237
238
239
240
  * 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
241
minerva (12.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
242
243
244
245
  * 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
246
  * Small improvement: option to remove additional overlays generated by custom
Piotr Gawron's avatar
Piotr Gawron committed
247
    semantic zoom
248
  * Small improvement: 'Reduced modulation' edge was displayed differently in
Piotr Gawron's avatar
Piotr Gawron committed
249
250
251
    CellDesigner and Minerva
  * Small improvement: user-friendly documentation for plugin URL field
  * Small improvement: plugins have to access information about active submap
252
253
254
255
  * 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
256
  * Feature: minerva is distributed using rpm packages
257
  * Small improvement: annotations from RHEA are handled
Piotr Gawron's avatar
Piotr Gawron committed
258
259
  * Small improvement: changing of Terms of Service url allows admin to reset
    the status of ToS acceptance for all users
260
261
  * 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
262
263
264
265
266
267
268
269
  * 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
270
  * Bug fix: when there is a problem with adjusting font in complexes (because
Piotr Gawron's avatar
Piotr Gawron committed
271
272
273
274
275
    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
276
  * Bug fix: double click on user add button disabled
Piotr Gawron's avatar
Piotr Gawron committed
277
278
  * Bug fix: privileges are mirrored correctly across different popups
  * Bug fix: plugin tab css fixed
279
  * Bug fix: uploading sbml file with no ids in glyphs returned error that
Piotr Gawron's avatar
Piotr Gawron committed
280
281
282
    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
283

Piotr Gawron's avatar
Piotr Gawron committed
284
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Oct 2018 13:00:00 +0200
285

Piotr Gawron's avatar
Piotr Gawron committed
286
minerva (12.0.4) stable; urgency=medium
287
  * Bug fix: CellDesigner modifications that are drawn as reaction are handled
Piotr Gawron's avatar
Piotr Gawron committed
288
289
290
    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
291
  * Bug fix: Tair database moved to https
292
  * Bug fix: Taxnomy database changed html output that resulted in problems
Piotr Gawron's avatar
Piotr Gawron committed
293
    with resolving species name to the id
294

Piotr Gawron's avatar
Piotr Gawron committed
295
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Sep 2018 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
296

Piotr Gawron's avatar
Piotr Gawron committed
297
298
299
300
301
302
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
303

Piotr Gawron's avatar
Piotr Gawron committed
304
305
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Aug 2018 11:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
306
307
308
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
309
    works properly
Piotr Gawron's avatar
Piotr Gawron committed
310
311
312
313
  * 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
314
  * Performance: tomcat inside docker image by default can use 3G of memory
Piotr Gawron's avatar
Piotr Gawron committed
315

316
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 31 Jul 2018 13:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
317

Piotr Gawron's avatar
Piotr Gawron committed
318
319
320
321
322
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
323
  * Bug fix: opening map could crash when CellDesigner file contained duplicate
Piotr Gawron's avatar
Piotr Gawron committed
324
    reaction id
Piotr Gawron's avatar
Piotr Gawron committed
325
326
  * Bug fix: map is repositioned when info window is outside of current view in
    OpenLayers library
327

328
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 24 Jul 2018 10:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
329

Piotr Gawron's avatar
Piotr Gawron committed
330
331
minerva (12.0.0) stable; urgency=medium
  * Feature: There is alternative OpenLayers map engine available
Piotr Gawron's avatar
Piotr Gawron committed
332
  * Feature: database connection configuration (login, password, host, etc)
Piotr Gawron's avatar
Piotr Gawron committed
333
    can be modified using /etc/minerva/db.properties file
334
  * Feature: searching for elements in submap gives marker on top map
Piotr Gawron's avatar
Piotr Gawron committed
335
336
    indicating the submap connection
  * Feature: similar search results are merged
Piotr Gawron's avatar
Piotr Gawron committed
337
  * Feature: visualization of protein structures by MolArt
Piotr Gawron's avatar
Piotr Gawron committed
338
  * Feature: reordering of data overlays is supported
339
  * Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA  annotators
Piotr Gawron's avatar
Piotr Gawron committed
340
341
342
343
344
345
346
  * 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
347
348
  * 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
349
350
351
352
353
354
355
356
357
358
  * 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
359
360
  * 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
361
362
363
  * 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
364
365
  * Small improvement: Data overlays can use source element identifiers for
    filtering
Piotr Gawron's avatar
Piotr Gawron committed
366
367
368
  * 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
369
  * Small improvement: auto complete functionality for drugs, mirnas and
Piotr Gawron's avatar
Piotr Gawron committed
370
    chemicals
Piotr Gawron's avatar
Piotr Gawron committed
371
  * Small improvement: columns value and type are not mutually exclusive in
Piotr Gawron's avatar
Piotr Gawron committed
372
373
374
375
    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
376
  * Small improvement: data overlays color scale contains configurable default
Piotr Gawron's avatar
Piotr Gawron committed
377
378
    middle color (for 0 values)
  * Small improvement: opening data overlay switch to empty background
Piotr Gawron's avatar
Piotr Gawron committed
379
380
381
382
383
384
385
386
387
388
389
390
391
  * 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
392
  * Bug fix: uploading of zip files created by mac doesn't crash due to
Piotr Gawron's avatar
Piotr Gawron committed
393
394
    .DS_Store folder
  * Bug fix: auto complete is case insensitive
Piotr Gawron's avatar
Piotr Gawron committed
395
  * Bug fix: google maps API 404 errors for non existing tiles are removed
Piotr Gawron's avatar
Piotr Gawron committed
396

Piotr Gawron's avatar
Piotr Gawron committed
397
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Jul 2018 12:00:00 +0200
398

399
400
401
402
403
404
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
405
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 23 Jul 2018 12:00:00 +0200
406

Piotr Gawron's avatar
Piotr Gawron committed
407
minerva (11.1.2) stable; urgency=medium
408
409
  * 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
410
411
412
413
  * 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
414
415
416
417
418
419
420
421
422
423
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
424
425
426
minerva (11.1.0) stable; urgency=high
  * User can provide Google Maps API key that must be registered in google
    cloud account
427
428
  * User data overlays must be Google Maps API terms of use compliant
  * Terms of Use added
429

430
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 05 Jun 2018 9:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
431
  
432
433
minerva (11.0.10) stable; urgency=medium
  * Bug fix: link from overview image to search result was broken
434

435
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Apr 2018 15:00:00 +0200
436

Piotr Gawron's avatar
Piotr Gawron committed
437
438
439
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
440

Piotr Gawron's avatar
Piotr Gawron committed
441
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
442

Piotr Gawron's avatar
Piotr Gawron committed
443
444
445
446
447
448
449
450
451
452
453
454
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
455
  * Bug fix: comments on submaps are visualized properly
Piotr Gawron's avatar
Piotr Gawron committed
456

Piotr Gawron's avatar
Piotr Gawron committed
457
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 05 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
458

Piotr Gawron's avatar
Piotr Gawron committed
459
460
461
462
463
464
465
466
467
468
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

469
minerva (11.0.6) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
470
471
  * Bug fix: fix a bug when entering invalid mirna id

472
473
474
 -- 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
475
  * Bug fix: fix on connection to drugbank database
476
477
  * Bug fix: posttranslational modification data was sometimes unavailable
    in search results panel
Piotr Gawron's avatar
Piotr Gawron committed
478

479
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 30 Nov 2017 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
480

481
minerva (11.0.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
482
  * Bug fix: fix on connection to taxonomy database
483
484
  * 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
485

486
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 09 Nov 2017 14:50:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
487

488
minerva (11.0.3) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
489
  * Bug fix: removing empty project removed images from all projects
490
491
492
493
494
495
496
497
498
  * 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
499
  * Bug fix: login issues when default page is in secure area
500
501
502
503

 -- 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
504
  * Bug fix: logout caused issues with session data
505
506
507
508
509

 -- 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
510
511
  * Bug fix: security issue - access to specific map can be restricted
    by the user login
512
513
  * Bug fix: sbgn import
  * Bug fix: mesh connector
Piotr Gawron's avatar
Piotr Gawron committed
514
  * Rest API (documentation can be found here:
515
516
    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
517
    corner (when Search tab is not open)
518
519
  * 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
520
521
    proper text box
  * Layout changes: the main one is that there are only 3 tab panels
522
523
524
525
526
527
528
529
530
    (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
531
532
  * Overlay presents description field if possible

533
534

 -- Piotr Gawron <piotr.gawron@uni.lu>  Sat, 04 Mar 2017 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
535

536
537
538
539
540
541
542
543
544
545
546
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
547
  * Bug fix: search for multiple drugs will not return more drugs than
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
    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
565
566
  * Bug fix: trigger reaction and physical stimulation reactions are no
    longer allowed (CellDesigner data model issue)
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
596
597
598
599
600
601
602
603
604
605
  * 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
606
607
608
609
610
611
  * 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
612
613
614
615
616

 -- 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
617
618
619
620
621
  * Searching by annotations
  * Errors from parsing data forwarded to client
  * Notification email system added
  * Warnings are downloadable
  * Complex map (composed from many small maps)
622
  * Visualization of Recon specific annotations
Piotr Gawron's avatar
Piotr Gawron committed
623
624
625
626
627
628
629
  * Versioning system
  * Galaxy connector
  * Miriam types report
  * Advanced annotation options
  * Uniprot annotation module
  * Customized validation of miriam annotations
  * Recon annotation service
630
  * Bug fix: Data autofill problem in user management
Piotr Gawron's avatar
Piotr Gawron committed
631
632
  * Bug fix: User privileges for adding project
  * Bug fix: Problem with some miriam entries in RDF format
633
  * Bug fix: Reporting of drawing problems
Piotr Gawron's avatar
Piotr Gawron committed
634
635
  * Bug fix: Visualization of posttranslationa modification
  * Bug fix: Drugbank problem after update of Drugbank interface
636
  * Bug fix: Session scope fixed (browsing many maps at the same time)
Piotr Gawron's avatar
Piotr Gawron committed
637
638
639
640
641
  * 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
642
643

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 21 Jul 2015 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
644

645
646
minerva (5) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
647
  * Additional checkboxes in upload model: annotate automatically, cache data, verify annotations
648
  * Popup window in admin panel that list warnings
Piotr Gawron's avatar
Piotr Gawron committed
649
650
  * Information about build
  * Parsing and annotation warnings for models in admin panel
651
  * Custom reaction visualization in upload overlay
Piotr Gawron's avatar
Piotr Gawron committed
652
653
654
655
656
  * 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
657
658

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 18 Dec 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
659

660
661
662
minerva (4) stable; urgency=low

  * Export of the part of the map into CellDesigner file
Piotr Gawron's avatar
Piotr Gawron committed
663
664
  * Logo files managable via config webpage
  * Import data from GO
665
666
667
  * 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
668
669
670
671
672
  * 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
673
674

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 11 Sep 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
675

676
677
678
minerva (3) stable; urgency=low

  * Drug targeting interface
Piotr Gawron's avatar
Piotr Gawron committed
679
680
681
  * Export to CellDesigner
  * Status page of all dependent services
  * Configuration page
682
683

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 5 Jun 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
684

685
686
687
minerva (2) stable; urgency=low

  * Upload of the CellDesigner map
Piotr Gawron's avatar
Piotr Gawron committed
688
689
  * Bug fix: Problem with touch interface after update of browsers engine
  * Bug fix: Problem in Safari when searching for elements
690
691

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 2 Apr 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
692

693
694
minerva (1) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
695
  * Initial release
696
697

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 4 Dec 2013 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
698