CHANGELOG 33.1 KB
Newer Older
1
minerva (12.3.0~alpha.0) unstable; urgency=low
2
3
  * Feature: annotators are more flexible - you can define set of input and 
    outputs used by annotator (#617)
Piotr Gawron's avatar
Piotr Gawron committed
4
5
  * Small improvement: validation of the organism and disease id on map upload
    added (#618)
6
7
8
9
  * Small improvement: added current username next to logout button in admin 
    panel (#660)
  * Small improvement: New comment dialog does not contain content of previous 
    comment dialog (#680)
Piotr Gawron's avatar
Piotr Gawron committed
10
  * Small improvement: Left logo is configurable (#731)
11
12
  * Small improvement: Plugin API provides list of overview images (#702)
  * Small improvement: Plugin API allows to show/hide overview images (#702)
13
  * Small improvement: Plugin API allows to trigger search on the map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
14
  * Small improvement: Plugin API allows to clear search results on map (#702)
15
16
  * Small improvement: edit/remove project button is disabled until project is 
    uploaded (#683)
17
18
  * Small improvement: warning about capslock is visible on login page when 
    necessary (#658)
Piotr Gawron's avatar
Piotr Gawron committed
19
20
  * Small improvement: names of columns in data overlay are unified: no 
    whitespace, "_" used as separator (#596)
21
22
  * Small improvement: list of references in drug panel contains PUBMED prefix
    (#666)
Piotr Gawron's avatar
Piotr Gawron committed
23
24
  * Small improvement: passwords to email account and ldap are not sent over 
    API (#732)
Piotr Gawron's avatar
Piotr Gawron committed
25
26
  * Small improvement: reactant/product/modifier specific colors are parsed 
    properly from CellDesigner file (#597)
27
28
  * Bug fix: progress bar of gene genome mapping upload is refreshing properly 
    (#728)
Piotr Gawron's avatar
Piotr Gawron committed
29
30
  * Bug fix: when editing project Disease and Organism could not be removed 
    (#616)
31
32
  * Bug fix: dashed line partially wasn't dashed in "Unknown Catalysis" and 
    "Unknown Inhibition" reactions (#664) 
33

Piotr Gawron's avatar
Piotr Gawron committed
34
minerva (12.2.0~beta.2) unstable; urgency=medium
35
  * Bug fix: order of the overlays is defined explicitly also for general
Piotr Gawron's avatar
Piotr Gawron committed
36
    overlays (#684)
Piotr Gawron's avatar
Piotr Gawron committed
37
  * Bug fix: files are saved in proper folder (#694, #670)
38
39
  * Bug fix: removing comments in a project asked for confirmation twice after
    edit project dialog for specific project was opened; closed and opened
40
    again (#697)
41
  * Bug fix: clicking on compartment border inside pathway should return
42
    compartment, not a pathway (#324)
43
  * Bug fix: clicking outside of the element sometimes resulted with the
44
    invalid element highlighted  (#324)
45
  * Bug fix: parent compartment/pathway use proper type name in left panel
46
    (#324)
47
  * Bug fix: editing/removing project requires Map Management privilege (#681)
48
  * Bug fix: when removeAllListeners is called list of registered listeners is
49
    cleaned (#687)
50
  * Bug fix: when plugin is removed the html elements associated with it are
51
    removed as well (#686)
Piotr Gawron's avatar
Piotr Gawron committed
52
  * Bug fix: when creating new user default privileges are set properly (#692)
53
54
  * Bug fix: import from SBML issue - reaction with product and modifier being
    the same element caused exception (#703)
55
  * Bug fix: plugin can be added after plugin has been removed in admin plugin
56
    panel (#686)
57
  * Bug fix: too many annotations (>=100) caused misaligning in the left panel
58
    (#708)
Piotr Gawron's avatar
Piotr Gawron committed
59
  * Bug fix: text was outside the popup window (#711)
60
61
62
63
64
65
66
  * Bug fix: custom semantic zooming contains multiple overlays checkbox was
    disabled (#715)
  * Bug fix: export to svg contains viewBox info (#716)
  * Bug fix: import from sbml with layout could crash when two elements
    occupied the exact same position (#717)
  * Bug fix: overlays added via API couldn't be visualized after refresh (#718)
  * Bug fix: Safari sometimes cached server responses and used wrong data, for
Piotr Gawron's avatar
Piotr Gawron committed
67
    example in admin panel configuration tab (#719)
68
  * Bug fix: description of transcription site is centered (#720)
69
  * Bug fix: selecting too few parameters in export doesn't throw reportable
70
    error (#721)
Piotr Gawron's avatar
Piotr Gawron committed
71
  * Bug fix: changes in selected checkbox in add project dialog block UI (#722)
Piotr Gawron's avatar
Piotr Gawron committed
72
  * Bug fix: providing invalid overlay id in url could break minerva (#726)
Piotr Gawron's avatar
Piotr Gawron committed
73
  * Bug fix: removing project that doesn't exist doesn't cause 500 error (#723)
74
  * Bug fix: Editing project with images and submaps could cause a problem
Piotr Gawron's avatar
Piotr Gawron committed
75
    (#725)
Piotr Gawron's avatar
Piotr Gawron committed
76
  * Bug fix: opening map with invalid id shows proper error message (#724)
Piotr Gawron's avatar
Piotr Gawron committed
77
78
  * Bug fix: Fixing an issue where search panel was not properly resized on
    expansion (#682)
Piotr Gawron's avatar
Piotr Gawron committed
79
80
  * Small improvement: highlighting table rows in admin panel uses better
    contrast color (#706)
Piotr Gawron's avatar
Piotr Gawron committed
81
82
83

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

Piotr Gawron's avatar
typo    
Piotr Gawron committed
84
minerva (12.2.0~beta.1) unstable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
85
  * Small improvement: list of publication can be filtered by submap (#614)
86
  * Small improvement: report bug utility shows confirmation dialog on success
Piotr Gawron's avatar
Piotr Gawron committed
87
88
    (#648)
  * Small improvement: size of add overlay window adjusted to show more data
89
90
    without scrollbars (#657)
  * Small improvement: all popup dialogs in the app have dialog specific css
Piotr Gawron's avatar
Piotr Gawron committed
91
92
    class names (#665)
  * Bug fix: loading icon is not overlapping input in the search panel (#404)
93
  * Bug fix: position of transcription sites in genes are computed properly
Piotr Gawron's avatar
Piotr Gawron committed
94
    (#553)
95
  * Bug fix: REQUEST AN ACCOUNT was enabled when associated email was invalid
Piotr Gawron's avatar
Piotr Gawron committed
96
    (#626)
97
  * Bug fix: layout exported to SBML can be properly visualized by COPASI
Piotr Gawron's avatar
Piotr Gawron committed
98
    (#654)
99
  * Bug fix: working with too many maps within the single session could crash
Piotr Gawron's avatar
Piotr Gawron committed
100
    connection to server (#651)
101
  * Bug fix: invalid pubmed id could crash listing/downloading publications
Piotr Gawron's avatar
Piotr Gawron committed
102
103
    (#656)
  * Bug fix: icons in safari sometimes disappear (#661)
104
  * Bug fix: downloading reference genome for the second time resulted in an
Piotr Gawron's avatar
Piotr Gawron committed
105
    error (#670)
106
  * Bug fix: plugin validation in admin panel improved to catch more problems
Piotr Gawron's avatar
Piotr Gawron committed
107
    (#672)
108
  * Bug fix: drawing corrupted heterodimer association in CellDesigner could
Piotr Gawron's avatar
Piotr Gawron committed
109
    crash map upload (#673)
110
  * Bug fix: custom semantic zooming didn't work with pathways imported from
Piotr Gawron's avatar
Piotr Gawron committed
111
112
113
114
    CellDesigner layers (#678)

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

Piotr Gawron's avatar
Piotr Gawron committed
115
116
minerva (12.2.0~beta.0) unstable; urgency=medium
  * Feature: bug report utility
117
  * Small improvement: JS plugin can create listener that is triggered on
Piotr Gawron's avatar
Piotr Gawron committed
118
119
    search results focus change

Piotr Gawron's avatar
Piotr Gawron committed
120
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 23 Jan 2019 15:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
121

Piotr Gawron's avatar
Piotr Gawron committed
122
123
124
125
126
127
128
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
129
130
  * Feature: url GET parameters support all kind of search and selected overlays
    highlight
131
  * Feature: user can create custom logging configuration in file
Piotr Gawron's avatar
Piotr Gawron committed
132
133
134
135
    /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
136
  * Feature: API tool providing possibility to transform different types of
Piotr Gawron's avatar
Piotr Gawron committed
137
    file formats
138
  * Feature: current state of the browsed map is reflected in the url (position,
Piotr Gawron's avatar
Piotr Gawron committed
139
140
141
    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
142
  * Small improvement: genetics information allows to provide information about
Piotr Gawron's avatar
Piotr Gawron committed
143
    modification on peptide level that could be visualized in MolArt
144
  * Small improvement: allow to control the background and font color of areas
Piotr Gawron's avatar
Piotr Gawron committed
145
    drawn from text areas in CellDesigner "layers"
146
  * Small improvement: config logo location is relative to the root minerva
Piotr Gawron's avatar
Piotr Gawron committed
147
148
    deployment directory
  * Small improvement: there is branding minerva logo in the left panel
149
150
151
152
153
154
155
156
157
158
159
160
  * 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
161
162
  * Small improvement: there is max size of the map in configuration panel that
    disables upload of too big files
163
  * Small improvement: hitting enter on login page logs in the user (no need to
Piotr Gawron's avatar
Piotr Gawron committed
164
    click on the login button)
165
  * Small improvement: refresh button in overlays panel (useful when data
Piotr Gawron's avatar
Piotr Gawron committed
166
167
168
    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
169
  * Small improvement: 'BACK TO MAP' link is available only when guest account
Piotr Gawron's avatar
Piotr Gawron committed
170
171
    has proper access level
  * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
172
173
    email account is provided
  * Small improvement: Plugin API allows to show/hide data overlays
Piotr Gawron's avatar
Piotr Gawron committed
174
  * Bug fix: export to CellDesigner align inhibition reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
175
  * Bug fix: export/import to/from SBML handles Heterodimer Association
Piotr Gawron's avatar
Piotr Gawron committed
176
    reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
177
  * Bug fix: logo doesn't need to be square
178
  * Bug fix: when clicking on a search link (in overview window), input in the
Piotr Gawron's avatar
Piotr Gawron committed
179
    left tab was not modified
180
  * Bug fix: in admin panel changing of genome version is blocking interface
Piotr Gawron's avatar
Piotr Gawron committed
181
    until data about url is retrieved
182
183
  * 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
184
185
  * Bug fix: export to SBGN did not export compartments
  * Bug fix: export of complex states to SBGN did not work
186
  * Bug fix: type of the data overlay can be defined in the file content
Piotr Gawron's avatar
Piotr Gawron committed
187
188
    (useful when uploading genetic variants)
  * Bug fix: CLEAR button clears comment checkbox if necessary
Piotr Gawron's avatar
Piotr Gawron committed
189
  * Bug fix: minerva install problem on ubuntu 16 fixed
Piotr Gawron's avatar
Piotr Gawron committed
190

Piotr Gawron's avatar
Piotr Gawron committed
191
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 11 Jan 2019 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
192

Sascha Herzinger's avatar
Sascha Herzinger committed
193
minerva (12.1.8) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
194
  * Bug fix: add a project reset users custom overlays limit to default (#679)
195
  * Bug fix: edit/remove project button was disabled based on Configuration
Piotr Gawron's avatar
Piotr Gawron committed
196
    Manage Privilege, but should be based on Project Manage Privilege (#681)
197
  * Bug fix: another minor problem with updating privileges introduced in
Piotr Gawron's avatar
Piotr Gawron committed
198
    12.1.6 fixed (#659)
Sascha Herzinger's avatar
Sascha Herzinger committed
199

Piotr Gawron's avatar
Piotr Gawron committed
200
201
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 8 Feb 2019 15:30:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
202
203
204
205
206
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
207
208
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
209
210
  * Bug fix: plugin API had sometimes problems with fetching reactions
    properly
Piotr Gawron's avatar
Piotr Gawron committed
211
212
  * 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
213
214
  * 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
215
  * Bug fix: fetching some drugs via API could cause 500
Piotr Gawron's avatar
Piotr Gawron committed
216

Piotr Gawron's avatar
Piotr Gawron committed
217
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Jan 2019 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
218

Piotr Gawron's avatar
Piotr Gawron committed
219
220
221
222
223
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
224
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 10 Jan 2019 14:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
225

226
minerva (12.1.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
227
  * Bug fix: no check for limit on custom data overlays fixed
228
  * Bug fix: error message improved when there is privilege problem during
Piotr Gawron's avatar
Piotr Gawron committed
229
    data overlay upload
Piotr Gawron's avatar
Piotr Gawron committed
230
  * Bug fix: upload of data overlay from admin panel didn't work
231
  * Bug fix: add project button is disabled when user doesn't have proper
Piotr Gawron's avatar
Piotr Gawron committed
232
    privileges ("Add project" privilege)
233
  * Bug fix: there are no more extra markers due to map wrapping
234
235
  * Bug fix: upload of the project failed when another project was removed
    during upload
Piotr Gawron's avatar
Piotr Gawron committed
236
  * Bug fix:  word wrapping fixed in overlay table for long overlay names
237
238
239

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

Piotr Gawron's avatar
Piotr Gawron committed
240
241
242
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
243
244
245
246
  * 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
247
248
249

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

Piotr Gawron's avatar
Piotr Gawron committed
250
251
252
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
253
  * Bug fix: integer configurtion options (like SMTP_PORT) are properly
Piotr Gawron's avatar
Piotr Gawron committed
254
255
    validated before saving
  * Bug fix: inside of reaction box wasn't properly aligned
Piotr Gawron's avatar
Piotr Gawron committed
256
  * Bug fix: too long data overlay name disturbed size of the map div and
Piotr Gawron's avatar
Piotr Gawron committed
257
258
259
260
261
    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
262
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Dec 2018 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
263

Piotr Gawron's avatar
Piotr Gawron committed
264
minerva (12.1.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
265
266
267
268
269
270
271
272
273
  * 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
274
minerva (12.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
275
276
277
278
  * 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
279
  * Small improvement: option to remove additional overlays generated by custom
Piotr Gawron's avatar
Piotr Gawron committed
280
    semantic zoom
281
  * Small improvement: 'Reduced modulation' edge was displayed differently in
Piotr Gawron's avatar
Piotr Gawron committed
282
283
284
    CellDesigner and Minerva
  * Small improvement: user-friendly documentation for plugin URL field
  * Small improvement: plugins have to access information about active submap
285
286
287
288
  * 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
289
  * Feature: minerva is distributed using rpm packages
290
  * Small improvement: annotations from RHEA are handled
Piotr Gawron's avatar
Piotr Gawron committed
291
292
  * Small improvement: changing of Terms of Service url allows admin to reset
    the status of ToS acceptance for all users
293
294
  * 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
295
296
297
298
299
300
301
302
  * 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
303
  * Bug fix: when there is a problem with adjusting font in complexes (because
Piotr Gawron's avatar
Piotr Gawron committed
304
305
306
307
308
    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
309
  * Bug fix: double click on user add button disabled
Piotr Gawron's avatar
Piotr Gawron committed
310
311
  * Bug fix: privileges are mirrored correctly across different popups
  * Bug fix: plugin tab css fixed
312
  * Bug fix: uploading sbml file with no ids in glyphs returned error that
Piotr Gawron's avatar
Piotr Gawron committed
313
314
315
    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
316

Piotr Gawron's avatar
Piotr Gawron committed
317
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Oct 2018 13:00:00 +0200
318

Piotr Gawron's avatar
Piotr Gawron committed
319
minerva (12.0.4) stable; urgency=medium
320
  * Bug fix: CellDesigner modifications that are drawn as reaction are handled
Piotr Gawron's avatar
Piotr Gawron committed
321
322
323
    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
324
  * Bug fix: Tair database moved to https
325
  * Bug fix: Taxnomy database changed html output that resulted in problems
Piotr Gawron's avatar
Piotr Gawron committed
326
    with resolving species name to the id
327

Piotr Gawron's avatar
Piotr Gawron committed
328
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Sep 2018 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
329

Piotr Gawron's avatar
Piotr Gawron committed
330
331
332
333
334
335
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
336

Piotr Gawron's avatar
Piotr Gawron committed
337
338
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Aug 2018 11:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
339
340
341
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
342
    works properly
Piotr Gawron's avatar
Piotr Gawron committed
343
344
345
346
  * 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
347
  * Performance: tomcat inside docker image by default can use 3G of memory
Piotr Gawron's avatar
Piotr Gawron committed
348

349
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 31 Jul 2018 13:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
350

Piotr Gawron's avatar
Piotr Gawron committed
351
352
353
354
355
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
356
  * Bug fix: opening map could crash when CellDesigner file contained duplicate
Piotr Gawron's avatar
Piotr Gawron committed
357
    reaction id
Piotr Gawron's avatar
Piotr Gawron committed
358
359
  * Bug fix: map is repositioned when info window is outside of current view in
    OpenLayers library
360

361
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 24 Jul 2018 10:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
362

Piotr Gawron's avatar
Piotr Gawron committed
363
364
minerva (12.0.0) stable; urgency=medium
  * Feature: There is alternative OpenLayers map engine available
Piotr Gawron's avatar
Piotr Gawron committed
365
  * Feature: database connection configuration (login, password, host, etc)
Piotr Gawron's avatar
Piotr Gawron committed
366
    can be modified using /etc/minerva/db.properties file
367
  * Feature: searching for elements in submap gives marker on top map
Piotr Gawron's avatar
Piotr Gawron committed
368
369
    indicating the submap connection
  * Feature: similar search results are merged
Piotr Gawron's avatar
Piotr Gawron committed
370
  * Feature: visualization of protein structures by MolArt
Piotr Gawron's avatar
Piotr Gawron committed
371
  * Feature: reordering of data overlays is supported
372
  * Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA  annotators
Piotr Gawron's avatar
Piotr Gawron committed
373
374
375
376
377
378
379
  * 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
380
381
  * 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
382
383
384
385
386
387
388
389
390
391
  * 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
392
393
  * 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
394
395
396
  * 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
397
398
  * Small improvement: Data overlays can use source element identifiers for
    filtering
Piotr Gawron's avatar
Piotr Gawron committed
399
400
401
  * 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
402
  * Small improvement: auto complete functionality for drugs, mirnas and
Piotr Gawron's avatar
Piotr Gawron committed
403
    chemicals
Piotr Gawron's avatar
Piotr Gawron committed
404
  * Small improvement: columns value and type are not mutually exclusive in
Piotr Gawron's avatar
Piotr Gawron committed
405
406
407
408
    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
409
  * Small improvement: data overlays color scale contains configurable default
Piotr Gawron's avatar
Piotr Gawron committed
410
411
    middle color (for 0 values)
  * Small improvement: opening data overlay switch to empty background
Piotr Gawron's avatar
Piotr Gawron committed
412
413
414
415
416
417
418
419
420
421
422
423
424
  * 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
425
  * Bug fix: uploading of zip files created by mac doesn't crash due to
Piotr Gawron's avatar
Piotr Gawron committed
426
427
    .DS_Store folder
  * Bug fix: auto complete is case insensitive
Piotr Gawron's avatar
Piotr Gawron committed
428
  * Bug fix: google maps API 404 errors for non existing tiles are removed
Piotr Gawron's avatar
Piotr Gawron committed
429

Piotr Gawron's avatar
Piotr Gawron committed
430
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Jul 2018 12:00:00 +0200
431

432
433
434
435
436
437
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
438
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 23 Jul 2018 12:00:00 +0200
439

Piotr Gawron's avatar
Piotr Gawron committed
440
minerva (11.1.2) stable; urgency=medium
441
442
  * 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
443
444
445
446
  * 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
447
448
449
450
451
452
453
454
455
456
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
457
458
459
minerva (11.1.0) stable; urgency=high
  * User can provide Google Maps API key that must be registered in google
    cloud account
460
461
  * User data overlays must be Google Maps API terms of use compliant
  * Terms of Use added
462

463
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 05 Jun 2018 9:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
464
  
465
466
minerva (11.0.10) stable; urgency=medium
  * Bug fix: link from overview image to search result was broken
467

468
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Apr 2018 15:00:00 +0200
469

Piotr Gawron's avatar
Piotr Gawron committed
470
471
472
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
473

Piotr Gawron's avatar
Piotr Gawron committed
474
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
475

Piotr Gawron's avatar
Piotr Gawron committed
476
477
478
479
480
481
482
483
484
485
486
487
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
488
  * Bug fix: comments on submaps are visualized properly
Piotr Gawron's avatar
Piotr Gawron committed
489

Piotr Gawron's avatar
Piotr Gawron committed
490
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 05 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
491

Piotr Gawron's avatar
Piotr Gawron committed
492
493
494
495
496
497
498
499
500
501
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

502
minerva (11.0.6) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
503
504
  * Bug fix: fix a bug when entering invalid mirna id

505
506
507
 -- 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
508
  * Bug fix: fix on connection to drugbank database
509
510
  * Bug fix: posttranslational modification data was sometimes unavailable
    in search results panel
Piotr Gawron's avatar
Piotr Gawron committed
511

512
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 30 Nov 2017 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
513

514
minerva (11.0.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
515
  * Bug fix: fix on connection to taxonomy database
516
517
  * 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
518

519
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 09 Nov 2017 14:50:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
520

521
minerva (11.0.3) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
522
  * Bug fix: removing empty project removed images from all projects
523
524
525
526
527
528
529
530
531
  * 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
532
  * Bug fix: login issues when default page is in secure area
533
534
535
536

 -- 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
537
  * Bug fix: logout caused issues with session data
538
539
540
541
542

 -- 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
543
544
  * Bug fix: security issue - access to specific map can be restricted
    by the user login
545
546
  * Bug fix: sbgn import
  * Bug fix: mesh connector
Piotr Gawron's avatar
Piotr Gawron committed
547
  * Rest API (documentation can be found here:
548
549
    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
550
    corner (when Search tab is not open)
551
552
  * 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
553
554
    proper text box
  * Layout changes: the main one is that there are only 3 tab panels
555
556
557
558
559
560
561
562
563
    (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
564
565
  * Overlay presents description field if possible

566
567

 -- Piotr Gawron <piotr.gawron@uni.lu>  Sat, 04 Mar 2017 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
568

569
570
571
572
573
574
575
576
577
578
579
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
580
  * Bug fix: search for multiple drugs will not return more drugs than
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
    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
598
599
  * Bug fix: trigger reaction and physical stimulation reactions are no
    longer allowed (CellDesigner data model issue)
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
  * 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
639
640
641
642
643
644
  * 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
645
646
647
648
649

 -- 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
650
651
652
653
654
  * Searching by annotations
  * Errors from parsing data forwarded to client
  * Notification email system added
  * Warnings are downloadable
  * Complex map (composed from many small maps)
655
  * Visualization of Recon specific annotations
Piotr Gawron's avatar
Piotr Gawron committed
656
657
658
659
660
661
662
  * Versioning system
  * Galaxy connector
  * Miriam types report
  * Advanced annotation options
  * Uniprot annotation module
  * Customized validation of miriam annotations
  * Recon annotation service
663
  * Bug fix: Data autofill problem in user management
Piotr Gawron's avatar
Piotr Gawron committed
664
665
  * Bug fix: User privileges for adding project
  * Bug fix: Problem with some miriam entries in RDF format
666
  * Bug fix: Reporting of drawing problems
Piotr Gawron's avatar
Piotr Gawron committed
667
668
  * Bug fix: Visualization of posttranslationa modification
  * Bug fix: Drugbank problem after update of Drugbank interface
669
  * Bug fix: Session scope fixed (browsing many maps at the same time)
Piotr Gawron's avatar
Piotr Gawron committed
670
671
672
673
674
  * 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
675
676

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 21 Jul 2015 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
677

678
679
minerva (5) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
680
  * Additional checkboxes in upload model: annotate automatically, cache data, verify annotations
681
  * Popup window in admin panel that list warnings
Piotr Gawron's avatar
Piotr Gawron committed
682
683
  * Information about build
  * Parsing and annotation warnings for models in admin panel
684
  * Custom reaction visualization in upload overlay
Piotr Gawron's avatar
Piotr Gawron committed
685
686
687
688
689
  * 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
690
691

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 18 Dec 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
692

693
694
695
minerva (4) stable; urgency=low

  * Export of the part of the map into CellDesigner file
Piotr Gawron's avatar
Piotr Gawron committed
696
697
  * Logo files managable via config webpage
  * Import data from GO
698
699
700
  * 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
701
702
703
704
705
  * 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
706
707

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 11 Sep 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
708

709
710
711
minerva (3) stable; urgency=low

  * Drug targeting interface
Piotr Gawron's avatar
Piotr Gawron committed
712
713
714
  * Export to CellDesigner
  * Status page of all dependent services
  * Configuration page
715
716

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 5 Jun 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
717

718
719
720
minerva (2) stable; urgency=low

  * Upload of the CellDesigner map
Piotr Gawron's avatar
Piotr Gawron committed
721
722
  * Bug fix: Problem with touch interface after update of browsers engine
  * Bug fix: Problem in Safari when searching for elements
723
724

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 2 Apr 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
725

726
727
minerva (1) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
728
  * Initial release
729
730

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 4 Dec 2013 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
731