CHANGELOG 41.6 KB
Newer Older
1
2
3
4
5
6
minerva (14.0.0~alpha.1) unstable; urgency=low
  * Small improvement: debian package can be installed on debian:buster (#879)
  * Feature removal: support for tomcat7 removed (#828)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 12 Aug 2019 10:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
7
minerva (14.0.0~alpha.0) unstable; urgency=low
8
  * Feature: security layer redesigned - privilege types and scope changed 
Piotr Gawron's avatar
Piotr Gawron committed
9
    (#636, #624)
Piotr Gawron's avatar
Piotr Gawron committed
10
  * Feature: log4j is replaced with log4j2 logging mechanism (#291)
11
  * Feature: database installed via debian package is done via dbconfig-commons
Piotr Gawron's avatar
Piotr Gawron committed
12
    (#469)
13
  * Feature: Replaced connection pool manager C3P0 with better maintained
14
15
    Hikari - restart of postgresql database doesn't require restart of tomcat 
    (#564)
Piotr Gawron's avatar
Piotr Gawron committed
16
  * Feature removal: BioCompendium annotator removed (#32)
Piotr Gawron's avatar
Piotr Gawron committed
17
18
19
  * Small improvement: anonymous login is no longer required - each API query 
    outside session is authorized with anonymous user privileges (#629)
  * Small improvement: bcrypt is used for password encryption (#387)
20
  * Small improvement: caching is active by default for new users when
Piotr Gawron's avatar
Piotr Gawron committed
21
    uploading project (#202)
22
  * Small improvement: when removing overlay in admin panel there is a
Piotr Gawron's avatar
Piotr Gawron committed
23
    confirmation dialog (#696)
24
  * Small improvement: overlay name is obligatory (#698)
25
26
  * Small improvement: list of projects in admin panel contains creation date 
    (#447)
Piotr Gawron's avatar
Piotr Gawron committed
27
  * Small improvement: links in list of publications open in new tab (#447)
28
  * Small improvement: target gene in search panel contains also information
29
    about type of database that identifies the target (#66)
30
31
  * Small improvement: redundant 'references' field in gene variants data 
    overlay is now deprecated (#850)
Piotr Gawron's avatar
Piotr Gawron committed
32
33
  * Small improvement: information about deprecated columns in data overlay is 
    visible in overlay list (#838)
34
  * Small improvement: publication list is resizeable (#740)
Piotr Gawron's avatar
Piotr Gawron committed
35
  * Small improvement: user list on project edit dialog is sortable (#808)
36
37
38
  * Bug fix: export to CellDesigner of reaction with two modifiers connected
    with boolean operator resulted was skipping some layout information
  * Bug fix: reaction in SBGNML file containing two products was improperly
Piotr Gawron's avatar
Piotr Gawron committed
39
    drawn
40
  * Bug fix: color handling in CellDesigner did not work properly for modifiers
41
42
    inside boolean gateway
  * Bug fix: CellDesigner file exported from minerva was not fully compliant
Piotr Gawron's avatar
Piotr Gawron committed
43
    with SBML standard (#831)
44
  * Bug fix: MiRNA targets are limited only to the organism associated with the
45
    map (#66)
46
  * Bug fix: Search drug by target element did not return values when this
47
    element was annotated automatically (#216)
Piotr Gawron's avatar
Piotr Gawron committed
48

49
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 09 Aug 2019 10:00:00 +0200
50

Piotr Gawron's avatar
Piotr Gawron committed
51
52
minerva (13.1.2) stable; urgency=medium
  * Bug fix: Information about problematic zip file is more specific (#865)
53
  * Bug fix: Url didn't contain list of opened plugins and they weren't reload
54
    automatically on refresh (#866)
Piotr Gawron's avatar
Piotr Gawron committed
55

56
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Jul 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
57

58
59
minerva (13.1.1) stable; urgency=medium
  * Bug fix: adding gene mapping before the genome caused an error (#835)
60
  * Bug fix: "Terms of Use" change to "Terms of Service" in all places (#843)
61
  * Bug fix: upgrade to 13.1.0 crashed on machines where every element was
62
    inside compartment (#856)
63
  * Bug fix: searching for some drugs in chembl didn't provide any results even
64
    though that data exists, for instance 'DORLIMOMAB ARITOX' (#842)
65
  * Bug fix: user wasn't logged out in all tabs when the log out event appeard
66
    in only one of them (#847)
67

Piotr Gawron's avatar
Piotr Gawron committed
68
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 2 Jul 2019 19:00:00 +0200
69

Piotr Gawron's avatar
Piotr Gawron committed
70
minerva (13.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
71
  * Feature: annotators are more flexible - you can define set of input and
72
    outputs used by annotator (#617)
Piotr Gawron's avatar
Piotr Gawron committed
73
74
  * Feature: changes in admin panel doesn't require saving - they are saved
    automatically (#676)
Piotr Gawron's avatar
Piotr Gawron committed
75
  * Feature: elements can have custom glyphs used for visualization (#487)
76
  * Small improvement: model_name renamed to map_name in data overlay columns
Piotr Gawron's avatar
Piotr Gawron committed
77
    (#827)
78
79
  * Small improvement: name, type, reference_genome_type and
    reference_genome_version column in genetic variant data overlay are
Piotr Gawron's avatar
Piotr Gawron committed
80
    deprecated (#827)
81
  * Small improvement: all bio entities have z-index associated with them
Piotr Gawron's avatar
Piotr Gawron committed
82
    (#487)
Piotr Gawron's avatar
Piotr Gawron committed
83
84
  * Small improvement: validation of the organism and disease id on map upload
    added (#618)
Piotr Gawron's avatar
Piotr Gawron committed
85
  * Small improvement: added current username next to logout button in admin
86
    panel (#660)
Piotr Gawron's avatar
Piotr Gawron committed
87
  * Small improvement: New comment dialog does not contain content of previous
88
    comment dialog (#680)
Piotr Gawron's avatar
Piotr Gawron committed
89
  * Small improvement: Left logo is configurable (#731)
90
  * Small improvement: list of element types in choose annotator dialog is
Ewa Smula's avatar
Ewa Smula committed
91
    sorted (#798)
92
93
  * Small improvement: Plugin API provides list of overview images (#702)
  * Small improvement: Plugin API allows to show/hide overview images (#702)
94
  * Small improvement: Plugin API allows to trigger search on the map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
95
  * Small improvement: Plugin API allows to clear search results on map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
96
  * Small improvement: edit/remove project button is disabled until project is
97
    uploaded (#683)
Piotr Gawron's avatar
Piotr Gawron committed
98
  * Small improvement: warning about capslock is visible on login page when
99
    necessary (#658)
Piotr Gawron's avatar
Piotr Gawron committed
100
  * Small improvement: names of columns in data overlay are unified: no
Piotr Gawron's avatar
Piotr Gawron committed
101
    whitespace, "_" used as separator (#596)
102
103
  * Small improvement: list of references in drug panel contains PUBMED prefix
    (#666)
Piotr Gawron's avatar
Piotr Gawron committed
104
  * Small improvement: list of projects is auto refreshed every 5 seconds if at
105
    least one of the project is uploading/removing (#610)
Piotr Gawron's avatar
Piotr Gawron committed
106
  * Small improvement: passwords to email account and ldap are not sent over
Piotr Gawron's avatar
Piotr Gawron committed
107
    API (#732)
Piotr Gawron's avatar
Piotr Gawron committed
108
  * Small improvement: reactant/product/modifier specific colors are parsed
Piotr Gawron's avatar
Piotr Gawron committed
109
    properly from CellDesigner file (#597)
Piotr Gawron's avatar
Piotr Gawron committed
110
  * Small improvement: Info tab contains information about disease and
111
    organism when info is provided
Piotr Gawron's avatar
Piotr Gawron committed
112
113
114
  * Small improvement: Info tab provides information about model annotations
    and submap tabs provide information about submaps annotations if applicable
    (#591)
115
116
  * Small improvement: uploading sbml file should automatically discover a file
    type (#784)
117
  * Small improvement: when plugin listeners crash the system notifies user
118
    about problem with a plugin (#767)
119
  * Small improvement: when exporting reaction and elements there is
Piotr Gawron's avatar
Piotr Gawron committed
120
    possibility to filter by (sub)map (#615)
121
  * Small improvement: during first opening of a map, the zoom level is
Piotr Gawron's avatar
Piotr Gawron committed
122
    automatically computed if no default information is provided (#776)
123
  * Small improvement: when adding new project columns "Root map", "Mapping
Piotr Gawron's avatar
Piotr Gawron committed
124
    file" and "Map type" are merged (#700)
Piotr Gawron's avatar
Piotr Gawron committed
125
  * Small improvement: allow admin to disable CORS check (#802)
126
  * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
127
    SemanticZoomLevelTransparency (#801)
128
  * Small improvement: export/import from SBML support z-index in LAYOUT
129
    extension
130
  * Bug fix: due to blocking of our requests from ctdbase the autocomplete for
Piotr Gawron's avatar
Piotr Gawron committed
131
132
133
134
135
136
137
138
    this database is disabled
  * Bug fix: deprecated columns in data overlay are not visible to the end user
    (#827)
  * Bug fix: invalid color in data overlay provides proper feedback to the user
    (#822)
  * Bug fix: genetic variant overlay without name caused problems (#832)
  * Bug fix: tair locus identifiers were used improperly - instead of id the
    name was used
139
  * Bug fix: plugin tab header wasn't properly resized after adding plugins
Piotr Gawron's avatar
Piotr Gawron committed
140
141
142
143
144
145
    that introduced second line for tab selection (#758)
  * Bug fix: invisible layer shouldn't be shown on the map (#813)
  * Bug fix: list of availbale annotators is sorted alphabetically (#815)
  * Bug fix: redirect url from export panel is fixed (#819)
  * Bug fix: allow to reupload the same file without closing add overlay dialog
    (#833)
146
  * Bug fix: gene_name column is allowed only in the genetic variant data
Piotr Gawron's avatar
Piotr Gawron committed
147
148
149
150
151
152
153
    overlay
  * Bug fix: protein types are sorted properly in "Select valid annotations"
    dialog (#815)
  * Bug fix: if there is a description of (sub)map then it is available in
    info/submap panel (#824)
  * Bug fix: empty type for data overlay is allowed (#827)
  * Bug fix: genetic variants data overlay was ignoring color parameter (#827)
154
  * Bug fix: asynchronous calls on showing/hiding data overlays might cause
Piotr Gawron's avatar
Piotr Gawron committed
155
    problems due to network latency (#830)
Piotr Gawron's avatar
Piotr Gawron committed
156
  * Bug fix: progress bar of gene genome mapping upload is refreshing properly
157
    (#728)
Piotr Gawron's avatar
Piotr Gawron committed
158
  * Bug fix: when editing project Disease and Organism could not be removed
Piotr Gawron's avatar
Piotr Gawron committed
159
    (#616)
Piotr Gawron's avatar
Piotr Gawron committed
160
161
162
  * Bug fix: dashed line partially wasn't dashed in "Unknown Catalysis" and
    "Unknown Inhibition" reactions (#664)
  * Bug fix: "Unknown Catalysis" and "Unknown Inhibition" reaction end is
163
    slightly separated from target phenotype (#664)
164
  * Bug fix: order of genomes in admin panel doesn't change after refreshing
165
    list of genomes (#761)
166
  * Bug fix: fixing situation when Molart started with variation overlay not
Piotr Gawron's avatar
Piotr Gawron committed
167
    having the aa change information
168
  * Bug fix: plugin contect element width is adjusted when link to tabs are
169
    wrapped in more than one line (#758)
Ewa Smula's avatar
Ewa Smula committed
170
  * Bug fix: export to CellDesigner preserve font size (#798)
171
  * Bug fix: layout data was ignored for some reactions when importing from
Piotr Gawron's avatar
Piotr Gawron committed
172
    SBML (#812)
173

Piotr Gawron's avatar
Piotr Gawron committed
174
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 27 Jun 2019 14:00:00 +0200
175

176
minerva (13.0.0) stable; urgency=medium
177
178
  * Bug fix: Since Oracle Java cannot be installed as debian dependency we use
    openjdk-8. Due to this dependency minerva can be no longer installed on
179
180
181
182
    Ubuntu-14 (#223)

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

Piotr Gawron's avatar
Piotr Gawron committed
183
184
minerva (12.2.3) stable; urgency=medium
  * Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790)
185
  * Bug fix: searching of chemicals stopped working due to expired SSL
Piotr Gawron's avatar
Piotr Gawron committed
186
    certificate on https://ctdbase.org/
187
  * Bug fix: remove button is disabled after starting removing of the data
188
    overlay (#791)
189
  * Bug fix: search autocomplete hint could be initially hidden (#793)
190
  * Bug fix: updating terms of use could crash when list of users was removed
191
    in separate tab or by another user (#797)
Piotr Gawron's avatar
Piotr Gawron committed
192
  * Bug fix: name of the checkbox in ADD PROJECT window adjusted (#799)
193
194
  * Bug fix: when user didn't have privileges to remove comments the button was
    active on pages other than page 1 (#792)
Piotr Gawron's avatar
Piotr Gawron committed
195
196
  * Bug fix: export of reaction to SBML didn't work when lines on the map were
    too short (#805)
Piotr Gawron's avatar
Piotr Gawron committed
197
198
199

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

Piotr Gawron's avatar
Piotr Gawron committed
200
minerva (12.2.2) stable; urgency=medium
201
  * Bug fix: downloading overlays didn't work from admin panel when project
Piotr Gawron's avatar
Piotr Gawron committed
202
    with different id than default map was accessed
203
  * Bug fix: change of owner of the data overlay in admin panel incorrectly
Piotr Gawron's avatar
Piotr Gawron committed
204
    ordered overlays (#777)
205
  * Bug fix: chemical search didn't use updated disease identifier, original
206
    disease id from project upload was used instead (#779)
207
  * Bug fix: user login with special characters (like '@')  could cause
Piotr Gawron's avatar
Piotr Gawron committed
208
    problems in admin panel (#780)
209
210
  * Bug fix: removing project without full control in the system (but with
    enough privileges to remove project) caused "Not enough privileges" error
211
    (#778)
212
  * Bug fix: export of custom properties (like synonyms) are properly encoded
Piotr Gawron's avatar
Piotr Gawron committed
213
    in CellDesigner xml (#785)
214
215
216
  * Bug fix: notification about not supported version in IE 11 fixed (#783)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 9 Apr 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
217

Piotr Gawron's avatar
Piotr Gawron committed
218
219
minerva (12.2.1) stable; urgency=medium
  * Bug fix: export of reaction colorsi in SBML is properly encoded (COPASI can
Piotr Gawron's avatar
Piotr Gawron committed
220
221
    read colors properly) (#744)
  * Bug fix: removing active plugin didn't switch plugin tab to the next loaded
222
    plugin (#757)
Piotr Gawron's avatar
Piotr Gawron committed
223
224
  * Bug fix: closed submap will not be reopened after page refresh (#763)
  * Bug fix: comment remove button is disabled for users without proper
225
    privileges (#766)
Piotr Gawron's avatar
Piotr Gawron committed
226
  * Bug fix: invalid pubmed identifier could break clicking on element
227
    containing it (#764, #765, #769)
Piotr Gawron's avatar
Piotr Gawron committed
228
  * Bug fix: cache for API queries is explicitly disabled - some queries could
229
    be mistakenly cached and the system behaviour might get unstable (#771)
Piotr Gawron's avatar
Piotr Gawron committed
230
231
232

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

Piotr Gawron's avatar
Piotr Gawron committed
233
minerva (12.2.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
234
  * Feature: bug report utility
Piotr Gawron's avatar
Piotr Gawron committed
235
236
  * Feature: url GET parameters support all kind of search and selected overlays
    highlight
237
  * Feature: user can create custom logging configuration in file
Piotr Gawron's avatar
Piotr Gawron committed
238
239
240
241
    /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
242
  * Feature: API tool providing possibility to transform different types of
Piotr Gawron's avatar
Piotr Gawron committed
243
    file formats
244
  * Feature: current state of the browsed map is reflected in the url (position,
Piotr Gawron's avatar
Piotr Gawron committed
245
    zoom, overlays, search queries, etc.)
Piotr Gawron's avatar
Piotr Gawron committed
246
247
248
249
250
  * Small improvement: highlighting table rows in admin panel uses better
    contrast color (#706)
  * Small improvement: list of publication can be filtered by submap (#614)
  * Small improvement: size of add overlay window adjusted to show more data
    without scrollbars (#657)
Piotr Gawron's avatar
Piotr Gawron committed
251
  * Small improvement: all popup dialogs in the application have dialog
Piotr Gawron's avatar
Piotr Gawron committed
252
253
254
    specific css class names (#665)
  * Small improvement: JS plugin can create listener that is triggered on
    search results focus change
Piotr Gawron's avatar
Piotr Gawron committed
255
256
  * Small improvement: export to SBML includes unit factors
  * Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
257
  * Small improvement: genetics information allows to provide information about
Piotr Gawron's avatar
Piotr Gawron committed
258
    modification on peptide level that could be visualized in MolArt
259
  * Small improvement: allow to control the background and font color of areas
Piotr Gawron's avatar
Piotr Gawron committed
260
    drawn from text areas in CellDesigner "layers"
261
  * Small improvement: config logo location is relative to the root minerva
Piotr Gawron's avatar
Piotr Gawron committed
262
263
    deployment directory
  * Small improvement: there is branding minerva logo in the left panel
264
265
266
267
268
269
270
271
272
273
274
275
  * 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
276
277
  * Small improvement: there is max size of the map in configuration panel that
    disables upload of too big files
278
  * Small improvement: hitting enter on login page logs in the user (no need to
Piotr Gawron's avatar
Piotr Gawron committed
279
    click on the login button)
280
  * Small improvement: refresh button in overlays panel (useful when data
Piotr Gawron's avatar
Piotr Gawron committed
281
282
283
    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
284
  * Small improvement: 'BACK TO MAP' link is available only when guest account
Piotr Gawron's avatar
Piotr Gawron committed
285
286
    has proper access level
  * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
287
288
    email account is provided
  * Small improvement: Plugin API allows to show/hide data overlays
Piotr Gawron's avatar
Piotr Gawron committed
289
  * Bug fix: Icons were sometimes not properly loaded on Safari (#661)
Piotr Gawron's avatar
Piotr Gawron committed
290
  * Bug fix: migration scripts are compatibile with postgres 9.3 version that
Piotr Gawron's avatar
Piotr Gawron committed
291
    is default on Ubuntu 14 (#762)
Piotr Gawron's avatar
Piotr Gawron committed
292
  * Bug fix: update/remove button is disabled when user has no privileges for
Piotr Gawron's avatar
Piotr Gawron committed
293
    managing overlays (#742)
Piotr Gawron's avatar
Piotr Gawron committed
294
  * Bug fix: when user cannot manage users information in overlays and users
Piotr Gawron's avatar
Piotr Gawron committed
295
    tab in edit project dialog is provided instead of hiding tabs (#756)
Piotr Gawron's avatar
Piotr Gawron committed
296
297
  * Bug fix: removing comments in a project asked for confirmation twice after
    edit project dialog for specific project was opened; closed and opened
Piotr Gawron's avatar
Piotr Gawron committed
298
299
    again (#697)
  * Bug fix: editing/removing project requires Map Management privilege (#681)
Piotr Gawron's avatar
Piotr Gawron committed
300
  * Bug fix: when removeAllListeners is called list of registered listeners is
Piotr Gawron's avatar
Piotr Gawron committed
301
    cleaned (#687)
Piotr Gawron's avatar
Piotr Gawron committed
302
  * Bug fix: when plugin is removed the html elements associated with it are
Piotr Gawron's avatar
Piotr Gawron committed
303
304
    removed as well (#686)
  * Bug fix: when creating new user default privileges are set properly (#692)
Piotr Gawron's avatar
Piotr Gawron committed
305
  * Bug fix: plugin can be added after plugin has been removed in admin plugin
Piotr Gawron's avatar
Piotr Gawron committed
306
    panel (#686)
Piotr Gawron's avatar
Piotr Gawron committed
307
  * Bug fix: too many annotations (>=100) caused misaligning in the left panel
Piotr Gawron's avatar
Piotr Gawron committed
308
    (#708)
Piotr Gawron's avatar
Piotr Gawron committed
309
310
311
  * Bug fix: export to svg contains viewBox info (#716)
  * Bug fix: overlays added via API couldn't be visualized after refresh (#718)
  * Bug fix: Safari sometimes cached server responses and used wrong data, for
Piotr Gawron's avatar
Piotr Gawron committed
312
313
    example in admin panel configuration tab (#719)
  * Bug fix: description of transcription site is centered (#720)
Piotr Gawron's avatar
Piotr Gawron committed
314
  * Bug fix: selecting too few parameters in export doesn't throw reportable
Piotr Gawron's avatar
Piotr Gawron committed
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
    error (#721)
  * Bug fix: providing invalid overlay id in url could break minerva (#726)
  * Bug fix: removing project that doesn't exist doesn't cause 500 error (#723)
  * Bug fix: opening map with invalid id shows proper error message (#724)
  * Bug fix: Fixing an issue where search panel was not properly resized on
    expansion (#682)
  * Bug fix: loading icon is not overlapping input in the search panel (#404)
  * Bug fix: position of transcription sites in genes are computed properly
    (#553)
  * Bug fix: REQUEST AN ACCOUNT was enabled when associated email was invalid
    (#626)
  * Bug fix: working with too many maps within the single session could crash
    connection to server (#651)
  * Bug fix: drawing corrupted heterodimer association in CellDesigner could
    crash map upload (#673)
Piotr Gawron's avatar
Piotr Gawron committed
330
  * Bug fix: export to CellDesigner align inhibition reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
331
  * Bug fix: export/import to/from SBML handles Heterodimer Association
Piotr Gawron's avatar
Piotr Gawron committed
332
    reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
333
  * Bug fix: logo doesn't need to be square
334
  * Bug fix: when clicking on a search link (in overview window), input in the
Piotr Gawron's avatar
Piotr Gawron committed
335
    left tab was not modified
336
  * Bug fix: in admin panel changing of genome version is blocking interface
Piotr Gawron's avatar
Piotr Gawron committed
337
    until data about url is retrieved
338
339
  * 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
340
341
  * Bug fix: export to SBGN did not export compartments
  * Bug fix: export of complex states to SBGN did not work
342
  * Bug fix: type of the data overlay can be defined in the file content
Piotr Gawron's avatar
Piotr Gawron committed
343
344
    (useful when uploading genetic variants)
  * Bug fix: CLEAR button clears comment checkbox if necessary
Piotr Gawron's avatar
Piotr Gawron committed
345
  * Bug fix: minerva install problem on ubuntu 18 fixed
Piotr Gawron's avatar
Piotr Gawron committed
346

Piotr Gawron's avatar
Piotr Gawron committed
347
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 25 Mar 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
348

Sascha Herzinger's avatar
Sascha Herzinger committed
349
minerva (12.1.8) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
350
  * Bug fix: add a project reset users custom overlays limit to default (#679)
351
  * Bug fix: edit/remove project button was disabled based on Configuration
Piotr Gawron's avatar
Piotr Gawron committed
352
    Manage Privilege, but should be based on Project Manage Privilege (#681)
353
  * Bug fix: another minor problem with updating privileges introduced in
Piotr Gawron's avatar
Piotr Gawron committed
354
    12.1.6 fixed (#659)
Sascha Herzinger's avatar
Sascha Herzinger committed
355

Piotr Gawron's avatar
Piotr Gawron committed
356
357
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 8 Feb 2019 15:30:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
358
359
360
361
362
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
363
364
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
365
366
  * Bug fix: plugin API had sometimes problems with fetching reactions
    properly
Piotr Gawron's avatar
Piotr Gawron committed
367
368
  * 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
369
370
  * 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
371
  * Bug fix: fetching some drugs via API could cause 500
Piotr Gawron's avatar
Piotr Gawron committed
372

Piotr Gawron's avatar
Piotr Gawron committed
373
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Jan 2019 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
374

Piotr Gawron's avatar
Piotr Gawron committed
375
376
377
378
379
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
380
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 10 Jan 2019 14:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
381

382
minerva (12.1.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
383
  * Bug fix: no check for limit on custom data overlays fixed
384
  * Bug fix: error message improved when there is privilege problem during
Piotr Gawron's avatar
Piotr Gawron committed
385
    data overlay upload
Piotr Gawron's avatar
Piotr Gawron committed
386
  * Bug fix: upload of data overlay from admin panel didn't work
387
  * Bug fix: add project button is disabled when user doesn't have proper
Piotr Gawron's avatar
Piotr Gawron committed
388
    privileges ("Add project" privilege)
389
  * Bug fix: there are no more extra markers due to map wrapping
390
391
  * Bug fix: upload of the project failed when another project was removed
    during upload
Piotr Gawron's avatar
Piotr Gawron committed
392
  * Bug fix:  word wrapping fixed in overlay table for long overlay names
393
394
395

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

Piotr Gawron's avatar
Piotr Gawron committed
396
397
398
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
399
400
401
402
  * 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
403
404
405

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

Piotr Gawron's avatar
Piotr Gawron committed
406
407
408
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
409
  * Bug fix: integer configurtion options (like SMTP_PORT) are properly
Piotr Gawron's avatar
Piotr Gawron committed
410
411
    validated before saving
  * Bug fix: inside of reaction box wasn't properly aligned
Piotr Gawron's avatar
Piotr Gawron committed
412
  * Bug fix: too long data overlay name disturbed size of the map div and
Piotr Gawron's avatar
Piotr Gawron committed
413
414
415
416
417
    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
418
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Dec 2018 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
419

Piotr Gawron's avatar
Piotr Gawron committed
420
minerva (12.1.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
421
422
423
424
425
426
427
428
429
  * 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
430
minerva (12.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
431
432
433
434
  * 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
435
  * Small improvement: option to remove additional overlays generated by custom
Piotr Gawron's avatar
Piotr Gawron committed
436
    semantic zoom
437
  * Small improvement: 'Reduced modulation' edge was displayed differently in
Piotr Gawron's avatar
Piotr Gawron committed
438
439
440
    CellDesigner and Minerva
  * Small improvement: user-friendly documentation for plugin URL field
  * Small improvement: plugins have to access information about active submap
441
442
443
444
  * 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
445
  * Feature: minerva is distributed using rpm packages
446
  * Small improvement: annotations from RHEA are handled
Piotr Gawron's avatar
Piotr Gawron committed
447
448
  * Small improvement: changing of Terms of Service url allows admin to reset
    the status of ToS acceptance for all users
449
450
  * 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
451
452
453
454
455
456
457
458
  * 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
459
  * Bug fix: when there is a problem with adjusting font in complexes (because
Piotr Gawron's avatar
Piotr Gawron committed
460
461
462
463
464
    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
465
  * Bug fix: double click on user add button disabled
Piotr Gawron's avatar
Piotr Gawron committed
466
467
  * Bug fix: privileges are mirrored correctly across different popups
  * Bug fix: plugin tab css fixed
468
  * Bug fix: uploading sbml file with no ids in glyphs returned error that
Piotr Gawron's avatar
Piotr Gawron committed
469
470
471
    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
472

Piotr Gawron's avatar
Piotr Gawron committed
473
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Oct 2018 13:00:00 +0200
474

Piotr Gawron's avatar
Piotr Gawron committed
475
minerva (12.0.4) stable; urgency=medium
476
  * Bug fix: CellDesigner modifications that are drawn as reaction are handled
Piotr Gawron's avatar
Piotr Gawron committed
477
478
479
    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
480
  * Bug fix: Tair database moved to https
481
  * Bug fix: Taxnomy database changed html output that resulted in problems
Piotr Gawron's avatar
Piotr Gawron committed
482
    with resolving species name to the id
483

Piotr Gawron's avatar
Piotr Gawron committed
484
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Sep 2018 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
485

Piotr Gawron's avatar
Piotr Gawron committed
486
487
488
489
490
491
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
492

Piotr Gawron's avatar
Piotr Gawron committed
493
494
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Aug 2018 11:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
495
496
497
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
498
    works properly
Piotr Gawron's avatar
Piotr Gawron committed
499
500
501
502
  * 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
503
  * Performance: tomcat inside docker image by default can use 3G of memory
Piotr Gawron's avatar
Piotr Gawron committed
504

505
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 31 Jul 2018 13:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
506

Piotr Gawron's avatar
Piotr Gawron committed
507
508
509
510
511
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
512
  * Bug fix: opening map could crash when CellDesigner file contained duplicate
Piotr Gawron's avatar
Piotr Gawron committed
513
    reaction id
Piotr Gawron's avatar
Piotr Gawron committed
514
515
  * Bug fix: map is repositioned when info window is outside of current view in
    OpenLayers library
516

517
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 24 Jul 2018 10:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
518

Piotr Gawron's avatar
Piotr Gawron committed
519
520
minerva (12.0.0) stable; urgency=medium
  * Feature: There is alternative OpenLayers map engine available
Piotr Gawron's avatar
Piotr Gawron committed
521
  * Feature: database connection configuration (login, password, host, etc)
Piotr Gawron's avatar
Piotr Gawron committed
522
    can be modified using /etc/minerva/db.properties file
523
  * Feature: searching for elements in submap gives marker on top map
Piotr Gawron's avatar
Piotr Gawron committed
524
525
    indicating the submap connection
  * Feature: similar search results are merged
Piotr Gawron's avatar
Piotr Gawron committed
526
  * Feature: visualization of protein structures by MolArt
Piotr Gawron's avatar
Piotr Gawron committed
527
  * Feature: reordering of data overlays is supported
528
  * Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA  annotators
Piotr Gawron's avatar
Piotr Gawron committed
529
530
531
532
533
534
535
  * 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
536
537
  * 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
538
539
540
541
542
543
544
545
546
547
  * 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
548
549
  * 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
550
551
552
  * 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
553
554
  * Small improvement: Data overlays can use source element identifiers for
    filtering
Piotr Gawron's avatar
Piotr Gawron committed
555
556
557
  * 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
558
  * Small improvement: auto complete functionality for drugs, mirnas and
Piotr Gawron's avatar
Piotr Gawron committed
559
    chemicals
Piotr Gawron's avatar
Piotr Gawron committed
560
  * Small improvement: columns value and type are not mutually exclusive in
Piotr Gawron's avatar
Piotr Gawron committed
561
562
563
564
    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
565
  * Small improvement: data overlays color scale contains configurable default
Piotr Gawron's avatar
Piotr Gawron committed
566
567
    middle color (for 0 values)
  * Small improvement: opening data overlay switch to empty background
Piotr Gawron's avatar
Piotr Gawron committed
568
569
570
571
572
573
574
575
576
577
578
579
580
  * 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
581
  * Bug fix: uploading of zip files created by mac doesn't crash due to
Piotr Gawron's avatar
Piotr Gawron committed
582
583
    .DS_Store folder
  * Bug fix: auto complete is case insensitive
Piotr Gawron's avatar
Piotr Gawron committed
584
  * Bug fix: google maps API 404 errors for non existing tiles are removed
Piotr Gawron's avatar
Piotr Gawron committed
585

Piotr Gawron's avatar
Piotr Gawron committed
586
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Jul 2018 12:00:00 +0200
587

588
589
590
591
592
593
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
594
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 23 Jul 2018 12:00:00 +0200
595

Piotr Gawron's avatar
Piotr Gawron committed
596
minerva (11.1.2) stable; urgency=medium
597
598
  * 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
599
600
601
602
  * 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
603
604
605
606
607
608
609
610
611
612
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
613
614
615
minerva (11.1.0) stable; urgency=high
  * User can provide Google Maps API key that must be registered in google
    cloud account
616
617
  * User data overlays must be Google Maps API terms of use compliant
  * Terms of Use added
618

619
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 05 Jun 2018 9:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
620
  
621
622
minerva (11.0.10) stable; urgency=medium
  * Bug fix: link from overview image to search result was broken
623

624
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Apr 2018 15:00:00 +0200
625

Piotr Gawron's avatar
Piotr Gawron committed
626
627
628
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
629

Piotr Gawron's avatar
Piotr Gawron committed
630
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
631

Piotr Gawron's avatar
Piotr Gawron committed
632
633
634
635
636
637
638
639
640
641
642
643
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
644
  * Bug fix: comments on submaps are visualized properly
Piotr Gawron's avatar
Piotr Gawron committed
645

Piotr Gawron's avatar
Piotr Gawron committed
646
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 05 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
647

Piotr Gawron's avatar
Piotr Gawron committed
648
649
650
651
652
653
654
655
656
657
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

658
minerva (11.0.6) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
659
660
  * Bug fix: fix a bug when entering invalid mirna id

661
662
663
 -- 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
664
  * Bug fix: fix on connection to drugbank database
665
666
  * Bug fix: posttranslational modification data was sometimes unavailable
    in search results panel
Piotr Gawron's avatar
Piotr Gawron committed
667

668
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 30 Nov 2017 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
669

670
minerva (11.0.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
671
  * Bug fix: fix on connection to taxonomy database
672
673
  * 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
674

675
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 09 Nov 2017 14:50:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
676

677
minerva (11.0.3) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
678
  * Bug fix: removing empty project removed images from all projects
679
680
681
682
683
684
685
686
687
  * 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
688
  * Bug fix: login issues when default page is in secure area
689
690
691
692

 -- 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
693
  * Bug fix: logout caused issues with session data
694
695
696
697
698

 -- 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
699
700
  * Bug fix: security issue - access to specific map can be restricted
    by the user login
701
702
  * Bug fix: sbgn import
  * Bug fix: mesh connector
Piotr Gawron's avatar
Piotr Gawron committed
703
  * Rest API (documentation can be found here:
704
705
    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
706
    corner (when Search tab is not open)
707
708
  * 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
709
710
    proper text box
  * Layout changes: the main one is that there are only 3 tab panels
711
712
713
714
715
716
717
718
719
    (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
720
721
  * Overlay presents description field if possible

722
723

 -- Piotr Gawron <piotr.gawron@uni.lu>  Sat, 04 Mar 2017 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
724

725
726
727
728
729
730
731
732
733
734
735
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
736
  * Bug fix: search for multiple drugs will not return more drugs than
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
    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
754
755
  * Bug fix: trigger reaction and physical stimulation reactions are no
    longer allowed (CellDesigner data model issue)
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
  * 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
795
796
797
798
799
800
  * 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
801
802
803
804
805

 -- 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
806
807
808
809
810
  * Searching by annotations
  * Errors from parsing data forwarded to client
  * Notification email system added
  * Warnings are downloadable
  * Complex map (composed from many small maps)
811
  * Visualization of Recon specific annotations
Piotr Gawron's avatar
Piotr Gawron committed
812
813
814
815
816
817
818
  * Versioning system
  * Galaxy connector
  * Miriam types report
  * Advanced annotation options
  * Uniprot annotation module
  * Customized validation of miriam annotations
  * Recon annotation service
819
  * Bug fix: Data autofill problem in user management
Piotr Gawron's avatar
Piotr Gawron committed
820
821
  * Bug fix: User privileges for adding project
  * Bug fix: Problem with some miriam entries in RDF format
822
  * Bug fix: Reporting of drawing problems
Piotr Gawron's avatar
Piotr Gawron committed
823
824
  * Bug fix: Visualization of posttranslationa modification
  * Bug fix: Drugbank problem after update of Drugbank interface
825
  * Bug fix: Session scope fixed (browsing many maps at the same time)
Piotr Gawron's avatar
Piotr Gawron committed
826
827
828
829
830
  * 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
831
832

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 21 Jul 2015 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
833

834
835
minerva (5) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
836
  * Additional checkboxes in upload model: annotate automatically, cache data, verify annotations
837
  * Popup window in admin panel that list warnings
Piotr Gawron's avatar
Piotr Gawron committed
838
839
  * Information about build
  * Parsing and annotation warnings for models in admin panel
840
  * Custom reaction visualization in upload overlay
Piotr Gawron's avatar
Piotr Gawron committed
841
842
843
844
845
  * 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
846
847

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 18 Dec 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
848

849
850
851
minerva (4) stable; urgency=low

  * Export of the part of the map into CellDesigner file
Piotr Gawron's avatar
Piotr Gawron committed
852
853
  * Logo files managable via config webpage
  * Import data from GO
854
855
856
  * 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
857
858
859
860
861
  * Bug fix: Visualization of residues in rna, antisense rna, proteins
  * Bug fix: Problem with touching bubbles on touch interface
  * Bug fix: Problem with special