CHANGELOG 44.7 KB
Newer Older
1
minerva (14.0.0~beta.0) unstable; urgency=low
Piotr Gawron's avatar
Piotr Gawron committed
2
3
  * Small improvement: sorting by columns that doesn't make sense in admin panel 
    is disabled (#895)
Piotr Gawron's avatar
Piotr Gawron committed
4
  * Small improvement: version of minerva is visible in map browser panel
Piotr Gawron's avatar
Piotr Gawron committed
5
6
  * Small improvement: CellDesigner layers are always visualized as pathways 
    (#813)
7
8
  * Bug fix: work on FF Private Window mode could cause logout or raise an 
    error on when opening new tab with minerva (#892)
9
10
  * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server 
    Error" (#889)
Piotr Gawron's avatar
Piotr Gawron committed
11
  * Bug fix: user without admin right can accept terms of service (#893)
12
13
  * Bug fix: user without admin or curator privileges shouldn't be able to 
    check logs (#894)
14
15
  * Bug fix: user without admin or curator privileges had issues with accesing
    and removing data overlays (#897, #898, #899, #903)
Piotr Gawron's avatar
Piotr Gawron committed
16
17
  * Bug fix: privilege checking on updating privileges, data overlays were not 
    sufficient and could lead to access escalation
18
  * Bug fix: user without privileges had edit map input options enabled
19
20
  * Bug fix: user without privileges had edit map input options for managing 
    project users
Piotr Gawron's avatar
Piotr Gawron committed
21
  * Bug fix: curator couldn't update data overlay in some situations (#905)
Piotr Gawron's avatar
Piotr Gawron committed
22
23
  * Bug fix: alignment of tabs fixed for dialogs: "Add Project", "Edit Genome", 
    "Edit Project", "Edit User" (#881)
Piotr Gawron's avatar
Piotr Gawron committed
24
25
  * Bug fix: all colors in boolean reaction (from CellDesigner) are processed 
    properly (#907)
26
27
  * Bug fix: proper line type for boolean reaction is used on the whole
    reaction (#908)
28
29
  * Bug fix: user with modify access to the project can edit it in admin panel
    (#901)
30
  * Bug fix: creating project with too long name hung (#916)
Piotr Gawron's avatar
Piotr Gawron committed
31
  * Bug fix: too long user login thrown an error (#915)
Piotr Gawron's avatar
Piotr Gawron committed
32
  * Bug fix: width of info window adjust to the content size (#903)
33
34
35

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 21 Aug 2019 21:00:00 +0200

36
37
minerva (14.0.0~alpha.1) unstable; urgency=low
  * Feature removal: support for tomcat7 removed (#828)
Piotr Gawron's avatar
Piotr Gawron committed
38
  * Small improvement: debian package can be installed on debian:buster (#879)
Piotr Gawron's avatar
Piotr Gawron committed
39
  * Bug fix: REST API bioEntities:search method didn't limit results to the
Piotr Gawron's avatar
Piotr Gawron committed
40
    submodel id (#860)
41
  * Bug fix: Empty Overlay colours were not preserved during export to
Piotr Gawron's avatar
Piotr Gawron committed
42
    CellDesigner (#714)
Piotr Gawron's avatar
Piotr Gawron committed
43
  * Bug fix: some project couldn't be accessed due to problem with migration of
Piotr Gawron's avatar
Piotr Gawron committed
44
    reaction with unknown boolean operator (#880)
Piotr Gawron's avatar
Piotr Gawron committed
45
  * Bug fix: problem with unloading plugin is properly handled (#884)
Piotr Gawron's avatar
Piotr Gawron committed
46
  * Bug fix: upload of invalid plugin doesn't add it to plugin tab and list of
47
    loaded plugins (#885)
Piotr Gawron's avatar
Piotr Gawron committed
48
  * Bug fix: link to molart was brokwn (#886)
49
  * Bug fix: context menu visualization fixed
50
  * Bug fix: problem with uploading projects (#887)
51

Piotr Gawron's avatar
Piotr Gawron committed
52
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 13 Aug 2019 21:00:00 +0200
53

Piotr Gawron's avatar
Piotr Gawron committed
54
minerva (14.0.0~alpha.0) unstable; urgency=low
Piotr Gawron's avatar
Piotr Gawron committed
55
  * Feature: security layer redesigned - privilege types and scope changed
Piotr Gawron's avatar
Piotr Gawron committed
56
    (#636, #624)
Piotr Gawron's avatar
Piotr Gawron committed
57
  * Feature: log4j is replaced with log4j2 logging mechanism (#291)
58
  * Feature: database installed via debian package is done via dbconfig-commons
Piotr Gawron's avatar
Piotr Gawron committed
59
    (#469)
60
  * Feature: Replaced connection pool manager C3P0 with better maintained
Piotr Gawron's avatar
Piotr Gawron committed
61
    Hikari - restart of postgresql database doesn't require restart of tomcat
62
    (#564)
Piotr Gawron's avatar
Piotr Gawron committed
63
  * Feature removal: BioCompendium annotator removed (#32)
Piotr Gawron's avatar
Piotr Gawron committed
64
  * Small improvement: anonymous login is no longer required - each API query
Piotr Gawron's avatar
Piotr Gawron committed
65
66
    outside session is authorized with anonymous user privileges (#629)
  * Small improvement: bcrypt is used for password encryption (#387)
67
  * Small improvement: caching is active by default for new users when
Piotr Gawron's avatar
Piotr Gawron committed
68
    uploading project (#202)
69
  * Small improvement: when removing overlay in admin panel there is a
Piotr Gawron's avatar
Piotr Gawron committed
70
    confirmation dialog (#696)
71
  * Small improvement: overlay name is obligatory (#698)
Piotr Gawron's avatar
Piotr Gawron committed
72
  * Small improvement: list of projects in admin panel contains creation date
73
    (#447)
Piotr Gawron's avatar
Piotr Gawron committed
74
  * Small improvement: links in list of publications open in new tab (#447)
75
  * Small improvement: target gene in search panel contains also information
76
    about type of database that identifies the target (#66)
Piotr Gawron's avatar
Piotr Gawron committed
77
  * Small improvement: redundant 'references' field in gene variants data
78
    overlay is now deprecated (#850)
Piotr Gawron's avatar
Piotr Gawron committed
79
  * Small improvement: information about deprecated columns in data overlay is
Piotr Gawron's avatar
Piotr Gawron committed
80
    visible in overlay list (#838)
81
  * Small improvement: publication list is resizeable (#740)
Piotr Gawron's avatar
Piotr Gawron committed
82
  * Small improvement: user list on project edit dialog is sortable (#808)
83
84
85
  * 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
86
    drawn
87
  * Bug fix: color handling in CellDesigner did not work properly for modifiers
88
89
    inside boolean gateway
  * Bug fix: CellDesigner file exported from minerva was not fully compliant
Piotr Gawron's avatar
Piotr Gawron committed
90
    with SBML standard (#831)
91
  * Bug fix: MiRNA targets are limited only to the organism associated with the
92
    map (#66)
93
  * Bug fix: Search drug by target element did not return values when this
94
    element was annotated automatically (#216)
Piotr Gawron's avatar
Piotr Gawron committed
95

96
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 09 Aug 2019 10:00:00 +0200
97

Piotr Gawron's avatar
Piotr Gawron committed
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
minerva (13.1.4) stable; urgency=medium
  * Bug fix:search by drugs didn't check synonyms in chembl database

 -- Piotr Gawron <piotr.gawron@uni.lu> Wed,  21 Aug 2019 17:00:00 +0200

minerva (13.1.3) stable; urgency=medium
  * Bug fix: refreshing list of projects or list of users doesn't change active
    page (#870)
  * Bug fix: submap list must be selected to export from every submap (#874)
  * Bug fix: export map as image properly uses bottom limit (#875)
  * Bug fix: reaction info window wasn't closed on CLEAR (#876)
  * Bug fix: name of the uploaded file is displayed when adding overlay (#849)

 -- Piotr Gawron <piotr.gawron@uni.lu> Wed,  14 Aug 2019 17:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
113
114
minerva (13.1.2) stable; urgency=medium
  * Bug fix: Information about problematic zip file is more specific (#865)
115
  * Bug fix: Url didn't contain list of opened plugins and they weren't reload
116
    automatically on refresh (#866)
Piotr Gawron's avatar
Piotr Gawron committed
117

118
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Jul 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
119

120
121
minerva (13.1.1) stable; urgency=medium
  * Bug fix: adding gene mapping before the genome caused an error (#835)
122
  * Bug fix: "Terms of Use" change to "Terms of Service" in all places (#843)
123
  * Bug fix: upgrade to 13.1.0 crashed on machines where every element was
124
    inside compartment (#856)
125
  * Bug fix: searching for some drugs in chembl didn't provide any results even
126
    though that data exists, for instance 'DORLIMOMAB ARITOX' (#842)
127
  * Bug fix: user wasn't logged out in all tabs when the log out event appeard
128
    in only one of them (#847)
129

Piotr Gawron's avatar
Piotr Gawron committed
130
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue,  2 Jul 2019 19:00:00 +0200
131

Piotr Gawron's avatar
Piotr Gawron committed
132
minerva (13.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
133
  * Feature: annotators are more flexible - you can define set of input and
134
    outputs used by annotator (#617)
Piotr Gawron's avatar
Piotr Gawron committed
135
136
  * Feature: changes in admin panel doesn't require saving - they are saved
    automatically (#676)
Piotr Gawron's avatar
Piotr Gawron committed
137
  * Feature: elements can have custom glyphs used for visualization (#487)
138
  * Small improvement: model_name renamed to map_name in data overlay columns
Piotr Gawron's avatar
Piotr Gawron committed
139
    (#827)
140
141
  * 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
142
    deprecated (#827)
143
  * Small improvement: all bio entities have z-index associated with them
Piotr Gawron's avatar
Piotr Gawron committed
144
    (#487)
Piotr Gawron's avatar
Piotr Gawron committed
145
146
  * Small improvement: validation of the organism and disease id on map upload
    added (#618)
Piotr Gawron's avatar
Piotr Gawron committed
147
  * Small improvement: added current username next to logout button in admin
148
    panel (#660)
Piotr Gawron's avatar
Piotr Gawron committed
149
  * Small improvement: New comment dialog does not contain content of previous
150
    comment dialog (#680)
Piotr Gawron's avatar
Piotr Gawron committed
151
  * Small improvement: Left logo is configurable (#731)
152
  * Small improvement: list of element types in choose annotator dialog is
Ewa Smula's avatar
Ewa Smula committed
153
    sorted (#798)
154
155
  * Small improvement: Plugin API provides list of overview images (#702)
  * Small improvement: Plugin API allows to show/hide overview images (#702)
156
  * Small improvement: Plugin API allows to trigger search on the map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
157
  * Small improvement: Plugin API allows to clear search results on map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
158
  * Small improvement: edit/remove project button is disabled until project is
159
    uploaded (#683)
Piotr Gawron's avatar
Piotr Gawron committed
160
  * Small improvement: warning about capslock is visible on login page when
161
    necessary (#658)
Piotr Gawron's avatar
Piotr Gawron committed
162
  * Small improvement: names of columns in data overlay are unified: no
Piotr Gawron's avatar
Piotr Gawron committed
163
    whitespace, "_" used as separator (#596)
164
165
  * Small improvement: list of references in drug panel contains PUBMED prefix
    (#666)
Piotr Gawron's avatar
Piotr Gawron committed
166
  * Small improvement: list of projects is auto refreshed every 5 seconds if at
167
    least one of the project is uploading/removing (#610)
Piotr Gawron's avatar
Piotr Gawron committed
168
  * Small improvement: passwords to email account and ldap are not sent over
Piotr Gawron's avatar
Piotr Gawron committed
169
    API (#732)
Piotr Gawron's avatar
Piotr Gawron committed
170
  * Small improvement: reactant/product/modifier specific colors are parsed
Piotr Gawron's avatar
Piotr Gawron committed
171
    properly from CellDesigner file (#597)
Piotr Gawron's avatar
Piotr Gawron committed
172
  * Small improvement: Info tab contains information about disease and
173
    organism when info is provided
Piotr Gawron's avatar
Piotr Gawron committed
174
175
176
  * Small improvement: Info tab provides information about model annotations
    and submap tabs provide information about submaps annotations if applicable
    (#591)
177
178
  * Small improvement: uploading sbml file should automatically discover a file
    type (#784)
179
  * Small improvement: when plugin listeners crash the system notifies user
180
    about problem with a plugin (#767)
181
  * Small improvement: when exporting reaction and elements there is
Piotr Gawron's avatar
Piotr Gawron committed
182
    possibility to filter by (sub)map (#615)
183
  * Small improvement: during first opening of a map, the zoom level is
Piotr Gawron's avatar
Piotr Gawron committed
184
    automatically computed if no default information is provided (#776)
185
  * Small improvement: when adding new project columns "Root map", "Mapping
Piotr Gawron's avatar
Piotr Gawron committed
186
    file" and "Map type" are merged (#700)
Piotr Gawron's avatar
Piotr Gawron committed
187
  * Small improvement: allow admin to disable CORS check (#802)
188
  * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
189
    SemanticZoomLevelTransparency (#801)
190
  * Small improvement: export/import from SBML support z-index in LAYOUT
191
    extension
192
  * Bug fix: due to blocking of our requests from ctdbase the autocomplete for
Piotr Gawron's avatar
Piotr Gawron committed
193
194
195
196
197
198
199
200
    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
201
  * Bug fix: plugin tab header wasn't properly resized after adding plugins
Piotr Gawron's avatar
Piotr Gawron committed
202
203
204
205
206
207
    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)
208
  * Bug fix: gene_name column is allowed only in the genetic variant data
Piotr Gawron's avatar
Piotr Gawron committed
209
210
211
212
213
214
215
    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)
216
  * Bug fix: asynchronous calls on showing/hiding data overlays might cause
Piotr Gawron's avatar
Piotr Gawron committed
217
    problems due to network latency (#830)
Piotr Gawron's avatar
Piotr Gawron committed
218
  * Bug fix: progress bar of gene genome mapping upload is refreshing properly
219
    (#728)
Piotr Gawron's avatar
Piotr Gawron committed
220
  * Bug fix: when editing project Disease and Organism could not be removed
Piotr Gawron's avatar
Piotr Gawron committed
221
    (#616)
Piotr Gawron's avatar
Piotr Gawron committed
222
223
224
  * 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
225
    slightly separated from target phenotype (#664)
226
  * Bug fix: order of genomes in admin panel doesn't change after refreshing
227
    list of genomes (#761)
228
  * Bug fix: fixing situation when Molart started with variation overlay not
Piotr Gawron's avatar
Piotr Gawron committed
229
    having the aa change information
230
  * Bug fix: plugin contect element width is adjusted when link to tabs are
231
    wrapped in more than one line (#758)
Ewa Smula's avatar
Ewa Smula committed
232
  * Bug fix: export to CellDesigner preserve font size (#798)
233
  * Bug fix: layout data was ignored for some reactions when importing from
Piotr Gawron's avatar
Piotr Gawron committed
234
    SBML (#812)
235

Piotr Gawron's avatar
Piotr Gawron committed
236
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 27 Jun 2019 14:00:00 +0200
237

238
minerva (13.0.0) stable; urgency=medium
239
240
  * 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
241
242
243
244
    Ubuntu-14 (#223)

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

Piotr Gawron's avatar
Piotr Gawron committed
245
246
minerva (12.2.3) stable; urgency=medium
  * Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790)
247
  * Bug fix: searching of chemicals stopped working due to expired SSL
Piotr Gawron's avatar
Piotr Gawron committed
248
    certificate on https://ctdbase.org/
249
  * Bug fix: remove button is disabled after starting removing of the data
250
    overlay (#791)
251
  * Bug fix: search autocomplete hint could be initially hidden (#793)
252
  * Bug fix: updating terms of use could crash when list of users was removed
253
    in separate tab or by another user (#797)
Piotr Gawron's avatar
Piotr Gawron committed
254
  * Bug fix: name of the checkbox in ADD PROJECT window adjusted (#799)
255
256
  * 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
257
258
  * 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
259
260
261

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

Piotr Gawron's avatar
Piotr Gawron committed
262
minerva (12.2.2) stable; urgency=medium
263
  * Bug fix: downloading overlays didn't work from admin panel when project
Piotr Gawron's avatar
Piotr Gawron committed
264
    with different id than default map was accessed
265
  * Bug fix: change of owner of the data overlay in admin panel incorrectly
Piotr Gawron's avatar
Piotr Gawron committed
266
    ordered overlays (#777)
267
  * Bug fix: chemical search didn't use updated disease identifier, original
268
    disease id from project upload was used instead (#779)
269
  * Bug fix: user login with special characters (like '@')  could cause
Piotr Gawron's avatar
Piotr Gawron committed
270
    problems in admin panel (#780)
271
272
  * Bug fix: removing project without full control in the system (but with
    enough privileges to remove project) caused "Not enough privileges" error
273
    (#778)
274
  * Bug fix: export of custom properties (like synonyms) are properly encoded
Piotr Gawron's avatar
Piotr Gawron committed
275
    in CellDesigner xml (#785)
276
277
278
  * 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
279

Piotr Gawron's avatar
Piotr Gawron committed
280
281
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
282
283
    read colors properly) (#744)
  * Bug fix: removing active plugin didn't switch plugin tab to the next loaded
284
    plugin (#757)
Piotr Gawron's avatar
Piotr Gawron committed
285
286
  * Bug fix: closed submap will not be reopened after page refresh (#763)
  * Bug fix: comment remove button is disabled for users without proper
287
    privileges (#766)
Piotr Gawron's avatar
Piotr Gawron committed
288
  * Bug fix: invalid pubmed identifier could break clicking on element
289
    containing it (#764, #765, #769)
Piotr Gawron's avatar
Piotr Gawron committed
290
  * Bug fix: cache for API queries is explicitly disabled - some queries could
291
    be mistakenly cached and the system behaviour might get unstable (#771)
Piotr Gawron's avatar
Piotr Gawron committed
292
293
294

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

Piotr Gawron's avatar
Piotr Gawron committed
295
minerva (12.2.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
296
  * Feature: bug report utility
Piotr Gawron's avatar
Piotr Gawron committed
297
298
  * Feature: url GET parameters support all kind of search and selected overlays
    highlight
299
  * Feature: user can create custom logging configuration in file
Piotr Gawron's avatar
Piotr Gawron committed
300
301
302
303
    /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
304
  * Feature: API tool providing possibility to transform different types of
Piotr Gawron's avatar
Piotr Gawron committed
305
    file formats
306
  * Feature: current state of the browsed map is reflected in the url (position,
Piotr Gawron's avatar
Piotr Gawron committed
307
    zoom, overlays, search queries, etc.)
Piotr Gawron's avatar
Piotr Gawron committed
308
309
310
311
312
  * 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
313
  * Small improvement: all popup dialogs in the application have dialog
Piotr Gawron's avatar
Piotr Gawron committed
314
315
316
    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
317
318
  * Small improvement: export to SBML includes unit factors
  * Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
319
  * Small improvement: genetics information allows to provide information about
Piotr Gawron's avatar
Piotr Gawron committed
320
    modification on peptide level that could be visualized in MolArt
321
  * Small improvement: allow to control the background and font color of areas
Piotr Gawron's avatar
Piotr Gawron committed
322
    drawn from text areas in CellDesigner "layers"
323
  * Small improvement: config logo location is relative to the root minerva
Piotr Gawron's avatar
Piotr Gawron committed
324
325
    deployment directory
  * Small improvement: there is branding minerva logo in the left panel
326
327
328
329
330
331
332
333
334
335
336
337
  * 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
338
339
  * Small improvement: there is max size of the map in configuration panel that
    disables upload of too big files
340
  * Small improvement: hitting enter on login page logs in the user (no need to
Piotr Gawron's avatar
Piotr Gawron committed
341
    click on the login button)
342
  * Small improvement: refresh button in overlays panel (useful when data
Piotr Gawron's avatar
Piotr Gawron committed
343
344
345
    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
346
  * Small improvement: 'BACK TO MAP' link is available only when guest account
Piotr Gawron's avatar
Piotr Gawron committed
347
348
    has proper access level
  * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
349
350
    email account is provided
  * Small improvement: Plugin API allows to show/hide data overlays
Piotr Gawron's avatar
Piotr Gawron committed
351
  * Bug fix: Icons were sometimes not properly loaded on Safari (#661)
Piotr Gawron's avatar
Piotr Gawron committed
352
  * Bug fix: migration scripts are compatibile with postgres 9.3 version that
Piotr Gawron's avatar
Piotr Gawron committed
353
    is default on Ubuntu 14 (#762)
Piotr Gawron's avatar
Piotr Gawron committed
354
  * Bug fix: update/remove button is disabled when user has no privileges for
Piotr Gawron's avatar
Piotr Gawron committed
355
    managing overlays (#742)
Piotr Gawron's avatar
Piotr Gawron committed
356
  * Bug fix: when user cannot manage users information in overlays and users
Piotr Gawron's avatar
Piotr Gawron committed
357
    tab in edit project dialog is provided instead of hiding tabs (#756)
Piotr Gawron's avatar
Piotr Gawron committed
358
359
  * 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
360
361
    again (#697)
  * Bug fix: editing/removing project requires Map Management privilege (#681)
Piotr Gawron's avatar
Piotr Gawron committed
362
  * Bug fix: when removeAllListeners is called list of registered listeners is
Piotr Gawron's avatar
Piotr Gawron committed
363
    cleaned (#687)
Piotr Gawron's avatar
Piotr Gawron committed
364
  * Bug fix: when plugin is removed the html elements associated with it are
Piotr Gawron's avatar
Piotr Gawron committed
365
366
    removed as well (#686)
  * Bug fix: when creating new user default privileges are set properly (#692)
Piotr Gawron's avatar
Piotr Gawron committed
367
  * Bug fix: plugin can be added after plugin has been removed in admin plugin
Piotr Gawron's avatar
Piotr Gawron committed
368
    panel (#686)
Piotr Gawron's avatar
Piotr Gawron committed
369
  * Bug fix: too many annotations (>=100) caused misaligning in the left panel
Piotr Gawron's avatar
Piotr Gawron committed
370
    (#708)
Piotr Gawron's avatar
Piotr Gawron committed
371
372
373
  * 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
374
375
    example in admin panel configuration tab (#719)
  * Bug fix: description of transcription site is centered (#720)
Piotr Gawron's avatar
Piotr Gawron committed
376
  * Bug fix: selecting too few parameters in export doesn't throw reportable
Piotr Gawron's avatar
Piotr Gawron committed
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
    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
392
  * Bug fix: export to CellDesigner align inhibition reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
393
  * Bug fix: export/import to/from SBML handles Heterodimer Association
Piotr Gawron's avatar
Piotr Gawron committed
394
    reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
395
  * Bug fix: logo doesn't need to be square
396
  * Bug fix: when clicking on a search link (in overview window), input in the
Piotr Gawron's avatar
Piotr Gawron committed
397
    left tab was not modified
398
  * Bug fix: in admin panel changing of genome version is blocking interface
Piotr Gawron's avatar
Piotr Gawron committed
399
    until data about url is retrieved
400
401
  * 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
402
403
  * Bug fix: export to SBGN did not export compartments
  * Bug fix: export of complex states to SBGN did not work
404
  * Bug fix: type of the data overlay can be defined in the file content
Piotr Gawron's avatar
Piotr Gawron committed
405
406
    (useful when uploading genetic variants)
  * Bug fix: CLEAR button clears comment checkbox if necessary
Piotr Gawron's avatar
Piotr Gawron committed
407
  * Bug fix: minerva install problem on ubuntu 18 fixed
Piotr Gawron's avatar
Piotr Gawron committed
408

Piotr Gawron's avatar
Piotr Gawron committed
409
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 25 Mar 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
410

Sascha Herzinger's avatar
Sascha Herzinger committed
411
minerva (12.1.8) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
412
  * Bug fix: add a project reset users custom overlays limit to default (#679)
413
  * Bug fix: edit/remove project button was disabled based on Configuration
Piotr Gawron's avatar
Piotr Gawron committed
414
    Manage Privilege, but should be based on Project Manage Privilege (#681)
415
  * Bug fix: another minor problem with updating privileges introduced in
Piotr Gawron's avatar
Piotr Gawron committed
416
    12.1.6 fixed (#659)
Sascha Herzinger's avatar
Sascha Herzinger committed
417

Piotr Gawron's avatar
Piotr Gawron committed
418
419
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 8 Feb 2019 15:30:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
420
421
422
423
424
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
425
426
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
427
428
  * Bug fix: plugin API had sometimes problems with fetching reactions
    properly
Piotr Gawron's avatar
Piotr Gawron committed
429
430
  * 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
431
432
  * 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
433
  * Bug fix: fetching some drugs via API could cause 500
Piotr Gawron's avatar
Piotr Gawron committed
434

Piotr Gawron's avatar
Piotr Gawron committed
435
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Jan 2019 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
436

Piotr Gawron's avatar
Piotr Gawron committed
437
438
439
440
441
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
442
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 10 Jan 2019 14:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
443

444
minerva (12.1.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
445
  * Bug fix: no check for limit on custom data overlays fixed
446
  * Bug fix: error message improved when there is privilege problem during
Piotr Gawron's avatar
Piotr Gawron committed
447
    data overlay upload
Piotr Gawron's avatar
Piotr Gawron committed
448
  * Bug fix: upload of data overlay from admin panel didn't work
449
  * Bug fix: add project button is disabled when user doesn't have proper
Piotr Gawron's avatar
Piotr Gawron committed
450
    privileges ("Add project" privilege)
451
  * Bug fix: there are no more extra markers due to map wrapping
452
453
  * Bug fix: upload of the project failed when another project was removed
    during upload
Piotr Gawron's avatar
Piotr Gawron committed
454
  * Bug fix:  word wrapping fixed in overlay table for long overlay names
455
456
457

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

Piotr Gawron's avatar
Piotr Gawron committed
458
459
460
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
461
462
463
464
  * 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
465
466
467

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

Piotr Gawron's avatar
Piotr Gawron committed
468
469
470
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
471
  * Bug fix: integer configurtion options (like SMTP_PORT) are properly
Piotr Gawron's avatar
Piotr Gawron committed
472
473
    validated before saving
  * Bug fix: inside of reaction box wasn't properly aligned
Piotr Gawron's avatar
Piotr Gawron committed
474
  * Bug fix: too long data overlay name disturbed size of the map div and
Piotr Gawron's avatar
Piotr Gawron committed
475
476
477
478
479
    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
480
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Dec 2018 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
481

Piotr Gawron's avatar
Piotr Gawron committed
482
minerva (12.1.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
483
484
485
486
487
488
489
490
491
  * 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
492
minerva (12.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
493
494
495
496
  * 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
497
  * Small improvement: option to remove additional overlays generated by custom
Piotr Gawron's avatar
Piotr Gawron committed
498
    semantic zoom
499
  * Small improvement: 'Reduced modulation' edge was displayed differently in
Piotr Gawron's avatar
Piotr Gawron committed
500
501
502
    CellDesigner and Minerva
  * Small improvement: user-friendly documentation for plugin URL field
  * Small improvement: plugins have to access information about active submap
503
504
505
506
  * 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
507
  * Feature: minerva is distributed using rpm packages
508
  * Small improvement: annotations from RHEA are handled
Piotr Gawron's avatar
Piotr Gawron committed
509
510
  * Small improvement: changing of Terms of Service url allows admin to reset
    the status of ToS acceptance for all users
511
512
  * 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
513
514
515
516
517
518
519
520
  * 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
521
  * Bug fix: when there is a problem with adjusting font in complexes (because
Piotr Gawron's avatar
Piotr Gawron committed
522
523
524
525
526
    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
527
  * Bug fix: double click on user add button disabled
Piotr Gawron's avatar
Piotr Gawron committed
528
529
  * Bug fix: privileges are mirrored correctly across different popups
  * Bug fix: plugin tab css fixed
530
  * Bug fix: uploading sbml file with no ids in glyphs returned error that
Piotr Gawron's avatar
Piotr Gawron committed
531
532
533
    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
534

Piotr Gawron's avatar
Piotr Gawron committed
535
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Oct 2018 13:00:00 +0200
536

Piotr Gawron's avatar
Piotr Gawron committed
537
minerva (12.0.4) stable; urgency=medium
538
  * Bug fix: CellDesigner modifications that are drawn as reaction are handled
Piotr Gawron's avatar
Piotr Gawron committed
539
540
541
    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
542
  * Bug fix: Tair database moved to https
543
  * Bug fix: Taxnomy database changed html output that resulted in problems
Piotr Gawron's avatar
Piotr Gawron committed
544
    with resolving species name to the id
545

Piotr Gawron's avatar
Piotr Gawron committed
546
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Sep 2018 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
547

Piotr Gawron's avatar
Piotr Gawron committed
548
549
550
551
552
553
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
554

Piotr Gawron's avatar
Piotr Gawron committed
555
556
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Aug 2018 11:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
557
558
559
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
560
    works properly
Piotr Gawron's avatar
Piotr Gawron committed
561
562
563
564
  * 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
565
  * Performance: tomcat inside docker image by default can use 3G of memory
Piotr Gawron's avatar
Piotr Gawron committed
566

567
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 31 Jul 2018 13:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
568

Piotr Gawron's avatar
Piotr Gawron committed
569
570
571
572
573
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
574
  * Bug fix: opening map could crash when CellDesigner file contained duplicate
Piotr Gawron's avatar
Piotr Gawron committed
575
    reaction id
Piotr Gawron's avatar
Piotr Gawron committed
576
577
  * Bug fix: map is repositioned when info window is outside of current view in
    OpenLayers library
578

579
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 24 Jul 2018 10:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
580

Piotr Gawron's avatar
Piotr Gawron committed
581
582
minerva (12.0.0) stable; urgency=medium
  * Feature: There is alternative OpenLayers map engine available
Piotr Gawron's avatar
Piotr Gawron committed
583
  * Feature: database connection configuration (login, password, host, etc)
Piotr Gawron's avatar
Piotr Gawron committed
584
    can be modified using /etc/minerva/db.properties file
585
  * Feature: searching for elements in submap gives marker on top map
Piotr Gawron's avatar
Piotr Gawron committed
586
587
    indicating the submap connection
  * Feature: similar search results are merged
Piotr Gawron's avatar
Piotr Gawron committed
588
  * Feature: visualization of protein structures by MolArt
Piotr Gawron's avatar
Piotr Gawron committed
589
  * Feature: reordering of data overlays is supported
590
  * Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA  annotators
Piotr Gawron's avatar
Piotr Gawron committed
591
592
593
594
595
596
597
  * 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
598
599
  * 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
600
601
602
603
604
605
606
607
608
609
  * 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
610
611
  * 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
612
613
614
  * 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
615
616
  * Small improvement: Data overlays can use source element identifiers for
    filtering
Piotr Gawron's avatar
Piotr Gawron committed
617
618
619
  * 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
620
  * Small improvement: auto complete functionality for drugs, mirnas and
Piotr Gawron's avatar
Piotr Gawron committed
621
    chemicals
Piotr Gawron's avatar
Piotr Gawron committed
622
  * Small improvement: columns value and type are not mutually exclusive in
Piotr Gawron's avatar
Piotr Gawron committed
623
624
625
626
    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
627
  * Small improvement: data overlays color scale contains configurable default
Piotr Gawron's avatar
Piotr Gawron committed
628
629
    middle color (for 0 values)
  * Small improvement: opening data overlay switch to empty background
Piotr Gawron's avatar
Piotr Gawron committed
630
631
632
633
634
635
636
637
638
639
640
641
642
  * 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
643
  * Bug fix: uploading of zip files created by mac doesn't crash due to
Piotr Gawron's avatar
Piotr Gawron committed
644
645
    .DS_Store folder
  * Bug fix: auto complete is case insensitive
Piotr Gawron's avatar
Piotr Gawron committed
646
  * Bug fix: google maps API 404 errors for non existing tiles are removed
Piotr Gawron's avatar
Piotr Gawron committed
647

Piotr Gawron's avatar
Piotr Gawron committed
648
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Jul 2018 12:00:00 +0200
649

650
651
652
653
654
655
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
656
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 23 Jul 2018 12:00:00 +0200
657

Piotr Gawron's avatar
Piotr Gawron committed
658
minerva (11.1.2) stable; urgency=medium
659
660
  * 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
661
662
663
664
  * 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
665
666
667
668
669
670
671
672
673
674
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
675
676
677
minerva (11.1.0) stable; urgency=high
  * User can provide Google Maps API key that must be registered in google
    cloud account
678
679
  * User data overlays must be Google Maps API terms of use compliant
  * Terms of Use added
680

681
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 05 Jun 2018 9:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
682
  
683
684
minerva (11.0.10) stable; urgency=medium
  * Bug fix: link from overview image to search result was broken
685

686
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Apr 2018 15:00:00 +0200
687

Piotr Gawron's avatar
Piotr Gawron committed
688
689
690
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
691

Piotr Gawron's avatar
Piotr Gawron committed
692
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
693

Piotr Gawron's avatar
Piotr Gawron committed
694
695
696
697
698
699
700
701
702
703
704
705
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
706
  * Bug fix: comments on submaps are visualized properly
Piotr Gawron's avatar
Piotr Gawron committed
707

Piotr Gawron's avatar
Piotr Gawron committed
708
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 05 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
709

Piotr Gawron's avatar
Piotr Gawron committed
710
711
712
713
714
715
716
717
718
719
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

720
minerva (11.0.6) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
721
722
  * Bug fix: fix a bug when entering invalid mirna id

723
724
725
 -- 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
726
  * Bug fix: fix on connection to drugbank database
727
728
  * Bug fix: posttranslational modification data was sometimes unavailable
    in search results panel
Piotr Gawron's avatar
Piotr Gawron committed
729

730
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 30 Nov 2017 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
731

732
minerva (11.0.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
733
  * Bug fix: fix on connection to taxonomy database
734
735
  * 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
736

737
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 09 Nov 2017 14:50:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
738

739
minerva (11.0.3) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
740
  * Bug fix: removing empty project removed images from all projects
741
742
743
744
745
746
747
748
749
  * 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
750
  * Bug fix: login issues when default page is in secure area
751
752
753
754

 -- 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
755
  * Bug fix: logout caused issues with session data
756
757
758
759
760

 -- 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
761
762
  * Bug fix: security issue - access to specific map can be restricted
    by the user login
763
764
  * Bug fix: sbgn import
  * Bug fix: mesh connector
Piotr Gawron's avatar
Piotr Gawron committed
765
  * Rest API (documentation can be found here:
766
767
    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
768
    corner (when Search tab is not open)
769
770
  * 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
771
772
    proper text box
  * Layout changes: the main one is that there are only 3 tab panels
773
774
775
776
777
778
779
780
781
    (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
782
783
  * Overlay presents description field if possible

784
785

 -- Piotr Gawron <piotr.gawron@uni.lu>  Sat, 04 Mar 2017 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
786

787
788
789
790
791
792
793
794
795
796
797
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
798
  * Bug fix: search for multiple drugs will not return more drugs than
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
    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
816
817
  * Bug fix: trigger reaction and physical stimulation reactions are no
    longer allowed (CellDesigner data model issue)
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
  * 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
857
858
859
860
861
862
  * 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
863
864
865
866
867

 -- 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
868
869
870
871
872
  * Searching by annotations
  * Errors from parsing data forwarded to client
  * Notification email system added
  * Warnings are downloadable
  * Complex map (composed from many small maps)
873
  * Visualization of Recon specific annotations
Piotr Gawron's avatar
Piotr Gawron committed
874
875
876
877
878
879