CHANGELOG 46.5 KB
Newer Older
Piotr Gawron's avatar
Piotr Gawron committed
1
2
3
minerva (14.0.3) stable; urgency=medium
  * Bug fix: parsing of CellDesigner files that contained substanceUnits could
    crash the upload (#985)
4
5
  * Bug fix: verificatin of version length added when uploading project 
    implemented (#978)
6
  * Bug fix: CLEAR button disappeard when plugin tab used to much space (#976)
Piotr Gawron's avatar
Piotr Gawron committed
7
8
9
10
11
12
13
14
  * Bug fix: removing data overlay refreshes list of overlays in info window 
    (#974)
  * Bug fix: general overlays are always on top of data overlays in info window
    (#975) 
  * Bug fix: refresh button in overlay panel synchronise list of general and
    user provided data overlays (#975)
  * Bug fix: changing order of data overlays is reflected in info window

Piotr Gawron's avatar
Piotr Gawron committed
15
16
17

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Oct 2019 9:00:00 +0200

18
19
20
21
22
minerva (14.0.2) stable; urgency=medium
  * Bug fix: Genetic data overlay uploaded prior to 14.0.0 crashed maps (#988)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 15 Oct 2019 11:00:00 +0200

23
24
25
26
27
28
minerva (14.0.1) stable; urgency=medium
  * Bug fix: maps that were annotated using old Biocompendium annotator could
    not load properly (#986)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 15 Oct 2019 9:00:00 +0200

29
30
31
32
33
34
35
36
37
38
39
40
minerva (14.0.0) stable; urgency=medium
  * Feature removal: BioCompendium annotator removed (#32)
  * Feature removal: support for tomcat7 removed (#828)
  * Feature: security layer redesigned - privilege types and scope changed
    (#636, #624)
  * Feature: log4j is replaced with log4j2 logging mechanism (#291)
  * Feature: database installed via debian package is done via dbconfig-commons
    (#469)
  * Feature: Replaced connection pool manager C3P0 with better maintained
    Hikari - restart of postgresql database doesn't require restart of tomcat
    (#564)
  * Small improvement: debian package can be installed on debian:buster (#879)
41
  * Small improvement: info window contains information about overlay No (#919)
42
43
  * Small improvement: sorting by columns that doesn't make sense in admin
    panel is disabled (#895)
Piotr Gawron's avatar
Piotr Gawron committed
44
  * Small improvement: version of minerva is visible in map browser panel
45
  * Small improvement: small info about annotator details is available in
46
    select annotators dialog (#923)
47
  * Small improvement: CellDesigner layers are always visualized as pathways
Piotr Gawron's avatar
Piotr Gawron committed
48
    (#813)
49
50
  * Small improvement: notification email uses minerva name and id of affected
    project (#926)
51
  * Small improvement: information about person who uploaded project is visible
Piotr Gawron's avatar
Piotr Gawron committed
52
    in list of projects (#927)
53
  * Small improvement: tab with list of glyphs is available when adding project
Piotr Gawron's avatar
Piotr Gawron committed
54
    with glyphs (#925)
55
  * Small improvement: BackgroundColor parameter should be assigned using ":"
56
    character (#929)
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
  * 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)
  * Small improvement: caching is active by default for new users when
    uploading project (#202)
  * Small improvement: when removing overlay in admin panel there is a
    confirmation dialog (#696)
  * Small improvement: overlay name is obligatory (#698)
  * Small improvement: list of projects in admin panel contains creation date
    (#447)
  * Small improvement: links in list of publications open in new tab (#447)
  * Small improvement: target gene in search panel contains also information
    about type of database that identifies the target (#66)
  * Small improvement: redundant 'references' field in gene variants data
    overlay is now deprecated (#850)
  * Small improvement: information about deprecated columns in data overlay is
    visible in overlay list (#838)
  * Small improvement: publication list is resizeable (#740)
  * Small improvement: user list on project edit dialog is sortable (#808)
  * Bug fix: exported SBML passes online validation (#831)
  * Bug fix: allow user to remove own comments (#931)
  * Bug fix: validation of project name length is provided (#950)
  * Bug fix: list of "Copy from" elements in "Select valid annotations" dialog 
    is shortened to used bio entity types (#911)
  * Bug fix: version of the project is limited to 20 characters (#951)
  * Bug fix: export to CD could misalign reaction lines that were imported from
    format that didn't require reaction line to be attached to the species (#933)
  * Bug fix: problem with uploading data_overlays with type included in header
    (#936)
86
  * Bug fix: work on FF Private Window mode could cause logout or raise an
87
    error on when opening new tab with minerva (#892)
88
  * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server
89
    Error" (#889)
Piotr Gawron's avatar
Piotr Gawron committed
90
  * Bug fix: edit project dialog verifies organism id  (#914)
91
  * Bug fix: all colors in boolean reaction (from CellDesigner) are processed
Piotr Gawron's avatar
Piotr Gawron committed
92
    properly (#907)
93
94
  * Bug fix: proper line type for boolean reaction is used on the whole
    reaction (#908)
95
96
  * Bug fix: creating project with too long name hung upload (#916)
  * Bug fix: too long user login threw an error (#915)
97
  * Bug fix: when uploading generic data overlay the type was not updated in
Piotr Gawron's avatar
Piotr Gawron committed
98
    case the type was not specified in the input file (#906)
99
  * Bug fix: list of types when copying from annotators contains only types
Piotr Gawron's avatar
Piotr Gawron committed
100
    that are selectable in the dialog (#911)
Piotr Gawron's avatar
Piotr Gawron committed
101
  * Bug fix: too long name for data overlay in info window is trimmed (#919)
Piotr Gawron's avatar
Piotr Gawron committed
102
  * Bug fix: too long name in general overlay list is wrapped (#857)
103
  * Bug fix: after genome is removed list of genomes is refreshed (#922)
Piotr Gawron's avatar
Piotr Gawron committed
104
  * Bug fix: REST API bioEntities:search method didn't limit results to the
Piotr Gawron's avatar
Piotr Gawron committed
105
    submodel id (#860)
106
  * Bug fix: Empty Overlay colours were not preserved during export to
Piotr Gawron's avatar
Piotr Gawron committed
107
    CellDesigner (#714)
Piotr Gawron's avatar
Piotr Gawron committed
108
  * Bug fix: problem with unloading plugin is properly handled (#884)
Piotr Gawron's avatar
Piotr Gawron committed
109
  * Bug fix: upload of invalid plugin doesn't add it to plugin tab and list of
110
    loaded plugins (#885)
111
112
113
  * 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
114
    drawn
115
  * Bug fix: color handling in CellDesigner did not work properly for modifiers
116
117
    inside boolean gateway
  * Bug fix: CellDesigner file exported from minerva was not fully compliant
Piotr Gawron's avatar
Piotr Gawron committed
118
    with SBML standard (#831)
119
  * Bug fix: MiRNA targets are limited only to the organism associated with the
120
    map (#66)
121
  * Bug fix: Search drug by target element did not return values when this
122
    element was annotated automatically (#216)
Piotr Gawron's avatar
Piotr Gawron committed
123

124
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 09 Oct 2019 12:00:00 +0200
125

Piotr Gawron's avatar
Piotr Gawron committed
126
minerva (13.2.0) stable; urgency=medium
127
  * Small improvement: MolArt v1.4 is used which provide information from
Piotr Gawron's avatar
Piotr Gawron committed
128
    PredictProtein (#913)
129
130
131
132
  * Bug fix: search by drugs didn't check synonyms in chembl database
  * Bug fix: verification of overlay type added (#917)
  * Bug fix: opening edit project/user dialog returned list of users/projects
    to the 1st page (#909)
133
134
  * Bug fix: show element title option wasn't influencing title visibility
    (#910)
Piotr Gawron's avatar
Piotr Gawron committed
135

Piotr Gawron's avatar
Piotr Gawron committed
136
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 29 Aug 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
137
138
139
140
141
142
143
144
145

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's avatar
Piotr Gawron committed
146
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 14 Aug 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
147

Piotr Gawron's avatar
Piotr Gawron committed
148
149
minerva (13.1.2) stable; urgency=medium
  * Bug fix: Information about problematic zip file is more specific (#865)
150
  * Bug fix: Url didn't contain list of opened plugins and they weren't reload
151
    automatically on refresh (#866)
Piotr Gawron's avatar
Piotr Gawron committed
152

153
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Jul 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
154

155
156
minerva (13.1.1) stable; urgency=medium
  * Bug fix: adding gene mapping before the genome caused an error (#835)
157
  * Bug fix: "Terms of Use" change to "Terms of Service" in all places (#843)
158
  * Bug fix: upgrade to 13.1.0 crashed on machines where every element was
159
    inside compartment (#856)
160
  * Bug fix: searching for some drugs in chembl didn't provide any results even
161
    though that data exists, for instance 'DORLIMOMAB ARITOX' (#842)
162
  * Bug fix: user wasn't logged out in all tabs when the log out event appeard
163
    in only one of them (#847)
164

Piotr Gawron's avatar
Piotr Gawron committed
165
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue,  2 Jul 2019 19:00:00 +0200
166

Piotr Gawron's avatar
Piotr Gawron committed
167
minerva (13.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
168
  * Feature: annotators are more flexible - you can define set of input and
169
    outputs used by annotator (#617)
Piotr Gawron's avatar
Piotr Gawron committed
170
171
  * Feature: changes in admin panel doesn't require saving - they are saved
    automatically (#676)
Piotr Gawron's avatar
Piotr Gawron committed
172
  * Feature: elements can have custom glyphs used for visualization (#487)
173
  * Small improvement: model_name renamed to map_name in data overlay columns
Piotr Gawron's avatar
Piotr Gawron committed
174
    (#827)
175
176
  * 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
177
    deprecated (#827)
178
  * Small improvement: all bio entities have z-index associated with them
Piotr Gawron's avatar
Piotr Gawron committed
179
    (#487)
Piotr Gawron's avatar
Piotr Gawron committed
180
181
  * Small improvement: validation of the organism and disease id on map upload
    added (#618)
Piotr Gawron's avatar
Piotr Gawron committed
182
  * Small improvement: added current username next to logout button in admin
183
    panel (#660)
Piotr Gawron's avatar
Piotr Gawron committed
184
  * Small improvement: New comment dialog does not contain content of previous
185
    comment dialog (#680)
Piotr Gawron's avatar
Piotr Gawron committed
186
  * Small improvement: Left logo is configurable (#731)
187
  * Small improvement: list of element types in choose annotator dialog is
Ewa Smula's avatar
Ewa Smula committed
188
    sorted (#798)
189
190
  * Small improvement: Plugin API provides list of overview images (#702)
  * Small improvement: Plugin API allows to show/hide overview images (#702)
191
  * Small improvement: Plugin API allows to trigger search on the map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
192
  * Small improvement: Plugin API allows to clear search results on map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
193
  * Small improvement: edit/remove project button is disabled until project is
194
    uploaded (#683)
Piotr Gawron's avatar
Piotr Gawron committed
195
  * Small improvement: warning about capslock is visible on login page when
196
    necessary (#658)
Piotr Gawron's avatar
Piotr Gawron committed
197
  * Small improvement: names of columns in data overlay are unified: no
Piotr Gawron's avatar
Piotr Gawron committed
198
    whitespace, "_" used as separator (#596)
199
200
  * Small improvement: list of references in drug panel contains PUBMED prefix
    (#666)
Piotr Gawron's avatar
Piotr Gawron committed
201
  * Small improvement: list of projects is auto refreshed every 5 seconds if at
202
    least one of the project is uploading/removing (#610)
Piotr Gawron's avatar
Piotr Gawron committed
203
  * Small improvement: passwords to email account and ldap are not sent over
Piotr Gawron's avatar
Piotr Gawron committed
204
    API (#732)
Piotr Gawron's avatar
Piotr Gawron committed
205
  * Small improvement: reactant/product/modifier specific colors are parsed
Piotr Gawron's avatar
Piotr Gawron committed
206
    properly from CellDesigner file (#597)
Piotr Gawron's avatar
Piotr Gawron committed
207
  * Small improvement: Info tab contains information about disease and
208
    organism when info is provided
Piotr Gawron's avatar
Piotr Gawron committed
209
210
211
  * Small improvement: Info tab provides information about model annotations
    and submap tabs provide information about submaps annotations if applicable
    (#591)
212
213
  * Small improvement: uploading sbml file should automatically discover a file
    type (#784)
214
  * Small improvement: when plugin listeners crash the system notifies user
215
    about problem with a plugin (#767)
216
  * Small improvement: when exporting reaction and elements there is
Piotr Gawron's avatar
Piotr Gawron committed
217
    possibility to filter by (sub)map (#615)
218
  * Small improvement: during first opening of a map, the zoom level is
Piotr Gawron's avatar
Piotr Gawron committed
219
    automatically computed if no default information is provided (#776)
220
  * Small improvement: when adding new project columns "Root map", "Mapping
Piotr Gawron's avatar
Piotr Gawron committed
221
    file" and "Map type" are merged (#700)
Piotr Gawron's avatar
Piotr Gawron committed
222
  * Small improvement: allow admin to disable CORS check (#802)
223
  * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
224
    SemanticZoomLevelTransparency (#801)
225
  * Small improvement: export/import from SBML support z-index in LAYOUT
226
    extension
227
  * Bug fix: due to blocking of our requests from ctdbase the autocomplete for
Piotr Gawron's avatar
Piotr Gawron committed
228
229
230
231
232
233
234
235
    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
236
  * Bug fix: plugin tab header wasn't properly resized after adding plugins
Piotr Gawron's avatar
Piotr Gawron committed
237
238
239
240
241
242
    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)
243
  * Bug fix: gene_name column is allowed only in the genetic variant data
Piotr Gawron's avatar
Piotr Gawron committed
244
245
246
247
248
249
250
    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)
251
  * Bug fix: asynchronous calls on showing/hiding data overlays might cause
Piotr Gawron's avatar
Piotr Gawron committed
252
    problems due to network latency (#830)
Piotr Gawron's avatar
Piotr Gawron committed
253
  * Bug fix: progress bar of gene genome mapping upload is refreshing properly
254
    (#728)
Piotr Gawron's avatar
Piotr Gawron committed
255
  * Bug fix: when editing project Disease and Organism could not be removed
Piotr Gawron's avatar
Piotr Gawron committed
256
    (#616)
Piotr Gawron's avatar
Piotr Gawron committed
257
258
259
  * 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
260
    slightly separated from target phenotype (#664)
261
  * Bug fix: order of genomes in admin panel doesn't change after refreshing
262
    list of genomes (#761)
263
  * Bug fix: fixing situation when Molart started with variation overlay not
Piotr Gawron's avatar
Piotr Gawron committed
264
    having the aa change information
265
  * Bug fix: plugin contect element width is adjusted when link to tabs are
266
    wrapped in more than one line (#758)
Ewa Smula's avatar
Ewa Smula committed
267
  * Bug fix: export to CellDesigner preserve font size (#798)
268
  * Bug fix: layout data was ignored for some reactions when importing from
Piotr Gawron's avatar
Piotr Gawron committed
269
    SBML (#812)
270

Piotr Gawron's avatar
Piotr Gawron committed
271
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 27 Jun 2019 14:00:00 +0200
272

273
minerva (13.0.0) stable; urgency=medium
274
275
  * 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
276
277
278
279
    Ubuntu-14 (#223)

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

Piotr Gawron's avatar
Piotr Gawron committed
280
281
minerva (12.2.3) stable; urgency=medium
  * Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790)
282
  * Bug fix: searching of chemicals stopped working due to expired SSL
Piotr Gawron's avatar
Piotr Gawron committed
283
    certificate on https://ctdbase.org/
284
  * Bug fix: remove button is disabled after starting removing of the data
285
    overlay (#791)
286
  * Bug fix: search autocomplete hint could be initially hidden (#793)
287
  * Bug fix: updating terms of use could crash when list of users was removed
288
    in separate tab or by another user (#797)
Piotr Gawron's avatar
Piotr Gawron committed
289
  * Bug fix: name of the checkbox in ADD PROJECT window adjusted (#799)
290
291
  * 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
292
293
  * 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
294
295
296

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

Piotr Gawron's avatar
Piotr Gawron committed
297
minerva (12.2.2) stable; urgency=medium
298
  * Bug fix: downloading overlays didn't work from admin panel when project
Piotr Gawron's avatar
Piotr Gawron committed
299
    with different id than default map was accessed
300
  * Bug fix: change of owner of the data overlay in admin panel incorrectly
Piotr Gawron's avatar
Piotr Gawron committed
301
    ordered overlays (#777)
302
  * Bug fix: chemical search didn't use updated disease identifier, original
303
    disease id from project upload was used instead (#779)
304
  * Bug fix: user login with special characters (like '@')  could cause
Piotr Gawron's avatar
Piotr Gawron committed
305
    problems in admin panel (#780)
306
307
  * Bug fix: removing project without full control in the system (but with
    enough privileges to remove project) caused "Not enough privileges" error
308
    (#778)
309
  * Bug fix: export of custom properties (like synonyms) are properly encoded
Piotr Gawron's avatar
Piotr Gawron committed
310
    in CellDesigner xml (#785)
311
312
313
  * 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
314

Piotr Gawron's avatar
Piotr Gawron committed
315
316
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
317
318
    read colors properly) (#744)
  * Bug fix: removing active plugin didn't switch plugin tab to the next loaded
319
    plugin (#757)
Piotr Gawron's avatar
Piotr Gawron committed
320
321
  * Bug fix: closed submap will not be reopened after page refresh (#763)
  * Bug fix: comment remove button is disabled for users without proper
322
    privileges (#766)
Piotr Gawron's avatar
Piotr Gawron committed
323
  * Bug fix: invalid pubmed identifier could break clicking on element
324
    containing it (#764, #765, #769)
Piotr Gawron's avatar
Piotr Gawron committed
325
  * Bug fix: cache for API queries is explicitly disabled - some queries could
326
    be mistakenly cached and the system behaviour might get unstable (#771)
Piotr Gawron's avatar
Piotr Gawron committed
327
328
329

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

Piotr Gawron's avatar
Piotr Gawron committed
330
minerva (12.2.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
331
  * Feature: bug report utility
Piotr Gawron's avatar
Piotr Gawron committed
332
333
  * Feature: url GET parameters support all kind of search and selected overlays
    highlight
334
  * Feature: user can create custom logging configuration in file
Piotr Gawron's avatar
Piotr Gawron committed
335
336
337
338
    /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
339
  * Feature: API tool providing possibility to transform different types of
Piotr Gawron's avatar
Piotr Gawron committed
340
    file formats
341
  * Feature: current state of the browsed map is reflected in the url (position,
Piotr Gawron's avatar
Piotr Gawron committed
342
    zoom, overlays, search queries, etc.)
Piotr Gawron's avatar
Piotr Gawron committed
343
344
345
346
347
  * 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
348
  * Small improvement: all popup dialogs in the application have dialog
Piotr Gawron's avatar
Piotr Gawron committed
349
350
351
    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
352
353
  * Small improvement: export to SBML includes unit factors
  * Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
354
  * Small improvement: genetics information allows to provide information about
Piotr Gawron's avatar
Piotr Gawron committed
355
    modification on peptide level that could be visualized in MolArt
356
  * Small improvement: allow to control the background and font color of areas
Piotr Gawron's avatar
Piotr Gawron committed
357
    drawn from text areas in CellDesigner "layers"
358
  * Small improvement: config logo location is relative to the root minerva
Piotr Gawron's avatar
Piotr Gawron committed
359
360
    deployment directory
  * Small improvement: there is branding minerva logo in the left panel
361
362
363
364
365
366
367
368
369
370
371
372
  * 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
373
374
  * Small improvement: there is max size of the map in configuration panel that
    disables upload of too big files
375
  * Small improvement: hitting enter on login page logs in the user (no need to
Piotr Gawron's avatar
Piotr Gawron committed
376
    click on the login button)
377
  * Small improvement: refresh button in overlays panel (useful when data
Piotr Gawron's avatar
Piotr Gawron committed
378
379
380
    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
381
  * Small improvement: 'BACK TO MAP' link is available only when guest account
Piotr Gawron's avatar
Piotr Gawron committed
382
383
    has proper access level
  * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
384
385
    email account is provided
  * Small improvement: Plugin API allows to show/hide data overlays
Piotr Gawron's avatar
Piotr Gawron committed
386
  * Bug fix: Icons were sometimes not properly loaded on Safari (#661)
Piotr Gawron's avatar
Piotr Gawron committed
387
  * Bug fix: migration scripts are compatibile with postgres 9.3 version that
Piotr Gawron's avatar
Piotr Gawron committed
388
    is default on Ubuntu 14 (#762)
Piotr Gawron's avatar
Piotr Gawron committed
389
  * Bug fix: update/remove button is disabled when user has no privileges for
Piotr Gawron's avatar
Piotr Gawron committed
390
    managing overlays (#742)
Piotr Gawron's avatar
Piotr Gawron committed
391
  * Bug fix: when user cannot manage users information in overlays and users
Piotr Gawron's avatar
Piotr Gawron committed
392
    tab in edit project dialog is provided instead of hiding tabs (#756)
Piotr Gawron's avatar
Piotr Gawron committed
393
394
  * 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
395
396
    again (#697)
  * Bug fix: editing/removing project requires Map Management privilege (#681)
Piotr Gawron's avatar
Piotr Gawron committed
397
  * Bug fix: when removeAllListeners is called list of registered listeners is
Piotr Gawron's avatar
Piotr Gawron committed
398
    cleaned (#687)
Piotr Gawron's avatar
Piotr Gawron committed
399
  * Bug fix: when plugin is removed the html elements associated with it are
Piotr Gawron's avatar
Piotr Gawron committed
400
401
    removed as well (#686)
  * Bug fix: when creating new user default privileges are set properly (#692)
Piotr Gawron's avatar
Piotr Gawron committed
402
  * Bug fix: plugin can be added after plugin has been removed in admin plugin
Piotr Gawron's avatar
Piotr Gawron committed
403
    panel (#686)
Piotr Gawron's avatar
Piotr Gawron committed
404
  * Bug fix: too many annotations (>=100) caused misaligning in the left panel
Piotr Gawron's avatar
Piotr Gawron committed
405
    (#708)
Piotr Gawron's avatar
Piotr Gawron committed
406
407
408
  * 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
409
410
    example in admin panel configuration tab (#719)
  * Bug fix: description of transcription site is centered (#720)
Piotr Gawron's avatar
Piotr Gawron committed
411
  * Bug fix: selecting too few parameters in export doesn't throw reportable
Piotr Gawron's avatar
Piotr Gawron committed
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
    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
427
  * Bug fix: export to CellDesigner align inhibition reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
428
  * Bug fix: export/import to/from SBML handles Heterodimer Association
Piotr Gawron's avatar
Piotr Gawron committed
429
    reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
430
  * Bug fix: logo doesn't need to be square
431
  * Bug fix: when clicking on a search link (in overview window), input in the
Piotr Gawron's avatar
Piotr Gawron committed
432
    left tab was not modified
433
  * Bug fix: in admin panel changing of genome version is blocking interface
Piotr Gawron's avatar
Piotr Gawron committed
434
    until data about url is retrieved
435
436
  * 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
437
438
  * Bug fix: export to SBGN did not export compartments
  * Bug fix: export of complex states to SBGN did not work
439
  * Bug fix: type of the data overlay can be defined in the file content
Piotr Gawron's avatar
Piotr Gawron committed
440
441
    (useful when uploading genetic variants)
  * Bug fix: CLEAR button clears comment checkbox if necessary
Piotr Gawron's avatar
Piotr Gawron committed
442
  * Bug fix: minerva install problem on ubuntu 18 fixed
Piotr Gawron's avatar
Piotr Gawron committed
443

Piotr Gawron's avatar
Piotr Gawron committed
444
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 25 Mar 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
445

Sascha Herzinger's avatar
Sascha Herzinger committed
446
minerva (12.1.8) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
447
  * Bug fix: add a project reset users custom overlays limit to default (#679)
448
  * Bug fix: edit/remove project button was disabled based on Configuration
Piotr Gawron's avatar
Piotr Gawron committed
449
    Manage Privilege, but should be based on Project Manage Privilege (#681)
450
  * Bug fix: another minor problem with updating privileges introduced in
Piotr Gawron's avatar
Piotr Gawron committed
451
    12.1.6 fixed (#659)
Sascha Herzinger's avatar
Sascha Herzinger committed
452

Piotr Gawron's avatar
Piotr Gawron committed
453
454
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 8 Feb 2019 15:30:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
455
456
457
458
459
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
460
461
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
462
463
  * Bug fix: plugin API had sometimes problems with fetching reactions
    properly
Piotr Gawron's avatar
Piotr Gawron committed
464
465
  * 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
466
467
  * 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
468
  * Bug fix: fetching some drugs via API could cause 500
Piotr Gawron's avatar
Piotr Gawron committed
469

Piotr Gawron's avatar
Piotr Gawron committed
470
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Jan 2019 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
471

Piotr Gawron's avatar
Piotr Gawron committed
472
473
474
475
476
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
477
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 10 Jan 2019 14:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
478

479
minerva (12.1.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
480
  * Bug fix: no check for limit on custom data overlays fixed
481
  * Bug fix: error message improved when there is privilege problem during
Piotr Gawron's avatar
Piotr Gawron committed
482
    data overlay upload
Piotr Gawron's avatar
Piotr Gawron committed
483
  * Bug fix: upload of data overlay from admin panel didn't work
484
  * Bug fix: add project button is disabled when user doesn't have proper
Piotr Gawron's avatar
Piotr Gawron committed
485
    privileges ("Add project" privilege)
486
  * Bug fix: there are no more extra markers due to map wrapping
487
488
  * Bug fix: upload of the project failed when another project was removed
    during upload
Piotr Gawron's avatar
Piotr Gawron committed
489
  * Bug fix:  word wrapping fixed in overlay table for long overlay names
490
491
492

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

Piotr Gawron's avatar
Piotr Gawron committed
493
494
495
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
496
497
498
499
  * 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
500
501
502

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

Piotr Gawron's avatar
Piotr Gawron committed
503
504
505
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
506
  * Bug fix: integer configurtion options (like SMTP_PORT) are properly
Piotr Gawron's avatar
Piotr Gawron committed
507
508
    validated before saving
  * Bug fix: inside of reaction box wasn't properly aligned
Piotr Gawron's avatar
Piotr Gawron committed
509
  * Bug fix: too long data overlay name disturbed size of the map div and
Piotr Gawron's avatar
Piotr Gawron committed
510
511
512
513
514
    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
515
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Dec 2018 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
516

Piotr Gawron's avatar
Piotr Gawron committed
517
minerva (12.1.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
518
519
520
521
522
523
524
525
526
  * 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
527
minerva (12.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
528
529
530
531
  * 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
532
  * Small improvement: option to remove additional overlays generated by custom
Piotr Gawron's avatar
Piotr Gawron committed
533
    semantic zoom
534
  * Small improvement: 'Reduced modulation' edge was displayed differently in
Piotr Gawron's avatar
Piotr Gawron committed
535
536
537
    CellDesigner and Minerva
  * Small improvement: user-friendly documentation for plugin URL field
  * Small improvement: plugins have to access information about active submap
538
539
540
541
  * 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
542
  * Feature: minerva is distributed using rpm packages
543
  * Small improvement: annotations from RHEA are handled
Piotr Gawron's avatar
Piotr Gawron committed
544
545
  * Small improvement: changing of Terms of Service url allows admin to reset
    the status of ToS acceptance for all users
546
547
  * 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
548
549
550
551
552
553
554
555
  * 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
556
  * Bug fix: when there is a problem with adjusting font in complexes (because
Piotr Gawron's avatar
Piotr Gawron committed
557
558
559
560
561
    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
562
  * Bug fix: double click on user add button disabled
Piotr Gawron's avatar
Piotr Gawron committed
563
564
  * Bug fix: privileges are mirrored correctly across different popups
  * Bug fix: plugin tab css fixed
565
  * Bug fix: uploading sbml file with no ids in glyphs returned error that
Piotr Gawron's avatar
Piotr Gawron committed
566
567
568
    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
569

Piotr Gawron's avatar
Piotr Gawron committed
570
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Oct 2018 13:00:00 +0200
571

Piotr Gawron's avatar
Piotr Gawron committed
572
minerva (12.0.4) stable; urgency=medium
573
  * Bug fix: CellDesigner modifications that are drawn as reaction are handled
Piotr Gawron's avatar
Piotr Gawron committed
574
575
576
    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
577
  * Bug fix: Tair database moved to https
578
  * Bug fix: Taxnomy database changed html output that resulted in problems
Piotr Gawron's avatar
Piotr Gawron committed
579
    with resolving species name to the id
580

Piotr Gawron's avatar
Piotr Gawron committed
581
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Sep 2018 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
582

Piotr Gawron's avatar
Piotr Gawron committed
583
584
585
586
587
588
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
589

Piotr Gawron's avatar
Piotr Gawron committed
590
591
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Aug 2018 11:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
592
593
594
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
595
    works properly
Piotr Gawron's avatar
Piotr Gawron committed
596
597
598
599
  * 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
600
  * Performance: tomcat inside docker image by default can use 3G of memory
Piotr Gawron's avatar
Piotr Gawron committed
601

602
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 31 Jul 2018 13:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
603

Piotr Gawron's avatar
Piotr Gawron committed
604
605
606
607
608
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
609
  * Bug fix: opening map could crash when CellDesigner file contained duplicate
Piotr Gawron's avatar
Piotr Gawron committed
610
    reaction id
Piotr Gawron's avatar
Piotr Gawron committed
611
612
  * Bug fix: map is repositioned when info window is outside of current view in
    OpenLayers library
613

614
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 24 Jul 2018 10:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
615

Piotr Gawron's avatar
Piotr Gawron committed
616
617
minerva (12.0.0) stable; urgency=medium
  * Feature: There is alternative OpenLayers map engine available
Piotr Gawron's avatar
Piotr Gawron committed
618
  * Feature: database connection configuration (login, password, host, etc)
Piotr Gawron's avatar
Piotr Gawron committed
619
    can be modified using /etc/minerva/db.properties file
620
  * Feature: searching for elements in submap gives marker on top map
Piotr Gawron's avatar
Piotr Gawron committed
621
622
    indicating the submap connection
  * Feature: similar search results are merged
Piotr Gawron's avatar
Piotr Gawron committed
623
  * Feature: visualization of protein structures by MolArt
Piotr Gawron's avatar
Piotr Gawron committed
624
  * Feature: reordering of data overlays is supported
625
  * Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA  annotators
Piotr Gawron's avatar
Piotr Gawron committed
626
627
628
629
630
631
632
  * 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
633
634
  * 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
635
636
637
638
639
640
641
642
643
644
  * 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
645
646
  * 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
647
648
649
  * 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
650
651
  * Small improvement: Data overlays can use source element identifiers for
    filtering
Piotr Gawron's avatar
Piotr Gawron committed
652
653
654
  * 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
655
  * Small improvement: auto complete functionality for drugs, mirnas and
Piotr Gawron's avatar
Piotr Gawron committed
656
    chemicals
Piotr Gawron's avatar
Piotr Gawron committed
657
  * Small improvement: columns value and type are not mutually exclusive in
Piotr Gawron's avatar
Piotr Gawron committed
658
659
660
661
    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
662
  * Small improvement: data overlays color scale contains configurable default
Piotr Gawron's avatar
Piotr Gawron committed
663
664
    middle color (for 0 values)
  * Small improvement: opening data overlay switch to empty background
Piotr Gawron's avatar
Piotr Gawron committed
665
666
667
668
669
670
671
672
673
674
675
676
677
  * 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
678
  * Bug fix: uploading of zip files created by mac doesn't crash due to
Piotr Gawron's avatar
Piotr Gawron committed
679
680
    .DS_Store folder
  * Bug fix: auto complete is case insensitive
Piotr Gawron's avatar
Piotr Gawron committed
681
  * Bug fix: google maps API 404 errors for non existing tiles are removed
Piotr Gawron's avatar
Piotr Gawron committed
682

Piotr Gawron's avatar
Piotr Gawron committed
683
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Jul 2018 12:00:00 +0200
684

685
686
687
688
689
690
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
691
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 23 Jul 2018 12:00:00 +0200
692

Piotr Gawron's avatar
Piotr Gawron committed
693
minerva (11.1.2) stable; urgency=medium
694
695
  * 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
696
697
698
699
  * 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
700
701
702
703
704
705
706
707
708
709
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
710
711
712
minerva (11.1.0) stable; urgency=high
  * User can provide Google Maps API key that must be registered in google
    cloud account
713
714
  * User data overlays must be Google Maps API terms of use compliant
  * Terms of Use added
715

716
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 05 Jun 2018 9:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
717
  
718
719
minerva (11.0.10) stable; urgency=medium
  * Bug fix: link from overview image to search result was broken
720

721
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Apr 2018 15:00:00 +0200
722

Piotr Gawron's avatar
Piotr Gawron committed
723
724
725
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
726

Piotr Gawron's avatar
Piotr Gawron committed
727
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
728

Piotr Gawron's avatar
Piotr Gawron committed
729
730
731
732
733
734
735
736
737
738
739
740
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
741
  * Bug fix: comments on submaps are visualized properly
Piotr Gawron's avatar
Piotr Gawron committed
742

Piotr Gawron's avatar
Piotr Gawron committed
743
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 05 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
744

Piotr Gawron's avatar
Piotr Gawron committed
745
746
747
748
749
750
751
752
753
754
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

755
minerva (11.0.6) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
756
757
  * Bug fix: fix a bug when entering invalid mirna id

758
759
760
 -- 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
761
  * Bug fix: fix on connection to drugbank database
762
763
  * Bug fix: posttranslational modification data was sometimes unavailable
    in search results panel
Piotr Gawron's avatar
Piotr Gawron committed
764

765
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 30 Nov 2017 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
766

767
minerva (11.0.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
768
  * Bug fix: fix on connection to taxonomy database
769
770
  * 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
771

772
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 09 Nov 2017 14:50:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
773

774
minerva (11.0.3) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
775
  * Bug fix: removing empty project removed images from all projects
776
777
778
779
780
781
782
783
784
  * 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
785
  * Bug fix: login issues when default page is in secure area
786
787
788
789

 -- 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
790
  * Bug fix: logout caused issues with session data
791
792
793
794
795

 -- 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
796
797
  * Bug fix: security issue - access to specific map can be restricted
    by the user login
798
799
  * Bug fix: sbgn import
  * Bug fix: mesh connector
Piotr Gawron's avatar
Piotr Gawron committed
800
  * Rest API (documentation can be found here:
801
802
    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
803
    corner (when Search tab is not open)
804
805
  * 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
806
807
    proper text box
  * Layout changes: the main one is that there are only 3 tab panels
808
809
810
811
812
813
814
815
816
    (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
817
818
  * Overlay presents description field if possible

819
820

 -- Piotr Gawron <piotr.gawron@uni.lu>  Sat, 04 Mar 2017 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
821

822
823
824
825
826
827
828
829
830
831
832
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
833
  * Bug fix: search for multiple drugs will not return more drugs than
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
    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