CHANGELOG 51.6 KB
Newer Older
Piotr Gawron's avatar
Piotr Gawron committed
1
minerva (14.0.8) stable; urgency=medium
2
  * Bug fix: API didn't allow to upload pluins with local url (#1084,
Piotr Gawron's avatar
Piotr Gawron committed
3
4
5
    regression 14.0.7)
  * Bug fix: upload of data overlay with two entries having different uniprot
    identifier but pointing to the same gene crashed (#1083)
6
  * Bug fix: don't allow to remove plugin twice (#1081)
7
8
  * Bug fix: upload of SBML file with very short reaction length could produce
    a map that couldn't be exported to SBML anymore (#1078)
9
  * Bug fix: import of structural state from SBGN-ML PD that cannot be
Piotr Gawron's avatar
Piotr Gawron committed
10
11
    normalized to residue is changed into structural state without losing
    information (#1062)
12
13
  * Bug fix: import of stimulation modifiers from SBGN-ML crashed converter
    (#1063)
Piotr Gawron's avatar
Piotr Gawron committed
14
15
  * Bug fix: export to SBGN files created from newt source produced corrupted
    disconnected reactions
Piotr Gawron's avatar
Piotr Gawron committed
16
  * Bug fix: upload from zip file allowed empty overlay name (#1065)
17
18
  * Bug fix: genome browser slider didn't work properly in Safari on
    non-default Browser zoom level (#1048)
19
20
  * Bug fix: project without background overlay but with some custom data
    overlays crashed with an error (#1066)
21
22
  * Bug fix: when session expires updating options in configuration panel threw
    unhandled error (#1068)
Piotr Gawron's avatar
Piotr Gawron committed
23
24
25

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 23 Jan 2020 12:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
26
27
28
29
30
31
minerva (14.0.7) stable; urgency=high
  * Bug fix: API allowed to provide malformed plugin url that could be used for
    xss attack (#1073)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 14 Jan 2020 17:00:00 +0200

32
33
34
minerva (14.0.6) stable; urgency=medium
  * Bug fix: opening map with no background overlays and search request in url
    provides proper error message (#1046)
35
36
  * Bug fix: search by identifier didn't consider identifiers added by
    annotators (#1047)
37
38
  * Bug fix: if map has SHOW OVERVIEW, the legend/comment/clear were not
    displayed at all (regresion 14.0.5, #1045)
39
40
  * Bug fix: when there is a problem with database during removing project, 
    project removal doesn't hang (#1058)
41
  * Bug fix: coloring of the reaction wasn't applied to center of reaction
Piotr Gawron's avatar
Piotr Gawron committed
42
    (regression 14.0.0, #1057)
43
44
  * Bug fix: genetic variant overlay improperly processed elements identified
    by miriam identifiers, like uniprot (#1059)
Piotr Gawron's avatar
Piotr Gawron committed
45
46
  * Bug fix: invalid information was provided for genetic variants overlay when
    map organism was defined (#1060)
47

Piotr Gawron's avatar
Piotr Gawron committed
48
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 19 Dec 2019 13:00:00 +0200
49

50
51
52
minerva (14.0.5) stable; urgency=medium
  * Bug fix: copy-paste of genetic-variant data overlay into Add overlay 
    content dialog could crash upload (#1040)
53
54
  * Bug fix: some annotators (like Cazy) were crashing on old installations 
    (#1029)
55
56
  * Bug fix: uploading a map that breaks postgres constraints hung upload of 
    the project (#1028)
57
58
59
  * Bug fix: uploading of the page with low internet connection speed could 
    produce empty screen for several seconds/minutes - now the loading icon is
    present (#1025)
60
  * Bug fix: search for NADH drug resulted in drug with empty name (#1018)
Piotr Gawron's avatar
Piotr Gawron committed
61
  * Bug fix: export to SBML didn't handle properly arrows (#1015)
62
  * Bug fix: Font colour of text area was preserved in Empty view (#1014)
63
  * Bug fix: exported sbml file always contain model identifier (#1013)
Piotr Gawron's avatar
Piotr Gawron committed
64
65
  * Bug fix: typo allel reverted to allele in overlay data (regression 14.0.0,
    #1012)
Piotr Gawron's avatar
Piotr Gawron committed
66
67
  * Bug fix: after loading/removing too many plugins it was impossible to load
    new plugins (#1011)
68
69
70
  * Bug fix: CLEAR button disappears after legend, comment checkboxes when 
    plugin tab used to much space (#976)

Piotr Gawron's avatar
Piotr Gawron committed
71
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 03 Dec 2019 12:00:00 +0200
72

Piotr Gawron's avatar
Piotr Gawron committed
73
minerva (14.0.4) stable; urgency=high
74
75
  * Bug fix: some SBGN files uploaded to minerva could not be exported to SBML
    due to problems with identifiers used by SBGN (#1006)
76
77
  * Bug fix: upload of data overlay with conflicting overlay types caused error
    (#998)
78
79
  * Bug fix: upload of sbml file with protein modifications inside complex 
    crashed visualization (#966)
80
81
  * Bug fix: list of overlays for admin and curator included also other people
    overlays (regression 14.0.3, #1008)
82
83
  * Bug fix: refresh button did not refresh overlay list after overlay was 
    removed over API (#997)
84

Piotr Gawron's avatar
Piotr Gawron committed
85
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 07 Nov 2019 11:00:00 +0200
86

Piotr Gawron's avatar
Piotr Gawron committed
87
minerva (14.0.3) stable; urgency=medium
88
89
  * Bug fix: default zoom level on main map works even when x or y are
    undefined (#993)
90
  * Bug fix: sbml parser had sometimes problems with combining layout and multi
Piotr Gawron's avatar
Piotr Gawron committed
91
    packages (#966)
Piotr Gawron's avatar
Piotr Gawron committed
92
93
  * Bug fix: parsing of CellDesigner files that contained substanceUnits could
    crash the upload (#985)
94
  * Bug fix: verification of version length added when uploading project
95
    implemented (#978)
96
  * Bug fix: CLEAR button disappeared when plugin tab used to much space (#976)
97
  * Bug fix: removing data overlay refreshes list of overlays in info window
Piotr Gawron's avatar
Piotr Gawron committed
98
99
    (#974)
  * Bug fix: general overlays are always on top of data overlays in info window
100
    (#975)
Piotr Gawron's avatar
Piotr Gawron committed
101
102
103
  * 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
104
  * Bug fix: opening map with no available background crashed (#964)
105
  * Bug fix: uploading SBGN file that does not pass xsd validation provides a
106
    warning, but does not fail upload (#937)
107
  * Bug fix: export of the map to SBML that was imported with older version
108
    (below 14.0.0) didn't produce valid SBML (#970)
109
110
  * Bug fix: fields in add project window are reinitialized after each open
    (#963)
111
  * Bug fix: filename case in uploaded zip files is preserved (#964)
112
  * Bug fix: +/- buttons were misaligned in genome browser (#942)
113
114
  * Bug fix: color of links in the left panel was unintentionally changed 
    (#990)
115
  * Bug fix: minerva logo in left panel is centred properly
116
  * Bug fix: width of search button icon was too big
Piotr Gawron's avatar
Piotr Gawron committed
117

Piotr Gawron's avatar
Piotr Gawron committed
118
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 18 Oct 2019 15:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
119

120
121
122
123
124
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

125
126
127
128
129
130
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

131
132
133
134
135
136
137
138
139
140
141
142
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)
143
  * Small improvement: info window contains information about overlay No (#919)
144
145
  * Small improvement: sorting by columns that doesn't make sense in admin
    panel is disabled (#895)
Piotr Gawron's avatar
Piotr Gawron committed
146
  * Small improvement: version of minerva is visible in map browser panel
147
  * Small improvement: small info about annotator details is available in
148
    select annotators dialog (#923)
149
  * Small improvement: CellDesigner layers are always visualized as pathways
Piotr Gawron's avatar
Piotr Gawron committed
150
    (#813)
151
152
  * Small improvement: notification email uses minerva name and id of affected
    project (#926)
153
  * Small improvement: information about person who uploaded project is visible
Piotr Gawron's avatar
Piotr Gawron committed
154
    in list of projects (#927)
155
  * Small improvement: tab with list of glyphs is available when adding project
Piotr Gawron's avatar
Piotr Gawron committed
156
    with glyphs (#925)
157
  * Small improvement: BackgroundColor parameter should be assigned using ":"
158
    character (#929)
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
  * 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)
188
  * Bug fix: work on FF Private Window mode could cause logout or raise an
189
    error on when opening new tab with minerva (#892)
190
  * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server
191
    Error" (#889)
Piotr Gawron's avatar
Piotr Gawron committed
192
  * Bug fix: edit project dialog verifies organism id  (#914)
193
  * Bug fix: all colors in boolean reaction (from CellDesigner) are processed
Piotr Gawron's avatar
Piotr Gawron committed
194
    properly (#907)
195
196
  * Bug fix: proper line type for boolean reaction is used on the whole
    reaction (#908)
197
198
  * Bug fix: creating project with too long name hung upload (#916)
  * Bug fix: too long user login threw an error (#915)
199
  * Bug fix: when uploading generic data overlay the type was not updated in
Piotr Gawron's avatar
Piotr Gawron committed
200
    case the type was not specified in the input file (#906)
201
  * Bug fix: list of types when copying from annotators contains only types
Piotr Gawron's avatar
Piotr Gawron committed
202
    that are selectable in the dialog (#911)
Piotr Gawron's avatar
Piotr Gawron committed
203
  * Bug fix: too long name for data overlay in info window is trimmed (#919)
Piotr Gawron's avatar
Piotr Gawron committed
204
  * Bug fix: too long name in general overlay list is wrapped (#857)
205
  * Bug fix: after genome is removed list of genomes is refreshed (#922)
Piotr Gawron's avatar
Piotr Gawron committed
206
  * Bug fix: REST API bioEntities:search method didn't limit results to the
Piotr Gawron's avatar
Piotr Gawron committed
207
    submodel id (#860)
208
  * Bug fix: Empty Overlay colours were not preserved during export to
Piotr Gawron's avatar
Piotr Gawron committed
209
    CellDesigner (#714)
Piotr Gawron's avatar
Piotr Gawron committed
210
  * Bug fix: problem with unloading plugin is properly handled (#884)
Piotr Gawron's avatar
Piotr Gawron committed
211
  * Bug fix: upload of invalid plugin doesn't add it to plugin tab and list of
212
    loaded plugins (#885)
213
214
215
  * 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
216
    drawn
217
  * Bug fix: color handling in CellDesigner did not work properly for modifiers
218
219
    inside boolean gateway
  * Bug fix: CellDesigner file exported from minerva was not fully compliant
Piotr Gawron's avatar
Piotr Gawron committed
220
    with SBML standard (#831)
221
  * Bug fix: MiRNA targets are limited only to the organism associated with the
222
    map (#66)
223
  * Bug fix: Search drug by target element did not return values when this
224
    element was annotated automatically (#216)
Piotr Gawron's avatar
Piotr Gawron committed
225

226
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 09 Oct 2019 12:00:00 +0200
227

Piotr Gawron's avatar
Piotr Gawron committed
228
minerva (13.2.0) stable; urgency=medium
229
  * Small improvement: MolArt v1.4 is used which provide information from
Piotr Gawron's avatar
Piotr Gawron committed
230
    PredictProtein (#913)
231
232
233
234
  * 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)
235
236
  * Bug fix: show element title option wasn't influencing title visibility
    (#910)
Piotr Gawron's avatar
Piotr Gawron committed
237

Piotr Gawron's avatar
Piotr Gawron committed
238
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 29 Aug 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
239
240
241
242
243
244
245
246
247

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
248
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 14 Aug 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
249

Piotr Gawron's avatar
Piotr Gawron committed
250
251
minerva (13.1.2) stable; urgency=medium
  * Bug fix: Information about problematic zip file is more specific (#865)
252
  * Bug fix: Url didn't contain list of opened plugins and they weren't reload
253
    automatically on refresh (#866)
Piotr Gawron's avatar
Piotr Gawron committed
254

255
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Jul 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
256

257
258
minerva (13.1.1) stable; urgency=medium
  * Bug fix: adding gene mapping before the genome caused an error (#835)
259
  * Bug fix: "Terms of Use" change to "Terms of Service" in all places (#843)
260
  * Bug fix: upgrade to 13.1.0 crashed on machines where every element was
261
    inside compartment (#856)
262
  * Bug fix: searching for some drugs in chembl didn't provide any results even
263
    though that data exists, for instance 'DORLIMOMAB ARITOX' (#842)
264
  * Bug fix: user wasn't logged out in all tabs when the log out event appeard
265
    in only one of them (#847)
266

Piotr Gawron's avatar
Piotr Gawron committed
267
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue,  2 Jul 2019 19:00:00 +0200
268

Piotr Gawron's avatar
Piotr Gawron committed
269
minerva (13.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
270
  * Feature: annotators are more flexible - you can define set of input and
271
    outputs used by annotator (#617)
Piotr Gawron's avatar
Piotr Gawron committed
272
273
  * Feature: changes in admin panel doesn't require saving - they are saved
    automatically (#676)
Piotr Gawron's avatar
Piotr Gawron committed
274
  * Feature: elements can have custom glyphs used for visualization (#487)
275
  * Small improvement: model_name renamed to map_name in data overlay columns
Piotr Gawron's avatar
Piotr Gawron committed
276
    (#827)
277
278
  * 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
279
    deprecated (#827)
280
  * Small improvement: all bio entities have z-index associated with them
Piotr Gawron's avatar
Piotr Gawron committed
281
    (#487)
Piotr Gawron's avatar
Piotr Gawron committed
282
283
  * Small improvement: validation of the organism and disease id on map upload
    added (#618)
Piotr Gawron's avatar
Piotr Gawron committed
284
  * Small improvement: added current username next to logout button in admin
285
    panel (#660)
Piotr Gawron's avatar
Piotr Gawron committed
286
  * Small improvement: New comment dialog does not contain content of previous
287
    comment dialog (#680)
Piotr Gawron's avatar
Piotr Gawron committed
288
  * Small improvement: Left logo is configurable (#731)
289
  * Small improvement: list of element types in choose annotator dialog is
Ewa Smula's avatar
Ewa Smula committed
290
    sorted (#798)
291
292
  * Small improvement: Plugin API provides list of overview images (#702)
  * Small improvement: Plugin API allows to show/hide overview images (#702)
293
  * Small improvement: Plugin API allows to trigger search on the map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
294
  * Small improvement: Plugin API allows to clear search results on map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
295
  * Small improvement: edit/remove project button is disabled until project is
296
    uploaded (#683)
Piotr Gawron's avatar
Piotr Gawron committed
297
  * Small improvement: warning about capslock is visible on login page when
298
    necessary (#658)
Piotr Gawron's avatar
Piotr Gawron committed
299
  * Small improvement: names of columns in data overlay are unified: no
Piotr Gawron's avatar
Piotr Gawron committed
300
    whitespace, "_" used as separator (#596)
301
302
  * Small improvement: list of references in drug panel contains PUBMED prefix
    (#666)
Piotr Gawron's avatar
Piotr Gawron committed
303
  * Small improvement: list of projects is auto refreshed every 5 seconds if at
304
    least one of the project is uploading/removing (#610)
Piotr Gawron's avatar
Piotr Gawron committed
305
  * Small improvement: passwords to email account and ldap are not sent over
Piotr Gawron's avatar
Piotr Gawron committed
306
    API (#732)
Piotr Gawron's avatar
Piotr Gawron committed
307
  * Small improvement: reactant/product/modifier specific colors are parsed
Piotr Gawron's avatar
Piotr Gawron committed
308
    properly from CellDesigner file (#597)
Piotr Gawron's avatar
Piotr Gawron committed
309
  * Small improvement: Info tab contains information about disease and
310
    organism when info is provided
Piotr Gawron's avatar
Piotr Gawron committed
311
312
313
  * Small improvement: Info tab provides information about model annotations
    and submap tabs provide information about submaps annotations if applicable
    (#591)
314
315
  * Small improvement: uploading sbml file should automatically discover a file
    type (#784)
316
  * Small improvement: when plugin listeners crash the system notifies user
317
    about problem with a plugin (#767)
318
  * Small improvement: when exporting reaction and elements there is
Piotr Gawron's avatar
Piotr Gawron committed
319
    possibility to filter by (sub)map (#615)
320
  * Small improvement: during first opening of a map, the zoom level is
Piotr Gawron's avatar
Piotr Gawron committed
321
    automatically computed if no default information is provided (#776)
322
  * Small improvement: when adding new project columns "Root map", "Mapping
Piotr Gawron's avatar
Piotr Gawron committed
323
    file" and "Map type" are merged (#700)
Piotr Gawron's avatar
Piotr Gawron committed
324
  * Small improvement: allow admin to disable CORS check (#802)
325
  * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
326
    SemanticZoomLevelTransparency (#801)
327
  * Small improvement: export/import from SBML support z-index in LAYOUT
328
    extension
329
  * Bug fix: due to blocking of our requests from ctdbase the autocomplete for
Piotr Gawron's avatar
Piotr Gawron committed
330
331
332
333
334
335
336
337
    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
338
  * Bug fix: plugin tab header wasn't properly resized after adding plugins
Piotr Gawron's avatar
Piotr Gawron committed
339
340
341
342
343
344
    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)
345
  * Bug fix: gene_name column is allowed only in the genetic variant data
Piotr Gawron's avatar
Piotr Gawron committed
346
347
348
349
350
351
352
    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)
353
  * Bug fix: asynchronous calls on showing/hiding data overlays might cause
Piotr Gawron's avatar
Piotr Gawron committed
354
    problems due to network latency (#830)
Piotr Gawron's avatar
Piotr Gawron committed
355
  * Bug fix: progress bar of gene genome mapping upload is refreshing properly
356
    (#728)
Piotr Gawron's avatar
Piotr Gawron committed
357
  * Bug fix: when editing project Disease and Organism could not be removed
Piotr Gawron's avatar
Piotr Gawron committed
358
    (#616)
Piotr Gawron's avatar
Piotr Gawron committed
359
360
361
  * 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
362
    slightly separated from target phenotype (#664)
363
  * Bug fix: order of genomes in admin panel doesn't change after refreshing
364
    list of genomes (#761)
365
  * Bug fix: fixing situation when Molart started with variation overlay not
Piotr Gawron's avatar
Piotr Gawron committed
366
    having the aa change information
367
  * Bug fix: plugin contect element width is adjusted when link to tabs are
368
    wrapped in more than one line (#758)
Ewa Smula's avatar
Ewa Smula committed
369
  * Bug fix: export to CellDesigner preserve font size (#798)
370
  * Bug fix: layout data was ignored for some reactions when importing from
Piotr Gawron's avatar
Piotr Gawron committed
371
    SBML (#812)
372

Piotr Gawron's avatar
Piotr Gawron committed
373
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 27 Jun 2019 14:00:00 +0200
374

375
minerva (13.0.0) stable; urgency=medium
376
377
  * 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
378
379
380
381
    Ubuntu-14 (#223)

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

Piotr Gawron's avatar
Piotr Gawron committed
382
383
minerva (12.2.3) stable; urgency=medium
  * Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790)
384
  * Bug fix: searching of chemicals stopped working due to expired SSL
Piotr Gawron's avatar
Piotr Gawron committed
385
    certificate on https://ctdbase.org/
386
  * Bug fix: remove button is disabled after starting removing of the data
387
    overlay (#791)
388
  * Bug fix: search autocomplete hint could be initially hidden (#793)
389
  * Bug fix: updating terms of use could crash when list of users was removed
390
    in separate tab or by another user (#797)
Piotr Gawron's avatar
Piotr Gawron committed
391
  * Bug fix: name of the checkbox in ADD PROJECT window adjusted (#799)
392
393
  * 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
394
395
  * 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
396
397
398

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

Piotr Gawron's avatar
Piotr Gawron committed
399
minerva (12.2.2) stable; urgency=medium
400
  * Bug fix: downloading overlays didn't work from admin panel when project
Piotr Gawron's avatar
Piotr Gawron committed
401
    with different id than default map was accessed
402
  * Bug fix: change of owner of the data overlay in admin panel incorrectly
Piotr Gawron's avatar
Piotr Gawron committed
403
    ordered overlays (#777)
404
  * Bug fix: chemical search didn't use updated disease identifier, original
405
    disease id from project upload was used instead (#779)
406
  * Bug fix: user login with special characters (like '@')  could cause
Piotr Gawron's avatar
Piotr Gawron committed
407
    problems in admin panel (#780)
408
409
  * Bug fix: removing project without full control in the system (but with
    enough privileges to remove project) caused "Not enough privileges" error
410
    (#778)
411
  * Bug fix: export of custom properties (like synonyms) are properly encoded
Piotr Gawron's avatar
Piotr Gawron committed
412
    in CellDesigner xml (#785)
413
414
415
  * 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
416

Piotr Gawron's avatar
Piotr Gawron committed
417
418
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
419
420
    read colors properly) (#744)
  * Bug fix: removing active plugin didn't switch plugin tab to the next loaded
421
    plugin (#757)
Piotr Gawron's avatar
Piotr Gawron committed
422
423
  * Bug fix: closed submap will not be reopened after page refresh (#763)
  * Bug fix: comment remove button is disabled for users without proper
424
    privileges (#766)
Piotr Gawron's avatar
Piotr Gawron committed
425
  * Bug fix: invalid pubmed identifier could break clicking on element
426
    containing it (#764, #765, #769)
Piotr Gawron's avatar
Piotr Gawron committed
427
  * Bug fix: cache for API queries is explicitly disabled - some queries could
428
    be mistakenly cached and the system behaviour might get unstable (#771)
Piotr Gawron's avatar
Piotr Gawron committed
429
430
431

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

Piotr Gawron's avatar
Piotr Gawron committed
432
minerva (12.2.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
433
  * Feature: bug report utility
Piotr Gawron's avatar
Piotr Gawron committed
434
435
  * Feature: url GET parameters support all kind of search and selected overlays
    highlight
436
  * Feature: user can create custom logging configuration in file
Piotr Gawron's avatar
Piotr Gawron committed
437
438
439
440
    /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
441
  * Feature: API tool providing possibility to transform different types of
Piotr Gawron's avatar
Piotr Gawron committed
442
    file formats
443
  * Feature: current state of the browsed map is reflected in the url (position,
Piotr Gawron's avatar
Piotr Gawron committed
444
    zoom, overlays, search queries, etc.)
Piotr Gawron's avatar
Piotr Gawron committed
445
446
447
448
449
  * 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
450
  * Small improvement: all popup dialogs in the application have dialog
Piotr Gawron's avatar
Piotr Gawron committed
451
452
453
    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
454
455
  * Small improvement: export to SBML includes unit factors
  * Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
456
  * Small improvement: genetics information allows to provide information about
Piotr Gawron's avatar
Piotr Gawron committed
457
    modification on peptide level that could be visualized in MolArt
458
  * Small improvement: allow to control the background and font color of areas
Piotr Gawron's avatar
Piotr Gawron committed
459
    drawn from text areas in CellDesigner "layers"
460
  * Small improvement: config logo location is relative to the root minerva
Piotr Gawron's avatar
Piotr Gawron committed
461
462
    deployment directory
  * Small improvement: there is branding minerva logo in the left panel
463
464
465
466
467
468
469
470
471
472
473
474
  * 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
475
476
  * Small improvement: there is max size of the map in configuration panel that
    disables upload of too big files
477
  * Small improvement: hitting enter on login page logs in the user (no need to
Piotr Gawron's avatar
Piotr Gawron committed
478
    click on the login button)
479
  * Small improvement: refresh button in overlays panel (useful when data
Piotr Gawron's avatar
Piotr Gawron committed
480
481
482
    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
483
  * Small improvement: 'BACK TO MAP' link is available only when guest account
Piotr Gawron's avatar
Piotr Gawron committed
484
485
    has proper access level
  * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
486
487
    email account is provided
  * Small improvement: Plugin API allows to show/hide data overlays
Piotr Gawron's avatar
Piotr Gawron committed
488
  * Bug fix: Icons were sometimes not properly loaded on Safari (#661)
Piotr Gawron's avatar
Piotr Gawron committed
489
  * Bug fix: migration scripts are compatibile with postgres 9.3 version that
Piotr Gawron's avatar
Piotr Gawron committed
490
    is default on Ubuntu 14 (#762)
Piotr Gawron's avatar
Piotr Gawron committed
491
  * Bug fix: update/remove button is disabled when user has no privileges for
Piotr Gawron's avatar
Piotr Gawron committed
492
    managing overlays (#742)
Piotr Gawron's avatar
Piotr Gawron committed
493
  * Bug fix: when user cannot manage users information in overlays and users
Piotr Gawron's avatar
Piotr Gawron committed
494
    tab in edit project dialog is provided instead of hiding tabs (#756)
Piotr Gawron's avatar
Piotr Gawron committed
495
496
  * 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
497
498
    again (#697)
  * Bug fix: editing/removing project requires Map Management privilege (#681)
Piotr Gawron's avatar
Piotr Gawron committed
499
  * Bug fix: when removeAllListeners is called list of registered listeners is
Piotr Gawron's avatar
Piotr Gawron committed
500
    cleaned (#687)
Piotr Gawron's avatar
Piotr Gawron committed
501
  * Bug fix: when plugin is removed the html elements associated with it are
Piotr Gawron's avatar
Piotr Gawron committed
502
503
    removed as well (#686)
  * Bug fix: when creating new user default privileges are set properly (#692)
Piotr Gawron's avatar
Piotr Gawron committed
504
  * Bug fix: plugin can be added after plugin has been removed in admin plugin
Piotr Gawron's avatar
Piotr Gawron committed
505
    panel (#686)
Piotr Gawron's avatar
Piotr Gawron committed
506
  * Bug fix: too many annotations (>=100) caused misaligning in the left panel
Piotr Gawron's avatar
Piotr Gawron committed
507
    (#708)
Piotr Gawron's avatar
Piotr Gawron committed
508
509
510
  * 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
511
512
    example in admin panel configuration tab (#719)
  * Bug fix: description of transcription site is centered (#720)
Piotr Gawron's avatar
Piotr Gawron committed
513
  * Bug fix: selecting too few parameters in export doesn't throw reportable
Piotr Gawron's avatar
Piotr Gawron committed
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
    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
529
  * Bug fix: export to CellDesigner align inhibition reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
530
  * Bug fix: export/import to/from SBML handles Heterodimer Association
Piotr Gawron's avatar
Piotr Gawron committed
531
    reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
532
  * Bug fix: logo doesn't need to be square
533
  * Bug fix: when clicking on a search link (in overview window), input in the
Piotr Gawron's avatar
Piotr Gawron committed
534
    left tab was not modified
535
  * Bug fix: in admin panel changing of genome version is blocking interface
Piotr Gawron's avatar
Piotr Gawron committed
536
    until data about url is retrieved
537
538
  * 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
539
540
  * Bug fix: export to SBGN did not export compartments
  * Bug fix: export of complex states to SBGN did not work
541
  * Bug fix: type of the data overlay can be defined in the file content
Piotr Gawron's avatar
Piotr Gawron committed
542
543
    (useful when uploading genetic variants)
  * Bug fix: CLEAR button clears comment checkbox if necessary
Piotr Gawron's avatar
Piotr Gawron committed
544
  * Bug fix: minerva install problem on ubuntu 18 fixed
Piotr Gawron's avatar
Piotr Gawron committed
545

Piotr Gawron's avatar
Piotr Gawron committed
546
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 25 Mar 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
547

Sascha Herzinger's avatar
Sascha Herzinger committed
548
minerva (12.1.8) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
549
  * Bug fix: add a project reset users custom overlays limit to default (#679)
550
  * Bug fix: edit/remove project button was disabled based on Configuration
Piotr Gawron's avatar
Piotr Gawron committed
551
    Manage Privilege, but should be based on Project Manage Privilege (#681)
552
  * Bug fix: another minor problem with updating privileges introduced in
Piotr Gawron's avatar
Piotr Gawron committed
553
    12.1.6 fixed (#659)
Sascha Herzinger's avatar
Sascha Herzinger committed
554

Piotr Gawron's avatar
Piotr Gawron committed
555
556
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 8 Feb 2019 15:30:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
557
558
559
560
561
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
562
563
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
564
565
  * Bug fix: plugin API had sometimes problems with fetching reactions
    properly
Piotr Gawron's avatar
Piotr Gawron committed
566
567
  * 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
568
569
  * 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
570
  * Bug fix: fetching some drugs via API could cause 500
Piotr Gawron's avatar
Piotr Gawron committed
571

Piotr Gawron's avatar
Piotr Gawron committed
572
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Jan 2019 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
573

Piotr Gawron's avatar
Piotr Gawron committed
574
575
576
577
578
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
579
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 10 Jan 2019 14:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
580

581
minerva (12.1.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
582
  * Bug fix: no check for limit on custom data overlays fixed
583
  * Bug fix: error message improved when there is privilege problem during
Piotr Gawron's avatar
Piotr Gawron committed
584
    data overlay upload
Piotr Gawron's avatar
Piotr Gawron committed
585
  * Bug fix: upload of data overlay from admin panel didn't work
586
  * Bug fix: add project button is disabled when user doesn't have proper
Piotr Gawron's avatar
Piotr Gawron committed
587
    privileges ("Add project" privilege)
588
  * Bug fix: there are no more extra markers due to map wrapping
589
590
  * Bug fix: upload of the project failed when another project was removed
    during upload
Piotr Gawron's avatar
Piotr Gawron committed
591
  * Bug fix:  word wrapping fixed in overlay table for long overlay names
592
593
594

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

Piotr Gawron's avatar
Piotr Gawron committed
595
596
597
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
598
599
600
601
  * 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
602
603
604

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

Piotr Gawron's avatar
Piotr Gawron committed
605
606
607
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
608
  * Bug fix: integer configurtion options (like SMTP_PORT) are properly
Piotr Gawron's avatar
Piotr Gawron committed
609
610
    validated before saving
  * Bug fix: inside of reaction box wasn't properly aligned
Piotr Gawron's avatar
Piotr Gawron committed
611
  * Bug fix: too long data overlay name disturbed size of the map div and
Piotr Gawron's avatar
Piotr Gawron committed
612
613
614
615
616
    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
617
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Dec 2018 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
618

Piotr Gawron's avatar
Piotr Gawron committed
619
minerva (12.1.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
620
621
622
623
624
625
626
627
628
  * 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
629
minerva (12.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
630
631
632
633
  * 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
634
  * Small improvement: option to remove additional overlays generated by custom
Piotr Gawron's avatar
Piotr Gawron committed
635
    semantic zoom
636
  * Small improvement: 'Reduced modulation' edge was displayed differently in
Piotr Gawron's avatar
Piotr Gawron committed
637
638
639
    CellDesigner and Minerva
  * Small improvement: user-friendly documentation for plugin URL field
  * Small improvement: plugins have to access information about active submap
640
641
642
643
  * 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
644
  * Feature: minerva is distributed using rpm packages
645
  * Small improvement: annotations from RHEA are handled
Piotr Gawron's avatar
Piotr Gawron committed
646
647
  * Small improvement: changing of Terms of Service url allows admin to reset
    the status of ToS acceptance for all users
648
649
  * 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
650
651
652
653
654
655
656
657
  * 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
658
  * Bug fix: when there is a problem with adjusting font in complexes (because
Piotr Gawron's avatar
Piotr Gawron committed
659
660
661
662
663
    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
664
  * Bug fix: double click on user add button disabled
Piotr Gawron's avatar
Piotr Gawron committed
665
666
  * Bug fix: privileges are mirrored correctly across different popups
  * Bug fix: plugin tab css fixed
667
  * Bug fix: uploading sbml file with no ids in glyphs returned error that
Piotr Gawron's avatar
Piotr Gawron committed
668
669
670
    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
671

Piotr Gawron's avatar
Piotr Gawron committed
672
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Oct 2018 13:00:00 +0200
673

Piotr Gawron's avatar
Piotr Gawron committed
674
minerva (12.0.4) stable; urgency=medium
675
  * Bug fix: CellDesigner modifications that are drawn as reaction are handled
Piotr Gawron's avatar
Piotr Gawron committed
676
677
678
    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
679
  * Bug fix: Tair database moved to https
680
  * Bug fix: Taxnomy database changed html output that resulted in problems
Piotr Gawron's avatar
Piotr Gawron committed
681
    with resolving species name to the id
682

Piotr Gawron's avatar
Piotr Gawron committed
683
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Sep 2018 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
684

Piotr Gawron's avatar
Piotr Gawron committed
685
686
687
688
689
690
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
691

Piotr Gawron's avatar
Piotr Gawron committed
692
693
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Aug 2018 11:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
694
695
696
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
697
    works properly
Piotr Gawron's avatar
Piotr Gawron committed
698
699
700
701
  * 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
702
  * Performance: tomcat inside docker image by default can use 3G of memory
Piotr Gawron's avatar
Piotr Gawron committed
703

704
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 31 Jul 2018 13:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
705

Piotr Gawron's avatar
Piotr Gawron committed
706
707
708
709
710
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
711
  * Bug fix: opening map could crash when CellDesigner file contained duplicate
Piotr Gawron's avatar
Piotr Gawron committed
712
    reaction id
Piotr Gawron's avatar
Piotr Gawron committed
713
714
  * Bug fix: map is repositioned when info window is outside of current view in
    OpenLayers library
715

716
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 24 Jul 2018 10:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
717

Piotr Gawron's avatar
Piotr Gawron committed
718
719
minerva (12.0.0) stable; urgency=medium
  * Feature: There is alternative OpenLayers map engine available
Piotr Gawron's avatar
Piotr Gawron committed
720
  * Feature: database connection configuration (login, password, host, etc)
Piotr Gawron's avatar
Piotr Gawron committed
721
    can be modified using /etc/minerva/db.properties file
722
  * Feature: searching for elements in submap gives marker on top map
Piotr Gawron's avatar
Piotr Gawron committed
723
724
    indicating the submap connection
  * Feature: similar search results are merged
Piotr Gawron's avatar
Piotr Gawron committed
725
  * Feature: visualization of protein structures by MolArt
Piotr Gawron's avatar
Piotr Gawron committed
726
  * Feature: reordering of data overlays is supported
727
  * Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA  annotators
Piotr Gawron's avatar
Piotr Gawron committed
728
729
730
731
732
733
734
  * 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
735
736
  * 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
737
738
739
740
741
742
743
744
745
746
  * 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
747
748
  * 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
749
750
751
  * 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
752
753
  * Small improvement: Data overlays can use source element identifiers for
    filtering
Piotr Gawron's avatar
Piotr Gawron committed
754
755
756
  * 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
757
  * Small improvement: auto complete functionality for drugs, mirnas and
Piotr Gawron's avatar
Piotr Gawron committed
758
    chemicals
Piotr Gawron's avatar
Piotr Gawron committed
759
  * Small improvement: columns value and type are not mutually exclusive in
Piotr Gawron's avatar
Piotr Gawron committed
760
761
762
763
    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
764
  * Small improvement: data overlays color scale contains configurable default
Piotr Gawron's avatar
Piotr Gawron committed
765
766
    middle color (for 0 values)
  * Small improvement: opening data overlay switch to empty background
Piotr Gawron's avatar
Piotr Gawron committed
767
768
769
770
771
772
773
774
775
776
777
778
779
  * 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
780
  * Bug fix: uploading of zip files created by mac doesn't crash due to
Piotr Gawron's avatar
Piotr Gawron committed
781
782
    .DS_Store folder
  * Bug fix: auto complete is case insensitive
Piotr Gawron's avatar
Piotr Gawron committed
783
  * Bug fix: google maps API 404 errors for non existing tiles are removed
Piotr Gawron's avatar
Piotr Gawron committed
784

Piotr Gawron's avatar
Piotr Gawron committed
785
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Jul 2018 12:00:00 +0200
786

787
788
789
790
791
792
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
793
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 23 Jul 2018 12:00:00 +0200
794

Piotr Gawron's avatar
Piotr Gawron committed
795
minerva (11.1.2) stable; urgency=medium
796
797
  * 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
798
799
800
801
  * 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
802
803
804
805
806
807
808
809
810
811
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
812
813
814
minerva (11.1.0) stable; urgency=high
  * User can provide Google Maps API key that must be registered in google
    cloud account