CHANGELOG 50.8 KB
Newer Older
1
minerva (15.0.0~alpha.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
2
  * Improvement: support for rendering colors in SBGNML added (#1009)
3
4
  * Small improvement: sort order of tables in admin panel is preserved among
    sessions (#836)
5
6
  * Small improvement: simple molecules in sbgn compliant view are drawn as 
    ellipses not circles (#796)
7
  * Small improvement: uploaded map is automatically cached (#983)
Piotr Gawron's avatar
Piotr Gawron committed
8
9
  * Small improvement: molart updated to version 1.5.0: Ability to show
    unobserved structure regions in the sequence view.
10
11
  * Small improvement: list of genomes is automatically refreshed during genome
    upload (#820)
Piotr Gawron's avatar
Piotr Gawron committed
12
  * Small improvement: items in context menu are reorganized (#787)
13
  * Small improvement: CellDesigner files from version 2.5 should be parseable
14
15
  * Bug fix: compartments limited by corner (left-top corner compartment, etc)
    are parsed properly from CellDesigner files
16
17
  * Bug fix: structural states of proteins are imported properly from SBGNML PD
    (#995)
18
  * Bug fix: clear button icon, refresh comments button and show overview
19
    button icons were missing (regression 15.0.0~alpha.0)
20
21
  * Bug fix: export to CellDesigner names with new line is properly handled
    (#930)
22
  * Bug fix: layout of the exported reactome pathways is fixed when reactome
23
    exporter violates SBGN specification (#707)
24
25
  * Bug fix: unknown catalysis boolean gate modifiers in CellDesigner are
    visualized with proper line type across all included modifiers (#957)
26
27
  * Bug fix: dimension of the modifications is the same as in minerva when
    exporting to SBGNML-PD (#554)
28

Piotr Gawron's avatar
Piotr Gawron committed
29
minerva (15.0.0~alpha.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
30
  * Improvement: logs provided for validation data model are structurized (#325)
Piotr Gawron's avatar
Piotr Gawron committed
31
  * Improvement: import/export of GPML implemented
Piotr Gawron's avatar
Piotr Gawron committed
32
  * Small improvement: compartments in not layouted SBML file are more
33
    scattered (#326)
34
35
  * Small improvement: when downloading a map results in too big file (>1MB)
    the content is compressed and returned as a zip file (#348)
Piotr Gawron's avatar
Piotr Gawron committed
36
37
  * Small improvement: confirmation dialog when removing "general view"
    overlays contain proper warning  (#809)
38
  * Small improvement: CellDesigner text area object can have "BorderColor"
Piotr Gawron's avatar
Piotr Gawron committed
39
    property defined (#806)
40
  * Small improvement: list of submaps is sorted alphabetically (#962)
41
42
  * Small improvement: notification about new releases of minerva added in
    admin panel (#961)
Piotr Gawron's avatar
Piotr Gawron committed
43
44
45
  * Small improvement: font awesome upgraded to 5.1 (new icon styles)
  * Small improvement: header contains login/logout button and access admin
    panel button (#982)
46
  * Bug fix: position of structural state is preserved on upload CellDesigner
Piotr Gawron's avatar
Piotr Gawron committed
47
    file (#671)
Piotr Gawron's avatar
Piotr Gawron committed
48
  * Bug fix: problematic notes doesn't crash CellDesigner upload (#968)
Piotr Gawron's avatar
Piotr Gawron committed
49

50
51
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 4 Nov 2019 11:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
52
minerva (14.0.4) stable; urgency=high
53
54
  * Bug fix: some SBGN files uploaded to minerva could not be exported to SBML
    due to problems with identifiers used by SBGN (#1006)
55
56
  * Bug fix: upload of data overlay with conflicting overlay types caused error
    (#998)
57
  * Bug fix: upload of sbml file with protein modifications inside complex
58
    crashed visualization (#966)
59
60
  * Bug fix: list of overlays for admin and curator included also other people
    overlays (regression 14.0.3, #1008)
61
  * Bug fix: refresh button did not refresh overlay list after overlay was
62
    removed over API (#997)
63

Piotr Gawron's avatar
Piotr Gawron committed
64
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 07 Nov 2019 11:00:00 +0200
65

Piotr Gawron's avatar
Piotr Gawron committed
66
minerva (14.0.3) stable; urgency=medium
67
68
  * Bug fix: default zoom level on main map works even when x or y are
    undefined (#993)
69
  * Bug fix: sbml parser had sometimes problems with combining layout and multi
Piotr Gawron's avatar
Piotr Gawron committed
70
    packages (#966)
Piotr Gawron's avatar
Piotr Gawron committed
71
72
  * Bug fix: parsing of CellDesigner files that contained substanceUnits could
    crash the upload (#985)
73
  * Bug fix: verification of version length added when uploading project
74
    implemented (#978)
75
  * Bug fix: CLEAR button disappeared when plugin tab used to much space (#976)
76
  * Bug fix: removing data overlay refreshes list of overlays in info window
Piotr Gawron's avatar
Piotr Gawron committed
77
78
    (#974)
  * Bug fix: general overlays are always on top of data overlays in info window
79
    (#975)
Piotr Gawron's avatar
Piotr Gawron committed
80
81
82
  * 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
83
  * Bug fix: opening map with no available background crashed (#964)
84
  * Bug fix: uploading SBGN file that does not pass xsd validation provides a
85
    warning, but does not fail upload (#937)
86
  * Bug fix: export of the map to SBML that was imported with older version
87
    (below 14.0.0) didn't produce valid SBML (#970)
88
89
  * Bug fix: fields in add project window are reinitialized after each open
    (#963)
90
  * Bug fix: filename case in uploaded zip files is preserved (#964)
91
  * Bug fix: +/- buttons were misaligned in genome browser (#942)
92
93
  * Bug fix: color of links in the left panel was unintentionally changed 
    (#990)
94
  * Bug fix: minerva logo in left panel is centred properly
95
  * Bug fix: width of search button icon was too big
Piotr Gawron's avatar
Piotr Gawron committed
96

Piotr Gawron's avatar
Piotr Gawron committed
97
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 18 Oct 2019 15:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
98

99
100
101
102
103
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

104
105
106
107
108
109
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

110
111
112
113
114
115
116
117
118
119
120
121
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)
122
  * Small improvement: info window contains information about overlay No (#919)
123
124
  * Small improvement: sorting by columns that doesn't make sense in admin
    panel is disabled (#895)
Piotr Gawron's avatar
Piotr Gawron committed
125
  * Small improvement: version of minerva is visible in map browser panel
126
  * Small improvement: small info about annotator details is available in
127
    select annotators dialog (#923)
128
  * Small improvement: CellDesigner layers are always visualized as pathways
Piotr Gawron's avatar
Piotr Gawron committed
129
    (#813)
130
131
  * Small improvement: notification email uses minerva name and id of affected
    project (#926)
132
  * Small improvement: information about person who uploaded project is visible
Piotr Gawron's avatar
Piotr Gawron committed
133
    in list of projects (#927)
134
  * Small improvement: tab with list of glyphs is available when adding project
Piotr Gawron's avatar
Piotr Gawron committed
135
    with glyphs (#925)
136
  * Small improvement: BackgroundColor parameter should be assigned using ":"
137
    character (#929)
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
  * 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)
167
  * Bug fix: work on FF Private Window mode could cause logout or raise an
168
    error on when opening new tab with minerva (#892)
169
  * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server
170
    Error" (#889)
Piotr Gawron's avatar
Piotr Gawron committed
171
  * Bug fix: edit project dialog verifies organism id  (#914)
172
  * Bug fix: all colors in boolean reaction (from CellDesigner) are processed
Piotr Gawron's avatar
Piotr Gawron committed
173
    properly (#907)
174
175
  * Bug fix: proper line type for boolean reaction is used on the whole
    reaction (#908)
176
177
  * Bug fix: creating project with too long name hung upload (#916)
  * Bug fix: too long user login threw an error (#915)
178
  * Bug fix: when uploading generic data overlay the type was not updated in
Piotr Gawron's avatar
Piotr Gawron committed
179
    case the type was not specified in the input file (#906)
180
  * Bug fix: list of types when copying from annotators contains only types
Piotr Gawron's avatar
Piotr Gawron committed
181
    that are selectable in the dialog (#911)
Piotr Gawron's avatar
Piotr Gawron committed
182
  * Bug fix: too long name for data overlay in info window is trimmed (#919)
Piotr Gawron's avatar
Piotr Gawron committed
183
  * Bug fix: too long name in general overlay list is wrapped (#857)
184
  * Bug fix: after genome is removed list of genomes is refreshed (#922)
Piotr Gawron's avatar
Piotr Gawron committed
185
  * Bug fix: REST API bioEntities:search method didn't limit results to the
Piotr Gawron's avatar
Piotr Gawron committed
186
    submodel id (#860)
187
  * Bug fix: Empty Overlay colours were not preserved during export to
Piotr Gawron's avatar
Piotr Gawron committed
188
    CellDesigner (#714)
Piotr Gawron's avatar
Piotr Gawron committed
189
  * Bug fix: problem with unloading plugin is properly handled (#884)
Piotr Gawron's avatar
Piotr Gawron committed
190
  * Bug fix: upload of invalid plugin doesn't add it to plugin tab and list of
191
    loaded plugins (#885)
192
193
194
  * 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
195
    drawn
196
  * Bug fix: color handling in CellDesigner did not work properly for modifiers
197
198
    inside boolean gateway
  * Bug fix: CellDesigner file exported from minerva was not fully compliant
Piotr Gawron's avatar
Piotr Gawron committed
199
    with SBML standard (#831)
200
  * Bug fix: MiRNA targets are limited only to the organism associated with the
201
    map (#66)
202
  * Bug fix: Search drug by target element did not return values when this
203
    element was annotated automatically (#216)
Piotr Gawron's avatar
Piotr Gawron committed
204

205
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 09 Oct 2019 12:00:00 +0200
206

Piotr Gawron's avatar
Piotr Gawron committed
207
minerva (13.2.0) stable; urgency=medium
208
  * Small improvement: MolArt v1.4 is used which provide information from
Piotr Gawron's avatar
Piotr Gawron committed
209
    PredictProtein (#913)
210
211
212
213
  * 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)
214
215
  * Bug fix: show element title option wasn't influencing title visibility
    (#910)
Piotr Gawron's avatar
Piotr Gawron committed
216

Piotr Gawron's avatar
Piotr Gawron committed
217
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 29 Aug 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
218
219
220
221
222
223
224
225
226

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
227
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 14 Aug 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
228

Piotr Gawron's avatar
Piotr Gawron committed
229
230
minerva (13.1.2) stable; urgency=medium
  * Bug fix: Information about problematic zip file is more specific (#865)
231
  * Bug fix: Url didn't contain list of opened plugins and they weren't reload
232
    automatically on refresh (#866)
Piotr Gawron's avatar
Piotr Gawron committed
233

234
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Jul 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
235

236
237
minerva (13.1.1) stable; urgency=medium
  * Bug fix: adding gene mapping before the genome caused an error (#835)
238
  * Bug fix: "Terms of Use" change to "Terms of Service" in all places (#843)
239
  * Bug fix: upgrade to 13.1.0 crashed on machines where every element was
240
    inside compartment (#856)
241
  * Bug fix: searching for some drugs in chembl didn't provide any results even
242
    though that data exists, for instance 'DORLIMOMAB ARITOX' (#842)
243
  * Bug fix: user wasn't logged out in all tabs when the log out event appeard
244
    in only one of them (#847)
245

Piotr Gawron's avatar
Piotr Gawron committed
246
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue,  2 Jul 2019 19:00:00 +0200
247

Piotr Gawron's avatar
Piotr Gawron committed
248
minerva (13.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
249
  * Feature: annotators are more flexible - you can define set of input and
250
    outputs used by annotator (#617)
Piotr Gawron's avatar
Piotr Gawron committed
251
252
  * Feature: changes in admin panel doesn't require saving - they are saved
    automatically (#676)
Piotr Gawron's avatar
Piotr Gawron committed
253
  * Feature: elements can have custom glyphs used for visualization (#487)
254
  * Small improvement: model_name renamed to map_name in data overlay columns
Piotr Gawron's avatar
Piotr Gawron committed
255
    (#827)
256
257
  * 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
258
    deprecated (#827)
259
  * Small improvement: all bio entities have z-index associated with them
Piotr Gawron's avatar
Piotr Gawron committed
260
    (#487)
Piotr Gawron's avatar
Piotr Gawron committed
261
262
  * Small improvement: validation of the organism and disease id on map upload
    added (#618)
Piotr Gawron's avatar
Piotr Gawron committed
263
  * Small improvement: added current username next to logout button in admin
264
    panel (#660)
Piotr Gawron's avatar
Piotr Gawron committed
265
  * Small improvement: New comment dialog does not contain content of previous
266
    comment dialog (#680)
Piotr Gawron's avatar
Piotr Gawron committed
267
  * Small improvement: Left logo is configurable (#731)
268
  * Small improvement: list of element types in choose annotator dialog is
Ewa Smula's avatar
Ewa Smula committed
269
    sorted (#798)
270
271
  * Small improvement: Plugin API provides list of overview images (#702)
  * Small improvement: Plugin API allows to show/hide overview images (#702)
272
  * Small improvement: Plugin API allows to trigger search on the map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
273
  * Small improvement: Plugin API allows to clear search results on map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
274
  * Small improvement: edit/remove project button is disabled until project is
275
    uploaded (#683)
Piotr Gawron's avatar
Piotr Gawron committed
276
  * Small improvement: warning about capslock is visible on login page when
277
    necessary (#658)
Piotr Gawron's avatar
Piotr Gawron committed
278
  * Small improvement: names of columns in data overlay are unified: no
Piotr Gawron's avatar
Piotr Gawron committed
279
    whitespace, "_" used as separator (#596)
280
281
  * Small improvement: list of references in drug panel contains PUBMED prefix
    (#666)
Piotr Gawron's avatar
Piotr Gawron committed
282
  * Small improvement: list of projects is auto refreshed every 5 seconds if at
283
    least one of the project is uploading/removing (#610)
Piotr Gawron's avatar
Piotr Gawron committed
284
  * Small improvement: passwords to email account and ldap are not sent over
Piotr Gawron's avatar
Piotr Gawron committed
285
    API (#732)
Piotr Gawron's avatar
Piotr Gawron committed
286
  * Small improvement: reactant/product/modifier specific colors are parsed
Piotr Gawron's avatar
Piotr Gawron committed
287
    properly from CellDesigner file (#597)
Piotr Gawron's avatar
Piotr Gawron committed
288
  * Small improvement: Info tab contains information about disease and
289
    organism when info is provided
Piotr Gawron's avatar
Piotr Gawron committed
290
291
292
  * Small improvement: Info tab provides information about model annotations
    and submap tabs provide information about submaps annotations if applicable
    (#591)
293
294
  * Small improvement: uploading sbml file should automatically discover a file
    type (#784)
295
  * Small improvement: when plugin listeners crash the system notifies user
296
    about problem with a plugin (#767)
297
  * Small improvement: when exporting reaction and elements there is
Piotr Gawron's avatar
Piotr Gawron committed
298
    possibility to filter by (sub)map (#615)
299
  * Small improvement: during first opening of a map, the zoom level is
Piotr Gawron's avatar
Piotr Gawron committed
300
    automatically computed if no default information is provided (#776)
301
  * Small improvement: when adding new project columns "Root map", "Mapping
Piotr Gawron's avatar
Piotr Gawron committed
302
    file" and "Map type" are merged (#700)
Piotr Gawron's avatar
Piotr Gawron committed
303
  * Small improvement: allow admin to disable CORS check (#802)
304
  * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
305
    SemanticZoomLevelTransparency (#801)
306
  * Small improvement: export/import from SBML support z-index in LAYOUT
307
    extension
308
  * Bug fix: due to blocking of our requests from ctdbase the autocomplete for
Piotr Gawron's avatar
Piotr Gawron committed
309
310
311
312
313
314
315
316
    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
317
  * Bug fix: plugin tab header wasn't properly resized after adding plugins
Piotr Gawron's avatar
Piotr Gawron committed
318
319
320
321
322
323
    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)
324
  * Bug fix: gene_name column is allowed only in the genetic variant data
Piotr Gawron's avatar
Piotr Gawron committed
325
326
327
328
329
330
331
    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)
332
  * Bug fix: asynchronous calls on showing/hiding data overlays might cause
Piotr Gawron's avatar
Piotr Gawron committed
333
    problems due to network latency (#830)
Piotr Gawron's avatar
Piotr Gawron committed
334
  * Bug fix: progress bar of gene genome mapping upload is refreshing properly
335
    (#728)
Piotr Gawron's avatar
Piotr Gawron committed
336
  * Bug fix: when editing project Disease and Organism could not be removed
Piotr Gawron's avatar
Piotr Gawron committed
337
    (#616)
Piotr Gawron's avatar
Piotr Gawron committed
338
339
340
  * 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
341
    slightly separated from target phenotype (#664)
342
  * Bug fix: order of genomes in admin panel doesn't change after refreshing
343
    list of genomes (#761)
344
  * Bug fix: fixing situation when Molart started with variation overlay not
Piotr Gawron's avatar
Piotr Gawron committed
345
    having the aa change information
346
  * Bug fix: plugin contect element width is adjusted when link to tabs are
347
    wrapped in more than one line (#758)
Ewa Smula's avatar
Ewa Smula committed
348
  * Bug fix: export to CellDesigner preserve font size (#798)
349
  * Bug fix: layout data was ignored for some reactions when importing from
Piotr Gawron's avatar
Piotr Gawron committed
350
    SBML (#812)
351

Piotr Gawron's avatar
Piotr Gawron committed
352
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 27 Jun 2019 14:00:00 +0200
353

354
minerva (13.0.0) stable; urgency=medium
355
356
  * 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
357
358
359
360
    Ubuntu-14 (#223)

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

Piotr Gawron's avatar
Piotr Gawron committed
361
362
minerva (12.2.3) stable; urgency=medium
  * Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790)
363
  * Bug fix: searching of chemicals stopped working due to expired SSL
Piotr Gawron's avatar
Piotr Gawron committed
364
    certificate on https://ctdbase.org/
365
  * Bug fix: remove button is disabled after starting removing of the data
366
    overlay (#791)
367
  * Bug fix: search autocomplete hint could be initially hidden (#793)
368
  * Bug fix: updating terms of use could crash when list of users was removed
369
    in separate tab or by another user (#797)
Piotr Gawron's avatar
Piotr Gawron committed
370
  * Bug fix: name of the checkbox in ADD PROJECT window adjusted (#799)
371
372
  * 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
373
374
  * 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
375
376
377

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

Piotr Gawron's avatar
Piotr Gawron committed
378
minerva (12.2.2) stable; urgency=medium
379
  * Bug fix: downloading overlays didn't work from admin panel when project
Piotr Gawron's avatar
Piotr Gawron committed
380
    with different id than default map was accessed
381
  * Bug fix: change of owner of the data overlay in admin panel incorrectly
Piotr Gawron's avatar
Piotr Gawron committed
382
    ordered overlays (#777)
383
  * Bug fix: chemical search didn't use updated disease identifier, original
384
    disease id from project upload was used instead (#779)
385
  * Bug fix: user login with special characters (like '@')  could cause
Piotr Gawron's avatar
Piotr Gawron committed
386
    problems in admin panel (#780)
387
388
  * Bug fix: removing project without full control in the system (but with
    enough privileges to remove project) caused "Not enough privileges" error
389
    (#778)
390
  * Bug fix: export of custom properties (like synonyms) are properly encoded
Piotr Gawron's avatar
Piotr Gawron committed
391
    in CellDesigner xml (#785)
392
393
394
  * 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
395

Piotr Gawron's avatar
Piotr Gawron committed
396
397
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
398
399
    read colors properly) (#744)
  * Bug fix: removing active plugin didn't switch plugin tab to the next loaded
400
    plugin (#757)
Piotr Gawron's avatar
Piotr Gawron committed
401
402
  * Bug fix: closed submap will not be reopened after page refresh (#763)
  * Bug fix: comment remove button is disabled for users without proper
403
    privileges (#766)
Piotr Gawron's avatar
Piotr Gawron committed
404
  * Bug fix: invalid pubmed identifier could break clicking on element
405
    containing it (#764, #765, #769)
Piotr Gawron's avatar
Piotr Gawron committed
406
  * Bug fix: cache for API queries is explicitly disabled - some queries could
407
    be mistakenly cached and the system behaviour might get unstable (#771)
Piotr Gawron's avatar
Piotr Gawron committed
408
409
410

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

Piotr Gawron's avatar
Piotr Gawron committed
411
minerva (12.2.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
412
  * Feature: bug report utility
Piotr Gawron's avatar
Piotr Gawron committed
413
414
  * Feature: url GET parameters support all kind of search and selected overlays
    highlight
415
  * Feature: user can create custom logging configuration in file
Piotr Gawron's avatar
Piotr Gawron committed
416
417
418
419
    /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
420
  * Feature: API tool providing possibility to transform different types of
Piotr Gawron's avatar
Piotr Gawron committed
421
    file formats
422
  * Feature: current state of the browsed map is reflected in the url (position,
Piotr Gawron's avatar
Piotr Gawron committed
423
    zoom, overlays, search queries, etc.)
Piotr Gawron's avatar
Piotr Gawron committed
424
425
426
427
428
  * 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
429
  * Small improvement: all popup dialogs in the application have dialog
Piotr Gawron's avatar
Piotr Gawron committed
430
431
432
    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
433
434
  * Small improvement: export to SBML includes unit factors
  * Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
435
  * Small improvement: genetics information allows to provide information about
Piotr Gawron's avatar
Piotr Gawron committed
436
    modification on peptide level that could be visualized in MolArt
437
  * Small improvement: allow to control the background and font color of areas
Piotr Gawron's avatar
Piotr Gawron committed
438
    drawn from text areas in CellDesigner "layers"
439
  * Small improvement: config logo location is relative to the root minerva
Piotr Gawron's avatar
Piotr Gawron committed
440
441
    deployment directory
  * Small improvement: there is branding minerva logo in the left panel
442
443
444
445
446
447
448
449
450
451
452
453
  * 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
454
455
  * Small improvement: there is max size of the map in configuration panel that
    disables upload of too big files
456
  * Small improvement: hitting enter on login page logs in the user (no need to
Piotr Gawron's avatar
Piotr Gawron committed
457
    click on the login button)
458
  * Small improvement: refresh button in overlays panel (useful when data
Piotr Gawron's avatar
Piotr Gawron committed
459
460
461
    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
462
  * Small improvement: 'BACK TO MAP' link is available only when guest account
Piotr Gawron's avatar
Piotr Gawron committed
463
464
    has proper access level
  * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
465
466
    email account is provided
  * Small improvement: Plugin API allows to show/hide data overlays
Piotr Gawron's avatar
Piotr Gawron committed
467
  * Bug fix: Icons were sometimes not properly loaded on Safari (#661)
Piotr Gawron's avatar
Piotr Gawron committed
468
  * Bug fix: migration scripts are compatibile with postgres 9.3 version that
Piotr Gawron's avatar
Piotr Gawron committed
469
    is default on Ubuntu 14 (#762)
Piotr Gawron's avatar
Piotr Gawron committed
470
  * Bug fix: update/remove button is disabled when user has no privileges for
Piotr Gawron's avatar
Piotr Gawron committed
471
    managing overlays (#742)
Piotr Gawron's avatar
Piotr Gawron committed
472
  * Bug fix: when user cannot manage users information in overlays and users
Piotr Gawron's avatar
Piotr Gawron committed
473
    tab in edit project dialog is provided instead of hiding tabs (#756)
Piotr Gawron's avatar
Piotr Gawron committed
474
475
  * 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
476
477
    again (#697)
  * Bug fix: editing/removing project requires Map Management privilege (#681)
Piotr Gawron's avatar
Piotr Gawron committed
478
  * Bug fix: when removeAllListeners is called list of registered listeners is
Piotr Gawron's avatar
Piotr Gawron committed
479
    cleaned (#687)
Piotr Gawron's avatar
Piotr Gawron committed
480
  * Bug fix: when plugin is removed the html elements associated with it are
Piotr Gawron's avatar
Piotr Gawron committed
481
482
    removed as well (#686)
  * Bug fix: when creating new user default privileges are set properly (#692)
Piotr Gawron's avatar
Piotr Gawron committed
483
  * Bug fix: plugin can be added after plugin has been removed in admin plugin
Piotr Gawron's avatar
Piotr Gawron committed
484
    panel (#686)
Piotr Gawron's avatar
Piotr Gawron committed
485
  * Bug fix: too many annotations (>=100) caused misaligning in the left panel
Piotr Gawron's avatar
Piotr Gawron committed
486
    (#708)
Piotr Gawron's avatar
Piotr Gawron committed
487
488
489
  * 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
490
491
    example in admin panel configuration tab (#719)
  * Bug fix: description of transcription site is centered (#720)
Piotr Gawron's avatar
Piotr Gawron committed
492
  * Bug fix: selecting too few parameters in export doesn't throw reportable
Piotr Gawron's avatar
Piotr Gawron committed
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
    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
508
  * Bug fix: export to CellDesigner align inhibition reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
509
  * Bug fix: export/import to/from SBML handles Heterodimer Association
Piotr Gawron's avatar
Piotr Gawron committed
510
    reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
511
  * Bug fix: logo doesn't need to be square
512
  * Bug fix: when clicking on a search link (in overview window), input in the
Piotr Gawron's avatar
Piotr Gawron committed
513
    left tab was not modified
514
  * Bug fix: in admin panel changing of genome version is blocking interface
Piotr Gawron's avatar
Piotr Gawron committed
515
    until data about url is retrieved
516
517
  * 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
518
519
  * Bug fix: export to SBGN did not export compartments
  * Bug fix: export of complex states to SBGN did not work
520
  * Bug fix: type of the data overlay can be defined in the file content
Piotr Gawron's avatar
Piotr Gawron committed
521
522
    (useful when uploading genetic variants)
  * Bug fix: CLEAR button clears comment checkbox if necessary
Piotr Gawron's avatar
Piotr Gawron committed
523
  * Bug fix: minerva install problem on ubuntu 18 fixed
Piotr Gawron's avatar
Piotr Gawron committed
524

Piotr Gawron's avatar
Piotr Gawron committed
525
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 25 Mar 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
526

Sascha Herzinger's avatar
Sascha Herzinger committed
527
minerva (12.1.8) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
528
  * Bug fix: add a project reset users custom overlays limit to default (#679)
529
  * Bug fix: edit/remove project button was disabled based on Configuration
Piotr Gawron's avatar
Piotr Gawron committed
530
    Manage Privilege, but should be based on Project Manage Privilege (#681)
531
  * Bug fix: another minor problem with updating privileges introduced in
Piotr Gawron's avatar
Piotr Gawron committed
532
    12.1.6 fixed (#659)
Sascha Herzinger's avatar
Sascha Herzinger committed
533

Piotr Gawron's avatar
Piotr Gawron committed
534
535
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 8 Feb 2019 15:30:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
536
537
538
539
540
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
541
542
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
543
544
  * Bug fix: plugin API had sometimes problems with fetching reactions
    properly
Piotr Gawron's avatar
Piotr Gawron committed
545
546
  * 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
547
548
  * 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
549
  * Bug fix: fetching some drugs via API could cause 500
Piotr Gawron's avatar
Piotr Gawron committed
550

Piotr Gawron's avatar
Piotr Gawron committed
551
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Jan 2019 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
552

Piotr Gawron's avatar
Piotr Gawron committed
553
554
555
556
557
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
558
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 10 Jan 2019 14:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
559

560
minerva (12.1.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
561
  * Bug fix: no check for limit on custom data overlays fixed
562
  * Bug fix: error message improved when there is privilege problem during
Piotr Gawron's avatar
Piotr Gawron committed
563
    data overlay upload
Piotr Gawron's avatar
Piotr Gawron committed
564
  * Bug fix: upload of data overlay from admin panel didn't work
565
  * Bug fix: add project button is disabled when user doesn't have proper
Piotr Gawron's avatar
Piotr Gawron committed
566
    privileges ("Add project" privilege)
567
  * Bug fix: there are no more extra markers due to map wrapping
568
569
  * Bug fix: upload of the project failed when another project was removed
    during upload
Piotr Gawron's avatar
Piotr Gawron committed
570
  * Bug fix:  word wrapping fixed in overlay table for long overlay names
571
572
573

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

Piotr Gawron's avatar
Piotr Gawron committed
574
575
576
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
577
578
579
580
  * 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
581
582
583

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

Piotr Gawron's avatar
Piotr Gawron committed
584
585
586
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
587
  * Bug fix: integer configurtion options (like SMTP_PORT) are properly
Piotr Gawron's avatar
Piotr Gawron committed
588
589
    validated before saving
  * Bug fix: inside of reaction box wasn't properly aligned
Piotr Gawron's avatar
Piotr Gawron committed
590
  * Bug fix: too long data overlay name disturbed size of the map div and
Piotr Gawron's avatar
Piotr Gawron committed
591
592
593
594
595
    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
596
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Dec 2018 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
597

Piotr Gawron's avatar
Piotr Gawron committed
598
minerva (12.1.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
599
600
601
602
603
604
605
606
607
  * 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
608
minerva (12.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
609
610
611
612
  * 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
613
  * Small improvement: option to remove additional overlays generated by custom
Piotr Gawron's avatar
Piotr Gawron committed
614
    semantic zoom
615
  * Small improvement: 'Reduced modulation' edge was displayed differently in
Piotr Gawron's avatar
Piotr Gawron committed
616
617
618
    CellDesigner and Minerva
  * Small improvement: user-friendly documentation for plugin URL field
  * Small improvement: plugins have to access information about active submap
619
620
621
622
  * 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
623
  * Feature: minerva is distributed using rpm packages
624
  * Small improvement: annotations from RHEA are handled
Piotr Gawron's avatar
Piotr Gawron committed
625
626
  * Small improvement: changing of Terms of Service url allows admin to reset
    the status of ToS acceptance for all users
627
628
  * 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
629
630
631
632
633
634
635
636
  * 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
637
  * Bug fix: when there is a problem with adjusting font in complexes (because
Piotr Gawron's avatar
Piotr Gawron committed
638
639
640
641
642
    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
643
  * Bug fix: double click on user add button disabled
Piotr Gawron's avatar
Piotr Gawron committed
644
645
  * Bug fix: privileges are mirrored correctly across different popups
  * Bug fix: plugin tab css fixed
646
  * Bug fix: uploading sbml file with no ids in glyphs returned error that
Piotr Gawron's avatar
Piotr Gawron committed
647
648
649
    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
650

Piotr Gawron's avatar
Piotr Gawron committed
651
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Oct 2018 13:00:00 +0200
652

Piotr Gawron's avatar
Piotr Gawron committed
653
minerva (12.0.4) stable; urgency=medium
654
  * Bug fix: CellDesigner modifications that are drawn as reaction are handled
Piotr Gawron's avatar
Piotr Gawron committed
655
656
657
    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
658
  * Bug fix: Tair database moved to https
659
  * Bug fix: Taxnomy database changed html output that resulted in problems
Piotr Gawron's avatar
Piotr Gawron committed
660
    with resolving species name to the id
661

Piotr Gawron's avatar
Piotr Gawron committed
662
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Sep 2018 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
663

Piotr Gawron's avatar
Piotr Gawron committed
664
665
666
667
668
669
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
670

Piotr Gawron's avatar
Piotr Gawron committed
671
672
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Aug 2018 11:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
673
674
675
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
676
    works properly
Piotr Gawron's avatar
Piotr Gawron committed
677
678
679
680
  * 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
681
  * Performance: tomcat inside docker image by default can use 3G of memory
Piotr Gawron's avatar
Piotr Gawron committed
682

683
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 31 Jul 2018 13:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
684

Piotr Gawron's avatar
Piotr Gawron committed
685
686
687
688
689
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
690
  * Bug fix: opening map could crash when CellDesigner file contained duplicate
Piotr Gawron's avatar
Piotr Gawron committed
691
    reaction id
Piotr Gawron's avatar
Piotr Gawron committed
692
693
  * Bug fix: map is repositioned when info window is outside of current view in
    OpenLayers library
694

695
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 24 Jul 2018 10:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
696

Piotr Gawron's avatar
Piotr Gawron committed
697
698
minerva (12.0.0) stable; urgency=medium
  * Feature: There is alternative OpenLayers map engine available
Piotr Gawron's avatar
Piotr Gawron committed
699
  * Feature: database connection configuration (login, password, host, etc)
Piotr Gawron's avatar
Piotr Gawron committed
700
    can be modified using /etc/minerva/db.properties file
701
  * Feature: searching for elements in submap gives marker on top map
Piotr Gawron's avatar
Piotr Gawron committed
702
703
    indicating the submap connection
  * Feature: similar search results are merged
Piotr Gawron's avatar
Piotr Gawron committed
704
  * Feature: visualization of protein structures by MolArt
Piotr Gawron's avatar
Piotr Gawron committed
705
  * Feature: reordering of data overlays is supported
706
  * Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA  annotators
Piotr Gawron's avatar
Piotr Gawron committed
707
708
709
710
711
712
713
  * 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
714
715
  * 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
716
717
718
719
720
721
722
723
724
725
  * 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
726
727
  * 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
728
729
730
  * 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
731
732
  * Small improvement: Data overlays can use source element identifiers for
    filtering
Piotr Gawron's avatar
Piotr Gawron committed
733
734
735
  * 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
736
  * Small improvement: auto complete functionality for drugs, mirnas and
Piotr Gawron's avatar
Piotr Gawron committed
737
    chemicals
Piotr Gawron's avatar
Piotr Gawron committed
738
  * Small improvement: columns value and type are not mutually exclusive in
Piotr Gawron's avatar
Piotr Gawron committed
739
740
741
742
    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
743
  * Small improvement: data overlays color scale contains configurable default
Piotr Gawron's avatar
Piotr Gawron committed
744
745
    middle color (for 0 values)
  * Small improvement: opening data overlay switch to empty background
Piotr Gawron's avatar
Piotr Gawron committed
746
747
748
749
750
751
752
753
754
755
756
757
758
  * 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
759
  * Bug fix: uploading of zip files created by mac doesn't crash due to
Piotr Gawron's avatar
Piotr Gawron committed
760
761
    .DS_Store folder
  * Bug fix: auto complete is case insensitive
Piotr Gawron's avatar
Piotr Gawron committed
762
  * Bug fix: google maps API 404 errors for non existing tiles are removed
Piotr Gawron's avatar
Piotr Gawron committed
763

Piotr Gawron's avatar
Piotr Gawron committed
764
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Jul 2018 12:00:00 +0200
765

766
767
768
769
770
771
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
772
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 23 Jul 2018 12:00:00 +0200
773

Piotr Gawron's avatar
Piotr Gawron committed
774
minerva (11.1.2) stable; urgency=medium
775
776
  * 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
777
778
779
780
  * 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
781
782
783
784
785
786
787
788
789
790
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
791
792
793
minerva (11.1.0) stable; urgency=high
  * User can provide Google Maps API key that must be registered in google
    cloud account
794
795
  * User data overlays must be Google Maps API terms of use compliant
  * Terms of Use added
796

797
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 05 Jun 2018 9:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
798
  
799
800
minerva (11.0.10) stable; urgency=medium
  * Bug fix: link from overview image to search result was broken
801

802
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Apr 2018 15:00:00 +0200
803

Piotr Gawron's avatar
Piotr Gawron committed
804
805
806
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
807

Piotr Gawron's avatar
Piotr Gawron committed
808
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
809

Piotr Gawron's avatar
Piotr Gawron committed
810
811
812
813
814
815
816
817
818
819
820
821
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