CHANGELOG 65.5 KB
Newer Older
1
2
3
minerva (15.0.2) stable; urgency=medium
  * Bug fix: annotations using identifiers.org urls sometimes required http and
    sometimes required https url (#1297)
Piotr Gawron's avatar
Piotr Gawron committed
4
  * Bug fix: map notes were not exported to GPML
5
6
  * Bug fix: reaction notes were not imported from GPML
  * Bug fix: export of notes could create invalid GPML file (#1299) 
7
8
  * Bug fix: there was an issue with exporting color and line type of reaction
    additional reactant/product (#1303) 
9
10
  * Bug fix: coordinates of children in compact complexes in CellDesigner were
    wrong (#1304) 
11
  * Bug fix: user data overlays were not removed when user was deleted (#1301)
12
13
  * Bug fix: kinetic parameters exported to SBML created invalid SBML file
    (#1305)
14
  * Bug fix: text area were not converted to GPML using conversion API (#1306)
Piotr Gawron's avatar
Piotr Gawron committed
15
16
  * Bug fix: name provided by user in comment dialog was not visible in admin
    panel (#1245)
Piotr Gawron's avatar
Piotr Gawron committed
17
18
  * Bug fix: bqmodel:isInstanceOf and bqmodel:hasInstance relation types were
    not handled properly (#1281)
19
20
21
22
  * Bug fix: "bqmodel:isInstanceOf", "bqmodel:hasInstance",
    "bqbiol:hasProperty", "bqbiol:isPropertyOf" and "bqbiol:hasTaxon" relation
    types are not supported by CellDedigner and are now transformed during
    export into something readable by CellDesigner (#1281)
23
  * Bug fix: at random time points there was an issue with cached data (#1323)
24
25
  * Bug fix: connection to DAPI timeouted sometimes which resulted in error
    when checking for all chemicals for specfific protein (#1324)
26
27
  * Bug fix: complex/compartment with empty name was incorrectly exported to
    CellDesigner (#1310)
28

29
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 1 Jul 2020 16:00:00 +0200
30

31
32
33
minerva (15.0.1) stable; urgency=medium
  * Bug fix: when there was problem with DAPI minerva threw unexpected error
    (#1316) 
34
  * Bug fix: DAPI connection must go over HTTPS (#1316)
35
36
37

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 26 Jun 2020 11:00:00 +0200

38
39
40
41
42
43
44
45
minerva (15.0.0) stable; urgency=medium
  * Backward incompatible: old connection to CTD is removed and replaced with
    new Data-API interface that closely check license compliance
  * Backward incompatible: old connection to DrugBank is removed and replaced
    with new Data-API interface that closely check license compliance
  * Backward incompatible: some custom fields (like transparency zoom level)
    are not exported to CellDesigner file (#1071)
  * Backward incompatible: truncation/association/dissociation points are
46
    represented as a dot in all new images/uploaded maps (#1265)
Piotr Gawron's avatar
Piotr Gawron committed
47
48
  * Backward incompatible: and/split points are represented as a dot in all new
    images/uploaded maps (#1253)
49
  * Backward incompatible: reaction will be on top of elements in maps uploaded
Piotr Gawron's avatar
Piotr Gawron committed
50
    from formats that does not contain z-index (#1251)
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
  * Backward incompatible: when uploading complex map with submap there is no
    possibility to change submap name (#947)
  * Improvement: logs provided for validation data model are structured (#325)
  * Improvement: import/export of GPML implemented
  * Improvement: API allows to merge files (#1208)
  * Improvement: export to SBGN/SBML/GPML format provides popup with list of
    warnings occurred in the translation process (#713)
  * Improvement: support for rendering colors in SBGNML added (#1009)
  * Small improvement: compartments in not layouted SBML file are more
    scattered (#326)
  * Small improvement: when downloading a map results in too big file (>1MB)
    the content is compressed and returned as a zip file (#348)
  * Small improvement: confirmation dialog when removing "general view"
    overlays contain proper warning  (#809)
  * Small improvement: CellDesigner text area object can have "BorderColor"
    property defined (#806)
  * Small improvement: list of submaps is sorted alphabetically (#962)
  * Small improvement: notification about new releases of minerva added in
    admin panel (#961)
  * Small improvement: font awesome upgraded to 5.1 (new icon styles)
  * Small improvement: header contains login/logout button and access admin
    panel button (#982)
  * Small improvement: autocomplete for chemical searches is enabled (#841)
Piotr Gawron's avatar
Piotr Gawron committed
74
75
  * Small improvement: "bqbiol:occursIn" and "bqmodel:isDerivedFrom" and
    handled in annotations (#1190),
76
77
  * Small improvement: 3DMET, Evidence Code Ontology, Kegg Glycan, LipidBank,
    Chemical Component Dictionary annotations are supported (#1190)
Piotr Gawron's avatar
Piotr Gawron committed
78
  * Small improvement: SWISS-model annotations are supported (#1249),
79
80
81
82
83
84
  * Small Improvement: SBO annotation support added (#1194)
  * Small improvement: support for annotations added: ChemIDplus, EcoGene,
    FlyBase, GeneDB, Intact, Kegg Drug, KNApSAcK, LIPID MAPS, NCBI Protein,
    PATO, RGD, SPIKE, TTD Drug, ZFIN BioEntity
  * Small Improvement: additional annotation uri qualifiers added: hasProperty,
    isPropertyOf (#1193)
Piotr Gawron's avatar
Piotr Gawron committed
85
  * Small improvement: small css improvement in info tab (#1104)
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
  * Small improvement: import/export to SBML of unit of information obtained
    from SBGN source is supported (#1088)
  * Small improvement: rounded rectangle is used to visualize Simple chemicals
    in SBGN-like view according to the newest SBGN specification (#1094)
  * Small improvement: after removing project is confirmed the system enforce
    waiting until remove status is confirmed (#1106)
  * Small improvement: when typing drug, list of autocomplete drugs should be
    available limited to the drugs that target something on the map (#641)
  * Small improvement: data not compliant with database constraints (for
    instance too long species identifiers) will be automatically adjust instead
    of crashing project upload (#1041)
  * Small improvement: reaction lines in SBML files without layout are set
    outside of the species (not in the center, #1023)
  * Small improvement: sort order of tables in admin panel is preserved among
    sessions (#836)
  * Small improvement: simple molecules in SBGN compliant view are drawn as
    ellipses not circles (#796)
  * Small improvement: uploaded map is automatically cached (#983)
  * Small improvement: molart updated to version 1.5.0: Ability to show
    unobserved structure regions in the sequence view.
  * Small improvement: list of genomes is automatically refreshed during genome
    upload (#820)
  * Small improvement: items in context menu are reorganized (#787)
  * Small improvement: CellDesigner files from version 2.5 should be parseable
  * Small improvement: plugins in admin panel can be revalidated to update info
    about the plugins (name, version)
  * Small improvement: there is possibility to define default plugins loaded
    with every opening of a map (#967)
  * Bug fix: pathways are visualized in image converter (#1266)
  * Bug fix: conversion of file containing BOM did not work (#1264)
  * Bug fix: proper color is parsed from CellDesigner species marked as 'brief'
Piotr Gawron's avatar
Piotr Gawron committed
117
118
  * Bug fix: upload of SBGN files didn't process unicode characters properly
    when server was running with encoding different than UTF-8 (#1142)
119
120
  * Bug fix: kinetic equation in reaction that referenced complex (instead of
    target species) crashed CellDesigner upload (#1212)
121
122
  * Bug fix: kinetic equation in SBML that used speciesReference id crashed
    upload (#1190)
123
124
  * Bug fix: layout reaction with duplicated reaction element crashed SBML
    upload (#1190)
125
  * Bug fix: conversion from SBML to CellDesigner escaped "<" twice (#1228)
Piotr Gawron's avatar
Piotr Gawron committed
126
  * Bug fix: Select annotation dialog width is at least 840px (#1210)
127
128
  * Bug fix: modifiers joined by operator were exported to SBML without line
    corresponding to the operator (#1199)
129
130
  * Bug fix: first state variable that does not match modification residue is
    translated to structural state when importing from SBGNML  (#1088)
131
132
  * Bug fix: exported SBML was not compliant with the standard when element
    name was empty (#1147)
133
134
  * Bug fix: invalid data overlays in uploaded zip file created "valid" project
    that could not be opened (#1086)
135
  * Bug fix: cardinality in SBGN-like view is drawn in separate unit (#1157)
136
  * Bug fix: notes from SBML are parsed with all html tags (#1196)
137
  * Bug fix: converter API append conversion warnings to generated output notes
Piotr Gawron's avatar
Piotr Gawron committed
138
  * Bug fix: newt use incorrect attributes when exporting render information
139
    that could not be parsed by minerva (#1127)
Piotr Gawron's avatar
Piotr Gawron committed
140
  * Bug fix: catalysis to protein was not parsed from SBGN file (#1116)
141
  * Bug fix: antisenseRNA shape is inferred from SBGN when antisenseRNA text is
142
    present in glyph label (#1114)
143
  * Bug fix: export to SBGN sometimes crashed due to concurrency issues (#1126)
144
145
  * Bug fix: CellDesigner models where start and end point of reaction was the
    same were not handled properly (#1131)
146
147
  * Bug fix: more than one authors in CellDesigner file were not parsed
    properly (#1156)
148
  * Bug fix: SBGN reaction with no reactants crashed map upload (#1148)
149
  * Bug fix: import from SBGN assigned invalid name to species that didn't have
Piotr Gawron's avatar
Piotr Gawron committed
150
    label defined (#1093)
Piotr Gawron's avatar
Piotr Gawron committed
151
152
  * Bug fix: drawing protein in SBGN-like style didn't handle properly
    dimension of the species for multimers bigger than 2 (#1091)
Piotr Gawron's avatar
Piotr Gawron committed
153
  * Bug fix: drawing of structural state in SBGN-like style uses
154
    RoundedRectangle instead of Ellipse which was not SBGN-compliant (#1095)
155
  * Bug fix: import from CellDesigner rounded alias dimension to integer
156
157
  * Bug fix: compartments limited by corner (left-top corner compartment, etc)
    are parsed properly from CellDesigner files
158
159
  * Bug fix: structural states of proteins are imported properly from SBGNML PD
    (#995)
160
161
  * Bug fix: export to CellDesigner names with new line is properly handled
    (#930)
162
  * Bug fix: layout of the exported reactome pathways is fixed when reactome
163
    exporter violates SBGN specification (#707)
164
165
  * Bug fix: unknown catalysis boolean gate modifiers in CellDesigner are
    visualized with proper line type across all included modifiers (#957)
166
167
  * Bug fix: dimension of the modifications is the same as in minerva when
    exporting to SBGNML-PD (#554)
168
  * Bug fix: position of structural state is preserved on upload CellDesigner
Piotr Gawron's avatar
Piotr Gawron committed
169
    file (#671)
Piotr Gawron's avatar
Piotr Gawron committed
170
  * Bug fix: problematic notes doesn't crash CellDesigner upload (#968)
Piotr Gawron's avatar
Piotr Gawron committed
171

172
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Jun 2020 11:00:00 +0200
173

Piotr Gawron's avatar
Piotr Gawron committed
174
175
176
minerva (14.0.13) stable; urgency=medium
  * Bug fix: chrome modified default css and service looked ugly in chrome
    (#1260)
Piotr Gawron's avatar
Piotr Gawron committed
177
178
  * Bug fix: uploaded HGNC identifiers that looks like "HGNC:HGNC:1234" are
    changed to "HGNC:1234" (#1252)
179
180
181
  * Bug fix: creating comment with too long name/email resulted in Internal
    Server Error - now the proper error message is returned (#1245)
  * Bug fix: user cannot put too long name in a comment dialog (#1245)
Piotr Gawron's avatar
Piotr Gawron committed
182
183
  * Bug fix: when url contained invalid submap id unhandled error was raised
    (#1243)
Piotr Gawron's avatar
Piotr Gawron committed
184
185
186

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 3 Jun 2020 17:00:00 +0200

187
188
189
minerva (14.0.12) stable; urgency=medium
  * Bug fix: comments on submaps were not visible (#1230)
  * Bug fix: removing comment from submap did not work
190
191
  * Bug fix: reaction name containing "<" character was exported inproperly to
    CellDesigner (#1227)
Piotr Gawron's avatar
Piotr Gawron committed
192
193
  * Bug fix: doi annotation was inproperly parsed from CellDesigner file and
    resulted in not clickable link (#1231)
194
  * Bug fix: when plugin data was too big 500 error was returned (#1232)
195
196
  * Bug fix: removing plugin in admin panel removes it from server permanently
    (#1211)
197
198
199

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 11 May 2020 17:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
200
201
202
203
minerva (14.0.11) stable; urgency=medium
  * Bug fix: complex with no border was inproperly imported from CellDesigner
    (#1198)
  * Bug fix: export to CellDesigner deal with CellDesigner issue that does not
204
    allow compartment species alias to be shorter than 2 characters (#1204)
Piotr Gawron's avatar
Piotr Gawron committed
205
206
207
208
209
210
211
212
213
214
215
  * Bug fix: kinetic parameters with INFINITY values could not be uploaded to
    minerva (#1202)
  * Bug fix: infinity value in kinetic parameter could not be parsed from
    CellDesigner file minerva (#1203)
  * Bug fix: author list inproperly presented author data when some fields were
    missing (#1201)
  * Bug fix: refreshing minerva page with more than one plugin opened might
    led to an error due to race condition (#1197)

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 31 Mar 2020 09:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
216
minerva (14.0.10) stable; urgency=medium
217
  * Bug fix: reaction without ports in SBGN crashed upload (#1065)
218
219
  * Bug fix: annotations using newer identifiers.org uri schema were truncated
    by one character (#1191)
220
  * Bug fix: long annotation string broke listing of annotations (#1155)
221

222
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Mar 2020 14:00:00 +0200
223

224
225
226
minerva (14.0.9) stable; urgency=medium
  * Bug fix: simultanous export to SBML of more than one file could result in
    500 Internal Server Error (#1110)
227
228
  * Bug fix: refresh data overlay did not hide data overlays that were removed
    and selected (#1097)
229
  * Bug fix: transparent complexes are shown with wrong color (#1103)
230
231
  * Bug fix: CellDesigner sometimes marked reduced notation reaction as
    reversible even though they were not visualized so (#1109)
232
233
  * Bug fix: when data overlay was being removed user could request to remove
    overlay second time and an error was thrown (#1121)
234
235
  * Bug fix: when data overlay name in zip uploaded zip file is not present the
    name of a file is used as overlay name (#1065)
236
  * Bug fix: uploading empty data overlay resulted in an error (#1123)
Piotr Gawron's avatar
Piotr Gawron committed
237
  * Bug fix: exporting map with glyphs crashed (#1130)
238
239
  * Bug fix: transcription factor on black&white gene are drawn in black
    (#1132)
240
241
242
243
  * Bug fix: when SBGN file contained consumption starting in process minerva
    crashed (#1063)
  * Bug fix: when SBGN file contained reaction where every node started in the
    same process port minerva crashed crashed (#1063)
Piotr Gawron's avatar
Piotr Gawron committed
244
245
246
  * Bug fix: activity flow reaction inside SBGN PD caused upload of map to
    crash
  * Bug fix: reaction without product in SBGN crashed upload of map
247
248
  * Bug fix: when SBGN production pointed directly to process instead of
    process port upload crashed
249
  * Bug fix: handle properly corrupted cached chembl drug data (#1140)
250

251
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 25 Feb 2020 15:00:00 +0200
252

Piotr Gawron's avatar
Piotr Gawron committed
253
minerva (14.0.8) stable; urgency=medium
254
  * Bug fix: API didn't allow to upload plugins with local url (#1084,
Piotr Gawron's avatar
Piotr Gawron committed
255
256
257
    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)
258
  * Bug fix: don't allow to remove plugin twice (#1081)
259
260
  * Bug fix: upload of SBML file with very short reaction length could produce
    a map that couldn't be exported to SBML anymore (#1078)
261
  * Bug fix: import of structural state from SBGN-ML PD that cannot be
Piotr Gawron's avatar
Piotr Gawron committed
262
263
    normalized to residue is changed into structural state without losing
    information (#1062)
264
265
  * Bug fix: import of stimulation modifiers from SBGN-ML crashed converter
    (#1063)
Piotr Gawron's avatar
Piotr Gawron committed
266
267
  * Bug fix: export to SBGN files created from newt source produced corrupted
    disconnected reactions
Piotr Gawron's avatar
Piotr Gawron committed
268
  * Bug fix: upload from zip file allowed empty overlay name (#1065)
269
270
  * Bug fix: genome browser slider didn't work properly in Safari on
    non-default Browser zoom level (#1048)
271
272
  * Bug fix: project without background overlay but with some custom data
    overlays crashed with an error (#1066)
273
274
  * Bug fix: when session expires updating options in configuration panel threw
    unhandled error (#1068)
Piotr Gawron's avatar
Piotr Gawron committed
275

Piotr Gawron's avatar
Piotr Gawron committed
276
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 28 Jan 2020 11:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
277

Piotr Gawron's avatar
Piotr Gawron committed
278
279
280
281
282
283
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

284
285
286
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)
287
288
  * Bug fix: search by identifier didn't consider identifiers added by
    annotators (#1047)
289
290
  * Bug fix: if map has SHOW OVERVIEW, the legend/comment/clear were not
    displayed at all (regresion 14.0.5, #1045)
291
  * Bug fix: when there is a problem with database during removing project,
292
    project removal doesn't hang (#1058)
293
  * Bug fix: coloring of the reaction wasn't applied to center of reaction
Piotr Gawron's avatar
Piotr Gawron committed
294
    (regression 14.0.0, #1057)
295
296
  * Bug fix: genetic variant overlay improperly processed elements identified
    by miriam identifiers, like uniprot (#1059)
Piotr Gawron's avatar
Piotr Gawron committed
297
298
  * Bug fix: invalid information was provided for genetic variants overlay when
    map organism was defined (#1060)
299

Piotr Gawron's avatar
Piotr Gawron committed
300
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 19 Dec 2019 13:00:00 +0200
301

302
minerva (14.0.5) stable; urgency=medium
303
  * Bug fix: copy-paste of genetic-variant data overlay into Add overlay
304
    content dialog could crash upload (#1040)
305
  * Bug fix: some annotators (like Cazy) were crashing on old installations
306
    (#1029)
307
  * Bug fix: uploading a map that breaks postgres constraints hung upload of
308
    the project (#1028)
309
  * Bug fix: uploading of the page with low internet connection speed could
310
311
    produce empty screen for several seconds/minutes - now the loading icon is
    present (#1025)
312
  * Bug fix: search for NADH drug resulted in drug with empty name (#1018)
Piotr Gawron's avatar
Piotr Gawron committed
313
  * Bug fix: export to SBML didn't handle properly arrows (#1015)
314
  * Bug fix: Font colour of text area was preserved in Empty view (#1014)
315
  * Bug fix: exported sbml file always contain model identifier (#1013)
Piotr Gawron's avatar
Piotr Gawron committed
316
317
  * Bug fix: typo allel reverted to allele in overlay data (regression 14.0.0,
    #1012)
Piotr Gawron's avatar
Piotr Gawron committed
318
319
  * Bug fix: after loading/removing too many plugins it was impossible to load
    new plugins (#1011)
320
  * Bug fix: CLEAR button disappears after legend, comment checkboxes when
321
322
    plugin tab used to much space (#976)

Piotr Gawron's avatar
Piotr Gawron committed
323
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 03 Dec 2019 12:00:00 +0200
324

Piotr Gawron's avatar
Piotr Gawron committed
325
minerva (14.0.4) stable; urgency=high
326
327
  * Bug fix: some SBGN files uploaded to minerva could not be exported to SBML
    due to problems with identifiers used by SBGN (#1006)
328
329
  * Bug fix: upload of data overlay with conflicting overlay types caused error
    (#998)
330
  * Bug fix: upload of sbml file with protein modifications inside complex
331
    crashed visualization (#966)
332
333
  * Bug fix: list of overlays for admin and curator included also other people
    overlays (regression 14.0.3, #1008)
334
  * Bug fix: refresh button did not refresh overlay list after overlay was
335
    removed over API (#997)
336

Piotr Gawron's avatar
Piotr Gawron committed
337
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 07 Nov 2019 11:00:00 +0200
338

Piotr Gawron's avatar
Piotr Gawron committed
339
minerva (14.0.3) stable; urgency=medium
340
341
  * Bug fix: default zoom level on main map works even when x or y are
    undefined (#993)
342
  * Bug fix: sbml parser had sometimes problems with combining layout and multi
Piotr Gawron's avatar
Piotr Gawron committed
343
    packages (#966)
Piotr Gawron's avatar
Piotr Gawron committed
344
345
  * Bug fix: parsing of CellDesigner files that contained substanceUnits could
    crash the upload (#985)
346
  * Bug fix: verification of version length added when uploading project
347
    implemented (#978)
348
  * Bug fix: CLEAR button disappeared when plugin tab used to much space (#976)
349
  * Bug fix: removing data overlay refreshes list of overlays in info window
Piotr Gawron's avatar
Piotr Gawron committed
350
351
    (#974)
  * Bug fix: general overlays are always on top of data overlays in info window
352
    (#975)
Piotr Gawron's avatar
Piotr Gawron committed
353
354
355
  * 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
356
  * Bug fix: opening map with no available background crashed (#964)
357
  * Bug fix: uploading SBGN file that does not pass xsd validation provides a
358
    warning, but does not fail upload (#937)
359
  * Bug fix: export of the map to SBML that was imported with older version
360
    (below 14.0.0) didn't produce valid SBML (#970)
361
362
  * Bug fix: fields in add project window are reinitialized after each open
    (#963)
363
  * Bug fix: filename case in uploaded zip files is preserved (#964)
364
  * Bug fix: +/- buttons were misaligned in genome browser (#942)
365
366
  * Bug fix: color of links in the left panel was unintentionally changed 
    (#990)
367
  * Bug fix: minerva logo in left panel is centred properly
368
  * Bug fix: width of search button icon was too big
Piotr Gawron's avatar
Piotr Gawron committed
369

Piotr Gawron's avatar
Piotr Gawron committed
370
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 18 Oct 2019 15:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
371

372
373
374
375
376
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

377
378
379
380
381
382
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

383
384
385
386
387
388
389
390
391
392
393
394
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)
395
  * Small improvement: info window contains information about overlay No (#919)
396
397
  * Small improvement: sorting by columns that doesn't make sense in admin
    panel is disabled (#895)
Piotr Gawron's avatar
Piotr Gawron committed
398
  * Small improvement: version of minerva is visible in map browser panel
399
  * Small improvement: small info about annotator details is available in
400
    select annotators dialog (#923)
401
  * Small improvement: CellDesigner layers are always visualized as pathways
Piotr Gawron's avatar
Piotr Gawron committed
402
    (#813)
403
404
  * Small improvement: notification email uses minerva name and id of affected
    project (#926)
405
  * Small improvement: information about person who uploaded project is visible
Piotr Gawron's avatar
Piotr Gawron committed
406
    in list of projects (#927)
407
  * Small improvement: tab with list of glyphs is available when adding project
Piotr Gawron's avatar
Piotr Gawron committed
408
    with glyphs (#925)
409
  * Small improvement: BackgroundColor parameter should be assigned using ":"
410
    character (#929)
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
  * 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)
440
  * Bug fix: work on FF Private Window mode could cause logout or raise an
441
    error on when opening new tab with minerva (#892)
442
  * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server
443
    Error" (#889)
Piotr Gawron's avatar
Piotr Gawron committed
444
  * Bug fix: edit project dialog verifies organism id  (#914)
445
  * Bug fix: all colors in boolean reaction (from CellDesigner) are processed
Piotr Gawron's avatar
Piotr Gawron committed
446
    properly (#907)
447
448
  * Bug fix: proper line type for boolean reaction is used on the whole
    reaction (#908)
449
450
  * Bug fix: creating project with too long name hung upload (#916)
  * Bug fix: too long user login threw an error (#915)
451
  * Bug fix: when uploading generic data overlay the type was not updated in
Piotr Gawron's avatar
Piotr Gawron committed
452
    case the type was not specified in the input file (#906)
453
  * Bug fix: list of types when copying from annotators contains only types
Piotr Gawron's avatar
Piotr Gawron committed
454
    that are selectable in the dialog (#911)
Piotr Gawron's avatar
Piotr Gawron committed
455
  * Bug fix: too long name for data overlay in info window is trimmed (#919)
Piotr Gawron's avatar
Piotr Gawron committed
456
  * Bug fix: too long name in general overlay list is wrapped (#857)
457
  * Bug fix: after genome is removed list of genomes is refreshed (#922)
Piotr Gawron's avatar
Piotr Gawron committed
458
  * Bug fix: REST API bioEntities:search method didn't limit results to the
Piotr Gawron's avatar
Piotr Gawron committed
459
    submodel id (#860)
460
  * Bug fix: Empty Overlay colours were not preserved during export to
Piotr Gawron's avatar
Piotr Gawron committed
461
    CellDesigner (#714)
Piotr Gawron's avatar
Piotr Gawron committed
462
  * Bug fix: problem with unloading plugin is properly handled (#884)
Piotr Gawron's avatar
Piotr Gawron committed
463
  * Bug fix: upload of invalid plugin doesn't add it to plugin tab and list of
464
    loaded plugins (#885)
465
466
467
  * 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
468
    drawn
469
  * Bug fix: color handling in CellDesigner did not work properly for modifiers
470
471
    inside boolean gateway
  * Bug fix: CellDesigner file exported from minerva was not fully compliant
Piotr Gawron's avatar
Piotr Gawron committed
472
    with SBML standard (#831)
473
  * Bug fix: MiRNA targets are limited only to the organism associated with the
474
    map (#66)
475
  * Bug fix: Search drug by target element did not return values when this
476
    element was annotated automatically (#216)
Piotr Gawron's avatar
Piotr Gawron committed
477

478
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 09 Oct 2019 12:00:00 +0200
479

Piotr Gawron's avatar
Piotr Gawron committed
480
minerva (13.2.0) stable; urgency=medium
481
  * Small improvement: MolArt v1.4 is used which provide information from
Piotr Gawron's avatar
Piotr Gawron committed
482
    PredictProtein (#913)
483
484
485
486
  * 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)
487
488
  * Bug fix: show element title option wasn't influencing title visibility
    (#910)
Piotr Gawron's avatar
Piotr Gawron committed
489

Piotr Gawron's avatar
Piotr Gawron committed
490
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 29 Aug 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
491
492
493
494
495
496
497
498
499

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
500
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 14 Aug 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
501

Piotr Gawron's avatar
Piotr Gawron committed
502
503
minerva (13.1.2) stable; urgency=medium
  * Bug fix: Information about problematic zip file is more specific (#865)
504
  * Bug fix: Url didn't contain list of opened plugins and they weren't reload
505
    automatically on refresh (#866)
Piotr Gawron's avatar
Piotr Gawron committed
506

507
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Jul 2019 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
508

509
510
minerva (13.1.1) stable; urgency=medium
  * Bug fix: adding gene mapping before the genome caused an error (#835)
511
  * Bug fix: "Terms of Use" change to "Terms of Service" in all places (#843)
512
  * Bug fix: upgrade to 13.1.0 crashed on machines where every element was
513
    inside compartment (#856)
514
  * Bug fix: searching for some drugs in chembl didn't provide any results even
515
    though that data exists, for instance 'DORLIMOMAB ARITOX' (#842)
516
  * Bug fix: user wasn't logged out in all tabs when the log out event appeard
517
    in only one of them (#847)
518

Piotr Gawron's avatar
Piotr Gawron committed
519
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue,  2 Jul 2019 19:00:00 +0200
520

Piotr Gawron's avatar
Piotr Gawron committed
521
minerva (13.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
522
  * Feature: annotators are more flexible - you can define set of input and
523
    outputs used by annotator (#617)
Piotr Gawron's avatar
Piotr Gawron committed
524
525
  * Feature: changes in admin panel doesn't require saving - they are saved
    automatically (#676)
Piotr Gawron's avatar
Piotr Gawron committed
526
  * Feature: elements can have custom glyphs used for visualization (#487)
527
  * Small improvement: model_name renamed to map_name in data overlay columns
Piotr Gawron's avatar
Piotr Gawron committed
528
    (#827)
529
530
  * 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
531
    deprecated (#827)
532
  * Small improvement: all bio entities have z-index associated with them
Piotr Gawron's avatar
Piotr Gawron committed
533
    (#487)
Piotr Gawron's avatar
Piotr Gawron committed
534
535
  * Small improvement: validation of the organism and disease id on map upload
    added (#618)
Piotr Gawron's avatar
Piotr Gawron committed
536
  * Small improvement: added current username next to logout button in admin
537
    panel (#660)
Piotr Gawron's avatar
Piotr Gawron committed
538
  * Small improvement: New comment dialog does not contain content of previous
539
    comment dialog (#680)
Piotr Gawron's avatar
Piotr Gawron committed
540
  * Small improvement: Left logo is configurable (#731)
541
  * Small improvement: list of element types in choose annotator dialog is
Ewa Smula's avatar
Ewa Smula committed
542
    sorted (#798)
543
544
  * Small improvement: Plugin API provides list of overview images (#702)
  * Small improvement: Plugin API allows to show/hide overview images (#702)
545
  * Small improvement: Plugin API allows to trigger search on the map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
546
  * Small improvement: Plugin API allows to clear search results on map (#702)
Piotr Gawron's avatar
Piotr Gawron committed
547
  * Small improvement: edit/remove project button is disabled until project is
548
    uploaded (#683)
Piotr Gawron's avatar
Piotr Gawron committed
549
  * Small improvement: warning about capslock is visible on login page when
550
    necessary (#658)
Piotr Gawron's avatar
Piotr Gawron committed
551
  * Small improvement: names of columns in data overlay are unified: no
Piotr Gawron's avatar
Piotr Gawron committed
552
    whitespace, "_" used as separator (#596)
553
554
  * Small improvement: list of references in drug panel contains PUBMED prefix
    (#666)
Piotr Gawron's avatar
Piotr Gawron committed
555
  * Small improvement: list of projects is auto refreshed every 5 seconds if at
556
    least one of the project is uploading/removing (#610)
Piotr Gawron's avatar
Piotr Gawron committed
557
  * Small improvement: passwords to email account and ldap are not sent over
Piotr Gawron's avatar
Piotr Gawron committed
558
    API (#732)
Piotr Gawron's avatar
Piotr Gawron committed
559
  * Small improvement: reactant/product/modifier specific colors are parsed
Piotr Gawron's avatar
Piotr Gawron committed
560
    properly from CellDesigner file (#597)
Piotr Gawron's avatar
Piotr Gawron committed
561
  * Small improvement: Info tab contains information about disease and
562
    organism when info is provided
Piotr Gawron's avatar
Piotr Gawron committed
563
564
565
  * Small improvement: Info tab provides information about model annotations
    and submap tabs provide information about submaps annotations if applicable
    (#591)
566
567
  * Small improvement: uploading sbml file should automatically discover a file
    type (#784)
568
  * Small improvement: when plugin listeners crash the system notifies user
569
    about problem with a plugin (#767)
570
  * Small improvement: when exporting reaction and elements there is
Piotr Gawron's avatar
Piotr Gawron committed
571
    possibility to filter by (sub)map (#615)
572
  * Small improvement: during first opening of a map, the zoom level is
Piotr Gawron's avatar
Piotr Gawron committed
573
    automatically computed if no default information is provided (#776)
574
  * Small improvement: when adding new project columns "Root map", "Mapping
Piotr Gawron's avatar
Piotr Gawron committed
575
    file" and "Map type" are merged (#700)
Piotr Gawron's avatar
Piotr Gawron committed
576
  * Small improvement: allow admin to disable CORS check (#802)
577
  * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
578
    SemanticZoomLevelTransparency (#801)
579
  * Small improvement: export/import from SBML support z-index in LAYOUT
580
    extension
581
  * Bug fix: due to blocking of our requests from ctdbase the autocomplete for
Piotr Gawron's avatar
Piotr Gawron committed
582
583
584
585
586
587
588
589
    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
590
  * Bug fix: plugin tab header wasn't properly resized after adding plugins
Piotr Gawron's avatar
Piotr Gawron committed
591
592
593
594
595
596
    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)
597
  * Bug fix: gene_name column is allowed only in the genetic variant data
Piotr Gawron's avatar
Piotr Gawron committed
598
599
600
601
602
603
604
    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)
605
  * Bug fix: asynchronous calls on showing/hiding data overlays might cause
Piotr Gawron's avatar
Piotr Gawron committed
606
    problems due to network latency (#830)
Piotr Gawron's avatar
Piotr Gawron committed
607
  * Bug fix: progress bar of gene genome mapping upload is refreshing properly
608
    (#728)
Piotr Gawron's avatar
Piotr Gawron committed
609
  * Bug fix: when editing project Disease and Organism could not be removed
Piotr Gawron's avatar
Piotr Gawron committed
610
    (#616)
Piotr Gawron's avatar
Piotr Gawron committed
611
612
613
  * 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
614
    slightly separated from target phenotype (#664)
615
  * Bug fix: order of genomes in admin panel doesn't change after refreshing
616
    list of genomes (#761)
617
  * Bug fix: fixing situation when Molart started with variation overlay not
Piotr Gawron's avatar
Piotr Gawron committed
618
    having the aa change information
619
  * Bug fix: plugin contect element width is adjusted when link to tabs are
620
    wrapped in more than one line (#758)
Ewa Smula's avatar
Ewa Smula committed
621
  * Bug fix: export to CellDesigner preserve font size (#798)
622
  * Bug fix: layout data was ignored for some reactions when importing from
Piotr Gawron's avatar
Piotr Gawron committed
623
    SBML (#812)
624

Piotr Gawron's avatar
Piotr Gawron committed
625
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 27 Jun 2019 14:00:00 +0200
626

627
minerva (13.0.0) stable; urgency=medium
628
629
  * 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
630
631
632
633
    Ubuntu-14 (#223)

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

Piotr Gawron's avatar
Piotr Gawron committed
634
635
minerva (12.2.3) stable; urgency=medium
  * Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790)
636
  * Bug fix: searching of chemicals stopped working due to expired SSL
Piotr Gawron's avatar
Piotr Gawron committed
637
    certificate on https://ctdbase.org/
638
  * Bug fix: remove button is disabled after starting removing of the data
639
    overlay (#791)
640
  * Bug fix: search autocomplete hint could be initially hidden (#793)
641
  * Bug fix: updating terms of use could crash when list of users was removed
642
    in separate tab or by another user (#797)
Piotr Gawron's avatar
Piotr Gawron committed
643
  * Bug fix: name of the checkbox in ADD PROJECT window adjusted (#799)
644
645
  * 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
646
647
  * 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
648
649
650

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

Piotr Gawron's avatar
Piotr Gawron committed
651
minerva (12.2.2) stable; urgency=medium
652
  * Bug fix: downloading overlays didn't work from admin panel when project
Piotr Gawron's avatar
Piotr Gawron committed
653
    with different id than default map was accessed
654
  * Bug fix: change of owner of the data overlay in admin panel incorrectly
Piotr Gawron's avatar
Piotr Gawron committed
655
    ordered overlays (#777)
656
  * Bug fix: chemical search didn't use updated disease identifier, original
657
    disease id from project upload was used instead (#779)
658
  * Bug fix: user login with special characters (like '@')  could cause
Piotr Gawron's avatar
Piotr Gawron committed
659
    problems in admin panel (#780)
660
661
  * Bug fix: removing project without full control in the system (but with
    enough privileges to remove project) caused "Not enough privileges" error
662
    (#778)
663
  * Bug fix: export of custom properties (like synonyms) are properly encoded
Piotr Gawron's avatar
Piotr Gawron committed
664
    in CellDesigner xml (#785)
665
666
667
  * 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
668

Piotr Gawron's avatar
Piotr Gawron committed
669
670
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
671
672
    read colors properly) (#744)
  * Bug fix: removing active plugin didn't switch plugin tab to the next loaded
673
    plugin (#757)
Piotr Gawron's avatar
Piotr Gawron committed
674
675
  * Bug fix: closed submap will not be reopened after page refresh (#763)
  * Bug fix: comment remove button is disabled for users without proper
676
    privileges (#766)
Piotr Gawron's avatar
Piotr Gawron committed
677
  * Bug fix: invalid pubmed identifier could break clicking on element
678
    containing it (#764, #765, #769)
Piotr Gawron's avatar
Piotr Gawron committed
679
  * Bug fix: cache for API queries is explicitly disabled - some queries could
680
    be mistakenly cached and the system behaviour might get unstable (#771)
Piotr Gawron's avatar
Piotr Gawron committed
681
682
683

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

Piotr Gawron's avatar
Piotr Gawron committed
684
minerva (12.2.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
685
  * Feature: bug report utility
Piotr Gawron's avatar
Piotr Gawron committed
686
687
  * Feature: url GET parameters support all kind of search and selected overlays
    highlight
688
  * Feature: user can create custom logging configuration in file
Piotr Gawron's avatar
Piotr Gawron committed
689
690
691
692
    /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
693
  * Feature: API tool providing possibility to transform different types of
Piotr Gawron's avatar
Piotr Gawron committed
694
    file formats
695
  * Feature: current state of the browsed map is reflected in the url (position,
Piotr Gawron's avatar
Piotr Gawron committed
696
    zoom, overlays, search queries, etc.)
Piotr Gawron's avatar
Piotr Gawron committed
697
698
699
700
701
  * 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
702
  * Small improvement: all popup dialogs in the application have dialog
Piotr Gawron's avatar
Piotr Gawron committed
703
704
705
    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
706
707
  * Small improvement: export to SBML includes unit factors
  * Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
708
  * Small improvement: genetics information allows to provide information about
Piotr Gawron's avatar
Piotr Gawron committed
709
    modification on peptide level that could be visualized in MolArt
710
  * Small improvement: allow to control the background and font color of areas
Piotr Gawron's avatar
Piotr Gawron committed
711
    drawn from text areas in CellDesigner "layers"
712
  * Small improvement: config logo location is relative to the root minerva
Piotr Gawron's avatar
Piotr Gawron committed
713
714
    deployment directory
  * Small improvement: there is branding minerva logo in the left panel
715
716
717
718
719
720
721
722
723
724
725
726
  * 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
727
728
  * Small improvement: there is max size of the map in configuration panel that
    disables upload of too big files
729
  * Small improvement: hitting enter on login page logs in the user (no need to
Piotr Gawron's avatar
Piotr Gawron committed
730
    click on the login button)
731
  * Small improvement: refresh button in overlays panel (useful when data
Piotr Gawron's avatar
Piotr Gawron committed
732
733
734
    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
735
  * Small improvement: 'BACK TO MAP' link is available only when guest account
Piotr Gawron's avatar
Piotr Gawron committed
736
737
    has proper access level
  * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
738
739
    email account is provided
  * Small improvement: Plugin API allows to show/hide data overlays
Piotr Gawron's avatar
Piotr Gawron committed
740
  * Bug fix: Icons were sometimes not properly loaded on Safari (#661)
Piotr Gawron's avatar
Piotr Gawron committed
741
  * Bug fix: migration scripts are compatibile with postgres 9.3 version that
Piotr Gawron's avatar
Piotr Gawron committed
742
    is default on Ubuntu 14 (#762)
Piotr Gawron's avatar
Piotr Gawron committed
743
  * Bug fix: update/remove button is disabled when user has no privileges for
Piotr Gawron's avatar
Piotr Gawron committed
744
    managing overlays (#742)
Piotr Gawron's avatar
Piotr Gawron committed
745
  * Bug fix: when user cannot manage users information in overlays and users
Piotr Gawron's avatar
Piotr Gawron committed
746
    tab in edit project dialog is provided instead of hiding tabs (#756)
Piotr Gawron's avatar
Piotr Gawron committed
747
748
  * 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
749
750
    again (#697)
  * Bug fix: editing/removing project requires Map Management privilege (#681)
Piotr Gawron's avatar
Piotr Gawron committed
751
  * Bug fix: when removeAllListeners is called list of registered listeners is
Piotr Gawron's avatar
Piotr Gawron committed
752
    cleaned (#687)
Piotr Gawron's avatar
Piotr Gawron committed
753
  * Bug fix: when plugin is removed the html elements associated with it are
Piotr Gawron's avatar
Piotr Gawron committed
754
755
    removed as well (#686)
  * Bug fix: when creating new user default privileges are set properly (#692)
Piotr Gawron's avatar
Piotr Gawron committed
756
  * Bug fix: plugin can be added after plugin has been removed in admin plugin
Piotr Gawron's avatar
Piotr Gawron committed
757
    panel (#686)
Piotr Gawron's avatar
Piotr Gawron committed
758
  * Bug fix: too many annotations (>=100) caused misaligning in the left panel
Piotr Gawron's avatar
Piotr Gawron committed
759
    (#708)
Piotr Gawron's avatar
Piotr Gawron committed
760
761
762
  * 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
763
764
    example in admin panel configuration tab (#719)
  * Bug fix: description of transcription site is centered (#720)
Piotr Gawron's avatar
Piotr Gawron committed
765
  * Bug fix: selecting too few parameters in export doesn't throw reportable
Piotr Gawron's avatar
Piotr Gawron committed
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
    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
781
  * Bug fix: export to CellDesigner align inhibition reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
782
  * Bug fix: export/import to/from SBML handles Heterodimer Association
Piotr Gawron's avatar
Piotr Gawron committed
783
    reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
784
  * Bug fix: logo doesn't need to be square
785
  * Bug fix: when clicking on a search link (in overview window), input in the
Piotr Gawron's avatar
Piotr Gawron committed
786
    left tab was not modified
787
  * Bug fix: in admin panel changing of genome version is blocking interface