CHANGELOG 26.7 KB
Newer Older
Piotr Gawron's avatar
Piotr Gawron committed
1
2
minerva (12.2.0~beta.0) unstable; urgency=medium
  * Feature: bug report utility
3
  * Small improvement: JS plugin can create listener that is triggered on
Piotr Gawron's avatar
Piotr Gawron committed
4
5
    search results focus change

Piotr Gawron's avatar
Piotr Gawron committed
6
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 23 Jan 2019 15:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
7

Piotr Gawron's avatar
Piotr Gawron committed
8
9
10
11
12
13
14
minerva (12.2.0~alpha.1) unstable; urgency=medium
  * Bug fix: problems with SBML-CellDesigner translation fixed
  * Bug fix: gitlab CI tests fixed

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 17 Jan 2019 15:00:00 +0200

minerva (12.2.0~alpha.0) unstable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
15
16
  * Feature: url GET parameters support all kind of search and selected overlays
    highlight
17
  * Feature: user can create custom logging configuration in file
Piotr Gawron's avatar
Piotr Gawron committed
18
19
20
21
    /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
22
  * Feature: API tool providing possibility to transform different types of
Piotr Gawron's avatar
Piotr Gawron committed
23
    file formats
24
  * Feature: current state of the browsed map is reflected in the url (position,
Piotr Gawron's avatar
Piotr Gawron committed
25
26
27
    zoom, overlays, search queries, etc.)
  * Small improvement: export to SBML includes unit factors
  * Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
28
  * Small improvement: genetics information allows to provide information about
Piotr Gawron's avatar
Piotr Gawron committed
29
    modification on peptide level that could be visualized in MolArt
30
  * Small improvement: allow to control the background and font color of areas
Piotr Gawron's avatar
Piotr Gawron committed
31
    drawn from text areas in CellDesigner "layers"
32
  * Small improvement: config logo location is relative to the root minerva
Piotr Gawron's avatar
Piotr Gawron committed
33
34
    deployment directory
  * Small improvement: there is branding minerva logo in the left panel
35
36
37
38
39
40
41
42
43
44
45
46
  * 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
47
48
  * Small improvement: there is max size of the map in configuration panel that
    disables upload of too big files
49
  * Small improvement: hitting enter on login page logs in the user (no need to
Piotr Gawron's avatar
Piotr Gawron committed
50
    click on the login button)
51
  * Small improvement: refresh button in overlays panel (useful when data
Piotr Gawron's avatar
Piotr Gawron committed
52
53
54
    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
55
  * Small improvement: 'BACK TO MAP' link is available only when guest account
Piotr Gawron's avatar
Piotr Gawron committed
56
57
    has proper access level
  * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
58
59
    email account is provided
  * Small improvement: Plugin API allows to show/hide data overlays
Piotr Gawron's avatar
Piotr Gawron committed
60
  * Bug fix: export to CellDesigner align inhibition reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
61
  * Bug fix: export/import to/from SBML handles Heterodimer Association
Piotr Gawron's avatar
Piotr Gawron committed
62
    reaction properly
Piotr Gawron's avatar
Piotr Gawron committed
63
  * Bug fix: logo doesn't need to be square
64
  * Bug fix: when clicking on a search link (in overview window), input in the
Piotr Gawron's avatar
Piotr Gawron committed
65
    left tab was not modified
66
  * Bug fix: in admin panel changing of genome version is blocking interface
Piotr Gawron's avatar
Piotr Gawron committed
67
    until data about url is retrieved
68
69
  * 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
70
71
  * Bug fix: export to SBGN did not export compartments
  * Bug fix: export of complex states to SBGN did not work
72
  * Bug fix: type of the data overlay can be defined in the file content
Piotr Gawron's avatar
Piotr Gawron committed
73
74
    (useful when uploading genetic variants)
  * Bug fix: CLEAR button clears comment checkbox if necessary
Piotr Gawron's avatar
Piotr Gawron committed
75
  * Bug fix: minerva install problem on ubuntu 16 fixed
Piotr Gawron's avatar
Piotr Gawron committed
76

Piotr Gawron's avatar
Piotr Gawron committed
77
 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 11 Jan 2019 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
78

Piotr Gawron's avatar
Piotr Gawron committed
79
80
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
81
82
  * Bug fix: plugin API had sometimes problems with fetching reactions
    properly
Piotr Gawron's avatar
Piotr Gawron committed
83
84
  * 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
85
86
  * 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
87
  * Bug fix: fetching some drugs via API could cause 500
Piotr Gawron's avatar
Piotr Gawron committed
88

Piotr Gawron's avatar
Piotr Gawron committed
89
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Jan 2019 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
90

Piotr Gawron's avatar
Piotr Gawron committed
91
92
93
94
95
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
96
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 10 Jan 2019 14:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
97

98
minerva (12.1.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
99
  * Bug fix: no check for limit on custom data overlays fixed
100
  * Bug fix: error message improved when there is privilege problem during
Piotr Gawron's avatar
Piotr Gawron committed
101
    data overlay upload
Piotr Gawron's avatar
Piotr Gawron committed
102
  * Bug fix: upload of data overlay from admin panel didn't work
103
  * Bug fix: add project button is disabled when user doesn't have proper
Piotr Gawron's avatar
Piotr Gawron committed
104
    privileges ("Add project" privilege)
105
  * Bug fix: there are no more extra markers due to map wrapping
106
107
  * Bug fix: upload of the project failed when another project was removed
    during upload
Piotr Gawron's avatar
Piotr Gawron committed
108
  * Bug fix:  word wrapping fixed in overlay table for long overlay names
109
110
111

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

Piotr Gawron's avatar
Piotr Gawron committed
112
113
114
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
115
116
117
118
  * 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
119
120
121

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

Piotr Gawron's avatar
Piotr Gawron committed
122
123
124
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
125
  * Bug fix: integer configurtion options (like SMTP_PORT) are properly
Piotr Gawron's avatar
Piotr Gawron committed
126
127
    validated before saving
  * Bug fix: inside of reaction box wasn't properly aligned
Piotr Gawron's avatar
Piotr Gawron committed
128
  * Bug fix: too long data overlay name disturbed size of the map div and
Piotr Gawron's avatar
Piotr Gawron committed
129
130
131
132
133
    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
134
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Dec 2018 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
135

Piotr Gawron's avatar
Piotr Gawron committed
136
minerva (12.1.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
137
138
139
140
141
142
143
144
145
  * 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
146
minerva (12.1.0) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
147
148
149
150
  * 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
151
  * Small improvement: option to remove additional overlays generated by custom
Piotr Gawron's avatar
Piotr Gawron committed
152
    semantic zoom
153
  * Small improvement: 'Reduced modulation' edge was displayed differently in
Piotr Gawron's avatar
Piotr Gawron committed
154
155
156
    CellDesigner and Minerva
  * Small improvement: user-friendly documentation for plugin URL field
  * Small improvement: plugins have to access information about active submap
157
158
159
160
  * 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
161
  * Feature: minerva is distributed using rpm packages
162
  * Small improvement: annotations from RHEA are handled
Piotr Gawron's avatar
Piotr Gawron committed
163
164
  * Small improvement: changing of Terms of Service url allows admin to reset
    the status of ToS acceptance for all users
165
166
  * 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
167
168
169
170
171
172
173
174
  * 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
175
  * Bug fix: when there is a problem with adjusting font in complexes (because
Piotr Gawron's avatar
Piotr Gawron committed
176
177
178
179
180
    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
181
  * Bug fix: double click on user add button disabled
Piotr Gawron's avatar
Piotr Gawron committed
182
183
  * Bug fix: privileges are mirrored correctly across different popups
  * Bug fix: plugin tab css fixed
184
  * Bug fix: uploading sbml file with no ids in glyphs returned error that
Piotr Gawron's avatar
Piotr Gawron committed
185
186
187
    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
188

Piotr Gawron's avatar
Piotr Gawron committed
189
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Oct 2018 13:00:00 +0200
190

Piotr Gawron's avatar
Piotr Gawron committed
191
minerva (12.0.4) stable; urgency=medium
192
  * Bug fix: CellDesigner modifications that are drawn as reaction are handled
Piotr Gawron's avatar
Piotr Gawron committed
193
194
195
    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
196
  * Bug fix: Tair database moved to https
197
  * Bug fix: Taxnomy database changed html output that resulted in problems
Piotr Gawron's avatar
Piotr Gawron committed
198
    with resolving species name to the id
199

Piotr Gawron's avatar
Piotr Gawron committed
200
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Sep 2018 17:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
201

Piotr Gawron's avatar
Piotr Gawron committed
202
203
204
205
206
207
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
208

Piotr Gawron's avatar
Piotr Gawron committed
209
210
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Aug 2018 11:00:00 +0200

Piotr Gawron's avatar
Piotr Gawron committed
211
212
213
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
214
    works properly
Piotr Gawron's avatar
Piotr Gawron committed
215
216
217
218
  * 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
219
  * Performance: tomcat inside docker image by default can use 3G of memory
Piotr Gawron's avatar
Piotr Gawron committed
220

221
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 31 Jul 2018 13:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
222

Piotr Gawron's avatar
Piotr Gawron committed
223
224
225
226
227
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
228
  * Bug fix: opening map could crash when CellDesigner file contained duplicate
Piotr Gawron's avatar
Piotr Gawron committed
229
    reaction id
Piotr Gawron's avatar
Piotr Gawron committed
230
231
  * Bug fix: map is repositioned when info window is outside of current view in
    OpenLayers library
232

233
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 24 Jul 2018 10:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
234

Piotr Gawron's avatar
Piotr Gawron committed
235
236
minerva (12.0.0) stable; urgency=medium
  * Feature: There is alternative OpenLayers map engine available
Piotr Gawron's avatar
Piotr Gawron committed
237
  * Feature: database connection configuration (login, password, host, etc)
Piotr Gawron's avatar
Piotr Gawron committed
238
    can be modified using /etc/minerva/db.properties file
239
  * Feature: searching for elements in submap gives marker on top map
Piotr Gawron's avatar
Piotr Gawron committed
240
241
    indicating the submap connection
  * Feature: similar search results are merged
Piotr Gawron's avatar
Piotr Gawron committed
242
  * Feature: visualization of protein structures by MolArt
Piotr Gawron's avatar
Piotr Gawron committed
243
  * Feature: reordering of data overlays is supported
244
  * Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA  annotators
Piotr Gawron's avatar
Piotr Gawron committed
245
246
247
248
249
250
251
  * 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
252
253
  * 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
254
255
256
257
258
259
260
261
262
263
  * 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
264
265
  * 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
266
267
268
  * 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
269
270
  * Small improvement: Data overlays can use source element identifiers for
    filtering
Piotr Gawron's avatar
Piotr Gawron committed
271
272
273
  * 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
274
  * Small improvement: auto complete functionality for drugs, mirnas and
Piotr Gawron's avatar
Piotr Gawron committed
275
    chemicals
Piotr Gawron's avatar
Piotr Gawron committed
276
  * Small improvement: columns value and type are not mutually exclusive in
Piotr Gawron's avatar
Piotr Gawron committed
277
278
279
280
    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
281
  * Small improvement: data overlays color scale contains configurable default
Piotr Gawron's avatar
Piotr Gawron committed
282
283
    middle color (for 0 values)
  * Small improvement: opening data overlay switch to empty background
Piotr Gawron's avatar
Piotr Gawron committed
284
285
286
287
288
289
290
291
292
293
294
295
296
  * 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
297
  * Bug fix: uploading of zip files created by mac doesn't crash due to
Piotr Gawron's avatar
Piotr Gawron committed
298
299
    .DS_Store folder
  * Bug fix: auto complete is case insensitive
Piotr Gawron's avatar
Piotr Gawron committed
300
  * Bug fix: google maps API 404 errors for non existing tiles are removed
Piotr Gawron's avatar
Piotr Gawron committed
301

Piotr Gawron's avatar
Piotr Gawron committed
302
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 16 Jul 2018 12:00:00 +0200
303

304
305
306
307
308
309
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
310
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 23 Jul 2018 12:00:00 +0200
311

Piotr Gawron's avatar
Piotr Gawron committed
312
minerva (11.1.2) stable; urgency=medium
313
314
  * 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
315
316
317
318
  * 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
319
320
321
322
323
324
325
326
327
328
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
329
330
331
minerva (11.1.0) stable; urgency=high
  * User can provide Google Maps API key that must be registered in google
    cloud account
332
333
  * User data overlays must be Google Maps API terms of use compliant
  * Terms of Use added
334

335
 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 05 Jun 2018 9:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
336
  
337
338
minerva (11.0.10) stable; urgency=medium
  * Bug fix: link from overview image to search result was broken
339

340
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 16 Apr 2018 15:00:00 +0200
341

Piotr Gawron's avatar
Piotr Gawron committed
342
343
344
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
345

Piotr Gawron's avatar
Piotr Gawron committed
346
 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
347

Piotr Gawron's avatar
Piotr Gawron committed
348
349
350
351
352
353
354
355
356
357
358
359
minerva (11.0.8) stable; urgency=medium
  * Bug fix: XSS vulnerability
  * Bug fix: "java.lang.IllegalStateException: getWriter()" exceptions
    in logs
  * Bug fix: crash for uploading and caching chemical data
  * Bug fix: disappearing tiles in submodels
  * Bug fix: max number of results is properly taken from configuration
  * Bug fix: overlay cannot be hidden before process of fetching data
    during opening is finished
  * Bug fix: redirection to login page when session expired and access to
    export page is requested
  * Bug fix: sometimes overlays couldn't be hidden in submaps
Piotr Gawron's avatar
Piotr Gawron committed
360
  * Bug fix: comments on submaps are visualized properly
Piotr Gawron's avatar
Piotr Gawron committed
361

Piotr Gawron's avatar
Piotr Gawron committed
362
 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 05 Feb 2018 18:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
363

Piotr Gawron's avatar
Piotr Gawron committed
364
365
366
367
368
369
370
371
372
373
minerva (11.0.7) stable; urgency=medium
  * Bug fix: redirection added when anonymous tries to access secured map
  * Bug fix: loading time of custom overlays is reduced
  * Bug fix: there should be no problem with symlink when upgrading debian
    package
  * Bug fix: number of services changed API address to https: pmceurope
    (pubmed), uniprot, ensembl, hgnc, recon, ctd database

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 18 Jan 2018 16:00:00 +0200

374
minerva (11.0.6) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
375
376
  * Bug fix: fix a bug when entering invalid mirna id

377
378
379
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 14 Dec 2017 16:00:00 +0200
 
minerva (11.0.5) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
380
  * Bug fix: fix on connection to drugbank database
381
382
  * Bug fix: posttranslational modification data was sometimes unavailable
    in search results panel
Piotr Gawron's avatar
Piotr Gawron committed
383

384
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 30 Nov 2017 16:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
385

386
minerva (11.0.4) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
387
  * Bug fix: fix on connection to taxonomy database
388
389
  * Bug fix: color coding for reactions (wrong color was chosen)
  * Bug fix: overlays with many reactions did not work properly
Piotr Gawron's avatar
Piotr Gawron committed
390

391
 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 09 Nov 2017 14:50:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
392

393
minerva (11.0.3) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
394
  * Bug fix: removing empty project removed images from all projects
395
396
397
398
399
400
401
402
403
  * Bug fix: clicking on map when left panel was hidden threw error
  * Bug fix: links to invalid annotations were opening invalid web page
  * Bug fix: service resolving miriam resources doesn't work over http
    anymore
  * Bug fix: chebi annotator doesn't work over http anymore

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 19 Oct 2017 13:50:00 +0200

minerva (11.0.2) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
404
  * Bug fix: login issues when default page is in secure area
405
406
407
408

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 25 Sep 2017 12:00:00 +0200

minerva (11.0.1) stable; urgency=medium
Piotr Gawron's avatar
Piotr Gawron committed
409
  * Bug fix: logout caused issues with session data
410
411
412
413
414

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 08 Sep 2017 12:00:00 +0200

minerva (11.0.0) stable; urgency=medium

Piotr Gawron's avatar
Piotr Gawron committed
415
416
  * Bug fix: security issue - access to specific map can be restricted
    by the user login
417
418
  * Bug fix: sbgn import
  * Bug fix: mesh connector
Piotr Gawron's avatar
Piotr Gawron committed
419
  * Rest API (documentation can be found here:
420
421
    https://git-r3lab.uni.lu/piotr.gawron/minerva/blob/master/README.md)
  * Selecting an element on the map shows info about it in the bottom left
Piotr Gawron's avatar
Piotr Gawron committed
422
    corner (when Search tab is not open)
423
424
  * Upload of data overlays allows to upload just names of the proteins
    (or other elements), it can be done via file or just by typing in the
Piotr Gawron's avatar
Piotr Gawron committed
425
426
    proper text box
  * Layout changes: the main one is that there are only 3 tab panels
427
428
429
430
431
432
433
434
435
    (search, overlay, info), so it should be easier to navigate

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 28 Aug 2017 12:00:00 +0200

minerva (10.0.5) stable; urgency=medium

  * Bug fix: interacting drugs can be found for RNAs
  * Bug fix: error handling improved on map upload
  * Bug fix: taxonomy ncbi server switched to https
Piotr Gawron's avatar
Piotr Gawron committed
436
437
  * Overlay presents description field if possible

438
439

 -- Piotr Gawron <piotr.gawron@uni.lu>  Sat, 04 Mar 2017 12:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
440

441
442
443
444
445
446
447
448
449
450
451
minerva (10.0.4) stable; urgency=medium

  * Bug fix: overlays colors are centered in white (not black)
  * Bug fix: export to CellDesigner fixed
  * Bug fix: DrugBank connector updated due to change in DrugBank website

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 29 Dec 2016 17:01:16 +0200

minerva (10.0.3) stable; urgency=medium

  * Bug fix: login cannot contain whitespace
Piotr Gawron's avatar
Piotr Gawron committed
452
  * Bug fix: search for multiple drugs will not return more drugs than
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
    queried for
  * Bug fix: drug list for some proteins (like RHOA) hung webpage
  * Bug fix: comments on submaps issue
  * Bug fix: link to submap from comment panel
  * Overlay coloring can be defined in Configuration

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 15 Dec 2016 15:01:16 +0200

minerva (10.0.2) stable; urgency=medium

  * Bug fix: markers for mirna targets visibility

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 29 Sep 2016 10:01:16 +0200

minerva (10.0.1) stable; urgency=medium

  * Bug fix: export to image
Piotr Gawron's avatar
Piotr Gawron committed
470
471
  * Bug fix: trigger reaction and physical stimulation reactions are no
    longer allowed (CellDesigner data model issue)
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
  * Bug fix: clicking on reactions in submaps

 -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 21 Sep 2016 13:01:16 +0200

minerva (10) stable; urgency=medium

  * Project info tab available for users
  * Management of overlays in admin panel
  * Bug fix: Visualization of text mining
  * Bug fix: Exception when accessing non-existing project
  * Bug fix: Zooming issue when searching for results on submaps
  * Bug fix: Out of memory when caching a lot of data
  * Bug fix: Corrupted drug names
  * Bug fix: Unexpected errors when uploading layouts
  * Bug fix: Coordinates in url
  * Bug fix: Hiding left panel
  * Bug fix: CellDesigner font size is processed properly
  * Bug fix: Search by reaction id is not case sensitive

 -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Aug 2016 13:01:16 +0200

minerva (9) stable; urgency=medium

  * Fix on install script of version 8 that crashed some new installations

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 29 Jun 2016 09:58:34 +0200

minerva (8) stable; urgency=medium

  * Micro RNA interface
  * Toxic chemicals interface
  * Data sets (layouts) visualized dynamically in the browser
  * Reverse query for drugs, chemicals, micro RNAs interfaces
  * Small bug fixes

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 14 Apr 2016 13:03:55 +0200

minerva (7) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
511
512
513
514
515
516
  * Uploaded datasets are available for download
  * Entrez annotator
  * Ensembl annotator
  * Valid/required annotations and used annotations saved in user profile
  * Export to pdf/png/jpg/svg
  * New web interface
517
518
519
520
521

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 3 Dec 2015 22:00:00 +0200

minerva (6) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
522
523
524
525
526
  * Searching by annotations
  * Errors from parsing data forwarded to client
  * Notification email system added
  * Warnings are downloadable
  * Complex map (composed from many small maps)
527
  * Visualization of Recon specific annotations
Piotr Gawron's avatar
Piotr Gawron committed
528
529
530
531
532
533
534
  * Versioning system
  * Galaxy connector
  * Miriam types report
  * Advanced annotation options
  * Uniprot annotation module
  * Customized validation of miriam annotations
  * Recon annotation service
535
  * Bug fix: Data autofill problem in user management
Piotr Gawron's avatar
Piotr Gawron committed
536
537
  * Bug fix: User privileges for adding project
  * Bug fix: Problem with some miriam entries in RDF format
538
  * Bug fix: Reporting of drawing problems
Piotr Gawron's avatar
Piotr Gawron committed
539
540
  * Bug fix: Visualization of posttranslationa modification
  * Bug fix: Drugbank problem after update of Drugbank interface
541
  * Bug fix: Session scope fixed (browsing many maps at the same time)
Piotr Gawron's avatar
Piotr Gawron committed
542
543
544
545
546
  * Bug fix: Asynchronous removing/adding maps
  * Bug fix: Export to CellDesigner rarely produced corrupted CellDesigner file
  * Bug fix: Recon annotations of reactions
  * Bug fix: Login problem when browsing not default map
  * Bug fix: Multimers are available for every element
547
548

 -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 21 Jul 2015 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
549

550
551
minerva (5) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
552
  * Additional checkboxes in upload model: annotate automatically, cache data, verify annotations
553
  * Popup window in admin panel that list warnings
Piotr Gawron's avatar
Piotr Gawron committed
554
555
  * Information about build
  * Parsing and annotation warnings for models in admin panel
556
  * Custom reaction visualization in upload overlay
Piotr Gawron's avatar
Piotr Gawron committed
557
558
559
560
561
  * Bug fix: Problem with touch interface on Windows 8.1
  * Bug fix: Google Maps API problem with floating bubbles
  * Bug fix: Error handling in admin panel
  * Bug fix: Reaction color in CellDesigner file
  * Bug fix: Reaction line width
562
563

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 18 Dec 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
564

565
566
567
minerva (4) stable; urgency=low

  * Export of the part of the map into CellDesigner file
Piotr Gawron's avatar
Piotr Gawron committed
568
569
  * Logo files managable via config webpage
  * Import data from GO
570
571
572
  * Custom overlay upload
  * Additional structural information imported from annotation service
  * Bug fix: Fonts and lines in hierarchical view
Piotr Gawron's avatar
Piotr Gawron committed
573
574
575
576
577
  * Bug fix: Visualization of residues in rna, antisense rna, proteins
  * Bug fix: Problem with touching bubbles on touch interface
  * Bug fix: Problem with special UTF-8 characters in CellDesigner file
  * Bug fix: Problem with users and session expire
  * Bug fix: Export problem
578
579

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 11 Sep 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
580

581
582
583
minerva (3) stable; urgency=low

  * Drug targeting interface
Piotr Gawron's avatar
Piotr Gawron committed
584
585
586
  * Export to CellDesigner
  * Status page of all dependent services
  * Configuration page
587
588

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 5 Jun 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
589

590
591
592
minerva (2) stable; urgency=low

  * Upload of the CellDesigner map
Piotr Gawron's avatar
Piotr Gawron committed
593
594
  * Bug fix: Problem with touch interface after update of browsers engine
  * Bug fix: Problem in Safari when searching for elements
595
596

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 2 Apr 2014 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
597

598
599
minerva (1) stable; urgency=low

Piotr Gawron's avatar
Piotr Gawron committed
600
  * Initial release
601
602

 -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 4 Dec 2013 22:00:00 +0200
Piotr Gawron's avatar
Piotr Gawron committed
603