Wiki source code of Releases

Version 136.1 by hbpadmin on 2022/06/14 11:29
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1 === **Collaboratory 2 release (2022-06-14)** ===
2
3 **Collaboratory.Lab**
4
5 * Integrated tvb-widgets ([[https:~~/~~/github.com/the-virtual-brain/tvb-widgets>>url:https://github.com/the-virtual-brain/tvb-widgets]])
6 * Fixed issue where kernel lost connection to the running notebook session
7
8 === **Collaboratory 2 release (2022-06-09) (Released)** ===
9
10 **Collaboratory.Wiki**
11
12 * Fixed issue with collab search, results now return public collabs appropriately.
13 * Extended API of the OIDC client managers app. [[Read more.>>https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20IAM/FAQ/OIDC%20Clients%20explained/1.%20Registering%20an%20OIDC%20client%20v2/]]
14 * Guest accounts: deploying script to deactivate guest accounts that have reached end of life.
15
16 **Collaboratory.Drive**
17
18 * Changes made to allow admins to monitor large file usage in the Drive.
19
20 === **Collaboratory 2 release (2022-05-12) (Released)** ===
21
22 **Collaboratory.Lab**
23
24 * Deploying an "Experimental" build of EBRAINS tools to the Lab.
25 ** Contains the latest version of participating tools.
26 ** Updated much more frequently than the official EBRAINS releases of participating tools.
27 ** Contrary to EBRAINS releases, experimental build only persists until the next deployment of the experimental build.
28 ** Please note that this is an experimental build, and as such, users should use it at their own risk. EBRAINS recommends the official releases instead.
29
30 === **Collaboratory 2 release (2022-05-11) (Released)** ===
31
32 **Collaboratory.Wiki**
33
34 * Fixing an issue discovered with users profile view.
35
36 === **Collaboratory 2 release (2022-05-10) (Released)** ===
37
38 **Collaboratory.Wiki**
39
40 * Guest account frontend released. To gain access please request sponsor role with justification via [[https:~~/~~/ebrains.eu/support>>https://ebrains.eu/support]]
41
42 === **Collaboratory 2 release (2022-04-26) (Released)** ===
43
44 **Collaboratory.Wiki**
45
46 * Update to guest account creation API.
47
48 === **Collaboratory 2 release (2022-04-12) (Released)** ===
49
50 **Collaboratory.Wiki**
51
52 * Initial guest account creation API released.
53
54 **Collaboratory.IAM**
55
56 * Initial version of updated OIDC client API released.
57
58 === **Collaboratory 2 release (2022-04-07) (Released)** ===
59
60 **Collaboratory.Wiki**
61
62 * Fixup on Units navigation UI
63 * New Collaboratory policies about public collabs, [[more info>>https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/New%20Collaboratory.wiki%20policy/]]
64
65 === **Collaboratory 2 release (2022-04-04)(Released)** ===
66
67 The EBRAINS logo is being updated throughout all of our services.
68
69 **Collaboratory.IAM**
70
71 * Keycloak has been upgraded to version 15
72
73 Note: Developers using Spring boot 2.4.0 may encounter issues contacting our services, to avoid any issues please upgrade to Spring boot 2.6.4
74
75 === **Collaboratory 2 release (2022-03-22) (Released)** ===
76
77 **Collaboratory.Lab**
78
79 * Improved environment variables (more details in [[FAQ>>https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Documentation%20Lab/FAQ/Creating%20and%20accessing%20environment%20variables%20/]]):
80 ** Added variables for the Docker image version
81 ** Support for environment variables has been added for URLs specifying an execution site (e.g. lab.ch.ebrains.eu/...). Up to now, environment variables were only supported fo URLs to the generic lab.ebrains.eu/...
82 * Added a new extension in the Lab to monitor HPC jobs launched through the Unicore interface. More info [[here>>https://github.com/the-virtual-brain/tvb-ext-unicore]].
83 ** To activate the extension in the JupyterLab context menu: View -> Activate Command Palette -> PyUnicore Task Stream
84 * Added support for the [[SWIG>>http://www.swig.org/]] tool. SWIG allows C/C++ libraries to be accessed in Python.
85
86 **Collaboratory.Wiki**
87
88 * Updated footer.
89
90 **Collaboratory.Office**
91
92 * Added a plugin that will open the collab a document is contained in. [[Read more>>doc:Collabs.the-collaboratory.Documentation Office.FAQ.Accessing a documents collab.WebHome]].
93
94 **Collaboratory.Drive **
95
96 * Added a button that will open the collab a document is contained in. [[Read more>>doc:Collabs.the-collaboratory.Documentation Drive.FAQ.Accessing a parent collab from inside the Drive.WebHome]].
97
98 **OpenShift Dev cluster**
99
100 * The NFS disk storage for all persistent volumes is being increased.
101
102 === **Collaboratory 2 release (2022-02-22) (Released)** ===
103
104 **Collaboratory.Lab**
105
106 * A new R kernel has been implemented in the Lab. Users can now select this kernel to use the R language in notebooks.
107 * The ebrains-drive lib is now available by default in new notebooks. The "pip install" command is no longer needed for Collaboratory.Drive integration.
108
109 === **Collaboratory 2 release (2022-02-16) (Released)** ===
110
111 **Collaboratory.IAM**
112
113 * When EBRAINS users log in the first time, they have occasionally seen an error message. This is resolved by this deployment.
114
115 **Collaboratory.Lab**
116
117 * We have fixed an issue with SSL certificates while using certain Python modules (e.g. requests) in the Lab.
118
119 === **Collaboratory 2 release (2022-02-08) (Released)** ===
120
121 **Collaboratory.Wiki**
122
123 * All common navigation elements in a collab (Drive, Team, Lab, Bucket) are now grouped together at the top of the left navigation panel.
124
125 **Collaboratory.Lab**
126
127 * Updated JupyterLab image to use latest version
128 ** Adds a debugger to the Lab, allowing users to debug their notebooks.
129 ** Includes native git integration
130 ** Allows the user to install extensions to JupyterLab
131 * Fixed issues with notebook exports (and re-enabled native PDF export)
132 * Added [[nbgitpuller>>https://jupyterhub.github.io/nbgitpuller/]] support
133 * Set bash as the default shell in the terminal
134 * Updated the JupyterLab extension to make [[Lab URL query parameters>>doc:Collabs.the-collaboratory.Documentation Lab.FAQ.Creating and accessing environment variables .WebHome]] available (now works with direct links to a specific openshift cluster)
135 * Reduced Docker image size to improve Collaboratory Lab load times.
136 * Fixed unknown user id issue in the Lab container
137 * Updated Jupyter Hub version
138
139 === **Collaboratory 2 release (2022-01-25) (Delayed, Released 27th)** ===
140
141 **Collaboratory.Wiki**
142
143 * Adding a new API to delete collabs. Details found [[here>>doc:Collabs.the-collaboratory.Documentation Wiki.API.WebHome]] after release.
144 * The "Get Collab" API has been updated, you can now use this API to search for exact title. Details found [[here>>doc:Collabs.the-collaboratory.Documentation Wiki.API.WebHome]] after release.
145 * Updates to the maintenance banner.
146
147 === **Collaboratory 2 release (2022-01-17) (Released)** ===
148
149 **Collaboratory.Lab**
150
151 * We are re-enabling the Juelich site selection for running your Notebooks on.
152
153 === **Collaboratory 2 release (2022-01-11) (Released)** ===
154
155 **Collaboratory.Wiki**
156
157 * The new Toast that appears if you have not filled in your PLUS profile has been updated to take into account more scenarios. The message and links will change dynamically based on a users situation.
158 * Upgrading XWiki to latest patch version.
159 * New policy released regarding collabs. [[Read more>>doc:Collabs.the-collaboratory.New Collaboratory\.wiki policy.WebHome]]
160
161 **Collaboratory.Drive**
162
163 * File uploads are now limited to 1GB or below in size.
164
165 === **Collaboratory 2 release (2021-12-14) (Released)** ===
166
167 **Collaboratory.Lab**
168
169 * Idle Labs are now kept running for up to 12 hours before being automatically closed.
170 * The Lab is aware of a new permission regarding user quotas. Lab users will be asked to grant the Lab this permission in their next session.
171 * The "Experimental" image is now becoming the Official EBRAINS image while the current  "Official EBRAINS" image will now be deprecated.
172 * The option to choose the Julich site is temporarily being disabled.
173
174 **Collaboratory.Wiki**
175
176 * Removed inactive EBRAINS user accounts from the results of user searches. These include the list displayed when trying to add a user to a collab's Team.
177 * The wording of the email received when you need to re-verify your account has been updated.
178 * You can no longer create collabs with duplicate titles.
179 * When using the "Collabs" search, filters will no longer be applied by default; instead you now need to select what filters you want to apply.
180 * A "Toast" popup will now remind you to fill out your PLUS profile if you have not already done so.
181
182 **Collaboratory.Bucket (Data-proxy)**
183
184 * file picker option added in the data-proxy. Data Proxy front UI can be parametrized with 2 query parameters: redirect_uri  and redirect_title . Once the user has selected files/folders in the UI, and clicks on the redirect button, he is redirected to the specified redirect_uri. The redirect_title is optional and allows to customize the redirect button in the UI.
185 * There is a new query parameter folder . When the user browses a bucket, the folder parameter is updated. That allows the user to share a link to a specific folder.
186 * Public buckets are now visible to anyone authenticated in the UI
187 * Public / Private toggle is visible to everyone but disabled by default. Only administrators can update the bucket privacy status.
188
189 === **Collaboratory 2 release (2021-12-07) (Released)** ===
190
191 **Collaboratory.Lab**
192
193 * The Lab now loads the Drive of the selected collab before loading the Drive of other collabs the user has access to. This reduces the time it takes for the selected collab's Drive to be accessible when starting up the Lab. This applies both to users opening the Lab from the Wiki navigation or from a link to a specific notebook.
194 * Notebooks can be exported to various views from the File > Export Notebook as menu. Some of those export options were no longer working and have been removed.
195
196 **Collaboratory.Wiki**
197
198 * The guided tour of the Wiki for users logging in the first time has been removed. Instead, feel free to check out individual tool tutorials that you can find on our [[documentation page.>>doc:Collabs.the-collaboratory.WebHome]]
199
200 === **Collaboratory 2 release (2021-11-10) (Released)** ===
201
202 **Collaboratory.Drive**
203
204 * We are deploying an upgrade to the Drive which should resolve multiple issues and adds new features including:
205 ** It improves Drive performance which had caused issues with Lab sessions left idling by users.
206 ** Its web interface updates dynamically when new files are created/deleted/renamed in a sub-folder of a collab's Drive.
207 ** It adds a new search file by filename in a given collab's Drive.
208 ** It adds a new "column view" in the web UI for browsing files in a collab's Drive.
209 ** Its web UI groups the public (shared) links and smart (internal) links to be managed via a common button and pop-up.
210 ** Its web UI adds color tagging to individual files.
211
212 (% class="wikigeneratedid" %)
213 **Collaboratory.Lab**
214
215 * The new version provides access to Lab sessions with more RAM for authorized users. Authorization can be requested by contacting [[https:~~/~~/ebrains.eu/support>>https://ebrains.eu/support]] with a motivation.
216
217 === **Collaboratory 2 release (2021-10-19) (Released)** ===
218
219 **Collaboratory.Lab**
220
221 * We have now added the ability for users to request larger amounts of memory for notebooks. For now, the best way to gain access to these larger notebooks is to [[contact support>>https://ebrains.eu/support/]] to request access.
222
223 **Collaboratory.Bucket**
224
225 * Users now have the ability to copy files from one bucket to another. You can do this when initially creating a bucket or at any time after creation via the Bucket UI.
226
227 === **Collaboratory 2 release (2021-10-11) (Released)** ===
228
229 **Collaboratory.Lab**
230
231 * We are adding a new Python kernel to the Collaboratory Lab in which pre-installed neuroscience tools are readily available. The new kernel is the one with "//**EBRAINS**//" in its name. Available tools in that kernel can be listed with the command "//**module avail**//". The new kernel will be available in the experimental Docker image of the Lab.
232
233 === **Collaboratory 2 release (2021-09-14) (Released)** ===
234
235 **Collaboratory.Wiki**
236
237 * Collabs will now have a "Contact Administrator" button that allows users to send a message to the administrators of a collab. The administrators will receive the message along with the details of the user that has sent the message.
238
239 === **Collaboratory 2 release (2021-09-03) (Released)** ===
240
241 **Collaboratory.Wiki**
242
243 * A new API is available to retrieve users emails based off a username, this is only available to users with the appropriate rights and will be detailed in the [[Wiki API>>doc:Collabs.the-collaboratory.Documentation Wiki.API.WebHome]] .
244 * The User API will now also return the "mitreid-sub", a unique identifier carried over from Collaboratory 1 that will be maintained in Collaboratory 2.
245 * The GET Users endpoint is now only available for authenticated users.
246
247 === **Collaboratory 2 release (2021-08-31) (Released)** ===
248
249 **Collaboratory 1**
250
251 * Account creation has been removed from Collaboratory 1 in preparation for Collaboratory 1 shutdown.
252
253 **Collaboratory.IAM**
254
255 * Users registering on Collaboratory 2 will now have a 16 digit numerical "Mitreid-sub" generated. This allows services using the "mitreid-sub" on Collaboratory 1 to continue using this field on Collaboratory 2.
256
257 **Collaboratory.Wiki**
258
259 * The collab creation form has been updated. When users click on "Create" they will now see a popup window informing them of the progress of the collab creation.
260
261 === **Collaboratory 2 release (2021-08-17) (Released)** ===
262
263 **Collaboratory.IAM**
264
265 * Users can check in the Wiki for their [[past login events>>https://iam.ebrains.eu/auth/realms/hbp/account/log]] (or from the wiki > user profile icon > basic profile > logs). The IAM update will pass the correct IP address from which the user logged in, instead of displaying the IP address 127.0.0.1.
266
267 **Collaboratory.Lab**
268
269 * Added a form for the user to select the Fenix site to run notebooks on.
270 * Activated the Fenix Jülich Supercomputing Centre execution site.
271 * Users visiting the Lab before visiting the Drive will now receive an appropriate error message.
272 * New environment variables have been added in the Notebook environment with:
273 ** the notebook filename,
274 ** the name of the collab containing the notebook file in its Drive,
275 ** the Fenix site where the notebook is executed, and
276 ** the Docker image in which the notebook is executed.
277 * View our [[sample notebook>>https://lab.ebrains.eu/user-redirect/lab/tree/shared/The%20Collaboratory/lab_env.ipynb?LAB_TEST=1]] on how to access these variables. NOTE: This notebook will not work until after tonight's deployment.
278 * Read the [[FAQ>>doc:Collabs.the-collaboratory.Documentation Lab.FAQ.Creating and accessing environment variables .WebHome]] for creating your own custom environment variables.
279
280 === **Collaboratory 2 release (2021-08-03) (Released)** ===
281
282 **Collaboratory.Wiki**
283
284 * Change 2 endpoints of the Collaboratory [[Wiki API>>doc:Collabs.the-collaboratory.Documentation Wiki.API.WebHome]] to also accept a Keycloak sub unique identifier as a search parameter.
285
286 === **Collaboratory 2 release (2021-07-20) (Released)** ===
287
288 **Collaboratory.Wiki**
289
290 * Collaboratory deletion now removes the associated Drive from the name, preventing duplicate Drives.
291 * Copying links from the Identity manager now works correctly.
292 * Backend changes made in preparation for future releases.
293 * Complete redesign of the Documentation which you will find in [[The Collaboratory>>doc:Collabs.the-collaboratory.WebHome]] collab.
294
295 === **Collaboratory 2 release (2021-07-06) (Released)** ===
296
297 **Collaboratory.Lab**
298
299 * Fixes and improvements to pyplot and matplotlib.
300 * Added NGL Viewer to interactively view molecular structures.
301 * Fixed permission issues in the notebook docker images that was were causing some libraries to throw warnings, the .cache dir is now writeable.
302 * Images have been cleaned by removing unnecessary libraries.
303
304 **Collaboratory.IAM**
305
306 * Fixed an issue where a user would occasionally be unable to delete a newly created collab.
307
308 **Collaboratory.Drive**
309
310 * Fixed an issue where linking directly to a document in a newly created private collab would provide an "Unable to view file" error.
311
312 === **Collaboratory 2 release (2021-06-22) (Released)** ===
313
314 **Collaboratory.Lab**
315
316 * Official EBRAINS Docker image~: Added R and rpy2.
317 * Experimental Docker image for EBRAINS tool developers: NFS Mount will now be available for developers. Added gcc10 and image optimisations.
318
319 === **Collaboratory 2 release (2021-06-14) (Released)** ===
320
321 **Collaboratory.Wiki **
322
323 * Fixed an issue causing new collabs to not have a Drive present.
324
325 === **Collaboratory 2 release (2021-06-10) (Released)** ===
326
327 **Collaboratory.Wiki **
328
329 * A small bug fix for the collab search page.
330
331 === **Collaboratory 2 release (2021-06-08) (Released)** ===
332
333 **As well as individual services, we have also changed how announcements are made, if more than one announcement is being made you now see an arrow to the left of the announcement banner that you can use to switch between announcements.**
334
335 **Collaboratory.Wiki **
336
337 * Added more filters to Collab search, you can now filter on collabs where you are a viewer, an editor or an admin.
338 * Collab Creation and collab settings forms have been updated, more descriptions have been added and the private or public collab choice is now a radio button.
339 * Instructions on how to get your collab as a highlighted collab have been published, if you visit the collab search page you will find a link to this new page just above the highlighted collabs.
340 * The collab page editor has been replaced by a full page editor instead of the current inline editor being used.
341
342 **Collaboratory.Lab**
343
344 * Users can now choose between 2 different images when launching a notebook, most users should keep using the Official EBRAINS image, however tool developers can now work on the experimental image.
345
346 **Collaboratory.Bucket**
347
348 * The ability for users to create permanent links is now available via the UI by right clicking on any file and choosing "Manage public link".
349
350 === **Collaboratory 2 release (2021-05-11) (Released)** ===
351
352 **The Collaboratory release on 11th May represents a large change in the functionality of the collab search page. Please [[contact support>>https://ebrains.eu/support/]] if you encounter any issues with this new functionality, thank you.**
353
354 **Collaboratory.Wiki**
355
356 * Large update to the collab search page functionality
357 ** Look and feel has been improved
358 ** You will now see "Highlighted collabs" when initially arriving on the page
359 ** You can now filter by "My favourite" collabs - Showing only those collabs that you have favourited (Small heart symbol on top right of a collab page)
360
361 **Collaboratory.Lab**
362
363 * Neuron installation has been fixed and updated to latest version.
364 * The "Copy shareable link" menu entry in the file browser of the Lab should now produce a correct URL without manual intervention.
365 * You can now use Environment variables populated from a URL, [[more information>>https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/how-to/Adding%20environment%20variables%20to%20Jupyter%20Notebooks/]]
366
367 **Collaboratory.Bucket**
368
369 * The ability for users to create permanent links is now available  (Via API only for now): [[API Documentation>>https://data-proxy.ebrains.eu/api/docs#/permalinks]]
370
371 === **Collaboratory 2 release (2021-04-28) (Partially released)** ===
372
373 **Due to the problem described in the "Drive issue" announcement, the Collaboratory release was delayed from 27th April to the 28th April**
374
375 **Collaboratory.Wiki**
376
377 * The new "Bucket" menu is now available in all collabs
378 * Various UI fixes.
379 * Collapsible macro styles have been updated.
380 * Fixed some issues with our Search functionality.
381 * Favourite collabs API has been developed for future integration into the UI.
382 * Added a report button to collabs, you can now report unused or inappropriate collabs.
383 * Issue for some users getting permission denied messages when they should not has been resolved.
384
385 **There was an issue during the release of the Lab, as such, the following has not yet been released and will be released on a different day.**
386
387 **Collaboratory.Lab**
388
389 * Nueron installation has been fixed and updated to latest version.
390 * The "Copy shareable link" button should now work without manual intervention.
391
392 === **Collaboratory 2 release (2021-04-13) (Released)** ===
393
394 **Collaboratory.Wiki**
395
396 * The new "Bucket" menu will be available in every new collab created, and will be rolled out to existing collab's in the coming days.
397 * Users logged into the wiki, should now automatically be logged into the lab in an iFrame instead of needing to login again.
398
399 === **Collaboratory 2 release (2021-03-30) (Released)** ===
400
401 The release going ahead on the 30th March will contain numerous upgrades and fixes throughout the Collaboratory Drive, Wiki and Lab.
402
403 **Collaboratory.Drive**
404
405 * Incorrect name formats are now automatically fixed
406 * Improvements to Automated tests.
407
408 **Collaboratory.Lab**
409
410 * Current Notebook image was rebuilt with extra extensions.  These are :  nbgitpuller,ipywidgets, jupyterlab-plotly, jupyter-matplotlib
411
412 **Collaboratory.Wiki**
413
414 * The "Favourite" button was moved to the top right of a collab page.
415 * New API added, this will allow users to get the Collab(CollabObject) via the DriveId - [[More information>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/Technical%20documentation/For%20Developers/Collaboratory%20API/]]
416 * Highlighted Collabs is now a responsive design.
417 * Improvements to Automated tests.
418
419 Note: This release will cause all running containers to be reset.
420
421 === Wiki update (2021-03-02) **(Released)** ===
422
423 As well as numerous bug fixes and small improvements to the Wiki, we are also upgrading the current version of XWiki(Version 10.11.9) to the most recent version of XWiki (Version 12.10.2). We are also adding a few fixes to its integration in the Wiki front end . A new feature was added: a new "Like" (Represented by a [[image:https://a.slack-edge.com/production-standard-emoji-assets/13.0/google-medium/2764-fe0f.png||alt=":heart:"]]) feature that is now available on Collab pages. For now, it can be used to show support and approval for any Collab page you like and use, in the future, we will be expanding upon this functionality. 
424
425 If you would like to see new features or feel certain functionality is required to improve the Collaboratory, please [[join the Collaboratory user group>>url:https://wiki.ebrains.eu/bin/view/Collabs/collaboratory-user-group/Joining%20the%20group/]], once joined, please do not hesitate to [[make your suggestions>>url:https://drive.ebrains.eu/lib/aac38e36-4bd9-48ee-9ae6-b876a65028aa/file/Collaboratory%20User%20Group%20-%20Suggestion%20box.docx]].
426
427 === EBRAINS ticketing system (2021-03-02) **(Released)** ===
428
429 The categories of tickets are being aligned to the description of [[services on the EBRAINS.eu website>>url:https://ebrains.eu/services/]]. We are using this opportunity to also upgrade the ticketing system to a more recent version.
430
431 === Collaboratory 2 release (2021-02-17) **(Released)** ===
432
433 The release going ahead on 17th February has the following enhancements.
434
435
436 1. Mounting a new "Shared" drive for the ability to easily share links from Seafile. So going forward, any links that need to be shared should be generated in the "Shared " drive. The original "/drive" will be kept so it does not break any of the already existing links.
437 1. OnlyOffice is being upgraded to the latest version. This should solve the issue listed below in the "Files locked in the Drive " section. The section will remain temporarily until it is verified this issue is fully fixed.
438 1. Seafile file system is being increased
439
440 === Collaboratory 1 maintenance **(Released)** ===
441
442 Collaboratory 1 services will be down from 18:00 CET [[(my timezone)>>url:https://everytimezone.com/s/4a9daa55]] Thursday Jan 7 for maintenance. The services are being re-hosted from the EPFL/BBP infrastructure to the Fenix infrastructure. The OIDC authentication service will be reactivated first (within 30 minutes); all other services will follow in the evening. Once the Collaboratory 1 services are back online, you may find that files added to the storage within the last days do not initially appear. This will be remedied overnight as we synchronize the storage. Thank you for your patience and understanding.
443
444 As a reminder the Collaboratory 1 services are deprecated and will be shut down in September 2021.
445
446 If you encounter issues with Collaboratory 1 after Friday 12:00 CET, please contact [[https:~~/~~/ebrains.eu/support>>url:https://ebrains.eu/support]]
447
448 The re-hosting was completed on Thursday evening. Some services relying on the Collaboratory 1 may need to be restarted to take into account the new DNS entries. Please notify [[support>>url:https://ebrains.eu/support]] of any issues you identify.