Activity

From 01/25/2015 to 02/23/2015

02/23/2015

11:33 pm Bug #5298 (Feedback): [SDKs] Should CollectionReader.all_streams() iterate lines in the manifest,...
A user just encountered an issue where their Crunch script had surprising behavior because an input manifest defined ... Brett Smith
11:14 pm Revision a5a4f79e (arvados): Added block to collection index map. Started using collection index ...
Started running summarize() methods after reading data from disk so that we can modify the summarization code and tes... Misha Zatsman
10:49 pm Revision d3f9fad0 (arvados): Fixed bug where I wasn't copied saved data.
Computed and logged summary of replication state. Misha Zatsman
10:13 pm Bug #5235: [Workbench] Pipeline instance "Re-run with latest" button occasionally returns Not fou...
Sorry, I don't think this is related to the middle button issue. I'm not really sure how to explain it other than it ... Bryan Cosca
09:52 pm Bug #5235: [Workbench] Pipeline instance "Re-run with latest" button occasionally returns Not fou...
Bryan,
Any chance you might be middle-clicking the button? That returns a 404, and would basically make this a du...
Brett Smith
09:54 pm Bug #4956: [API] cannot create collections with very large manifests
Here's the log:... Peter Amstutz
08:24 pm Bug #4956: [API] cannot create collections with very large manifests
Was able to recreate the error. Notes:
* This is a severely degenerate manifest. There are many instances of seq...
Peter Amstutz
09:50 pm Bug #4520 (Resolved): [SDKs] arv copy should respect --project-uuid when saving destination Colle...
Applied in changeset arvados|commit:f0fe7273c1851cb93e9edd58c0b60d3590b222ed. Peter Amstutz
09:40 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Peter Amstutz wrote:
> * Updated test.
Please assert that the first put returns the right hash (so we're sure it ...
Brett Smith
09:35 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
* Don't encode manifest_text by default to avoid double-encode faults.
* Coerce unicode strings to ascii in put(). ...
Peter Amstutz
08:38 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Peter Amstutz wrote:
> Brett Smith wrote:
>
> > Please change this condition to @isinstance(data, str)@ to accept...
Brett Smith
08:16 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Brett Smith wrote:
> Please change this condition to @isinstance(data, str)@ to accept subclasses, and add a test....
Peter Amstutz
07:51 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Reviewing commit:a47dc2b
Peter Amstutz wrote:
> > * The docker_image_hash link is copied incorrectly. The name s...
Brett Smith
07:15 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Brett Smith wrote:
> Reviewing commit:74784b3.
>
> * The code to take a source collection and turn it into a coll...
Peter Amstutz
03:07 am Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Reviewing commit:74784b3.
* The code to take a source collection and turn it into a collection on dst (including n...
Brett Smith
09:49 pm Revision f0fe7273 (arvados): Merge branch '4520-arv-copy-project-uuid' closes #4520
Peter Amstutz
09:48 pm Revision 8a5790d5 (arvados): 4520: Tweak test that put(u'foo') does the right thing.
Peter Amstutz
09:47 pm Task #5238 (Resolved): Review 4520-arv-copy-project-uuid
Peter Amstutz
02:44 am Task #5238 (In Progress): Review 4520-arv-copy-project-uuid
Brett Smith
09:43 pm Bug #3785: [Crunch] Job log collections should be stored with the same owner_uuid (and therefore ...
Radhika Chippada wrote:
> Peter,
> The update to set the owner_uuid for the log itself looks good.
>
> Just a c...
Peter Amstutz
06:28 pm Bug #3785: [Crunch] Job log collections should be stored with the same owner_uuid (and therefore ...
Peter,
The update to set the owner_uuid for the log itself looks good.
Just a couple of questions.
* Is it po...
Radhika Chippada
09:41 pm Revision 6b5b6890 (arvados): Added flags to write network data and then read it back. This is use...
Unfortunately had to switch H,L fields in blockdigest from private to public, otherwise they would not be exported. Misha Zatsman
09:36 pm Revision a4bc2867 (arvados): 4520: Coerce unicode strings to ascii in put(). Use result.content ...
literal result bytes) instead result.text (returns unicode) when processing
Keep responses.
Peter Amstutz
09:10 pm Revision f387f8bb (arvados): 3785: Log tab is no longer suppressed for anonymous users.
Peter Amstutz
08:20 pm Feature #5297: [Workbench] Enable users to share with any other user
I know I did some work on the API server end to make it possible for all users to see basic information about each ot... Brett Smith
08:17 pm Feature #5297 (New): [Workbench] Enable users to share with any other user
As a user, I would like to share my pipeline with another random user, but I currently cannot because he's not in my ... Bryan Cosca
08:18 pm Bug #5285: [SDKs] arv-run-pipeline-instance does not use 'settings.conf' file like other 'arv' tools
This tool already uses the Arvados class from the Ruby SDK, which reads from the configuration file. However, it als... Brett Smith
08:17 pm Revision 7b0d3939 (arvados): 4520: manifest_text() is utf-8 encoded by default so it can be safel...
Keep. Add test that calling put() with a unicode string raises an error.
Fetching user uuid in arv-copy uses num_ret...
Peter Amstutz
08:03 pm Story #3490: [Workbench] Create and edit pipeline templates
Bryan suggested http://json.parser.online.fr/ for inspiration in the related ticket. Brett Smith
08:03 pm Feature #5291 (Closed): [Workbench] Editing pipeline templates on Workbench
Duplicates #3490. Brett Smith
03:29 pm Feature #5291 (Closed): [Workbench] Editing pipeline templates on Workbench
It would be cool to have something like this: http://json.parser.online.fr/ with the collapsible objects Bryan Cosca
07:59 pm Bug #3434: No workbench user interface for sharing collections
Not sure why we deferred this? We just got a user request for it. Brett Smith
07:44 pm Bug #5294 (Closed): [SDKs] Make arv-copy useful for copying a Docker image
Peter's doing the code parts in #4520. Documentation should be covered in #5288. Closing a duplicate of those. Brett Smith
04:42 pm Bug #5294 (Closed): [SDKs] Make arv-copy useful for copying a Docker image
It's handy to be able to copy a Docker image collection from one project to another. However, because Arvados needs ... Brett Smith
07:41 pm Revision 248d2ebb (arvados): Added BlockToReplication field to collection.ReadCollections.
Lots of other little cleanup. Misha Zatsman
07:30 pm Bug #5292 (Closed): [Node Manager] Failed to recognize busy node on qr1hi
Caused by #4751. Brett Smith
07:04 pm Bug #5292: [Node Manager] Failed to recognize busy node on qr1hi
Saw something similar with qr1hi-8i9sb-en76y3f8yrtjitc. When it entered the queue, Node Manager booted several nodes... Brett Smith
04:07 pm Bug #5292 (Closed): [Node Manager] Failed to recognize busy node on qr1hi
This morning on qr1hi, the single minimum compute node was up (qr1hi-7ekkf-09hjulgcrpxp1iw), and running a job (qr1hi... Brett Smith
07:17 pm Revision a47dc2bc (arvados): 4520: Better checking to see if collection already exists at the des...
Set args.project_uuid to default value (current user uuid) if not set on
command line to simplify code.
Peter Amstutz
06:55 pm Revision f70584ec (arvados): 4520: Bonus fix because arv-copy was giving KeepClient.put() unicode...
instead of byte strings. KeepClient will now reject that. Peter Amstutz
06:54 pm Revision b7642ef6 (arvados): 4520: Refactor code to create the collection record. Also refactore...
which creates Docker metadata links so that copying any collection which
represents a Docker image will also copy ove...
Peter Amstutz
06:23 pm Task #5295 (In Progress): Review 3785-job-log-collection-owner
Radhika Chippada
04:43 pm Task #5295 (Resolved): Review 3785-job-log-collection-owner
Peter Amstutz
06:20 pm Feature #5296 (New): [Workbench] Extend Sharing tab to collections
Right now, in workbench, projects can be shared with other users/groups in workbench but not collections. It would b... Abram Connelly
06:02 pm February development review: Sharing is caring
Once you've found an interesting result in your analysis, you don't want to keep it to yourself. You want to share i... Brett Smith
04:45 pm Revision d960e97b (arvados): 3785: Upload job log to collection with --project-uuid same owner_uu...
Peter Amstutz
04:42 pm Task #5271 (Resolved): Fix crunch-job
Peter Amstutz
03:52 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
qr1hi-8i9sb-mcla1dzm2zrpl0t is a rerun of the exact same original job, and it died the exact same way. My test must ... Brett Smith
03:50 pm Bug #5277 (Resolved): FUSE does not parse timestamps with fraction of a second
Applied in changeset arvados|commit:b5cd9c9b9b160f316f9df6dda155df8a67cb8188. Peter Amstutz
03:44 am Bug #5277: FUSE does not parse timestamps with fraction of a second
commit:98f1b83 is good to merge. I've updated arvados-dev and Jenkins to build a ciso8601 .deb to fulfill the depend... Brett Smith
03:48 pm Revision b5cd9c9b (arvados): Merge branch '5277-fuse-mtime-fix' closes #5277
Peter Amstutz
03:47 pm Task #5278 (Resolved): Review 5277-fuse-mtime-fix
Peter Amstutz
03:07 am Task #5278 (In Progress): Review 5277-fuse-mtime-fix
Brett Smith
03:44 pm Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
If you don't have the OpenSSL wrapper that it wants to use, it will silently disable the feature. That might be what... Peter Amstutz
03:57 am Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
Peter Amstutz wrote:
> Doesn't work (default Debian packages in Jesse):
>
> * python-requests 2.4.3-4
> * python...
Brett Smith
03:35 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Brett Smith wrote:
> The whole suite of non-classes and extra @createFooCollection()@ constructor methods here is ...
Peter Amstutz
03:20 pm Bug #4232: [Workbench] Pipeline instances with many components should render quickly (on pipeline...
Reviewing commit:ad2792e
* You can remove the PipelineInstance#dependency_search method from API server as well. ...
Brett Smith
03:16 pm Revision ad69b48e (arvados): Merge branch 'master' into 4823-python-sdk-writable-collection-api
Peter Amstutz
03:16 pm Revision 25485439 (arvados): 4823: Clean up imports in collection.py
Peter Amstutz
03:10 pm Bug #5192 (Resolved): [API] Disallow changing the name of a repository record (by non-admin users)
Both API and Workbench already disallow a non-admin user from changing a repository name.
* API: repository.rb -> ...
Radhika Chippada
03:04 pm Bug #5192 (In Progress): [API] Disallow changing the name of a repository record (by non-admin us...
Radhika Chippada
02:44 pm Revision 3070d89e (arvados): 4823: Handle edge cases of files named '.' so that the FUSE test pas...
tests for invalid manifests. Defer populating CollectionReader streams until
needed to avoid extra copy of the manif...
Peter Amstutz
03:45 am Task #5280 (In Progress): Review 5246-update-urllib3
Brett Smith
03:41 am Revision 91a75ac3 (arvados): 5277: Build .deb for new ciso8601 dependency.
Refs #5277. Brett Smith
03:41 am Revision 91a75ac3 (arvados-dev): 5277: Build .deb for new ciso8601 dependency.
Refs #5277. Brett Smith

02/21/2015

06:06 pm Bug #4232: [Workbench] Pipeline instances with many components should render quickly (on pipeline...
Branch prepared with latest master, and with what I believe are the conclusions. That is, in the end I've removed the... Phil Hodgson
01:34 pm Revision 78fc2408 (arvados-dev): authkeys file need not be 0700...
0600 is sufficient.
Caught by Christoph. I don't actually think there is any possibility of this
being used to atta...
Sitaram Chamarty
01:33 pm Revision 9cd1e373 (arvados-dev): allow gitolite-shell to be used as "$SHELL"...
Experts only; no support and no docs.
Idea courtesy "calestyo"; see mails on Feb 20 or so in this:
https://groups.go...
Sitaram Chamarty
09:21 am Revision ad2792ed (arvados): 4232: revert experimental change to using find? for each of the jobs...
Phil Hodgson
09:11 am Revision c4fa80c6 (arvados): Merge branch 'master' into 4232-slow-pipes-n-jobs
Phil Hodgson

02/20/2015

10:40 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
I created a small Perl script that fetched the failing task, and fed its output to a flattened version of create_outp... Brett Smith
08:08 pm Bug #5283 (In Progress): [Crunch] crunch-job apparently died while collating job's output
Brett Smith
03:00 pm Bug #5283: [Crunch] crunch-job apparently died while collating job's output
qr1hi-8i9sb-gnwpoyq1fgc2vky is a job that's almost identical, except the Crunch script explicitly sets its task's suc... Brett Smith
10:35 pm Feature #4823: [SDKs] Good Collection API for Python SDK
The FUSE "edge cases" test revealed some awkward interactions between POSIX semantics and what's expressable in manif... Brett Smith
02:19 pm Feature #4823: [SDKs] Good Collection API for Python SDK
> * CollectionReader should fit into this hierarchy somehow. You're literally copying huge swaths of code from Colle... Brett Smith
08:58 pm Revision 93d38f3c (arvados): 4823: Fix tests broken by prior refactoring. Renamed 'api.py' to 'a...
so it wouldn't be awkwardly shadowed by the 'api' method. Peter Amstutz
08:26 pm Revision 664ca60e (arvados): make carousel arrows more obvious
Nancy Ouyang
06:29 pm Revision 62e3f155 (arvados): 4823: Refactoring. ReadOnly Collection is now CollectionReader, rep...
CollectionReader implementation (but maintains the same public API). Peter Amstutz
02:55 pm Story #5250 (In Progress): [Documentation] (recurring) Write blog post in first three days of sprint
Brett Smith
02:43 pm Bug #5288 (Resolved): [Documentation] Write user guide for arv-copy
Write a guide that walks a user through the process of starting from no configuration, and using arv-copy to copy a p... Brett Smith
02:21 pm Feature #5284: [Docker] Auto setup as much as possible for new users
Alternatively, maybe we shouldn't do any automatic user setup at all, and instead make sure the user is consistently ... Brett Smith
01:57 pm Revision 26b15b2f (sso-provider): 4601: Add indexes to enforce uniqueness on users.uuid and
authentications.[provider, uid] Peter Amstutz
03:51 am Revision 7b070ca1 (sso-provider): Merge branch '4601-openid-migrate-to-oauth2' into login_via_ema...
Peter Amstutz
03:51 am Revision 17ae8c64 (sso-provider): Add note about action mailer
Peter Amstutz
03:44 am Revision cb81985a (sso-provider): 4601: Improve configuration comments
Peter Amstutz
03:43 am Revision 71814268 (sso-provider): Local database sign up and sign in works!
Peter Amstutz
03:07 am Revision 4d479d06 (sso-provider): 4601: Generate uuid as part of creating new user record
Peter Amstutz
02:53 am Feature #4601: [SSO] Migrate OpenId users to OAuth/Google+
4601-openid-migrate-to-oauth2
* To support multiple providers, start using the "authentications" table.
** Migrat...
Peter Amstutz
02:20 am Feature #4601 (In Progress): [SSO] Migrate OpenId users to OAuth/Google+
Peter Amstutz
02:36 am Revision c9b81415 (sso-provider): 4601: Correctly create OAuth2 authentication record after findi...
authentication. Peter Amstutz
02:21 am Task #5286 (Resolved): Review 4601-openid-migrate-to-oauth2 (sso-provider)
Peter Amstutz
02:21 am Revision 551bae0f (sso-provider): 4601: Provide uuid in place of OpenId 2.0 for identity_url, for...
compatability with current master API server. Peter Amstutz
02:20 am Task #4421 (Resolved): API server can migrate users from OpenID to OpenID Connect
Peter Amstutz
02:06 am Bug #5285 (Resolved): [SDKs] arv-run-pipeline-instance does not use 'settings.conf' file like oth...
Having the file ... Abram Connelly

02/19/2015

10:13 pm Revision 20608e8c (sso-provider): 4601: Migrating user from OpenId 2.0 to OAuth2 works, new user ...
Peter Amstutz
10:04 pm Feature #5284 (New): [Docker] Auto setup as much as possible for new users
The API server Docker image is configured with auto_setup_new_users, but none of the related settings like auto_setup... Brett Smith
09:12 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Reviewing commit:f39118d. I have read more into the implementations for this round, which informs some of my discuss... Brett Smith
08:51 pm Revision f3d6ca90 (sso-provider): 4601: Migrate identity_url to authentications table.
Peter Amstutz
07:55 pm Revision 63ee2945 (sso-provider): 4601: Initial work in establishing how to get the openid_id fro...
flow to be able to do migration. Peter Amstutz
07:46 pm Revision d8856736 (arvados): Fix typo on doc homepage.
No issue # Ward Vandewege
06:58 pm Bug #5283 (Resolved): [Crunch] crunch-job apparently died while collating job's output
See qr1hi-8i9sb-ds95g67jm2jpmnd. The last line in the log says "collate", which means that we've entered @create_out... Brett Smith
06:55 pm Bug #4956: [API] cannot create collections with very large manifests
Re-ran the job and got the same error: qr1hi-8i9sb-77epylk1ecakg3a Peter Amstutz
04:07 pm Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
For reference, the github issue for this bug was:
https://github.com/shazow/urllib3/issues/412
Peter Amstutz
03:55 pm Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
Tracked it down. The bug is in urllib3 and is fixed in 1.10.
Peter Amstutz
03:36 pm Bug #5246: [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError when tryin...
This appears to be a requests and/or urllib3 bug. The "OpenSSL.SSL.WantWriteError" exception is a non-fatal error th... Peter Amstutz
04:00 pm Revision 71aa90b8 (arvados): 5246: Add minimum version constraint on urllib3 because of bug #5246
Peter Amstutz
03:59 pm Task #5280 (Closed): Review 5246-update-urllib3
Peter Amstutz
03:44 pm Task #5102 (In Progress): Try to reproduce
Peter Amstutz
03:33 pm Task #5268 (In Progress): Investigate further
Peter Amstutz
03:20 pm Revision 98f1b834 (arvados): 5277: Add test for mtime. Use ciso8601 module to parse arvados time...
Peter Amstutz
03:18 pm Task #5279 (Resolved): Add test and fix
Peter Amstutz
03:18 pm Task #5279 (Resolved): Add test and fix
Peter Amstutz
03:17 pm Task #5278 (Resolved): Review 5277-fuse-mtime-fix
Peter Amstutz
03:16 pm Bug #5277 (In Progress): FUSE does not parse timestamps with fraction of a second
Peter Amstutz
02:38 pm Bug #5277 (Resolved): FUSE does not parse timestamps with fraction of a second
Peter Amstutz
02:42 pm Support #5251 (In Progress): [Support] Fix bugs and write tests (first half)
Ward Vandewege
02:39 pm Revision f39118da (arvados): 4823: Revert FUSE changes unrelated to ThreadSafeApiCache
Peter Amstutz
02:32 pm Revision 0d63ac0c (arvados): Merge branch 'master' into 4823-python-sdk-writable-collection-api
Peter Amstutz
02:32 pm Revision 27fe76f5 (arvados): 4823: Fix fuse tests for SafeApi -> ThreadSafeApiCache changes. Add...
of mtime assertions. Peter Amstutz

02/18/2015

10:51 pm Bug #5276 (Resolved): [Workbench] Log graph pop up shows when there is no log graph
!log_graph_popup_shows.gif! Bryan Cosca
09:32 pm Task #5275 (Resolved): Specify desired behavior
Tom Clegg
09:32 pm Task #5274 (Resolved): Avoid parsing tokens in child's stderr
Tom Clegg
09:31 pm Task #5273 (Resolved): Add test
Tom Clegg
09:31 pm Task #5272 (Resolved): Detect CORS failure and display error message
Use a horrible hack like timeouts if necessary. Tom Clegg
09:30 pm Task #5271 (Resolved): Fix crunch-job
Peter Amstutz
09:27 pm Task #5270 (Resolved): write Draft 2 spec
Peter Amstutz
09:26 pm Task #5268 (Resolved): Investigate further
Peter Amstutz
09:20 pm Bug #5267 (New): [Node Manager] add one integration test for node manager
Ward Vandewege
09:16 pm Task #5266 (Closed): Detect various AJAX errors and ensure fail handler runs
Tom Clegg
09:15 pm Task #5265 (Closed): Add tests for redirect, timeout, and error
Tom Clegg
09:12 pm Task #5263 (Resolved): Add API mocking facility
Tom Clegg
09:11 pm Task #5262 (Resolved): Update install doc page
Tom Clegg
09:03 pm Bug #4957: [SDKs] arv keep put blows up when trying to put a danging symlink
Tom Clegg wrote:
> Perhaps rsync's behavior in the face of IO errors is a good model to follow. "Some stuff failed a...
Ward Vandewege
09:02 pm Bug #4957: [SDKs] arv keep put blows up when trying to put a danging symlink
Perhaps rsync's behavior in the face of IO errors is a good model to follow. "Some stuff failed along the way, so exi... Tom Clegg
08:46 pm Bug #4426: [Documentation] Support searching documentation
Suggest using site:doc.arvados.org and delegating to Google search Peter Amstutz
08:43 pm Feature #5261 (Resolved): [Workbench] Show project description in its own tab
The description tab should become the leftmost tab.
This tab should be the initially displayed tab -- unless the d...
Tom Clegg
08:20 pm Feature #5260 (New): [Tests] Implement long-running keepstore services in run-tests, similar to w...
Tom Clegg
08:18 pm Feature #5259 (New): [Tests] Reduce dependency on integration tests
Tom Clegg
08:16 pm Task #5213 (Resolved): Review branch: 4759-timestamp-precision
Tom Clegg
08:16 pm Task #5221 (Resolved): Review branch: 5186-collection-with-empty-properties
Radhika Chippada
08:16 pm Task #4947 (Resolved): Provide example to science team
Peter Amstutz
08:16 pm Story #5257 (Resolved): [CWL] write draft 2 spec
Peter Amstutz
07:46 pm Feature #5256 (Resolved): [OPS] Make it possible to kick off a Jenkins build for an arbitrary com...
Ward Vandewege
07:43 pm Bug #5255 (New): [Testing] Add a new unit-test-only build step to the build pipeline, before the ...
Ward Vandewege
07:42 pm Feature #5254 (New): [Testing] Make run-tests.sh able to run only unit tests or integration tests...
Ward Vandewege
06:44 pm Support #5252 (Resolved): [Support] Fix bugs and write tests (second half)
Ward Vandewege
06:44 pm Support #5251 (Resolved): [Support] Fix bugs and write tests (first half)
Ward Vandewege
06:43 pm Story #5250 (Resolved): [Documentation] (recurring) Write blog post in first three days of sprint
Ward Vandewege
06:41 pm Bug #4232: [Workbench] Pipeline instances with many components should render quickly (on pipeline...
Phil Hodgson wrote:
> Suggesting that we merge in the removal of the rendering of the "dependencies" in the API and ...
Brett Smith
06:39 pm Task #5249 (Resolved): Write up implementation summary on wiki
Tom Clegg
06:38 pm Task #5167 (Resolved): Figure out appropriate scope for first implementation
Tom Clegg
06:37 pm Feature #5072 (Resolved): [Documentation] (recurring) Refresh user documentation
Tom Clegg
06:37 pm Task #5248 (Resolved): [Documentation] Add public projects (anonymous access) to documentation.
We have a bunch of sharing features. We should have a page on the documentation site that explains them all. Ward Vandewege
06:37 pm Feature #5247 (Resolved): [Documentation] (recurring) Refresh user documentation
Ward Vandewege
06:19 pm Story #2659 (Resolved): [Workbench] Anonymous user can access publicly shared data using Workbenc...
Ward Vandewege
05:45 pm Support #5071 (Resolved): [Support] Fix bugs and write tests (second half)
Ward Vandewege
04:52 pm Revision 78ca9c5c (arvados): closes #5197
Merge branch '5197-collection-name-owner-unique' Radhika Chippada
04:48 pm Bug #5194: [Documentation] User guide doesn't link to or acknowledge new "Getting Started" section
This is great, thanks. Peter Amstutz
04:43 pm Bug #5246 (Resolved): [OPS] Write to keep.qr1hi.arvadosapi.com raising OpenSSL.SSL.WantWriteError...
WTF?... Peter Amstutz
04:20 pm Revision 7383891f (arvados-dev): Reflect deploy changes in run-deploy.sh
Refs #5226 Ward Vandewege
04:20 pm Revision 7383891f (arvados): Reflect deploy changes in run-deploy.sh
Refs #5226 Ward Vandewege
03:32 pm Bug #5207: [API] Collection expires_at should be a full timestamp, not just a date.
expires_at should absolutely be a timestamp just like all the others.
Suggest a unit test that verifies every *_at...
Tom Clegg
03:31 pm Revision cbccf62a (arvados): 4759: Update Node Manager to parse new Arvados API timestamps.
Refs #4759. Brett Smith
02:43 pm Bug #5145: [Workbench] Combining collections should separate files with identical names, not conc...
so in here: qr1hi-j7d0g-0x4b08b68zanwxh
I have new collection and new collection (2)
I have foo.txt in each of them...
Bryan Cosca

02/17/2015

11:20 pm Bug #5194 (Resolved): [Documentation] User guide doesn't link to or acknowledge new "Getting Star...
Applied in changeset arvados|commit:9c8bad50218730ac2c640f8e1c00fd12f2f174e4. Anonymous
11:04 pm Bug #5194 (In Progress): [Documentation] User guide doesn't link to or acknowledge new "Getting S...
Nancy Ouyang
11:03 pm Bug #5194 (New): [Documentation] User guide doesn't link to or acknowledge new "Getting Started" ...
* I kept "finished" because hopefully they ran their first pipeline in addition to reading the guide
* fixed
* fixed
Nancy Ouyang
10:53 pm Bug #5194 (In Progress): [Documentation] User guide doesn't link to or acknowledge new "Getting S...
Radhika Chippada
10:52 pm Bug #5194: [Documentation] User guide doesn't link to or acknowledge new "Getting Started" section
Review comments:
Looks much better and clears the confusion with disconnected "Getting started" sections. Just a f...
Radhika Chippada
10:29 pm Bug #5194: [Documentation] User guide doesn't link to or acknowledge new "Getting Started" section
Note about task #5243:
This is a quick fix only.
* I disambiguated "user guide" vs "getting started" sections with...
Nancy Ouyang
11:20 pm Task #5243 (Resolved): Review branch 5194-quickfix-disambiguate-gettingstarted-sections
Applied in changeset arvados|commit:9c8bad50218730ac2c640f8e1c00fd12f2f174e4. Anonymous
10:55 pm Task #5243 (In Progress): Review branch 5194-quickfix-disambiguate-gettingstarted-sections
Radhika Chippada
10:22 pm Task #5243 (Resolved): Review branch 5194-quickfix-disambiguate-gettingstarted-sections
This is a quick fix only. I disambiguated the new "getting started" section from the "getting started" subsection in ... Nancy Ouyang
11:16 pm Revision 9c8bad50 (arvados): closes #5243, #5194 Merge branch '5194-quickfix-disambiguate-getting...
Nancy Ouyang
11:07 pm Revision efb77a42 (arvados): Merge branch '3408-production-datamanager' refs #3408
Misha Zatsman
11:06 pm Revision a5f72c4a (arvados): 5194: minor fixes
Nancy Ouyang
11:06 pm Revision f5a88673 (arvados): Merge branch 'master' into 3408-production-datamanager refs #3408
Misha Zatsman
11:02 pm Revision 83ea6e36 (arvados): Changes to allow datamanager to run indefinitely:
Logger's worker goroutine returns after final write.
minutes-between-runs flag specifies how many minutes to wait bet...
Misha Zatsman
11:00 pm Task #5222 (Resolved): Review 4138-node-manager-gce-wip
Applied in changeset arvados|commit:319503f1a8eda9fb9cea0bff038ad437e88ebeac. Brett Smith
11:00 pm Feature #4138 (Resolved): [Node Manager] Support Google Cloud Platform in node manager
Applied in changeset arvados|commit:319503f1a8eda9fb9cea0bff038ad437e88ebeac. Brett Smith
10:02 pm Feature #4138: [Node Manager] Support Google Cloud Platform in node manager
Brett Smith wrote:
> Tom Clegg wrote:
> > * services/nodemanager/doc/gce.example.cfg seems to have forked the docum...
Tom Clegg
03:44 pm Feature #4138: [Node Manager] Support Google Cloud Platform in node manager
Tom Clegg wrote:
> * services/nodemanager/doc/gce.example.cfg seems to have forked the documentation in ec2.example....
Brett Smith
10:55 pm Revision 319503f1 (arvados): Merge branch '4138-node-manager-gce-wip'
Closes #4138, #5222.
Thanks, Tim.
Brett Smith
10:49 pm Revision c51fe8e8 (arvados): 4138: Refactor out Node Manager DriverTestMixin.
Brett Smith
10:49 pm Revision d6d290bf (arvados): 4138: Prepare Node Manager GCE driver for production.
* Set node metadata in more appropriate places.
* Bridge more differences between GCE and EC2, like the fact that
s...
Brett Smith
10:49 pm Revision d32bbed0 (arvados): 4138: Revamp Node Manager driver proxying in BaseComputeNodeDriver.
Accessing attributes through a super() proxy does not invoke
__getattr__ on base classes, so the old implementation m...
Brett Smith
10:49 pm Revision 9d6a6eca (arvados): 4138: support for Google Cloud Engine.
* Added:
** nodemanager/arvnodeman/computenode/drivers/gce.py
** nodemanager/doc/gce.example.cfg
** nodemanager/tests...
Tim Pierce
10:49 pm Revision 5884b7c4 (arvados): 4138: Fix noop Node Manager EC2 driver tests.
The previous tests simply instantiated the driver, then checked that a
mock method was truthy (which it will always b...
Brett Smith
10:49 pm Revision b5249ac7 (arvados): 4138: Refactor common Node Manager driver initialization to base dri...
Brett Smith
10:49 pm Revision 708630d0 (arvados): 4138: Simplify Node Manager GCE credential handling.
Because libcloud's GCE driver accepts a key path as a constructor
argument, it's relatively straightforward to put al...
Brett Smith
10:49 pm Revision 51d417f9 (arvados): 4138: GCE fixes
The 'network_id' parameter needs to be delivered as 'location' in GCE.
The ping_url parameter is now delivered in th...
Tim Pierce
10:49 pm Revision 45fdc95e (arvados): 4138: general GCE fixes
* JSON credential file
** GCE credentials are delivered as a JSON string (and the key is formatted as a multi-line RS...
Tim Pierce
10:49 pm Revision a6837612 (arvados): 4138: updated unit test
Corrected test_create_includes_ping_secret to account for delivering the
ping secret via metadata in GCE.
Tim Pierce
10:49 pm Revision af52e497 (arvados): 4138: code review feedback
Tim Pierce
10:46 pm Feature #5245 (New): [Documentation] Show footer with date last updated
A "date last updated" footer on each doc page will help users troubleshoot if any documentation falls out of date and... Nancy Ouyang
10:19 pm Revision 95053e5f (arvados): 5194: Quickfix, disambiguated getting started and user guide section...
Nancy Ouyang
10:10 pm Story #3408: [Keep] Implement Production Data Manager
Peter Amstutz wrote:
> * The Arvados convention for timestamps is to end in "_at" so runInfo["started_at"] instead o...
Misha Zatsman
09:37 pm Revision 1713f54c (arvados): Merge branch '3408-production-datamanager' refs #3408
Misha Zatsman
09:33 pm Bug #5211: [Documentation] Top Navbar of docs homepage not suitable for small window
This happens in-between "super small" where it turns into a mobile-friendly page, and "big" when the top navbar is flat. Nancy Ouyang
09:30 pm Revision 6100a423 (arvados): More changes in response to Peter's review.
Started referencing keep servers by uuid.
Moved more logger init code into constructor call.
Switched logged timestam...
Misha Zatsman
09:23 pm Bug #5240 (Closed): Create spec of Public Project list
Bryan Cosca
09:21 pm Bug #5240 (Closed): Create spec of Public Project list
make sure descriptions are had in all collections, templates, projects, subprojects, etc. Bryan Cosca
09:22 pm Story #5239 (Closed): Create public RNA seq tuxedo pipeline
Bryan Cosca
09:21 pm Story #5239 (Closed): Create public RNA seq tuxedo pipeline
Bowtie > Tophat > cufflinks > HTSeq Bryan Cosca
09:20 pm Bug #4520 (In Progress): [SDKs] arv copy should respect --project-uuid when saving destination Co...
Peter Amstutz
09:16 pm Bug #4520: [SDKs] arv copy should respect --project-uuid when saving destination Collection
Notes:
It should now correctly respect --project-uuid for collections, templates, pipeline instances, and docker i...
Peter Amstutz
09:12 pm Task #5238 (Resolved): Review 4520-arv-copy-project-uuid
Peter Amstutz
09:12 pm Task #5114 (Resolved): Fix
Peter Amstutz
07:59 pm Task #5114 (In Progress): Fix
Peter Amstutz
09:04 pm Revision 74784b33 (arvados): 4520: tested copying, fixed bad 'properties' field
Peter Amstutz
09:02 pm Feature #5090 (Resolved): [Documentation] Add some direct links on doc.arvados.org to the most us...
Nancy Ouyang
09:01 pm Task #5196 (Resolved): Review branch 5090-doc-to-homepage
Nancy Ouyang
08:53 pm Revision 546b44cf (arvados): refs #5090 Merge branch '5090-doc-to-homepage'
Nancy Ouyang
08:16 pm Revision bef0f85f (arvados): 4520: --project-uuid now used for owner_uuid on all create() calls.
Peter Amstutz
08:10 pm Feature #5237 (New): [Workbench] Pipeline re-run dialog should offer docker image choices (latest...
Tom Clegg
07:46 pm Task #5031: Review/feedback
Wiki page is ready for another round of feedback. Brett Smith
07:45 pm Story #3603: [Crunch] Design good Crunch task API, including considerations about "jobs-within-jo...
I've updated "the wiki page":https://arvados.org/projects/arvados/wiki/Python_SDK with our current thinking about the... Brett Smith
06:46 pm Revision f3250432 (arvados): 3408: Merge branch 'master' into 3408-production-datamanager
Tom Clegg
06:43 pm Feature #4823: [SDKs] Good Collection API for Python SDK
Brett Smith wrote:
>
> h2. What am I reviewing?
>
> A lot of the code in this branch is meant to provide API su...
Peter Amstutz
06:39 pm Bug #5235 (New): [Workbench] Pipeline instance "Re-run with latest" button occasionally returns N...
This has happened to me maybe 3 or so times in the last 100-200 attempts, hard to reproduce, maybe its just an intern... Bryan Cosca
06:36 pm Revision 50d3be92 (arvados): 4823: Record manifest_text response from API server. Give better na...
some tests. Peter Amstutz
06:29 pm Revision bd53829c (arvados): refs #4926 Merge branch '4926-rename-share.png'
Nancy Ouyang
05:35 pm Bug #4759 (Resolved): [API] greater than filter is treated as greater than or equals for modifica...
Applied in changeset arvados|commit:3598c3003a7987cca5c0536ba8206ec40c1c3649. Anonymous
05:07 pm Bug #4759: [API] greater than filter is treated as greater than or equals for modification time.
Tom, that is fine. I also used "humans" in several tests earlier for the same reason. We can deal with them when we d... Radhika Chippada
05:04 pm Bug #4759: [API] greater than filter is treated as greater than or equals for modification time.
Radhika Chippada wrote:
> One minor comment about the tests. In the python test_timestamp_inequality_filter, why use...
Tom Clegg
04:37 pm Bug #4759: [API] greater than filter is treated as greater than or equals for modification time.
Tom, yes, I agree that "2015-02-17" should mean "2015-02-17T00:00:00.000000000Z" and all the updates look good.
On...
Radhika Chippada
06:41 am Bug #4759: [API] greater than filter is treated as greater than or equals for modification time.
4759-timestamp-precision-TC now has
commit:5517f02 4759: Add functional tests for timestamp precision.
commit:6ee...
Tom Clegg
05:16 pm Revision 20b2d6f7 (arvados): Merge branch 'master' into 4823-python-sdk-writable-collection-api
Peter Amstutz
05:15 pm Revision 503c616f (arvados): 4823: More tests and fixes for updating and merging from remote api ...
Tests pass. Peter Amstutz
05:09 pm Bug #5233 (New): [Tests] Eliminate system globals in test suites
It should be possible to run jenkins/run-tests.sh on two source trees concurrently on the same machine (using either ... Tom Clegg
05:07 pm Revision 3598c300 (arvados): Merge branch '4759-timestamp-precision-TC' closes #4759
Tom Clegg
04:50 pm Task #5219 (Resolved): Review branch: 5096-wb-collection-name-or-desc-update
Radhika Chippada
04:11 pm Bug #4232: [Workbench] Pipeline instances with many components should render quickly (on pipeline...
Suggesting that we merge in the removal of the rendering of the "dependencies" in the API and call it a day, with the... Phil Hodgson
03:42 pm Revision 28467b48 (arvados): 4138: Fixup GCE shutdown window docs.
Brett Smith
03:38 pm Revision 37916fad (arvados): 4138: Fixup GCE boot time calculations.
Store boot time in node metadata when we create a node. Assume 0 if
that's not available.
Brett Smith
03:30 pm Bug #5220 (Resolved): [Workbench] for collections shared anonymously, do not show the 'Sharing an...
Applied in changeset arvados|commit:d54738ad3b2fde0207cf1ebbdc6f4360cd141d90. Radhika Chippada
03:16 pm Bug #5220: [Workbench] for collections shared anonymously, do not show the 'Sharing and Permissio...
I added one whitespace cleanup commit on this branch, thanks, LGTM.
Please pull in that commit and merge!
Ward Vandewege
03:25 pm Revision d54738ad (arvados): closes #5220
Merge branch '5220-no-sharing-box-for-anon-user' Radhika Chippada
03:20 pm Revision 177e076e (arvados): 4926: renamed share.png to sharing.png due to adblock on firefox
Nancy Ouyang
03:17 pm Task #5225 (Resolved): Review branch: 5220-no-sharing-box-for-anon-user
Ward Vandewege
03:15 pm Task #5225 (In Progress): Review branch: 5220-no-sharing-box-for-anon-user
Ward Vandewege
03:13 pm Revision 96e0115f (arvados): 5220: whitespace cleanup.
Ward Vandewege
02:26 pm Revision 39e2e62f (arvados): 4138: Fixup GCE config e-mail address.
Brett Smith
06:35 am Revision 5517f022 (arvados): 4759: Add functional tests for timestamp precision.
Tom Clegg
06:06 am Revision 6ee389b7 (arvados): 4759: Add test for inequality filters.
Tom Clegg
03:35 am Revision 4f8b2d75 (arvados): 4759: Ignore args to as_json.
Tom Clegg
02:36 am Task #5165 (Resolved): Review 3410-replication-attrs
Tom Clegg
12:27 am Revision fe7c0afe (arvados): 4759: add (options = nil) to time_format -> as_json method. Several ...
SELECT "logs".* FROM "logs" WHERE (logs.id >= 7) ORDER BY id asc LIMIT 20
Error publishing event: wrong number of arg...
Radhika Chippada

02/16/2015

11:59 pm Revision afa3f1f4 (arvados): 4759: do not use modified_at getter method; test passes but still ot...
Radhika Chippada
11:34 pm Bug #5220: [Workbench] for collections shared anonymously, do not show the 'Sharing and Permissio...
Notes about the update:
* I hid the "Sharing and permissions" box when anonymous access is the context.
* I sho...
Radhika Chippada
10:52 pm Bug #5220 (In Progress): [Workbench] for collections shared anonymously, do not show the 'Sharing...
Radhika Chippada
06:03 pm Bug #5220: [Workbench] for collections shared anonymously, do not show the 'Sharing and Permissio...
Brett Smith wrote:
> For background, Workbench used to be quieter in this scenario. The message was added during re...
Ward Vandewege
11:31 pm Task #5225 (Resolved): Review branch: 5220-no-sharing-box-for-anon-user
Radhika Chippada
11:30 pm Revision 58f8ab40 (arvados): 5220: do not show "Sharing and permissions" box when an anonymous us...
Radhika Chippada
10:50 pm Bug #5189 (Resolved): [Workbench] Manage account does not show repositories directly owned by user
Applied in changeset arvados|commit:1ee6ce5be0c86c1d2e903252ba2a70694be5cf31. Radhika Chippada
10:46 pm Bug #5189: [Workbench] Manage account does not show repositories directly owned by user
Thanks Brett. Merged into master after making the update. Radhika Chippada
09:35 pm Bug #5189: [Workbench] Manage account does not show repositories directly owned by user
Radhika Chippada wrote:
> Brett, I need separate lists @my_repositories (which has the list of repositories for the ...
Brett Smith
09:16 pm Bug #5189: [Workbench] Manage account does not show repositories directly owned by user
Brett, I need separate lists @my_repositories (which has the list of repositories for the links + owned repositories)... Radhika Chippada
07:12 pm Bug #5189: [Workbench] Manage account does not show repositories directly owned by user
Reviewing commit:45d8d01
This code calls @Repository.where(owner_uuid: current_user.uuid)@ twice. This can make t...
Brett Smith
04:34 pm Bug #5189 (In Progress): [Workbench] Manage account does not show repositories directly owned by ...
Radhika Chippada
10:49 pm Revision 37affe0f (arvados): Merge branch 'master' into 4759-timestamp-precision
Radhika Chippada
10:46 pm Task #5223 (Resolved): Review branch: 5189-manage-acct-shows-own-repos
Radhika Chippada
06:51 pm Task #5223 (In Progress): Review branch: 5189-manage-acct-shows-own-repos
Brett Smith
04:35 pm Task #5223 (Resolved): Review branch: 5189-manage-acct-shows-own-repos
Radhika Chippada
10:46 pm Revision 1ee6ce5b (arvados): closes #5189
Merge branch '5189-manage-acct-shows-own-repos' Radhika Chippada
10:45 pm Revision c99e40c1 (arvados): 5189: a little cleanup
Radhika Chippada
10:28 pm Revision 1578bb43 (arvados): Merge branch 'master' into 5189-manage-acct-shows-own-repos
Radhika Chippada
10:24 pm Revision 40e9d6a0 (arvados): 4759: added time_format.rb initializer
Radhika Chippada
10:13 pm Feature #4138: [Node Manager] Support Google Cloud Platform in node manager
Only a couple of comments at commit:8f28c53... with the caveat that I'm still pretty new at libcloud/nodemanager:
...
Tom Clegg
09:51 pm Revision 6cd9106d (arvados): Merge branch 'master' into 4759-timestamp-precision
Conflicts:
services/api/test/integration/collections_api_test.rb
Radhika Chippada
09:49 pm Revision 5f905666 (arvados): 4823: Add new tests for BufferBlock, BlockManager, saving, updating....
changes on variable naming. Remove splitting code from splitfastq. Peter Amstutz
09:00 pm Story #3410 (Resolved): [API] Rename collection "desired replication" attributes, add model const...
Applied in changeset arvados|commit:d87717b4ec885059183ef6d7fa6780c343338455. Anonymous
05:32 pm Story #3410 (In Progress): [API] Rename collection "desired replication" attributes, add model co...
Tom Clegg
08:28 am Story #3410: [API] Rename collection "desired replication" attributes, add model constraints
Radhika Chippada wrote:
> “args.replication is how many copies we instruct Arvados to maintain (by passing it in col...
Tom Clegg
08:58 pm Revision 87ab50f7 (arvados): 5197: needed one more udpate
Radhika Chippada
08:53 pm Revision d87717b4 (arvados): Merge branch '3410-replication-attrs' closes #3410 refs #5011
Tom Clegg
08:49 pm Revision 20abd5d5 (arvados): Merge branch 'master' into 5197-collection-name-owner-unique
Conflicts:
services/api/db/structure.sql
Radhika Chippada
08:41 pm Revision 0fd86b97 (arvados): 5197: down migration working
Radhika Chippada
08:31 pm Revision 8c629ffa (arvados): Merge branch 'master' into 5197-collection-name-owner-unique
Radhika Chippada
08:31 pm Revision a002d3ef (arvados): 5197: updated migration script
Radhika Chippada
08:02 pm Revision daaeb7a2 (arvados): Fix typo in COPYING.
No issue # Ward Vandewege
07:49 pm Revision 399366e7 (arvados): 5197: update the collection_owner_uuid_name_unique index to use expi...
Radhika Chippada
07:13 pm Revision eff37344 (arvados): 3410: Merge branch 'master' into 3410-replication-attrs
Conflicts:
services/api/test/fixtures/collections.yml
services/api/test/unit/collection_test.rb
Tom Clegg
07:07 pm Revision fb179796 (arvados): 5197: write a failing test
Radhika Chippada
07:05 pm Task #5222 (In Progress): Review 4138-node-manager-gce-wip
Tom Clegg
04:15 pm Task #5222 (Resolved): Review 4138-node-manager-gce-wip
Brett Smith
07:02 pm Bug #4759: [API] greater than filter is treated as greater than or equals for modification time.
Replaced 4759-timestamp-precision-TC with much nicer commit:5f2d5f9.
Tom Clegg
04:42 pm Bug #4759: [API] greater than filter is treated as greater than or equals for modification time.
It doesn't seem quite right to make the models' attribute methods start returning strings instead of ActiveSupport::T... Tom Clegg
07:00 pm Revision 5f2d5f96 (arvados): 4759: Use ISO 8601 timestamps with fractional seconds in API responses.
Tom Clegg
05:54 pm Bug #5096: [Workbench] Avoid passing manifest_text around the network too much when updating and ...
Brett, thanks for the suggestion. This is much more efficient and accomplishes the goal more effectively. I made this... Radhika Chippada
05:23 pm Bug #5096: [Workbench] Avoid passing manifest_text around the network too much when updating and ...
Reviewing commit:23c1bc6
When we're doing small updates, the new update method skips a lot of the encoding work in...
Brett Smith
05:50 pm Revision fd172dd6 (arvados): refs #5096
Merge branch '5096-wb-collection-name-or-desc-update' Radhika Chippada
05:46 pm Revision 5e003c8f (arvados): Merge branch 'master' into 5096-wb-collection-name-or-desc-update
Conflicts:
apps/workbench/test/controllers/collections_controller_test.rb
Radhika Chippada
05:42 pm Revision f842b72b (arvados): 5096: more efficient update method override.
Radhika Chippada
05:32 pm Task #5205 (Resolved): Review 5200-anonymous-download
Tom Clegg
04:35 pm Bug #5095 (Resolved): [FUSE] arv-mount takes up too much memory and occassionally crashes when li...
Applied in changeset arvados|commit:8b90f80efca772efd2697ffc70d7809c32564171. Peter Amstutz
04:20 pm Bug #5095: [FUSE] arv-mount takes up too much memory and occassionally crashes when listing large...
Peter Amstutz wrote:
> Now at commit:ef4e4a3
This is good to merge. Thanks.
Brett Smith
04:00 pm Bug #5095: [FUSE] arv-mount takes up too much memory and occassionally crashes when listing large...
Brett Smith wrote:
> Reviewing commit:4106786.
>
> * Directory uses the current time as the default mtime. Colle...
Peter Amstutz
03:54 pm Bug #5095 (In Progress): [FUSE] arv-mount takes up too much memory and occassionally crashes when...
Peter Amstutz
03:19 am Bug #5095: [FUSE] arv-mount takes up too much memory and occassionally crashes when listing large...
Reviewing commit:4106786.
* Directory uses the current time as the default mtime. CollectionDirectory overrides t...
Brett Smith
04:33 pm Revision 6ab55057 (arvados): Merge branch 'master' into 5189-manage-acct-shows-own-repos
Radhika Chippada
04:33 pm Revision 8b90f80e (arvados): Merge branch '5095-fuse-ls-takes-forever' closes #5095
Peter Amstutz
04:33 pm Task #5219 (In Progress): Review branch: 5096-wb-collection-name-or-desc-update
Brett Smith
04:33 pm Task #5216 (Resolved): Review 5095-fuse-ls-takes-forever
Peter Amstutz
02:58 am Task #5216 (In Progress): Review 5095-fuse-ls-takes-forever
Brett Smith
04:32 pm Revision 446785a1 (arvados): 4823: Notes on how the mocking works with requests.Session
Peter Amstutz
04:30 pm Bug #4464 (Resolved): [Workbench] Collections tab loads forever on a specific project
The project named in this bug now loads very quickly, so I'm marking this as closed. Admittedly there's been some fa... Brett Smith
04:29 pm Revision 45d8d010 (arvados): 5189: include owned repositories in the list of repositories returne...
Radhika Chippada
04:26 pm Revision 4b79e0e7 (arvados): 4759: Use ISO 8601 timestamps with fractional seconds in API responses.
Tom Clegg
04:12 pm Revision 8f28c530 (arvados): 4138: Prepare Node Manager GCE driver for production.
* Set node metadata in more appropriate places.
* Bridge more differences between GCE and EC2, like the fact that
s...
Brett Smith
04:12 pm Revision 58be160a (arvados): 4138: Fix noop Node Manager EC2 driver tests.
The previous tests simply instantiated the driver, then checked that a
mock method was truthy (which it will always b...
Brett Smith
04:12 pm Revision 82bb5282 (arvados): 4138: Revamp Node Manager driver proxying in BaseComputeNodeDriver.
Accessing attributes through a super() proxy does not invoke
__getattr__ on base classes, so the old implementation m...
Brett Smith
04:12 pm Revision 1e0fa596 (arvados): 4138: Refactor out Node Manager DriverTestMixin.
Brett Smith
04:12 pm Revision 6bd3ba96 (arvados): 4138: Refactor common Node Manager driver initialization to base dri...
Brett Smith
04:12 pm Revision 0d0a1fe0 (arvados): 4138: Simplify Node Manager GCE credential handling.
Because libcloud's GCE driver accepts a key path as a constructor
argument, it's relatively straightforward to put al...
Brett Smith
04:12 pm Revision 36929497 (arvados): 4138: updated unit test
Corrected test_create_includes_ping_secret to account for delivering the
ping secret via metadata in GCE.
Tim Pierce
04:12 pm Revision 0d0de386 (arvados): 4138: GCE fixes
The 'network_id' parameter needs to be delivered as 'location' in GCE.
The ping_url parameter is now delivered in th...
Tim Pierce
04:12 pm Revision c2fb3f57 (arvados): 4138: code review feedback
Tim Pierce
04:12 pm Revision 650bd4ae (arvados): 4138: support for Google Cloud Engine.
* Added:
** nodemanager/arvnodeman/computenode/drivers/gce.py
** nodemanager/doc/gce.example.cfg
** nodemanager/tests...
Tim Pierce
04:12 pm Revision 2b6cfad3 (arvados): 4138: general GCE fixes
* JSON credential file
** GCE credentials are delivered as a JSON string (and the key is formatted as a multi-line RS...
Tim Pierce
04:01 pm Revision ef4e4a34 (arvados): 5095: _mtime on collection defaults to 0 instead of time.time().
Peter Amstutz
03:59 pm Revision f22dda84 (arvados): Merge branch 'master' into 4823-python-sdk-writable-collection-api
Conflicts:
sdk/python/tests/arvados_testutil.py
services/fuse/arvados_fuse/__init__.py
Peter Amstutz
03:49 pm Task #5213 (In Progress): Review branch: 4759-timestamp-precision
Tom Clegg
03:11 pm Revision 7b877a2b (arvados): 5095: Set _mtime when the collection object is updated.
Peter Amstutz
02:00 pm Bug #5186 (Resolved): [Workbench] Collection viewing broken for collections with empty (but non-n...
Applied in changeset arvados|commit:0cefa4c0f3c1b16884b04d6273bd8730166d69ba. Radhika Chippada
01:58 pm Bug #5186: [Workbench] Collection viewing broken for collections with empty (but non-nil) propert...
Thanks for the review feedback Brett. I removed the unnecessary statement from the collection_controller. I added a g... Radhika Chippada
03:54 am Bug #5186: [Workbench] Collection viewing broken for collections with empty (but non-nil) propert...
At commit:7ef2780
Radhika Chippada wrote:
> * My tests passed with or without "accept_attribute_as_json :properti...
Brett Smith
01:56 pm Revision 0cefa4c0 (arvados): closes #5186
Merge branch '5186-collection-with-empty-properties' Radhika Chippada
01:54 pm Revision 4c5352de (arvados): 5186: a few more test assertions.
Radhika Chippada
08:12 am Revision 11e1ee67 (arvados): 3410: Update comments.
Tom Clegg
08:12 am Revision 1e423bd9 (arvados): 3410: Fix search index so [old versions of] tests pass after down-mi...
Tom Clegg
08:11 am Revision 938338a3 (arvados): 3410: Fix overly sensitive test.
Tom Clegg
03:20 am Task #5221 (In Progress): Review branch: 5186-collection-with-empty-properties
Brett Smith
02:47 am Bug #5217 (Closed): [API] Cannot rename a new collection in a project to a previous collection na...
Duplicate of #5197. Brett Smith

02/15/2015

09:03 pm Bug #5096 (In Progress): [Workbench] Avoid passing manifest_text around the network too much when...
Radhika Chippada
08:58 pm Bug #5186: [Workbench] Collection viewing broken for collections with empty (but non-nil) propert...
* This error is happening because the properties attribute is not serialized as hash on the API server.
* I update...
Radhika Chippada
08:53 pm Bug #5186 (In Progress): [Workbench] Collection viewing broken for collections with empty (but no...
Radhika Chippada
08:54 pm Task #5221 (Resolved): Review branch: 5186-collection-with-empty-properties
Radhika Chippada
08:48 pm Revision 7ef27804 (arvados): 5186: collection properties attribute is a hash
Radhika Chippada
06:25 pm Bug #5187 (Resolved): [Workbench] PNG is not available/is empty when it really isnt
Confirmed fixed, caused by the same issue as #5176. Ward Vandewege
04:12 pm Bug #5198: [Workbench] Middle clicking on Run this pipeline brings fiddlesticks
This is almost certainly the same basic problem as #4291. We really need to be using form buttons in any situation w... Brett Smith
04:08 pm Bug #5220: [Workbench] for collections shared anonymously, do not show the 'Sharing and Permissio...
For background, Workbench used to be quieter in this scenario. The message was added during review of #4291 as a deb... Brett Smith
02:27 am Bug #5220 (Resolved): [Workbench] for collections shared anonymously, do not show the 'Sharing an...

It just shows "Your API token is not authorized to manage collection sharing links.".
Quick fix: remove the box....
Ward Vandewege
04:57 am Story #3410: [API] Rename collection "desired replication" attributes, add model constraints
* I understand replication strategy better after your first response above. Also agree with your comments about "conf... Radhika Chippada
01:41 am Story #3410: [API] Rename collection "desired replication" attributes, add model constraints
Radhika Chippada wrote:
> * I am understanding this implementation as follows. For each collection, replication_desi...
Tom Clegg
01:20 am Revision 1f7a6b50 (arvados): 3410: Update comments.
Tom Clegg
12:56 am Revision 08c575dc (arvados): 3410: Rename maybe_clear_redundancy_confirmed to maybe_clear_replica...
Tom Clegg
12:35 am Feature #5011 (Resolved): [SDKs] arv-put accepts --replication argument (saved with collection re...
Tom Clegg
12:35 am Task #5206 (Resolved): Review 5011-thread-safe-test
Tom Clegg

02/14/2015

11:48 pm Task #5219 (Resolved): Review branch: 5096-wb-collection-name-or-desc-update
Radhika Chippada
11:47 pm Task #5218 (Resolved): [Workbench] Do not send manifest_text when only name or description is bei...
Radhika Chippada
10:29 pm Task #5218 (Resolved): [Workbench] Do not send manifest_text when only name or description is bei...
Radhika Chippada
11:46 pm Revision 23c1bc62 (arvados): 5096: if only collection name or description is being updated, do no...
Radhika Chippada
10:02 pm Revision 175c31a1 (arvados): Ensure result order is predictable, even if client-provided orders d...
Fixes intermittent test failures. Example (from
https://ci.curoverse.com/job/arvados-api-server/1305/console):
Group...
Tom Clegg
10:02 pm Revision e1999050 (arvados): Merge branch '5011-thread-safe-test' refs #5011
Tom Clegg
08:51 pm Task #5195 (Resolved): Review branch: 5185-collections-tab-zero-size-issue
Radhika Chippada
08:48 pm Story #3410: [API] Rename collection "desired replication" attributes, add model constraints
* I am understanding this implementation as follows. For each collection, replication_desired can be set (by admin); ... Radhika Chippada
08:46 pm Task #5165 (In Progress): Review 3410-replication-attrs
Radhika Chippada
07:21 pm Revision 02d27b88 (arvados-dev): When run-tests.sh is invoked to only run the api server tests, d...
spin up an api server for all the tests that will not be run.
No issue #
Ward Vandewege
07:21 pm Revision 02d27b88 (arvados): When run-tests.sh is invoked to only run the api server tests, do not
spin up an api server for all the tests that will not be run.
No issue #
Ward Vandewege
07:06 pm Revision be33b03f (arvados-dev): Make pip install quiet, no point in printing loads of useless wa...
(looking at you, PyYAML!).
No issue #
Ward Vandewege
07:06 pm Revision be33b03f (arvados): Make pip install quiet, no point in printing loads of useless warnings
(looking at you, PyYAML!).
No issue #
Ward Vandewege
01:40 pm Bug #5200 (Resolved): [Workbench] on public project, collection downloads require login
Applied in changeset arvados|commit:da298b0d96a1e49a1330a4486dcbe22d92d1d743. Ward Vandewege
01:37 pm Bug #5200: [Workbench] on public project, collection downloads require login
LGTM, going to merge it now because it's urgent. Ward Vandewege
01:39 pm Revision da298b0d (arvados): Merge branch '5200-anonymous-download'
Closes #5200 Ward Vandewege
01:39 pm Revision d27fd3e2 (arvados): Merge branch 'master' into 5200-anonymous-download
Ward Vandewege

02/13/2015

10:19 pm Revision 520008a5 (arvados): Minor fixes, see #5090
Nancy Ouyang
10:18 pm Feature #5090: [Documentation] Add some direct links on doc.arvados.org to the most useful redmin...
1. fixed "we are open source"
2. fixed link
3. see image -- on my screen, the right column is too short, that is wh...
Nancy Ouyang
07:36 pm Feature #5090: [Documentation] Add some direct links on doc.arvados.org to the most useful redmin...
* I think it would nice to say “We are open source” in “Want to contribute?” bullet point, even if it is already stat... Radhika Chippada
10:02 pm Revision 8a504ad5 (arvados): Merge branch 'master' into 3408-production-datamanager
Tom Clegg
09:25 pm Revision b7bd673a (arvados): Added different event types for started, partially complete and fina...
Misha Zatsman
09:25 pm Revision 43538243 (arvados): Moved some logging code from datamananager to loggerutil.
Misha Zatsman
09:25 pm Revision e88d1643 (arvados): Improved erorr message to make it clear what's a size and what's a t...
Misha Zatsman
09:25 pm Revision 3a1face2 (arvados): Updated logger to do all work in a dedicated goroutine, so we don't ...
Misha Zatsman
09:25 pm Revision 75f4b706 (arvados): Renamed timestamp fields to begin with "time_"
Misha Zatsman
09:25 pm Revision e5840cee (arvados): Now fetch Keep Server Status and record it to the log. Renamed some ...
Misha Zatsman
09:25 pm Revision 17800e7d (arvados): Added Logger.MutateLog() on Tom's suggestion. Tried it out in one in...
Misha Zatsman
09:25 pm Revision c2b8ab70 (arvados): Added comment, ran gofmt.
Misha Zatsman
09:25 pm Revision 4df1175e (arvados): A bunch of changes, most in response to Peter's review.
Logger:
Edit() and Record() have been replaced with the single Update() method which takes a function as input (sugge...
Misha Zatsman
09:25 pm Revision 6db8f01a (arvados): Renamed BlockDigest's ToString() to String() to implement fmt.String...
Misha Zatsman
09:25 pm Revision 2d2f3bed (arvados): gofmt'd all my source code. No other changes.
Misha Zatsman
09:25 pm Revision 7924fe7d (arvados): Finished adding logging to keep.GetServerContents but have not teste...
Misha Zatsman
09:25 pm Revision 144e2388 (arvados): Started logging in keep.go. More work to be done.
Misha Zatsman
09:25 pm Revision 4879e0e2 (arvados): Started reading collections and keep data in parallel. Moved some lo...
Misha Zatsman
09:25 pm Revision 2415e93f (arvados): Removed channel awareness from keep.GetServerContents().
Misha Zatsman
09:25 pm Revision 6221a500 (arvados): Broke keep.GetServerContents() into smaller functions.
Misha Zatsman
09:25 pm Revision 3f74a758 (arvados): ran gofmt
Misha Zatsman
09:25 pm Revision e0889a8f (arvados): Created loggerutil to hold common datamanager logger code. Moved Fat...
Misha Zatsman
09:25 pm Revision 2ee02486 (arvados): Moved some logic from datamanager.go to keep.go.
Misha Zatsman
09:25 pm Revision 5bcba288 (arvados): Merge branch 'master' of git.curoverse.com:arvados into 3408-product...
Conflicts resolved:
services/api/Gemfile
services/api/Gemfile.lock
Misha Zatsman
09:23 pm Revision 3d63bc27 (arvados): Switched batch size to 50. Added logging of batch size.
Misha Zatsman
09:23 pm Revision b14bc80d (arvados): Added ForceRecord() method to enable writing remaining log changes b...
Misha Zatsman
09:23 pm Revision 4851f29a (arvados): Switched Logger edit hooks to write hooks so they'll trigger less of...
Misha Zatsman
09:23 pm Revision 95cbdf59 (arvados): Added recording of fatal errors to logger.
Misha Zatsman
09:23 pm Revision 97009575 (arvados): Added memory alloc in use to stats exported to log. Also added EditH...
Misha Zatsman
09:23 pm Revision 1c87e0d7 (arvados): Added structure to data manager log entries, grouping similar fields.
Misha Zatsman
09:23 pm Revision e7ef642f (arvados): Added ability to turn off logging by passing an empty string as the ...
Misha Zatsman
09:23 pm Revision 08fbba82 (arvados): Started focusing on Keep Server responses again. Switched to using b...
Misha Zatsman
09:23 pm Revision 3594ad79 (arvados): Added logger to write log messages that grow over time. Not working ...
Misha Zatsman
09:23 pm Revision 1a68b00b (arvados): Added support for MinimumWriteInterval.
Misha Zatsman
09:23 pm Revision 0cf4805d (arvados): Fixed bugs in logger, changed interface some, added documentation.
Still need to add support for MinimunWriteInterval. Misha Zatsman
09:23 pm Revision 367a6fbc (arvados): Started using Logger in data manager and collections.
Misha Zatsman
09:23 pm Revision fbfd3b4c (arvados): Added string copying to try to reduce memory usage, didn't seem to w...
Misha Zatsman
09:23 pm Revision 9cf25951 (arvados): Fixed heap profile writing so that we overwrite previous heap profil...
Misha Zatsman
09:23 pm Revision d7f6013f (arvados): Switched from strings to BlockDigests to hold block digests more eff...
Runs to completion! Misha Zatsman
09:23 pm Revision 2ccc3eda (arvados): Started parsing modification date as a timestamp instead of leaving ...
Misha Zatsman
09:23 pm Revision 25d58aaf (arvados): Added blockdigest class to store digests more efficiently. This has ...
Misha Zatsman
09:23 pm Revision dab166a0 (arvados): Changes to manifest that I forgot to add to previous checking.
Misha Zatsman
09:23 pm Revision fb62ab31 (arvados): Long overdue checkin of data manager. Current code runs, but uses wa...
Misha Zatsman
09:23 pm Revision af550e54 (arvados): Added reporting of disk usage. This is the Collection Storage of eac...
But it does not include the size of projects owned by the user (projects and subprojects are each reported as their o... Misha Zatsman
09:23 pm Revision 9684e729 (arvados): Started reading index from keep servers.
Added lots of code to handle unexpected results from keep server. Misha Zatsman
09:23 pm Revision a224de26 (arvados): Started reading response from keep server.
Misha Zatsman
09:22 pm Revision 63cb5c23 (arvados): Merge branch 'master' of git.curoverse.com:arvados into 3408-product...
Tom Clegg
09:22 pm Revision 4106786a (arvados): 5095: Record mtime() from group#contents
Peter Amstutz
09:17 pm Bug #5217: [API] Cannot rename a new collection in a project to a previous collection name that w...
I worked around it by adding a space at the end of each collection name. Bryan Cosca
09:14 pm Bug #5217 (Closed): [API] Cannot rename a new collection in a project to a previous collection na...
!duplicateinproj.png!
I had a collection named 1KG chr1-22 VCF which I just removed from that project. I then copi...
Bryan Cosca
09:12 pm Revision cc569957 (arvados): 5095: Don't check update when getting mtime().
Peter Amstutz
09:10 pm Task #5216 (Resolved): Review 5095-fuse-ls-takes-forever
Peter Amstutz
08:50 pm Bug #5037 (Resolved): [SDKs] Improve Python SDK thread safety and document pitfalls
Applied in changeset arvados|commit:1128f6e0d62f71f4ee91ab609c918ae5bb291edd. Anonymous
08:30 pm Bug #5215: [Workbench] When a pipeline is run using "output_name = false," the job outputs links ...
... Tom Clegg
07:41 pm Bug #5215 (Resolved): [Workbench] When a pipeline is run using "output_name = false," the job out...
Pipeline instance: https://workbench.qr1hi.arvadosapi.com/pipeline_instances/qr1hi-d1hrv-1l0u0jhw34tmxu7
Job (in t...
Radhika Chippada
07:59 pm Bug #3855: [SDK] New keep mount is very slow on initial usage
As of commit:91abe26 it is still slow. This is a project with 885 collections: ... Ward Vandewege
07:24 pm Feature #5214 (New): [SDKs] Use sphinx to render for Python SDK docs
Peter Amstutz
07:03 pm Task #5203 (Resolved): Review 4839-worker-state
Tom Clegg
07:03 pm Revision 1128f6e0 (arvados): Merge branch '5037-nonocache' closes #5037
Tom Clegg
07:01 pm Task #5172 (Resolved): Review 5030-hide-graph-until-data
Tom Clegg
06:56 pm Task #5213 (Resolved): Review branch: 4759-timestamp-precision
Radhika Chippada
06:56 pm Bug #4759 (In Progress): [API] greater than filter is treated as greater than or equals for modif...
* Added a getter method for collection modified_at attribute with formatting to include milliseconds in api responses... Radhika Chippada
06:53 pm Feature #5011: [SDKs] arv-put accepts --replication argument (saved with collection record)
Tom Clegg wrote:
> Brett Smith wrote:
> > Instead of writing our own threadsafe_iter, would it be possible to just ...
Brett Smith
05:44 pm Feature #5011: [SDKs] arv-put accepts --replication argument (saved with collection record)
Brett Smith wrote:
> Reviewing 5011-thread-safe-test at commit:3068c62
>
> Instead of writing our own threadsafe_...
Tom Clegg
04:03 pm Feature #5011: [SDKs] arv-put accepts --replication argument (saved with collection record)
Reviewing 5011-thread-safe-test at commit:3068c62
Instead of writing our own threadsafe_iter, would it be possible...
Brett Smith
12:05 am Feature #5011 (In Progress): [SDKs] arv-put accepts --replication argument (saved with collection...
Tom Clegg
06:50 pm Bug #5030 (Resolved): [Workbench] Stats graph display for job without stats is confusing
Applied in changeset arvados|commit:1bcfe8651af341c6e7cd01a19443c7c288efa932. Anonymous
06:43 pm Revision 7eae56ff (arvados): 4759: add a getter method for collection.modified_at attribute with ...
Radhika Chippada
06:31 pm Support #5071 (In Progress): [Support] Fix bugs and write tests (second half)
Radhika Chippada
06:30 pm Bug #5211 (Resolved): [Documentation] Top Navbar of docs homepage not suitable for small window
Nancy Ouyang
06:17 pm Revision 1bcfe865 (arvados): Merge branch '5030-hide-graph-until-data' closes #5030
Tom Clegg
05:39 pm Revision 50df4956 (arvados): 5011: Use a threadsafe wrapper to feed side effects to mocks.
Tom Clegg
05:39 pm Revision d5809a1e (arvados): 5011: Fix unreliable test.
The collection writer was (sometimes) consuming the last 200 response
even though it could write 3 copies without it....
Tom Clegg
05:33 pm Task #5196: Review branch 5090-doc-to-homepage
Fixed branch name. Nancy Ouyang
05:11 pm Task #5178: Review sigint branch on arvados-dev
Well, it seems rvm does some additional magic to prevent ^C from working properly while any ruby program is running. ... Tom Clegg
03:24 pm Task #5178: Review sigint branch on arvados-dev
Nope, that's not what it does for me at all. Here's an example where I hit ctrl-c during a test:... Ward Vandewege
05:29 am Task #5178: Review sigint branch on arvados-dev
Ward Vandewege wrote:
> This doesn't quite seem to work for me. I see 'interrupted' when I interrupt for example the...
Tom Clegg
02:52 am Task #5178: Review sigint branch on arvados-dev
This doesn't quite seem to work for me. I see 'interrupted' when I interrupt for example the api server tests, but th... Ward Vandewege
04:33 pm Bug #5207 (Resolved): [API] Collection expires_at should be a full timestamp, not just a date.
Is there a reason why it is set as Date instead of timestamp? Radhika Chippada
04:01 pm Task #5206 (In Progress): Review 5011-thread-safe-test
Brett Smith
12:04 am Task #5206 (Resolved): Review 5011-thread-safe-test
Tom Clegg
12:05 am Task #5124 (Resolved): Use server-provided default replication level as default in arv-put and Co...
Tom Clegg
12:04 am Revision 3068c620 (arvados): 5011: Fix unreliable test.
The collection writer was (sometimes) consuming the last 200 response
even though it could write 3 copies without it....
Tom Clegg

02/12/2015

11:56 pm Revision aad2a353 (arvados): 5011: Use a threadsafe_iter wrapper to feed side effects to mocks.
Tom Clegg
11:23 pm Revision 60637551 (arvados): 5200: Fix overly sensitive fuse test. (Do not fail every time a fixt...
Tom Clegg
11:23 pm Task #5205 (Resolved): Review 5200-anonymous-download
Tom Clegg
10:42 pm Revision 398a5ef0 (arvados): 5200: Do not fail tests if application.yml is missing: defaults are ...
Tom Clegg
10:12 pm Revision f8f654db (arvados): 4823: Style cleanup on docstrings, renamed some single-letter variab...
more descriptive. Peter Amstutz
10:09 pm Revision 820ce7ad (arvados): 5200: Enable anonymous file view/download.
Tom Clegg
09:22 pm Bug #5204 (Closed): Collections in Pathomap exhibit 0 bytes. [blocker for public sharing]
Bryan Cosca
09:17 pm Bug #5204: Collections in Pathomap exhibit 0 bytes. [blocker for public sharing]
project: qr1hi-j7d0g-4857aevkuybaxm1 Bryan Cosca
09:16 pm Bug #5204 (Closed): Collections in Pathomap exhibit 0 bytes. [blocker for public sharing]
!0bytes-coll-data.png! Bryan Cosca
07:50 pm Bug #4839 (Resolved): [Node Manager] Should look at Arvados node's crunch_worker_state, not info[...
Applied in changeset arvados|commit:91abe2648d8ca1a3a5185e94beb505ad33db9e2c. Anonymous
07:23 pm Bug #4839: [Node Manager] Should look at Arvados node's crunch_worker_state, not info['slurm_state']
commit:61fd9276 is good to merge. Thanks. Brett Smith
07:24 pm Revision 91abe264 (arvados): Merge branch '4839-worker-state' closes #4839
Tom Clegg
07:23 pm Task #5203 (In Progress): Review 4839-worker-state
Brett Smith
06:34 pm Task #5203 (Resolved): Review 4839-worker-state
Tom Clegg
06:55 pm Story #4904 (Resolved): [SDKs] Use websockets to restart/reconfigure a web service running on a V...
Applied in changeset arvados|commit:a67bb34f6f19662f0a30e4aa670774c4595cb7a4. Peter Amstutz
06:46 pm Story #4904: [SDKs] Use websockets to restart/reconfigure a web service running on a VM whenever ...
Reviewing commit:5dbf5c8.
Peter Amstutz wrote:
> Brett Smith wrote:
> > * On my system, using our own Docker pac...
Brett Smith
06:53 pm Revision a67bb34f (arvados): Merge branch '4904-arv-web' closes #4904
Peter Amstutz
06:52 pm Revision 7a14311a (arvados): Merge branch 'master' into 4904-arv-web
Peter Amstutz
06:52 pm Revision 2917d8c1 (arvados): 4904: Remove extraneous ciddir and cidfilepath. Explicit non-zero e...
when an ArgumentError is caught. Peter Amstutz
06:51 pm Task #5018 (Resolved): Review 4904-arv-web
Peter Amstutz
06:41 pm Revision 8ae4b934 (arvados): 4823: Revert settings mistakenly added to application.yml.example
Peter Amstutz
06:35 pm Revision f6b88a9e (arvados): Merge branch 'master' into 4823-python-sdk-writable-collection-api
Conflicts:
sdk/python/arvados/collection.py
sdk/python/tests/test_keep_client.py
Peter Amstutz
06:35 pm Revision 61fd9276 (arvados): 4839: Use node[crunch_worker_state], not node[info][slurm_state], to...
Tom Clegg
06:34 pm Task #5169 (Resolved): Heed crunch_worker_state
Tom Clegg
03:58 pm Task #5169 (In Progress): Heed crunch_worker_state
Tom Clegg
06:33 pm Revision 03d58fa9 (arvados-dev): Clean up and exit on SIGINT.
Tom Clegg
06:33 pm Revision 03d58fa9 (arvados): Clean up and exit on SIGINT.
Tom Clegg
06:02 pm Feature #5202 (New): Hash individual files in collections.
It would be very helpful to have hashes for the individual files in a collection available by default. This supports... Peter Amstutz
06:00 pm Bug #4957: [SDKs] arv keep put blows up when trying to put a danging symlink
See also #3815 Peter Amstutz
05:53 pm Feature #5201 (New): [SDKs] arv-put --description X --properties P should set respective attrs on...
Tom Clegg
04:43 pm Revision 857d5a70 (arvados): Node Manager daemon tests avoid checking monitor.is_alive().
Checking is_alive() creates race conditions, because we might check
the actor's live state before it's had a chance t...
Brett Smith
04:22 pm Bug #5199: Searching does not work right when editing pipeline template
I confused ctrl+r and ctrl+w. Bryan Cosca
04:22 pm Bug #5199 (Closed): Searching does not work right when editing pipeline template
Bryan Cosca
03:38 pm Bug #5199 (Closed): Searching does not work right when editing pipeline template
!arv-editsearching.gif! Bryan Cosca
04:22 pm Revision 2d03ecf4 (arvados-dev): Make tmp/cache during workbench install. No issue #
Tom Clegg
04:22 pm Revision 2d03ecf4 (arvados): Make tmp/cache during workbench install. No issue #
Tom Clegg
04:22 pm Revision e8492641 (arvados): Default to TESTOPTS=-v for rake test.
(except workbench performance tests, because Minitest bug)
No issue #
Tom Clegg
04:22 pm Revision e8492641 (arvados-dev): Default to TESTOPTS=-v for rake test.
(except workbench performance tests, because Minitest bug)
No issue #
Tom Clegg
04:04 pm Bug #5200 (Resolved): [Workbench] on public project, collection downloads require login
Ward Vandewege
03:57 pm Revision d4b03f24 (arvados): Fix undependable test (incorrectly assumed a particular job would be...
Tom Clegg
03:34 pm Bug #5198 (Resolved): [Workbench] Middle clicking on Run this pipeline brings fiddlesticks
!middleclickrun.gif! Bryan Cosca
03:19 pm Revision ff3e4c60 (arvados): Merge branch '4951-request-vm-TC' refs #4951
Tom Clegg
03:17 pm Bug #4988 (Closed): [SDKs] Fix incompatibility between Python packages and newer virtualenv
Brett Smith
03:13 pm Revision fcfc0065 (arvados): 4951: Empty out ActionMailer::Base.deliveries so we can count delive...
Tom Clegg
03:05 pm Bug #5095: [FUSE] arv-mount takes up too much memory and occassionally crashes when listing large...
Related to #4464? Peter Amstutz
02:47 pm Revision d90460b1 (arvados): 4951: incorporate review feedback to move request_shell_access.js in...
Radhika Chippada
12:08 pm Feature #4951: [Workbench] When a user does not have access to a VM, provide a way to contact the...
* I incorrectly used button_to (which cannot be used to submit without form_to) for the request button. It unfortunat... Radhika Chippada
08:18 am Revision cde755bd (arvados): 4951: Rearrange js to make use of Rails built-ins. Add generic AJAX ...
Tom Clegg
08:06 am Revision 54819e39 (arvados): 4951: Add localStorage to browser dependency checks.
Tom Clegg
02:55 am Bug #4759: [API] greater than filter is treated as greater than or equals for modification time.
* We do have more precision in our tables than we are returning. Below is an example row from my db
whose modified_a...
Radhika Chippada
02:36 am Task #5196 (Resolved): Review branch 5090-doc-to-homepage
Changed navbars, homepage, to let /doc/index.html function as homepage. Specifically: homepage title is "Arvados", to... Nancy Ouyang
02:29 am Revision 17f61182 (arvados): Changed navbars, homepage, to let /doc/index.html function as homepage
Nancy Ouyang
01:58 am Revision 5b7ee6cb (arvados): 4951: fix comment in test
Radhika Chippada
12:45 am Bug #5185 (Resolved): [Workbench] Project lists all collections as zero size as of 6bf9ae1
Applied in changeset arvados|commit:5d3d32d5532d39f1ef85a9e01b9b70cd28cf3579. Radhika Chippada
12:32 am Revision 31f83b25 (arvados): 4951: update test to also verify that an email was sent when request...
Radhika Chippada
12:23 am Revision 02d728b8 (arvados): Merge branch 'master' into 4951-request-vm
Radhika Chippada
12:22 am Revision 5d3d32d5 (arvados): closes #5185
Merge branch '5185-collections-tab-zero-size-issue' Radhika Chippada

02/11/2015

11:47 pm Revision d302307a (arvados): 3410: Fix munge_manifest_locators!: don't skip locators that have no...
Also, fix portable_manifest_text: do not add a trailing + to a locator
that has no size hint.
Portable data hash of ...
Tom Clegg
11:47 pm Revision 966bd977 (arvados): 3410: Add replication attributes (and rules about updating them) to ...
Tom Clegg
11:47 pm Revision d62b7338 (arvados): 3410: Add tests for replication attributes.
Tom Clegg
11:47 pm Revision ec0c0f54 (arvados): 3410: Add default_collection_replication to config and discovery doc.
Tom Clegg
11:47 pm Revision 353a72e6 (arvados): 3410: Rename redundancy -> replication columns.
Tom Clegg
11:46 pm Revision b17ed3b4 (arvados): 5185: remove the unnecessary test because another test is covering t...
Radhika Chippada
11:44 pm Revision e759c71e (arvados): 5185: do not display description at all in Project -> Data collectio...
Radhika Chippada
11:40 pm Revision 498a97e6 (arvados): 4951: button_to cannot be used to submit; instead change to link_to
Radhika Chippada
10:53 pm Bug #5185: [Workbench] Project lists all collections as zero size as of 6bf9ae1
Implemented Step 1: if description is available, display it in the description column; otherwise display the modified... Radhika Chippada
08:20 pm Bug #5185 (In Progress): [Workbench] Project lists all collections as zero size as of 6bf9ae1
Radhika Chippada
08:19 pm Bug #5185: [Workbench] Project lists all collections as zero size as of 6bf9ae1
Tom said on IRC:
12:11 tomclegg: I'm inclined to say 5185 should be: step 1. Don't say "0 bytes" when we don't hav...
Radhika Chippada
01:44 pm Bug #5185: [Workbench] Project lists all collections as zero size as of 6bf9ae1
This may be due to the work from #4464 (where manifest text is omitted while loading projects -> Data collections tab... Radhika Chippada
01:00 am Bug #5185 (Resolved): [Workbench] Project lists all collections as zero size as of 6bf9ae1
In projects, all collections are listed as "0 bytes Collection". Visible on 4xphq and su92l, for example:
https:...
Ward Vandewege
10:52 pm Task #5195 (Resolved): Review branch: 5185-collections-tab-zero-size-issue
Radhika Chippada
10:32 pm Revision cd00c7d6 (arvados): 5185: in project data collections tab, show description when availab...
Radhika Chippada
10:16 pm Feature #4951: [Workbench] When a user does not have access to a VM, provide a way to contact the...
Looking at commit:1de8e55
* How/why does $.ajax('/') work? shouldn't that point to /users/request_shell_access?
*...
Tom Clegg
10:00 pm Feature #4951 (Resolved): [Workbench] When a user does not have access to a VM, provide a way to ...
Applied in changeset arvados|commit:26ac1b2f41916d1f4040073a15dfae5f1b294cb5. Radhika Chippada
09:50 pm Feature #4951: [Workbench] When a user does not have access to a VM, provide a way to contact the...
May be https://stackoverflow.com/questions/5985839/bug-with-firefox-disabled-attribute-of-input-not-resetting-when-re... Peter Amstutz
09:36 pm Feature #4951: [Workbench] When a user does not have access to a VM, provide a way to contact the...
Here's the HTML for the button. I suspect Firefox is interpreting @disabled=""@ as disabled.... Peter Amstutz
09:34 pm Feature #4951: [Workbench] When a user does not have access to a VM, provide a way to contact the...
I can't click on the button either. Peter Amstutz
09:22 pm Feature #4951: [Workbench] When a user does not have access to a VM, provide a way to contact the...
After I click "Send request for shell access" and then reload the page, the "Send request for shell access" button is... Peter Amstutz
04:01 pm Feature #4951: [Workbench] When a user does not have access to a VM, provide a way to contact the...
* What's the purpose of wrapping @localStorage.getItem(item)@ and @localStorage.removeItem(item)@ with @getLocalStora... Peter Amstutz
09:56 pm Bug #5194 (Resolved): [Documentation] User guide doesn't link to or acknowledge new "Getting Star...
The User Guide has its own section labled "Getting started" which is confusing with the new (much better) "Getting St... Peter Amstutz
09:55 pm Task #5144 (Resolved): Review branch: 4951-request-vm
Radhika Chippada
09:49 pm Story #3408: [Keep] Implement Production Data Manager
* The Arvados convention for timestamps is to end in "_at" so runInfo["started_at"] instead of runInfo["time_start"] ... Peter Amstutz
09:35 pm Revision 26ac1b2f (arvados): closes #4951
Merge branch '4951-request-vm' Radhika Chippada
09:01 pm Revision 5dbf5c8e (arvados): Merge branch 'master' into 4904-arv-web
Conflicts:
sdk/python/arvados/events.py
Peter Amstutz
08:48 pm Revision c9ff7436 (arvados): 4904: Detach from Docker container to get cid from stdout instead of...
with cid file. Poll "docker ps" to check if the container is still running. Fixed bugs.
Updated documentation.
Peter Amstutz
08:46 pm Story #4904: [SDKs] Use websockets to restart/reconfigure a web service running on a VM whenever ...
Brett Smith wrote:
> Reviewing commit:8233bab
>
> h2. Bugs
>
> * On my system, using our own Docker package, t...
Peter Amstutz
08:05 pm Revision 1de8e55b (arvados): Merge branch 'master' into 4951-request-vm
Radhika Chippada
08:05 pm Feature #5110 (Resolved): [Workbench] Use full text search instead of 'ilike' when searching with...
Applied in changeset arvados|commit:b80db28cdd536077e5effe6c08af079532c2059b. Radhika Chippada
06:17 pm Feature #5110: [Workbench] Use full text search instead of 'ilike' when searching with a user-ent...
Reviewing commit:31e1554. Just one small thing: a couple of pipeline instance integration tests switched from using ... Brett Smith
08:03 pm Task #5184 (Resolved): Review branch: 5110-workbench-full-text-search
Radhika Chippada
05:45 pm Task #5184 (In Progress): Review branch: 5110-workbench-full-text-search
Brett Smith
08:02 pm Revision b80db28c (arvados): closes #5110
Merge branch '5110-workbench-full-text-search' Radhika Chippada
08:01 pm Revision f16b7abe (arvados): 5110: update a comment in test; this comment was reflecting ui from ...
Radhika Chippada
07:58 pm Revision 148ff097 (arvados): 5110: update couple more tests to do a single visit to page than vis...
Radhika Chippada
07:49 pm Revision d3a9326a (arvados): Merge branch 'master' into 5110-workbench-full-text-search
Radhika Chippada
07:39 pm Feature #5193 (New): [Workbench] Public project page should encourage visitors to try using Arvad...
Tom Clegg
07:33 pm Revision da2492bf (arvados): 4904: Refactor arv-web main() into ArvWeb class. Add CollectionDire...
Peter Amstutz
07:07 pm Revision f5a30607 (arvados): 4951: Incorporate review feedback. Always show the request button, a...
Radhika Chippada
05:47 pm Bug #5192 (Resolved): [API] Disallow changing the name of a repository record (by non-admin users)
Currently, a regular user can rename a repository, but the new name will resolve to a new empty repository: the conte... Peter Amstutz
05:42 pm Bug #5037: [SDKs] Improve Python SDK thread safety and document pitfalls
5037-nonocache LGTM Peter Amstutz
05:41 pm Task #5170 (Resolved): Review 5037-nonocache
Peter Amstutz
05:05 pm Revision 4993b8b4 (arvados): Merge branch 'master' into 4951-request-vm
Radhika Chippada
04:39 pm Bug #5190 (Resolved): [Workbench] Tell admins not to put hyphens in repository names
Something removes dashes from repository names before creating the actual repository.
However, nobody told the API...
Peter Amstutz
04:19 pm Bug #5189 (Resolved): [Workbench] Manage account does not show repositories directly owned by user
The manage account page only shows repositories for which there are permission links. It should also show repositori... Peter Amstutz
03:40 pm Bug #5136: arv-run arv-keep command gives error while running
Hi Sabarish,
There was a problem with our Python packaging that was resulting in an outdated package being install...
Peter Amstutz
03:18 pm Bug #4988: [SDKs] Fix incompatibility between Python packages and newer virtualenv
I think the real bug here was #5175: we were generating version numbers that were not PEP 440-compliant, and would no... Brett Smith
12:26 pm Bug #5030: [Workbench] Stats graph display for job without stats is confusing
Review notes:
I focused on the "actual" changes (though the diff is 680 lines long due to moving js code into a ne...
Radhika Chippada
12:24 pm Task #5172 (In Progress): Review 5030-hide-graph-until-data
Radhika Chippada
07:44 am Task #5173 (Resolved): Review 4958-old-browser-alert
Tom Clegg
07:27 am Bug #5183 (Resolved): [Workbench] Job reuse modal test fails intermittently
Tom Clegg
03:37 am Bug #5187: [Workbench] PNG is not available/is empty when it really isnt
Oh, I think I misspoke. So I was able to view it because I ran it locally (not using arvados) and scp to my local lin... Bryan Cosca
03:24 am Bug #5187: [Workbench] PNG is not available/is empty when it really isnt
Hmm, on my Debian box I'm also seeing an empty file (download) and a broken inline image. The view icon leads to a br... Ward Vandewege
03:23 am Bug #5187: [Workbench] PNG is not available/is empty when it really isnt
created from qr1hi-8i9sb-59ma32lkl4f3a4j Bryan Cosca
03:03 am Bug #5187 (Resolved): [Workbench] PNG is not available/is empty when it really isnt
qr1hi-4zz18-wt6rncs9d6kpotq, the file Admixture\040PATHOMAP_P00553-833-SNPs.png is not viewable in the collection, al... Bryan Cosca
01:11 am Feature #4823: [SDKs] Good Collection API for Python SDK
Looking at commit:8128b45. The comments here are pretty high-level. I haven't even read many of the method implemen... Brett Smith
01:10 am Bug #5186 (Resolved): [Workbench] Collection viewing broken for collections with empty (but non-n...

I have a collection (su92l-4zz18-kf7cytopq8suzi0) with a properties attribute that has the value {}. I was able to ...
Ward Vandewege

02/10/2015

10:55 pm Bug #4958 (Resolved): [Workbench] Show an alert message below top nav when running in an unsuppor...
Applied in changeset arvados|commit:6bf9ae122958b25b4a22447f67fb11cf24765d97. Anonymous
10:40 pm Bug #4958: [Workbench] Show an alert message below top nav when running in an unsupported browser.
LGTM Radhika Chippada
10:30 pm Bug #4958: [Workbench] Show an alert message below top nav when running in an unsupported browser.
> * The “browser is missing” alert has right margin but no left margin. I think it does not look pretty due to this u... Tom Clegg
08:24 pm Bug #4958: [Workbench] Show an alert message below top nav when running in an unsupported browser.
Review comments:
* The “browser is missing” alert has right margin but no left margin. I think it does not look pr...
Radhika Chippada
10:50 pm Revision 6bf9ae12 (arvados): Merge branch '4958-old-browser-alert' closes #4958
Tom Clegg
10:12 pm Revision 5923d0fa (arvados): 4958: Merge branch 'master' into 4958-old-browser-alert
Tom Clegg
10:08 pm Revision 58bf2ad2 (arvados): 4958: Tweak wording. Fix margins.
Tom Clegg
10:02 pm Revision 8676d8d8 (arvados): 4958: Test WebSocket support.
Tom Clegg
10:02 pm Revision fb181d96 (arvados): 4958: Rename test file.
Tom Clegg
09:42 pm Revision b599ef92 (arvados): Fix javascript errors when closing modal. refs #5183
Tom Clegg
09:23 pm Revision 67a48253 (arvados): 5183: Disable animation on modal. (It seems to cause intermittent te...
Tom Clegg
09:04 pm Revision f31ff926 (arvados): 5183: retry if the radio button is not selected.
Radhika Chippada
08:51 pm Revision b8ca977e (arvados): Merge branch 'master' into 5183-fix-job-rerun-test
Radhika Chippada
08:28 pm Task #5173 (In Progress): Review 4958-old-browser-alert
Radhika Chippada
07:39 pm Revision f74b087c (arvados): 5183: revert back previous update and add an assertion to check if t...
Radhika Chippada
07:20 pm Task #5163 (Resolved): Review 5160-share-with-anonymous-group-wip
Applied in changeset arvados|commit:0215bf7b8c61d59462a476d850af999105856177. Brett Smith
03:46 am Task #5163 (In Progress): Review 5160-share-with-anonymous-group-wip
Radhika Chippada
07:20 pm Bug #5160 (Resolved): [API] Non-admin can't share a project publicly on qr1hi
Applied in changeset arvados|commit:0215bf7b8c61d59462a476d850af999105856177. Brett Smith
07:19 pm Bug #5160: [API] Non-admin can't share a project publicly on qr1hi
Radhika Chippada wrote:
> Do we also want remove the "anonymous user" from the "share with users" selection list? It...
Brett Smith
05:36 pm Bug #5160: [API] Non-admin can't share a project publicly on qr1hi
Brett, thanks for the update. Looks very good as far as sharing with groups is concerned.
Do we also want remove ...
Radhika Chippada
04:36 pm Bug #5160: [API] Non-admin can't share a project publicly on qr1hi
Radhika Chippada wrote:
> * I am quite concerned about the user experience. A user can share a project with anonymou...
Brett Smith
03:50 am Bug #5160: [API] Non-admin can't share a project publicly on qr1hi
Review comments:
* Everything looks good and worked as expected (except the below concern)
* I am quite concern...
Radhika Chippada
07:15 pm Revision 0215bf7b (arvados): Merge branch '5160-share-with-anonymous-group-wip'
Closes #5160, #5163. Brett Smith
07:11 pm Revision 045bce46 (arvados): 5160: Make anonymous group fixture match database seed.
Refer to /services/api/app/models/database_seeds.rb. Brett Smith
07:11 pm Revision 34d6dc1f (arvados): 5160: Workbench hides anonymous sharing when browsing disabled.
This commit updates Workbench to filter out the anonymous group from
the group sharing modal when anonymous browsing ...
Brett Smith
07:11 pm Revision d9e2de2e (arvados): 5160: Fix typo in Workbench default config comments.
Brett Smith
07:11 pm Revision 710b0356 (arvados): 5160: All users have API read permission to anonymous group.
Workbench makes public data available to everyone by including the
anonymous user API token as a reader token for eve...
Brett Smith
06:13 pm Bug #5183: [Workbench] Job reuse modal test fails intermittently
Above screenshots are with... Tom Clegg
06:07 pm Bug #5183: [Workbench] Job reuse modal test fails intermittently
I suspect the modal is still animating (moving down the page) when capybara chooses a coordinate to click and then cl... Tom Clegg
05:46 pm Bug #5183 (In Progress): [Workbench] Job reuse modal test fails intermittently
Radhika Chippada
05:49 pm Revision 545879af (arvados): 5183: test fails intermittently looking for the script version; henc...
Radhika Chippada
04:33 pm Revision f102390c (arvados): 5160: Workbench hides anonymous sharing when browsing disabled.
This commit updates Workbench to filter out the anonymous group from
the group sharing modal when anonymous browsing ...
Brett Smith
04:25 pm Revision 4e31431a (arvados): 5160: Make anonymous group fixture match database seed.
Refer to /services/api/app/models/database_seeds.rb. Brett Smith
04:06 pm Task #5184 (Resolved): Review branch: 5110-workbench-full-text-search
Radhika Chippada
04:05 pm Task #5161 (Resolved): Review branch: 4523-full-text-search
Radhika Chippada
04:01 pm Revision 31e1554c (arvados): Merge branch 'master' into 5110-workbench-full-text-search
Radhika Chippada
03:58 pm Revision 9b6b5f0b (arvados): refs #4523 : Add postgres full text search support
Merge branch '4523-full-text-search' Radhika Chippada
03:47 pm Revision 07f50aff (arvados): 5110: update comment
Radhika Chippada
03:46 pm Bug #4523: [Workbench] Search dialog giving error when searching in "All projects" in qr1hi
LGTM @ commit:330a46e Tom Clegg
03:42 pm Revision ae7e8221 (arvados): Merge branch '4523-full-text-search' into 5110-workbench-full-text-s...
Radhika Chippada
03:42 pm Revision f6089c82 (arvados): Merge branch 'master' into 5110-workbench-full-text-search
Radhika Chippada
03:41 pm Revision a934fcf8 (arvados): Merge branch 'master' into 4523-full-text-search
Radhika Chippada
03:37 pm Revision 9045c252 (arvados-dev): Merge branch 'master' into sigint
Tom Clegg
02:55 pm Revision 26d0d60c (arvados): 5037: Remove git tags from SDK version restrictions.
Tom Clegg
02:55 pm Revision 46efb1e7 (arvados): 5037: Merge branch 'master' into 5037-nonocache
Tom Clegg
02:53 pm Revision bf231ad8 (arvados): 5037: Remove git tags from SDK version restrictions.
Tom Clegg
02:51 pm Revision 672ecf75 (arvados): 5037: Merge branch 'master' into 5037-nonocache
Tom Clegg
02:00 pm Revision 6b0bd956 (arvados): 5160: Fix typo in Workbench default config comments.
Brett Smith
04:39 am Revision fc8e5729 (arvados): Fix typo.
refs #4754 Ward Vandewege
04:39 am Revision 6c63e6c0 (arvados): Make sure tmp/cache exists before we run our performance test suite.
refs #4754 Ward Vandewege
04:39 am Revision 6c63e6c0 (arvados-dev): Make sure tmp/cache exists before we run our performance test su...
refs #4754 Ward Vandewege
04:36 am Revision 41d0494a (arvados): Run the performance tests the documented way. This is possible after
commit d65b683af52e072b3d179b6f32edfbf37e108011 has been merged in the
arvados repository.
refs #4754
Ward Vandewege
04:36 am Revision 41d0494a (arvados-dev): Run the performance tests the documented way. This is possible a...
commit d65b683af52e072b3d179b6f32edfbf37e108011 has been merged in the
arvados repository.
refs #4754
Ward Vandewege
04:35 am Revision d65b683a (arvados): Also add minitest and friends to the performance group.
Refs #4754 Ward Vandewege
04:32 am Revision c9f5db97 (arvados): Revert "We need tmp/cache to exist before we can run performance tests"
refs #4754
This reverts commit c882575c856e01313cf2caf2e4ead1f27bfb33ae.
Ward Vandewege
04:03 am Revision f7ec673c (arvados): Merge branch '4523-full-text-search' into 5110-workbench-full-text-s...
Radhika Chippada
04:02 am Revision b8148b3b (arvados): Merge branch 'master' into 4523-full-text-search
Radhika Chippada
03:46 am Revision abcdf588 (arvados-dev): Add a script to run our performance tests.
refs #4754 Ward Vandewege
03:46 am Revision abcdf588 (arvados): Add a script to run our performance tests.
refs #4754 Ward Vandewege
03:45 am Revision c882575c (arvados): We need tmp/cache to exist before we can run performance tests
refs #4754 Ward Vandewege
03:25 am Revision 525d5d63 (arvados): Make sure the performance testing gems are available when workbench is
run in the performance rails environment.
refs #4754
Ward Vandewege
02:50 am Revision 538caa06 (arvados): 5110: full text search seems to treat '_' characters as spaces. Thus...
are also fetched since '1' is a common word and ignored. Hence, update the test to use more specific search filters. Radhika Chippada
02:39 am Revision 8d6532d6 (arvados): Added different event types for started, partially complete and fina...
Misha Zatsman
02:36 am Revision 9f1fafa8 (arvados): Merge branch '4523-full-text-search' into 5110-workbench-full-text-s...
Radhika Chippada
02:34 am Revision 330a46e9 (arvados): 4523: add search test looking for '_' which is ignored by full text ...
Radhika Chippada
02:27 am Revision fefce5e8 (arvados): Merge branch 'master' into 4523-full-text-search
Radhika Chippada
02:11 am Revision 40e42c38 (arvados): Moved some logging code from datamananager to loggerutil.
Misha Zatsman
01:55 am Revision bdf093d2 (arvados): Updated logger to do all work in a dedicated goroutine, so we don't ...
Misha Zatsman
01:15 am Revision 204f433a (arvados): 5176: Update Gemfiles with current arvados gem.
Refs #5176. Closes #5181. Brett Smith
01:12 am Revision 9b61792d (arvados): Merge branch '5176-escape-filenames'
Closes #5176, #5180. Brett Smith
01:12 am Revision 16b72095 (arvados): 5176: Update API Collections test to accommodate new fixtures.
Brett Smith

02/09/2015

11:33 pm Revision e73af668 (arvados): 5110: append :* to search filter to enable prefix matching; server n...
Radhika Chippada
11:06 pm Bug #5183 (Resolved): [Workbench] Job reuse modal test fails intermittently
This is the error when it happens:... Brett Smith
10:56 pm Revision b6a7a62f (arvados): 5176: Update Gemfile.lock.
Tom Clegg
10:48 pm Revision 0b102fac (arvados): Merge branch '4523-full-text-search' into 5110-workbench-full-text-s...
Radhika Chippada
10:47 pm Revision 79aca915 (arvados): Merge branch 'master' into 4523-full-text-search
Radhika Chippada
10:45 pm Revision b21b81e6 (arvados): 4523: update tests to include :* in the filters sent rather than exp...
Radhika Chippada
10:45 pm Revision aaffcb23 (arvados): 5176: Update bundles.
Tom Clegg
10:38 pm Revision f3e822f9 (arvados): Revert 11339c91. Don't use virtualenv to build packages.
fpm and virtualenv don't play nicely together. Under virtualenv, fpm
ends up building Python packages that include t...
Brett Smith
10:38 pm Revision f3e822f9 (arvados-dev): Revert 11339c91. Don't use virtualenv to build packages.
fpm and virtualenv don't play nicely together. Under virtualenv, fpm
ends up building Python packages that include t...
Brett Smith
10:37 pm Revision 20f5b178 (arvados): 5176: Fix broken fixtures, add tests.
Tom Clegg
10:31 pm Task #5164 (Closed): Review branch: 4926-fix-imagesizes
Nancy Ouyang
02:46 pm Task #5164 (In Progress): Review branch: 4926-fix-imagesizes
commit:348801d is good to merge. Thanks! Brett Smith
10:29 pm Revision fb4921f5 (arvados): refs #4926 #5072 Merge branch '4926-fix-imagesizes'
Nancy Ouyang
10:15 pm Task #5140 (Resolved): Review 4464-api-project-contents-wip
Applied in changeset arvados|commit:1d4a39ab3e97c031683ada9f6c98e4c7365fa414. Brett Smith
10:10 pm Revision 1d4a39ab (arvados): Merge branch '4464-api-project-contents-wip'
Refs #4464. Closes #5140. Brett Smith
10:09 pm Revision f6ab9be0 (arvados): 4464: Simplify API collection list method docs.
Brett Smith
10:09 pm Revision b59b310e (arvados): 4464: Remove API group contents include_linked parameter.
With Tom's permission. Brett Smith
10:09 pm Revision 1963df31 (arvados): 4464: Document API group contents parameters.
Brett Smith
10:09 pm Revision 231242b6 (arvados): 4464: API group contents no longer include manifests.
This change achieves symmetry with the collections list method, which
doesn't return manifests unless you expressly r...
Brett Smith
10:02 pm Revision e2da84c1 (arvados): 5176: Add more Ruby SDK tests for empty manifests.
I wrote these while trying to diagnose other issues in the branch.
They didn't reveal anything directly, but it seems...
Brett Smith
10:00 pm Bug #4464: [Workbench] Collections tab loads forever on a specific project
Radhika Chippada wrote:
> Documentation updates
>
> * "Retrieve a list of items which are associated with the giv...
Brett Smith
04:54 pm Bug #4464: [Workbench] Collections tab loads forever on a specific project
Review feedback:
Documentation updates
* "Retrieve a list of items which are associated with the given group ...
Radhika Chippada
09:40 pm Revision 7c5a88da (arvados): 4464: Simplify API collection list method docs.
Brett Smith
09:01 pm Revision d6ec5672 (arvados): 5175: Avoid egg_info name conflicts with pip.
pip does its own subclassing of egg_info. Installing with pip fails
if setup.py includes an egg_info class that is p...
Brett Smith
08:23 pm Revision 75721248 (arvados): 4523: update full text search record_filter to not append :* for pre...
Radhika Chippada
07:49 pm Bug #5182: [Workbench] CORS error uploading via browser - better JS error handling needed
We're hitting the keepproxy connection limit. We need better error reporting. Ward Vandewege
06:09 pm Bug #5182: [Workbench] CORS error uploading via browser - better JS error handling needed
Using arvados-python-client-0.1.20141016164709.8297039 ("latest" via pip at this time)
Possibly related?...
Peter Amstutz
06:05 pm Bug #5182 (Resolved): [Workbench] CORS error uploading via browser - better JS error handling needed
Firefox 35.0.1 on OS X 10.6.8
Trying to upload via browser
Javascript console:
The connection to wss://ws.qr...
Peter Amstutz
07:09 pm Bug #5175 (Resolved): [SDKs] Fix Python package versions so they can be uploaded to pypi
Tom Clegg
05:32 pm Bug #5175: [SDKs] Fix Python package versions so they can be uploaded to pypi
(12:14:23 PM) Me: tomclegg: As far as I can see, we should give up completely on ever trying to include the git commi... Brett Smith
07:09 pm Task #5177 (Resolved): Review 5175-pep-440 (arvados + arvados-dev)
Tom Clegg
04:38 pm Task #5177 (In Progress): Review 5175-pep-440 (arvados + arvados-dev)
Brett Smith
03:26 am Task #5177 (Resolved): Review 5175-pep-440 (arvados + arvados-dev)
commit:f8067dd Tom Clegg
06:28 pm Revision f85132f1 (arvados): Merge branch '5175-pep-440' refs #5175
Tom Clegg
06:28 pm Revision 2e9f5f1a (arvados): 5715: Sort imports.
Tom Clegg
06:28 pm Revision 71c05eec (arvados): 5175: Revert change to find_packages(), it gets confused by run_test...
Tom Clegg
05:31 pm Revision f32690a4 (arvados): 5175: Include README for Node Manager packages.
Brett Smith
05:31 pm Revision df507d6c (arvados): 5175: Do not add +sha1 tag to Python packages ever.
PEP 440 is clear that the local version tag is for distributors who
are patching an upstream release. That's not us;...
Brett Smith
05:13 pm Revision 4982008e (arvados): 4523: Add tests for some edge cases.
Tom Clegg
05:13 pm Revision 77daa609 (arvados): 4523: Fix up whitespace.
Tom Clegg
05:12 pm Revision bd720586 (arvados): 4523: Remove unneeded else.
Tom Clegg
04:20 pm Revision 2527b9cd (arvados): 5176: Add spaces-in-filenames tests.
Tom Clegg
03:49 pm Revision dd645c9e (arvados): 5176: Fix handling of escape sequences in manifest filenames.
Tom Clegg
02:25 pm Support #5070 (Resolved): [Support] Fix bugs and write tests (first half)
Brett Smith
06:26 am Bug #5179 (Resolved): [Workbench] [SDKs] Incorrect collection display when stream has entries wit...
!directorystructuredoesnthold.png!
Here, temp_admix_files-PATHOMAP_P00553_1k should be a directory with those file...
Bryan Cosca
03:31 am Bug #5030 (In Progress): [Workbench] Stats graph display for job without stats is confusing
Tom Clegg
03:31 am Bug #4958 (In Progress): [Workbench] Show an alert message below top nav when running in an unsup...
Tom Clegg
03:28 am Task #5178 (Resolved): Review sigint branch on arvados-dev
Tom Clegg
02:28 am Revision c9e19eb6 (arvados): 5110: clean up pipeline instances integration tests a bit. and remov...
"scroll pipeline instances page for with search filter" that are neither searching nor scrolling. Radhika Chippada

02/08/2015

11:59 pm Revision 3385feb3 (arvados-dev): Clean up and exit on SIGINT.
Tom Clegg
11:57 pm Revision 4bac34e0 (arvados-dev): 5175: Build test packages with --sha1-tag.
Tom Clegg
11:53 pm Revision f8067dd1 (arvados): 5175: Do not add +sha1 tag unless --sha1-tag flag given.
Tom Clegg
11:51 pm Bug #5175 (Resolved): [SDKs] Fix Python package versions so they can be uploaded to pypi
Tom Clegg
09:56 pm Revision cb793583 (arvados): Merge branch '4523-full-text-search' into 5110-workbench-full-text-s...
Radhika Chippada
09:22 pm Revision cda964ac (arvados): 4523: update full text search to append ':*' for each word to suppor...
Radhika Chippada
08:54 pm Revision 2e5ac62b (arvados): Merge branch 'master' into 4523-full-text-search
Conflicts:
services/api/test/unit/collection_test.rb
Radhika Chippada
08:46 am Revision b48e7f0c (arvados): 4958: Add tests.
Tom Clegg
05:30 am Revision 145f9bbd (arvados): 4958: Add tests.
Tom Clegg
05:30 am Task #5174 (Resolved): Add test case
Tom Clegg
02:52 am Task #5174 (Resolved): Add test case
Tom Clegg
02:52 am Task #5173 (Resolved): Review 4958-old-browser-alert
commit:b48e7f0 Tom Clegg
02:52 am Task #5171 (Resolved): Check UA string and JS features, throw alert if missing.
Tom Clegg
02:26 am Revision 7a71d74c (arvados): 4958: Avoid squishing dax's aspect ratio when window is narrow.
Tom Clegg
02:25 am Revision ff49b114 (arvados): 4958: Detect old browsers and recommend upgrading.
We use a plain .js file in /public instead of the asset pipeline, and
don't rely on any JS libraries. This gives the ...
Tom Clegg
12:47 am Revision b6050a81 (arvados-dev): test suite: write user.* settings to ~/.gitconfig.local...
...instead of ~/.gitconfig, and add an include.path in it Sitaram Chamarty

02/07/2015

10:37 am Task #5171 (In Progress): Check UA string and JS features, throw alert if missing.
Tom Clegg
09:30 am Task #5171 (Resolved): Check UA string and JS features, throw alert if missing.
Tom Clegg
10:36 am Revision f5a0a633 (arvados): 5030: Hide cpu/mem/io graph until data points arrive.
Tom Clegg
10:36 am Task #5172 (Resolved): Review 5030-hide-graph-until-data
Tom Clegg
10:36 am Task #5168 (Resolved): Hide graph div until data points arrive
Tom Clegg
10:03 am Task #5168 (In Progress): Hide graph div until data points arrive
Tom Clegg
07:27 am Task #5168 (Resolved): Hide graph div until data points arrive
Tom Clegg
10:15 am Revision 78596140 (arvados): 5030: Move log graph javascript into its own file.
Tom Clegg
10:11 am Revision d500cb7d (arvados-dev): sshkeys-lint: refactor keytype and accept ed25519
sshkeys-lint was rejecting Ed25519 type keys, and also not detecting
ecdsa keys for shell users; refactor the key typ...
Robin H. Johnson
09:56 am Revision 11339c91 (arvados-dev): Use virtualenv to get a newer setuptools that doesn't munge Pyth...
Tom Clegg
09:56 am Revision 11339c91 (arvados): Use virtualenv to get a newer setuptools that doesn't munge Python v...
Tom Clegg
09:29 am Task #5170 (Resolved): Review 5037-nonocache
Tom Clegg
09:29 am Task #5166 (Resolved): Remove cache=False from Python SDK clients (bump version requirements inst...
Tom Clegg
09:24 am Task #5166 (In Progress): Remove cache=False from Python SDK clients (bump version requirements i...
Tom Clegg
03:51 am Task #5166 (Resolved): Remove cache=False from Python SDK clients (bump version requirements inst...
Tom Clegg
08:59 am Revision 2d788382 (arvados): 5037: Use a newer Python SDK (with no connection cache) instead of c...
Tom Clegg
07:28 am Task #5123 (Resolved): Review 5011-arv-put-replication
Tom Clegg
07:28 am Task #5169 (Resolved): Heed crunch_worker_state
Tom Clegg
07:26 am Task #5167 (Resolved): Figure out appropriate scope for first implementation
Tom Clegg
07:25 am Task #5161 (In Progress): Review branch: 4523-full-text-search
Tom Clegg
07:24 am Story #3021 (Resolved): [Tests] Make jenkins tests run faster.
Tom Clegg
07:23 am Task #5129 (Resolved): Review 3021-leave-api-running (arvados)
Tom Clegg
07:22 am Task #5130 (Resolved): Review 3021-leave-api-running (arvados-dev)
Tom Clegg
07:22 am Task #5125 (Resolved): Review branch: 2659-anonymous-share-projects
Tom Clegg
06:44 am Revision 346b1324 (arvados-dev): fix ugliness in http output when only base URL is given
Sitaram Chamarty
03:45 am Task #5165 (Resolved): Review 3410-replication-attrs
commit:d302307 Tom Clegg
03:45 am Task #5101 (Resolved): Write tests
Tom Clegg
03:45 am Task #5100 (Resolved): Write migration
Tom Clegg
02:36 am Revision 755faba1 (arvados): 3410: Fix munge_manifest_locators!: don't skip locators that have no...
Also, fix portable_manifest_text: do not add a trailing + to a locator
that has no size hint.
Portable data hash of ...
Tom Clegg
02:34 am Revision 3de9172e (arvados): 3410: Add tests for replication attributes.
Tom Clegg
02:34 am Revision 1361ff30 (arvados): 3410: Add replication attributes (and rules about updating them) to ...
Tom Clegg
02:34 am Revision fc0bdda6 (arvados): 3410: Add default_collection_replication to config and discovery doc.
Tom Clegg
02:34 am Revision 6f7820b3 (arvados): 3410: Rename redundancy -> replication columns.
Tom Clegg

02/06/2015

11:50 pm Feature #5011 (Resolved): [SDKs] arv-put accepts --replication argument (saved with collection re...
Applied in changeset arvados|commit:64c70939c414881de61ac65512701d0ba4068786. Anonymous
10:32 pm Feature #5011: [SDKs] arv-put accepts --replication argument (saved with collection record)
Tom Clegg wrote:
> > * Please add @replication_desired@ to the API schema documentation. It would be ideal to add a...
Brett Smith
06:46 pm Feature #5011: [SDKs] arv-put accepts --replication argument (saved with collection record)
Brett Smith wrote:
> * Please add unit tests for @replication_desired@. At least one for case where redundancy is d...
Tom Clegg
10:58 pm Revision d7f1a63c (arvados): Merge branch '3021-leave-api-running' refs #3021
Tom Clegg
10:58 pm Revision d7f1a63c (arvados-dev): Merge branch '3021-leave-api-running' refs #3021
Tom Clegg
10:53 pm Revision 64c70939 (arvados): Merge branch '5011-arv-put-replication' closes #5011
Tom Clegg
10:53 pm Revision d1338635 (arvados): 5011: Fix comment about when local_store_* methods get used.
Tom Clegg
10:47 pm Task #5164 (Closed): Review branch: 4926-fix-imagesizes
The varying image sizes were causing the image carousel to bounce around in size. I re-cropped all the images to a co... Nancy Ouyang
10:43 pm Revision 348801d4 (arvados): 4926: Fixed images to be consistently 900x500
Nancy Ouyang
10:30 pm Revision afef0760 (arvados): Merge branch '3021-leave-api-running' refs #3021
Tom Clegg
10:11 pm Story #3021: [Tests] Make jenkins tests run faster.
3021-leave-api-running LGTM Peter Amstutz
06:07 pm Story #3021: [Tests] Make jenkins tests run faster.
Turns out keepproxy and passenger seem to work fine with a recently-used port, so I changed find_available_port to "b... Tom Clegg
05:34 pm Story #3021: [Tests] Make jenkins tests run faster.
This looks unusual. Could this be a clue about the undependable FuseTagsUpdateTest failure?... Tom Clegg
01:45 am Story #3021: [Tests] Make jenkins tests run faster.
Peter Amstutz wrote:
> Still getting the foo_tag failure. This is running the whole test suite. With @--only servi...
Tom Clegg
10:00 pm Bug #5105: [Workbench] AJAX content loaders should not follow a redirect to the welcome page and ...
Such overlay.
I am pretty 80% sure this means an auto-refresh AJAX request received [a redirect, which yielded] a ...
Tom Clegg
09:53 pm Task #5163 (Resolved): Review 5160-share-with-anonymous-group-wip
Brett Smith
09:52 pm Revision 48884625 (arvados): 5160: All users have API read permission to anonymous group.
Workbench makes public data available to everyone by including the
anonymous user API token as a reader token for eve...
Brett Smith
09:26 pm Task #5140 (In Progress): Review 4464-api-project-contents-wip
Radhika Chippada
09:22 pm Revision eab43fcf (arvados): 5110: use full text search operator '@@' instead of 'ilike'
Radhika Chippada
09:15 pm Revision 9b59cd2f (arvados): 4523: slightly modified full text search condition.
Radhika Chippada
07:58 pm Bug #4957: [SDKs] arv keep put blows up when trying to put a danging symlink
Ward Vandewege wrote:
> Yeah, I think the desired behavior would be that arv keep put skips any files it can not upl...
Brett Smith
07:54 pm Bug #3500 (Resolved): docker --rm not always cleaning up containers correctly.
Believed to be fixed in recent versions of Docker. Peter Amstutz
07:43 pm Story #3651 (Resolved): Running programs from Keep
Fixed in #4838 Peter Amstutz
07:42 pm Story #3937 (Closed): [Workbench] Design collection trash behavior
Tom Clegg
07:31 pm Bug #5162 (New): [Crunch] crunch-dispatch should use the API instead of running in the API server...
Included:
* Move crunch-dispatch into services/crunch-dispatch
* A test case that relies on the real API (provided ...
Tom Clegg
07:23 pm Task #5161 (Resolved): Review branch: 4523-full-text-search
This has the server-side full text search implementation. Once this branch is merged into master, the workbench can b... Radhika Chippada
06:53 pm Bug #5160 (Resolved): [API] Non-admin can't share a project publicly on qr1hi
When you try, the modal reports an error that the tail UUID …-anonymouspublic could not be found.
At first glance,...
Brett Smith
06:47 pm Revision 1eda4774 (arvados): Merge branch 'master' into 4523-full-text-search
Radhika Chippada
06:47 pm Revision 71a556d7 (arvados): 5011: Merge branch 'master' into 5011-arv-put-replication
Tom Clegg
06:46 pm Feature #4951: [Workbench] When a user does not have access to a VM, provide a way to contact the...
Peter, thanks for your suggestion. I now moved the logic to show / hide the request access button using jQuery ready ... Radhika Chippada
03:03 pm Feature #4951: [Workbench] When a user does not have access to a VM, provide a way to contact the...
In workbench routes.rb:... Peter Amstutz
06:43 pm Revision f2e686e1 (arvados): 4951: remove unused id from link
Radhika Chippada
06:42 pm Revision 9f0f926a (arvados): 5011: Make docstring less scary.
Tom Clegg
06:39 pm Revision f414dc4c (arvados): Merge branch 'master' into 4951-request-vm
Radhika Chippada
06:38 pm Revision 180498df (arvados): 4951: localStorage lookup much simplified and handled during page lo...
Radhika Chippada
06:36 pm Bug #5136: arv-run arv-keep command gives error while running
Hi Peter,
Finally found out the problem.Pip was from python 2.6.I changed it to python 2.7.Now after this ,if I inst...
Sabarish Subramanian
06:34 pm Revision 8a8450dc (arvados): 3021: Bugfix for arvados_fuse.TagsDirectory to correctly merge tag l...
with existing TagsDirectory entries. Peter Amstutz
05:46 pm Revision 7939a927 (arvados): 3021: Use bind(0.0.0.0, 0) instead of grep /proc/net/tcp to find a p...
Tom Clegg
05:01 pm Revision 54873fcd (arvados): Relax version limit of python-daemon dependencies.
We imposed this limit in 9c2e673ba96ba5d11e56a4aba67157e64dfe01e2.
The issues seem to be ironed out as of version 2.0...
Brett Smith
04:55 pm Revision 6772d21b (arvados-dev): 3021: Remove obsolete accommodation for buggy python-daemon.
This bug has been fixed in newer versions. Refs #3021. Brett Smith
04:55 pm Revision 6772d21b (arvados): 3021: Remove obsolete accommodation for buggy python-daemon.
This bug has been fixed in newer versions. Refs #3021. Brett Smith
03:53 pm Bug #5145: [Workbench] Combining collections should separate files with identical names, not conc...
Bryan,
Can you please explain the original bug/failure in more detail? Specifically, I'd like to know what tool y...
Brett Smith
03:34 pm Bug #5025: [Docker] Make it easy to add data from the host system to containers
(10:29:26 AM) <tetron> https://stackoverflow.com/questions/7934027/process-local-override-of-name-resolution
(10:30:...
Brett Smith
03:13 pm Bug #5147 (New): [Docker] Make API server root URL in discovery document easier to resolve
If you start the Arvados docker containers in the normal way, the API server's discovery document says @"baseUrl":"ht... Brett Smith
01:56 pm Revision 8cd7249b (arvados): Merge branch 'master' into 4523-full-text-search
Radhika Chippada
01:02 pm Revision c6566ea3 (arvados): 4951: actually add test assertion to verify that request access butt...
Radhika Chippada
12:49 pm Revision f7cc825b (arvados): 4951: add test assertion to verify that request access button was no...
Radhika Chippada
12:36 pm Revision a41baffe (arvados): Merge branch 'master' into 4951-request-vm
Radhika Chippada
05:04 am Revision a94e15ca (arvados): 3021: Merge branch 'master' into 3021-leave-api-running
Conflicts:
sdk/python/tests/test_websockets.py
Tom Clegg
04:59 am Revision aa613a59 (arvados): 3021: We use passenger in dev and test environments, too.
Tom Clegg
01:37 am Revision dd72a4de (arvados): 3021: Make sure any unexpected openssl output ends up on stderr.
Tom Clegg

02/05/2015

11:31 pm Revision 0ea383a2 (arvados): 3021: Reduce race potential by resetting database after fuse unmounts.
Tom Clegg
11:12 pm Revision 21a824c1 (arvados): 3021: Remove unused variable.
Tom Clegg
11:00 pm Bug #5137: [SDKs] Add Python version test 2.7 <= sys.version_info < 3
In order for the proposal to work, the old version of Python has to be able to compile and run @arvados/__init__.py@ ... Brett Smith
02:44 pm Bug #5137 (New): [SDKs] Add Python version test 2.7 <= sys.version_info < 3
<tetron> brett: regarding #5136 any thoughts on how to warn the user if they are using Python < 2.7 ?
<brett> tetron...
Peter Amstutz
10:37 pm Revision c722a8bb (arvados): 3021: Use kwargs to pass options through make_mount(). Dry up FuseTa...
Tom Clegg
10:20 pm Task #5143 (Resolved): Review 5141-workbench-numeric-inputs-wip
Applied in changeset arvados|commit:e5b8f6826a2034c0c7d7142cff3fb02f64fb8831. Brett Smith
09:19 pm Task #5143 (In Progress): Review 5141-workbench-numeric-inputs-wip
Peter Amstutz
09:18 pm Task #5143 (Resolved): Review 5141-workbench-numeric-inputs-wip
Brett Smith
10:20 pm Bug #5141 (Resolved): [Workbench] Should permit all numeric values for numeric pipeline inputs, n...
Applied in changeset arvados|commit:e5b8f6826a2034c0c7d7142cff3fb02f64fb8831. Brett Smith
10:08 pm Bug #5141: [Workbench] Should permit all numeric values for numeric pipeline inputs, not just int...
Brett Smith wrote:
> Peter Amstutz wrote:
> > However, (correct me if I'm wrong), I believe the "number" type did e...
Peter Amstutz
09:51 pm Bug #5141: [Workbench] Should permit all numeric values for numeric pipeline inputs, not just int...
Peter Amstutz wrote:
> However, (correct me if I'm wrong), I believe the "number" type did ensure that the "value" f...
Brett Smith
09:40 pm Bug #5141: [Workbench] Should permit all numeric values for numeric pipeline inputs, not just int...
I don't have a problem with treating it like a string on the browser side if the editing form is being obnoxious.
...
Peter Amstutz
09:26 pm Bug #5141 (In Progress): [Workbench] Should permit all numeric values for numeric pipeline inputs...
Brett Smith
07:20 pm Bug #5141 (Resolved): [Workbench] Should permit all numeric values for numeric pipeline inputs, n...
Currently, when a pipeline input has dataclass: numeric, Workbench lets users specify that with an numeric X-Editable... Brett Smith
10:14 pm Revision e5b8f682 (arvados): Merge branch '5141-workbench-numeric-inputs-wip'
Closes #5141, #5143. Brett Smith
10:13 pm Revision 12dee1eb (arvados): 5141: Workbench permits float values for number pipeline inputs.
Previously, when a pipeline input had the number dataclass, we
rendered the input form with type=number. However, th...
Brett Smith
10:02 pm Revision 7b9ca2a2 (arvados): 3021: Give up earlier if ARVADOS_TEST_API_HOST is set but reset() fa...
Tom Clegg
10:02 pm Revision 7acac83d (arvados): 3021: Reset env vars in any reset(), not just in start().
Tom Clegg
09:58 pm Revision f6c53e0e (arvados-dev): 3021: Print reassuring messages about expected warning messages ...
Tom Clegg
09:58 pm Revision f6c53e0e (arvados): 3021: Print reassuring messages about expected warning messages duri...
Tom Clegg
09:57 pm Revision 36d6d160 (arvados): Avoid optional disk cache usage if it is owned by a different user. ...
Tom Clegg
09:45 pm Task #5144 (In Progress): Review branch: 4951-request-vm
Peter Amstutz
09:24 pm Task #5144 (Resolved): Review branch: 4951-request-vm
Radhika Chippada
09:45 pm Bug #5135 (Resolved): [Workbench] Ensure modal button order is consistent
Applied in changeset arvados|commit:e20040092b47f79365637dd8e26156d95ab5c6ee. Brett Smith
09:27 pm Bug #5135 (In Progress): [Workbench] Ensure modal button order is consistent
Brett Smith
09:43 pm Revision e2004009 (arvados): 5135: Workbench consistently orders modal buttons.
Primary buttons should be first from the right, following Bootstrap
conventions and Tom's edict. Closes #5135.
Brett Smith
09:38 pm Bug #5145 (Resolved): [Workbench] Combining collections should separate files with identical name...
collection uuid
foo.txt hash 123
add foo.txt hash 234 to collection uuid
Currently this fails, is there a way ...
Bryan Cosca
09:33 pm Revision a11c56ef (arvados): Merge branch 'master' into 4523-full-text-search
Conflicts:
services/api/db/structure.sql
Radhika Chippada
09:29 pm Revision 5b70a11a (arvados): 4523: preparing to merge master
Radhika Chippada
09:29 pm Revision dac304f9 (arvados): 3021: Set env var to empty string instead of removing it. Unsetenv i...
Tom Clegg
09:22 pm Revision c5fa3f7b (arvados): Merge branch 'master' into 4951-request-vm
Radhika Chippada
09:22 pm Revision 1a78ca15 (arvados): 5011: Add forward compatibility, so we don't need backward compatibi...
Tom Clegg
09:20 pm Revision 826cb14a (arvados): 4951: when a request for shell access is made, remember this in html...
Radhika Chippada
09:20 pm Revision 8128b451 (arvados): 4823: Remove commented out StreamWriter code from much earlier versi...
Peter Amstutz
09:18 pm Revision dba51ea8 (arvados): 5141: Workbench permits float values for number pipeline inputs.
Previously, when a pipeline input had the number dataclass, we
rendered the input form with type=number. However, th...
Brett Smith
09:17 pm Revision cef69b16 (arvados): Merge branch 'master' into 4823-python-sdk-writable-collection-api
Peter Amstutz
09:14 pm Revision 08c3828a (arvados): 4823: Fix instance of Collection -> CollectionRoot. Tweaked a coupl...
Peter Amstutz
09:01 pm Story #3021: [Tests] Make jenkins tests run faster.
Still getting the foo_tag failure. This is running the whole test suite. With @--only services/fuse@ it passes.
...
Peter Amstutz
09:03 am Story #3021: [Tests] Make jenkins tests run faster.
Peter Amstutz wrote:
> A couple of gem install warnings (non fatal?)
To minimize downloading the internet, I put ...
Tom Clegg
08:15 pm Revision 4204a3c2 (arvados): 5011: Add tests and comments for redundancy vs. replication_desired ...
Tom Clegg
08:14 pm Revision 1147248a (arvados): 5011: Fix up docstring.
Tom Clegg
08:06 pm Task #5103 (Resolved): Implement live sync, merge
Peter Amstutz
08:04 pm Revision 19f7fd5e (arvados): 4823: Added apiconfig option to arvados.api() to accept a dict with
ARVADOS_API_HOST and ARVADOS_API_TOKEN keys. Expanded comments on Collections
object. Added convenience wrappers fo...
Peter Amstutz
07:23 pm Story #5142 (New): [DRAFT] [API] Enrich supported dataclass values for pipeline templates
<tomclegg> tetron: is this an opportunity to "do whatever cwl does"?
<tetron> unfortunately I don't have a good answ...
Brett Smith
07:03 pm Feature #5011: [SDKs] arv-put accepts --replication argument (saved with collection record)
Reviewing commit:cbf80c0. Thank you very much for DRYing up the test infrastructure. This is much nicer.
* Pleas...
Brett Smith
05:17 pm Feature #5011: [SDKs] arv-put accepts --replication argument (saved with collection record)
Brett Smith wrote:
> Reviewing commit:655b69e. Unfortunately, I got these test failures:
>
> [...]
>
> This s...
Tom Clegg
06:46 pm Revision da63a23e (arvados): 4823: Add root_collection() to make it easier to find the root. Adj...
semantics of save(), renamed save_as() to save_newC(). Now call save() on
close() when in SYNC_LIVE. Release readfr...
Peter Amstutz
06:16 pm Revision 1e2e0e4f (arvados): Merge branch '4472-save-partial-output' closes #4472
Tom Clegg
05:25 pm Bug #4464: [Workbench] Collections tab loads forever on a specific project
4464-api-project-contents-wip is up for review to implement the change in the last comment. It also does some relate... Brett Smith
05:24 pm Task #5140 (Resolved): Review 4464-api-project-contents-wip
Brett Smith
05:11 pm Revision fef79101 (arvados): 4823: Rename @_synchronized -> @synchronized and @_must_be_writable ...
Peter Amstutz
05:05 pm Revision cbf80c08 (arvados): 5011: Dry up three different solutions for mocking keep_services().a...
Tom Clegg
04:58 pm Revision 84c0cf99 (arvados): 4464: API group contents no longer include manifests.
This change achieves symmetry with the collections list method, which
doesn't return manifests unless you expressly r...
Brett Smith
04:33 pm Feature #5139 (New): [SDKs] arv-get should support getting multiple files by shell glob
for example arv-get uuid/*.vcf grabs all the vcfs Bryan Cosca
04:26 pm Revision 66f42779 (arvados): 4823: Another merge conflict test.
Peter Amstutz
04:22 pm Revision bac1bf1f (arvados): 4823: Files now fall under collection's lock. Add tests for merge c...
Add modified flag to collections to detect deletions. Peter Amstutz
03:34 pm Feature #5138 (New): [SDKs] arv-run-pipeline-instance should accept project and title parameters
When running 'arv-run-pipeline-instance' there is no option to associate the pipeline generated to a project. This m... Abram Connelly
02:41 pm Bug #5136: arv-run arv-keep command gives error while running
Hi Sabarish, how are you installing the Arvados Python SDK? Did you install using "pip" or are you running from the ... Peter Amstutz
02:40 pm Revision 56ad3038 (arvados): 5011: Merge branch 'master' into 5011-arv-put-replication
Tom Clegg
02:28 am Revision b2059022 (arvados): 3021: In start(), if a stale server is already running (but we can't...
Tom Clegg
02:27 am Revision 13f83b93 (arvados): 3021: Check whether a randomly selected port is available before usi...
Tom Clegg
02:25 am Revision 64416e47 (arvados): 3021: Don't worry about env vars, run_test_server.py does that.
Tom Clegg
02:25 am Revision dcba3e2c (arvados): 4951: trailing white space
Radhika Chippada
02:21 am Revision e1523c51 (arvados): 4951: add tests for request shell access feature.
Radhika Chippada

02/04/2015

11:54 pm Revision 9fc99919 (arvados): 4951: add ajax handling for request shell access button.
Radhika Chippada
10:35 pm Revision 0c8f599d (arvados): 3021: Fix use of inaccessible global in atexit handler.
Tom Clegg
10:28 pm Revision d1957808 (arvados): 3021: Remove ARVADOS_KEEP_PROXY support. (If you need to interfere
with the discovery mechanism from out-of-process, use some combination
of HTTP_PROXY, NO_PROXY, and a generic proxy s...
Tom Clegg
10:15 pm Revision 1f8fcb02 (arvados): 3021: Set up a proxy-only keepclient manually, instead of communicat...
Tom Clegg
10:13 pm Revision 2cf42c27 (arvados): 3021: Tidy up (and document) the choice of exactly which server we e...
Tom Clegg
10:11 pm Revision bd6f1751 (arvados): 3021: Fix misspelled variable.
Tom Clegg
09:27 pm Revision 5c0430fd (arvados): 4823: Switched order of diff (now gives a diff *to* the target colle...
instead of *from* the target collection). Peter Amstutz
09:22 pm Bug #5136: arv-run arv-keep command gives error while running
Thank you @Peter. I installed python 2.7.Now I get the following error if I run arv-run
'import site' failed; use -...
Sabarish Subramanian
08:52 pm Bug #5136: arv-run arv-keep command gives error while running
It appears you are using Python 2.6. Unfortunately, the Arvados SDK only supports Python 2.7. Are you able to upgrade? Peter Amstutz
08:40 pm Bug #5136 (New): arv-run arv-keep command gives error while running
If I run arv-run command, I get the following error:
Traceback (most recent call last):
File "/usr/bin/arv-run", ...
Sabarish Subramanian
09:04 pm Revision d4285076 (arvados): 4823: Add tests for Collection diff and apply.
Peter Amstutz
08:54 pm Revision cd3019ce (arvados): Diagnostics testing: The test fails because there are 2 Run buttons ...
Radhika Chippada
08:46 pm Revision a9e07ecb (arvados): 4464: Document API group contents parameters.
Brett Smith
08:46 pm Revision 734ded9a (arvados): 4464: Remove API group contents include_linked parameter.
With Tom's permission. Brett Smith
07:31 pm Story #3021: [Tests] Make jenkins tests run faster.
A couple of gem install warnings (non fatal?)... Peter Amstutz
07:04 pm Revision 90af4cd8 (arvados): Merge branch 'master' into 4951-request-vm
Radhika Chippada
07:00 pm Revision c58a2c83 (arvados): Merge branch '2659-anonymous-share-projects' refs #2659
Tom Clegg
06:56 pm Revision 9ae339f1 (arvados): 5011: Convert comment to docstring.
Tom Clegg
06:56 pm Revision 3d0c0753 (arvados): 5011: Sync local_store_put/get() signatures to put/get(). Add docstr...
Tom Clegg
06:54 pm Revision 288413d1 (arvados): 5011: Use None, not 0, to signify default replication.
Tom Clegg
06:36 pm Bug #4464: [Workbench] Collections tab loads forever on a specific project
This project contains several collections with large (50+MiB) manifests. The API request times out because the API s... Brett Smith
06:00 pm Bug #4464 (In Progress): [Workbench] Collections tab loads forever on a specific project
Brett Smith
06:29 pm Revision 378c32cf (arvados): 4951: send mail to request shell access to user
Radhika Chippada
06:27 pm Task #5130 (In Progress): Review 3021-leave-api-running (arvados-dev)
Peter Amstutz
06:26 pm Task #5129 (In Progress): Review 3021-leave-api-running (arvados)
Peter Amstutz
06:22 pm Revision c30d3a7c (arvados): 4823: Implemented diff/apply/update methods for Collection synchroni...
Peter Amstutz
05:38 pm Revision 35c50eb2 (arvados): 2659: Use a partial instead of a switch block for the not-so-generic...
Tom Clegg
05:01 pm Revision 08b3d5b9 (arvados): 2659: Use assert_operator to help debug unreliable test.
Tom Clegg
04:43 pm Story #3126: [API] Support use of anonymous git url (like github https) as repository in jobs.create
*bump* This would be really useful for me! Sarah Guthrie
04:24 pm Revision 12abd300 (arvados): 2659: Split skip_around_filter back into two separate cases. 063c546...
Tom Clegg
04:01 pm Feature #4561: [SDKs] Refactor run-command so it can be used as an SDK by scripts in a git tree
(comments from IRC)
Now that we have the "deploy SDK into container" feature, moving most of run-command's functio...
Peter Amstutz
03:46 pm Feature #5011: [SDKs] arv-put accepts --replication argument (saved with collection record)
Reviewing commit:655b69e. Unfortunately, I got these test failures:... Brett Smith
03:12 pm Task #5123 (In Progress): Review 5011-arv-put-replication
Brett Smith
02:59 pm Revision cad21664 (arvados): 5131: Document run-command's escape sequences.
Refs #5131. Brett Smith
02:44 pm Feature #4951 (In Progress): [Workbench] When a user does not have access to a VM, provide a way ...
Radhika Chippada
02:24 pm Bug #5135 (Resolved): [Workbench] Ensure modal button order is consistent
These modals have the primary button first from the right:
* application/_choose.html.erb
* application/_report_i...
Brett Smith
02:22 pm Revision fefdb915 (arvados): 2659: Do not turn on anonymous config by default in test mode; inste...
Also convert some of the simple integration tests into controller tests. Radhika Chippada
02:12 pm Bug #5134: [SDKs] CLI tools fail or warn when current working directory is gone
From IRC follow-up:
* Calling @arv-keepdocker@ directly produced the warning @sh: 0: getcwd() failed: No such file...
Brett Smith
01:40 am Bug #5134 (New): [SDKs] CLI tools fail or warn when current working directory is gone
arv keep docker --no-pull bcosc/all-tools
/usr/local/rvm/gems/ruby-2.1.5@global/gems/rubygems-bundler-1.4.4/lib/ruby...
Bryan Cosca
05:00 am Revision de6150af (arvados): 2659: add publicly accessible pipeline instance and template to the ...
Radhika Chippada
03:23 am Revision bf9d2be7 (arvados): Merge branch '2659-anonymous-share-projects' of git.curoverse.com:ar...
Radhika Chippada
03:23 am Revision e31b4ee6 (arvados): Merge branch 'master' of git.curoverse.com:arvados into 2659-anonymo...
Radhika Chippada
03:16 am Revision 549f0a0d (arvados): 2659: Fix infinite recursion while creating system_user.
Tom Clegg
03:16 am Revision e98e77b8 (arvados): 2659: Fix up chicken-and-egg conditions in seed setup.
Tom Clegg
12:32 am Revision fa166d52 (arvados): Merge branch '2659-anonymous-share-projects' of git.curoverse.com:ar...
Radhika Chippada
12:31 am Revision 74b859d9 (arvados): 2659: tests do not "assume" that anonymous configuration is enabled.
Radhika Chippada
12:24 am Revision 970766e3 (arvados): 2659: Token fail during download is 404 when anon token is enabled, ...
Tom Clegg
12:24 am Revision 18b5b6fa (arvados): 2659: Fix anonymous token test.
Tom Clegg

02/03/2015

11:46 pm Revision af84e178 (arvados-dev): info: get description from the 'gitweb.description'
Sitaram Chamarty
11:20 pm Revision 56714c8d (arvados): 2659: add test cases where anonymous config is turned off for collec...
Radhika Chippada
11:19 pm Revision 60789154 (arvados): 2659: Add separate test for "run pipeline" notification when anonymo...
Tom Clegg
10:22 pm Revision 063c5461 (arvados): 2659: Do not ask to skip_around_filter(only:...) and skip_around_fil...
Tom Clegg
09:37 pm Revision 130b8d31 (arvados): 4823: Add tests for Collection.clone and Collection.merge
Peter Amstutz
09:33 pm Revision e0619201 (arvados): 2659: Check anon config at runtime instead of boot time in skip_befo...
Tom Clegg
09:07 pm Feature #5133 (New): [Crunch] Use uncommitted code in a git work tree to run a dockerized crunch ...
Tom Clegg
08:59 pm Revision a7b16675 (arvados): 4823: Add Collection.copy tests
Peter Amstutz
08:55 pm Task #5132 (Resolved): Review 5131-run-command-consume-backslashes-wip
Applied in changeset arvados|commit:906aa5e3427c1e89e5f426191e33af4b1c27fc7e. Brett Smith
08:43 pm Task #5132 (Resolved): Review 5131-run-command-consume-backslashes-wip
Brett Smith
08:55 pm Bug #5131 (Resolved): [Crunch] run-command passes escape backslashes through
Applied in changeset arvados|commit:906aa5e3427c1e89e5f426191e33af4b1c27fc7e. Brett Smith
07:20 pm Bug #5131 (In Progress): [Crunch] run-command passes escape backslashes through
Brett Smith
07:15 pm Bug #5131 (Resolved): [Crunch] run-command passes escape backslashes through
run-command lets you prefix characters with a backslash to prevent it from interpreting them. However, when you do t... Brett Smith
08:51 pm Revision 501a707f (arvados-dev): * Only source /etc/profile.d/rvm.sh if it exists and is a regula...
* Fix typo
No issue #
Ward Vandewege
08:51 pm Revision 501a707f (arvados): * Only source /etc/profile.d/rvm.sh if it exists and is a regular file
* Fix typo
No issue #
Ward Vandewege
08:49 pm Revision 3253570c (arvados-dev): * Only source /etc/profile.d/rvm.sh if it exists and is a regula...
* Fix typo
No issue #
Ward Vandewege
08:48 pm Revision 906aa5e3 (arvados): Merge branch '5131-run-command-consume-backslashes-wip'
Closes #5131, #5132. Brett Smith
08:40 pm Revision b495d8bd (arvados): 5131: run-command consumes escape backslashes.
run-command has long recognized backslashes to inhibit
substitution, but it was leaving those backslashes in the stri...
Brett Smith
08:24 pm Revision 4d8209df (arvados): 2659: Remove obsolete "don't create jobs in workbench" rule.
Tom Clegg
07:57 pm Revision afabee43 (arvados): 2659: Update test to match changed error message.
Tom Clegg
07:56 pm Revision 5b749587 (arvados): 2659: Remove obsolete "don't create collections in workbench" rule.
Tom Clegg
07:28 pm Revision 1b39a6e1 (arvados): 2659: Back out unneeded condition. Fix up whitespace.
Tom Clegg
07:27 pm Revision 416c5436 (arvados): 2659: Toggle features according to editable? and creatable? instead ...
Tom Clegg
07:26 pm Revision 8192c879 (arvados): 4823: Fix bugs, fix tests, existing tests pass again. Still need to...
Peter Amstutz
07:14 pm Revision 4cd97b2c (arvados): 2659: Fix indentation.
Tom Clegg
07:13 pm Revision 0d2e6cf3 (arvados): 2659: Use Collection.creatable? to toggle selection actions.
Tom Clegg
06:56 pm Revision 9fcabe97 (arvados): 2659: Reload seeds (system_user et al.) after cache is cleared. Be m...
Tom Clegg
06:41 pm Revision b9a8de22 (arvados): 5087: API server uses a crunch-job with bugfix.
Refs #5087. Brett Smith
06:34 pm Revision 9ea36303 (arvados): 2659: Set group_class=role on anonymous group, change name to "Anony...
Tom Clegg
04:44 pm Revision 89a8208e (arvados): 2659: Fix crash in /users/current when not logged in.
Tom Clegg
04:24 pm Support #5070 (In Progress): [Support] Fix bugs and write tests (first half)
Brett Smith
04:24 pm Story #5069 (Resolved): [Documentation] (recurring) Write blog post in first three days of sprint
https://arvados.org/blogs/27 Brett Smith
04:20 pm Revision f56d3a68 (arvados): Merge branch 'master' into 4823-python-sdk-writable-collection-api
Peter Amstutz
04:19 pm Revision 07032047 (arvados): 4823: Added merge(), live sync. Removed deferred _populate().
Peter Amstutz
04:18 pm Revision e1104f98 (arvados): 2659: Fix up 404 page.
Tom Clegg
04:11 pm January development review: Gotta go fast!
Arvados can already save researchers a lot of time just by keeping track of their data and analysis work. You never ... Brett Smith
03:40 pm Revision 17c5cc48 (arvados): 2659: Fix crashes when current_user is nil.
Tom Clegg
03:29 pm Revision 42fc0557 (arvados): 2659: Send anonymous token as a reader token with all requests.
Tom Clegg
03:20 pm Revision 7edde478 (arvados): 2659: Finally understood the mystery behind the "anonymous tests are...
There is a permission link fixture for anonymous group. I needed to create read permission link for anonymous user.
(...
Radhika Chippada
03:06 pm Task #5103 (In Progress): Implement live sync, merge
Peter Amstutz
01:33 pm Revision ec27ba2a (arvados): 2659: Expect redirect to login page when show method is executed in ...
Something is overriding the configured value from application.default.yml when the test is executed along with all ot... Radhika Chippada
01:08 pm Revision 50ab35e7 (arvados): 2659: fix test assertion
Radhika Chippada
12:00 pm Revision 4bc67f80 (arvados): 2659: enable anonymous user config in test environment.
Radhika Chippada
05:14 am Revision b23240bd (arvados): 2659: add a "you are not logged in" warning in 404 page.
Radhika Chippada
03:40 am Revision 33e6d335 (arvados): Merge branch 'master' into 2659-anonymous-share-projects
Radhika Chippada
03:39 am Revision 03428065 (arvados): 2659: skip require_thread_api_token filter only when anonymous confi...
Radhika Chippada

02/02/2015

11:23 pm Revision 9a6559f9 (arvados): 2659: Do not require login for project tab_counts method as well.
Remove anonymous login tests for /users and /groups pages since we are no longer doing session establishment for anon... Radhika Chippada
10:15 pm Revision 64e9180b (arvados): 2659: load @prov_svg outside of the 'if current_user' block so that ...
Radhika Chippada
09:39 pm Revision 89d4aec6 (arvados): 2659: prevent nil exception when a content hash link is clicked by a...
Radhika Chippada
09:29 pm Task #5130 (Resolved): Review 3021-leave-api-running (arvados-dev)
This can't be merged/used without 3021-leave-api-running (arvados) Tom Clegg
09:28 pm Task #5129 (Resolved): Review 3021-leave-api-running (arvados)
Tom Clegg
09:27 pm Task #4986 (Resolved): Refactor run_test_server.py to use API database reset rather than restarti...
Tom Clegg
08:55 pm Story #4904: [SDKs] Use websockets to restart/reconfigure a web service running on a VM whenever ...
On second thought, I have a couple of ideas that would be slightly less hacky without going all the way backwards.
Peter Amstutz
08:49 pm Story #4904: [SDKs] Use websockets to restart/reconfigure a web service running on a VM whenever ...
Will go back to the "shut down the container, shut down the mount, start a new mount, start a new container" approach... Peter Amstutz
08:16 pm Story #4904: [SDKs] Use websockets to restart/reconfigure a web service running on a VM whenever ...
Reviewing commit:8233bab
h2. Bugs
* On my system, using our own Docker package, the service refresh causes the ...
Brett Smith
08:53 pm Revision 7dcac823 (arvados): 4823: Add copyinto()
Peter Amstutz
08:50 pm Revision 96326e98 (arvados): 2659: anonymous token handling in api client updated
Radhika Chippada
08:20 pm Revision d4879073 (arvados): 2659: no need for permit_anonymous_browsing_for_public_data filter; ...
Radhika Chippada
08:16 pm Revision 951149b9 (arvados): 4823: Refactored Collection into SynchronizedCollectionBase, Subcoll...
Collection. Added clone(). Added method decorators for locking. Peter Amstutz
08:06 pm Revision 16e6df55 (arvados): 2659: is_anonymous helper method is not needed anymore.
Radhika Chippada
08:00 pm Revision 7f2c45b1 (arvados): 2659: do not include "You are viewing public data" in topnav when an...
Radhika Chippada
07:50 pm Revision 89fb910b (arvados): Documentation cleanup: CLI SDK:
- merge some information from the wiki.
- reorganize things a bit.
No issue #
Ward Vandewege
07:36 pm Revision 4470ba26 (arvados): 3021: Use `passenger stop` to shut down passenger. Restore database ...
Tom Clegg
07:30 pm Revision 411ce5bc (arvados): 2659: instead of setting up a session as anonymous user, just use an...
Radhika Chippada
04:44 pm Feature #5128 (New): [DRAFT] [FUSE] arv-mount supports FUSE for OS X
Peter Amstutz
03:27 pm Revision a526319c (arvados-dev): 3021: Fix up some error checking.
Tom Clegg
03:27 pm Revision a526319c (arvados): 3021: Fix up some error checking.
Tom Clegg
03:19 pm Revision 438752b8 (arvados): 4823: Added SYNC mode constants.
Peter Amstutz
03:14 pm Bug #5127 (New): [Docs] Note apt key information in Python package READMEs
Our Python client packages tell you how to install the software via apt. Those instructions need to be expanded to n... Brett Smith
03:03 pm Feature #5126 (New): [DRAFT] [SDKs] "arv-vc" command line tool supporting VCS workflow for collec...
Concept: arv-vc tool supporting version control system workflow over collections.
(This assumes a svn-like workflo...
Peter Amstutz
02:33 pm Revision 5bb11227 (arvados): 4823: Adding @_synchronized to protect arvfile and block manager. U...
docstrings to PEP 257 and PEP 287. Peter Amstutz
02:00 pm Task #5125 (Resolved): Review branch: 2659-anonymous-share-projects
Radhika Chippada
01:57 pm Story #2659: [Workbench] Anonymous user can access publicly shared data using Workbench and curl
Branch '2659-anonymous-share-projects' implemented workbench support for anonymous users. Some details:
* Updated ...
Radhika Chippada
01:46 pm Revision 876ca867 (arvados): 2659: add some more text assertions; several of the same tests are f...
Radhika Chippada
12:08 pm Revision 332015d1 (arvados): 2659: remove most of the user-based tests since they are covered in ...
Radhika Chippada
10:29 am Revision e925baa0 (arvados-dev): 3021: Cache packages with bundle package --all
Tom Clegg
10:29 am Revision e925baa0 (arvados): 3021: Cache packages with bundle package --all
Tom Clegg
10:27 am Revision a6969ab9 (arvados-dev): 3021: Let integration tests write to the api server log before r...
Tom Clegg
10:27 am Revision a6969ab9 (arvados): 3021: Let integration tests write to the api server log before rotat...
Tom Clegg
10:25 am Revision 3e70317d (arvados-dev): 3021: Try bundle install --local before resorting to downloading...
Tom Clegg
10:25 am Revision 3e70317d (arvados): 3021: Try bundle install --local before resorting to downloading the...
Tom Clegg
08:41 am Revision d01477c5 (arvados): 3021: gitignore **/vendor
Tom Clegg
08:10 am Revision 5c1cee51 (arvados): 3021: Use run_test_server.py instead of the special workbench way of...
Tom Clegg
08:05 am Revision 440a0665 (arvados-dev): 3021: Leave an API server running while test suites run.
Tom Clegg
08:05 am Revision 440a0665 (arvados): 3021: Leave an API server running while test suites run.
Tom Clegg
08:04 am Revision 8ea68a13 (arvados): 3021: Use run_test_server.py instead of the special workbench way of...
Tom Clegg
05:42 am Revision 73d8ff76 (arvados): 2659: slightly improved test flows
Radhika Chippada
05:29 am Revision a1ad1f1d (arvados): 3021: Round up various implementations of "run test servers" into an...
* Get the API host, port, and admin token from the run_test_server.py
--auth output, instead of guessing localhost:...
Tom Clegg
05:29 am Revision 13181107 (arvados): 3021: Refactor run_test_server.
* Always start API server with both https:// and wss:// enabled. Use
mocks to test the websocket-not-available case...
Tom Clegg
05:11 am Revision 62eaf394 (arvados): 2659: add completed job fixture in publicly accessible project and t...
Radhika Chippada
03:01 am Revision 3ffc4fd3 (arvados): 3021: Do not start a test server if ARVADOS_TEST_API_HOST is set.
Tom Clegg
02:56 am Revision 1aa04543 (arvados-dev): 3021: Set ARVADOS_TEST_API_INSTALLED so workbench doesn't try to...
Tom Clegg
02:15 am Revision c4320ec0 (arvados-dev): 3021: Leave an API server running while test suites run.
Tom Clegg
02:11 am Revision c3086805 (arvados): 3021: Round up various implementations of "run test servers" into an...
* Get the API host, port, and admin token from the run_test_server.py
--auth output, instead of guessing localhost:...
Tom Clegg
01:59 am Revision 68f0e2be (arvados): 3021: Refactor run_test_server.
* Always start API server with both https:// and wss:// enabled. Use
mocks to test the websocket-not-available case...
Tom Clegg
01:22 am Revision 2c447c25 (arvados): 2659: (1) Update link_to_if_arvados_object method to display an obje...
Otherwise, an anonymous user will always see 404 when such a link is clicked.
(2) In the unlikely event of an anonymo...
Radhika Chippada
12:21 am Revision 48580ba7 (arvados): 3021: Propagate unhandled exceptions back to the caller instead of r...
Tom Clegg
12:15 am Revision 0d32948a (arvados): 3021: Add comment about IPv4/IPv6 trap in websocket client.
Tom Clegg

02/01/2015

08:09 pm Revision 1a462bc4 (arvados): 2659: It appears that a job's log file is stored in a user's Home pr...
Due to this, when an anonymous user accesses the job from the publicly accessible project, the Log tab is failing.
He...
Radhika Chippada
05:42 pm Revision 6b972e17 (arvados): 2659: show job cancel button only when user is_active.
Radhika Chippada
05:15 pm Revision 9f931ff8 (arvados): 2659: more asserts in dashboard testing
Radhika Chippada
04:40 pm Revision 4d1e5c05 (arvados): 2659: trailing white space
Radhika Chippada
04:38 pm Revision 7f6d2dbe (arvados): Merge branch 'master' into 2659-anonymous-share-projects
Radhika Chippada
04:30 pm Revision c8f0f0c5 (arvados): 2659: Collection show_files shows selection dropdown (which has only...
Also, dashboard displays the 'Run a pipeline' selector for active users. Upated anonymous user test to verify dashboa... Radhika Chippada
04:22 pm Revision 487dc409 (arvados): 5037: Fix tearDown error handling in PySDK Websockets test.
I accidentally broke this in 51f9e6cb. That version would crash if
the test failed to assign self.ws. Refactor to b...
Brett Smith
04:01 am Revision b6ca3da4 (arvados): 2659: hide job re-run button when user is inactive and add fixtures ...
Radhika Chippada
01:35 am Revision 0507f73c (arvados): 5011: Fix run_and_find_collection so it works without --portable-dat...
Tom Clegg
01:35 am Revision a2e9008a (arvados): 5011: 3410: Export client-specified redundancy as replication_desired.
Tom Clegg
01:34 am Revision cb6a13cd (arvados): 5011: Use replication=2 if unspecified.
Tom Clegg

01/31/2015

10:42 pm Revision 934fa5ac (arvados): 2659: show tab buttons, selection actions etc only when the current_...
Radhika Chippada
06:06 pm Revision 71d9ea52 (arvados): 2659: when an anonymous user is accessing public data, offer "Log in...
Radhika Chippada
05:45 pm Revision 94a3addb (arvados): 2659: add text message "You are viewing public data" to top nav when...
Radhika Chippada
03:38 pm Revision 5dbde597 (arvados): 2659: add permit_anonymous_browsing_for_public_data
Radhika Chippada
07:21 am Revision f9a0cb85 (arvados): 3021: gitignore rotated log files.
Tom Clegg

01/30/2015

10:21 pm Task #5124 (Resolved): Use server-provided default replication level as default in arv-put and Co...
Tom Clegg
10:20 pm Task #5123 (Resolved): Review 5011-arv-put-replication
Tom Clegg
10:20 pm Revision 655b69e4 (arvados): 5011: Add --replication option to CLI docs.
Tom Clegg
10:19 pm Task #5122 (Resolved): Update docs
Tom Clegg
10:12 pm Task #5122 (Resolved): Update docs
Tom Clegg
10:12 pm Task #5120 (Resolved): Add --replication arg to arv-put
Tom Clegg
10:12 pm Task #5120 (Resolved): Add --replication arg to arv-put
Tom Clegg
10:12 pm Revision 774bc42d (arvados): 5011: Add --replication argument to arv-put.
Tom Clegg
10:12 pm Revision bed95fb1 (arvados): 5011: Add replication argument to CollectionWriter.
Tom Clegg
10:12 pm Task #5121 (Resolved): Add replication=X kwarg to CollectionWriter and friends
Tom Clegg
10:12 pm Task #5121 (Resolved): Add replication=X kwarg to CollectionWriter and friends
Tom Clegg
09:51 pm Story #2659: [Workbench] Anonymous user can access publicly shared data using Workbench and curl
To make projects#show work for anonymous users:
* ApplicationController#check_user_agreements should return true if ...
Tom Clegg
09:40 pm Revision facbf48d (arvados): Merge branch 'master' into 4823-python-sdk-writable-collection-api
Peter Amstutz
09:28 pm Task #5117 (Resolved): Review 5037-python-sdk-thread-safe
Tom Clegg
08:29 pm Task #5117 (In Progress): Review 5037-python-sdk-thread-safe
Brett Smith
06:28 pm Task #5117 (Resolved): Review 5037-python-sdk-thread-safe
Tom Clegg
08:42 pm Revision 9af0808e (arvados): Merge branch '5037-python-sdk-thread-safe' refs #5037
Tom Clegg
08:40 pm Revision 9fb82043 (arvados): 5037: Mention where this cache is, instead of describing what a cach...
Tom Clegg
08:28 pm Bug #5037: [SDKs] Improve Python SDK thread safety and document pitfalls
Now we're at commit:1eeb668. My commits add a test for the new behavior, fix a Websockets test that broke for me (al... Brett Smith
07:32 pm Bug #5037: [SDKs] Improve Python SDK thread safety and document pitfalls
commit:ae7a6c9 on 5037-python-sdk-thread-safe Tom Clegg
05:38 pm Bug #5037 (In Progress): [SDKs] Improve Python SDK thread safety and document pitfalls
Tom Clegg
03:25 pm Bug #5037: [SDKs] Improve Python SDK thread safety and document pitfalls
We just got a report that the GATK-merge-call Crunch script, included with Arvados, is failing because of this issue.... Brett Smith
08:24 pm Revision 44cbe230 (arvados): 5037: Add test for new PySDK API cache behavior.
Brett Smith
08:24 pm Revision 1eeb6688 (arvados): 5037: Remove unnecessary cache=False from arv-copy.
Brett Smith
08:24 pm Revision 51f9e6cb (arvados): 5037: Fix race condition in PySDK Websockets test.
This might just be bad luck, but for some reason when testing Tom's
changes I ran into a situation where this test fa...
Brett Smith
08:15 pm Feature #4601: [SSO] Migrate OpenId users to OAuth/Google+
Related work from wikifarm
* "Google login button":https://github.com/tomclegg/wikifarm/blob/master/src/web/login.ph...
Tom Clegg
07:56 pm Feature #4601: [SSO] Migrate OpenId users to OAuth/Google+
Updated strategy
# Change API server:
#* If SSO provider gives us an identity_url field, log in the same way we've ...
Tom Clegg
07:15 pm Feature #4601: [SSO] Migrate OpenId users to OAuth/Google+
Some thoughts:
* SSO migration: Start Using multiple authorizations feature of SSO server in order to support not...
Peter Amstutz
07:00 pm Task #5015 (Resolved): Review branch 4562-crunch-tools-docs-wip
Applied in changeset arvados|commit:088bc7b980536ee2b27c8abf4bfc09c348000589. Brett Smith
07:00 pm Bug #4562 (Resolved): [Documentation] Wiki page: explain appropriate use cases for arv-run vs. ru...
Applied in changeset arvados|commit:088bc7b980536ee2b27c8abf4bfc09c348000589. Brett Smith
04:28 pm Bug #4562: [Documentation] Wiki page: explain appropriate use cases for arv-run vs. run-command v...
Peter Amstutz wrote:
> My concern with the current draft is that is a bit too wordy to be a "brief" summary, while a...
Brett Smith
06:58 pm Revision 088bc7b9 (arvados): Merge branch '4562-crunch-tools-docs-wip'
Closes #4562, #5015. Brett Smith
06:57 pm Revision 4215621e (arvados): 4562: Add Crunch tools overview to the documentation.
Brett Smith
06:46 pm Feature #5119 (New): [OPS] Write a wrapper script that calls packer to generate customized docker...
Ward Vandewege
06:46 pm Revision 0882568e (arvados): 4562: Fixups suggested by office discussion.
Brett Smith
06:45 pm Feature #5118 (In Progress): [OPS] Use packer to generate docker images for our various services
Ward Vandewege
06:28 pm Task #5116 (Resolved): Remove connection pooling feature from arvados.api()
Tom Clegg
05:37 pm Task #5116 (In Progress): Remove connection pooling feature from arvados.api()
Tom Clegg
05:37 pm Task #5116 (Resolved): Remove connection pooling feature from arvados.api()
Tom Clegg
06:22 pm Task #4959 (Resolved): Write up [[Authentication]] page
Tom Clegg
06:20 pm Revision ae7a6c9a (arvados): 5037: Remove connection pool. Now, api(cache=False) refers only to t...
Tom Clegg
04:58 pm Revision 8233babd (arvados): 4904: Fix documentation issues. Add comments to arv-web.py.
Peter Amstutz
04:23 pm Revision e72f4e3b (arvados): 4562: Add Crunch tools overview to the documentation.
Brett Smith
04:10 pm Revision 29e2e288 (arvados): 4904: Handle failure to delete non-existent cidfile. Fix docker_ima...
Peter Amstutz
04:03 pm Revision 63ea99a3 (arvados): 4904: Finally figured out a (hopefully) reliable way of sending SIGH...
service inside Docker container to get it to refresh. Peter Amstutz
03:41 pm Revision ef91d974 (arvados-dev): add missing include path to GL_LIBDIR
In src/triggers/post-compile/update-description-file and
src/triggers/post-compile/update-gitweb-daemon-from-options ...
Robert Schiele
03:01 pm Bug #4922 (Resolved): [Crunch] google-api-python-client fails to install
The original job didn't specify an arvados_sdk_version, so changing crunch-job's install process for that would not c... Brett Smith
07:26 am Revision 5ae2677e (arvados): 4472: Include output of failed tasks when generating job output mani...
Tom Clegg
01:38 am Story #3408: [Keep] Implement Production Data Manager
Peter Amstutz wrote:
> * the keep servers report should include number of blocks on the service, disk space in use...
Misha Zatsman
01:32 am Revision c37ed03a (arvados): Renamed timestamp fields to begin with "time_"
Misha Zatsman
01:25 am Revision af0728d3 (arvados): Now fetch Keep Server Status and record it to the log. Renamed some ...
Misha Zatsman

01/29/2015

10:13 pm Revision 04a8e038 (arvados): 4904: Eliminate downtime switching collections.
* Now re-uses CollectionDirectory and loads new collection contents instead of
unmounting and remounting. Now sends ...
Peter Amstutz
09:38 pm Task #5012 (Closed): Confirm fix
Brett Smith
09:37 pm Bug #4922 (New): [Crunch] google-api-python-client fails to install
qr1hi-8i9sb-o9719vud1ro9wzh successfully reproduced the issue. Unfortunately this is not fixed. Brett Smith
09:30 pm Feature #5034: [Workbench] Show content statistics/summary (total size, number of files) at top o...
In "This collection was the output of:" maybe change this to "This collection was uploaded by" if its not an output o... Bryan Cosca
08:31 pm Task #5114 (Resolved): Fix
Peter Amstutz
08:11 pm Story #4930 (Resolved): [FUSE] Design: specify behavior for writable arv-mount
Tom Clegg
05:53 pm Story #4930 (In Progress): [FUSE] Design: specify behavior for writable arv-mount
Tom Clegg
07:59 pm Feature #5110 (Resolved): [Workbench] Use full text search instead of 'ilike' when searching with...
Tom Clegg
07:55 pm Task #5109 (Resolved): Add "import files from another collection" API to Ruby SDK
Tom Clegg
07:54 pm Task #3736 (Closed): [SDKs] Document Python Crunch SDK
I'm unhooking this from #3603, now that that has become more focused on design specifically. Documentation should ha... Brett Smith
07:54 pm Task #5108 (Resolved): Implement internal representation for collections in Ruby SDK (analogous t...
Tom Clegg
07:53 pm Task #5107 (Resolved): Add collections#rename and collections#delete methods to Ruby SDK
Tom Clegg
07:41 pm Bug #4174 (Resolved): [Documentation] Write a wiki page describing desired bug workflow
Ward Vandewege
07:41 pm Bug #4174: [Documentation] Write a wiki page describing desired bug workflow
Now done on
https://arvados.org/projects/orvos-private/wiki/Support_team
Ward Vandewege
07:39 pm Task #4580 (Closed): Review 4138-node-manager-google-cloud
Brett Smith
07:19 pm Story #3410: [API] Rename collection "desired replication" attributes, add model constraints
Peter Amstutz wrote:
> What's the difference between @redundancy_confirmed@ and @redundancy_confirmed_at@ ? If @red...
Tom Clegg
06:31 pm Story #4927 (Resolved): [SSO] Decide overall single sign-on strategy
Tom Clegg
06:21 pm Feature #4601: [SSO] Migrate OpenId users to OAuth/Google+
Priorities for this story, in order:
# allow existing users (who signed up using Google OpenID) to log in after logi...
Tom Clegg
06:17 pm Bug #4523: [Workbench] Search dialog giving error when searching in "All projects" in qr1hi
Tom,
* Added the ArgumentError when individual columns are used in filter
* Added tests to cover this condition
* ...
Radhika Chippada
03:52 pm Bug #4523: [Workbench] Search dialog giving error when searching in "All projects" in qr1hi
Looking at 4523-full-text-search at commit:316eca14...
Currently, the filter attribute(s) provided by the client a...
Tom Clegg
06:13 pm Revision 7d76a3fb (arvados): 4523: full-text search is not supported for individual columns and o...
Radhika Chippada
04:41 pm Bug #4562 (In Progress): [Documentation] Wiki page: explain appropriate use cases for arv-run vs....
Ward Vandewege
03:37 pm Bug #4562: [Documentation] Wiki page: explain appropriate use cases for arv-run vs. run-command v...
I don't want to spend a lot of time wrangling over this, so I'll try to make this the last round of comments.
My c...
Peter Amstutz
03:24 pm Bug #4562: [Documentation] Wiki page: explain appropriate use cases for arv-run vs. run-command v...
Peter Amstutz wrote:
> Here's a brainstorm, how about a table that provides some kind of brief side-by-side summary?...
Brett Smith
04:41 pm Story #3603 (In Progress): [Crunch] Design good Crunch task API, including considerations about "...
Ward Vandewege
04:36 pm Story #4687 (Resolved): [Crunch] Support Brad Chapman to port bcbio tools and workflows to CWL
Ward Vandewege
04:35 pm Support #4929 (Resolved): [Support] Fix bugs and write tests (second half)
Ward Vandewege
03:36 pm Bug #5105 (Resolved): [Workbench] AJAX content loaders should not follow a redirect to the welcom...
!login_bug.png!
this happens when I have >2 tabs of curoverse open and then I log out in one of the tabs. I've see...
Bryan Cosca
03:09 pm Feature #4727: [Workbench] Feature requests/suggestions for shared collection download page
Brett Smith wrote:
> For what it's worth, we will probably be reluctant to add links to the page that point to anyth...
Tom Clegg
03:08 pm Revision 1060cff7 (arvados): Merge branch 'master' into 4904-arv-web
Peter Amstutz
02:59 am Revision a533cde8 (arvados): 4523: full-text search migration script renamed
Radhika Chippada
02:56 am Revision 981c7264 (arvados): Merge branch 'master' into 4523-full-text-search
Radhika Chippada
02:56 am Revision 9fbf8925 (arvados): 4523: prepare to merge master into branch
Radhika Chippada
01:50 am Feature #3686 (Resolved): [Workbench] Provide a sharing tab for repositories similar to setting u...
Applied in changeset arvados|commit:2717e707ce048dd9b47754d620663a76256958cf. Radhika Chippada
01:46 am Feature #3686: [Workbench] Provide a sharing tab for repositories similar to setting up sharing f...
Thanks Brett. Addressed all of these suggestions and merged into master. Radhika Chippada
01:48 am Feature #5104 (Resolved): [SDKs] Add Ruby SDK methods for manipulating collection contents (renam...
Tom Clegg
01:46 am Task #5088 (Resolved): Review branch: 3686-sharing-repositories (one more time, for repository li...
Radhika Chippada
01:45 am Revision 2717e707 (arvados): closes #3686
Merge branch '3686-sharing-repositories' Radhika Chippada
01:43 am Revision 390d1935 (arvados): Merge branch 'master' into 3686-sharing-repositories
Radhika Chippada
01:41 am Revision c67f0508 (arvados): 3686: correct one test assertion and refine some other assertions.
Radhika Chippada

01/28/2015

11:10 pm Bug #4918 (Resolved): [Workbench] Input chooser for new pipelines hides the "file choose" menu on...
Applied in changeset arvados|commit:a51da9f0338017a7c193dcb36fc957b9ab71e4b1. Anonymous
06:42 pm Bug #4918 (In Progress): [Workbench] Input chooser for new pipelines hides the "file choose" menu...
Tom Clegg
11:08 pm Feature #3686: [Workbench] Provide a sharing tab for repositories similar to setting up sharing f...
Reviewing commit:1ceddc7. This is very nice; thanks very much for following up on everything.
* If I'm following ...
Brett Smith
10:11 pm Feature #3686: [Workbench] Provide a sharing tab for repositories similar to setting up sharing f...
Made all suggested enhancements. In addition, added an exclusive Share link instead of making the name clickable for ... Radhika Chippada
03:47 pm Feature #3686 (In Progress): [Workbench] Provide a sharing tab for repositories similar to settin...
Reviewing commit:194eaad
* For the repository link, I don't see a need to use @raw()@ to escape the repository nam...
Brett Smith
10:51 pm Revision a51da9f0 (arvados): Fix preview pane disappearing on narrow displays. closes #4918
Tom Clegg
10:40 pm Bug #5074 (Resolved): [SDKs] CLI client and Ruby SDK should recover from (and avoid creating) unr...
Applied in changeset arvados|commit:0fb26747fa229d6b19ec911b907259a8e84acd83. Brett Smith
08:20 pm Bug #5074: [SDKs] CLI client and Ruby SDK should recover from (and avoid creating) unreadable dis...
LGTM Peter Amstutz
08:12 pm Bug #5074: [SDKs] CLI client and Ruby SDK should recover from (and avoid creating) unreadable dis...
Peter Amstutz wrote:
> Consider not reporting an error in this case, because it is nonfatal and the user probably ca...
Brett Smith
07:05 pm Bug #5074: [SDKs] CLI client and Ruby SDK should recover from (and avoid creating) unreadable dis...
The code looks good. I appreciate that you moved the logic to the Ruby SDK.
So I intentionally corrupted the cach...
Peter Amstutz
10:37 pm Revision 0fb26747 (arvados): Merge branch '5074-ruby-sdk-discovery-cache-wip'
Closes #5074, #5091. Brett Smith
10:36 pm Revision 14b6221c (arvados): 5074: CLI SDK uses Google API client extensions from Ruby SDK.
Brett Smith
10:35 pm Revision d2299e01 (arvados): 5074: Improve discovery document caching in Ruby SDK.
* Report a warning if there's an error reading or parsing a cached
discovery document.
* Cache discovery documents ...
Brett Smith
10:32 pm Story #4904: [SDKs] Use websockets to restart/reconfigure a web service running on a VM whenever ...
Reviewing commit:b4fd2ab
h2. arv-web
I double-checked that I was running arvados_fuse from the branch, but I ge...
Brett Smith
05:21 pm Story #4904: [SDKs] Use websockets to restart/reconfigure a web service running on a VM whenever ...
commit:b4fd2ab4 looks pretty good.
I haven't scrutinized the code (or docs) as a proper review. I noticed a couple...
Tom Clegg
10:25 pm Feature #4905 (Closed): [Workbench] Make repository-sharing feature accessible from Manage Accoun...
Link was added to Manage Account page in #3686. Tom Clegg
09:52 pm Feature #4601: [SSO] Migrate OpenId users to OAuth/Google+
2. Instead of a URL to identify users, SSO server should assign user ids that are compatible with existing arvados us... Peter Amstutz
09:48 pm Revision 1ceddc71 (arvados): 3686: add unit and controller tests for repository updates
Radhika Chippada
09:43 pm Task #5103 (Resolved): Implement live sync, merge
Peter Amstutz
09:42 pm Task #5102 (Resolved): Try to reproduce
Peter Amstutz
09:41 pm Task #5101 (Resolved): Write tests
Peter Amstutz
09:41 pm Task #5100 (Resolved): Write migration
Peter Amstutz
09:40 pm Task #4947 (In Progress): Provide example to science team
Peter Amstutz
09:34 pm Story #3410: [API] Rename collection "desired replication" attributes, add model constraints
What's the difference between @redundancy_confirmed@ and @redundancy_confirmed_at@ ? If @redundancy_confirmed@ is ju... Peter Amstutz
09:22 pm Task #5091 (Resolved): Review 5074-ruby-sdk-discovery-cache-wip
Peter Amstutz
07:17 pm Task #5091 (In Progress): Review 5074-ruby-sdk-discovery-cache-wip
Peter Amstutz
09:13 pm Story #3408: [Keep] Implement Production Data Manager
In logger Update(), ForceUpdate() and several other places, prefer the following pattern (note the l.lock.Unlock() m... Peter Amstutz
08:46 pm Bug #4903 (Resolved): [Crunch] ensure that JOB_WORK and TASK_WORK directories exist for Docker jobs
Confirmed that the crunch-job fix is now effective. Tested in job qr1hi-4zz18-d2f9i56o1m9dkr7. Brett Smith
08:28 pm Story #5098 (Closed): [Keep] Design: using Arvados to browse, and run jobs on, input data that is...
See
* [[Keep service hints]]
* [[Keep S3 gateway]]
Tom Clegg
08:16 pm Task #5018 (In Progress): Review 4904-arv-web
Brett Smith
08:08 pm Revision d59deccc (arvados): 5074: Fixup Ruby SDK discovery cache warnings.
Brett Smith
07:39 pm Bug #5095: [FUSE] arv-mount takes up too much memory and occassionally crashes when listing large...
Possible problems/solutions:
* arv-mount is retrieving the manifest_text for all those collections, even though it d...
Tom Clegg
04:52 pm Bug #5095 (Resolved): [FUSE] arv-mount takes up too much memory and occassionally crashes when li...
On lightning-dev2 (qr1hi), in the home directory of my keep mount (/home/abram/keep/home), doing an 'ls' causes arv-m... Abram Connelly
07:34 pm Feature #5097 (New): [SDKs] CLI tools support project paths in addition to uuids
It's awkward and user-unfriendly to have to always copy and paste project UUIDs from the browser to the command line,... Peter Amstutz
07:27 pm Bug #5026: [API] Prohibit leaving jobs in an inconsistent state (e.g., state=queued with non-null...
Possible solution:
* Certain job attributes (output, log) should only be allowed to change (including from null to n...
Tom Clegg
07:25 pm Story #3198: [FUSE] Writable streaming arv-mount
Detailed semantics and discussion in #4930 Peter Amstutz
07:19 pm Bug #5037: [SDKs] Improve Python SDK thread safety and document pitfalls
Suggest:
* Ignore cache=False or cache=True
* Add new flag discoveryCache=False to turn off discovery doc caching (...
Tom Clegg
07:17 pm Task #4949 (Resolved): Sketch out how to port bcbio-nextgen StandardPipeline
Peter Amstutz
07:12 pm Bug #5030: [Workbench] Stats graph display for job without stats is confusing
Suggest:
* Make the graph div hidden by default. display:none or whatever.
* show() the graph using a cheesy[1] ani...
Tom Clegg
07:09 pm Bug #4805: [Workbench] Workbench provenance graph tabs appear empty when graph is very large
The "smart scroll" javascript is supposed to adjust the size of the DOM box that renders the SVG, so that you get act... Peter Amstutz
06:59 pm Bug #4991: [API] Make user.send_profile_created_notification detect preference changes better
Could add a comment about shortcomings of this trigger. API "update" call always replaces the hash with a new one. Tom Clegg
06:47 pm Bug #5096 (Resolved): [Workbench] Avoid passing manifest_text around the network too much when up...
Examples:
* Workbench should not send manifest_text to API in an update() request when only name/description is bein...
Tom Clegg
06:43 pm Revision 805ad01a (arvados): 3686: update the repository row to offer an exclusive Share link tha...
Radhika Chippada
06:43 pm Task #5044 (Resolved): Review 5010-trash-button-for-collections
Peter Amstutz
06:42 pm Task #5017 (Resolved): Review 5016-ctrl-c-arv-ws
Peter Amstutz
06:41 pm Bug #4562: [Documentation] Wiki page: explain appropriate use cases for arv-run vs. run-command v...
@01/22/2015 05:10 pm
Much better.
Here's a brainstorm, how about a table that provides some kind of brief side-...
Peter Amstutz
06:29 pm Revision e2999ea6 (arvados): 3686: verify repositories testing uses hard coded repo info.
Radhika Chippada
04:42 pm Bug #4399 (Resolved): [Tests] Fix whatever sometimes causes Jenkins tests to fail with ECONNREFUSED
We believe we've done this in the Workbench branch of #3021. If we see it happen again, let's reopen this. Brett Smith
04:30 pm Task #4902 (Resolved): Use a fixture instead of calling "run a pipeline" in the set of 8 "rerun p...
Applied in changeset arvados|commit:687f94f0e17dca2639ce1704b18f483f2e6bedb3. Radhika Chippada
04:16 pm Task #4902: Use a fixture instead of calling "run a pipeline" in the set of 8 "rerun pipeline ins...
Radhika,
commit:ddc4a3c is good to merge. Thanks.
Brett Smith
04:27 pm Task #5092 (Resolved): Review branch: 4902-use-fixture-to-rerun-pipelines
Brett reviewed this update. Radhika Chippada
04:14 pm Task #4939 (Resolved): Review and discuss
Peter Amstutz
04:11 pm Revision 7ee4b2b5 (arvados): Merge branch 'master' into 3686-sharing-repositories
Radhika Chippada
04:07 pm Revision 687f94f0 (arvados): closes #4902
Merge branch '4902-use-fixture-to-rerun-pipelines' Radhika Chippada
04:07 pm Story #5094 (New): [Workbench] Make pipeline rerun UI more like jobs'
#4878 changed the Workbench interface for running jobs to better present and explain the different options. I think ... Brett Smith
04:06 pm Revision 4884240e (arvados): Merge branch 'master' into 4902-use-fixture-to-rerun-pipelines
Radhika Chippada
03:48 pm Revision c6c4e8a6 (arvados): Merge branch 'master' into 3686-sharing-repositories
Radhika Chippada
02:54 pm Task #5088 (In Progress): Review branch: 3686-sharing-repositories (one more time, for repository...
Brett Smith
02:15 am Feature #4926 (Resolved): [Documentation] (recurring) Refresh user documentation
Radhika Chippada
12:42 am Revision 62028379 (arvados): refs #4878
Merge branch '4878-rerun-job' Radhika Chippada
12:40 am Revision a29c6fb9 (arvados): 4878: add back the tab buttons partial.
Radhika Chippada

01/27/2015

11:30 pm Task #5067 (Resolved): Review branch: 4878-rerun-job-bcs-wip
Applied in changeset arvados|commit:4926ecdc0ab989d329fbb75e447469ed4efee184. Brett Smith
11:30 pm Bug #4878 (Resolved): [Workbench] clarify purpose of "re-run latest" button on jobs#show.
Applied in changeset arvados|commit:4926ecdc0ab989d329fbb75e447469ed4efee184. Brett Smith
11:11 pm Bug #4878: [Workbench] clarify purpose of "re-run latest" button on jobs#show.
Brett Smith wrote:
> Because this branch is implementing a pure interface change, I don't believe it should be neces...
Brett Smith
07:46 pm Bug #4878: [Workbench] clarify purpose of "re-run latest" button on jobs#show.
Radhika Chippada wrote:
> * I removed the “re-run using same version” button. In the re-run dialog, if a job has no ...
Brett Smith
05:40 pm Bug #4878: [Workbench] clarify purpose of "re-run latest" button on jobs#show.
* I removed the “re-run using same version” button. In the re-run dialog, if a job has no newer version, I am hiding ... Radhika Chippada
11:25 pm Revision 4926ecdc (arvados): Merge branch '4878-rerun-job-bcs-wip'
Closes #4878, #5067. Brett Smith
11:09 pm Revision 82955105 (arvados): 4878: Refactor Workbench "Re-run job" button for more code reuse.
* Avoid adding new routes: add the modal directly to the job show
page, and submit the new work with the existing j...
Brett Smith
09:47 pm Task #5092 (Resolved): Review branch: 4902-use-fixture-to-rerun-pipelines
Radhika Chippada
09:46 pm Task #4902 (In Progress): Use a fixture instead of calling "run a pipeline" in the set of 8 "reru...
Implemented in 4902-use-fixture-to-rerun-pipelines branch. Radhika Chippada
09:43 pm Revision ddc4a3cd (arvados): 4902: re-run pipeline instance tests use fixtures instead of creatin...
Radhika Chippada
09:29 pm Task #5091 (Resolved): Review 5074-ruby-sdk-discovery-cache-wip
Brett Smith
09:28 pm Revision 59adfc15 (arvados): 5074: CLI SDK uses Google API client extensions from Ruby SDK.
Brett Smith
09:22 pm Revision 0f556c8b (arvados): 5074: Improve discovery document caching in Ruby SDK.
* Report a warning if there's an error reading or parsing a cached
discovery document.
* Cache discovery documents ...
Brett Smith
08:59 pm Revision 77d1908a (arvados): 4878: update the popup display to not display radio button when only...
Radhika Chippada
08:55 pm Revision 6e43023a (arvados): Merge branch 'master' into 4878-rerun-job
Radhika Chippada
08:00 pm Bug #5074 (In Progress): [SDKs] CLI client and Ruby SDK should recover from (and avoid creating) ...
Brett Smith
06:43 pm Revision 643bf501 (arvados): refs #4523
Merge branch '4523-search-index' Radhika Chippada
06:30 pm Revision 194eaad9 (arvados): Merge branch 'master' into 3686-sharing-repositories
Radhika Chippada
06:28 pm Bug #4523: [Workbench] Search dialog giving error when searching in "All projects" in qr1hi
Tom, addressed all your comments. I also simplified has_description check further. Thanks. Radhika Chippada
03:18 pm Bug #4523: [Workbench] Search dialog giving error when searching in "All projects" in qr1hi
At commit:68bc991 on 4523-search-index, just a couple of minor suggestions:
* Instead of <code class="ruby">index_co...
Tom Clegg
06:20 pm Revision 1e133a2a (arvados): 4523: a little bit simpler script
Radhika Chippada
05:38 pm Revision 3957f3db (arvados): Merge branch 'master' into 4523-search-index
Radhika Chippada
05:00 pm Revision ef2d3688 (arvados): Merge branch '5087-fix-crunch-sigpipe-wip'
Closes #5087, #5089. Brett Smith
05:00 pm Revision 99a25735 (arvados): 5087: crunch-job installer feeds tar incrementally.
When the input we give to tar is large enough (greater than 4-5MiB),
writing it all in one shot causes tar to die, an...
Brett Smith
02:54 pm Story #3603: [Crunch] Design good Crunch task API, including considerations about "jobs-within-jo...
But, if we can't schedule things perfectly up-front, we can patch things over after-the-fact. Here's one idea:
Pe...
Brett Smith
02:21 pm Story #3603: [Crunch] Design good Crunch task API, including considerations about "jobs-within-jo...
Brett Smith wrote:
> This is the disconnect I probably spent the most time struggling with in the design: there is z...
Brett Smith
02:23 pm Revision 4a701056 (arvados): 4878: show only the re-run popup option
Radhika Chippada
01:27 am Revision 7079475c (arvados): Improved erorr message to make it clear what's a size and what's a t...
Misha Zatsman
01:06 am Revision 097d0c20 (arvados): Renamed BlockDigest's ToString() to String() to implement fmt.String...
Misha Zatsman

01/26/2015

10:51 pm Story #3603: [Crunch] Design good Crunch task API, including considerations about "jobs-within-jo...
Tom Clegg wrote:
> Brett Smith wrote:
> > maybe raise an exception if a WorkMethod assigns an instance variable—"Ot...
Brett Smith
04:25 pm Story #3603: [Crunch] Design good Crunch task API, including considerations about "jobs-within-jo...
Brett Smith wrote:
> maybe raise an exception if a WorkMethod assigns an instance variable—"Other WorkMethods won't ...
Tom Clegg
01:35 am Story #3603: [Crunch] Design good Crunch task API, including considerations about "jobs-within-jo...
Tom Clegg wrote:
> I think the question of what to put in @__main__@ is confusing in that we're putting a bunch of m...
Brett Smith
09:17 pm Revision 2cdf1644 (arvados): Merge branch 'master' into 4878-rerun-job
Radhika Chippada
08:54 pm Bug #4878: [Workbench] clarify purpose of "re-run latest" button on jobs#show.
Radhika Chippada wrote:
> Branch 4878-rerun-job ready for review.
Reviewing commit:2926892
h2. The story
I ...
Brett Smith
08:51 pm Revision fcd5763d (arvados): Wording tweaks for doc.arvados.org.
No issue # Ward Vandewege
08:50 pm Story #2659: [Workbench] Anonymous user can access publicly shared data using Workbench and curl
There is now an active customer request around this. Customer would like to create a project to share with his team. ... Jonathan Sheffi
08:04 pm Feature #5090 (Resolved): [Documentation] Add some direct links on doc.arvados.org to the most us...
After this, the doc.arvados.org content can appear at the arvados.org root, and visitors will still be able to find a... Tom Clegg
07:43 pm Task #5067 (In Progress): Review branch: 4878-rerun-job-bcs-wip
Brett Smith
07:02 pm Revision 9b4131b9 (arvados): 5087: crunch-job installer feeds tar incrementally.
When the input we give to tar is large enough (greater than 4-5MiB),
writing it all in one shot causes tar to die, an...
Brett Smith
06:35 pm Bug #4232: [Workbench] Pipeline instances with many components should render quickly (on pipeline...
Timed a few runs again. Here on the qr1hi shell:... Phil Hodgson
04:47 pm Revision a86762d9 (arvados): 4232: remove "dependencies" entries from examples in the tutorials i...
Phil Hodgson
04:05 pm Revision 0ba8a5a0 (arvados): Merge branch '4340-arv-ws-fix-ssl-warning'
Closes #4340 Ward Vandewege
04:04 pm Revision f5d68241 (arvados): Merge branch 'master' into 4340-arv-ws-fix-ssl-warning
Ward Vandewege
04:04 pm Revision 71a9cb71 (arvados): A few tweaks based on review feedback.
refs #4340 Ward Vandewege
04:03 pm Revision 9ac2a7d6 (arvados): 4232: remove uselessness (commented out code and other wastes of spa...
Phil Hodgson
03:55 pm Bug #5010 (Resolved): [Workbench] Trash button on collections lists should set expires_at instead...
Applied in changeset arvados|commit:e89251c160ae409f8af2f9ecae5ffb210ccd0a8d. Tim Pierce
03:53 pm Bug #5010: [Workbench] Trash button on collections lists should set expires_at instead of moving ...
Tim Pierce wrote:
> Thanks for checking the integration tests. I've removed those assertions at commit:ffa928f
T...
Brett Smith
03:27 pm Bug #5010: [Workbench] Trash button on collections lists should set expires_at instead of moving ...
Thanks for checking the integration tests. I've removed those assertions at commit:ffa928f
This code now passes a...
Tim Pierce
03:12 pm Bug #5010: [Workbench] Trash button on collections lists should set expires_at instead of moving ...
Tim Pierce wrote:
> Tests added at commit:6f3e7bf
These are great, thanks for following up on that. I like every...
Brett Smith
03:52 pm Revision e89251c1 (arvados): Merge branch '5010-trash-button-for-collections'
Fixes #5010. Tim Pierce
03:24 pm Revision ffa928f7 (arvados): 5010: fixed integration test
Fixed a failing integration test that checked for the presence of a
collection in the Home project after being delete...
Tim Pierce
03:08 pm Revision f8af0c6c (arvados): Merge branch 'master' into 4232-slow-pipes-n-jobs
Phil Hodgson
03:01 pm Story #3532: [Keep] Keepstore queries API server to verify tokens
After talking to Tim, I am assigning this to me. Tim will guide me through the development as needed. Radhika Chippada

01/25/2015

09:18 pm Story #3603: [Crunch] Design good Crunch task API, including considerations about "jobs-within-jo...
Brett Smith wrote:
> When this file actually is the Crunch script named in a job, then the code under this condition...
Tom Clegg
03:05 pm Story #3603: [Crunch] Design good Crunch task API, including considerations about "jobs-within-jo...
Let me talk about implementation concerns for a minute, because I think that's my main source of worry about the idea... Brett Smith
12:25 am Story #3603: [Crunch] Design good Crunch task API, including considerations about "jobs-within-jo...
Here's a strawman for "how modules call one another's methods":... Tom Clegg
08:04 am Revision e79f335b (arvados-dev): writable: 'status' subcommand changes...
- allow users with RW to use it
- fix bug where, when a repo's writable status is checked, the global status
...
Sitaram Chamarty
03:23 am Revision 16c5d87a (arvados): 3686: improve manage account page test to click on the repository link.
Radhika Chippada
02:50 am Revision 22ded15b (arvados): 3686: enhance manage account test to also verify a writable repository.
Radhika Chippada
 

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