Activity

From 06/21/2015 to 07/20/2015

07/20/2015

09:52 pm Bug #6663: [Documentation] Document git repository setup
I might be missing something, but as a new user I expected `arvados-git-httpd` and the `git` package itself to be all... Joshua Randall
09:32 pm Bug #6663: [Documentation] Document git repository setup
Josh, your original bug report made me realize we have a number of deficiencies here. I hope you don't mind if I exp... Brett Smith
09:42 pm June development review: Writing to FUSE on Red Hat installs
A couple of major new developments landed in the last Arvados development sprint. Whether you're using Arvados to an... Brett Smith
07:57 pm Story #6473: [SDKs] arv-ws supports an option to show events starting from a given time
commit:17e8c59deca04137f66ece7837f96599ff82f4de
* Enhanced PollClient to support last_log_id and added additional ...
Radhika Chippada
03:25 pm Story #6473: [SDKs] arv-ws supports an option to show events starting from a given time
- Changes to EventClient look good.
- You need to implement the same last_log_id feature in PollClient. Please ex...
Peter Amstutz
01:13 pm Story #6473: [SDKs] arv-ws supports an option to show events starting from a given time
Branch 6473-fetch-events-starting-at at commit:1c6515a4445e9fd79961c9c8caf21528f16d9399
- The subscribe method now...
Radhika Chippada
07:44 pm Revision 106df13f (arvados): closes #6587
Merge branch '6587-workbench-webshell-login-documentation' Radhika Chippada
07:42 pm Revision 7879727a (arvados): Merge branch 'master' into 6587-workbench-webshell-login-documentation
Radhika Chippada
07:40 pm Story #6465 (Resolved): [Tests] Optimize workbench integration tests
Applied in changeset arvados|commit:ddb83a220cd6f3b62171c3c374c58e553d82a5d6. Manoj Malipeddu
07:26 pm Story #6465: [Tests] Optimize workbench integration tests
Explained in chat:
Because the test is actually checking that the Textile rendering is turning "Link to object" i...
Peter Amstutz
06:58 pm Story #6465: [Tests] Optimize workbench integration tests
I'm a little puzzled by this test. Doesn't "refute_includes" check that @"Link to object"@ is *not* in the response?... Peter Amstutz
03:38 pm Story #6465: [Tests] Optimize workbench integration tests
In commit:7253b0d4cdf9612a4c0de0ca849979cec5e8d382:
Changed tests to use the wildcard match less often.
Manoj Malipeddu
07:39 pm Revision 17e8c59d (arvados): 6473: PollClient also supports last_log_id argument.
Radhika Chippada
07:36 pm Revision ddb83a22 (arvados): closes #6465
Merge branch '6465-optimize-workbench-integration-tests' Manoj Malipeddu
07:35 pm Revision c4c8e9b0 (arvados): 6465: Added back bundled with
Manoj Malipeddu
07:35 pm Bug #6661 (Resolved): install docs reference non existant debian/ubuntu package
Applied in changeset arvados|commit:cd25f265349e86fab2fbe81959747ce112986806. Brett Smith
07:33 pm Story #3408 (Resolved): [Keep] Implement Production Data Manager
Marking as resolved because the last push from Misha is merged and further development will occur through new stories... Peter Amstutz
07:31 pm Revision 6a2f46b1 (arvados): Merge branch 'master' into 6465-optimize-workbench-integration-tests
Manoj Malipeddu
07:27 pm Revision cd25f265 (arvados): 6661: Install docs refer to arvados-git-httpd package and binary.
The code refers to itself as arv-git-httpd, but the package is named
arvados-git-httpd, and includes the binary under...
Brett Smith
07:24 pm Revision 2ad8f9cc (arvados): 6465: Added comments to explain test "find a project and edit descri...
with link to object". Manoj Malipeddu
07:24 pm Bug #6659: [SDKs] arv-copy dumps a stack trace when dst_git_push_url == None
At the point in time I reported this, it was because of #6605 - I only had https access configured and this did not w... Joshua Randall
07:11 pm Bug #6659: [SDKs] arv-copy dumps a stack trace when dst_git_push_url == None
Josh, can you please let us know what your API server has for the @git_repo_ssh_base@ and @git_repo_https_base@ setti... Brett Smith
07:22 pm Bug #6674 (Resolved): [Documentation] Don't recommend nginx16 Software Collection
We always use nginx in conjunction with Phusion Passenger. The Phusion Passenger repository includes its own nginx a... Brett Smith
07:18 pm Bug #4560 (Closed): [Documentation] We need a link to arv-copy in user guide.
We did #5288 instead. Brett Smith
07:17 pm Bug #6658: arv-copy dumps a stack track when `git` has an error
I guess I would expect something more succinct like:
"Command exited with error %d: `%s`\n%s\n" % (command_exit_co...
Joshua Randall
06:52 pm Bug #6658: arv-copy dumps a stack track when `git` has an error
I just pushed a fix for the name error in arvados.util. However, this just means that you'll now see a stack trace f... Brett Smith
06:51 pm Revision 6e5e1c72 (arvados): Merge branch 'master' into 6473-fetch-events-starting-at
Radhika Chippada
06:50 pm Revision b2310164 (arvados): 6658: Fix exception name errors in PySDK arvados.util.
Refs #6658. Brett Smith
06:39 pm Bug #6657: [SDKs] arv-copy has an unhelpful error message when `git` command is not available
We should implement this exactly as specified. arv-copy should check for git *up front* so it can report this error ... Brett Smith
06:38 pm Bug #6656 (Resolved): python-arvados-python-client package should depend on git
I'm not sure we want to make the entire package depend on git, because you can use a lot of it (the underlying SDK, t... Brett Smith
06:36 pm Revision d30c7f8b (arvados-dev): 6656: python-arvados-python-client Recommends: git.
Because arv-copy uses it. Refs #6656. Brett Smith
06:36 pm Revision d30c7f8b (arvados): 6656: python-arvados-python-client Recommends: git.
Because arv-copy uses it. Refs #6656. Brett Smith
06:23 pm Revision b08e9735 (arvados): 6587: minor text updates
Radhika Chippada
06:14 pm Bug #6652: [API] Error "Owner uuid must refer to a user with a username" when creating a new repo...
In commit:61d432f332dd9314f8c4cd57c2393e80e8ecef59:
System menu test now skips repositories and test has been move...
Manoj Malipeddu
06:09 pm Revision 61d432f3 (arvados): 6652: Moved system menu test into application_layout_test.
Manoj Malipeddu
06:05 pm Task #6671 (Resolved): Review branch: 6619-doc-update
Radhika Chippada
05:29 pm Task #6671 (In Progress): Review branch: 6619-doc-update
Peter Amstutz
02:45 pm Task #6671 (Resolved): Review branch: 6619-doc-update
Radhika Chippada
06:05 pm Story #6617 (Resolved): [Workbench] [Documentation] Display https url in repositories panel in ma...
Applied in changeset arvados|commit:f7c152d3ca9a753812bd7729ceb6cb8a23b12fce. Radhika Chippada
05:44 pm Story #6617: [Workbench] [Documentation] Display https url in repositories panel in manage_accoun...
Reviewing 6617-doc-repo-https-url
* "If you are prompted for username and password when you try to git clone using...
Peter Amstutz
01:30 pm Story #6617: [Workbench] [Documentation] Display https url in repositories panel in manage_accoun...
Verified that the clone with https url works in staging. Merged into master. Manoj Malipeddu
05:59 pm Revision a1ed06fc (arvados): Merge branch 'master' into 6587-workbench-webshell-login-documentation
Radhika Chippada
05:56 pm Revision ee29db4a (arvados): refs #6619
Merge branch '6619-doc-update' Radhika Chippada
05:55 pm Revision 70e832c1 (arvados): 6619: git config update
Radhika Chippada
05:51 pm Revision e0ab53ea (arvados): Merge branch 'master' into 6619-doc-update
Radhika Chippada
05:50 pm Revision f7c152d3 (arvados): closes #6617
Merge branch '6617-doc-repo-https-url' Radhika Chippada
05:50 pm Revision 0b19163c (arvados): 6617: minor text update
Radhika Chippada
05:49 pm Feature #6619: [Deployment] [Documentation] Install system-wide git credential helper for arvados...
"Configure git to use the ARVADOS_API_TOKEN environment variable to authenticate to gitolite."
That's not quite ri...
Peter Amstutz
05:47 pm Revision 4a35a164 (arvados): Merge branch 'master' into 6617-doc-repo-https-url
Radhika Chippada
05:04 pm Task #6673 (Resolved): merge 6221-write-trash-list only once keepstore is deployed with -no-delet...
Peter Amstutz
03:36 pm Revision 37e6d6e6 (arvados): Merge branch 'master' into 6473-fetch-events-starting-at
Radhika Chippada
03:35 pm Revision 7253b0d4 (arvados): 6465-Made changes that were recommended.
Manoj Malipeddu
03:31 pm Task #6670 (In Progress): Review branch: 6617-doc-repo-https-url
Peter Amstutz
01:51 pm Task #6670 (Resolved): Review branch: 6617-doc-repo-https-url
Radhika Chippada
03:13 pm Task #6660 (Resolved): Display https url in repositories panel in manage_account page
Radhika Chippada
03:04 pm Task #6536 (In Progress): Review branch: 6473-fetch-events-starting-at
Peter Amstutz
02:49 pm Task #6633 (Resolved): Review 6610-login-without-ssh-key
Tom Clegg
02:49 pm Task #6618 (Resolved): Review 5898-listen-race
Tom Clegg
02:47 pm Bug #6499: [Documentation] Review 6438-multiplatform-install-guide-wip
Comments on 6438-multiplatform-install-guide-TC at commit:cd6710e.
I'm not sure how I feel about including instruc...
Brett Smith
02:45 pm Task #6629 (Resolved): Review 6221-write-trash-list
Peter Amstutz
02:35 pm Revision edb109c2 (arvados): 6617: updated git config doc
Radhika Chippada
02:34 pm Revision caa9e89d (arvados): Revert "6362: Allow config/application.yml to override environments/...
In Rails 3 (actionpack 3.2.17), changing asset configuration to
production settings in load_config.rb breaks the rake...
Tom Clegg
02:33 pm Revision 1d5e009a (arvados): Revert "Revert "6362: Change config precedence order.""
This reverts commit 61187968f0e9268430b967ce37a79d9384ec7e3c.
Wrong commit reverted.
refs #6362
Tom Clegg
02:32 pm Revision 78e32484 (arvados): 6619: add git config to shell setup page.
Radhika Chippada
02:27 pm Revision 61187968 (arvados): Revert "6362: Change config precedence order."
In Rails 3 (actionpack 3.2.17), changing asset configuration to
production settings in load_config.rb breaks the rake...
Tom Clegg
02:15 pm Task #6648 (In Progress): Review 6438-multiplatform-install-guide-TC
Brett Smith
01:51 pm Task #6665 (Resolved): Review Branch 6617-display-https-url
Radhika Chippada
01:49 pm Revision 77aeb6fd (arvados): 6617: add note if prompted for user name during git clone using http...
Radhika Chippada
01:37 pm Revision 94afae23 (arvados): Merge branch 'master' into 6617-display-https-url
Radhika Chippada
01:29 pm Revision a1e6ebc7 (arvados): refs #6617
Merge branch '6617-display-https-url' Manoj Malipeddu
01:19 pm Revision 84698df0 (arvados): 6473: create ancestor object before subscribe
Radhika Chippada

07/18/2015

11:21 pm Task #6503 (Resolved): Parameterize the upload script to upload packages for the specified distri...
Brett Smith
11:21 pm Task #6502 (Resolved): Extract existing uploader code from run-build-packages.sh into a separate ...
Brett Smith
11:20 pm Revision 1e766639 (arvados-dev): 6497: Separate package build and uploader scripts.
This lets us avoid redundant uploads as we build for multiple targets,
and lets us better customize the upload proces...
Brett Smith
09:08 pm Bug #6497 (In Progress): [Deployment] Separate package upload portions of run-build-packages.sh t...
Brett Smith
09:01 pm Story #6473: [SDKs] arv-ws supports an option to show events starting from a given time
Tom Clegg wrote:
> My understanding of the feature we want:
> * Give me events matching A,B,C that happen after tim...
Brett Smith
08:51 pm Bug #6666: [Node Manager] Sometimes raises GoogleBaseError: u'Invalid fingerprint.'
The exception is ugly, but FWIW, this exception appearing in the logs is not a huge deal. It means the node's metada... Brett Smith
05:37 pm Revision e621ee47 (arvados): Merge branch 'master' of git.curoverse.com:arvados into 6473-fetch-e...
Radhika Chippada
01:21 pm Revision 1c6515a4 (arvados): 6473: include last_log_id when start_time argument is provided.
Radhika Chippada
06:34 am Revision 706f34d3 (arvados): Revert "6362: Update bootstrap gem."
This reverts commit ed8897b942f147afccf8eeac1025861ffe2f1690.
refs #6362
Tom Clegg

07/17/2015

08:11 pm Revision 9ac57b0b (arvados): Merge branch '6362-asset-config' refs #6362
Tom Clegg
08:06 pm Revision 50419ea6 (arvados): 6221: SendTrashLists only return non-nil array on error.
Peter Amstutz
07:53 pm Revision 210883bc (arvados): Merge branch 'master' into 6473-fetch-events-starting-at
Radhika Chippada
07:46 pm Bug #6221: [Data Manager] implement Delete
Peter Amstutz wrote:
> Tom Clegg wrote:
>
> > You could de-duplicate TestSendTrashListError and TestSendTrashList...
Tom Clegg
05:30 pm Bug #6221: [Data Manager] implement Delete
Tom Clegg wrote:
> You could de-duplicate TestSendTrashListError and TestSendTrashListError2 by doing something li...
Peter Amstutz
02:53 pm Bug #6221: [Data Manager] implement Delete
Peter Amstutz wrote:
> Tom Clegg wrote:
> > Indeed, error reporting for "mtime mismatch" is better now, thanks. (Pr...
Tom Clegg
07:44 pm Revision 91b7b7fd (arvados): 6221: Pass server to sendTrashListError(), use NewUnstartedServer()
Peter Amstutz
06:57 pm Task #6665 (In Progress): Review Branch 6617-display-https-url
Tom Clegg
02:29 pm Task #6665 (Resolved): Review Branch 6617-display-https-url
Manoj Malipeddu
06:56 pm Story #6617: [Workbench] [Documentation] Display https url in repositories panel in manage_accoun...
Changes look good, thanks.
We need to add guidance about how to authenticate when using the @https://@ urls. I'm o...
Tom Clegg
02:26 pm Story #6617: [Workbench] [Documentation] Display https url in repositories panel in manage_accoun...
In commit:db2584826ed9aadb162b8bd6d25e164565bbab8b
Display https url in repositories panel in manage_account page
...
Manoj Malipeddu
01:02 pm Story #6617 (In Progress): [Workbench] [Documentation] Display https url in repositories panel in...
Radhika Chippada
06:48 pm Story #6465: [Tests] Optimize workbench integration tests
Comments:
In "find a project and edit description to html description"...
Peter Amstutz
06:42 pm Bug #6652: [API] Error "Owner uuid must refer to a user with a username" when creating a new repo...
In commit:4999699d7614f214eb8718b85c5c30e9fb382c23:
Added tests for the system menu and the pages in the dropdown ...
Manoj Malipeddu
06:39 pm Revision 4999699d (arvados): 6652-Added tests for the system menu and each of the pages in the
dropdown menu. Manoj Malipeddu
06:20 pm Revision acacdd86 (arvados): 6617: update documentation to include https git url
Radhika Chippada
06:04 pm Story #6473: [SDKs] arv-ws supports an option to show events starting from a given time
I think the code, the flag description, and the feature we wanted are three different things.
Flag description: "A...
Tom Clegg
05:32 pm Revision f51b562b (arvados): 6221: SendTrashLists() returns errors. Tests updated.
Peter Amstutz
03:37 pm Feature #6667 (New): [SDKs] Support HTTP proxy configuration using env vars
In some setups, client cannot make HTTP requests directly to Arvados, but can connect through a (non-transparent) HTT... Tom Clegg
03:11 pm Revision 85b29e4d (arvados): Merge branch 'master' into 6587-workbench-webshell-login-documentation
Radhika Chippada
03:10 pm Bug #6604 (Resolved): [Workbench] Notification menu should not prompt the user to upload an SSH k...
Applied in changeset arvados|commit:702ce6c3da9a1b09a2ed546fd3da775d21bd703b. Manoj Malipeddu
03:07 pm Bug #6604: [Workbench] Notification menu should not prompt the user to upload an SSH key when a W...
LGTM Radhika Chippada
03:08 pm Task #6662 (In Progress): Document https url in repositories
Radhika Chippada
01:11 pm Task #6662 (Resolved): Document https url in repositories
Radhika Chippada
03:06 pm Revision 702ce6c3 (arvados): closes #6604
Merge branch '6604-notification-menu-no-prompt' Manoj Malipeddu
03:05 pm Task #6650 (Resolved): Review Branch 6604-notification-menu-no-prompt
Radhika Chippada
02:54 pm Revision fb9730d1 (arvados): 6587: Documentation to access an arvados VM using webshell. Updated ...
"checking environment" to also include webshell doc page link. Radhika Chippada
02:41 pm Bug #6666 (Duplicate): [Node Manager] Sometimes raises GoogleBaseError: u'Invalid fingerprint.'
arvados-node-manager 0.1.20150511215048 gave exception... Nico César
02:23 pm Bug #6664 (New): [Tests] Generate code coverage reports for Go code in Jenkins test suite
See
* https://blog.golang.org/cover
* https://github.com/mattn/goveralls
* http://jmcvetta.github.io/blog/2013/08/...
Tom Clegg
02:21 pm Revision db258482 (arvados): 6617-Display https url in repositories panel in manage_account page ...
if https url is being shows in user_manage_account_test. Manoj Malipeddu
01:20 pm Bug #6663 (Resolved): [Documentation] Document git repository setup
The install docs don't say much about setting up git repositories. They should explain:
* Git repositories must l...
Joshua Randall
01:08 pm Bug #6661: install docs reference non existant debian/ubuntu package
The same goes for farther down in the docs in terms of the command name (on my system it appears to be `arvados-git-h... Joshua Randall
01:06 pm Bug #6661 (Resolved): install docs reference non existant debian/ubuntu package
The install docs at: http://doc.arvados.org/install/install-arv-git-httpd.html
Refer to installing the git service...
Joshua Randall
01:07 pm Revision 6ba447b8 (arvados): 6604-Updated assert statements.
Manoj Malipeddu
01:04 pm Task #6660 (Resolved): Display https url in repositories panel in manage_account page
Radhika Chippada
12:58 pm Bug #6659 (New): [SDKs] arv-copy dumps a stack trace when dst_git_push_url == None
# arv-copy -vvvv --src qr1hi --dst 7lnae --project-uuid 7lnae-j7d0g-9r429yt0rcrdl8x --dst-git-repo jr17/qr1hi qr1hi-p... Joshua Randall
12:50 pm Bug #6658 (New): arv-copy dumps a stack track when `git` has an error
When git encounters a Permission denied error, I get the following output from arv-copy:
# arv-copy --verbose --s...
Joshua Randall
12:39 pm Bug #6657 (Resolved): [SDKs] arv-copy has an unhelpful error message when `git` command is not av...
When arv-copy is asked to copy a pipeline template recursively to a --dst-git-repo, it requires the `git` command in ... Joshua Randall
12:36 pm Bug #6656 (Resolved): python-arvados-python-client package should depend on git
arv-copy from python-arvados-python-client requires the `git` binary for some actions, but the package does not depen... Joshua Randall

07/16/2015

10:02 pm Revision c9182875 (arvados-dev): run-deploy.sh improvements: remove the need for a .ssh/config en...
the shortname of each API server. Thanks for the suggestion Nico.
No issue #
Ward Vandewege
10:02 pm Revision c9182875 (arvados): run-deploy.sh improvements: remove the need for a .ssh/config entry for
the shortname of each API server. Thanks for the suggestion Nico.
No issue #
Ward Vandewege
08:46 pm Bug #6652: [API] Error "Owner uuid must refer to a user with a username" when creating a new repo...
This might be easy to fix by moving @self.owner_uuid ||= current_user.uuid@ into a @before_validation@ method.
(Ob...
Tom Clegg
08:15 pm Bug #6652 (Resolved): [API] Error "Owner uuid must refer to a user with a username" when creating...
Ways to create a new repo:
* Admin gear menu → Repositories → "Add a new repository" button -- *fail*
* U...
Radhika Chippada
08:17 pm Revision cd6710e9 (arvados): 6438: Back out dependency on lsb_release command.
Tom Clegg
08:12 pm Revision f63e86a3 (arvados): 6221: Add SendTrashLists() test. Propagate errors from BuildTrashLi...
Peter Amstutz
08:00 pm Bug #6221: [Data Manager] implement Delete
Tom Clegg wrote:
> Indeed, error reporting for "mtime mismatch" is better now, thanks. (Printing actual/expected mti...
Peter Amstutz
03:04 pm Bug #6221: [Data Manager] implement Delete
Indeed, error reporting for "mtime mismatch" is better now, thanks. (Printing actual/expected mtime would be even bet... Tom Clegg
01:30 pm Bug #6221 (In Progress): [Data Manager] implement Delete
Peter Amstutz
01:29 pm Bug #6221: [Data Manager] implement Delete
Tom Clegg wrote:
> HostPort() now returns @scheme://host:port@ and should be renamed accordingly.
>
> trash_list....
Peter Amstutz
07:37 pm Bug #6651 (New): "This website is under heavy load" error makes a parsing error
/usr/local/arvados/install-arvados-tokens.rb production... Nico César
07:30 pm Task #6650 (Resolved): Review Branch 6604-notification-menu-no-prompt
Manoj Malipeddu
07:20 pm Revision 12ca8452 (arvados): Merge branch '5898-listen-race' refs #5898
Tom Clegg
07:18 pm Revision 1856a3a1 (arvados): Merge branch 'master' of git.curoverse.com:arvados into 6465-optimiz...
Manoj Malipeddu
07:17 pm Bug #6649 (New): [Documentation] webshell installation
The documentation of how to install shellinabox and libpam_arvados is missing.
We've done all this in puppet for ...
Nico César
07:15 pm Bug #6604: [Workbench] Notification menu should not prompt the user to upload an SSH key when a W...
In commit:25e646a708d1d91aebcf8db80b8ae1fafa044034:
Removed notification for SSH key if web shell is configured.
...
Manoj Malipeddu
03:07 pm Bug #6604 (In Progress): [Workbench] Notification menu should not prompt the user to upload an SS...
Manoj Malipeddu
07:13 pm Bug #6499: [Documentation] Review 6438-multiplatform-install-guide-wip
6438-multiplatform-install-guide-TC fixes some stumbling blocks I've run into so far.
(Still more testing to do.)
Tom Clegg
07:12 pm Task #6648 (Resolved): Review 6438-multiplatform-install-guide-TC
Tom Clegg
07:03 pm Revision 3267722e (arvados): 6438: Add missing steps to SSO installation.
Tom Clegg
07:01 pm Revision 25e646a7 (arvados): 6604- Disabled SSH public key notification when shell_in_a_box_url
is configured. Manoj Malipeddu
06:55 pm Story #6647 (New): Choose an option to make better service discoveries in deployments
One of the main pain points is that a admin user has to add the new resource to the API server in order to be active.... Nico César
06:39 pm Revision 9ba9d82d (arvados): 6438: Use urandom instead of md5(hostname) for UUID. Avoid using Rub...
Tom Clegg
06:39 pm Revision b687f3af (arvados): 6438: Merge debian and ubuntu sections. The same recipe works for both.
Tom Clegg
06:39 pm Revision 56cd4a8d (arvados): 6438: Add missing "apt-get update". Give a command to add the packag...
Replace version table with $(lsb_release -cs). Tom Clegg
06:39 pm Revision 64c1ab20 (arvados): 6438: Use uuid_prefix (more) consistently.
Tom Clegg
06:39 pm Revision 030f8a1f (arvados): 6438: Add specific commands for nginx16 and postgresql92 Software Co...
Tom Clegg
06:39 pm Revision baf9f2f3 (arvados): 6438: Drop wget dependency. Update ./configure flags for Ruby 2.1.6.
Tom Clegg
06:39 pm Revision eaa31258 (arvados): 6438: Bring back package dependencies for "build Ruby from source" o...
These used to be documented earlier in the process, but were removed. Tom Clegg
06:39 pm Revision 5eeae0d3 (arvados): 6438: Add some missing steps to rvm recipe. Install rvm as root.
Tom Clegg
06:33 pm Revision 041af479 (arvados): 5898: Use lsof instead of fuser -- fuser 1234/tcp just hangs on some...
Tom Clegg
05:49 pm Feature #6619 (Resolved): [Deployment] [Documentation] Install system-wide git credential helper ...
Nico César
05:17 pm Bug #6643 (Resolved): [FUSE] Crash on del self._by_uuid[obj.cache_uuid]
It appears that when certain API server requests fail, the internal state of FUSE is left in an inconsistent state th... Peter Amstutz
03:01 pm Story #6642 (New): [API] Include a mechanism to automatically trust some clients
"Trusted client setting" in http://doc.arvados.org/install/install-workbench-app.html deployments more complicated.
...
Nico César
02:54 pm Revision 22f68d30 (arvados): 6473: remove incorrect format tests; it appears that #6451 strikes a...
Radhika Chippada
01:54 pm Revision 7da85b85 (arvados): 6221: Add trash_list_test.go
Peter Amstutz
01:05 pm Revision a45c162a (arvados): 6473: some more error tests
Radhika Chippada
01:04 pm Bug #6627 (Closed): [Workbench] bundler isnt installed
Oops! that was an oversight from my side...
closing the ticket
Nico César
11:37 am Bug #6640 (Resolved): [Workbench] Ensure projects menu consistently shows all "my projects"
h2. Background
I (Brett) have attached two screenshots of the projects menu pulldown in two tabs opened back-to-ba...
Brett Smith
03:47 am Story #6473: [SDKs] arv-ws supports an option to show events starting from a given time
What changed:
* Added additional start_time argument to arv-ws. Expected format is listed as "YYYY-MM-DD hh:mm:ss"...
Radhika Chippada
03:32 am Story #6473 (In Progress): [SDKs] arv-ws supports an option to show events starting from a given ...
Radhika Chippada
03:28 am Revision ca8e8224 (arvados): Merge branch 'master' into 6473-fetch-events-starting-at
Radhika Chippada
03:23 am Revision 7748c0b5 (arvados): 6473: add start_time additional argument to arv-ws
Radhika Chippada
03:14 am Revision ef2d37b1 (arvados-dev): Make sure jessie packages end up in the jessie repository.
No issue # Ward Vandewege
03:14 am Revision ef2d37b1 (arvados): Make sure jessie packages end up in the jessie repository.
No issue # Ward Vandewege
02:59 am Revision 9cc673cf (arvados): We need to force-tag the arvados/jobs docker image.
No issue # Ward Vandewege
02:59 am Revision 9cc673cf (arvados-dev): We need to force-tag the arvados/jobs docker image.
No issue # Ward Vandewege
02:53 am Revision 86cc2e4b (arvados): freight is already smart enough to do atomic updates.
No issue # Ward Vandewege
02:53 am Revision 86cc2e4b (arvados-dev): freight is already smart enough to do atomic updates.
No issue # Ward Vandewege
01:55 am Revision 30945c85 (arvados-dev): Add dockerfiles/build-all-build-containers.sh script
refs #6504 Ward Vandewege
01:55 am Revision 30945c85 (arvados): Add dockerfiles/build-all-build-containers.sh script
refs #6504 Ward Vandewege
01:33 am Revision 7365909f (arvados): arvdock realclean/deepclean should not delete images tagged as arvad...
No issue # Ward Vandewege

07/15/2015

11:27 pm Bug #6638 (Resolved): [Deployment] Python package backports should declare their C dependencies
h2. Original bug report
If installing on a bare bones debian or ubuntu machine, the python-arvados-python-client p...
Joshua Randall
09:50 pm Bug #6635: [Documentation] document installation of node manager
Document it for who? Ourselves, or the public?
The latter is lower-priority, since people installing dynamic clus...
Brett Smith
05:27 pm Bug #6635 (New): [Documentation] document installation of node manager
For example, it requires a system token created with
arv api_client_authorization create_system_auth \
--sc...
Ward Vandewege
09:35 pm Bug #5898 (Resolved): [Tests] Race condition in test_KeepProxyTest1 (tests.test_keep_client.KeepP...
Applied in changeset arvados|commit:8e1477dea24ed50b09c055092314fb6522c5a114. Tom Clegg
09:30 pm Bug #5898: [Tests] Race condition in test_KeepProxyTest1 (tests.test_keep_client.KeepProxyTestCas...
10 seconds, done. Thanks. Tom Clegg
09:07 pm Bug #5898: [Tests] Race condition in test_KeepProxyTest1 (tests.test_keep_client.KeepProxyTestCas...
review d2b707bb7c6dde27095130296f05e998ab90f3e1
LGTM .. I 'll make timeout=10 since 2 seconds could be too littl...
Nico César
09:30 pm Revision 036140f3 (arvados): 6221: Fix error reporting. Fix keepstore not to delete blocks with ...
mtime. Add unit test for BuildTrashLists. Peter Amstutz
09:29 pm Revision 8e1477de (arvados): Merge branch '5898-listen-race' closes #5898
Tom Clegg
09:28 pm Revision df070cb9 (arvados): 5898: Wait for servers to start *listening* before running integrati...
Tom Clegg
09:13 pm Bug #6627: [Workbench] bundler isnt installed
The first section of the page is "Install prerequisites," and "Ruby 2.1 and bundler" is included in that list. It al... Brett Smith
02:00 pm Bug #6627 (Closed): [Workbench] bundler isnt installed
I follow the documentation http://doc.arvados.org/install/install-workbench-app.html and thwe step /usr/local/bin/ar... Nico César
08:24 pm Revision c790738a (arvados): 6362: Allow config/application.yml to override environments/*.rb in ...
Tom Clegg
08:10 pm Bug #6610 (Resolved): [API] [Webshell] shell accounts should be created even if the user has not ...
Applied in changeset arvados|commit:97374cec874aaaaeb92eeb962bf580bdba199be9. Tom Clegg
06:46 pm Bug #6610: [API] [Webshell] shell accounts should be created even if the user has not added an SS...
Disregard previous comment, misunderstood the purpose of this change. LGTM. Peter Amstutz
06:39 pm Bug #6610: [API] [Webshell] shell accounts should be created even if the user has not added an SS...
Peter Amstutz wrote:
> Does it make sense to include VMs without ssh keys even when webshell is not enabled in the w...
Peter Amstutz
06:30 pm Bug #6610: [API] [Webshell] shell accounts should be created even if the user has not added an SS...
Does it make sense to include VMs without ssh keys even when webshell is not enabled in the workbench configuration? Peter Amstutz
08:01 pm Revision ed8897b9 (arvados): 6362: Update bootstrap gem.
See https://github.com/twbs/bootstrap-sass/issues/653 Tom Clegg
07:47 pm Revision 97374cec (arvados): Merge branch '6610-login-without-ssh-key' closes #6610
Tom Clegg
07:41 pm Revision 0af57aeb (arvados): 6362: Update bootstrap gem.
Tom Clegg
07:41 pm Revision 318e3d18 (arvados): 6362: Change config precedence order.
Before: environments/*.rb, Rails defaults, application.yml,
application.default.yml.
After: application.yml, applica...
Tom Clegg
07:37 pm Revision 14dbdda4 (arvados): Merge branch 'master' of git.curoverse.com:arvados into 6465-optimiz...
Manoj Malipeddu
07:37 pm Story #6465: [Tests] Optimize workbench integration tests
In commit:c3a7bb61e982ff5b0747204b79c4ca759c19b537:
Added tests to collections_controller_test:
can view empty co...
Manoj Malipeddu
03:57 pm Story #6465 (In Progress): [Tests] Optimize workbench integration tests
Manoj Malipeddu
12:36 pm Story #6465: [Tests] Optimize workbench integration tests
In commit:e59b42354a10079ecd579a1dbe53c39a20d05313:
Added test to projects_controller_test:
#{username} can see p...
Manoj Malipeddu
07:36 pm Feature #6619: [Deployment] [Documentation] Install system-wide git credential helper for arvados...
Nico Cesar wrote:
> (.. I agree on all the stuff cutted here...)
>
> Tom Clegg wrote:
> > I figured using sys...
Ward Vandewege
07:28 pm Revision c3a7bb61 (arvados): 6465-Added tests to collections_controller_test, removed 4 tests
from collections_test and one test from collections_upload_test. Manoj Malipeddu
07:23 pm Bug #6221: [Data Manager] implement Delete
HostPort() now returns @scheme://host:port@ and should be renamed accordingly.
trash_list.go is shamelessly copied...
Tom Clegg
06:32 pm Task #6632 (In Progress): Review Branch 6465-optimize-workbench-integration-tests
Peter Amstutz
03:58 pm Task #6632 (Resolved): Review Branch 6465-optimize-workbench-integration-tests
Manoj Malipeddu
05:31 pm Task #6633 (In Progress): Review 6610-login-without-ssh-key
Peter Amstutz
04:32 pm Task #6633 (Resolved): Review 6610-login-without-ssh-key
Tom Clegg
05:29 pm Revision a7d40e5a (arvados): Add datamanager tests. refs #3408
Peter Amstutz
05:29 pm Revision a7d40e5a (arvados-dev): Add datamanager tests. refs #3408
Peter Amstutz
05:14 pm Revision 0a0ca0b1 (arvados-dev): Build python3-websocket-client packages, which is now a dependen...
python3-docker-py, which is a dependency for arvados-docker-cleaner.
No issue #
Ward Vandewege
05:14 pm Revision 0a0ca0b1 (arvados): Build python3-websocket-client packages, which is now a dependency for
python3-docker-py, which is a dependency for arvados-docker-cleaner.
No issue #
Ward Vandewege
04:32 pm Revision 46da2daa (arvados): 6610: Include all user->VM login permission, even for users without ...
Tom Clegg
03:39 pm Task #6631 (In Progress): Review 6611-send-pull-list
Peter Amstutz
03:32 pm Revision eca9e074 (arvados): 6611: Send pull lists to keepstore
Peter Amstutz
03:20 pm Bug #6602: [Workbench] Pipeline components tab preloads all tasks; times out for jobs with many t...
(Summary of engineering discussion + some more detail)
h2. Current metrics
The current "scaling factor" metric ...
Tom Clegg
03:05 pm Task #6629 (In Progress): Review 6221-write-trash-list
Peter Amstutz
03:02 pm Task #6629 (Resolved): Review 6221-write-trash-list
Peter Amstutz
03:02 pm Revision 0d9da683 (arvados): Merge branch '6221-datamanager-delete' refs #6221
Peter Amstutz
03:02 pm Task #6615 (Resolved): Support sending trash lists from data manager
Peter Amstutz
03:02 pm Task #6620 (Resolved): Review 6221-datamanager-delete @ 66380d0
Peter Amstutz
03:00 pm Revision b0b276ff (arvados): 6221: Successfully writes trash lists.
Peter Amstutz
02:39 pm Bug #5288: [Documentation] Write user guide for arv-copy
Thanks for reviewing my first commit :) Bryan Cosca
02:35 pm Bug #5288 (Resolved): [Documentation] Write user guide for arv-copy
Bryan Cosca
01:33 pm Bug #5288: [Documentation] Write user guide for arv-copy
Looks very good. Just a couple more minor things.
* Typo in “The uuid can be found in the collection displace page...
Radhika Chippada
02:33 pm Revision 66c19e11 (arvados): Merge branch '5288-arv-copy-documentation' refs #5288
bryan
02:23 pm Task #6286 (Closed): Review branch: 5288-arv-copy-documentation
Bryan Cosca
02:21 pm Revision 1d827136 (arvados): Note #16
bryan
12:43 pm Revision 2c3c9f64 (arvados): Merge branch 'master' into 6465-optimize-workbench-integration-tests
Manoj Malipeddu
12:22 pm Revision e59b4235 (arvados): 6465-Added tests to project_controllers_test and users_controller
test and removed tests from users_test. Manoj Malipeddu
02:06 am Revision 2578d032 (arvados): 6221: Generate trash list, not sent to keep servers yet.
Peter Amstutz

07/14/2015

10:32 pm Feature #6619: [Deployment] [Documentation] Install system-wide git credential helper for arvados...
(.. I agree on all the stuff cutted here...)
Tom Clegg wrote:
> I figured using system level config would make...
Nico César
08:38 pm Feature #6619: [Deployment] [Documentation] Install system-wide git credential helper for arvados...
Nico Cesar wrote:
> Personally I don't like doing --system level configurations because we could be using git clone ...
Tom Clegg
07:47 pm Feature #6619: [Deployment] [Documentation] Install system-wide git credential helper for arvados...
Personally I don't like doing --system level configurations because we could be using git clone for other stuff, with... Nico César
07:18 pm Feature #6619 (Resolved): [Deployment] [Documentation] Install system-wide git credential helper ...
Git can be configured to use the ARVADOS_API_TOKEN environment variable to authenticate to gitolite. A single-user se... Tom Clegg
08:48 pm Revision beab0d6b (arvados): Note #15
bryan
08:47 pm Bug #5288: [Documentation] Write user guide for arv-copy
Radhika Chippada wrote:
> * lets -> let’s ?
Done
> * “beta cloud instance qr1hi” Can we add the site url also?...
Bryan Cosca
08:15 pm Bug #5288: [Documentation] Write user guide for arv-copy
Bryan Cosca wrote:
> Radhika Chippada wrote:
> > * Not sure about this: “This part of the tutorial assumes that you...
Brett Smith
07:55 pm Bug #5288: [Documentation] Write user guide for arv-copy

* lets -> let’s ?
* “beta cloud instance qr1hi” Can we add the site url also? Some thing like “beta cloud inst...
Radhika Chippada
06:00 pm Bug #5288: [Documentation] Write user guide for arv-copy
Radhika Chippada wrote:
> Review feedback for commit:9d52ea83290cab293229815286579ab6a1584f9e
>
> * Title: “Arv-...
Bryan Cosca
03:33 pm Bug #5288: [Documentation] Write user guide for arv-copy
Review feedback for commit:9d52ea83290cab293229815286579ab6a1584f9e
* Title: “Arv-copy” -> should it be “arc-copy...
Radhika Chippada
08:43 pm Bug #6221: [Data Manager] implement Delete
LGTM @ commit:421c879 Tom Clegg
08:15 pm Bug #6221: [Data Manager] implement Delete
6221-datamanager-delete @ commit:66380d0
This changes the default to @never_delete==true@ but doesn't get as far a...
Tom Clegg
08:35 pm Revision 0628f0c1 (arvados): added note #13
bryan
08:34 pm Revision 421c879e (arvados): 6221: Check never_delete must be true.
Peter Amstutz
08:30 pm Bug #6219 (Resolved): [FUSE] [Performance] Add performance tests for FUSE
Applied in changeset arvados|commit:39c75ea686e2326508fd8e3d0be31cdde7906597. Radhika Chippada
08:23 pm Bug #6219: [FUSE] [Performance] Add performance tests for FUSE

* Using FUSE for a collection with streams: 2, files_per_stream: 200, bytes_per_file: 1
|create collection|list ...
Radhika Chippada
08:04 pm Bug #6219: [FUSE] [Performance] Add performance tests for FUSE
Peter Amstutz wrote:
> I'm not entirely sure this answers the performance questions about FUSE that I would want to ...
Brett Smith
02:01 pm Bug #6219: [FUSE] [Performance] Add performance tests for FUSE
I'm not entirely sure this answers the performance questions about FUSE that I would want to ask, but this branch has... Peter Amstutz
08:15 pm Task #6620 (In Progress): Review 6221-datamanager-delete @ 66380d0
Tom Clegg
07:36 pm Task #6620 (Resolved): Review 6221-datamanager-delete @ 66380d0
Peter Amstutz
08:13 pm Revision 39c75ea6 (arvados): closes #6219
Merge branch '6219-fuse-performance-testing' Radhika Chippada
08:13 pm Revision 8b8673b6 (arvados): Merge branch 'master' into 6219-fuse-performance-testing
Radhika Chippada
07:07 pm Revision 8f589475 (arvados): Fixed more syntax errors
bryan
07:02 pm Task #6618 (Resolved): Review 5898-listen-race
Tom Clegg
07:01 pm Bug #5898 (In Progress): [Tests] Race condition in test_KeepProxyTest1 (tests.test_keep_client.Ke...
Tom Clegg
07:00 pm Revision 7adf48e3 (arvados): Fixed syntax
bryan
06:53 pm Story #6617 (Resolved): [Workbench] [Documentation] Display https url in repositories panel in ma...
Background: When logged in to a shell node via SSH, you can access git repositories via SSH (like git@git.zzzzz.arvad... Radhika Chippada
06:19 pm Revision d5dbaeb5 (arvados): Fixed more comments
bryan
06:12 pm Task #6613 (Resolved): Merge 3408
Peter Amstutz
06:10 pm Task #6613 (Resolved): Merge 3408
Peter Amstutz
06:12 pm Task #6615 (In Progress): Support sending trash lists from data manager
Peter Amstutz
06:11 pm Task #6615 (Resolved): Support sending trash lists from data manager
Peter Amstutz
06:11 pm Bug #6610 (In Progress): [API] [Webshell] shell accounts should be created even if the user has n...
Tom Clegg
01:36 pm Bug #6610 (Resolved): [API] [Webshell] shell accounts should be created even if the user has not ...
Ward Vandewege
06:11 pm Task #6616 (Resolved): Fix
Peter Amstutz
06:11 pm Task #6616 (Resolved): Fix
Peter Amstutz
06:10 pm Bug #6602: [Workbench] Pipeline components tab preloads all tasks; times out for jobs with many t...
Calculating "CPU time" (actually node-slot time) seems to be the sole purpose of fetching all tasks.
IMO we should...
Tom Clegg
06:02 pm Revision 66380d0e (arvados): 6221: Make never_delete true by default, make trash_worker respect n...
test. Peter Amstutz
06:01 pm Revision 60399224 (arvados): Fixed some changes but need to add copy git repos
bryan
05:53 pm Revision 9053b511 (arvados): added png and need to switch to 6014 to grab the url
bryan
05:49 pm Revision e06a7fe8 (arvados): 6362: Update bootstrap gem.
Tom Clegg
05:49 pm Revision 949e7831 (arvados): 6362: Change config precedence order.
Before: environments/*.rb, Rails defaults, application.yml,
application.default.yml.
After: application.yml, applica...
Tom Clegg
05:45 pm Bug #6484 (Resolved): [FUSE] fsync on read-only collection returns EROFS
Applied in changeset arvados|commit:5e27876fa4d3faf3b973282bfb4f152c02345bdc. Peter Amstutz
04:12 pm Bug #6484: [FUSE] fsync on read-only collection returns EROFS
LGTM Radhika Chippada
05:44 pm Task #6108 (Resolved): Review data manager
Peter Amstutz
05:44 pm Task #6609 (Resolved): Review 6484-fuse-fsync-erofs
Peter Amstutz
04:12 pm Task #6609 (In Progress): Review 6484-fuse-fsync-erofs
Radhika Chippada
01:24 pm Task #6609 (Resolved): Review 6484-fuse-fsync-erofs
Peter Amstutz
05:40 pm Revision 5e27876f (arvados): Merge branch '6484-fuse-fsync-erofs' closes #6484
Peter Amstutz
05:40 pm Revision f78434fc (arvados): Merge branch 'github-3408-production-datamanager' refs #3408
Peter Amstutz
05:39 pm Revision 0e57453d (arvados): Merge branch 'master' into github-3408-production-datamanager
Conflicts:
services/datamanager/keep/keep.go
Peter Amstutz
05:22 pm Revision 5d17dfc6 (arvados): Merge branch 'master' into 6219-fuse-performance-testing
Radhika Chippada
03:15 pm Bug #6014 (Resolved): [Documentation] Document repository creation in the Arvados tutorial
Applied in changeset arvados|commit:bb8a8e8ab7dc201dccf8f2f3cf243e63ba8d14cd. Radhika Chippada
02:39 pm Bug #6014: [Documentation] Document repository creation in the Arvados tutorial
LGTM, feel free to merge. Bryan Cosca
03:10 pm Revision bb8a8e8a (arvados): closes #6014
Merge branch '6014-repo-creation-doc' Radhika Chippada
03:10 pm Revision 4a5c16b7 (arvados): Merge branch 'master' into 6014-repo-creation-doc
Radhika Chippada
02:42 pm Task #6612 (New): Report trash and pull queue & worker status in keepstore /status.json
Tom Clegg
02:41 pm Task #6285 (Closed): Review branch: 6014-repo-creation-doc
Bryan Cosca
02:37 pm Feature #6611 (Closed): [Data Manager] Act on pull lists for underreplicated blocks
By design, Data Manager fixed underreplicated blocks by sending "pull lists" to the keepstore servers.
Currently, ...
Tom Clegg
02:31 pm Revision 9d52ea83 (arvados): added _arv_copy_expectations
bryan
02:00 pm Task #6452 (Resolved): Review branch: 6219-fuse-performance-testing (from 3198-writable-fuse) branch
Peter Amstutz
01:32 pm Task #6286 (In Progress): Review branch: 5288-arv-copy-documentation
Radhika Chippada
09:31 am Revision 1d806839 (arvados): API server installation doc clones arvados over the network.
Now that we've moved away from a source-based install, there isn't
necessarily a checkout anywhere on the host. This...
Brett Smith
09:24 am Bug #6604: [Workbench] Notification menu should not prompt the user to upload an SSH key when a W...
Joshua Randall wrote:
> From a user point of view, I probably wouldn't mind if I got the notification from Dax once ...
Brett Smith
08:47 am Bug #6604: [Workbench] Notification menu should not prompt the user to upload an SSH key when a W...
From a user point of view, I probably wouldn't mind if I got the notification from Dax once that suggested I might wa... Joshua Randall
09:14 am Story #6588: [Workbench] UX - webshell login button placement
Radhika Chippada wrote:
> One thought: How about we add a right-justified button/dropdown menu in the breadcrumbs na...
Brett Smith
01:02 am Revision ea0e43b2 (arvados-dev): Make sure we have a conference/environments/production.rb file s...
we generate the workbench assets correctly before packaging.
refs #6362
Ward Vandewege
01:02 am Revision ea0e43b2 (arvados): Make sure we have a conference/environments/production.rb file so that
we generate the workbench assets correctly before packaging.
refs #6362
Ward Vandewege

07/13/2015

09:43 pm Revision 9007e669 (arvados): 6484: Ignore filehandle flush if object is not writable.
Peter Amstutz
09:34 pm Bug #6499: [Documentation] Review 6438-multiplatform-install-guide-wip
#6589, #6590, and #6591 are known issues. Brett Smith
09:16 pm Revision 726cc580 (arvados): closes #6445
Merge branch '6445-incorrect-task-runtime-calc' Radhika Chippada
09:11 pm Revision ad237560 (arvados): 6014: minor updates
Radhika Chippada
09:08 pm Bug #6014: [Documentation] Document repository creation in the Arvados tutorial
!addnewrepobox6.png! Bryan Cosca
09:06 pm Bug #6014: [Documentation] Document repository creation in the Arvados tutorial
!addnewrepobox5.png! Bryan Cosca
08:20 pm Bug #6014: [Documentation] Document repository creation in the Arvados tutorial
A couple notes:
I vote for a name like "*Adding* a new Arvados repository". We have words like Accessing, Running,...
Bryan Cosca
09:03 pm Bug #6593: [SDKs] arv-get should use the stdout FD directly, rather than opening /dev/stdout
"Chapter and verse for the curious":http://lkml.iu.edu/hypermail/linux/kernel/0808.0/3091.html.
Brett Smith
04:44 pm Bug #6593 (Resolved): [SDKs] arv-get should use the stdout FD directly, rather than opening /dev/...
A process can always write to fd 1, but it may not always be able to open @/dev/stdout@. In particular, if a user in... Brett Smith
08:28 pm Revision ee42981c (arvados): 6445: update the job status line also to use the job's finished_at t...
Radhika Chippada
08:26 pm Revision 7e5b8ba9 (arvados): Merge branch 'master' into 6445-incorrect-task-runtime-calc
Radhika Chippada
08:19 pm Task #6365 (Resolved): Write runner using cwltool and run-command
Peter Amstutz
08:17 pm Task #6464 (Resolved): Review 6264-run-command-task-env
Peter Amstutz
08:04 pm Bug #6606 (New): [Workbench] Provide a GUI interface to arv-copy
[This needs collaboration to find the sweet spot between what's currently doable, what's prudent from a security pers... Brett Smith
08:01 pm Bug #6605 (Resolved): [SDKs] arv-copy can copy git repositories hosted by arv-git-httpd with no S...
Functional requirements:
* When reading Git repositories from the source cluster, it should try to read it through...
Brett Smith
07:55 pm Task #6285 (In Progress): Review branch: 6014-repo-creation-doc
Bryan Cosca
07:53 pm Bug #6604 (Resolved): [Workbench] Notification menu should not prompt the user to upload an SSH k...
Now Web shells are available, users do not need to upload an SSH key to fully use Arvados. Dax should not prompt the... Brett Smith
07:49 pm Bug #6603 (Duplicate): [Workbench] Pipeline components tab preloads all tasks; times out for jobs...
Brett Smith
07:49 pm Bug #6603 (Duplicate): [Workbench] Pipeline components tab preloads all tasks; times out for jobs...
@app/views/pipeline_instances/_show_components_running.html.erb@ includes the line <code class="ruby">tasks = JobTask... Brett Smith
07:48 pm Bug #6602 (Resolved): [Workbench] Pipeline components tab preloads all tasks; times out for jobs ...
h2. The bug
@app/views/pipeline_instances/_show_components_running.html.erb@ includes the line <code class="ruby">...
Brett Smith
07:40 pm Bug #6601 (New): [API] Do not accept an empty SSH key as valid
When a user creates a new AuthorizedKey, the API server validates that the key represents real key material, to help ... Brett Smith
07:37 pm Bug #6600 (Resolved): [SDKs] All PySDK functions that make API calls must support a num_retries a...
Most of the convenience functions in @__init__.py@ currently don't: @current_job@, @current_task@, @one_task_per_inpu... Brett Smith
07:33 pm Bug #6599 (New): [SDKs] Whenever `arv` has an invalid resource name argument, it should complain ...
Consider this terminal session:... Brett Smith
07:29 pm Bug #6598 (Resolved): [Crunch] Fix crunch-job's update_progress_stats post-5717
crunch-job's update_proress_stats function updates the job's tasks summary. It assumes that the number of running jo... Brett Smith
07:19 pm Story #6465: [Tests] Optimize workbench integration tests
In commit:5106490f
Removed test from projects_test:
Add a new name, then edit it, without creating a duplicate
...
Manoj Malipeddu
03:34 pm Story #6465: [Tests] Optimize workbench integration tests
In commit:a00eab83a1a2636f5c18be8109f73bf050d1ec88
Removed test from project_test:
project viewer can't see proje...
Manoj Malipeddu
01:38 pm Story #6465: [Tests] Optimize workbench integration tests
In commit:fc2dc01f:
Removed tests from project_test:
Find a project and edit description to textile description
...
Manoj Malipeddu
07:14 pm Revision 5106490f (arvados): 6465- Removed test "edit name and verify that a duplicate is not
created" from projects integration test to application controller
test.
Manoj Malipeddu
07:10 pm Revision 7bd12f51 (arvados): 6014: Add "add new repository" page to create a tutorial repository,...
Radhika Chippada
06:06 pm Bug #5288 (In Progress): [Documentation] Write user guide for arv-copy
Bryan Cosca
05:17 pm Bug #5288: [Documentation] Write user guide for arv-copy
Radhika, this is ready for review.
I left the example very general, so in order to follow, you need to use your ow...
Bryan Cosca
05:17 pm Task #6286: Review branch: 5288-arv-copy-documentation
Ready for review. Bryan Cosca
05:02 pm Revision 6196d328 (arvados): Ready for review
bryan
05:00 pm Revision becec5ef (arvados): changed formatting of cluster1 and cluster2
bryan
04:56 pm Revision 0581bd67 (arvados): changed arv-copy expectations and moved around words in the html file
bryan
04:47 pm Revision e3ab22d0 (arvados): changed formatting and added words
bryan
04:41 pm Bug #6592 (Resolved): [Crunch] crunch-job should handle cleanup step failures like install step f...
A compute node was running a Keep mount for a non-Crunch user on the system. When work was dispatched to this system... Brett Smith
04:34 pm Bug #6591 (Resolved): [Documentation] Improve suggested nginx configuration
In the installation guide for API server and Workbench:
* Add the definition of the @$external_client@ configurati...
Brett Smith
04:32 pm Bug #6590 (Resolved): [Documentation] Improve documentation of API server configuration variables
In the API server installation guide:
# Under the header "Configure the API server," near the end of the discussio...
Brett Smith
04:27 pm Bug #6589 (Resolved): [Documentation] API installation guide needs to set ARVADOS_WEBSOCKETS in P...
Without this, running Puma just runs another API server, which is not expected or desired behavior. Brett Smith
03:41 pm Revision 5b311db1 (arvados): Added documentation for copying collections and pipeline templates a...
bryan
03:41 pm Story #6096 (Resolved): [OPS] Implement a process to regularly deploy a Docker image for running ...
Ward Vandewege
03:40 pm Task #6586 (Resolved): figure out arv-keepdocker permissions issue on 4xphq
Ward Vandewege
03:40 pm Task #6586 (In Progress): figure out arv-keepdocker permissions issue on 4xphq
Ward Vandewege
03:39 pm Revision 5b7eaf60 (arvados-dev): run_deploy.sh improvements:
* Make sure that group_class is included when creating the public docker
images project.
* Document the required pe...
Ward Vandewege
03:39 pm Revision 5b7eaf60 (arvados): run_deploy.sh improvements:
* Make sure that group_class is included when creating the public docker
images project.
* Document the required pe...
Ward Vandewege
03:36 pm Revision f42c7e3d (arvados): Merge branch 'master' into 6465-optimize-workbench-integration-tests
Manoj Malipeddu
03:18 pm Revision a00eab83 (arvados): 6465-Moved test "project viewer can't see project sharing tab" from
projects integration test to projects controller test. Manoj Malipeddu

07/12/2015

07:40 pm Story #6588 (Resolved): [Workbench] UX - webshell login button placement
h2. Phase 1
Split "manage account" page into distinct pages. Each has its own link in the "person" drop-down, whic...
Radhika Chippada

07/11/2015

12:58 am Task #6292 (Resolved): Review branch: 6279-web-shell-client
Tom Clegg
12:58 am Task #6293 (Resolved): Review 6218-python-sdk-perf @ commit:d4c6c7c
Tom Clegg

07/10/2015

10:46 pm Revision 340a9ffa (arvados): refs #6279
Merge branch '6279-web-shell-client' Radhika Chippada
10:44 pm Revision 20524cb8 (arvados): 6279: open the webshell client in a blank window.
Radhika Chippada
09:52 pm Task #6586 (Resolved): figure out arv-keepdocker permissions issue on 4xphq
In docker-jobs-image ci run:
Status: Downloaded newer image for arvados/jobs:c47db46c7f2aac3ad1b099d8716c44dbb9f8b...
Ward Vandewege
08:20 pm Task #6573 (Resolved): review 6569-smarter-jobs-image
Ward Vandewege
03:18 am Task #6573 (Resolved): review 6569-smarter-jobs-image
Ward Vandewege
08:20 pm Task #6528 (Resolved): split off arvados/jobs docker image from docker image
Ward Vandewege
02:08 am Task #6528 (In Progress): split off arvados/jobs docker image from docker image
Ward Vandewege
08:20 pm Task #6569 (Resolved): clean up and test arvados/jobs image
Ward Vandewege
02:08 am Task #6569 (In Progress): clean up and test arvados/jobs image
Ward Vandewege
08:18 pm Revision 5ee1f6c0 (arvados): Merge branch '6569-smarter-jobs-image'
closes #6569 Ward Vandewege
08:18 pm Revision 5fa837af (arvados): Merge branch 'master' into 6569-smarter-jobs-image
Ward Vandewege
07:43 pm Revision 6e3e3c5c (arvados): Change _config.yaml to point to arv-copy.html.textile.liquid
bryan
07:03 pm Feature #6574 (New): [Workbench] [Webshell] Rough edges in web shell
Warning: laundry list. Might need to be prioritize bits and/or split into separate stories.
* More robust username...
Tom Clegg
06:45 pm Story #6279 (Resolved): [Workbench] Integrate a Web shell client
Applied in changeset arvados|commit:c47db46c7f2aac3ad1b099d8716c44dbb9f8bbf6. Tom Clegg
05:26 pm Story #6279: [Workbench] Integrate a Web shell client
Tom said:
> I think a4926df fixes the infinite loop of failed requests.
Yes, the infinite loop issue is resolved ...
Radhika Chippada
04:57 pm Story #6279: [Workbench] Integrate a Web shell client
Try branch at commit:1010035
I think commit:a4926df fixes the infinite loop of failed requests.
Tom Clegg
03:49 pm Story #6279: [Workbench] Integrate a Web shell client
Radhika Chippada wrote:
> * First a simple one: You said, "maybe open in a separate smaller window, -more like a "re...
Tom Clegg
03:01 pm Story #6279: [Workbench] Integrate a Web shell client
I logged into webshell client through my workbench (using of course my older revision at commit:f19af568) and I notic... Radhika Chippada
01:00 am Story #6279: [Workbench] Integrate a Web shell client
Tom:
Thanks much for the config updates and route updates. So much better.
That said, I see some big issues in th...
Radhika Chippada
06:39 pm Revision c47db46c (arvados): Merge branch '6279-web-shell-client' closes #6279
Tom Clegg
06:07 pm Revision 4690e2bf (arvados): Add debian8 as a build target.
No issue # Ward Vandewege
06:07 pm Revision 4690e2bf (arvados-dev): Add debian8 as a build target.
No issue # Ward Vandewege
05:35 pm Revision abe3b885 (arvados): 6279: Hide "reconnect" button because it doesn't auto-login.
Tom Clegg
04:55 pm Revision 10100356 (arvados): 6279: Provide feedback that authentication token has been sent.
Tom Clegg
04:45 pm Revision a4926dfa (arvados): 6279: Do not retry a request that "timed out" in less than 2 seconds.
In this case it's probably not a timeout -- more likely a CORS problem
that the browser is not allowed to report to t...
Tom Clegg
03:18 pm Revision 6929750b (arvados): 6279: Do not set content-length headers in XHR.
According to error messages in Chrome console:
Refused to set unsafe header "Content-Length"
ShellInABox.sendReque...
Tom Clegg
03:16 pm Revision 264391e4 (arvados): 6279: Move keyboard assets to /public/webshell/
Tom Clegg
03:09 pm Revision 5f7a1bf5 (arvados): 6438: Merge debian and ubuntu sections. The same recipe works for both.
Tom Clegg
03:02 pm Revision 1fdb31ed (arvados): 6438: Use urandom instead of md5(hostname) for UUID. Avoid using Rub...
Tom Clegg
03:00 pm Revision 6c38124b (arvados): 6438: Add missing "apt-get update". Give a command to add the packag...
Replace version table with $(lsb_release -cs). Tom Clegg
02:58 pm Revision 959ab858 (arvados): Make sure to add python-virtualenv to the Docker arvados/jobs image.
refs #6569 Ward Vandewege
02:58 pm Revision 453cdbc1 (arvados): 6438: Add specific commands for nginx16 and postgresql92 Software Co...
Tom Clegg
02:55 pm Bug #6014 (In Progress): [Documentation] Document repository creation in the Arvados tutorial
Radhika Chippada
02:44 pm Revision ad7c6e10 (arvados): 6445: when a task does not have finished_at time, use the finished_a...
Radhika Chippada
01:32 pm Revision 5b349796 (arvados): Merge branch '6222-memory-status' refs #6222
Tom Clegg
03:19 am Revision c8307689 (arvados): Merge branch 'master' into 6569-smarter-jobs-image
Ward Vandewege
03:11 am Story #6218: [SDKs] [Performance] Add performance tests for Python SDK collection methods
Tom Clegg wrote:
> Brett Smith wrote:
> > Apparently iteration happens at a low enough level that it becomes invisi...
Brett Smith
03:05 am Story #6218 (Resolved): [SDKs] [Performance] Add performance tests for Python SDK collection methods
Applied in changeset arvados|commit:97f5239f053b1691d7f2cb56230386921f8ea4d4. Tom Clegg
03:00 am Story #6218: [SDKs] [Performance] Add performance tests for Python SDK collection methods
Brett Smith wrote:
> Reviewing 6218-python-sdk-perf @ commit:d4c6c7c.
>
> Code issues:
>
> * It looks like the...
Tom Clegg
03:02 am Revision 97f5239f (arvados): Merge branch '6218-python-sdk-perf' closes #6218
Tom Clegg
03:01 am Revision 1088f784 (arvados): 6218: Generate profiling data for a few arvados.collection.Collectio...
Tom Clegg
03:00 am Revision 64736a9f (arvados): Make sure that mkimage-debootstrap.sh uses -f when tagging docker
images.
refs #6528
Ward Vandewege
02:20 am Revision dee0d839 (arvados): Make sure that mkimage-debootstrap.sh does not try to do an interactive
docker run when there's no tty.
refs #6528
Ward Vandewege
02:09 am Revision 2414412b (arvados): Make the arvados/jobs image leaner.
refs #6569 Ward Vandewege
02:01 am Revision bdfbb8c1 (arvados-dev): Build arvados/jobs docker image separately from the others.
refs #6528 Ward Vandewege
02:01 am Revision bdfbb8c1 (arvados): Build arvados/jobs docker image separately from the others.
refs #6528 Ward Vandewege

07/09/2015

09:50 pm Story #6572 (Resolved): [Documentation] Install guide demonstrates how to copy a pipeline from Cu...
Use case: an administrator just went through the install guide, and now they have a nice, shiny new cluster. What do... Brett Smith
09:28 pm Bug #6571 (New): [Workbench] Project description styled differently based on whether or not the u...
The "Read" screenshot shows what the project description looks like to a user who only has read permission on a proje... Nancy Ouyang
09:17 pm Bug #6483: [Workbench] Additional shell groups are not added to original Link object
Ward, please stop filing two bugs in one. :P In this case, the problem with the script is already #6403. Brett Smith
09:15 pm Bug #6563: 504 Gateway Time-out api error
Ran into it again here:
https://cloud.curoverse.com/collections/8e8d0fb98db3c0b6a9e39617a68d3dad+91/qr1hi-8i9sb-v6...
Bryan Cosca
07:13 pm Bug #6563 (New): 504 Gateway Time-out api error
I ran a 20 node job using GATK tools. Everything was configured to use 4 threads, I set the max number of samples per... Bryan Cosca
09:13 pm Bug #6538 (Resolved): arv-mount failing on shell.su92l
Fixed in commit:4f77c778, plus a deploy. Brett Smith
09:02 pm Task #6292 (In Progress): Review branch: 6279-web-shell-client
Tom Clegg
09:02 pm Story #6279: [Workbench] Integrate a Web shell client
First of all, this is awesome.
h2. Some fixes
I've fixed a few things and pushd to 6279-web-shell-client @ comm...
Tom Clegg
02:14 pm Story #6279: [Workbench] Integrate a Web shell client
I noticed one issue after logout. I clicked on the Login link in my_account page and now I am in the shell terminal. ... Radhika Chippada
01:54 am Story #6279: [Workbench] Integrate a Web shell client
Regarding branch 6279-web-shell-client at commit:c5e726c:
* Added /webshell as a route to workbench and it display...
Radhika Chippada
01:06 am Story #6279: [Workbench] Integrate a Web shell client
The '-' and '_' are not working in Firefox. Upon googling, found this URL that suggested a workaround: https://code.g... Radhika Chippada
08:46 pm Task #6290 (Resolved): Review specification
Peter Amstutz
08:39 pm Story #6570: [DRAFT] [Workbench] More encouragement for users to send feedback
I am still gathering functional requirements on this story. We won't work on it until it's very well-specified. Brett Smith
08:35 pm Story #6570 (New): [DRAFT] [Workbench] More encouragement for users to send feedback
We want to encourage users to both report problems, and send feature requests or other ideas.
Right now the primar...
Brett Smith
08:38 pm Revision eb4fb547 (arvados): 6279: Move webshell action into VirtualMachinesController, tweak for...
* Document config var
* Accept formatting references like %{hostname} and %{uuid} in config
var instead of always ...
Tom Clegg
08:07 pm Task #6569 (Resolved): clean up and test arvados/jobs image
No longer needed: rvm, gems, fuse Ward Vandewege
08:03 pm Story #6218: [SDKs] [Performance] Add performance tests for Python SDK collection methods
Reviewing 6218-python-sdk-perf @ commit:d4c6c7c.
Code issues:
* It looks like the benchmark class expects a rea...
Brett Smith
06:17 pm Task #6293 (In Progress): Review 6218-python-sdk-perf @ commit:d4c6c7c
Brett Smith
06:14 pm Task #6301 (Resolved): Review
Radhika Chippada
06:09 pm Story #2256 (Resolved): [Workbench] Users can access an Arvados shell through the Web
Nico César
06:08 pm Task #6288 (Closed): Review
Nico César
06:08 pm Task #6512 (Resolved): make arvados_pam.py read from /etc/default/ for its configuration.
this is done and deployed Nico César
05:46 pm Revision 89685545 (arvados): 6438: Add some missing steps to rvm recipe. Install rvm as root.
Tom Clegg
03:45 pm Revision 2fed32a4 (arvados): 6438: Bring back package dependencies for "build Ruby from source" o...
These used to be documented earlier in the process, but were removed. Tom Clegg
03:38 pm Revision e39a5e06 (arvados): 6438: Drop wget dependency. Update ./configure flags for Ruby 2.1.6.
Tom Clegg
03:32 pm Story #6265: [CWL] Contribute to the CWL specification
For the benefit of any future readers, most of the concerns above were addressed in https://github.com/common-workflo... Brett Smith
07:05 am Story #6265 (Resolved): [CWL] Contribute to the CWL specification
Peter Amstutz
03:27 pm Story #3408 (In Progress): [Keep] Implement Production Data Manager
Brett Smith
03:26 pm Story #3408 (Rejected): [Keep] Implement Production Data Manager
To spell out a little better what should happen with the issue this sprint:
* Does the outstanding Data Manager br...
Brett Smith
03:24 pm Bug #6157: [Documentation] Explain extra steps needed when compute hostnames are not fooN
Updating the description to reflect our post-#6156 world. We now support any kind of "fooN" schema, not just compute... Brett Smith
02:35 pm Story #6477: [Documentation] Clarify the use of Docker within shared and private VMs
(Review discussion happened in the review ticket, #6535.) Brett Smith
02:35 pm Story #6477 (Resolved): [Documentation] Clarify the use of Docker within shared and private VMs
Brett Smith
02:34 pm Task #6535 (Resolved): Review wiki update 33
Brett Smith
02:31 pm Task #6535: Review wiki update 33
Yeah that makes sense. Feel free to resolve this then. Bryan Cosca
02:28 pm Task #6535: Review wiki update 33
Bryan Cosca wrote:
> Both "arv keep docker" and "arv-keepdocker" seem to work on my shell, why did you choose the la...
Brett Smith
02:16 pm Task #6535: Review wiki update 33
One question:
Both "arv keep docker" and "arv-keepdocker" seem to work on my shell, why did you choose the latter ...
Bryan Cosca
02:23 pm Bug #6499: [Documentation] Review 6438-multiplatform-install-guide-wip
To help avoid duplicating too much work, I suggest you start from a base distro image, then follow the instructions t... Brett Smith
01:36 pm Bug #6499 (In Progress): [Documentation] Review 6438-multiplatform-install-guide-wip
Tom Clegg
02:14 pm Revision f19af568 (arvados): 6279: added shell_in_a_box url as comment
Radhika Chippada
01:43 pm Revision 1db6a725 (arvados): 6279: Noticed that enabled.gif is also needed. I see this one when I...
and use the reset option. Added this gif. Radhika Chippada
01:36 pm Task #6526 (In Progress): Try Ubuntu 12.04 install
Tom Clegg
01:36 pm Task #6525 (In Progress): Try CentOS 6 install
Tom Clegg
01:37 am Revision c5e726ce (arvados): 6279: add some comments
Radhika Chippada
01:07 am Revision 1d730509 (arvados): i6279: The '-' and '_' are not working in Firefox. Upon googling, fo...
https://code.google.com/p/shellinabox/issues/detail?id=202 Radhika Chippada
12:26 am Revision 8d0355a4 (arvados): Merge branch 'master' into 6279-web-shell-client
Radhika Chippada
12:25 am Revision 4e416c98 (arvados): 6279: if hostname ends with .shell, strip it.
Radhika Chippada

07/08/2015

09:56 pm Story #6477 (In Progress): [Documentation] Clarify the use of Docker within shared and private VMs
Brett Smith
09:56 pm Task #6535: Review wiki update 33
Bryan, this is ready for you to review. You can "see the Textile diff on the wiki":https://arvados.org/projects/arva... Brett Smith
08:21 pm Task #6535 (Resolved): Review wiki update 33
Brett Smith
09:44 pm Revision d2b707bb (arvados): 5898: Wait for servers to start *listening* before running integrati...
Tom Clegg
09:25 pm Bug #6358 (Resolved): [SDKs] Python Keep client uses wrong probe order for put()
Applied in changeset arvados|commit:4f77c7788c6fc3a6cc9cd90ff231d837fdec7cc4. Brett Smith
09:19 pm Revision 4f77c778 (arvados): 6358: Declare FUSE driver's dependency on llfuse >= 0.40.
The workaround added in 08284382 requires this version. Below that,
llfuse's Queue at least lives in a different pla...
Brett Smith
09:06 pm Bug #6538 (Resolved): arv-mount failing on shell.su92l
I had been running an old arv-mount on my $HOME/keep directory, one that had debugging turned out, I think to try and... Abram Connelly
08:58 pm Task #6360 (Resolved): add arvados API token libpam python module for shellinabox via puppet for ...
Nico César
08:58 pm Task #6360: add arvados API token libpam python module for shellinabox via puppet for shell nodes.
This is packaged and puppet installs it and configures it. Nico César
08:54 pm Story #6282 (Resolved): [Crunch] Write stories for implementation of Crunch v2
Tom Clegg
08:44 pm Revision e76418b0 (arvados): qiuck fix to arvados-pam vulnerability
no issue # Nico César
08:31 pm Revision 2edb46e6 (arvados-dev): Add dependency on libpam-python to the libarvados-pam package.
refs #2256 Ward Vandewege
08:31 pm Revision 2edb46e6 (arvados): Add dependency on libpam-python to the libarvados-pam package.
refs #2256 Ward Vandewege
08:21 pm Task #6536 (Resolved): Review branch: 6473-fetch-events-starting-at
Radhika Chippada
08:20 pm Task #6533 (Resolved): Review arvados-dev branch 6497-separate-package-upload-wip
Brett Smith
08:11 pm Task #6528 (Resolved): split off arvados/jobs docker image from docker image
then put it in a separate build step in front of the deploy step Ward Vandewege
08:05 pm Task #6526 (Resolved): Try Ubuntu 12.04 install
Tom Clegg
08:03 pm Task #6525 (Resolved): Try CentOS 6 install
Tom Clegg
08:02 pm Task #6524 (Resolved): Review 6157-worker-hostnames
Tom Clegg
07:16 pm Feature #6520 (Resolved): [Node Manager] [Crunch2] Take queued containers into account when compu...
Add one node to the wishlist for each queued container, just like we currently add one (or more) nodes to the wishlis... Tom Clegg
07:13 pm Feature #6517: Port arvados-libpam to centos

the debian version /etc/default/shellinabox in CentOS is /etc/sysconfig/shellinaboxd
OPTS="-s /shell_url:AUT...
Nico César
07:01 pm Feature #6517 (New): Port arvados-libpam to centos
we're currently supporting a deb version of arvados-libpam.
we need to make the same for Centos 6.6 ...
Nico César
07:13 pm Story #3408: [Keep] Implement Production Data Manager
Peter, please sync up with me about the current state of this branch, and let's figure out next steps for it. Brett Smith
07:11 pm Feature #6280: [SDKs] Go SDK can return an io.Reader for a given collection record and filename
Because development on this story is done in spare time, I'm kicking it out of the sprint cycle. It should not be bu... Brett Smith
07:09 pm Feature #6519 (Resolved): [Workbench] [Crunch2] index and show pages for Containers and Container...
In the first implementation, this does not need to be very extensive:
* Display a table so a developer can use it fo...
Tom Clegg
07:02 pm Feature #6518 (Resolved): [Crunch] [Crunch2] Dispatch containers via slurm
When containers appear in the queue, use SLURM to execute them on worker nodes.
For now, the queue is arvados.v1.c...
Tom Clegg
06:59 pm Task #6453 (Resolved): Review 6377-dev-startup
Tom Clegg
06:56 pm Revision 99c4b804 (arvados): Merge branch '6377-dev-startup' refs #6377
Tom Clegg
06:56 pm Revision c1aed40e (arvados-dev): Add libpam-arvados package build to run-build-packages.
refs #6384 Ward Vandewege
06:56 pm Revision c1aed40e (arvados): Add libpam-arvados package build to run-build-packages.
refs #6384 Ward Vandewege
06:46 pm Revision 484f12ee (arvados): Merge branch 'master' into 6279-web-shell-client
Radhika Chippada
06:43 pm Story #6279: [Workbench] Integrate a Web shell client
Radhika, try using:
https://webshell.4xphq.arvadosapi.com/shell/
it will expect username.
then it will expect...
Nico César
06:15 pm Task #6384 (Resolved): package libpam-arvados
Applied in changeset arvados|commit:3cf223a0d4374e6fc743439826f49adaf29f21cb. Nico César
06:10 pm Story #6171: [FUSE] Document the writable FUSE mount
(time warp here)
Two distinct(?) doc stories here:
# "limitations of write support" is probably what Peter means ...
Tom Clegg
04:15 pm Story #6171 (Resolved): [FUSE] Document the writable FUSE mount
We are going to call the current documentation good enough, and close the ticket.
The main thing in the descriptio...
Brett Smith
06:09 pm Revision 3cf223a0 (arvados): Merge branch '6384-libpam-arvados'
closes #6384 Nico César
05:58 pm Revision 19891e47 (arvados): Whitespace fixes
refs #6384 Ward Vandewege
05:57 pm Revision 3d3f2504 (arvados): Merge branch 'master' into 6384-libpam-arvados
Ward Vandewege
05:53 pm Revision 45c2b55b (arvados): 6384: reverting names
Nico César
05:27 pm Bug #6510: Keep upload using 'arv-put' from 'abe.shell.su92l' is getting 0.5Mb/s upload rate
A sampling of upload times:
2351M 2m11.719s
2265M 2m6.404s
2361M 19m46.000s
2307M 1m35.493s
5202M 4m47.064s
2...
Abram Connelly
03:10 pm Bug #6510: Keep upload using 'arv-put' from 'abe.shell.su92l' is getting 0.5Mb/s upload rate
As of this writing it's slowed down again and no longer getting ~10Mb/s. Abram Connelly
03:07 pm Bug #6510: Keep upload using 'arv-put' from 'abe.shell.su92l' is getting 0.5Mb/s upload rate
I am transferring a small portion of files located on an Amazon S3 bucket to su92l. I'm using the '/data' directory ... Abram Connelly
03:00 pm Bug #6510: Keep upload using 'arv-put' from 'abe.shell.su92l' is getting 0.5Mb/s upload rate

I'm seeing much faster upload than that with bmon. How are you measuring the arv put speed?
I note that you are ...
Ward Vandewege
02:32 pm Bug #6510 (New): Keep upload using 'arv-put' from 'abe.shell.su92l' is getting 0.5Mb/s upload rate
Uploading a collection from my shell node, abe.shell.su92l, using 'arv-put' is getting a rate of 0.5Mb/s. I'm trying... Abram Connelly
05:04 pm Support #6267 (Resolved): Support users and triage bugs (second half)
Ward Vandewege
04:50 pm Bug #5499 (Duplicate): [SDKs] arv-copy fails to create collection after copying many blocks
Ward agrees with the GCP firewall theory, so we're going to figure that was the issue and close this. Brett Smith
04:48 pm Task #6512: make arvados_pam.py read from /etc/default/ for its configuration.
Nico Cesar wrote:
> two minor changes
>
> 1. shellinabox is shellinaboxd for debian package version .... change ...
Ward Vandewege
04:28 pm Task #6512: make arvados_pam.py read from /etc/default/ for its configuration.
two minor changes
1. shellinabox is shellinaboxd for debian package version .... change that in the name of the /...
Nico César
03:38 pm Task #6512: make arvados_pam.py read from /etc/default/ for its configuration.
I added a arvados_pam file that should go in /etc/default
the code is untested.
Nico César
03:11 pm Task #6512 (In Progress): make arvados_pam.py read from /etc/default/ for its configuration.
Nico César
03:07 pm Task #6512 (Resolved): make arvados_pam.py read from /etc/default/ for its configuration.
Work from 6384-libpam-arvados Ward Vandewege
04:47 pm Revision a5c2ae6b (arvados): Rename file
refs #2256 Ward Vandewege
04:38 pm Story #6316 (Rejected): [OPS] run-build-packages publishes RPMs over HTTP
We did #6317 instead. Brett Smith
04:19 pm Revision c416e64c (arvados): Fix path for arvados_pam.py
refs #2256 Ward Vandewege
04:09 pm Revision c01e6aed (arvados): Fix typo.
refs #2256 Ward Vandewege
03:40 pm Revision de98daba (arvados): Merge branch 'master' into 6465-optimize-workbench-integration-tests
Manoj Malipeddu
03:34 pm Revision fc2dc01f (arvados): 6465-Removed two description based tests in projects integration tes...
Kept one description test in projects integration test to check if the edit description button works. Manoj Malipeddu
03:30 pm Revision 5a9684ac (arvados): added /etc/default/arvados_pam as a parameter
refs #6512 Nico César
03:01 pm Bug #5898: [Tests] Race condition in test_KeepProxyTest1 (tests.test_keep_client.KeepProxyTestCas...
These tests are still failing intermittently.
* test_KeepAuthenticatedSignedTest
* test_KeepAuthenticatedUnsignedTe...
Tom Clegg
02:13 pm Revision 76e03aef (arvados): Fix typo. No issue #
Tom Clegg
02:09 pm Revision aa569f0b (arvados): Merge branch '6389-add-dockerfiles'
Closes #6389, #6456. Brett Smith
02:09 pm Revision aa569f0b (arvados-dev): Merge branch '6389-add-dockerfiles'
Closes #6389, #6456. Brett Smith
02:08 pm Revision 08c24c27 (arvados): 6388: Add Dockerfile to build packages on CentOS 6.
Brett Smith
02:08 pm Revision 8f04915e (arvados): 6389: Add Makefile to support Docker builds.
Brett Smith
02:08 pm Revision 08c24c27 (arvados-dev): 6388: Add Dockerfile to build packages on CentOS 6.
Brett Smith
02:08 pm Revision 8f04915e (arvados-dev): 6389: Add Makefile to support Docker builds.
Brett Smith
02:07 pm Revision 5dfd1323 (arvados): 6389: Dockerfiles include the CMD to build packages.
Brett Smith
02:07 pm Revision 73f6f1bb (arvados-dev): Add dockerfiles for Debian7 and Ubuntu1204
refs #6389 Ward Vandewege
02:07 pm Revision 73f6f1bb (arvados): Add dockerfiles for Debian7 and Ubuntu1204
refs #6389 Ward Vandewege
02:07 pm Revision 5dfd1323 (arvados-dev): 6389: Dockerfiles include the CMD to build packages.
Brett Smith
02:06 pm Story #6281 (Resolved): [Crunch] Describe how it looks when Crunch v1 jobs run under Crunch v2
Tom Clegg
02:06 pm Task #6295 (Resolved): Review
Tom Clegg
02:04 pm Support #6266 (Resolved): Support users and triage bugs (first half)
Ward Vandewege
01:59 pm Revision 510a6b6a (arvados): Fix up git log statements:
* remove duplication between -n1 and --max-count=1
* make sure every git log statement has --first-parent
refs #6096
Ward Vandewege
01:59 pm Revision 510a6b6a (arvados-dev): Fix up git log statements:
* remove duplication between -n1 and --max-count=1
* make sure every git log statement has --first-parent
refs #6096
Ward Vandewege
05:56 am Revision 2ecf7efb (arvados): 6377: Update docs to use application.yml instead of omniauth.rb for ...
Tom Clegg
05:36 am Revision 85de04ad (arvados): 6377: Fix reversed condition in "site application.yml is optional" fix.
Tom Clegg
05:36 am Revision 71ba12ca (arvados): 6377: Avoid "incompatible encoding" errors by using blank template0 ...
Tom Clegg
05:36 am Revision acfbb648 (arvados): 6377: Support loading omniauth config from application.yml.
Tom Clegg
05:36 am Revision 158b18f0 (arvados): 6377: Use fork of themes_for_rails with fixed gemspec.
Allows installing with current bundler versions, which treat the invalid
gemspec as an error.
Tom Clegg
05:36 am Revision 9fbb2bbd (arvados): 6377: Fix crash if no asset pipeline.
Tom Clegg
05:36 am Revision e56ea5c6 (arvados): 6377: Update ruby to 2.1.6. Remove bundler version pin (not needed s...
Tom Clegg
02:30 am Revision 260e4dc4 (arvados): Merge branch 'master' into 6279-web-shell-client
Radhika Chippada
02:28 am Revision 8375bf07 (arvados): 6279: add login link in VM panel of manage_account page that takes u...
Radhika Chippada
02:05 am Revision 6086e2a5 (arvados): Small fixes for run-deploy.sh
refs #6096 Ward Vandewege
02:05 am Revision 6086e2a5 (arvados-dev): Small fixes for run-deploy.sh
refs #6096 Ward Vandewege

07/07/2015

09:35 pm Task #6503 (Resolved): Parameterize the upload script to upload packages for the specified distri...
Brett Smith
09:35 pm Task #6502 (Resolved): Extract existing uploader code from run-build-packages.sh into a separate ...
Brett Smith
09:24 pm Task #6119 (Resolved): Review 6096-deploy-jobs-image
Ward Vandewege
09:21 pm Bug #6499: [Documentation] Review 6438-multiplatform-install-guide-wip
This a branch that was prepared and merged at the end of last sprint because of external time constraints. Fortunate... Brett Smith
08:34 pm Bug #6499 (Resolved): [Documentation] Review 6438-multiplatform-install-guide-wip
Brett Smith
09:12 pm Revision 0a139ea3 (arvados-dev): Make run-deploy.rb install the correct version of the arvados/jobs
docker image on deploy.
refs #6096
Ward Vandewege
09:12 pm Revision 0a139ea3 (arvados): Make run-deploy.rb install the correct version of the arvados/jobs
docker image on deploy.
refs #6096
Ward Vandewege
09:05 pm Task #6479 (Resolved): Review 5989-api-all-repos-permissions-wip
Applied in changeset arvados|commit:5608a875c36101c791e35c474abf5e3900aad071. Brett Smith
09:05 pm Bug #5989 (Resolved): [API] API server repositories permissions list doesn't list repositories wi...
Applied in changeset arvados|commit:5608a875c36101c791e35c474abf5e3900aad071. Brett Smith
09:04 pm Bug #5989: [API] API server repositories permissions list doesn't list repositories without keys
Nico Cesar wrote:
> nice. ...
Brett Smith
03:38 pm Bug #5989: [API] API server repositories permissions list doesn't list repositories without keys
reviewed 0e239ef805b8c6eda936073197cf96d0329db048
This the API change looks good to me.
BTW: I see ...
Nico César
09:02 pm Revision 5608a875 (arvados): Merge branch '5989-api-all-repos-permissions-wip'
Closes #5989, #6479. Brett Smith
08:56 pm Revision e06ea339 (arvados): 5989: API repo perms method always returns all repos.
Previously the method would not return repositories that were not
accessible to any authorized key. This change help...
Brett Smith
08:43 pm Revision 734a6693 (arvados): 6377: Missing application.yml is not an error.
Tom Clegg
08:33 pm Bug #6497 (Resolved): [Deployment] Separate package upload portions of run-build-packages.sh to a...
The old way: we had a single shell script, run-build-packages.sh, that built .debs from our source repository, and up... Brett Smith
08:31 pm Revision 2359eabb (arvados): 6222: Add memory stats to status.json.
Reduce malloc activity in status.json.
Remove abandoned GetVolumeStatus, and move its tests over to
volume_unix_test...
Tom Clegg
07:42 pm Revision 3eedcb35 (arvados): Add arvados_pam.py and shellinabox pam configuration file.
Refs #2256 Ward Vandewege
07:41 pm Revision 9df4975a (arvados): 5989: create directory structure for temp files
refs #5989 bug_1 Nico César
07:41 pm Revision 25d47183 (arvados): 5989: bug_1 added puppet repository patch
this is duplicated code from:
puppet/modules/arvados-git-server/templates/usr-local-arvados-update-gitolite.rb.erb
...
Nico César
07:28 pm Story #6279 (In Progress): [Workbench] Integrate a Web shell client
Radhika Chippada
03:11 pm Story #6279: [Workbench] Integrate a Web shell client
Ok we have this half working. (API token as password will be solved when #6384 is finished.)
But you can see progr...
Nico César
06:51 pm Story #6096: [OPS] Implement a process to regularly deploy a Docker image for running jobs to Arv...
Nico Cesar wrote:
> I'm checking 2b93735fc87e447301afafe6556d8571afef2bcf
>
> I see that there are 3 commits on 6...
Ward Vandewege
06:00 pm Bug #6481: [Crunch] Job infinitely stuck in Queued state after Sanity check fails 1
The node (not the job) has a problem, so the sanity check is doing its job here. The job shouldn't fail: it hasn't ev... Tom Clegg
04:10 pm Support #6357 (Resolved): Review curoverse.link
Tom Clegg
04:08 pm Task #6488 (Resolved): Fail collection.create/update calls with invalid manifests.
Blocked by #6486 and #6487 Tom Clegg
04:07 pm Task #6487 (Resolved): Summarize invalid manifests present in production servers' databases
Tom Clegg
04:05 pm Task #6486 (Resolved): Review production logs to confirm no real clients are submitting any inval...
This should be done after the logging feature has been deployed for at least 2 weeks. Tom Clegg
03:45 pm Bug #5677 (Resolved): [API] Silence harmless message "ERROR: must be owner of extension plpgsql"
Applied in changeset arvados|commit:da80f4a198e734313a7991466244083dabd64b00. Tom Clegg
01:26 pm Bug #5677: [API] Silence harmless message "ERROR: must be owner of extension plpgsql"
Reviewed. LGTM. Radhika Chippada
03:42 pm Revision da80f4a1 (arvados): Merge branch '5677-plpgsql-warning' closes #5677
Tom Clegg
03:41 pm Revision c428f31a (arvados): 5677: Edit structure.sql after db:structure:dump: avoid warnings whe...
Tom Clegg
03:30 pm Story #6218: [SDKs] [Performance] Add performance tests for Python SDK collection methods
6218-python-sdk-perf @ commit:d4c6c7c
* This branch isn't a complete solution, but it provides some data points.
...
Tom Clegg
03:28 pm Revision d4c6c7cb (arvados): 6218: Generate profiling data for a few arvados.collection.Collectio...
Tom Clegg
03:03 pm Task #6383: package shellinabox-2.14
done.
tested on https://webshell.9tee4.arvadosapi.com/science/
it's working
Nico César
03:02 pm Task #6453 (In Progress): Review 6377-dev-startup
Radhika Chippada
03:02 pm Task #6454 (Resolved): Review 5677-plpgsql-warning
Radhika Chippada
02:47 pm Task #6410 (Resolved): create a puppet manifest to handle reverse proxy and CORS in switchyard's ...
This is resolved and tryied out in https://webshell.9tee4.arvadosapi.com/shell Nico César
02:00 pm Revision 09ae9c32 (arvados): 6377: Update ruby to 2.1.6.
Tom Clegg
01:46 pm Task #6478 (Resolved): Review Branch 6466-disable-public-projects
Manoj Malipeddu
01:15 pm Revision cfcfa1c4 (arvados): Merge branch 'master' into 6465-optimize-workbench-integration-tests
Manoj Malipeddu
01:15 pm Bug #6466 (Resolved): [Workbench] Add configuration knob to enable/disable public projects listing
Applied in changeset arvados|commit:fdb63be9fde8ea69e78e68f77bb0ab00a79a8d6f. Manoj Malipeddu
01:08 pm Revision fdb63be9 (arvados): closes #6466
Merge branch '6466-disable-public-projects' Manoj Malipeddu
01:07 pm Revision c0082c57 (arvados): Merge branch 'master' into 6466-disable-public-projects
Manoj Malipeddu
04:45 am Bug #6484 (Resolved): [FUSE] fsync on read-only collection returns EROFS
Calling fsync() on a read-only collection returns EROFS (read-only filesystem error) instead of doing nothing. This ... Peter Amstutz
04:09 am Bug #6483 (Resolved): [Workbench] Additional shell groups are not added to original Link object
It is not possible to add a group through workbench if a user is already in a group. The form description says that t... Ward Vandewege
02:31 am Revision cdfd69a4 (arvados): 6264: Fix bin/cwl-runner to import correct module.
Peter Amstutz

07/06/2015

09:45 pm Bug #6455 (Resolved): [Documentation] Fix oversights in compute installation docs
Applied in changeset arvados|commit:770927dbfa1fb16b3075d1581dc66f4e7a623631. Brett Smith
02:49 am Bug #6455: [Documentation] Fix oversights in compute installation docs
I have a branch that includes this as part of #6438. Brett Smith
09:45 pm Bug #6438 (Resolved): [Documentation] Update Rails server installation guides to use packages
Applied in changeset arvados|commit:770927dbfa1fb16b3075d1581dc66f4e7a623631. Brett Smith
09:37 pm Revision 770927db (arvados): Merge branch '6438-multiplatform-install-guide-wip'
Closes #6438, #6455. Refs #6388. Brett Smith
09:37 pm Revision 80a9fa66 (arvados): 6438: Modernize Rails server installation guides.
Document the package-based installation procedure, and associated
Nginx configuration.
Brett Smith
09:37 pm Revision f721928e (arvados): 6388: Add CentOS 6.6 instructions to install docs.
Brett Smith
09:37 pm Revision fa92bc75 (arvados): 6455: Include more steps in Crunch install docs.
* Document the necessary API server configuration change for
crunch-dispatch.
* Document Docker installation.
* Not...
Brett Smith
09:29 pm Revision d79d6e77 (arvados): 6438: Modernize Rails server installation guides.
Document the package-based installation procedure, and associated
Nginx configuration.
Brett Smith
09:29 pm Revision f6f12a6e (arvados): 6388: Add CentOS 6.6 instructions to install docs.
Brett Smith
09:29 pm Revision 5298486a (arvados): 6455: Include more steps in Crunch install docs.
* Document the necessary API server configuration change for
crunch-dispatch.
* Document Docker installation.
* Not...
Brett Smith
08:47 pm Bug #6466: [Workbench] Add configuration knob to enable/disable public projects listing
LGTM @ commit:5792237, thanks.
Tom Clegg
01:40 pm Bug #6466: [Workbench] Add configuration knob to enable/disable public projects listing
Remember to remove the link in source:apps/workbench/app/views/layouts/body.html.erb when configuration causes its ta... Tom Clegg
08:45 pm Task #6383: package shellinabox-2.14
I got it working just changing /etc/default/shellinabox:... Nico César
02:43 pm Task #6383: package shellinabox-2.14
I'll take this ticket
Let's install them using puppet ( and check how the configuration will be etc- etc)
Nico César
01:04 pm Task #6383 (Resolved): package shellinabox-2.14
This package is already available in mainline Debian (both Wheezy and Jessie). Ward Vandewege
08:35 pm Story #6482 (New): [Workbench] Show the weather of running jobs
"Is there somewhere where technical outage updates are kept?"
If jobs are consistently failing due to compute node...
Bryan Cosca
08:21 pm Task #6478 (In Progress): Review Branch 6466-disable-public-projects
Tom Clegg
08:18 pm Bug #6308 (Resolved): Words in description breaks awkwardly in Public Projects page
Tom Clegg
08:14 pm Bug #6481 (New): [Crunch] Job infinitely stuck in Queued state after Sanity check fails 1
Looking at: https://cloud.curoverse.com/pipeline_instances/qr1hi-d1hrv-0ohrxciza6yival#Log
It seems that
Sanit...
Bryan Cosca
08:01 pm Bug #6219: [FUSE] [Performance] Add performance tests for FUSE
Thanks Peter for the comments. I updated the branch to profile smaller code fragments. Please take another look. Radhika Chippada
03:09 pm Bug #6219: [FUSE] [Performance] Add performance tests for FUSE
In @magicDirTestMoveFiles_oneEachIntoAnother@
The @@profiled@ annotation is around a loop which calls "pool.apply"...
Peter Amstutz
08:00 pm Revision c74c5d27 (arvados): 6219: remove couple profiling statements for the tests.
Radhika Chippada
07:51 pm Revision 62f27bcb (arvados): 6219: refactor functions and profile smaller fuse related blocks of ...
Radhika Chippada
06:00 pm Revision 57922375 (arvados): 6466 - Update body html for enable public page and added tests to pr...
Manoj Malipeddu
05:47 pm Revision 50abee31 (arvados): 6264: Move cwlrunner into its own module.
Peter Amstutz
05:33 pm Revision 67b77eb3 (arvados): 6219: profile even smaller portions of code
Radhika Chippada
05:29 pm Revision b3677ac8 (arvados): Merge branch '6388-package-scripts-redhat-support-wip'
Refs #6388. Closes #6480. Brett Smith
05:29 pm Revision b3677ac8 (arvados-dev): Merge branch '6388-package-scripts-redhat-support-wip'
Refs #6388. Closes #6480. Brett Smith
04:15 pm Feature #6013 (Resolved): [Workbench] clean up 'setup user' behavior in the admin interface
Applied in changeset arvados|commit:09fcf10ff841e5032145936385b406412674a368. Radhika Chippada
03:32 pm Feature #6013: [Workbench] clean up 'setup user' behavior in the admin interface
reviewed 160aa31a20a754b165f0184d712fba8b65519125
looks good to me.
Nico César
04:09 pm Task #6298 (Resolved): Review branch: 6013-cleanup-setup-impl
Radhika Chippada
04:08 pm Revision 09fcf10f (arvados): closes #6013
Merge branch '6013-cleanup-setup-impl' Radhika Chippada
03:40 pm Feature #6280 (In Progress): [SDKs] Go SDK can return an io.Reader for a given collection record ...
Tom Clegg
03:40 pm Story #6218 (In Progress): [SDKs] [Performance] Add performance tests for Python SDK collection m...
Tom Clegg
03:00 pm Revision 19d9f3dd (arvados-dev): 6388: Fixup Makefile for Debian jessie.
Brett Smith
02:33 pm Support #6357 (Feedback): Review curoverse.link
Tom Clegg
02:26 pm Revision 400c39aa (arvados): 6388: Extend API server upgrade script to do initial database setup.
This will let administrators duplicating a lot of logic that already
exists in the script.
Brett Smith
02:26 pm Revision 400c39aa (arvados-dev): 6388: Extend API server upgrade script to do initial database se...
This will let administrators duplicating a lot of logic that already
exists in the script.
Brett Smith
01:58 pm Task #6410: create a puppet manifest to handle reverse proxy and CORS in switchyard's nginx
certs are there. I'm reviewing this task and see if it's ready to close Nico César
01:28 pm Revision b67167e7 (arvados): 6465 - Moved test for anonymous user accessing collection in a share...
to controller. Manoj Malipeddu
12:56 pm Task #6384 (In Progress): package libpam-arvados
Ward Vandewege
12:28 pm Revision 61600bd3 (arvados): Add arvados_pam.py and shellinabox pam configuration file.
Refs #2256 Ward Vandewege

07/05/2015

10:11 pm Revision 287590ce (arvados-dev): 6388: Rails package upgrade scripts support Red Hat systems.
* Red Hat doesn't use the www-data account name.
* When nginx is installed from a Software Collection, it may have a
...
Brett Smith
10:11 pm Revision 287590ce (arvados): 6388: Rails package upgrade scripts support Red Hat systems.
* Red Hat doesn't use the www-data account name.
* When nginx is installed from a Software Collection, it may have a
...
Brett Smith
03:55 pm Revision 9932d701 (arvados): Bugfix config:check error detection in Rails upgrade scripts.
The previous code was capturing the exit status of echo, which isn't
very interesting. No issue #.
Brett Smith
03:55 pm Revision 9932d701 (arvados-dev): Bugfix config:check error detection in Rails upgrade scripts.
The previous code was capturing the exit status of echo, which isn't
very interesting. No issue #.
Brett Smith
03:16 pm Story #6265: [CWL] Contribute to the CWL specification
Peter Amstutz wrote:
> CWL draft 2 is ready for review.
Trying to describe little copyedits in prose always seems...
Brett Smith
11:40 am Bug #5989: [API] API server repositories permissions list doesn't list repositories without keys
Brett Smith wrote:
> Brett Smith wrote:
> > We are iterating over permissions instead of repositories, and that's e...
Brett Smith
11:39 am Task #6479 (Resolved): Review 5989-api-all-repos-permissions-wip
Brett Smith
11:39 am Task #6291 (Resolved): Review 5989-bug_1
Brett Smith
11:39 am Revision 0e239ef8 (arvados): 5989: API repo perms method always returns all repos.
Previously the method would not return repositories that were not
accessible to any authorized key. This change help...
Brett Smith
11:35 am Story #6264: [CWL] Prototype Arvados CWL pipeline runner
Reviewing 6264-cwl-runner @ 53755b6
Considering the circumstances, I think this is good to merge. I would like to...
Brett Smith

07/03/2015

09:09 pm Feature #6013: [Workbench] clean up 'setup user' behavior in the admin interface
Notes about updates in 6013-cleanup-setup-impl branch:
* All the items listed in the description are addressed.
...
Radhika Chippada
08:58 pm Feature #6013 (In Progress): [Workbench] clean up 'setup user' behavior in the admin interface
Radhika Chippada
09:03 pm Revision 160aa31a (arvados): 6013: revert back the deactivate user button leading text in workben...
Radhika Chippada
08:56 pm Revision 0db099d9 (arvados): 6013: update user notification email upon setup.
Radhika Chippada
07:44 pm Revision cf8786f7 (arvados): 6013: remove "repository" from user setup popup in workbench
Radhika Chippada
04:09 pm Task #6478 (Resolved): Review Branch 6466-disable-public-projects
Manoj Malipeddu
04:06 pm Revision 87e9c0e2 (arvados): 6466:Added config parameter to disable public projects page and adde...
Manoj Malipeddu
03:53 pm Bug #6466 (In Progress): [Workbench] Add configuration knob to enable/disable public projects lis...
Manoj Malipeddu
03:35 pm Story #6477 (Resolved): [Documentation] Clarify the use of Docker within shared and private VMs
The "Port a Pipeline wiki page":https://arvados.org/projects/arvados/wiki/Port_a_Pipeline describes the process of in... Bryan Cosca
02:23 am Story #6476 (Resolved): [Workbench] actions#show should be implemented without requiring an API t...
It should be possible to share /action?uuid=FOO URLs to public projects. Right now this doesn't work because Workben... Brett Smith

07/02/2015

09:10 pm Feature #6013: [Workbench] clean up 'setup user' behavior in the admin interface
Updating the description to reflect the recent conversation on this ticket. The current description should be implem... Brett Smith
09:05 pm Bug #5989: [API] API server repositories permissions list doesn't list repositories without keys
Brett Smith wrote:
> We are iterating over permissions instead of repositories, and that's exactly the problem: the ...
Brett Smith
02:23 pm Bug #5989: [API] API server repositories permissions list doesn't list repositories without keys
The code in 5989-bug_1 is good. See e-mail about deployment issues. Thanks. Brett Smith
06:37 pm Story #6473 (Resolved): [SDKs] arv-ws supports an option to show events starting from a given time
arv-ws can live tail the logs for a given pipeline or job, but it won't go back in time. If you want to see logs alr... Brett Smith
05:55 pm Revision 6e7c96b2 (arvados): 6465: Moved the test "anonymous user accesses collection in shared p...
Manoj Malipeddu
05:15 pm Feature #6468 (New): Move arvados-mailchimp-plugin to a public repo
Nico César
03:11 pm Bug #6466 (Resolved): [Workbench] Add configuration knob to enable/disable public projects listing
This should be a simple boolean knob in application.yml. If it is false, /projects/public should return 404, just as... Brett Smith
02:39 pm Revision 76e74a7f (arvados): Merge branch '5989-bug_1' merge with puppet repo "copy and paste" to...
refs #5989 Nico César
02:35 pm Revision 0ebc3631 (arvados): 5989: bug_1 added puppet repository patch
this is duplicated code from:
puppet/modules/arvados-git-server/templates/usr-local-arvados-update-gitolite.rb.erb
...
Nico César
02:25 pm Revision 8048e6da (arvados): Merge branch '6264-run-command-task-env' refs #6264
Peter Amstutz
02:13 pm Task #6291 (In Progress): Review 5989-bug_1
Brett Smith
01:01 pm Task #6291: Review 5989-bug_1
Bug 1 is ready to review Nico César
02:09 pm Story #6264: [CWL] Prototype Arvados CWL pipeline runner
6264-run-command-task-env @ commit:15ccbba is good to merge.
One thing I noticed is that if the user specifies a n...
Brett Smith
01:51 pm Task #6294 (In Progress): Review 6264-cwl-runner
Peter Amstutz
01:47 pm Revision 15ccbbab (arvados): 6264: Add task.env to documentation.
Peter Amstutz
01:23 pm Story #6465 (Resolved): [Tests] Optimize workbench integration tests
Convert any integration tests that can be controller tests into controller tests to reduce run time. Radhika Chippada
03:23 am Task #6464 (In Progress): Review 6264-run-command-task-env
Peter Amstutz
03:23 am Task #6464 (Resolved): Review 6264-run-command-task-env
Peter Amstutz
03:05 am Revision 53755b6c (arvados): 6264: Support EnvVarRequirement and CreateFileRequirement.
Peter Amstutz

07/01/2015

10:15 pm Story #6405: [Workbench] Allow additional curation of the public projects listing
This will be done in a future sprint when we can have some more planning around use cases and functional requirements. Brett Smith
03:34 pm Story #6405: [Workbench] Allow additional curation of the public projects listing
Brett Smith wrote:
> For any installation that wants to let all users add stuff to the featured projects page, that ...
Tom Clegg
03:28 pm Story #6405: [Workbench] Allow additional curation of the public projects listing
There are a couple of points to address. One is which features are desired (and how urgently). Here's my understandin... Tom Clegg
03:10 pm Story #6405: [Workbench] Allow additional curation of the public projects listing
Radhika Chippada wrote:
> "moving the featured projects into anonymously shared *featured projects* project" : If we...
Brett Smith
09:58 pm Bug #5989: [API] API server repositories permissions list doesn't list repositories without keys
Nico Cesar wrote:
> About bug 2 on line 233 I see:
>
> [...]
>
> That's Brett's code from 39b48294
>
> *why...
Brett Smith
09:01 pm Bug #5989: [API] API server repositories permissions list doesn't list repositories without keys
About bug 2 on line 233 I see:... Nico César
08:29 pm Bug #5989 (In Progress): [API] API server repositories permissions list doesn't list repositories...
brach 5989-bug_1 should thave the fix. How do we test this? Nico César
09:43 pm Revision 508d3b10 (arvados): Merge branch '6264-run-command-task-env' into 6264-cwl-runner
Peter Amstutz
09:43 pm Revision e4895820 (arvados): 6264: Support setting environment variables.
Peter Amstutz
09:41 pm Revision 25e66d09 (arvados): Support job reuse, CreateFileRequirement, and EnvVarRequirement
Peter Amstutz
09:32 pm Task #6410: create a puppet manifest to handle reverse proxy and CORS in switchyard's nginx
I pushed configuration to puppet. Now we need certificates for all the cluster that we have to have the correct
...
Nico César
08:23 pm Revision 34ec4990 (arvados): 5989: create directory structure for temp files
refs #5989 bug_1 Nico César
07:44 pm Story #6315 (Duplicate): [OPS] run-build-packages builds RPMs
This happened in #6388. Brett Smith
06:54 pm Story #6281: [Crunch] Describe how it looks when Crunch v1 jobs run under Crunch v2
Wiki pages:
* [[Crunch1-in-Crunch2]]
* [[Crunch2 migration]]
Still hoping to rename "Job" to "Container" in Crun...
Tom Clegg
06:48 pm Task #6314 (Resolved): Crunch1-in-Crunch2 wiki page
Tom Clegg
03:41 pm Story #6279: [Workbench] Integrate a Web shell client
See webshell.zip attachment,
It should have all the minimal expression files to login.
see index.html for the ...
Nico César
03:11 pm Bug #6219: [FUSE] [Performance] Add performance tests for FUSE
Radhika Chippada wrote:
> The branch now contains test that lists a project's contents as well.
Thanks. And list...
Brett Smith
02:43 pm Task #6365 (In Progress): Write runner using cwltool and run-command
Peter Amstutz
01:44 pm Bug #6455 (Resolved): [Documentation] Fix oversights in compute installation docs
For crunch-dispatch:
* Set @crunch_job_wrapper: :slurm_immediate@
On compute nodes:
* Set up crunch user, wi...
Brett Smith
12:25 pm Revision 59e45dbc (arvados): Invoke crunch-job with `/usr/bin/env perl`.
No issue #. Brett Smith
02:54 am Task #6454 (Resolved): Review 5677-plpgsql-warning
Tom Clegg
02:54 am Task #6453 (Resolved): Review 6377-dev-startup
Tom Clegg
02:53 am Revision d0a2405d (arvados): 6264: CollectionFsAccess falls back reading local files.
Peter Amstutz
02:47 am Revision e6003097 (arvados): 6377: Avoid "incompatible encoding" errors by using blank template0 ...
Tom Clegg

06/30/2015

11:07 pm Bug #6219: [FUSE] [Performance] Add performance tests for FUSE
The branch now contains test that lists a project's contents as well. Radhika Chippada
06:45 pm Bug #6219: [FUSE] [Performance] Add performance tests for FUSE
Radhika Chippada wrote:
> I did not add test to retrieve project contents at this time.
Was there some obstacle t...
Brett Smith
04:30 pm Bug #6219: [FUSE] [Performance] Add performance tests for FUSE
Regarding branch 6219-fuse-performance-testing:
* This branch is from 3198-writable-fuse branch
* Includes some...
Radhika Chippada
04:23 pm Bug #6219 (In Progress): [FUSE] [Performance] Add performance tests for FUSE
Radhika Chippada
11:05 pm Revision fdb655af (arvados): 6219: add test to list contents of a project with many collections.
Radhika Chippada
06:56 pm Revision d8c6d08d (arvados): 6377: Create user-specified tmpdirs if necessary. refs #6377
Tom Clegg
06:56 pm Revision e18701a4 (arvados): 6377: Don't try to uninstall arvados* gems if they are not installed.
Fixes run-tests failure when no Ruby SDK is installed on the test host
and tmpdirs are new/empty. refs #6377
Tom Clegg
06:56 pm Revision d8c6d08d (arvados-dev): 6377: Create user-specified tmpdirs if necessary. refs #6377
Tom Clegg
06:56 pm Revision e18701a4 (arvados-dev): 6377: Don't try to uninstall arvados* gems if they are not insta...
Fixes run-tests failure when no Ruby SDK is installed on the test host
and tmpdirs are new/empty. refs #6377
Tom Clegg
05:54 pm Revision 5f18d6be (arvados): 6219: remove unused imports
Radhika Chippada
05:52 pm Revision 0effb930 (arvados): 6264: Passes 29/35 conformance tests. Some debugging and feature ad...
Peter Amstutz
04:25 pm Task #6452 (Resolved): Review branch: 6219-fuse-performance-testing (from 3198-writable-fuse) branch
Radhika Chippada
04:10 pm Revision 56753cd6 (arvados): 6219: add back the test with files with multiple blocks that I lost ...
Radhika Chippada
03:20 pm Bug #6438 (In Progress): [Documentation] Update Rails server installation guides to use packages
Brett Smith
03:20 pm Revision ea3b83da (arvados): 6377: Fix reversed condition in "site application.yml is optional" fix.
Tom Clegg
03:19 pm Revision ab72d767 (arvados): 6377: Use fork of themes_for_rails with fixed gemspec.
Allows installing with current bundler versions, which treat the invalid
gemspec as an error.
Tom Clegg
03:14 pm Story #6405: [Workbench] Allow additional curation of the public projects listing
A few concerns about this approach.
* "moving the featured projects into anonymously shared *featured projects* pr...
Radhika Chippada
03:07 pm Revision 222c3bb0 (arvados): 6377: Support loading omniauth config from application.yml.
Tom Clegg
01:46 am Revision deff6c26 (arvados): 6219: some more magic dir based testing
Radhika Chippada

06/29/2015

11:32 pm Revision 094c9628 (arvados): Merge branch '3198-writable-fuse' into 6219-fuse-performance-testing
Radhika Chippada
11:32 pm Revision fc69579b (arvados): Merge branch '3198-writable-fuse' of git.curoverse.com:arvados into ...
Radhika Chippada
11:31 pm Revision 88393d2f (arvados): 6219: some more magic dir based testing
Radhika Chippada
09:13 pm Revision 9d209cb3 (arvados): 6264: Uploads files and Docker images, can almost run jobs.
Peter Amstutz
08:59 pm Revision f266a0aa (arvados-dev): 6388: Add Dockerfile to build packages on CentOS 6.
Brett Smith
08:56 pm Revision 8b7923ab (arvados-dev): 6389: Add Makefile to support Docker builds.
Brett Smith
08:56 pm Revision 4e6b8664 (arvados-dev): 6389: Dockerfiles include the CMD to build packages.
Brett Smith
08:19 pm Revision 3b06308d (arvados): 6219: magic dir test in progress
Radhika Chippada
08:14 pm Revision c5e5db25 (arvados): 6264: First pass complete, ready for testing.
Peter Amstutz
06:18 pm Revision 264344dc (arvados-dev): Add rsync to the repo update command in run-build-packages.
No issue # Ward Vandewege
06:18 pm Revision 264344dc (arvados): Add rsync to the repo update command in run-build-packages.
No issue # Ward Vandewege
06:10 pm Revision 8f10d54c (arvados): 6264: Arvados CWL runner prototype work in progress.
Peter Amstutz
03:38 pm Story #6171 (In Progress): [FUSE] Document the writable FUSE mount
Peter Amstutz
03:38 pm Story #6281 (In Progress): [Crunch] Describe how it looks when Crunch v1 jobs run under Crunch v2
Peter Amstutz
03:38 pm Story #6282 (In Progress): [Crunch] Write stories for implementation of Crunch v2
Peter Amstutz
03:24 pm Feature #6442: [Workbench] [API] Support "world-readable, but not world-searchable" permission on...
Two ways Workbench could remember the secret part of the project's secret link when browsing the project's contents
...
Tom Clegg
03:20 pm Support #6267 (In Progress): Support users and triage bugs (second half)
Peter Amstutz
03:20 pm Story #6264 (In Progress): [CWL] Prototype Arvados CWL pipeline runner
Peter Amstutz
03:20 pm Story #6265 (In Progress): [CWL] Contribute to the CWL specification
Peter Amstutz
03:00 pm Revision 26b4ea99 (arvados): Dockerfile had an error. fixed
no issue # Nico César
02:53 pm Revision 18c93ee7 (arvados): we need to manually install python-pyasn1=0.1.7 python-pyasn1-module...
apt-get install are less quiet now too.
no issue #
Nico César
02:50 pm Bug #6443 (New): Git commit was not found when specified in template
https://cloud.curoverse.com/pipeline_instances/qr1hi-d1hrv-ohtq9mf6hqg7myj
Here, I set the script version of Run-SNP...
Bryan Cosca
01:58 pm Revision ccdaab65 (arvados): added more verbosity to Dockerfiles so we can show them in ci.curove...
no issue # Nico César

06/27/2015

10:03 pm Feature #6442 (New): [Workbench] [API] Support "world-readable, but not world-searchable" permiss...
This is similar to the "get a link to share" feature that's already available for collections, but the shareable link... Tom Clegg
09:57 pm Story #6405: [Workbench] Allow additional curation of the public projects listing
It sounds to me like we have a "public projects" page but what we really want is a "featured projects" page.
That ...
Tom Clegg
01:28 pm Bug #6439: [Workbench] Copying jobs causes "SubmitIdReused" error if submit_id is not null
It's hard to make "copy job" work well in the general case. Even if we restrict it to copying Completed/Failed jobs, ... Tom Clegg
01:05 pm Bug #6440 (Resolved): [Workbench] Improper quoting of error message
Applied in changeset arvados|commit:b17c7d97723d99909868d3435b449ab4e95f1708. Tom Clegg

06/26/2015

10:51 pm Bug #6358: [SDKs] Python Keep client uses wrong probe order for put()
Running arv-put and arv-get with ARVADOS_DEBUG=2 should generate enough log messages to see whether the servers are a... Tom Clegg
10:28 pm Revision b17c7d97 (arvados): 6440: Display AJAX errors as text, not HTML. closes #6440
Tom Clegg
09:22 pm Bug #6440 (Resolved): [Workbench] Improper quoting of error message
Encountering #6439 the error was not quoted properly, so instead of this somewhat helpful clue... Tom Clegg
09:17 pm Bug #6439 (New): [Workbench] Copying jobs causes "SubmitIdReused" error if submit_id is not null
While copying jobs and pipelines into a project:... Tom Clegg
09:09 pm Revision a0c5e16c (arvados): Make sure to also build a backported package for python-llfuse. We need
it for writeable fuse.
refs #3198
Ward Vandewege
09:09 pm Revision a0c5e16c (arvados-dev): Make sure to also build a backported package for python-llfuse. ...
it for writeable fuse.
refs #3198
Ward Vandewege
09:07 pm Revision 46a766ea (arvados-dev): Add dockerfiles for Debian7 and Ubuntu1204
refs #6389 Ward Vandewege
07:52 pm Revision 554300e7 (arvados): Fix bad CollectionReader reference in arv-put.
No issue #. Brett Smith
07:41 pm Revision 0e301da8 (arvados): Update comment references from 'debs' to 'packages'.
refs #6389 Ward Vandewege
07:41 pm Revision 0e301da8 (arvados-dev): Update comment references from 'debs' to 'packages'.
refs #6389 Ward Vandewege
07:40 pm Revision 4044a636 (arvados): Drop built packages into packages/$TARGET instead of the old 'debs' ...
Also, fix the 'find' test so that built packages are actually added to
the repository after upload.
refs #6389
Ward Vandewege
07:40 pm Revision 4044a636 (arvados-dev): Drop built packages into packages/$TARGET instead of the old 'de...
Also, fix the 'find' test so that built packages are actually added to
the repository after upload.
refs #6389
Ward Vandewege
07:04 pm Revision f5d864c9 (arvados): Add ubuntu1204 target to run-build-packages.sh
refs #6389 Ward Vandewege
07:04 pm Revision f5d864c9 (arvados-dev): Add ubuntu1204 target to run-build-packages.sh
refs #6389 Ward Vandewege
07:00 pm Bug #6438 (Resolved): [Documentation] Update Rails server installation guides to use packages
Brett Smith
06:55 pm Revision 598d191d (arvados-dev): Regex match fixes in the character class match for $FPM_RESULTS:
a) we want to match a literal dot, not any character
b) bash 4.2 does not support escaping a dash to include it in t...
Ward Vandewege
06:55 pm Revision 598d191d (arvados): Regex match fixes in the character class match for $FPM_RESULTS:
a) we want to match a literal dot, not any character
b) bash 4.2 does not support escaping a dash to include it in t...
Ward Vandewege
06:29 pm Revision 79be7ea2 (arvados): 6219: add test to create collection and read contents using magic dir.
Radhika Chippada
05:24 pm Story #6311: [Maybe] [SDKs] Support caching Keep blocks in memcached
Couple of things could make this much more troublesome than #3640:
* Orchestrating turning up/down memcached when jo...
Tom Clegg
03:45 pm Story #6432 (Resolved): [SDKs] PySDK supports Red Hat system CA certs
Applied in changeset arvados|commit:416a99c2039e879cefc67dd0764b8544ef6c2d53. Brett Smith
03:39 pm Story #6432: [SDKs] PySDK supports Red Hat system CA certs
reviewing 6432-pysdk-more-ca-certs-wip at commit:798218c8505a784877251e2424d39c8204895e20
Code looks good, tests p...
Ward Vandewege
01:47 pm Story #6432: [SDKs] PySDK supports Red Hat system CA certs
6432-pysdk-more-ca-certs-wip is up for review.
I thought about whether it made any sense to write a test, and ulti...
Brett Smith
03:42 pm Revision 416a99c2 (arvados): Merge branch '6432-pysdk-more-ca-certs-wip'
Closes #6432, #6434. Brett Smith
03:42 pm Revision 9b910084 (arvados): 6432: Python SDK can find and use CA certs on Red Hat.
Brett Smith
03:39 pm Task #6434 (Resolved): Review 6432-pysdk-more-ca-certs-wip
Ward Vandewege
03:35 pm Task #6434 (In Progress): Review 6432-pysdk-more-ca-certs-wip
Ward Vandewege
01:42 pm Task #6434 (Resolved): Review 6432-pysdk-more-ca-certs-wip
Brett Smith
03:19 pm Revision 7759a62c (arvados): Missing application.yml is not an error. No issue #
Tom Clegg
03:02 pm Bug #6436 (New): [Workbench] Pipeline template description display is difficult to read when maki...
Pipeline template descriptions are displayed over the "component, script, parameter, value" information. This makes t... Sarah Guthrie
03:00 pm Bug #6234 (Resolved): [Workbench] Admins should be able to edit their own user records, and view ...
Applied in changeset arvados|commit:665b0fbe5f57866f9d0183a08e713fe07e8db8de. Radhika Chippada
02:56 pm Bug #6234: [Workbench] Admins should be able to edit their own user records, and view other users...
Peter Amstutz wrote:
> Per our discussion, it is extremely confusing when you are viewing the home project of (or an...
Brett Smith
02:56 pm Task #6300 (Resolved): Review branch: 6234-user-edit-self
Radhika Chippada
02:36 pm Revision 665b0fbe (arvados): closes #6234
Merge branch '6234-user-edit-self' Radhika Chippada
02:34 pm Revision 2d4198a0 (arvados): Merge branch 'master' into 6234-user-edit-self
Radhika Chippada
01:12 pm Revision 5cb61be1 (arvados): 6388: CentOS needs backports for python-daemon and its dependencies.
Refs #6388. Brett Smith
01:12 pm Revision 5cb61be1 (arvados-dev): 6388: CentOS needs backports for python-daemon and its dependenc...
Refs #6388. Brett Smith
01:12 pm Revision 3465b6a8 (arvados): 6219: minor test updates
Radhika Chippada
06:58 am Bug #5677 (In Progress): [API] Silence harmless message "ERROR: must be owner of extension plpgsql"
5677-plpgsql-warning @ commit:02a3aa9 Tom Clegg
06:56 am Revision 02a3aa90 (arvados): 5677: Edit structure.sql after db:structure:dump: avoid warnings whe...
Tom Clegg
04:25 am Revision a1819526 (arvados): 6219: first draft at fuse performance testing.
Radhika Chippada
03:39 am Revision ca279f2c (arvados-dev): Additionally build and upload cwl-runner package. no issue #
Peter Amstutz
03:39 am Revision ca279f2c (arvados): Additionally build and upload cwl-runner package. no issue #
Peter Amstutz
02:19 am Revision f5cb4310 (arvados): Merge branch 'master' into 6219-fuse-performance-testing
Radhika Chippada

06/25/2015

11:36 pm Revision 798218c8 (arvados): 6432: Python SDK can find and use CA certs on Red Hat.
Brett Smith
11:10 pm Story #6432 (Resolved): [SDKs] PySDK supports Red Hat system CA certs
Right now the Python SDK knows how to find and use the Debian system CA certs file (@/etc/ssl/certs/ca-certificates.c... Brett Smith
08:29 pm Story #6429 (Resolved): [API] [Crunch2] Implement "containers" and "container requests" tables, m...
See [[Containers API]] and [[Crunch2 migration]]
For this initial implementation, focus on implementing and testin...
Peter Amstutz
07:53 pm Revision 6dc673b9 (arvados-dev): login patch because DockerHub is not friendly
no issue # Nico César
07:53 pm Revision 6dc673b9 (arvados): login patch because DockerHub is not friendly
no issue # Nico César
07:37 pm Bug #3573: [Workbench] When showing a shared project, do not include "Home" in breadcrumbs.
Updated version after meeting:
Given the following ownership hierarchy, where @A <--- B@ signifies "B.owner_uuid==...
Tom Clegg
07:33 pm Revision 3eecec6d (arvados-dev): Merge branch '6388-python-backports-wip'
Refs #6388. Closes #6425. Brett Smith
07:33 pm Revision 3eecec6d (arvados): Merge branch '6388-python-backports-wip'
Refs #6388. Closes #6425. Brett Smith
07:31 pm Story #6171: [FUSE] Document the writable FUSE mount
I think this is already mostly done in #3198, what do you think? Peter Amstutz
07:29 pm Bug #6234: [Workbench] Admins should be able to edit their own user records, and view other users...
Moving further discussion of breadcrumbs to #3573. Tom Clegg
06:28 pm Bug #6234: [Workbench] Admins should be able to edit their own user records, and view other users...
Proposed behavior for breadcrumb rendering:
* When looking at your home project or a subproject of your home proje...
Peter Amstutz
05:58 pm Bug #6234: [Workbench] Admins should be able to edit their own user records, and view other users...
Per our discussion, it is extremely confusing when you are viewing the home project of (or any project owned by) anot... Peter Amstutz
07:22 pm Revision c6de6999 (arvados-dev): 6388: Improve portability of Python backports in run-build-packa...
* Prefix package names with the same prefix used by the interpreter
package, to avoid conflicts with system package...
Brett Smith
07:22 pm Revision c6de6999 (arvados): 6388: Improve portability of Python backports in run-build-packages.
* Prefix package names with the same prefix used by the interpreter
package, to avoid conflicts with system package...
Brett Smith
07:19 pm Revision f4fcedfa (arvados-dev): 6388: CentOS 6 needs Python daemon and llfuse backported.
Brett Smith
07:19 pm Revision f4fcedfa (arvados): 6388: CentOS 6 needs Python daemon and llfuse backported.
Brett Smith
07:18 pm Revision 0b1b5713 (arvados): 6388: Build specific backport versions for Python OAuth dependencies.
Brett Smith
07:18 pm Revision 0b1b5713 (arvados-dev): 6388: Build specific backport versions for Python OAuth dependen...
Brett Smith
07:16 pm Revision 0181b121 (arvados-dev): 6388: Build PyCURL with NSS on CentOS 6.
Brett Smith
07:16 pm Revision 0181b121 (arvados): 6388: Build PyCURL with NSS on CentOS 6.
Brett Smith
07:10 pm Task #6066 (Resolved): Review 3198-writable-fuse
Peter Amstutz
06:01 pm Story #3198: [FUSE] Writable streaming arv-mount
Tom Clegg wrote:
> > Instead of speculating, let's wait to see what performance profiling says.
>
> Exactly. So...
Peter Amstutz
05:55 pm Story #3198 (Resolved): [FUSE] Writable streaming arv-mount
Applied in changeset arvados|commit:5b3187552676947ee74e4b652e7a04d3d9b9a3a4. Peter Amstutz
05:49 pm Story #3198: [FUSE] Writable streaming arv-mount
Peter Amstutz wrote:
> > OK... please don't forget to do that. ;) Fortunately it doesn't have to be the exact publis...
Tom Clegg
02:42 pm Story #3198: [FUSE] Writable streaming arv-mount
Tom Clegg wrote:
> By the way, in case this is related to the test-case-in-process strategy (but also because it s...
Peter Amstutz
05:55 pm Feature #4775 (Resolved): [SDKs] Add files to an existing Collection with CLI tools
Applied in changeset arvados|commit:5b3187552676947ee74e4b652e7a04d3d9b9a3a4. Peter Amstutz
05:55 pm Revision 1ec9e370 (arvados): Update arvados_fuse version dependency on arvados-python-client. re...
Peter Amstutz
05:52 pm Revision 5b318755 (arvados): Merge branch '3198-writable-fuse' closes #3198
Peter Amstutz
03:54 pm Revision 76edfd71 (arvados-dev): 6388: Remove old --apt-server switch from run-build-packages.
Refs #6388. Brett Smith
03:54 pm Revision 76edfd71 (arvados): 6388: Remove old --apt-server switch from run-build-packages.
Refs #6388. Brett Smith
03:41 pm Revision 121e7a81 (arvados): Merge branch '6388-centos-packages-wip'
Refs #6388. Closes #6411. Brett Smith
03:41 pm Revision 121e7a81 (arvados-dev): Merge branch '6388-centos-packages-wip'
Refs #6388. Closes #6411. Brett Smith
02:44 pm Task #6300 (In Progress): Review branch: 6234-user-edit-self
Peter Amstutz
02:30 pm Revision 41538c32 (arvados): 3198: Rename --enable-write to --read-write. Tweak docs.
Peter Amstutz

06/24/2015

09:47 pm Revision 82807388 (arvados): 6388: run-build-packages introspects more Python environment.
* Look for easy_install under a few different names.
* On CentOS, query the package that provides each Python, and li...
Brett Smith
09:47 pm Revision 82807388 (arvados-dev): 6388: run-build-packages introspects more Python environment.
* Look for easy_install under a few different names.
* On CentOS, query the package that provides each Python, and li...
Brett Smith
09:06 pm Revision 53ad1144 (arvados): 6388: Fix Arvados Perl SDK package build.
Brett Smith
09:06 pm Revision 53ad1144 (arvados-dev): 6388: Fix Arvados Perl SDK package build.
Brett Smith
08:44 pm Revision e5561b32 (arvados): 6388: Backport pycurl package everywhere.
We need the very latest version per #6073. Brett Smith
08:44 pm Revision e5561b32 (arvados-dev): 6388: Backport pycurl package everywhere.
We need the very latest version per #6073. Brett Smith
08:22 pm Story #6265: [CWL] Contribute to the CWL specification
CWL draft 2 is ready for review.
The specification is online at
https://common-workflow-language.github.io/draf...
Peter Amstutz
07:55 pm Task #6119: Review 6096-deploy-jobs-image
9 days ago I reviewit and forgot to reassign it to Ward. Now I'm doing it Nico César
07:36 pm Revision 46a6199f (arvados): Merge branch 'master' into 3198-writable-fuse
Radhika Chippada
06:59 pm Task #6364 (Resolved): Process remaining draft 2 change requests
Peter Amstutz
06:59 pm Task #6290 (In Progress): Review specification
Peter Amstutz
05:57 pm Revision 2f56fdaf (arvados): 6388: Remove version munging from Python package builds.
This code was added to accommodate version numbers that did *not*
comply with PEP 440. We've since fixed those, and ...
Brett Smith
05:57 pm Revision 2f56fdaf (arvados-dev): 6388: Remove version munging from Python package builds.
This code was added to accommodate version numbers that did *not*
comply with PEP 440. We've since fixed those, and ...
Brett Smith
05:51 pm Revision aac6af89 (arvados-dev): 6388: run-build-packages records python2.7 dependency where needed.
Brett Smith
05:51 pm Revision aac6af89 (arvados): 6388: run-build-packages records python2.7 dependency where needed.
Brett Smith
05:24 pm Revision 0e13d045 (arvados-dev): 6388: Add distro targets to run-build-packages.
This will provide us a single mechanism to make sure that packages are
built to run on a particular distribution: not...
Brett Smith
05:24 pm Revision 0e13d045 (arvados): 6388: Add distro targets to run-build-packages.
This will provide us a single mechanism to make sure that packages are
built to run on a particular distribution: not...
Brett Smith
03:50 pm Task #6404 (Resolved): Review
Tom Clegg
02:47 pm Task #6410 (In Progress): create a puppet manifest to handle reverse proxy and CORS in switchyard...
Nico César
02:28 pm Task #6410 (Resolved): create a puppet manifest to handle reverse proxy and CORS in switchyard's ...
Nico César
02:27 pm Task #6372 (Resolved): Review branch: 6218-add-performance-profiling-to-python-sdk
Radhika Chippada
02:24 pm Revision 69107d28 (arvados): refs #6218
Merge branch '6218-add-performance-profiling-to-python-sdk' Radhika Chippada
02:23 pm Task #6371 (Resolved): Add performance profiling framework to python sdk
Radhika Chippada
02:22 pm Revision 3104ab72 (arvados): 6218: update the exception handling.
Radhika Chippada
02:17 pm Story #6218: [SDKs] [Performance] Add performance tests for Python SDK collection methods
Radhika Chippada wrote:
> Tom, thanks for noticing the symlink issue; I corrected it. Please check.
Looks good, t...
Tom Clegg
01:58 pm Revision a8a79114 (arvados): 6218: correct exception handling.
Radhika Chippada

06/23/2015

09:01 pm Bug #6356: [Crunch] crunch-job retried a permanently failed task
It looks like what happened is:
# The task failed.
# reapchildren noticed this, and did the usual end-of-task wor...
Brett Smith
07:53 pm Story #6408 (Duplicate): [Workbench] Collection file views are sortable
Brett Smith
07:52 pm Story #6408 (Duplicate): [Workbench] Collection file views are sortable
Brett Smith
07:50 pm Story #6407 (Closed): [Workbench] Collection file trees are collapsible
Brett Smith
07:16 pm Story #6405: [Workbench] Allow additional curation of the public projects listing
A related issue is how to make sure there is a clean presentation of public projects and datasets (mostly for new use... Nancy Ouyang
07:11 pm Story #6405 (New): [Workbench] Allow additional curation of the public projects listing
Sasha says an opt-in approach is generally preferable to opt-out.
Possible approaches:
* Link objects that spec...
Brett Smith
06:16 pm Task #6404 (In Progress): Review
Tom Clegg
06:16 pm Task #6404 (Resolved): Review
Tom Clegg
06:13 pm Task #6295 (In Progress): Review
Peter Amstutz
06:13 pm Task #6301 (In Progress): Review
Peter Amstutz
06:13 pm Story #6282: [Crunch] Write stories for implementation of Crunch v2
crunch v2 stories
API server changes
- support container, container requests
Crunch v1 shim
- runs in a con...
Peter Amstutz
06:12 pm Story #6281: [Crunch] Describe how it looks when Crunch v1 jobs run under Crunch v2
Crunch v2 runs "containers" not jobs
Container can expose ports and act as a service
Crunch v1 runs shim API se...
Peter Amstutz
05:50 pm Feature #6013: [Workbench] clean up 'setup user' behavior in the admin interface
Ward Vandewege wrote:
> Ah. Yeah, we should probably make that work. Where do you want me to put that ticket? Just f...
Brett Smith
05:48 pm Feature #6013: [Workbench] clean up 'setup user' behavior in the admin interface
Brett Smith wrote:
> Ward Vandewege wrote:
> > Okay, that's fair. I looked at the version on 4xphq and that does se...
Ward Vandewege
05:36 pm Feature #6013: [Workbench] clean up 'setup user' behavior in the admin interface
Ward Vandewege wrote:
> Okay, that's fair. I looked at the version on 4xphq and that does seem fine. I assume that i...
Brett Smith
04:59 pm Feature #6013: [Workbench] clean up 'setup user' behavior in the admin interface
Brett Smith wrote:
> Ward Vandewege wrote:
> > Admin functions should be very simple and very straightforward. Thin...
Ward Vandewege
05:30 pm Revision f0d1f993 (arvados): 6388: Remove Debianisms from run-build-packages.
Make sure function and variable names don't refer to Debian when they
can also be used for Red Hat.
Brett Smith
05:30 pm Revision f0d1f993 (arvados-dev): 6388: Remove Debianisms from run-build-packages.
Make sure function and variable names don't refer to Debian when they
can also be used for Red Hat.
Brett Smith
05:20 pm Task #6364 (In Progress): Process remaining draft 2 change requests
Peter Amstutz
03:21 pm Story #6320 (Resolved): [OPS] Shell account creation script supports `groups` properties in can_l...
Brett Smith
02:33 pm Support #6357: Review curoverse.link
h3. adopt? replace curover.se?
This service implicitly offers to forever do Y when presented with link X, but the ...
Tom Clegg
02:21 pm Revision d7e0ab96 (arvados): 6320: Update Workbench test for active user VM setup.
Now that the test fixtures give the active user access to testvm2,
this test needs to be updated to account for it, j...
Brett Smith
02:13 pm Revision 628654aa (arvados): Remove unused modules from PySDK setup.py.
No issue #. Brett Smith
01:46 pm Story #6387 (New): [SDKs] arv-put progress meter scales based on file size, rather than being fix...
If you upload a small file with arv-put, the final progress meter will often say:... Brett Smith
01:33 pm Story #6218: [SDKs] [Performance] Add performance tests for Python SDK collection methods
Tom, thanks for noticing the symlink issue; I corrected it. Please check.
Also, regarding the comment in performan...
Radhika Chippada
01:25 pm Revision eac37feb (arvados): 6218: update the symlink and comment
Radhika Chippada

06/22/2015

09:01 pm Story #6218: [SDKs] [Performance] Add performance tests for Python SDK collection methods
Works for me.
I've pushed 6218-add-performance-profiling-to-python-sdk-TC with a couple of changes:
* Profiling r...
Tom Clegg
09:00 pm Task #6283 (Resolved): Review 4410-slurm-fails-are-tempfails-wip
Applied in changeset arvados|commit:ad7679cfe57733940f8461097ee01bfd97997ce6. Brett Smith
09:00 pm Bug #4410 (Resolved): [Crunch] crunch-job should exit tempfail when a SLURM node fails
Applied in changeset arvados|commit:ad7679cfe57733940f8461097ee01bfd97997ce6. Brett Smith
05:25 pm Bug #4410: [Crunch] crunch-job should exit tempfail when a SLURM node fails
> > No difference to behavior, but as an explanation, this comment should be the "else" part of if jobrecord.state ==... Tom Clegg
08:55 pm Revision ad7679cf (arvados): Merge branch '4410-slurm-fails-are-tempfails-wip'
Closes #4410, #6283. Brett Smith
08:55 pm Revision 1f40455a (arvados): 6218: Refactor profiler as a decorator
Tom Clegg
08:49 pm Revision 24b4d1ad (arvados): 4410: crunch-dispatch logs crunch-job exit later.
This makes it easier to log the exit code, and makes the logs look
nicer because the exit log doesn't interrupt crunc...
Brett Smith
08:49 pm Revision b269c28f (arvados): 4410: Crunch retries jobs when all SLURM nodes fail.
See the ticket for detailed background discussion and implementation
rationale, especially notes 13 and 14.
This req...
Brett Smith
08:45 pm Task #6384: package libpam-arvados
Here are the 2 files you need.
you should rename nico_pam.py to something more meaningful
shelinabox is /etc/pa...
Nico César
07:45 pm Task #6384 (Resolved): package libpam-arvados
Ward Vandewege
08:41 pm Revision 24fa04e6 (arvados): 6218: Refactor profiler as a decorator
Tom Clegg
07:45 pm Task #6383 (Resolved): package shellinabox-2.14
Ward Vandewege
07:41 pm Task #6372 (In Progress): Review branch: 6218-add-performance-profiling-to-python-sdk
Tom Clegg
06:37 pm Story #2256: [Workbench] Users can access an Arvados shell through the Web

# -buy 1 certificate per installation *.zzzzz.arvadosapi.com OR webshell.zzzzz.arvadosapi.com- DONE
# -make sure...
Nico César
06:33 pm Bug #6382 (New): [Workbench] Searching through a collection using regex should accept $ instead o...
Not sure how else to phrase this, (I expected something to work but it didn't.)
!regexinsidecollections.gif!
Bryan Cosca
06:19 pm Task #6360 (In Progress): add arvados API token libpam python module for shellinabox via puppet f...
Nico César
05:40 pm Story #6380 (New): Reading a new collection from keep takes extra time
When testing out how samtools merge looks at files, I ran some tests here:... Bryan Cosca
03:38 pm Story #3198: [FUSE] Writable streaming arv-mount
Peter Amstutz wrote:
> > (@del self.pool@ doesn't delete anything: it just unbinds the variable, which seems just as...
Tom Clegg
03:31 pm Revision ae63accf (arvados): 6218: fix typo in sample test
Radhika Chippada
 

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