Tom Clegg [Tue, 11 Mar 2014 20:29:18 +0000 (16:29 -0400)]
Bump versions, change optional=false to required=true, set dataclass
for bwa-aln input.
Tom Clegg [Tue, 11 Mar 2014 20:27:55 +0000 (16:27 -0400)]
Fix giving up on a pipeline prematurely when a component is waiting
for an output produced by a component later in the components.each()
loop.
Peter Amstutz [Tue, 11 Mar 2014 20:27:22 +0000 (16:27 -0400)]
Merge branch 'master' of git.clinicalfuture.com:arvados
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
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Peter Amstutz [Tue, 11 Mar 2014 20:26:59 +0000 (16:26 -0400)]
Merge branch '2107-update-documentation'
Brett Smith [Tue, 11 Mar 2014 20:12:11 +0000 (16:12 -0400)]
doc: Note warning for get one collection block.
Added per discussion with Tom. We're also interested in fixing the
warning, but in the meantime, this is worth documenting.
Brett Smith [Tue, 11 Mar 2014 20:08:19 +0000 (16:08 -0400)]
doc: Improve "How Keep Works" flow.
This addresses the fact that this page was broken off from the
original Keep tutorial page.
Tim Pierce [Tue, 11 Mar 2014 19:53:33 +0000 (15:53 -0400)]
Merge branch 'master' of git.clinicalfuture.com:arvados
Brett Smith [Tue, 11 Mar 2014 19:28:05 +0000 (15:28 -0400)]
doc: Make CLI pipeline run up-to-date.
This refreshes Keep hashes and the output format of `arv pipeline run`.
Brett Smith [Tue, 11 Mar 2014 19:26:52 +0000 (15:26 -0400)]
doc: Improve flow of CLI pipeline run.
The previous version assumed that we already had a static pipeline
template. That's no longer true under the current flow, so instruct
the user to make one at the start of the tutorial.
Peter Amstutz [Tue, 11 Mar 2014 19:21:41 +0000 (15:21 -0400)]
Merge branch 'master' of git.clinicalfuture.com:arvados
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
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Peter Amstutz [Tue, 11 Mar 2014 19:21:28 +0000 (15:21 -0400)]
Bugfixes to provenance graph:
* Fixed url generation to use correct protocol (http/https)
* Fixed generic node description
* Fixed direction of provenance graph
Tom Clegg [Tue, 11 Mar 2014 18:58:44 +0000 (14:58 -0400)]
Report error message and propagate exit code if subprocess.call() fails.
Tim Pierce [Tue, 11 Mar 2014 18:48:49 +0000 (14:48 -0400)]
Update instructions to use build.sh. (refs #2221)
Brett Smith [Tue, 11 Mar 2014 18:11:22 +0000 (14:11 -0400)]
doc: Consistent style in outside program tutorial.
Brett Smith [Tue, 11 Mar 2014 18:04:39 +0000 (14:04 -0400)]
doc: Consistent style in new pipeline tutorial.
Brett Smith [Tue, 11 Mar 2014 17:50:08 +0000 (13:50 -0400)]
doc: Small bugfixes for first pipeline template.
Peter Amstutz [Tue, 11 Mar 2014 18:34:58 +0000 (14:34 -0400)]
Ran linkchecker and fixed links.
Peter Amstutz [Tue, 11 Mar 2014 18:18:12 +0000 (14:18 -0400)]
Added liquid template to link to next and previous pages.
Tom Clegg [Tue, 11 Mar 2014 18:05:59 +0000 (14:05 -0400)]
Fix user_agreements/sign* routing again.
Tom Clegg [Tue, 11 Mar 2014 17:56:15 +0000 (13:56 -0400)]
Fix route method on user_agreements/sign.
Brett Smith [Tue, 11 Mar 2014 16:33:55 +0000 (12:33 -0400)]
doc: Bold `you` in tutorial-parallel's job spec.
Brett Smith [Tue, 11 Mar 2014 15:43:40 +0000 (11:43 -0400)]
doc: Fix hello-world-fixed.py name in job-debug.
Brett Smith [Tue, 11 Mar 2014 15:31:09 +0000 (11:31 -0400)]
doc: Consistent style for `you` in job-debug.
Brett Smith [Tue, 11 Mar 2014 15:24:07 +0000 (11:24 -0400)]
doc: Update job1's expected output.
Pete changed this script so that the output filename has a leading
`./`. This commit updates the tutorial to match.
Brett Smith [Tue, 11 Mar 2014 16:05:50 +0000 (12:05 -0400)]
doc: Highlight `you` in the first script job spec.
Brett Smith [Tue, 11 Mar 2014 15:10:44 +0000 (11:10 -0400)]
doc: Suggest setting User in .ssh/config.
Tom Clegg [Tue, 11 Mar 2014 17:28:49 +0000 (13:28 -0400)]
Update comment to refer to correct default-config file.
Tom Clegg [Tue, 11 Mar 2014 17:03:45 +0000 (13:03 -0400)]
Fix left nav order in Install section.
Tom Clegg [Tue, 11 Mar 2014 17:02:48 +0000 (13:02 -0400)]
Add api server package dependencies and update config instructions.
Peter Amstutz [Tue, 11 Mar 2014 16:36:11 +0000 (12:36 -0400)]
Removed h1. titles from pages because it is now part of the page template.
Peter Amstutz [Tue, 11 Mar 2014 16:22:57 +0000 (12:22 -0400)]
More documentation updates and reorganization.
Tom Clegg [Tue, 11 Mar 2014 16:03:51 +0000 (12:03 -0400)]
Remove PYTHONPATH hack.
Peter Amstutz [Tue, 11 Mar 2014 15:38:58 +0000 (11:38 -0400)]
Finished first draft of tutorial running pipeline from workbench.
Peter Amstutz [Tue, 11 Mar 2014 14:52:19 +0000 (10:52 -0400)]
Reorganizing documentation work in progress, checkpointing so that Brett can start looking through it.
Tom Clegg [Tue, 11 Mar 2014 04:29:40 +0000 (00:29 -0400)]
Add instructions for installing with new versions of pip.
Tom Clegg [Tue, 11 Mar 2014 04:07:40 +0000 (00:07 -0400)]
Fix namespace bug in write_directory_tree(max_manifest_depth=0).
Tom Clegg [Tue, 11 Mar 2014 01:02:35 +0000 (21:02 -0400)]
Add python-pip to Python SDK install dependencies
Tom Clegg [Mon, 10 Mar 2014 23:54:10 +0000 (19:54 -0400)]
Add arvados-cli dependency to Gemfile.
Peter Amstutz [Mon, 10 Mar 2014 21:08:46 +0000 (17:08 -0400)]
Merge branch '2042-new-collection-from-selected-files'
Peter Amstutz [Mon, 10 Mar 2014 21:04:48 +0000 (17:04 -0400)]
Merge branch 'master' of git.clinicalfuture.com:arvados
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
Peter Amstutz [Mon, 10 Mar 2014 21:00:49 +0000 (17:00 -0400)]
Removed out of order link to next tutorial.
Peter Amstutz [Mon, 10 Mar 2014 21:00:20 +0000 (17:00 -0400)]
Updating and reorganizing tutorials based on new features and feedback.
Tom Clegg [Mon, 10 Mar 2014 20:49:24 +0000 (16:49 -0400)]
Rename preload_all_models to zz_* so it runs after load_config.
Tom Clegg [Mon, 10 Mar 2014 20:38:00 +0000 (16:38 -0400)]
Default to using a random secret_token in test mode.
Tom Clegg [Mon, 10 Mar 2014 20:34:14 +0000 (16:34 -0400)]
Add missing config variable to test.rb.example. Thanks, #2076!
Tom Clegg [Mon, 10 Mar 2014 20:26:57 +0000 (16:26 -0400)]
Rename load_config to zz_load_config so initializers/secret_token.rb
gets loaded before we check for missing config settings.
refs #2076
Tom Clegg [Mon, 10 Mar 2014 20:09:16 +0000 (16:09 -0400)]
Merge branch '2189-log-in-as-user'
closes #2189
Tom Clegg [Mon, 10 Mar 2014 20:09:04 +0000 (16:09 -0400)]
Merge branch '2076-check-config-at-boot'
closes #2076
Tom Clegg [Mon, 10 Mar 2014 20:08:29 +0000 (16:08 -0400)]
Merge branch 'master' into 2189-log-in-as-user
Tom Clegg [Mon, 10 Mar 2014 20:05:31 +0000 (16:05 -0400)]
Rename config[.defaults].yml to application[.default].yml
Tom Clegg [Mon, 10 Mar 2014 19:58:49 +0000 (15:58 -0400)]
Merge branch 'master' into 2076-check-config-at-boot
Peter Amstutz [Mon, 10 Mar 2014 17:40:29 +0000 (13:40 -0400)]
* Added README with information about building/viewing the docs.
* Added arvados_workbench_host
* Can now specify baseurl, arvados_workbench_host, and arvados_api_host on the command line to override _config.yml
* Added liquid tag {% code 'file' as language %} for syntax highlighting via coderay
Tom Clegg [Mon, 10 Mar 2014 17:21:55 +0000 (13:21 -0400)]
Fix incorrect API endpoints in api/schema/
Peter Amstutz [Fri, 7 Mar 2014 22:05:59 +0000 (17:05 -0500)]
Merge branch '2049-run-job-from-workbench-correct' of git.clinicalfuture.com:arvados into 2049-run-job-from-workbench-correct
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
Peter Amstutz [Fri, 7 Mar 2014 22:04:54 +0000 (17:04 -0500)]
render_editable_subattribute() uses link_to_if_arvados_object() if the field is not editable.
Peter Amstutz [Fri, 7 Mar 2014 21:55:42 +0000 (16:55 -0500)]
* Pipeline components are topologically sorted based on :output_of, then sorted lexically.
* Refactored code to render pipeline components to be consistent across pipeline instance page and pipeline template page.
* Added "pipelines" tab that shows pipelines that were created from the current template. Uses the pipeline_instances/show_recent partial.
Tom Clegg [Fri, 7 Mar 2014 21:49:47 +0000 (16:49 -0500)]
Fix CollectionReader treating any collection with additional +hints as
an empty manifest.
Now, accept hash+size+anyhints as a UUID, and if the argument looks
like neither a UUID nor a manifest, raise an exception instead of
proceeding with undefined results.
Ward Vandewege [Fri, 7 Mar 2014 20:17:57 +0000 (15:17 -0500)]
We can't have dependencies on unpublished gems checked in; they break
deploy.
Tom Clegg [Fri, 7 Mar 2014 20:02:14 +0000 (15:02 -0500)]
Merge branch '1844-blob-signature'
Tom Clegg [Fri, 7 Mar 2014 20:02:00 +0000 (15:02 -0500)]
Merge branch 'master' into 1844-blob-signature
Peter Amstutz [Fri, 7 Mar 2014 19:46:34 +0000 (14:46 -0500)]
Merge remote-tracking branch 'refs/remotes/origin/2049-run-job-from-workbench-TC' into 2049-run-job-from-workbench-correct
Tim Pierce [Fri, 7 Mar 2014 19:35:49 +0000 (14:35 -0500)]
Code review for 1844-blob-signature: documentation, slight refactoring (refs #1844)
Peter Amstutz [Fri, 7 Mar 2014 18:43:01 +0000 (13:43 -0500)]
Merge remote-tracking branch 'origin/master' into 2042-new-collection-from-selected-files
Peter Amstutz [Fri, 7 Mar 2014 18:41:42 +0000 (13:41 -0500)]
Merge remote-tracking branch 'origin/master' into 2049-run-job-from-workbench-correct
Tom Clegg [Fri, 7 Mar 2014 18:37:03 +0000 (13:37 -0500)]
Fix check for crunch-job missing from path, and run it as arv-crunch-job.
Peter Amstutz [Fri, 7 Mar 2014 18:34:24 +0000 (13:34 -0500)]
Fixed styling of selection dropdown menu.
Menu no longer dismisses when clicking a checkbox to remove an item.
Selected files no longer have /./ in the middle.
Fixed nil error when non-file or non-collection items are in the selection list.
Fixed head_kind and tail_kind.
Made a comment about inline x-editable.
Tom Clegg [Fri, 7 Mar 2014 18:31:59 +0000 (13:31 -0500)]
Fix crash when job script is nil.
Tom Clegg [Fri, 7 Mar 2014 16:28:11 +0000 (11:28 -0500)]
Add arvados-cli dependency
Tom Clegg [Fri, 7 Mar 2014 16:26:52 +0000 (11:26 -0500)]
Obey ARVADOS_API_HOST_INSECURE
Peter Amstutz [Fri, 7 Mar 2014 15:16:56 +0000 (10:16 -0500)]
Provenance graphing bugfixes
Tom Clegg [Thu, 6 Mar 2014 22:54:07 +0000 (17:54 -0500)]
Add arv-normalize to python SDK package.
Peter Amstutz [Thu, 6 Mar 2014 22:10:22 +0000 (17:10 -0500)]
Fixed bug when selection list was cleared.
Fixed rendering collections in provenance graph.
Peter Amstutz [Thu, 6 Mar 2014 20:55:19 +0000 (15:55 -0500)]
Merge remote-tracking branch 'origin/master' into 2042-new-collection-from-selected-files
Peter Amstutz [Thu, 6 Mar 2014 20:49:49 +0000 (15:49 -0500)]
Fixed data title
Peter Amstutz [Thu, 6 Mar 2014 20:49:25 +0000 (15:49 -0500)]
Improvements and bugfixes refs #2242.
* Added tooltip to "play" button on pipeline templates page.
* Adjusted play button styling.
* Added a little bit of text to tell the user what to do on the parameter editing page.
* Moved "run pipeline" button to the tab bar row.
* Fixed the "-selection-" and "-recent-" dividers to be invalid selections.
* Tweaked editing popup label to say "set value for xxx" instead of "update xxx"
* Refactored status labels and progress bars for jobs and pipelines into partials that should be used everywhere consistently
* Fixed automatic refresh of pipeline instance page to emit ajax:complete event, and fixed shown.bs.tab event to catch all events and then apply the selector, instead of having to use the selector to attach events to specific DOM nodes (which breaks when the page is refreshed.)
Peter Amstutz [Wed, 5 Mar 2014 21:56:39 +0000 (16:56 -0500)]
Fixed progress bar alignment on Firefox.
Peter Amstutz [Wed, 5 Mar 2014 20:03:58 +0000 (15:03 -0500)]
Running pipeline from workbench works!
Tom Clegg [Wed, 5 Mar 2014 19:46:09 +0000 (14:46 -0500)]
Add "rake config:check" task. refs #2076
radhika chippada [Wed, 5 Mar 2014 17:22:16 +0000 (12:22 -0500)]
Merge branch '2107-radhika-user-guide-minor-updates'
radhika chippada [Wed, 5 Mar 2014 17:20:17 +0000 (12:20 -0500)]
Fix Task#2268 by removing the extra space character
Peter Amstutz [Wed, 5 Mar 2014 17:17:41 +0000 (12:17 -0500)]
Merge remote-tracking branch 'origin/master' into 2049-run-job-from-workbench
Peter Amstutz [Wed, 5 Mar 2014 14:58:35 +0000 (09:58 -0500)]
Successfully starts first stage of active pipelines.
Tom Clegg [Wed, 5 Mar 2014 09:35:45 +0000 (04:35 -0500)]
Read configuration from config.defaults.yml and config.yml.
Refuse to start if any configs are set to nil in config.default.yml
and not overridden in config/environments/*.rb or config.yml.
refs #2076
Tom Clegg [Wed, 5 Mar 2014 05:30:12 +0000 (00:30 -0500)]
Add "Log in as user" button in Admin pane on users#show.
refs #2189
Peter Amstutz [Wed, 5 Mar 2014 02:57:40 +0000 (21:57 -0500)]
Fixed default inactive user page.
Tom Clegg [Tue, 4 Mar 2014 22:12:25 +0000 (17:12 -0500)]
Add signing and verification code for blob permissions
radhika chippada [Tue, 4 Mar 2014 20:31:31 +0000 (15:31 -0500)]
Merge branch 'master' into 2107-radhika-user-guide-minor-updates
Conflicts:
doc/_config.yml
Tom Clegg [Tue, 4 Mar 2014 18:01:03 +0000 (13:01 -0500)]
Document baseurl and change to a useful default.
Tom Clegg [Tue, 4 Mar 2014 17:31:54 +0000 (12:31 -0500)]
Use require instead of rake_require. Fixes "Can't find
zenweb/tasks".
See
https://github.com/seattlerb/zenweb/commit/
4a28f3c8d766be7066658706d49b675d2a0f94ad
Peter Amstutz [Tue, 4 Mar 2014 16:50:19 +0000 (11:50 -0500)]
Working on having crunch-dispatch manage pipelines.
Peter Amstutz [Tue, 4 Mar 2014 15:52:00 +0000 (10:52 -0500)]
Merge remote-tracking branch 'origin/master' into 2049-run-job-from-workbench
radhika chippada [Mon, 3 Mar 2014 20:17:42 +0000 (15:17 -0500)]
minor updates to user guide
Peter Amstutz [Mon, 3 Mar 2014 19:02:22 +0000 (14:02 -0500)]
Added section about installing libwarehouse-perl.
Peter Amstutz [Mon, 3 Mar 2014 19:02:05 +0000 (14:02 -0500)]
Gemfile update using ruby 2.1.1
tetron [Mon, 3 Mar 2014 16:51:57 +0000 (11:51 -0500)]
Merge pull request #1 from gitaway/patch-1
Correct parameterized input collection reference
Phil Hodgson [Mon, 3 Mar 2014 16:40:15 +0000 (11:40 -0500)]
Correct parameterized input collection reference
Attempting to follow the tutorial I was blocked because the UUID for the alternate input supplied as a command line parameter was incomplete. This can be easily overlooked because in fact the final filtered output is a zero-length file in either case: it's just that currently it is zero-length only because its input is empty!
Ward Vandewege [Mon, 3 Mar 2014 16:33:54 +0000 (11:33 -0500)]
Be consistent in referring to the 'All users' group.
Peter Amstutz [Sat, 1 Mar 2014 02:36:00 +0000 (21:36 -0500)]
Fixed broken links in documentation that were using {{site.basedoc}} instead of {{site.baseurl}}.
Fixed some other links so that documentation can be browsed from file:///
Made some updates to API server setup guide.
Tom Clegg [Sat, 1 Mar 2014 00:29:34 +0000 (16:29 -0800)]
Fix jobs.cancel and add integration test. closes #2258
Tom Clegg [Sat, 1 Mar 2014 00:15:38 +0000 (16:15 -0800)]
Fix usage message dependent on credentials. Remove unused argparse import.