Brett Smith [Thu, 20 Mar 2014 21:26:48 +0000 (17:26 -0400)]
workbench: Fix typo in application.default.yml.
Brett Smith [Thu, 20 Mar 2014 21:24:24 +0000 (17:24 -0400)]
workbench: Make integration test settings default.
We know that these settings should work out of the box, given the
settings in the API server's `rails` script. Making them the default
makes it easier to get the tests running.
Brett Smith [Wed, 19 Mar 2014 18:50:21 +0000 (14:50 -0400)]
workbench: Document integration test dependencies.
This adds appropriate notes to the installation guide, and suggestions
to application.yml.example.
Brett Smith [Wed, 19 Mar 2014 16:24:37 +0000 (12:24 -0400)]
workbench: Add basic login integration tests.
Brett Smith [Wed, 19 Mar 2014 16:10:51 +0000 (12:10 -0400)]
workbench: Add VM integration tests.
This is the "start test" that Ward suggested I implement to start off.
It's easy but not trivial: it requires JavaScript support and filling
out a form.
Brett Smith [Wed, 19 Mar 2014 16:09:51 +0000 (12:09 -0400)]
workbench: Use Poltergeist for integration tests.
This is faster and will enable us to run integration tests on the
build server.
PhantomJS (http://phantomjs.org/) has to be installed in the $PATH for
this to work.
Brett Smith [Wed, 19 Mar 2014 15:44:49 +0000 (11:44 -0400)]
workbench: Add integration test helper module.
This provide a base test class that provides the Capybara DSL and a
couple of convenience methods. It also specifies a test runner class
that sets up the API server consistently, with the proper environment.
Brett Smith [Wed, 19 Mar 2014 15:42:30 +0000 (11:42 -0400)]
workbench: Add Capybara gem for integration tests.
Brett Smith [Mon, 17 Mar 2014 18:48:02 +0000 (14:48 -0400)]
js: Add identifiers to X-Editable templates.
This gives the form elements name and id attributes, as appropriate.
This will make it easier for us to refer to them in integration tests.
Tom Clegg [Fri, 14 Mar 2014 17:42:20 +0000 (13:42 -0400)]
Merge branch '2257-inequality-conditions'
closes #2257
Tom Clegg [Fri, 14 Mar 2014 17:38:23 +0000 (13:38 -0400)]
Add "filters" param to discovery document, add deprecation note to
"where" param description.
Brett Smith [Fri, 14 Mar 2014 17:34:29 +0000 (13:34 -0400)]
api: Improve compute_node_domain handling.
The default value was causing test failures on my machine because the
ERB evaluated to an empty string. And we want to avoid this causing
any DNS lookups during tests. Now we make the default false (in line
with our other compute_node_* settings), and suggest a change in
application.yml.example to demonstrate how it should be set.
I also fixed up the example about compute_node_nameservers while I was
at it.
This closes #2351.
Tom Clegg [Fri, 14 Mar 2014 14:31:03 +0000 (10:31 -0400)]
Make integer attributes searchable, add test cases.
Tom Clegg [Fri, 14 Mar 2014 14:17:46 +0000 (10:17 -0400)]
Merge branch 'master' into 2257-inequality-conditions
Tom Clegg [Thu, 13 Mar 2014 15:49:46 +0000 (11:49 -0400)]
Fix order of steps in install doc, add git_repositories_dir
instructions, remove troublesome default config.
Brett Smith [Thu, 13 Mar 2014 16:28:25 +0000 (12:28 -0400)]
doc: Make Workbench install guide up-to-date.
* Configure the application with `application.yml` instead of
`config/environments/*.rb`.
* Consistently capitalize Workbench.
Peter Amstutz [Thu, 13 Mar 2014 13:50:21 +0000 (09:50 -0400)]
Formatting tweaking to look good on github.
Peter Amstutz [Thu, 13 Mar 2014 13:48:29 +0000 (09:48 -0400)]
Added more links to information in README.
Peter Amstutz [Thu, 13 Mar 2014 13:31:02 +0000 (09:31 -0400)]
Added a README with pointers to the documentation, COPYING with license information, the relevant licenses, as well as a license section to the user guide.
Tom Clegg [Thu, 13 Mar 2014 04:17:06 +0000 (00:17 -0400)]
Fix crash in render_error(not_an_exception), and use raise() rather
than calling render_error() directly from ApplicationController#save
and #update
Tom Clegg [Thu, 13 Mar 2014 04:04:34 +0000 (00:04 -0400)]
Add sqlite3 to Gemfile so database.yml.sample works unmodified
Tom Clegg [Wed, 12 Mar 2014 22:11:15 +0000 (18:11 -0400)]
Fix configured uuid_prefix and force_ssl getting overwritten by application.rb
Tom Clegg [Wed, 12 Mar 2014 22:10:32 +0000 (18:10 -0400)]
Remove some stumbling blocks in default/example configs
Peter Amstutz [Thu, 13 Mar 2014 02:21:49 +0000 (22:21 -0400)]
Fixed typo in secret_token.rb
Peter Amstutz [Thu, 13 Mar 2014 02:19:20 +0000 (22:19 -0400)]
Updated workbench documentation.
Peter Amstutz [Thu, 13 Mar 2014 01:53:57 +0000 (21:53 -0400)]
Working on improving install documentation.
Peter Amstutz [Thu, 13 Mar 2014 01:08:33 +0000 (21:08 -0400)]
Added section on setting up SSO server
Peter Amstutz [Wed, 12 Mar 2014 19:29:18 +0000 (15:29 -0400)]
Adds scopes: ["all"] when creating a new api client authorization, because database schema does not permit have a null scopes column.
Peter Amstutz [Wed, 12 Mar 2014 19:26:29 +0000 (15:26 -0400)]
Replaces postgres-specific 'now()' with standard SQL CURRENT_TIMESTAMP
Render checks that opts which are passed in are valid before trying to use it.
Ward Vandewege [Wed, 12 Mar 2014 16:15:04 +0000 (12:15 -0400)]
URL change for the auth server.
Ward Vandewege [Tue, 11 Mar 2014 22:22:12 +0000 (18:22 -0400)]
Fix links to docs in workbench
Tom Clegg [Tue, 11 Mar 2014 20:50:05 +0000 (16:50 -0400)]
Update Gemfile to use latest arv-run-pipeline
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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# the commit.
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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# the commit.
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.
#
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# 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/
Tom Clegg [Sun, 9 Mar 2014 07:36:36 +0000 (03:36 -0400)]
Advertise filters param in discovery doc.
Tom Clegg [Sun, 9 Mar 2014 07:33:50 +0000 (03:33 -0400)]
Move where=[] to filters=[]
Tom Clegg [Fri, 7 Mar 2014 23:13:15 +0000 (18:13 -0500)]
Support where=[[attr,operator,operand],...] parameter
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.