Tim Pierce [Thu, 13 Mar 2014 21:58:57 +0000 (17:58 -0400)]
Merge branch 'master' into 2221-complete-docker
Tim Pierce [Thu, 13 Mar 2014 21:57:57 +0000 (17:57 -0400)]
Save logs to a temp file and commit to Keep via 'arv keep put'. Refs #2221.
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
Tim Pierce [Wed, 12 Mar 2014 22:17:42 +0000 (18:17 -0400)]
Fix RVM install bug (rvm-installer --ruby doesn't work in Docker?) refs #2221
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.
Tim Pierce [Wed, 12 Mar 2014 18:43:38 +0000 (14:43 -0400)]
Merge branch 'master' into 2221-complete-docker
Conflicts:
doc/user/topics/tutorial-job-debug.html.textile.liquid
doc/user/tutorials/tutorial-keep.html.textile.liquid
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
Tim Pierce [Tue, 11 Mar 2014 21:36:13 +0000 (17:36 -0400)]
install_sdk.sh: install the arvados-cli gem and all prerequisites. (refs #2221)
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.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# 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 19:54:22 +0000 (15:54 -0400)]
Merge branch 'master' into 2221-complete-docker
Tim Pierce [Tue, 11 Mar 2014 19:53:33 +0000 (15:53 -0400)]
Merge branch 'master' of git.clinicalfuture.com:arvados
Tim Pierce [Tue, 11 Mar 2014 19:52:53 +0000 (15:52 -0400)]
Small documentation fixes for installing. refs #2221
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.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# 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
Tim Pierce [Tue, 11 Mar 2014 19:10:43 +0000 (15:10 -0400)]
Merge branch 'master' into 2221-complete-docker
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.
Tim Pierce [Tue, 11 Mar 2014 17:54:55 +0000 (13:54 -0400)]
Fix bugs introduced from merge with (refs #2221)
* build.rb: be smarter about preparing SSH key and building config.yml
* build.sh: correct the check for ruby 1.9.3
* base: CURL and SSL libraries are now prerequisites
* apiserver: compute_node_domain must be set
* workbench: secret_token needs to be installed before rake precompile
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.
Tim Pierce [Tue, 11 Mar 2014 14:13:25 +0000 (10:13 -0400)]
Merge branch 'master' into 2221-complete-docker
Tim Pierce [Tue, 11 Mar 2014 14:12:55 +0000 (10:12 -0400)]
Force ruby1.9.3 install. (refs #2221)
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.
Tim Pierce [Mon, 10 Mar 2014 21:14:44 +0000 (17:14 -0400)]
Fix bugs for Ubunto 12.04 and 13.10. (refs #2221)
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
Tim Pierce [Mon, 10 Mar 2014 17:45:59 +0000 (13:45 -0400)]
Make build.sh executable. (refs #2221)
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/
Tim Pierce [Mon, 10 Mar 2014 15:08:19 +0000 (11:08 -0400)]
Add build.sh wrapper for build.rb, to make sure Ruby is installed. (Refs #2221)
Tim Pierce [Mon, 10 Mar 2014 14:49:41 +0000 (10:49 -0400)]
Merge branch 'master' into 2221-complete-docker
Tim Pierce [Fri, 7 Mar 2014 23:57:30 +0000 (18:57 -0500)]
install.rb: generate config.yml file on demand if necessary. Refs #2221.
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.