[ARVADOS] updated: 08eb585acafb30111d81c40f7e4b2c97d5fa4786
git at public.curoverse.com
git at public.curoverse.com
Wed Mar 26 13:02:41 EDT 2014
Summary of changes:
apps/workbench/Gemfile | 9 +-
apps/workbench/Gemfile.lock | 31 +
apps/workbench/README.rdoc | 261 --------
apps/workbench/README.textile | 19 +
apps/workbench/app/assets/javascripts/editable.js | 9 +
.../api_client_authorizations_controller.rb | 9 +-
.../app/controllers/application_controller.rb | 3 +-
.../controllers/pipeline_templates_controller.rb | 5 +-
apps/workbench/app/controllers/users_controller.rb | 63 ++-
apps/workbench/app/helpers/application_helper.rb | 14 +-
apps/workbench/app/models/arvados_api_client.rb | 34 +-
apps/workbench/app/models/arvados_base.rb | 31 +-
apps/workbench/app/models/arvados_resource_list.rb | 11 +
.../app/views/application/_paging.html.erb | 8 +-
.../app/views/layouts/application.html.erb | 6 +-
.../app/views/users/_show_activity.html.erb | 4 +
apps/workbench/app/views/users/activity.html.erb | 72 +++
apps/workbench/config/application.default.yml | 12 +-
.../config/environments/development.rb.example | 20 -
.../config/environments/production.rb.example | 19 -
apps/workbench/config/environments/test.rb.example | 19 -
apps/workbench/config/routes.rb | 1 +
apps/workbench/lib/tasks/config_check.rake | 13 +-
apps/workbench/test/integration/logins_test.rb | 14 +
apps/workbench/test/integration/smoke_test.rb | 39 ++
.../test/integration/virtual_machines_test.rb | 17 +
apps/workbench/test/integration_helper.rb | 77 +++
doc/README | 31 -
doc/README.textile | 58 ++
.../install-workbench-app.html.textile.liquid | 2 -
.../tutorials/tutorial-keep.html.textile.liquid | 2 +-
.../tutorial-new-pipeline.html.textile.liquid | 1 -
sdk/cli/bin/arv | 21 +-
sdk/cli/bin/crunch-job | 65 ++-
.../api/app/controllers/application_controller.rb | 2 +-
.../controllers/arvados/v1/schema_controller.rb | 23 +-
.../app/controllers/arvados/v1/users_controller.rb | 49 ++-
services/api/app/models/commit.rb | 19 +-
services/api/app/models/user.rb | 152 +++++
services/api/config/application.default.yml | 12 +-
services/api/config/application.yml.example | 7 +-
.../api/config/environments/development.rb.example | 39 --
.../api/config/environments/production.rb.example | 42 --
services/api/config/environments/test.rb.example | 40 --
services/api/config/routes.rb | 4 +-
services/api/lib/tasks/config_check.rake | 13 +-
services/api/script/crunch-dispatch.rb | 2 +-
services/api/script/rails | 4 -
services/api/script/setup-new-user.rb | 66 ++
.../arvados/v1/collections_controller_test.rb | 22 +
.../arvados/v1/schema_controller_test.rb | 2 +-
.../functional/arvados/v1/users_controller_test.rb | 645 ++++++++++++++++++++
.../api/test/integration/collections_api_test.rb | 12 +
services/api/test/integration/permissions_test.rb | 244 ++++++++
services/api/test/unit/user_test.rb | 280 +++++++++-
55 files changed, 2079 insertions(+), 600 deletions(-)
delete mode 100644 apps/workbench/README.rdoc
create mode 100644 apps/workbench/README.textile
create mode 100644 apps/workbench/app/views/users/_show_activity.html.erb
create mode 100644 apps/workbench/app/views/users/activity.html.erb
create mode 100644 apps/workbench/test/integration/logins_test.rb
create mode 100644 apps/workbench/test/integration/smoke_test.rb
create mode 100644 apps/workbench/test/integration/virtual_machines_test.rb
create mode 100644 apps/workbench/test/integration_helper.rb
delete mode 100644 doc/README
create mode 100644 doc/README.textile
create mode 100755 services/api/script/setup-new-user.rb
create mode 100644 services/api/test/integration/permissions_test.rb
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commit 08eb585acafb30111d81c40f7e4b2c97d5fa4786
Merge: 019c624 61a6b0d
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Mar 26 13:02:24 2014 -0400
Merge branch '1741-internal-git-repo' of git.clinicalfuture.com:arvados into 1741-internal-git-repo
commit 019c624eb61e8bd87bc505fc066473ce85a2a268
Merge: d4936db 921c13a
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Mar 26 13:01:15 2014 -0400
Merge branch 'master' into 1741-internal-git-repo
Also changes application.default.yml to use /var/lib instead of /var/cache.
Conflicts:
doc/README
doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
diff --cc doc/README.textile
index 0000000,23a82fe..f88d304
mode 000000,100644..100644
--- a/doc/README.textile
+++ b/doc/README.textile
@@@ -1,0 -1,52 +1,58 @@@
+ h1. Arvados documentation
+
+ This is the source code for "doc.arvados.org":http://doc.arvados.org.
+
+ Here's how to build the HTML pages locally so you can preview your updates before you commit and push.
+
+ Additional information is available on the "'Documentation' page on the Arvados wiki":https://arvados.org/projects/arvados/wiki/Documentation.
+
+ h2. 0. Install dependencies
+
+ <pre>
+ arvados/doc$ bundle install
+ </pre>
+
+ h2. 1. Generate HTML pages
+
+ <pre>
+ arvados/doc$ rake
+ </pre>
+
++Alternately, to make the documentation browsable on the local filesystem:
++
++<pre>
++arvados/doc$ rake generate baseurl=$PWD/.site
++</pre>
++
+ h2. 2. Preview HTML pages
+
+ <pre>
+ arvados/doc$ rake run
+ [2014-03-10 09:03:41] INFO WEBrick 1.3.1
+ [2014-03-10 09:03:41] INFO ruby 2.1.1 (2014-02-24) [x86_64-linux]
+ [2014-03-10 09:03:41] INFO WEBrick::HTTPServer#start: pid=8926 port=8000
+ </pre>
+
+ Preview the rendered pages at "http://localhost:8000":http://localhost:8000.
+
+ h2. 3. Publish HTML pages inside Workbench
+
+ (or some other web site)
+
+ You can set @baseurl@ (the URL prefix for all internal links), @arvados_api_host@ and @arvados_workbench_host@ without changing @_config.yml@:
+
+ <pre>
+ arvados/doc$ rake generate baseurl=/doc arvados_api_host=xyzzy.arvadosapi.com
+ </pre>
+
+ Make the docs appear at {workbench_host}/doc by creating a symbolic link in Workbench's @public@ directory, pointing to the generated HTML tree.
+
+ <pre>
+ arvados/doc$ ln -sn ../../../doc/.site ../apps/workbench/public/doc
+ </pre>
+
+ h2. 4. Delete generated files
+
+ <pre>
+ arvados/doc$ rake realclean
+ </pre>
diff --cc doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
index a4bad58,d218c3b..132bc9d
--- a/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-new-pipeline.html.textile.liquid
@@@ -71,5 -69,5 +71,4 @@@ Now, use @arv pipeline_template create
</code></pre>
</notextile>
-Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":http://{{ site.arvados_workbench_host }}/pipeline_templates page.
-
+Your new pipeline template will appear on the "Workbench %(rarr)→% Compute %(rarr)→% Pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_instances page.
-
diff --cc services/api/config/application.default.yml
index c1382b6,e46ff5d..298b001
--- a/services/api/config/application.default.yml
+++ b/services/api/config/application.default.yml
@@@ -45,17 -45,7 +45,17 @@@ common
secret_token: ~
uuid_prefix: <%= Digest::MD5.hexdigest(`hostname`).to_i(16).to_s(36)[0..4] %>
- git_repositories_dir: /var/cache/git
+ # Git repositories must be readable by api server, or you won't be
+ # able to submit crunch jobs. To pass the test suites, put a clone
+ # of the arvados tree in {git_repositories_dir}/arvados.git or
+ # {git_repositories_dir}/arvados/.git
- git_repositories_dir: /var/cache/git
++ git_repositories_dir: /var/lib/arvados/git
+
+ # This is a (bare) repository that stores commits used in jobs. When a job
- # runs, the source commits are first fetched into this repository, then
- # deployed to compute nodes. This should NOT be a subdirectory of
- # {git_repositiories_dir}.
- git_internal_dir: /var/cache/arvados/internal.git
++ # runs, the source commits are first fetched into this repository, then this
++ # repository is used to deploy to compute nodes. This should NOT be a
++ # subdirectory of {git_repositiories_dir}.
++ git_internal_dir: /var/lib/arvados/internal.git
# :none or :slurm_immediate
crunch_job_wrapper: :none
commit d4936db54192ca158104fb734c6d154e28397c56
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Mar 26 09:50:53 2014 -0400
Added explicit configuration parameter git_internal_dir. Needs to be tested.
diff --git a/services/api/app/models/commit.rb b/services/api/app/models/commit.rb
index 4df5198..ec2c0e0 100644
--- a/services/api/app/models/commit.rb
+++ b/services/api/app/models/commit.rb
@@ -11,7 +11,7 @@ class Commit < ActiveRecord::Base
# "apps:HEAD"
# def self.find_by_commit_ish(commit_ish)
- # if only_valid_chars.match(commit_ish)
+ # if only_valid_chars.match(commit_ish)
# logger.warn "find_by_commit_ish called with string containing invalid characters: '#{commit_ish}'"
# return nil
# end
@@ -39,11 +39,9 @@ class Commit < ActiveRecord::Base
# nil
# end
- ARVADOS_INTERNAL = "_arvados_internal.git"
-
def self.find_commit_range(current_user, repository, minimum, maximum, exclude)
only_valid_chars = /[^A-Za-z0-9_-]/
- if only_valid_chars.match(minimum) || only_valid_chars.match(maximum)
+ if only_valid_chars.match(minimum) || only_valid_chars.match(maximum)
logger.warn "find_commit_range called with string containing invalid characters: '#{minimum}', '#{maximum}'"
return nil
end
@@ -51,7 +49,7 @@ class Commit < ActiveRecord::Base
if minimum and minimum.empty?
minimum = nil
end
-
+
if !maximum
maximum = "HEAD"
end
@@ -98,11 +96,11 @@ class Commit < ActiveRecord::Base
exclude.each do |e|
IO.foreach("|git rev-list --max-count=1 #{e}") do |line|
resolved_exclude.push(line.strip)
- end
+ end
end
end
- if minimum
+ if minimum
# Get the commit hash for the lower bound
min_hash = nil
IO.foreach("|git rev-list --max-count=1 #{minimum}") do |line|
@@ -111,12 +109,12 @@ class Commit < ActiveRecord::Base
# If not found, nothing else to do
next if !min_hash
-
+
# Now find all commits between them
#puts "git rev-list #{min_hash}..#{max_hash}"
IO.foreach("|git rev-list #{min_hash}..#{max_hash}") do |line|
hash = line.strip
- commits.push(hash) if !resolved_exclude or !resolved_exclude.include? hash
+ commits.push(hash) if !resolved_exclude or !resolved_exclude.include? hash
end
commits.push(min_hash) if !resolved_exclude or !resolved_exclude.include? min_hash
@@ -171,9 +169,10 @@ class Commit < ActiveRecord::Base
@repositories = {}
@gitdirbase = Rails.configuration.git_repositories_dir
Dir.foreach @gitdirbase do |repo|
- next if repo.match /^\./ or repo == ARVADOS_INTERNAL
+ next if repo.match /^\./
git_dir = File.join(@gitdirbase,
repo.match(/\.git$/) ? repo : File.join(repo, '.git'))
+ next if git_dir == Rails.configuration.git_internal_dir
repo_name = repo.sub(/\.git$/, '')
@repositories[repo_name] = {git_dir: git_dir}
end
diff --git a/services/api/config/application.default.yml b/services/api/config/application.default.yml
index e46ff5d..c1382b6 100644
--- a/services/api/config/application.default.yml
+++ b/services/api/config/application.default.yml
@@ -45,8 +45,18 @@ common:
secret_token: ~
uuid_prefix: <%= Digest::MD5.hexdigest(`hostname`).to_i(16).to_s(36)[0..4] %>
+ # Git repositories must be readable by api server, or you won't be
+ # able to submit crunch jobs. To pass the test suites, put a clone
+ # of the arvados tree in {git_repositories_dir}/arvados.git or
+ # {git_repositories_dir}/arvados/.git
git_repositories_dir: /var/cache/git
+ # This is a (bare) repository that stores commits used in jobs. When a job
+ # runs, the source commits are first fetched into this repository, then
+ # deployed to compute nodes. This should NOT be a subdirectory of
+ # {git_repositiories_dir}.
+ git_internal_dir: /var/cache/arvados/internal.git
+
# :none or :slurm_immediate
crunch_job_wrapper: :none
diff --git a/services/api/config/application.yml.example b/services/api/config/application.yml.example
index 488c4bd..9162fc4 100644
--- a/services/api/config/application.yml.example
+++ b/services/api/config/application.yml.example
@@ -37,10 +37,5 @@ test:
secret_token: <%= rand(2**512).to_s(36) %>
common:
-
- # Git repositories must be readable by api server, or you won't be
- # able to submit crunch jobs. To pass the test suites, put a clone
- # of the arvados tree in {git_repositories_dir}/arvados.git or
- # {git_repositories_dir}/arvados/.git
- #
#git_repositories_dir: /var/cache/git
+ #git_internal_dir: /var/cache/arvados/internal.git
diff --git a/services/api/script/crunch-dispatch.rb b/services/api/script/crunch-dispatch.rb
index a90479c..7d42e14 100755
--- a/services/api/script/crunch-dispatch.rb
+++ b/services/api/script/crunch-dispatch.rb
@@ -152,7 +152,7 @@ class Dispatcher
require 'shellwords'
- arvados_internal = File.join(Rails.configuration.git_repositories_dir, Commit::ARVADOS_INTERNAL)
+ arvados_internal = Rails.configuration.git_internal_dir
if not File.exists? arvados_internal
$stderr.puts `mkdir -p #{arvados_internal.shellescape} && cd #{arvados_internal.shellescape} && git init --bare`
end
@@ -166,7 +166,7 @@ class Dispatcher
untake(job)
next
end
-
+
$stderr.puts `cd #{arvados_internal.shellescape} && git fetch --no-tags #{src_repo.shellescape} && git tag #{job.uuid.shellescape} #{job.script_version.shellescape}`
cmd_args << crunch_job_bin
@@ -174,7 +174,7 @@ class Dispatcher
cmd_args << job_auth.api_token
cmd_args << '--job'
cmd_args << job.uuid
- cmd_args << '--git-dir'
+ cmd_args << '--git-dir'
cmd_args << arvados_internal
$stderr.puts "dispatch: #{cmd_args.join ' '}"
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