[ARVADOS] updated: 3cd8626eda1618b9f2be293fc01c29f3d00973a7
git at public.curoverse.com
git at public.curoverse.com
Wed Jan 22 17:06:27 EST 2014
Summary of changes:
apps/admin/setup-new-user.rb | 2 +-
apps/workbench/.gitignore | 3 +
apps/workbench/Gemfile | 1 +
apps/workbench/Gemfile.lock | 3 +
apps/workbench/app/assets/javascripts/users.js | 40 ++
.../app/assets/stylesheets/application.css | 18 +
.../app/controllers/application_controller.rb | 15 +-
.../app/controllers/collections_controller.rb | 65 ++-
.../app/controllers/sessions_controller.rb | 2 +-
.../app/controllers/user_agreements_controller.rb | 2 +-
apps/workbench/app/controllers/users_controller.rb | 7 +
apps/workbench/app/helpers/application_helper.rb | 47 ++-
apps/workbench/app/models/arvados_api_client.rb | 48 ++-
apps/workbench/app/models/arvados_base.rb | 6 +
apps/workbench/app/models/arvados_resource_list.rb | 4 +
apps/workbench/app/models/node.rb | 3 +
apps/workbench/app/models/repository.rb | 3 +
apps/workbench/app/models/user.rb | 4 +
apps/workbench/app/models/virtual_machine.rb | 4 +-
.../views/application/_arvados_attr_value.html.erb | 21 +
.../app/views/application/_arvados_object.html.erb | 42 ++
.../application/_arvados_object_attr.html.erb | 19 +-
.../app/views/application/_index.html.erb | 19 +-
.../workbench/app/views/application/error.json.erb | 1 +
.../app/views/authorized_keys/create.js.erb | 1 +
.../app/views/authorized_keys/index.html.erb | 4 +-
.../app/views/collections/_index_tbody.html.erb | 27 +
.../workbench/app/views/collections/index.html.erb | 60 +-
apps/workbench/app/views/collections/index.js.erb | 4 +
apps/workbench/app/views/collections/show.html.erb | 29 +-
.../app/views/layouts/application.html.erb | 15 +-
.../app/views/repositories/index.html.erb | 8 +-
.../app/views/user_agreements/index.html.erb | 46 +-
.../views/users/{home.html.erb => _home.html.erb} | 13 +-
.../app/views/users/_notifications.html.erb | 46 +-
.../app/views/users/_quick_links.html.erb | 10 -
apps/workbench/app/views/users/_tables.html.erb | 63 ++-
apps/workbench/app/views/users/home.html.erb | 74 +---
apps/workbench/app/views/users/welcome.html.erb | 15 +-
.../app/views/virtual_machines/index.html.erb | 4 +-
.../config/environments/development.rb.example | 9 +
.../config/environments/production.rb.example | 9 +
apps/workbench/config/environments/test.rb.example | 9 +
apps/workbench/config/routes.rb | 2 +
.../test/fixtures/api_client_authorizations.yml | 11 -
apps/workbench/test/fixtures/authorized_keys.yml | 11 -
apps/workbench/test/fixtures/collections.yml | 11 -
apps/workbench/test/fixtures/groups.yml | 11 -
apps/workbench/test/fixtures/humans.yml | 11 -
apps/workbench/test/fixtures/job_tasks.yml | 11 -
apps/workbench/test/fixtures/jobs.yml | 11 -
apps/workbench/test/fixtures/links.yml | 11 -
apps/workbench/test/fixtures/logs.yml | 11 -
apps/workbench/test/fixtures/nodes.yml | 11 -
.../workbench/test/fixtures/pipeline_instances.yml | 11 -
.../workbench/test/fixtures/pipeline_templates.yml | 11 -
apps/workbench/test/fixtures/repositories.yml | 11 -
apps/workbench/test/fixtures/specimens.yml | 11 -
apps/workbench/test/fixtures/traits.yml | 11 -
apps/workbench/test/fixtures/users.yml | 11 -
apps/workbench/test/fixtures/virtual_machines.yml | 11 -
.../api_client_authorizations_controller_test.rb | 3 -
.../functional/authorized_keys_controller_test.rb | 3 -
.../test/functional/collections_controller_test.rb | 3 -
.../test/functional/groups_controller_test.rb | 3 -
.../test/functional/humans_controller_test.rb | 3 -
.../test/functional/job_tasks_controller_test.rb | 3 -
.../test/functional/jobs_controller_test.rb | 3 -
.../test/functional/links_controller_test.rb | 3 -
.../test/functional/logs_controller_test.rb | 3 -
.../test/functional/nodes_controller_test.rb | 45 --
.../pipeline_instances_controller_test.rb | 3 -
.../pipeline_templates_controller_test.rb | 3 -
.../functional/repositories_controller_test.rb | 3 -
.../test/functional/sessions_controller_test.rb | 3 -
.../test/functional/specimens_controller_test.rb | 3 -
.../test/functional/traits_controller_test.rb | 3 -
.../test/functional/users_controller_test.rb | 3 -
.../functional/virtual_machines_controller_test.rb | 3 -
crunch_scripts/pgp-survey-import | 12 +-
doc/Gemfile | 2 +-
doc/Gemfile.lock | 18 +-
doc/Rakefile | 1 +
doc/_config.yml | 3 +
doc/_includes/navbar_left.html | 2 +-
doc/_includes/navbar_top.html | 1 +
doc/_includes/run-md5sum.py | 35 ++
doc/_layouts/default.html | 7 +-
doc/api/schema/Link.textile | 65 ++-
doc/api/schema/Log.textile | 12 +-
doc/css/bootstrap.css | 4 +-
doc/gen_api_method_docs.py | 102 ++++
doc/gen_api_schema_docs.py | 77 +++
doc/images/glyphicons-halflings-white.png | Bin 0 -> 8777 bytes
doc/images/glyphicons-halflings.png | Bin 0 -> 12799 bytes
doc/index.html | 7 +-
doc/install/create-standard-objects.textile | 16 +
doc/install/index.md | 5 +-
doc/install/install-api-server.md | 2 +-
doc/install/install-workbench-app.md | 2 +-
doc/mkpydoc.sh | 5 +
doc/sdk/index.textile | 12 +
.../python}/crunch-utility-libraries.textile | 48 +-
doc/sdk/python/python.textile | 10 +
.../reference => sdk/python}/sdk-python.textile | 18 +-
doc/user/getting_started/community.textile | 25 +
doc/user/getting_started/ssh-access.textile | 29 +-
doc/user/reference/sdk-cli.textile | 7 +-
.../tutorials/running-external-program.textile | 65 ++
doc/user/tutorials/tutorial-firstscript.textile | 22 +-
.../tutorial-gatk-variantfiltration.textile | 11 +-
doc/user/tutorials/tutorial-job-debug.textile | 6 +-
doc/user/tutorials/tutorial-job1.textile | 33 +-
doc/user/tutorials/tutorial-keep.textile | 25 +-
doc/user/tutorials/tutorial-new-pipeline.textile | 12 +-
doc/user/tutorials/tutorial-parallel.textile | 10 +-
doc/user/tutorials/tutorial-trait-search.textile | 45 +-
doc/zenweb-liquid.rb | 22 +
docker/Makefile | 19 +-
docker/mkimage-debootstrap.sh | 8 +-
sdk/cli/Gemfile | 5 +-
sdk/cli/Gemfile.lock | 16 +-
sdk/cli/arvados-cli.gemspec | 5 +-
sdk/cli/bin/arv | 94 +++-
sdk/cli/bin/arv-tag | 230 +++++++
sdk/cli/test/test_arv-put.rb | 36 +-
sdk/cli/test/test_arv-tag.rb | 106 ++++
sdk/python/arvados/__init__.py | 638 ++------------------
sdk/python/arvados/collection.py | 215 +++++++
sdk/python/arvados/keep.py | 251 ++++++++
sdk/python/arvados/stream.py | 225 +++++++
sdk/ruby/arvados.gemspec | 2 +-
.../api/app/controllers/application_controller.rb | 62 ++-
.../v1/api_client_authorizations_controller.rb | 17 +-
.../arvados/v1/collections_controller.rb | 59 ++-
.../arvados/v1/keep_disks_controller.rb | 9 +-
.../app/controllers/arvados/v1/nodes_controller.rb | 5 +
.../controllers/arvados/v1/schema_controller.rb | 4 +-
.../arvados/v1/user_agreements_controller.rb | 4 +
services/api/app/controllers/static_controller.rb | 2 +-
services/api/app/models/arvados_model.rb | 8 +
services/api/app/models/authorized_key.rb | 19 +
services/api/app/models/collection.rb | 16 +-
.../api/config/environments/development.rb.example | 3 +
.../api/config/environments/production.rb.example | 3 +
services/api/config/environments/test.rb.example | 3 +
services/api/script/rails | 2 +-
.../arvados/v1/collections_controller_test.rb | 38 ++
148 files changed, 2544 insertions(+), 1448 deletions(-)
create mode 100644 apps/workbench/app/assets/javascripts/users.js
create mode 100644 apps/workbench/app/views/application/_arvados_attr_value.html.erb
create mode 100644 apps/workbench/app/views/application/error.json.erb
create mode 100644 apps/workbench/app/views/authorized_keys/create.js.erb
create mode 100644 apps/workbench/app/views/collections/_index_tbody.html.erb
create mode 100644 apps/workbench/app/views/collections/index.js.erb
copy apps/workbench/app/views/users/{home.html.erb => _home.html.erb} (85%)
delete mode 100644 apps/workbench/app/views/users/_quick_links.html.erb
delete mode 100644 apps/workbench/test/fixtures/api_client_authorizations.yml
delete mode 100644 apps/workbench/test/fixtures/authorized_keys.yml
delete mode 100644 apps/workbench/test/fixtures/collections.yml
delete mode 100644 apps/workbench/test/fixtures/groups.yml
delete mode 100644 apps/workbench/test/fixtures/humans.yml
delete mode 100644 apps/workbench/test/fixtures/job_tasks.yml
delete mode 100644 apps/workbench/test/fixtures/jobs.yml
delete mode 100644 apps/workbench/test/fixtures/links.yml
delete mode 100644 apps/workbench/test/fixtures/logs.yml
delete mode 100644 apps/workbench/test/fixtures/nodes.yml
delete mode 100644 apps/workbench/test/fixtures/pipeline_instances.yml
delete mode 100644 apps/workbench/test/fixtures/pipeline_templates.yml
delete mode 100644 apps/workbench/test/fixtures/repositories.yml
delete mode 100644 apps/workbench/test/fixtures/specimens.yml
delete mode 100644 apps/workbench/test/fixtures/traits.yml
delete mode 100644 apps/workbench/test/fixtures/users.yml
delete mode 100644 apps/workbench/test/fixtures/virtual_machines.yml
create mode 100644 doc/_includes/run-md5sum.py
create mode 100755 doc/gen_api_method_docs.py
create mode 100755 doc/gen_api_schema_docs.py
create mode 100644 doc/images/glyphicons-halflings-white.png
create mode 100644 doc/images/glyphicons-halflings.png
create mode 100755 doc/mkpydoc.sh
create mode 100644 doc/sdk/index.textile
rename doc/{user/reference => sdk/python}/crunch-utility-libraries.textile (91%)
create mode 100644 doc/sdk/python/python.textile
rename doc/{user/reference => sdk/python}/sdk-python.textile (87%)
create mode 100644 doc/user/getting_started/community.textile
create mode 100644 doc/user/tutorials/running-external-program.textile
create mode 100644 doc/zenweb-liquid.rb
create mode 100755 sdk/cli/bin/arv-tag
create mode 100644 sdk/cli/test/test_arv-tag.rb
create mode 100644 sdk/python/arvados/collection.py
create mode 100644 sdk/python/arvados/keep.py
create mode 100644 sdk/python/arvados/stream.py
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commit 3cd8626eda1618b9f2be293fc01c29f3d00973a7
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Jan 22 17:07:08 2014 -0500
Zenweb work in progress, adding plugin for liquid so we hopefully don't have to rewrite our pages.
diff --git a/doc/Gemfile b/doc/Gemfile
index ea40d14..ad695f0 100644
--- a/doc/Gemfile
+++ b/doc/Gemfile
@@ -1,4 +1,4 @@
source 'https://rubygems.org'
gem 'zenweb'
-gem 'zenweb-textile'
+gem 'liquid'
diff --git a/doc/Gemfile.lock b/doc/Gemfile.lock
index 608a001..5de90b1 100644
--- a/doc/Gemfile.lock
+++ b/doc/Gemfile.lock
@@ -1,28 +1,30 @@
GEM
remote: https://rubygems.org/
specs:
- RedCloth (4.2.9)
coderay (1.1.0)
- kramdown (0.14.2)
+ kramdown (1.3.1)
less (1.2.21)
mutter (>= 0.4.2)
treetop (>= 1.4.2)
+ liquid (2.6.1)
+ makerakeworkwell (1.0.3)
+ rake (>= 0.9.2, < 11)
mutter (0.5.3)
polyglot (0.3.3)
+ rake (10.1.1)
treetop (1.4.15)
polyglot
polyglot (>= 0.3.1)
- zenweb (3.0.0.b3)
+ zenweb (3.3.1)
coderay (~> 1.0)
- kramdown (~> 0.13)
+ kramdown (~> 1.0)
less (~> 1.2)
- zenweb-textile (0.0.1)
- RedCloth (~> 4.2.9)
- zenweb (= 3.0.0.b3)
+ makerakeworkwell (~> 1.0)
+ rake (>= 0.9, < 11)
PLATFORMS
ruby
DEPENDENCIES
+ liquid
zenweb
- zenweb-textile
diff --git a/doc/Rakefile b/doc/Rakefile
index 12f87b1..65d2855 100644
--- a/doc/Rakefile
+++ b/doc/Rakefile
@@ -3,4 +3,5 @@
require "rubygems"
require "zenweb/tasks"
load "zenweb-textile.rb"
+load "zenweb-liquid.rb"
diff --git a/doc/_config.yml b/doc/_config.yml
index b3a6eea..cd13810 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -1,6 +1,7 @@
exclude: ["Rakefile", "tmp"]
baseurl: /doc
arvados_api_host: qr1hi.arvadosapi.com
+layout: default
navbar:
userguide:
- Getting Started
diff --git a/doc/install/index.md b/doc/install/index.md
index 210c47a..39b3d97 100644
--- a/doc/install/index.md
+++ b/doc/install/index.md
@@ -3,7 +3,7 @@ layout: default
navsection: installguide
title: Overview
navorder: 0
----
+...
{% include alert-stub.html %}
diff --git a/doc/install/install-api-server.md b/doc/install/install-api-server.md
index dbae3da..c959e1b 100644
--- a/doc/install/install-api-server.md
+++ b/doc/install/install-api-server.md
@@ -3,7 +3,7 @@ layout: default
navsection: installguide
title: Install the API server
navorder: 1
----
+...
{% include alert-stub.html %}
diff --git a/doc/install/install-workbench-app.md b/doc/install/install-workbench-app.md
index 6c63598..c598785 100644
--- a/doc/install/install-workbench-app.md
+++ b/doc/install/install-workbench-app.md
@@ -3,7 +3,7 @@ layout: default
navsection: installguide
title: Install the Arvados workbench application
navorder: 2
----
+...
{% include alert-stub.html %}
diff --git a/doc/sdk/index.textile b/doc/sdk/index.textile
index 4224b59..ee001d9 100644
--- a/doc/sdk/index.textile
+++ b/doc/sdk/index.textile
@@ -3,7 +3,7 @@ layout: default
navsection: sdk
title: "SDK Reference"
navorder: 0
----
+...
h1. Arvados SDK Reference
diff --git a/doc/sdk/python/python.textile b/doc/sdk/python/python.textile
index 4d6900b..4483cd9 100644
--- a/doc/sdk/python/python.textile
+++ b/doc/sdk/python/python.textile
@@ -5,6 +5,6 @@ navmenu: Python
title: "PyDoc Reference"
navorder: 30
no_nav_left: true
----
+...
notextile. <iframe src="arvados/" style="width:100%; height:100%; border:none" />
diff --git a/doc/user/getting_started/community.textile b/doc/user/getting_started/community.textile
index 9a2aeca..7c63038 100644
--- a/doc/user/getting_started/community.textile
+++ b/doc/user/getting_started/community.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Getting Started
title: Arvados Community and Getting Help
navorder: 11
----
+...
h1. Arvados Community and Getting Help
diff --git a/doc/user/tutorials/running-external-program.textile b/doc/user/tutorials/running-external-program.textile
index f23fae8..a1a7873 100644
--- a/doc/user/tutorials/running-external-program.textile
+++ b/doc/user/tutorials/running-external-program.textile
@@ -4,7 +4,7 @@ navsection: userguide
navmenu: Tutorials
title: "Running external programs"
navorder: 18
----
+...
h1. Running external programs
diff --git a/doc/zenweb-liquid.rb b/doc/zenweb-liquid.rb
new file mode 100644
index 0000000..f301aa4
--- /dev/null
+++ b/doc/zenweb-liquid.rb
@@ -0,0 +1,22 @@
+require 'zenweb'
+
+module ZenwebLiquid
+ VERSION = '0.0.1'
+end
+
+module Zenweb
+ class Page
+
+ ##
+ # Render a page's liquid and return the intermediate result
+ def render_liquid page, content, binding = TOPLEVEL_BINDING
+ require 'liquid'
+
+ unless defined? @liquid_template then
+ @liquid_template = Liquid::Template.parse(content).render()
+ end
+
+ @liquid_template.render(binding)
+ end
+ end
+end
commit 3dc2b0008be4e09b47f73aeeb97d005cd7836619
Merge: 91e4be4 2c71507
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Jan 22 11:37:45 2014 -0500
Merge remote-tracking branch 'origin' into 1786-replace-jekyll-with-zenweb
diff --cc doc/_config.yml
index 108ec24,274ae9b..b3a6eea
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@@ -11,3 -10,5 +11,5 @@@ navbar
- Concepts
- API Methods
- Schema
+ sdk:
- - Python
++ - Python
diff --cc doc/sdk/python/crunch-utility-libraries.textile
index 679138d,95a3780..c0b54fa
--- a/doc/sdk/python/crunch-utility-libraries.textile
+++ b/doc/sdk/python/crunch-utility-libraries.textile
@@@ -1,10 -1,10 +1,10 @@@
---
layout: default
- navsection: userguide
- navmenu: Reference
+ navsection: sdk
+ navmenu: Python
title: "Crunch utility libraries"
- navorder: 31
+ navorder: 20
----
+...
h1. Crunch utility libraries
diff --cc doc/sdk/python/sdk-python.textile
index d9b1e5d,81a61f0..2e9660e
--- a/doc/sdk/python/sdk-python.textile
+++ b/doc/sdk/python/sdk-python.textile
@@@ -1,12 -1,12 +1,12 @@@
---
layout: default
- navsection: userguide
- navmenu: Reference
+ navsection: sdk
+ navmenu: Python
title: "Python SDK"
- navorder: 23
+ navorder: 10
----
+...
- h1. Reference: Python SDK
+ h1. Python SDK
The Python SDK provides a generic set of wrappers so you can make API calls easily. It performs some validation before connecting to the API server: for example, it refuses to do an API call if a required parameter is missing.
diff --cc doc/user/reference/sdk-cli.textile
index fd8e86d,058f1b3..5a7753c
--- a/doc/user/reference/sdk-cli.textile
+++ b/doc/user/reference/sdk-cli.textile
@@@ -2,11 -2,11 +2,11 @@@
layout: default
navsection: userguide
navmenu: Reference
- title: "Command line SDK"
+ title: "Command line interface"
navorder: 22
----
+...
- h1. Reference: Command line SDK
+ h1. Reference: Command Line Interface
If you are logged in to an Arvados VM, the command line SDK should be installed. Try:
diff --cc doc/user/tutorials/tutorial-firstscript.textile
index b03aaa3,b582eef..daa71fa
--- a/doc/user/tutorials/tutorial-firstscript.textile
+++ b/doc/user/tutorials/tutorial-firstscript.textile
@@@ -4,9 -4,9 +4,9 @@@ navsection: userguid
navmenu: Tutorials
title: "Writing a Crunch script"
navorder: 13
----
+...
- h1. Tutorial: Writing a Crunch script
+ h1. Writing a Crunch script
In this tutorial, we will write the "hash" script demonstrated in the first tutorial.
diff --cc doc/user/tutorials/tutorial-gatk-variantfiltration.textile
index 5e985c8,779761a..1748565
--- a/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
+++ b/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
@@@ -4,9 -4,9 +4,9 @@@ navsection: userguid
navmenu: Tutorials
title: "Using GATK with Arvados"
navorder: 16
----
+...
- h1. Tutorial: Using GATK with Arvados
+ h1. Using GATK with Arvados
This tutorials demonstrates how to use the Genome Analysis Toolkit (GATK) with Arvados. In this example we will install GATK and then create a VariantFiltration job to assign pass/fail scores to variants in a VCF file.
diff --cc doc/user/tutorials/tutorial-job-debug.textile
index ad01eaa,6be687c..570713b
--- a/doc/user/tutorials/tutorial-job-debug.textile
+++ b/doc/user/tutorials/tutorial-job-debug.textile
@@@ -4,9 -4,9 +4,9 @@@ navsection: userguid
navmenu: Tutorials
title: "Debugging a Crunch script"
navorder: 14
----
+...
- h1. Tutorial: Debugging a Crunch script
+ h1. Debugging a Crunch script
To test changes to a script by running a job, the change must be pushed into @git@, the job queued asynchronously, and the actual execution may be run on any compute server. As a result, debugging a script can be difficult and time consuming. This tutorial demonstrates using @arv-crunch-job@ to run your job in your local VM. This avoids the job queue and allows you to execute the script from your uncomitted git tree.
diff --cc doc/user/tutorials/tutorial-job1.textile
index f920019,53d2342..be159db
--- a/doc/user/tutorials/tutorial-job1.textile
+++ b/doc/user/tutorials/tutorial-job1.textile
@@@ -4,9 -4,9 +4,9 @@@ navsection: userguid
navmenu: Tutorials
title: "Running a Crunch job"
navorder: 12
----
+...
- h1. Tutorial: Running a crunch job
+ h1. Running a crunch job
This tutorial introduces the concepts and use of the Crunch job system using the @arv@ command line tool and Arvados Workbench.
diff --cc doc/user/tutorials/tutorial-keep.textile
index 2220ce1,6683498..eb0f969
--- a/doc/user/tutorials/tutorial-keep.textile
+++ b/doc/user/tutorials/tutorial-keep.textile
@@@ -4,9 -4,9 +4,9 @@@ navsection: userguid
navmenu: Tutorials
title: "Storing and Retrieving data using Arvados Keep"
navorder: 11
----
+...
- h1. Tutorial: Storing and Retrieving data using Arvados Keep
+ h1. Storing and Retrieving data using Arvados Keep
This tutorial introduces you to the Arvados file storage system.
diff --cc doc/user/tutorials/tutorial-new-pipeline.textile
index 3eb9796,101d6ac..ee92090
--- a/doc/user/tutorials/tutorial-new-pipeline.textile
+++ b/doc/user/tutorials/tutorial-new-pipeline.textile
@@@ -4,9 -4,9 +4,9 @@@ navsection: userguid
navmenu: Tutorials
title: "Constructing a Crunch pipeline"
navorder: 15
----
+...
- h1. Tutorial: Constructing a Crunch pipeline
+ h1. Constructing a Crunch pipeline
A pipeline in Arvados is a collection of crunch scripts, in which the output from one script may be used as the input to another script.
diff --cc doc/user/tutorials/tutorial-parallel.textile
index 3f278a7,8a61184..1cad88c
--- a/doc/user/tutorials/tutorial-parallel.textile
+++ b/doc/user/tutorials/tutorial-parallel.textile
@@@ -4,9 -4,9 +4,9 @@@ navsection: userguid
navmenu: Tutorials
title: "Parallel Crunch tasks"
navorder: 15
----
+...
- h1. Tutorial: Parallel Crunch tasks
+ h1. Parallel Crunch tasks
In the tutorial "writing a crunch script,":tutorial-firstscript.html our script used a "for" loop to compute the md5 hashes for each file in sequence. This approach, while simple, is not able to take advantage of the compute cluster with multiple nodes and cores to speed up computation by running tasks in parallel. This tutorial will demonstrate how to create parallel Crunch tasks.
diff --cc doc/user/tutorials/tutorial-trait-search.textile
index 89492d2,d7fe50b..1fcbbc3
--- a/doc/user/tutorials/tutorial-trait-search.textile
+++ b/doc/user/tutorials/tutorial-trait-search.textile
@@@ -4,9 -4,9 +4,9 @@@ navsection: userguid
navmenu: Tutorials
title: "Querying the Metadata Database"
navorder: 16
----
+...
- h1. Tutorial: Querying the Metadata Database
+ h1. Querying the Metadata Database
This tutorial introduces the Arvados Metadata Database. The Metadata Database stores information about files in Keep. This example will use the Python SDK to find public WGS (Whole Genome Sequencing) data for people who have reported a certain medical condition.
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