[ARVADOS] updated: f91c73aba940adf1e9fbd530d102931af45a63c5
git at public.curoverse.com
git at public.curoverse.com
Wed May 7 00:12:48 EDT 2014
Summary of changes:
doc/api/methods.html.textile.liquid | 39 +++++++++++++++++---
doc/install/install-api-server.html.textile.liquid | 2 +-
.../install-workbench-app.html.textile.liquid | 30 ++++++++++++---
doc/sdk/python/sdk-python.html.textile.liquid | 10 +++---
services/api/lib/record_filters.rb | 13 +++++--
.../functional/arvados/v1/jobs_controller_test.rb | 36 ++++++++++++++++++
6 files changed, 108 insertions(+), 22 deletions(-)
via f91c73aba940adf1e9fbd530d102931af45a63c5 (commit)
via a04d67ef0823d6c87e8515cfe6cf88793ef5e3bb (commit)
via df2ce01533175ff7190a5d13fdca4b61f22befd3 (commit)
from f493dd4dfab89c228fab05e2b46851211c7fc586 (commit)
Those revisions listed above that are new to this repository have
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commit f91c73aba940adf1e9fbd530d102931af45a63c5
Author: Tom Clegg <tom at curoverse.com>
Date: Wed May 7 00:12:12 2014 -0400
Document "filters" feature. Add missing "!=" and "not in" operators.
diff --git a/doc/api/methods.html.textile.liquid b/doc/api/methods.html.textile.liquid
index 57d058e..da15df8 100644
--- a/doc/api/methods.html.textile.liquid
+++ b/doc/api/methods.html.textile.liquid
@@ -24,12 +24,39 @@ filters=[["owner_uuid","=","xyzzy-tpzed-a4lcehql0dv2u25"]]
table(table table-bordered table-condensed).
|*Parameter name*|*Value*|*Description*|
-|limit |integer|Maximum number of resources to return|
-|offset |integer|Skip the first 'offset' objects|
-|filters |array |Conditions for selecting resources to return|
-|order |array |List of fields to use to determine sorting order for returned objects|
-|select |array |Specify which fields to return|
-|distinct|boolean|true: (default) do not return duplicate objects<br> false: permitted to return duplicates|
+|limit |integer|Maximum number of resources to return.|
+|offset |integer|Skip the first 'offset' resources that match the given filter conditions.|
+|filters |array |Conditions for selecting resources to return (see below).|
+|order |array |Attributes to use as sort keys to determine the order resources are returned, each optionally followed by @asc@ or @desc@ to indicate ascending or descending order.
+Example: @["head_uuid asc","modified_at desc"]@
+Default: @["created_at desc"]@|
+|select |array |Set of attributes to include in the response.
+Example: @["head_uuid","tail_uuid"]@
+Default: all available attributes, minus "manifest_text" in the case of collections.|
+|distinct|boolean|@true@: (default) do not return duplicate objects
+ at false@: permitted to return duplicates|
+
+h3. Filters
+
+The value of the @filters@ parameter is an array of conditions. The @list@ method returns only the resources that satisfy all of the given conditions. In other words, the conjunction @AND@ is implicit.
+
+Each condition is expressed as an array with three elements: @[attribute, operator, operand]@.
+
+table(table table-bordered table-condensed).
+|_. Index|_. Element|_. Type|_. Description|_. Examples|
+|0|attribute|string|Name of the attribute to compare|@script_version@, @head_uuid@|
+|1|operator|string|Comparison operator|@>@, @>=@, @like@, @not in@|
+|2|operand|string, array, or null|Value to compare with the resource attribute|@"d00220fb%"@, @"1234"@, @["foo","bar"]@, @nil@|
+
+The following operators are available.
+
+table(table table-bordered table-condensed).
+|_. Operator|_. Operand type|_. Example|
+|@<@, @<=@, @>=@, @>@, @like@|string|@["script_version","like","d00220fb%"]@|
+|@=@, @!=@|string or null|@["tail_uuid","=","xyzzy-j7d0g-fffffffffffffff"]@
+@["tail_uuid","!=",null]@|
+|@in@, @not in@|array of strings|@["script_version","in",["master","d00220fb38d4b85ca8fc28a8151702a2b9d1dec5"]]@|
+|@is_a@|string|@["head_uuid","is_a","arvados#pipelineInstance"]@|
h2. Create
diff --git a/services/api/lib/record_filters.rb b/services/api/lib/record_filters.rb
index d7e556b..d3727d3 100644
--- a/services/api/lib/record_filters.rb
+++ b/services/api/lib/record_filters.rb
@@ -8,7 +8,7 @@
module RecordFilters
# Input:
- # +filters+ Arvados filters as list of lists.
+ # +filters+ array of conditions, each being [column, operator, operand]
# +ar_table_name+ name of SQL table
#
# Output:
@@ -29,8 +29,11 @@ module RecordFilters
raise ArgumentError.new("Invalid attribute '#{attr}' in filter")
end
case operator.downcase
- when '=', '<', '<=', '>', '>=', 'like'
+ when '=', '<', '<=', '>', '>=', '!=', 'like'
if operand.is_a? String
+ if operator == '!='
+ operator = '<>'
+ end
cond_out << "#{ar_table_name}.#{attr} #{operator} ?"
if (# any operator that operates on value rather than
# representation:
@@ -41,13 +44,15 @@ module RecordFilters
param_out << operand
elsif operand.nil? and operator == '='
cond_out << "#{ar_table_name}.#{attr} is null"
+ elsif operand.nil? and operator == '!='
+ cond_out << "#{ar_table_name}.#{attr} is not null"
else
raise ArgumentError.new("Invalid operand type '#{operand.class}' "\
"for '#{operator}' operator in filters")
end
- when 'in'
+ when 'in', 'not in'
if operand.is_a? Array
- cond_out << "#{ar_table_name}.#{attr} IN (?)"
+ cond_out << "#{ar_table_name}.#{attr} #{operator} (?)"
param_out << operand
else
raise ArgumentError.new("Invalid operand type '#{operand.class}' "\
diff --git a/services/api/test/functional/arvados/v1/jobs_controller_test.rb b/services/api/test/functional/arvados/v1/jobs_controller_test.rb
index af8f729..d671e94 100644
--- a/services/api/test/functional/arvados/v1/jobs_controller_test.rb
+++ b/services/api/test/functional/arvados/v1/jobs_controller_test.rb
@@ -177,6 +177,42 @@ class Arvados::V1::JobsControllerTest < ActionController::TestCase
'zzzzz-8i9sb-pshmckwoma9plh7']
end
+ test "search jobs by uuid with 'not in' query" do
+ authorize_with :active
+ get :index, {
+ filters: [['uuid', 'not in', ['zzzzz-8i9sb-pshmckwoma9plh7']]]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_not_equal [], found, "'not in' query returned nothing"
+ assert_not_includes found, 'zzzzz-8i9sb-pshmckwoma9plh7',
+ "'not in' query returned the very thing I did not want"
+ end
+
+ test "search jobs by uuid with '!=' query" do
+ authorize_with :active
+ get :index, {
+ filters: [['uuid', '!=', 'zzzzz-8i9sb-pshmckwoma9plh7']]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:uuid)
+ assert_not_equal [], found, "'!=' query returned nothing"
+ assert_not_includes found, 'zzzzz-8i9sb-pshmckwoma9plh7',
+ "'!=' query returned the very thing I did not want"
+ end
+
+ test "search jobs by output with '!= nil' query" do
+ authorize_with :active
+ get :index, {
+ filters: [['output', '!=', nil]]
+ }
+ assert_response :success
+ found = assigns(:objects).collect(&:output)
+ assert_not_equal [], found, "'!= nil' query returned nothing"
+ assert_not_includes found, nil,
+ "'!= nil' query returned the very thing I did not want"
+ end
+
test "search jobs by started_at with < query" do
authorize_with :active
get :index, {
commit a04d67ef0823d6c87e8515cfe6cf88793ef5e3bb
Author: Tom Clegg <tom at curoverse.com>
Date: Tue May 6 19:40:27 2014 -0400
Fix up workbench and apiserver install docs.
diff --git a/doc/install/install-api-server.html.textile.liquid b/doc/install/install-api-server.html.textile.liquid
index 3e70a67..0d721fc 100644
--- a/doc/install/install-api-server.html.textile.liquid
+++ b/doc/install/install-api-server.html.textile.liquid
@@ -141,7 +141,7 @@ To enable streaming so users can monitor crunch jobs in real time, add to your P
</code></pre>
</notextile>
-h2. Add an admin user
+h2(#admin-user). Add an admin user
Point your browser to the API server's login endpoint:
diff --git a/doc/install/install-workbench-app.html.textile.liquid b/doc/install/install-workbench-app.html.textile.liquid
index c9395c6..eaf4ede 100644
--- a/doc/install/install-workbench-app.html.textile.liquid
+++ b/doc/install/install-workbench-app.html.textile.liquid
@@ -25,7 +25,12 @@ Install graphviz.
h2. Download the source tree
-Please follow the instructions on the "Download page":https://arvados.org/projects/arvados/wiki/Download in the wiki.
+<notextile>
+<pre><code>~$ <span class="userinput">cd $HOME</span> # (or wherever you want to install)
+~$ <span class="userinput">git clone https://github.com/curoverse/arvados.git</span>
+</code></pre></notextile>
+
+See also: "Downloading the source code":https://arvados.org/projects/arvados/wiki/Download on the Arvados wiki.
The Workbench application is in @apps/workbench@ in the source tree.
@@ -59,21 +64,28 @@ Copy @config/application.yml.example@ to @config/application.yml@ and edit it ap
* Set @secret_token@ to the string you generated with @rake secret at .
* Point @arvados_login_base@ and @arvados_v1_base@ at your "API server":install-api-server.html
* @site_name@ can be any string to identify this Workbench.
-* Assuming that the SSL certificate you use for development isn't signed by a CA, make sure @arvados_insecure_https@ is @true at .
+* If the SSL certificate you use for development isn't signed by a CA, make sure @arvados_insecure_https@ is @true at .
Copy @config/piwik.yml.example@ to @config/piwik.yml@ and edit to suit.
-h3. Apache/Passenger (optional)
+h2. Start a standalone server
-Set up Apache and Passenger. Point them to the apps/workbench directory in the source tree.
+For testing and development, the easiest way to get started is to run the web server that comes with Rails.
+
+<notextile>
+<pre><code>~/arvados/apps/workbench$ <span class="userinput">bundle exec rails server --port=3031</span>
+</code></pre>
+</notextile>
+
+Point your browser to <notextile><code>http://<b>your.host</b>:3031/</code></notextile>.
h2. Trusted client setting
-Log in to Workbench once (this ensures that the Arvados API server has a record of the Workbench client).
+Log in to Workbench once to ensure that the Arvados API server has a record of the Workbench client. (It's OK if Workbench says your account hasn't been activated yet. We'll deal with that next.)
In the API server project root, start the rails console. Locate the ApiClient record for your Workbench installation (typically, while you're setting this up, the @last@ one in the database is the one you want), then set the @is_trusted@ flag for the appropriate client record:
-<notextile><pre><code>~/arvados/services/api$ <span class="userinput">RAILS_ENV=development bundle exec rails console</span>
+<notextile><pre><code>~/arvados/services/api$ <span class="userinput">bundle exec rails console</span>
irb(main):001:0> <span class="userinput">wb = ApiClient.all.last; [wb.url_prefix, wb.created_at]</span>
=> ["https://workbench.example.com/", Sat, 19 Apr 2014 03:35:12 UTC +00:00]
irb(main):002:0> <span class="userinput">include CurrentApiClient</span>
@@ -82,3 +94,9 @@ irb(main):003:0> <span class="userinput">act_as_system_user do wb.update_attr
=> true
</code></pre>
</notextile>
+
+h2. Activate your own account
+
+Unless you already activated your account when installing the API server, the first time you log in to Workbench you will see a message that your account is awaiting activation.
+
+Activate your own account and give yourself administrator privileges by following the instructions in the "'Add an admin user' section of the API server install page":install-api-server.html#admin-user.
commit df2ce01533175ff7190a5d13fdca4b61f22befd3
Author: Tom Clegg <tom at curoverse.com>
Date: Tue May 6 19:40:19 2014 -0400
Fix prompt paths.
diff --git a/doc/sdk/python/sdk-python.html.textile.liquid b/doc/sdk/python/sdk-python.html.textile.liquid
index d563d6e..eef9a24 100644
--- a/doc/sdk/python/sdk-python.html.textile.liquid
+++ b/doc/sdk/python/sdk-python.html.textile.liquid
@@ -41,11 +41,11 @@ h4. Option 2: build and install from source
<notextile>
<pre>
-$ <code class="userinput">sudo apt-get install python-dev libattr1-dev libfuse-dev pkg-config</code>
-$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
-$ <code class="userinput">cd arvados/sdk/python</code>
-$ <code class="userinput">./build.sh</code>
-$ <code class="userinput">sudo python setup.py install</code>
+~$ <code class="userinput">sudo apt-get install python-dev libattr1-dev libfuse-dev pkg-config</code>
+~$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+~$ <code class="userinput">cd arvados/sdk/python</code>
+~/arvados/sdk/python$ <code class="userinput">./build.sh</code>
+~/arvados/sdk/python$ <code class="userinput">sudo python setup.py install</code>
</pre>
</notextile>
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