[ARVADOS] updated: 52a3016af3ff21b8fb5402bf70d0aab07f5ee486

git at public.curoverse.com git at public.curoverse.com
Tue May 6 21:47:15 EDT 2014


Summary of changes:
 apps/workbench/.gitignore                          |    3 +
 apps/workbench/Gemfile                             |    5 +
 apps/workbench/Gemfile.lock                        |    8 +
 .../app/assets/javascripts/application.js          |    1 -
 apps/workbench/app/assets/javascripts/editable.js  |   55 ++++-
 apps/workbench/app/assets/javascripts/folders.js   |   12 +
 ..._authorizations.js.coffee => folders.js.coffee} |    0
 apps/workbench/app/assets/javascripts/selection.js |   18 +-
 .../app/assets/stylesheets/application.css.scss    |   72 +++--
 .../app/assets/stylesheets/cards.css.scss          |   85 +++++
 .../{jobs.css.scss => folders.css.scss}            |    2 +-
 .../app/assets/stylesheets/sb-admin.css.scss       |  164 ++++++++++
 .../workbench/app/assets/stylesheets/selection.css |   22 +-
 .../app/controllers/actions_controller.rb          |   42 ++-
 .../app/controllers/application_controller.rb      |   47 ++-
 .../app/controllers/collections_controller.rb      |    1 -
 .../app/controllers/folders_controller.rb          |   99 ++++++
 .../workbench/app/controllers/groups_controller.rb |    7 +-
 apps/workbench/app/helpers/application_helper.rb   |   21 +-
 apps/workbench/app/helpers/folders_helper.rb       |    2 +
 .../app/helpers/pipeline_instances_helper.rb       |    1 -
 apps/workbench/app/models/arvados_base.rb          |   48 +++-
 apps/workbench/app/models/arvados_resource_list.rb |    6 +
 apps/workbench/app/models/collection.rb            |    5 +
 apps/workbench/app/models/group.rb                 |   10 +
 apps/workbench/app/models/log.rb                   |    5 +
 .../app/views/application/_content.html.erb        |    2 +-
 .../application/_delete_object_button.html.erb     |    2 +-
 .../views/application/_show_object_button.html.erb |    3 +
 .../app/views/application/_show_recent.html.erb    |   21 +-
 .../workbench/app/views/application/index.html.erb |    6 +-
 .../app/views/folders/_show_my_folders.html.erb    |    2 +
 .../views/folders/_show_shared_with_me.html.erb    |    2 +
 .../workbench/app/views/folders/remove_item.js.erb |    5 +
 apps/workbench/app/views/folders/show.html.erb     |  193 ++++++++++++
 .../app/views/layouts/application.html.erb         |  321 ++++++++++----------
 apps/workbench/app/views/logs/show.html.erb        |    1 -
 apps/workbench/config/routes.rb                    |    3 +
 .../folders_controller_test.rb}                    |    2 +-
 apps/workbench/test/integration/folders_test.rb    |   48 +++
 apps/workbench/test/integration/smoke_test.rb      |    2 +-
 apps/workbench/test/integration/users_test.rb      |   51 ++--
 .../test/integration/virtual_machines_test.rb      |    4 +-
 apps/workbench/test/integration_helper.rb          |   26 ++
 apps/workbench/test/test_helper.rb                 |   21 ++
 .../test/unit/helpers/folders_helper_test.rb       |    4 +
 doc/api/index.html.textile.liquid                  |    2 -
 doc/api/schema/Collection.html.textile.liquid      |    2 +-
 doc/sdk/java/index.html.textile.liquid             |   43 ++--
 doc/sdk/ruby/index.html.textile.liquid             |    2 +-
 sdk/java/ArvadosSDKJavaExample.java                |   20 +-
 sdk/java/pom.xml                                   |  149 +++++-----
 sdk/ruby/.gitignore                                |    1 +
 sdk/ruby/Gemfile.lock                              |   58 ----
 services/api/.gitignore                            |    2 +
 services/api/Gemfile                               |    6 +-
 services/api/Gemfile.lock                          |   10 +-
 .../api/app/controllers/application_controller.rb  |   67 ----
 .../controllers/arvados/v1/groups_controller.rb    |   68 ++++
 .../app/controllers/user_sessions_controller.rb    |    3 +-
 services/api/app/models/arvados_model.rb           |   20 ++
 services/api/app/models/group.rb                   |    1 +
 services/api/app/models/user.rb                    |    4 +
 services/api/test/fixtures/specimens.yml           |   18 ++
 .../arvados/v1/groups_controller_test.rb           |   37 +++
 .../api/test/integration/user_sessions_test.rb     |   28 ++
 services/api/test/test_helper.rb                   |   21 ++
 67 files changed, 1486 insertions(+), 536 deletions(-)
 create mode 100644 apps/workbench/app/assets/javascripts/folders.js
 copy apps/workbench/app/assets/javascripts/{api_client_authorizations.js.coffee => folders.js.coffee} (100%)
 create mode 100644 apps/workbench/app/assets/stylesheets/cards.css.scss
 copy apps/workbench/app/assets/stylesheets/{jobs.css.scss => folders.css.scss} (64%)
 create mode 100644 apps/workbench/app/assets/stylesheets/sb-admin.css.scss
 create mode 100644 apps/workbench/app/controllers/folders_controller.rb
 create mode 100644 apps/workbench/app/helpers/folders_helper.rb
 create mode 100644 apps/workbench/app/views/application/_show_object_button.html.erb
 create mode 100644 apps/workbench/app/views/folders/_show_my_folders.html.erb
 create mode 100644 apps/workbench/app/views/folders/_show_shared_with_me.html.erb
 create mode 100644 apps/workbench/app/views/folders/remove_item.js.erb
 create mode 100644 apps/workbench/app/views/folders/show.html.erb
 delete mode 100644 apps/workbench/app/views/logs/show.html.erb
 copy apps/workbench/test/{unit/job_test.rb => functional/folders_controller_test.rb} (57%)
 create mode 100644 apps/workbench/test/integration/folders_test.rb
 create mode 100644 apps/workbench/test/unit/helpers/folders_helper_test.rb
 delete mode 100644 sdk/ruby/Gemfile.lock
 create mode 100644 services/api/test/integration/user_sessions_test.rb

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commit 52a3016af3ff21b8fb5402bf70d0aab07f5ee486
Merge: e65b2e6 69141a1
Author: radhika <radhika at curoverse.com>
Date:   Tue May 6 21:47:04 2014 -0400

    Merge branch 'master' into 2525-java-sdk


commit e65b2e685833e1d850c8d671fd1df9d4e4fea4a3
Merge: fdbea9e ba764a7
Author: radhika <radhika at curoverse.com>
Date:   Tue May 6 21:34:04 2014 -0400

    Merge branch 'master' into 2525-java-sdk


commit fdbea9e3c225a3184f8f7c2fac52abde643603c6
Author: radhika <radhika at curoverse.com>
Date:   Tue May 6 21:33:26 2014 -0400

    2525: Address review feedback.

diff --git a/doc/sdk/java/index.html.textile.liquid b/doc/sdk/java/index.html.textile.liquid
index d249835..f39d9c5 100644
--- a/doc/sdk/java/index.html.textile.liquid
+++ b/doc/sdk/java/index.html.textile.liquid
@@ -14,9 +14,7 @@ h3. Introdution
   
 * The Java SDK is implemented as a maven project. Hence, you would need a working
 maven environment to be able to build the source code. If you do not have maven setup,
-you may find the following link useful. 
-
-<code class="userinput">http://maven.apache.org/guides/getting-started/maven-in-five-minutes.html</code>
+you may find the "Maven in 5 Minutes":http://maven.apache.org/guides/getting-started/maven-in-five-minutes.html link useful. 
 
 * In this document $ARVADOS_HOME is used to refer to the directory where
 arvados code is cloned in your system. For ex: $ARVADOS_HOME = $HOME/arvados
@@ -24,27 +22,23 @@ arvados code is cloned in your system. For ex: $ARVADOS_HOME = $HOME/arvados
 
 h3. Setting up the environment
 
-* The SDK requires a running Arvados API server. The information about the
-  	  API server needs to be passed to the SDK using environment variables or
-  	  during the construction of the Arvados instance.
-  	  
-* Below are the details about the environment variables and example setup
-  	  statements for a .bashrc file.
-  	
+* The SDK requires a running Arvados API server. The following information
+  	  about the API server needs to be passed to the SDK using environment
+  	  variables or during the construction of the Arvados instance.
+
 <notextile>
 <pre>
 ARVADOS_API_TOKEN: API client token to be used to authorize with API server.
-$ <code class="userinput">export ARVADOS_API_TOKEN=z40gplmla6i58rsg96jhg5u41ewdl5rj4g1py2s6e2lsc3</code>
 
 ARVADOS_API_HOST: Host name of the API server.
-$ <code class="userinput">export ARVADOS_API_HOST=localhost:3001</code>
 
 ARVADOS_API_HOST_INSECURE: Set this to true if you are using self-signed
-certificates and would like to bypass certificate validations.
-$ <code class="userinput">export ARVADOS_API_HOST_INSECURE=true</code>
+    certificates and would like to bypass certificate validations.
 </pre>
 </notextile>
 
+* Please see "api-tokens":{{site.baseurl}}/user/reference/api-tokens.html for full details.
+  	  
 
 h3. Building the Arvados SDK
 
@@ -116,15 +110,26 @@ h3. Using the SDK in eclipse
 
 * To develop in eclipse, you can use the provided <code class="userinput">eclipse project</code>
 
-* Install <code class="userinput">m2eclipse</code> plugin in your eclipse
-* Set <code class="userinput">M2_REPO</code> in eclipse to your <code class="userinput">.m2/repository</code> directory
+* Install "m2eclipse":https://www.eclipse.org/m2e/ plugin in your eclipse
+
+* Set <code class="userinput">M2_REPO</code> classpath variable in eclipse to point to your local repository.
+The local repository is usually located in your home directory at <code class="userinput">$HOME/.m2/repository</code>.
 
-* Open the SDK project in eclipse
 <notextile>
 <pre>
-File -> Import -> Existing Projects into Workspace -> Next -> Browse
-and select $ARVADOS_HOME/sdk/java
+In Eclipse IDE:
+Window -> Preferences -> Java -> Build Path -> Classpath Variables
+    Click on the "New..." button and add a new 
+    M2_REPO variable and set it to your local Maven repository
 </pre>
 </notextile>
 
 
+* Open the SDK project in eclipse
+<notextile>
+<pre>
+In Eclipse IDE:
+File -> Import -> Existing Projects into Workspace -> Next -> Browse
+    and select $ARVADOS_HOME/sdk/java
+</pre>
+</notextile>
diff --git a/sdk/java/ArvadosSDKJavaExample.java b/sdk/java/ArvadosSDKJavaExample.java
index 40ff9b6..3c47f66 100644
--- a/sdk/java/ArvadosSDKJavaExample.java
+++ b/sdk/java/ArvadosSDKJavaExample.java
@@ -14,7 +14,14 @@ import java.util.Map;
 
 public class ArvadosSDKJavaExample {
   /** Make sure the following environment variables are set before using Arvados:
-   *      ARVADOS_API_TOKEN, ARVADOS_API_HOST, ARVADOS_API_HOST_INSECURE
+   *      ARVADOS_API_TOKEN, ARVADOS_API_HOST and ARVADOS_API_HOST_INSECURE 
+   *      Set ARVADOS_API_HOST_INSECURE to true if you are using self-singed
+   *      certificates in development and want to bypass certificate validations.
+   *
+   *  If you are not using env variables, you can pass them to Arvados constructor.
+   *
+   *  Please refer to http://doc.arvados.org/api/index.html for a complete list
+   *      of the available API methods.
    */
   public static void main(String[] args) throws Exception {
     String apiName = "arvados";
@@ -22,7 +29,8 @@ public class ArvadosSDKJavaExample {
 
     Arvados arv = new Arvados(apiName, apiVersion);
 
-    // Make a users.list call
+    // Make a users list call. Here list on users is the method being invoked.
+    // Expect a Map containing the list of users as the response.
     System.out.println("Making an arvados users.list api call");
 
     Map<String, Object> params = new HashMap<String, Object>();
@@ -36,15 +44,15 @@ public class ArvadosSDKJavaExample {
     Map firstUser = (Map)items.get(0);
     String userUuid = (String)firstUser.get("uuid");
     
-    // Make a users.get call on the uuid obtained above
-    System.out.println("Making a users.get call for " + userUuid);
+    // Make a users get call on the uuid obtained above
+    System.out.println("\n\n\nMaking a users.get call for " + userUuid);
     params = new HashMap<String, Object>();
     params.put("uuid", userUuid);
     response = arv.call("users", "get", params);
     System.out.println("Arvados users.get:\n" + response);
 
-    // Make a pipeline_templates.list call
-    System.out.println("Making a pipeline_templates.list call.");
+    // Make a pipeline_templates list call
+    System.out.println("\n\n\nMaking a pipeline_templates.list call.");
 
     params = new HashMap<String, Object>();
     response = arv.call("pipeline_templates", "list", params);
diff --git a/sdk/java/pom.xml b/sdk/java/pom.xml
index b89e482..53e8f75 100644
--- a/sdk/java/pom.xml
+++ b/sdk/java/pom.xml
@@ -34,17 +34,17 @@
       <artifactId>log4j</artifactId>
       <version>1.2.16</version>
     </dependency>
+    <dependency>
+      <groupId>com.googlecode.json-simple</groupId>
+      <artifactId>json-simple</artifactId>
+      <version>1.1.1</version>
+    </dependency>
 
     <dependency>
       <groupId>junit</groupId>
       <artifactId>junit</artifactId>
       <version>4.8.1</version>
     </dependency>
-    <dependency>
-      <groupId>com.googlecode.json-simple</groupId>
-      <artifactId>json-simple</artifactId>
-      <version>1.1.1</version>
-    </dependency>
   </dependencies>
 
   <build>

commit 733269172b6b9802c2a00a8f8d19d6a520546a67
Merge: 35fb8a1 17b0eec
Author: radhika <radhika at curoverse.com>
Date:   Tue May 6 16:30:39 2014 -0400

    Merge branch 'master' into 2525-java-sdk


commit 35fb8a1cd59d1dc0ad4be89c64e8b48c750faaeb
Author: radhika <radhika at curoverse.com>
Date:   Tue May 6 12:28:17 2014 -0400

    2525: correct indentation for pom.xml

diff --git a/sdk/java/pom.xml b/sdk/java/pom.xml
index 33ba1e5..b89e482 100644
--- a/sdk/java/pom.xml
+++ b/sdk/java/pom.xml
@@ -10,9 +10,9 @@
 
   <dependencies>
     <dependency>
-    	<groupId>com.google.apis</groupId>
-    	<artifactId>google-api-services-discovery</artifactId>
-    	<version>v1-rev42-1.18.0-rc</version>
+      <groupId>com.google.apis</groupId>
+      <artifactId>google-api-services-discovery</artifactId>
+      <version>v1-rev42-1.18.0-rc</version>
     </dependency>
     <dependency>
       <groupId>com.google.api-client</groupId>
@@ -20,88 +20,87 @@
       <version>1.18.0-rc</version>
     </dependency>
     <dependency>
-    	<groupId>com.google.http-client</groupId>
-    	<artifactId>google-http-client-jackson2</artifactId>
-    	<version>1.18.0-rc</version>
+      <groupId>com.google.http-client</groupId>
+      <artifactId>google-http-client-jackson2</artifactId>
+      <version>1.18.0-rc</version>
     </dependency>
     <dependency>
-    	<groupId>com.google.guava</groupId>
-    	<artifactId>guava</artifactId>
-    	<version>r05</version>
+      <groupId>com.google.guava</groupId>
+      <artifactId>guava</artifactId>
+      <version>r05</version>
     </dependency>
     <dependency>
-  	<groupId>log4j</groupId>
-	<artifactId>log4j</artifactId>
-	<version>1.2.16</version>
+      <groupId>log4j</groupId>
+      <artifactId>log4j</artifactId>
+      <version>1.2.16</version>
     </dependency>
-                    
+
     <dependency>
-	  <groupId>junit</groupId>
-	  <artifactId>junit</artifactId>
-	  <version>4.8.1</version>
-	</dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <version>4.8.1</version>
+    </dependency>
     <dependency>
-        <groupId>com.googlecode.json-simple</groupId>
-        <artifactId>json-simple</artifactId>
-        <version>1.1.1</version>
-	</dependency>
+      <groupId>com.googlecode.json-simple</groupId>
+      <artifactId>json-simple</artifactId>
+      <version>1.1.1</version>
+    </dependency>
   </dependencies>
 
   <build>
     <finalName>arvados-sdk-1.0</finalName>
-	
+
     <plugins>
-       <plugin>
-          <groupId>org.apache.maven.plugins</groupId>
-          <artifactId>maven-compiler-plugin</artifactId>
-          <version>3.1</version>
-          <configuration>
-            <source>1.6</source>
-            <target>1.6</target>
-          </configuration>
-       </plugin>
-        <plugin>
-          <groupId>org.apache.maven.plugins</groupId>
-          <artifactId>maven-assembly-plugin</artifactId>
-          <executions>
-            <execution>
-              <goals>
-                <goal>attached</goal>
-              </goals>
-              <phase>package</phase>
-              <configuration>
-                <descriptorRefs>
-                  <descriptorRef>jar-with-dependencies</descriptorRef>
-                </descriptorRefs>
-                <archive>
-                  <manifest>
-                    <mainClass>org.arvados.sdk.Arvados</mainClass>
-                  </manifest>
-                  <manifestEntries>
-                    <!--<Premain-Class>Your.agent.class</Premain-Class>
-                    <Agent-Class>Your.agent.class</Agent-Class>-->
-                    <Can-Redefine-Classes>true</Can-Redefine-Classes>
-                    <Can-Retransform-Classes>true</Can-Retransform-Classes>
-                  </manifestEntries>
-                </archive>
-              </configuration>
-            </execution>
-          </executions>
-        </plugin>
-      </plugins>
-      <resources>
-    	<resource>
-          <directory>src/main/resources</directory>
-            <targetPath>${basedir}/target/classes</targetPath>
-            <includes>
-              <include>log4j.properties</include>
-            </includes>    	
-          <filtering>true</filtering>      
-        </resource>
-    	<resource>
-          <directory>src/test/resources</directory>      
-          <filtering>true</filtering>      
-        </resource>
-      </resources>
-    </build>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-compiler-plugin</artifactId>
+        <version>3.1</version>
+        <configuration>
+          <source>1.6</source>
+          <target>1.6</target>
+        </configuration>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-assembly-plugin</artifactId>
+        <executions>
+          <execution>
+            <goals>
+              <goal>attached</goal>
+            </goals>
+            <phase>package</phase>
+            <configuration>
+              <descriptorRefs>
+                <descriptorRef>jar-with-dependencies</descriptorRef>
+              </descriptorRefs>
+              <archive>
+                <manifest>
+                  <mainClass>org.arvados.sdk.Arvados</mainClass>
+                </manifest>
+                <manifestEntries>
+                  <!--<Premain-Class>Your.agent.class</Premain-Class> <Agent-Class>Your.agent.class</Agent-Class> -->
+                  <Can-Redefine-Classes>true</Can-Redefine-Classes>
+                  <Can-Retransform-Classes>true</Can-Retransform-Classes>
+                </manifestEntries>
+              </archive>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+    <resources>
+      <resource>
+        <directory>src/main/resources</directory>
+        <targetPath>${basedir}/target/classes</targetPath>
+        <includes>
+          <include>log4j.properties</include>
+        </includes>
+        <filtering>true</filtering>
+      </resource>
+      <resource>
+        <directory>src/test/resources</directory>
+        <filtering>true</filtering>
+      </resource>
+    </resources>
+  </build>
 </project>

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