[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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