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Getting Started
Make sure you can run the HelloWorld workflow. In three xterms do the following:
(1) Start the HelloWorld Activity worker
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- Console https://console.aws.amazon.com/swf/home
- Documentation https://aws.amazon.com/documentation/swf/
- be sure to read the AWS Flow Framework Developer Guide
- User forum https://forums.aws.amazon.com/forum.jspa?forumID=133
- AWS Java SDK http://aws.amazon.com/sdkforjava/
- be sure to look at the sample code in
aws-java-sdk-x.y.z/samples/AwsFlowFramework/
- be sure to look at the sample code in
- Make sure you are able to build and run Synapse locally. See Developer Bootstrap for instructions.
SageBio Workflow Examples
Hello World
Make sure you can run the HelloWorld workflow https://sagebionetworks.jira.com/source/browse/PLFM/trunk/lib/lib-workflow
In three shells do the following:
(1) Start the HelloWorld Activity worker
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~/platform/trunk/lib/lib-workflow>export MAVEN_OPTS=-javaagent:/Users/deflaux/.m2/repository/org/aspectj/aspectjweaver/1.6.10/aspectjweaver-1.6.10.jar ; mvn exec:java -Dexec.mainClass="com.amazonaws.services.simpleworkflow.flow.examples.helloworld.ActivityHost" [INFO] Scanning for projects... [INFO] Searching repository for plugin with prefix: 'exec'. [INFO] --------------------------------------------------------------- [INFO] Building--------- [INFO] Building Workflow Library [INFO] task-segment: [exec:java] [INFO] ------------------------------------------------------------------------ [INFO] Preparing exec:java [INFO] No goals needed for project - skipping [INFO] [exec:java {execution: default-cli}] [URLClassLoader@5898bbf6] info AspectJ Weaver Version 1.6.10 built on Friday Oct 22, 2010 at 03:50:26 GMT [URLClassLoader@5898bbf6] info register classloader java.net.URLClassLoader@5898bbf6 [URLClassLoader@5898bbf6] info using configuration /Users/deflaux/platform/trunk/lib/lib-workflow/target/classes/META-INF/aop.xml [URLClassLoader@5898bbf6] info register aspect com.amazonaws.services.simpleworkflow.flow.aspectj.AsynchronousAspect [URLClassLoader@5898bbf6] info register aspect com.amazonaws.services.simpleworkflow.flow.aspectj.ExponentialRetryAspect start: GenericActivityWorker [super=GenericActivityWorker[service=com.amazonaws.services.simpleworkflow.AmazonSimpleWorkflowClient@1769df00, domain=dev, taskListToPoll=HelloWorld, identity=6022@dhcp149230.fhcrc.org, backoffInitialInterval=100, backoffMaximumInterval=60000, backoffCoefficient=2.0], taskExecutorThreadPoolSize=100] 0 [com.amazonaws.services.simpleworkflow.flow.examples.helloworld.ActivityHost.main()] INFO com.amazonaws.services.simpleworkflow.flow.worker.GenericWorker - start: GenericActivityWorker [super=GenericActivityWorker[service=com.amazonaws.services.simpleworkflow.AmazonSimpleWorkflowClient@1769df00, domain=dev, taskListToPoll=HelloWorld, identity=6022@dhcp149230.fhcrc.org, backoffInitialInterval=100, backoffMaximumInterval=60000, backoffCoefficient=2.0], taskExecutorThreadPoolSize=100] Activity Worker Started for Task List: HelloWorld Please press any key to terminate service. |
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~/platform/trunk/lib/lib-workflow>export MAVEN_OPTS=-javaagent:/Users/deflaux/.m2/repository/org/aspectj/aspectjweaver/1.6.10/aspectjweaver-1.6.10.jar ; mvn exec:java -Dexec.mainClass="com.amazonaws.services.simpleworkflow.flow.examples.helloworld.WorkflowExecutionStarter"
[INFO] Scanning for projects...
[INFO] Searching repository for plugin with prefix: 'exec'.
[INFO] ------------------------------------------------------------------------
[INFO] Building Workflow Library
[INFO] task-segment: [exec:java]
[INFO] ------------------------------------------------------------------------
[INFO] Preparing exec:java
[INFO] No goals needed for project - skipping
[INFO] [exec:java {execution: default-cli}]
[URLClassLoader@1d162212] info AspectJ Weaver Version 1.6.10 built on Friday Oct 22, 2010 at 03:50:26 GMT
[URLClassLoader@1d162212] info register classloader java.net.URLClassLoader@1d162212
[URLClassLoader@1d162212] info using configuration /Users/deflaux/platform/trunk/lib/lib-workflow/target/classes/META-INF/aop.xml
[URLClassLoader@1d162212] info register aspect com.amazonaws.services.simpleworkflow.flow.aspectj.AsynchronousAspect
[URLClassLoader@1d162212] info register aspect com.amazonaws.services.simpleworkflow.flow.aspectj.ExponentialRetryAspect
Started helloWorld workflow with workflowId="c4bc4010-d1b6-4415-8d9a-40b7c410c1a5" and runId="57e222a2-52fb-4318-9cea-359bd5fdf11a"
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESSFUL
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 4 seconds
[INFO] Finished at: Mon Feb 27 16:40:56 PST 2012
[INFO] Final Memory: 14M/81M
[INFO] ------------------------------------------------------------------------
~/platform/trunk/lib/lib-workflow> |
(4) Each time you run the Initiator, you should see some "hello world!" messages in the Activity worker output. If not, log into the AWS console and look at the SWF tab to see what's going on with your workflows.
MetaGenomics Pipeline
https://sagebionetworks.jira.com/source/browse/PLFM/trunk/tools/gePipeline
TcgaWorkflow
https://sagebionetworks.jira.com/source/browse/PLFM/trunk/tools/tcgaWorkflow
How to run it:
(1) run a local instance of Synapse with some TCGA datasets created
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(2) run the decider java -javaagent:/Users/deflaux/Downloads/aws-java-sdk-1.3.3/third-party/aspectj-1.6/aspectjweaver.jar -cp ~/platform/trunk/tools/tcgaWorkflow/target/tcgaWorkflow-
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0.11-SNAPSHOT.jar org.sagebionetworks.workflow.curation.TcgaWorkflowDeciderService
(3) run the activity worker java -javaagent:/Users/deflaux/Downloads/aws-java-sdk-1.3.3/third-party/aspectj-1.6/aspectjweaver.jar -cp ~/platform/trunk/tools/tcgaWorkflow/target/tcgaWorkflow-0.11-SNAPSHOT.jar org.sagebionetworks.workflow.curation.TcgaWorkflowActivityService
(4) Run the initiator java -javaagent:/Users/deflaux/Downloads/aws-java-sdk-1.3.3/third-party/aspectj-1.6/aspectjweaver.jar -cp ~/platform/trunk/tools/
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(4) Each time you run the Initiator, you should see some "hello world!" messages in the Activity worker output. If not, log into the AWS console and look at the SWF tab to see what's going on with your workflows.tcgaWorkflow/target/tcgaWorkflow-0.11-SNAPSHOT.jar org.sagebionetworks.workflow.curation.TcgaWorkflowInitiator
How to make a new workflow
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This can happen when the activity or workflow code throws a runtime exception such as a NullPointerException. Unfortunately the unit testing framework provided by SWF does not log them.
"java.lang.IllegalStateException",{"cause":null,"message":"not ready","localizedMessage":"not ready"
Promise Variables were used Incorrectly
This happens when you try to access a Promise variable in a context that does not ensure that the value must be "ready". Here is an anti-example:
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Promise<String> message = client.formulateNotificationMessage(layerId);
client.notifyFollowers(Promise.asPromise(NOTIFICATION_SNS_TOPIC),
Promise.asPromise(NOTIFICATION_SUBJECT),
message); |
Load-Time Weaving Not Enabled
This can also happen when you have @Asynchronous annotations but aspectj weaving is not correctly configured and enabled. Make sure:(1) loadsure load-time weaving is enabled by passing JVM argument -javaagent:/Path/To/aspectj-1.6/aspectjweaver.jar
for mvn exec:java you do this via setting the environment variable
Code Block export MAVEN_OPTS=-javaagent:/Path/To/aspectj-1.6/aspectjweaver.jar
for the surefire plugin, this is configured via
Code Block <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-surefire-plugin</artifactId> <configuration> <forkMode>pertest</forkMode> <argLine>-javaagent:${settings.localRepository}/org/aspectj/aspectjweaver/${org.aspectj.version}/aspectjweaver-${org.aspectj.version}.jar</argLine> </configuration> </plugin>for Java it might look something like this
Code Block java -javaagent:/Users/deflaux/Downloads/a-java-sdk-1.3.3/third-party/aspectj-1.6/aspectjweaver.jar -cp target/tcgaWorkflow-0.11-SNAPSHOT.jar org.sagebionetworks.workflow.curation.TcgaWorkflowInitiator
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Load-Time Weaving Not Configured
This can also happen when you have @Asynchronous annotations but aspectj weaving is not correctly configured. Make sure load-time weaving is configured correctly in PLFM/trunk/lib/lib-workflow/src/main/resources/META-INF/aop.xml You should see some log output like the following:
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