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From samin...@apache.org
Subject [4/5] git commit: https://issues.apache.org/jira/browse/AIRAVATA-1047
Date Wed, 05 Mar 2014 01:26:34 GMT
https://issues.apache.org/jira/browse/AIRAVATA-1047


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/cead776c
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/cead776c
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/cead776c

Branch: refs/heads/master
Commit: cead776ce4e45a48c708b21d0dce24b321d94e47
Parents: 0ec292f
Author: Saminda Wijeratne <samindaw@gmail.com>
Authored: Tue Mar 4 20:24:55 2014 -0500
Committer: Saminda Wijeratne <samindaw@gmail.com>
Committed: Tue Mar 4 20:24:55 2014 -0500

----------------------------------------------------------------------
 modules/distribution/airavata-server/pom.xml    | 109 ++++++-------------
 .../src/main/assembly/bin-assembly.xml          |  72 ++++--------
 .../resources/conf/airavata-server.properties   |  78 +++++++------
 3 files changed, 102 insertions(+), 157 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/cead776c/modules/distribution/airavata-server/pom.xml
----------------------------------------------------------------------
diff --git a/modules/distribution/airavata-server/pom.xml b/modules/distribution/airavata-server/pom.xml
index aeda70b..06ea0e8 100644
--- a/modules/distribution/airavata-server/pom.xml
+++ b/modules/distribution/airavata-server/pom.xml
@@ -123,7 +123,7 @@
                     </execution>
                 </executions>
             </plugin>
-            <plugin>
+            <!--plugin>
                 <artifactId>maven-antrun-plugin</artifactId>
                 <executions>
                     <execution>
@@ -183,7 +183,7 @@
                         </goals>
                     </execution>
                 </executions>
-            </plugin>
+            </plugin-->
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>build-helper-maven-plugin</artifactId>
@@ -198,16 +198,6 @@
                         <configuration>
                             <artifacts>
                                 <artifact>
-                                    <file>${airavata.webapp.war.zip}</file>
-                                    <type>zip</type>
-                                    <classifier>war</classifier>
-                                </artifact>
-                                <artifact>
-                                    <file>${airavata.webapp.war.tar.gz}</file>
-                                    <type>tar.gz</type>
-                                    <classifier>war</classifier>
-                                </artifact>
-                                <artifact>
                                     <file>${airavata.bin.zip}</file>
                                     <type>zip</type>
                                     <classifier>bin</classifier>
@@ -320,72 +310,72 @@
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>json</artifactId>
+            <artifactId>airavata-standalone-server</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-messenger-client</artifactId>
+            <artifactId>airavata-common-utils</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-messenger-commons</artifactId>
+            <artifactId>airavata-orchestrator-service</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-registry-api</artifactId>
+            <artifactId>airavata-orchestrator-core</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-registry-service</artifactId>
+            <artifactId>airavata-registry-api</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-workflow-execution-context</artifactId>
+            <artifactId>airavata-gfac-schema-utils</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-workflow-tracking</artifactId>
+            <artifactId>airavata-workflow-execution-context</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-core</artifactId>
+            <artifactId>airavata-registry-cpi</artifactId>
             <version>${project.version}</version>
         </dependency>
-	<dependency>
+        <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-ec2</artifactId>
+            <artifactId>airavata-jpa-registry</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-credential-store</artifactId>
+            <artifactId>airavata-data-models</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-schema-utils</artifactId>
+            <artifactId>airavata-credential-store</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-common-utils</artifactId>
+            <artifactId>airavata-gfac-core</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-message-box</artifactId>
+            <artifactId>airavata-client-api</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-message-broker</artifactId>
+            <artifactId>airavata-message-monitor</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
@@ -395,70 +385,61 @@
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-workflow-model-component</artifactId>
+            <artifactId>airavata-messenger-commons</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-client-api</artifactId>
+            <artifactId>airavata-messenger-client</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-xbaya-gui</artifactId>
+            <artifactId>airavata-workflow-tracking</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-message-monitor</artifactId>
+            <artifactId>gsissh</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>apache-airavata-samples</artifactId>
+            <artifactId>airavata-model-utils</artifactId>
             <version>${project.version}</version>
-			<type>zip</type>
-        </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcprov-jdk16</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.openjpa</groupId>
-            <artifactId>openjpa-all</artifactId>
-            <version>2.2.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-jpa-registry</artifactId>
+            <artifactId>airavata-job-monitor</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-rest-mappings</artifactId>
+            <artifactId>airavata-api-server</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-rest-services</artifactId>
+	    <groupId>org.apache.airavata</groupId>
+	    <artifactId>apache-airavata-samples</artifactId>
+	    <type>zip</type>
             <version>${project.version}</version>
         </dependency>
         <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-embedded-tomcat</artifactId>
-            <version>${project.version}</version>
+            <groupId>org.bouncycastle</groupId>
+            <artifactId>bcprov-jdk16</artifactId>
         </dependency>
         <dependency>
+            <groupId>org.apache.openjpa</groupId>
+            <artifactId>openjpa-all</artifactId>
+            <version>2.2.0</version>
+        </dependency>
+
+        <dependency>
             <groupId>org.apache.shiro</groupId>
             <artifactId>shiro-core</artifactId>
             <version>1.2.1</version>
         </dependency>
         <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-security</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
             <groupId>com.sun.jersey</groupId>
             <artifactId>jersey-client</artifactId>
             <version>${jersey.version}</version>
@@ -466,26 +447,6 @@
         <!--dependency> <groupId>org.apache.airavata</groupId> <artifactId>airavata-common-utils</artifactId>
<version>${project.version}</version> 
             </dependency -->
         <dependency>
-            <groupId>org.apache.tomcat</groupId>
-            <artifactId>tomcat-jasper</artifactId>
-            <version>7.0.22</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.tomcat</groupId>
-            <artifactId>tomcat-jasper-el</artifactId>
-            <version>7.0.22</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.tomcat</groupId>
-            <artifactId>tomcat-jsp-api</artifactId>
-            <version>7.0.22</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.tomcat.embed</groupId>
-            <artifactId>tomcat-embed-core</artifactId>
-            <version>7.0.22</version>
-        </dependency>
-        <dependency>
             <groupId>javax.servlet</groupId>
             <artifactId>javax.servlet-api</artifactId>
             <version>3.0.1</version>

http://git-wip-us.apache.org/repos/asf/airavata/blob/cead776c/modules/distribution/airavata-server/src/main/assembly/bin-assembly.xml
----------------------------------------------------------------------
diff --git a/modules/distribution/airavata-server/src/main/assembly/bin-assembly.xml b/modules/distribution/airavata-server/src/main/assembly/bin-assembly.xml
index 423f0c5..399e0f0 100644
--- a/modules/distribution/airavata-server/src/main/assembly/bin-assembly.xml
+++ b/modules/distribution/airavata-server/src/main/assembly/bin-assembly.xml
@@ -161,21 +161,6 @@
 
         <!-- ********************** Copy samples ********************** -->
         <fileSet>
-            <directory>${project.build.directory}/samples/services</directory>
-            <outputDirectory>repository/services
-            </outputDirectory>
-            <includes>
-                <include>*.aar</include>
-            </includes>
-        </fileSet>
-        <fileSet>
-            <directory>${project.build.directory}/samples/workflows</directory>
-            <outputDirectory>samples/workflows</outputDirectory>
-            <includes>
-                <include>*.xwf</include>
-            </includes>
-        </fileSet>
-        <fileSet>
             <directory>${project.build.directory}/samples/applications</directory>
             <outputDirectory>samples</outputDirectory>
             <includes>
@@ -226,30 +211,29 @@
                 <include>org.apache.xmlbeans:xmlbeans</include>
                 <include>com.amazonaws:aws-java-sdk</include>
                 <include>net.java.dev.jets3t:jets3t</include>
-                <include>org.apache.airavata:airavata-registry-api</include>
-                <include>org.apache.airavata:airavata-workflow-execution-context</include>
-                <include>org.apache.airavata:airavata-workflow-tracking</include>
-                <include>org.apache.airavata:airavata-gfac-core</include>
-                <include>org.apache.airavata:airavata-gfac-ec2</include>
-                <include>org.apache.airavata:airavata-credential-store</include>
-                <include>org.apache.airavata:airavata-messenger-client</include>
-                <include>org.apache.airavata:airavata-messenger-commons</include>
-                <include>org.apache.airavata:airavata-gfac-schema-utils</include>
-                <include>org.apache.airavata:airavata-common-utils</include>
-                <include>org.apache.airavata:airavata-workflow-model-core:jar</include>
-                <include>org.apache.airavata:airavata-workflow-model-component:jar</include>
-                <include>org.apache.airavata:airavata-message-monitor:jar</include>
-                <include>org.apache.airavata:airavata-client-api:jar</include>
-                <include>org.apache.airavata:airavata-jpa-registry:jar</include>
-                <include>org.apache.airavata:airavata-rest-mappings:jar</include>
-                <include>org.apache.airavata:airavata-rest-client:jar</include>
-                <include>org.apache.airavata:airavata-embedded-tomcat:jar</include>
-                <include>org.apache.airavata:airavata-interpreter-service:jar</include>
-                <include>org.apache.airavata:airavata-rest-mappings</include>
-                <include>org.apache.airavata:airavata-rest-services</include>
-                <include>org.apache.airavata:airavata-security</include>
-                <include>org.apache.airavata:json</include>
-                <include>org.apache.airavata:gsissh</include>
+                <include>org.apache.airavata:airavata-standalone-server:jar</include>
+		<include>org.apache.airavata:airavata-common-utils:jar</include>
+		<include>org.apache.airavata:airavata-orchestrator-service:jar</include>
+		<include>org.apache.airavata:airavata-orchestrator-core:jar</include>
+		<include>org.apache.airavata:airavata-registry-api:jar</include>
+		<include>org.apache.airavata:airavata-gfac-schema-utils:jar</include>
+		<include>org.apache.airavata:airavata-workflow-execution-context:jar</include>
+		<include>org.apache.airavata:airavata-registry-cpi:jar</include>
+		<include>org.apache.airavata:airavata-jpa-registry:jar</include>
+		<include>org.apache.airavata:airavata-data-models:jar</include>
+		<include>org.apache.airavata:airavata-credential-store:jar</include>
+		<include>org.apache.airavata:airavata-gfac-core:jar</include>
+		<include>org.apache.airavata:airavata-client-api:jar</include>
+		<include>org.apache.airavata:airavata-message-monitor:jar</include>
+		<include>org.apache.airavata:airavata-workflow-model-core:jar</include>
+		<include>org.apache.airavata:airavata-messenger-commons:jar</include>
+		<include>org.apache.airavata:airavata-messenger-client:jar</include>
+		<include>org.apache.airavata:airavata-workflow-tracking:jar</include>
+		<include>org.apache.airavata:gsissh:jar</include>
+		<include>org.apache.airavata:airavata-model-utils:jar</include>
+		<include>org.apache.airavata:airavata-job-monitor:jar</include>
+		<include>org.apache.airavata:airavata-api-server:jar</include>
+		<include>org.apache.airavata:airavata-api-stubs:jar</include>
                 <include>org.apache.openjpa:openjpa-all:jar</include>
                 <include>com.sun.jersey:jersey-client:jar</include>
                 <include>com.sun.jersey:jersey-core:jar</include>
@@ -336,15 +320,7 @@
 				unicore end-->
             </includes>
         </dependencySet>
-        <dependencySet>
-            <outputDirectory>repository/services</outputDirectory>
-            <includes>
-                <include>org.apache.airavata:airavata-message-box:jar</include>
-                <include>org.apache.airavata:airavata-message-broker:jar</include>
-                <include>org.apache.airavata:airavata-xbaya-gui:jar</include>
-                <include>org.apache.airavata:airavata-registry-service:jar</include>
-            </includes>
-        </dependencySet>
+        
     </dependencySets>
 
 </assembly>

http://git-wip-us.apache.org/repos/asf/airavata/blob/cead776c/modules/distribution/airavata-server/src/main/resources/conf/airavata-server.properties
----------------------------------------------------------------------
diff --git a/modules/distribution/airavata-server/src/main/resources/conf/airavata-server.properties
b/modules/distribution/airavata-server/src/main/resources/conf/airavata-server.properties
index 5858962..ee67de3 100644
--- a/modules/distribution/airavata-server/src/main/resources/conf/airavata-server.properties
+++ b/modules/distribution/airavata-server/src/main/resources/conf/airavata-server.properties
@@ -20,7 +20,7 @@
 
 ###########################################################################
 #
-#  This properties file provides configuration for all Airavata Services: 
+#  This properties file provides configuration for all Airavata Services:
 #  Registry, Workflow Interpreter, GFac, Message Broker, Message Box
 #
 ###########################################################################
@@ -28,15 +28,15 @@
 ###########################################################################
 # Airavata Embedded-Tomcat Server Configuration
 ###########################################################################
-# By default, tomcat runs on port 80. If the port is changed, it will be  
-#  have to be specified with port properties. This will be picked up by 
+# By default, tomcat runs on port 80. If the port is changed, it will be
+#  have to be specified with port properties. This will be picked up by
 #  the registry service to register the service end-points.
 
 port=8080
 
-# Axis2 server automatically picks up IP address from axis configuration, 
-#  but some DHCP enables machines do not report correct ip addresses,  
-#  in which case, the IP address can be manually specified. 
+# Axis2 server automatically picks up IP address from axis configuration,
+#  but some DHCP enables machines do not report correct ip addresses,
+#  in which case, the IP address can be manually specified.
 
 #ip=192.2.33.12
 
@@ -48,6 +48,7 @@ port=8080
 system.gateway=default
 system.user=admin
 system.password=admin
+airavata.server.url=http://localhost:8080/airavata/services/registry
 
 ###########################################################################
 # Airavata Registry Configuration
@@ -63,7 +64,7 @@ registry.jdbc.password=airavata
 start.derby.server.mode=true
 validationQuery=SELECT 1 from Configuration
 jpa.connection.properties=MaxActive=10,MaxIdle=5,MinIdle=2,MaxWait=60000,testWhileIdle=true,testOnBorrow=true
-# Properties to setup registry service 
+# Properties to setup registry service
 default.registry.user=admin
 default.registry.password=admin
 default.registry.password.hash.method=SHA
@@ -79,7 +80,7 @@ default.registry.gateway=default
 #class.user.workflow.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry
 #class.published.workflow.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry
 
-###########################################################################
+############################################################    ###############
 # Airavata Workflow Interpreter Configurations
 ###########################################################################
 
@@ -98,12 +99,11 @@ gfac.embedded=true
 ###########################################################################
 
 myproxy.server=myproxy.teragrid.org
-myproxy.user=username
-myproxy.pass=password
+myproxy.user=ogce
+myproxy.pass=
 myproxy.life=3600
 # XSEDE Trusted certificates can be downloaded from https://software.xsede.org/security/xsede-certs.tar.gz
-trusted.cert.location=/path/to/trusted/certificates
-
+trusted.cert.location=/Users/lahirugunathilake/Downloads/certificates
 # SSH PKI key pair or ssh password can be used SSH based authentication is used.
 # if user specify both password authentication gets the higher preference
 
@@ -129,16 +129,16 @@ trusted.cert.location=/path/to/trusted/certificates
 broker.jdbc.driver=org.apache.derby.jdbc.EmbeddedDriver
 broker.jdbc.url=jdbc:derby:wsmg;create=true;user=airavata;password=airavata
 
-# Note: This database will only be used  if 'broker.storage.type=persistent' 
+# Note: This database will only be used  if 'broker.storage.type=persistent'
 #       is set in advanced properties below.
 # MySql database configuration
 #broker.jdbc.driver=com.mysql.jdbc.Driver
 #broker.jdbc.url=jdbc:mysql://localhost:3306/wsmg?user=airavata&password=airavata
 
 ###########################################################################
-# Airavata Message Box Basic Configurations, 
+# Airavata Message Box Basic Configurations,
 #  the Advanced section provides detailed custom configuration properties.
-###########################################################################  
+###########################################################################
 
 # Default derby database
 msgBox.jdbc.driver=org.apache.derby.jdbc.EmbeddedDriver
@@ -202,10 +202,10 @@ broker.delivery.method=serial
 #number of message delivery failures before a url become black listed (default is 2)
 #broker.msg.delivery.retries=2
 
-#time period (in seconds) a url will be kept blacklisted (default is 5 seconds) 
-#consumer.expiration.time.gap=5 
+#time period (in seconds) a url will be kept blacklisted (default is 5 seconds)
+#consumer.expiration.time.gap=5
 
-#maximum number of messages to be send to a one consumer/url at time. 
+#maximum number of messages to be send to a one consumer/url at time.
 #applicable if 'broker.delivery.method' is 'pcrew' . (default is 10)
 
 #sending.batch.size=10
@@ -215,7 +215,7 @@ broker.delivery.method=serial
 
 #
 # Advanced Message Box Configurations
-# 
+#
 msgBox.usedatabase=true
 messagePreservationDays=2
 messagePreservationHours=0
@@ -233,12 +233,12 @@ class.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.Airava
 # AMQP Notification Configuration
 ###########################################################################
 amqp.notification.enable=1
- 
+
 amqp.broker.host=localhost
 amqp.broker.port=5672
 amqp.broker.username=guest
 amqp.broker.password=guest
- 
+
 amqp.sender=org.apache.airavata.wsmg.client.amqp.rabbitmq.AMQPSenderImpl
 amqp.topic.sender=org.apache.airavata.wsmg.client.amqp.rabbitmq.AMQPTopicSenderImpl
 amqp.broadcast.sender=org.apache.airavata.wsmg.client.amqp.rabbitmq.AMQPBroadcastSenderImpl
@@ -252,17 +252,25 @@ registry.service.wsdl=http://localhost:${port}/${server.context-root}/services/R
 # If false, disables two phase commit when submitting jobs
 TwoPhase=true
 
-# credential store specific parameters
-credential.store.keystore.url=airavata.jks
-credential.store.keystore.alias=airavata
-credential.store.keystore.password=airavata
-notifier.enabled=false
-#period in milliseconds
-notifier.duration=5000
-
-email.server=smtp.googlemail.com
-email.server.port=465
-email.user=airavata
-email.password=xxx
-email.ssl=true
-email.from=airavata@apache.org
\ No newline at end of file
+
+###---------------------------Monitoring module Configurations---------------------------###
+#This will be the primary monitoring tool which runs in airavata, in future there will be
multiple monitoring
+#mechanisms and one would be able to start a monitor
+primaryMonitor=org.apache.airavata.job.monitor.impl.pull.qstat.QstatMonitor
+#We do not support a secondaray monitoring at this point or host specific monitoring
+secondaryMonitor=org.apache.airavata.job.monitor.impl.push.amqp.AMQPMonitor
+#This is the amqp related configuration and this lists down the Rabbitmq host, this is an
xsede specific configuration
+amqp.hosts=info1.dyn.teragrid.org,info2.dyn.teragrid.org
+connection.name=xsede_private
+
+
+###---------------------------Orchestrator module Configurations---------------------------###
+job.submitter=org.apache.airavata.orchestrator.core.impl.EmbeddedGFACJobSubmitter
+job.validator=org.apache.airavata.orchestrator.core.validator.impl.SimpleAppDataValidator
+submitter.interval=10000
+threadpool.size=10
+start.submitter=true
+embedded.mode=true
+enable.validation=false
+
+


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