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From sma...@apache.org
Subject svn commit: r1178878 - in /incubator/airavata/site/trunk: content/airavata/about/ content/airavata/architecture/ templates/
Date Tue, 04 Oct 2011 17:48:37 GMT
Author: smarru
Date: Tue Oct  4 17:48:36 2011
New Revision: 1178878

URL: http://svn.apache.org/viewvc?rev=1178878&view=rev
Log:
adding architecture docs

Added:
    incubator/airavata/site/trunk/content/airavata/architecture/airavata-registry.png   (with
props)
    incubator/airavata/site/trunk/content/airavata/architecture/airavata.png   (with props)
    incubator/airavata/site/trunk/content/airavata/architecture/messenger-overview.png   (with
props)
    incubator/airavata/site/trunk/content/airavata/architecture/overview.mdtext
    incubator/airavata/site/trunk/content/airavata/architecture/registry.mdtext
    incubator/airavata/site/trunk/content/airavata/architecture/workflow-suite.png   (with
props)
    incubator/airavata/site/trunk/content/airavata/architecture/workflow.mdtext
    incubator/airavata/site/trunk/content/airavata/architecture/ws-messenger.mdtext
Modified:
    incubator/airavata/site/trunk/content/airavata/about/history.mdtext
    incubator/airavata/site/trunk/templates/sidenav.mdtext

Modified: incubator/airavata/site/trunk/content/airavata/about/history.mdtext
URL: http://svn.apache.org/viewvc/incubator/airavata/site/trunk/content/airavata/about/history.mdtext?rev=1178878&r1=1178877&r2=1178878&view=diff
==============================================================================
--- incubator/airavata/site/trunk/content/airavata/about/history.mdtext (original)
+++ incubator/airavata/site/trunk/content/airavata/about/history.mdtext Tue Oct  4 17:48:36
2011
@@ -28,7 +28,7 @@ Cyberinfrastructure systems to enable fa
 LEAD goals required to create a dynamically adaptive, on-demand, grid-enabled workflow system

 supporting long running applications and on-demand computing. LEAD has subsequently produced
close 
 to 450 research publications combined in all disciplines. The resulting software framework
was built 
-on the concepts of service oriented architectures powering the LEAD Gateway Portal~\cite{leadportal}.

+on the concepts of service oriented architectures powering the LEAD Gateway Portal.
 
 ## Open Gateway Computing Environments
 

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==============================================================================
--- incubator/airavata/site/trunk/content/airavata/architecture/overview.mdtext (added)
+++ incubator/airavata/site/trunk/content/airavata/architecture/overview.mdtext Tue Oct  4
17:48:36 2011
@@ -0,0 +1,63 @@
+Title:     Airavata Gateway Framework
+Notice:    Licensed to the Apache Software Foundation (ASF) under one
+           or more contributor license agreements.  See the NOTICE file
+           distributed with this work for additional information
+           regarding copyright ownership.  The ASF licenses this file
+           to you under the Apache License, Version 2.0 (the
+           "License"); you may not use this file except in compliance
+           with the License.  You may obtain a copy of the License at
+           .
+             http://www.apache.org/licenses/LICENSE-2.0
+           .
+           Unless required by applicable law or agreed to in writing,
+           software distributed under the License is distributed on an
+           "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+           KIND, either express or implied.  See the License for the
+           specific language governing permissions and limitations
+           under the License.
+
+Apache Airavata is a software toolkit with features to compose, manage, execute, and monitor
small
+to large scale applications and workflows on computational resources ranging from local clusters
to 
+national grids and computing clouds. 
+
+Airavata builds on general concepts of service oriented computing, distributed messaging,
and 
+workflow composition and orchestration. The services primarly communicate using SOAP messages.

+In addition to the basic Web services specifications like SOAP and WSDL, the Web services
also 
+support WS-Addressing and WS-Messaging. WS-Addressing is used to provide an asynchronous

+communication mechanism for the services to communicate. All the communication channels are
secured 
+using https as the transport layer.
+
+Airavata features Dynamic Service Binding where in a proxy service accepts an input message
intended
+to a target application Web service instance invoked by a workflow engine. The proxy service
binds 
+an appropriate running Web service instance by looking up in XRegistry. When no Web service

+instances are available, a new instance of the GFac service is created.
+
+Airavata's primary goal is to support long running applications and workflows on distributed
computational resources. 
+The architecture is designed to be modular, componentized 
+software framework as illustrated in the following Figure. The goal of the Airavata framework
is minimalist 
+architectural design (i.e., a thin layer), a conceptually simple to understand architecture;
and easier to install, 
+maintain and use. Its salient feature includes using components by themselves or as an integrated
solution.
+
+![Airavata Overview](/airavata/architecture/airavata.png "Airavata Overview")
+
+## Airavata Features
+* desktop tools and browser-based web interface components for managing applications, workflows
and generated data. 
+* sophisticated server-side tools for registering and managing scientific applications on
computational resources. 
+* graphical user interfaces to construct, execute, control, manage and reuse of scientific
workflows.
+* interfacing and interoperability with with various external (third party) data, workflow
and provenance management tools.
+
+## Airavata Components
+* XBaya Workflow Suite - includes a GUI for workflow composition and monitoring. The workflows
can be 
+interpreted at each step providing dynamic interactive capabilities. The composed workflow
can be 
+exported to various workflow languages like BPEL, SCUFL, Condor DAG, Jython and Java. 
+The defacto workflow enacting engine used is Airavata Workflow Engine. In the future, it
will be Apache ODE.
+* GFac - an application wrapper service that can be used to wrap command line-driven science

+applications and make them into robust, network- accessible services. This component is build
on 
+Axis2 web service stack. 
+and constructed workflows.
+* WS-Messenger - a publish-subscribe based message broker implemented on top of Apache
Axis2 web 
+services stack. It implements the WS-Eventing and WS-Notifications specifications and incorporates

+a message box component that facilities communications with clients behind firewalls and
overcomes 
+network glitches. As an example, the workflow execution engine sends out events in various
stages,
+including start, end, failure, successful invocation, of its workflow execution.
+* Registry-API: A thick client registry API for Airavata to put and get documents. Current
JCR implementation is supported by Jack-Rabbit.
\ No newline at end of file

Added: incubator/airavata/site/trunk/content/airavata/architecture/registry.mdtext
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==============================================================================
--- incubator/airavata/site/trunk/content/airavata/architecture/registry.mdtext (added)
+++ incubator/airavata/site/trunk/content/airavata/architecture/registry.mdtext Tue Oct  4
17:48:36 2011
@@ -0,0 +1,44 @@
+Title:     Information and Data Registry
+Notice:    Licensed to the Apache Software Foundation (ASF) under one
+           or more contributor license agreements.  See the NOTICE file
+           distributed with this work for additional information
+           regarding copyright ownership.  The ASF licenses this file
+           to you under the Apache License, Version 2.0 (the
+           "License"); you may not use this file except in compliance
+           with the License.  You may obtain a copy of the License at
+           .
+             http://www.apache.org/licenses/LICENSE-2.0
+           .
+           Unless required by applicable law or agreed to in writing,
+           software distributed under the License is distributed on an
+           "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+           KIND, either express or implied.  See the License for the
+           specific language governing permissions and limitations
+           under the License.
+
+Airavata provides capabilities for an integrated workflow and data management system. The
information and data has to be persisted into a registry 
+service. To adhere to the philosophies of Airavata for layering over existing stable third
party components, Airavata usage is consolidated into a 
+thick-client API. This API allows the pluggability of the infrastructure and avoids locks
in into any specific registry architectures. 
+This follwing figure summerizes the use of the registry.
+
+![Airavata Registry Usage](/airavata/architecture/airavata-registry.png "Airavata Registry
Usage")
+
+## JCR Specification:
+The Content Repository for Java Technology specification, developed under the Java Community
Process JSR-170, 
+aims to standardize Java API to repositiries. The specification provides a unified API under
the javax.jcr namespace that allows you to
+access any specification-compliant repository implementation in a vendor-neutral manner.
A major advantage of JSR-170 is that it is not 
+tied to any particular underlying architecture. The back-end data storage for a JSR-170 implementation,
for instance, may be a filesystem, 
+a WebDAV repository, an XML-backed system, or even an SQL database. Furthermore, the export
and import facilities of JSR-170 allow an integrator
+to switch seamlessly between content back ends and JCR implementations. Finally, the JCR
provides a straightforward interface that can be layered 
+on top of a wide variety of existing content repositories, while simultaneously standardizing
complex functionality such as versioning, 
+access control, and searching. There are open source implementations of JSR-170 such as Apache
Jackrabbit, Alfresco and WSO2 Registry.
+
+##Airavata Registry API
+When implementing registry functionality to store data and retrieve data we did not want
to have locking for any custom API's to content 
+repository implementations. Airavata tried to integrate with existing repositories without
having to re-invent the wheel. 
+JCR-2.0 specification and the JSR-170 implementation is plugged in to Apache Airavata system.
The Airavata specific API layers over 
+the generic JCR API and is integrated with Apache Jackrabbit implementation. The API is modularized
as a common component reused by XBaya and 
+GFac components to store and retrieve data. In addition to the service information, the registry
is used to catalog workflow consumed inputs
+and generated output data. The registry is also used to advertise and retrieve persistent
service information. The use of the registry for 
+GFac service registration allows for late service binding and supporting large number of
applications provided by the inherent load balance 
+capabilities. 
\ No newline at end of file

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==============================================================================
--- incubator/airavata/site/trunk/content/airavata/architecture/workflow.mdtext (added)
+++ incubator/airavata/site/trunk/content/airavata/architecture/workflow.mdtext Tue Oct  4
17:48:36 2011
@@ -0,0 +1,76 @@
+Title:     Airavata Workflow Suite
+Notice:    Licensed to the Apache Software Foundation (ASF) under one
+           or more contributor license agreements.  See the NOTICE file
+           distributed with this work for additional information
+           regarding copyright ownership.  The ASF licenses this file
+           to you under the Apache License, Version 2.0 (the
+           "License"); you may not use this file except in compliance
+           with the License.  You may obtain a copy of the License at
+           .
+             http://www.apache.org/licenses/LICENSE-2.0
+           .
+           Unless required by applicable law or agreed to in writing,
+           software distributed under the License is distributed on an
+           "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+           KIND, either express or implied.  See the License for the
+           specific language governing permissions and limitations
+           under the License.
+
+Airavata XBaya workflow system provides a programming model that allows the scientist to
program experiments using 
+service-oriented architecture that would abstract the complexities of the underlying middleware.

+Airavata XBaya provides interfaces for composition, execution and monitoring of the workflows
as illustrated in the following Figure. 
+Airavata XBaya consist of convenient GUI interface for workflow composition, workflow enactment

+engine/interface for workflow enactment and workflow monitoring module. 
+
+![Airavata Workflow Suite](/airavata/architecture/workflow-suite.png  "Airavata Workflow
Suite")
+
+## Workflow Composition
+Airavata XBaya by design decouples composition and monitoring from the orchestration of the
workflow although it does provide an embedded workflow 
+enactment engine integrated with the workbench. As a scientific workflow suite XBaya is often
expected to run long running computations thus it 
+often delegates the workflow execution to a persistent orchestration engine and XBaya workbench
can monitor the progress of the workflow asynchronously. The workbench provides a convenient
drag and drop GUI for SOA based service composition along with other functionalities like
service discovery, registry lookup and workflow experiment management.
+
+## Workflow orchestration
+XBaya provides a unique pluggable architecture for selecting the orchestration engine. When
a user composes a workflow using XBaya workbench 
+it builds an abstract Directed Acyclic Graph (DAG) which is independent of any workflow runtime.
There are pluggable compiler modules that are 
+capable of producing workflow execution scripts for target runtimes. The above Figure illustrated
how the DAG can compiled into different runtimes. 
+Currently XBaya supports BPEL 2.0 and Apache ODE; SCUFL and Taverna; DAGMAN and Pegasus;
Jython scripts and XBaya Interpreter Service.
+
+Each of these workflow runtimes have their own strengths, for example, Apache ODE is a robust
SOA based workflow orchestration engine well suited 
+for long running applications. Pegasus workflow system is well suited for parametric sweeps
whereas XBaya Interpreter engine is strong in dynamic 
+and user interactive workflow execution. It is also capable of generating a Jython script
that can be executed in any Jython runtime independent 
+of any of the workflow infrastructure.
+
+## Workflow interpreter
+XBaya provides a inbuilt workflow enactment engine that provides extremely dynamic and interactive
workflow execution. 
+As the name suggests the workflow interpreter provides an interpreted workflow execution
framework rather than the compiled workflow execution 
+environments. In this context the interpreted workflow means at that execution framework
executed tasks in the XBaya DAG as and when the tasks 
+become runnable. Once the user composes the workflow and launches the workflow the workflow
interpreter will start executing the workflow DAG. 
+Topological sort of the DAG provides execution ordering of the tasks which allow the identification
of the initial ready task set and incrementally 
+adding new tasks to the ready list as previous tasks finish execution. What is unique about
this type of execution model is it allows the user 
+to pause the execution of the workflow as necessary and update the DAG’s execution states
or even the DAG itself and resume execution and the 
+changes are immediately picked up by the workflow interpreter.
+
+Workflow interpreter can be used as an embedded workflow enactment engine within XBaya GUI
or as an interpreter service that may run as a persistent 
+service. The functionality provided by the workflow interpreter allows fine gain control
over the workflow execution which translates into following 
+functionalities.
+* Static workflow interactions
+* Dynamic change workflow inputs, workflow rerun.
+* Stop, pause, resume execution of the workflow. Pause workflow at a particular (debug) point
+* Dynamic change in point of execution, workflow smart rerun.
+* Fault handling and exception models	 
+* Dynamic workflow interactions
+* Reconfiguration of workflow activity
+* Dynamic addition of activities to the DAG.
+* Dynamic remove or replace of activity to the DAG.
+
+## Workflow monitoring:
+XBaya workbench allows the user to monitor the progress of the workflow in real-time. Monitoring
includes the services which are currently executing, 
+those that are done. It also provides state of the job submissions to the batch job queues
and status of the data transfer. Workflow monitoring in 
+XBaya workbench work in two modes; synchronous mode and asynchronous mode. The synchronous
mode only applies when XBaya interpreter runs embedded in 
+the workbench. This allows the execution engine to be aware of which task are ready, running,
finished and waiting and thus accordingly update the 
+DAG execution state. But when the workflow execution is delegated to a persistant service
like Apache ODE serve or XBaya interpreter service, 
+it is necessary to have asynchronous monitoring. This is achieved using the WS-Eventing based
notification messages published by different components 
+of the workflow  system. If a user launches a workflow instance a unique topic will be associated
with that instance and all the workflow components
+like workflow engine, Factory service will publish status notification about the workflow
to the event bus using the topic assigned to the workflow 
+instance. This asynchronous monitoring is truly asynchronous where the user can launch the
workflow, start monitoring, loose internet connectivity and
+once reconnected the XBaya workbench will bring back the monitoring to the current execution
state of the workflow.

Added: incubator/airavata/site/trunk/content/airavata/architecture/ws-messenger.mdtext
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--- incubator/airavata/site/trunk/content/airavata/architecture/ws-messenger.mdtext (added)
+++ incubator/airavata/site/trunk/content/airavata/architecture/ws-messenger.mdtext Tue Oct
 4 17:48:36 2011
@@ -0,0 +1,80 @@
+Title:     WS-Messenger System
+Notice:    Licensed to the Apache Software Foundation (ASF) under one
+           or more contributor license agreements.  See the NOTICE file
+           distributed with this work for additional information
+           regarding copyright ownership.  The ASF licenses this file
+           to you under the Apache License, Version 2.0 (the
+           "License"); you may not use this file except in compliance
+           with the License.  You may obtain a copy of the License at
+           .
+             http://www.apache.org/licenses/LICENSE-2.0
+           .
+           Unless required by applicable law or agreed to in writing,
+           software distributed under the License is distributed on an
+           "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+           KIND, either express or implied.  See the License for the
+           specific language governing permissions and limitations
+           under the License.
+
+Airavata WS-Messenger is a Web Services-based Messaging System for Service-Oriented Computing
and is
+an implementation of [WS-Notification][wsn] and [WS-Eventing][wse] specifications. The message
format 
+can be automatically converted between the two specifications. The subscription request type
+(Ws-Notification or WS-Eventing) for a listener determines the message format that the notification

+consumer will receive. If WS-Notification subscription request is received by the broker,
it will 
+send WS-Notification messages to the listener. Similarly, if WS-Eventing subscription is
received 
+by the broker, the broker will produce WS-Eventing messages for that listener. The publisher
can 
+publish messages in either format. The consumers will recieve messages in the format they
subscribed 
+irrespective of the format the message is published.
+
+The WS-Messenger guarantees scalable, reliable and efficient message delivery. WS-Messenger
contains 
+sub-components of Message broker, Message box and WS-Messenger client libraries. 
+WS-Messenger acts like the nervous system within Airavata infrastructure but can very well
be integrated 
+into any WS-Eventing/WS-Notification standard compliant infrastructures. The Messenger is
deployed as a 
+Axis2 service providing inherent support for different transports including HTTP 1.0, HTTP
1.1 and JMS. 
+Custom transport protocols can be plugged in using the Axis2 framework's transport plug-ins.

+WS-Messenger is integrated with Mysql and Apache Derby database implementations. 
+The embedded Derby database is deployed within the same Java process. The system also supports
persistent 
+subscriptions and notifications which will tolerate failures and restarts of the application
server. 
+
+The following figure illustrates the high level overview of the WS-Messenger 
+![WS Messenger Overview](/airavata/architecture/messenger-overview.png "WS Messenger Overview")
+
+## WS-Messenger Modules 
+
+1. Message Broker: The broker handles filtering/delivering messages to even sinks and subscription
management. 
+WS-Messenger support filtering messages based on XPath expression and topic expression. Message
broker is implemented on 
+Web services specifications and provide the mediation between WS-Eventing Specification and
WS-Notification Specifications. 
+WS-Eventing and WS-Notification specifications are two competing specifications defining
the interfaces for Web services-based 
+publish/subscribe systems.  The Web Services interfaces and the notification message formats
defined in these two 
+specifications are fundamentally different. WS-Messenger provides a mediation approach facilitating
interoperability with supported services. 
+WS-Messenger can automatically convert the notification message formats to makes sure that
the message “on the wire” can be understood by the 
+event consumers. For example, a WS-Notification  consumer can receive notification messages
published by a WS-Eventing publisher and vice versa. 
+The event consumer type is determined by the subscription request message type. Here we assume
that the subscribers and the event 
+consumers use the same specification. This is a valid assumption for most cases since the
subscribers needs to know the location of the event consumers.
+The message delivering schema is implemented by consumer blacklisting to minimize the overhead
of message delivering failures. 
+Message delivering performance has been implemented with a parallel message delivering sub
system. The blocking I/O overhead is reduced 
+configuring the NIO transport. WS-Messenger uses the NIO transport provided by Apache Synapse
project to enable non-blocking I/O in Axis2. 
+3. Message Box: WS-Messenger decouples the consumer tolerating network failures and firewalls.

+The Message box acts like an intermediate notification storage between broker and the event
sink. Users can simply create a message box and 
+provide the message box URL as the event sink URL during the subscription. When messages
are publishing to message broker notifications will 
+send to the message box and it stores the incoming messages in to database or keep them in
memory based on the WS-Messenger configuration. 
+Message box Service has operations  to pull the messages from the message box so whenever
actual event sink is ready to pull the messages out 
+from message box they simply have to invoke the message Pulling API and take the notifications.
When the message box is no longer needed, 
+the subscriber can send another web service request to destroy the message box.This is a
useful feature in a scenario where event source cannot 
+send notifications directly to even sink running behind the firewall. This deployment is
a very common firewall configuration between DMZ and green zone 
+in an enterprise deployment.provide a web service interface for subscribers behind the firewalls.
+
+## Airavata Usage of the WS-Messenger
+Within Airavata, the WS-Messenger is used for user and system communications between GFac,
XBaya and Workflow Intepreter. 
+XBaya in monitoring mode subscribes to a pre-specified topic to which Workflow Engine and
GFac are publishing status notifications. 
+XBaya is instrumented to react to the messages to illustrate workflow progress by means of
color coding of tasks being executed.
+
+The following steps illustrates the usage in detail:
+* XBaya creates a message Box, subscribes to it and then invokes a workflow, with the created
message box EPR passed in context.  
+* Then XBaya sends a subscription request to WS-Messenger with a particular topic and message
box URL received as the event sink. 
+* Then workflow notifiers in XBaya send the notifications using the same topic to the message
broker.
+* Individual application services created by GFac are instrumented to publish detailed status
and send progress to the EPR received in workflow execution context.
+* XBaya translates the messages into graphical colors and input and output extractions.
+
+  [wsn]:  http://www.oasis-open.org/committees/wsn/
+  [wse]:  http://www.w3.org/Submission/WS-Eventing/

Modified: incubator/airavata/site/trunk/templates/sidenav.mdtext
URL: http://svn.apache.org/viewvc/incubator/airavata/site/trunk/templates/sidenav.mdtext?rev=1178878&r1=1178877&r2=1178878&view=diff
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--- incubator/airavata/site/trunk/templates/sidenav.mdtext (original)
+++ incubator/airavata/site/trunk/templates/sidenav.mdtext Tue Oct  4 17:48:36 2011
@@ -8,9 +8,10 @@
 # Architecture
 
   - [Airavata Overview](/airavata/architecture/overview.html)
-  - [WS Messenger](/airavata/architecture/ws-messenger.html)
-  - [XBaya](/airavata/architecture/workflow/xbaya.html)
   - [GFac](/airavata/architecture/gfac/gfac.html)
+  - [Workflow Suite](/airavata/architecture/workflow.html)
+  - [WS Messenger](/airavata/architecture/ws-messenger.html)
+  - [Registry API](/airavata/architecture/registry.html)
 
 # Community
 



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