Triana User Guide
Contents
1. gt should be replaced by the users appropriate details e Text in this font signifies the unix command line prompt the text following it will be the command to type 2 2 2 CVSRoot and Passwords The CVSROOT you should you will depend on whether you have read only pserver access or write ext access This document assumes pserver if you don t know then ask the person who gave you your user name and password For the Core Triana and default Toolbxes repositories there is anonymous pserver access use the username lt anonymous gt with no password just hit return at the password prompt 2 2 3 A Word About Directory Structure For administration reasons Triana is split into a number of different packages which are stored in various CVS repositories Some of these are project specific and not public so don t assume that because something is listed in this document that you will be able to get the source code from the CVS server The public packages are 1 Core Triana The Triana Environment itself 2 Toolboxes The default toolboxes that come with Triana 3 Toolboxes dev The unstable toolboxes that developers are currently work ing with Use at you own risk The project specific packages are 1 GEO The Gravitational Waves tools 2 Gravity Example tools from the book Gravity From The Ground Up by Bernard Schutz 3 GriPhyN Tools from collaboration work with the GriPhyN project T2. 5 2 Advanced loollechiniques s 24 424 A ee eee 19 5 2 1 Showing and Hiding a Unit s Parameter Panel 19 5 2 2 Pausing Unit Execution yla acy 4 Pay aa 20 5 3 Triana as a Workflow Editor 04 23 6 Demos 24 111 List of Figures 2 1 example build properties file 4 oe a eae a ae ke es 8 3 1 Web Service Configuration Dialog i a 20 02 Se eas 10 3 2 Webservice tools inthe Tool Tree 1 ua ana bao hee sew 11 3 3 Using StringGen and StringViewer to provide input to and dis play the output from a temperature conversion web service 12 3 4 A simple bible translation workflow 14 3 5 Generating viewing complex data types using WSTypeGen and WOT Y Pe VICWER a Sep a dng ih ule A Ge he cong Spe Ale a dad 15 3 6 Dialog for deploying a task group task as a web service 16 3 7 Using xsd tools to ensure standard input output XML types are used when deploying a web Service o oo 17 lv Chapter 1 Overview 1 1 Introduction Chapter 2 Getting Started 2 1 Download Installation and Configuration Step 1 Download Download the latest Triana release from http www trianacode org Step 2 Set Environment Variable Set an environment variable for your system TRIANA for Unix like systems or TRIANA for Windows to point the top level triana directory the location that you saved and unpacked the download to e g from the command prompt set TRIAN
3. are in the Common Input and Common Output packages respectively In this workflow StringGen provides the input for BibleVerses If we double click on StringGen and enter Genesis 1 1 7 in the input dialog then this input 2Online documentation for BabelFish and BibleVerses can be found at www xmethods net 13 File Edit Run Tools Services Options Window Help DOHA DXHBX ASOD Q C WebServices Q BabelFish ES BabeFish A bankvalidate StringGen1 o Barcode Generator ennaviewar Barnes and Noble Pri asic R m Rate Ini Figure 3 4 A simple bible translation workflow will cause BibleVerses to extract the first seven verses from the bible Genesis chapter 1 verses 1 to 7 The output from BibleVerses is used to provide the second input for BabelFish which is the text that is translated The first input to BabelFish is provided by StringGen1 This is the languages that the text should be translated from to Using StringGen1 to specify en_fr indicates we wish to translate from English to French The output from BabelFish is sent to StringViewer Pressing the play icon on the tool bar will run the bible translation workflow we have created and hopefully the Genesis 1 1 7 extract from the bible translated into French will be displayed in String Viewer double click on String View view the result 3 2 6 Complex Data Types In Triana there are two ways to handle
4. select the directories project toolboxes project toolboxes dev project toolboxes_other 2 2 6 Other Install You can actually have your toolbox modules anywhere you like in your file system and still have the build process pick them up and compile them In the file build xml there is a commented section titled USER EDITABLE PROP ERTIES within this section there are a number of commented out proper ties for the various toolbox modules Uncomment any of these and set them to the appropriate location to override the default locations Alternatively add a file called build properties with the appropriate lines containing propertyname value 2 3 Workflow Basics 2 3 1 Simple Workflow Example 2 3 2 Group Tools Chapter 3 Distributed Computing with Triana 3 1 Overview 3 2 Web Services An important current paradigm in distributed computing is web services Web services are remote software components accessible using standard network protocols and with defined XML based interfaces Already a large number of web service components are available via the Internet and increasingly legacy applications are being wrapped in web service interfaces In Triana terms web services function exactly as locally available tools A web service receives input data performs some operation on that data and returns results Due to this similarity Triana allows the user use web services within a workflow as if they are standard t
5. task becoming completely red indicates that the deployment has been successful and that the web service is ready to be used As mentioned before web services deployed using Triana can be used either within Triana or by third party users 16 File Edit Run Tools Services Options Window Help DSeBA RXBBX ASOM an Packages defaut unta Diemut Y SystemOut A C Timer A Distribute Group Q C WebServices wstynecen i xsd_string y wstypeViewer E D xsd_boolean a E a SubString Bi xsd_double C xsd int O xsd_string xsd_string1 File E Job C Demos C Editing Figure 3 7 Using xsd tools to ensure standard input output XML types are used when deploying a web service The input and output data types for deployed web services are automatically determined by Triana If the input output types from the task being distributed coincide with a standard XML type e g java lang String java lang Integer etc then that standard XML type is assigned For non standard types Triana assigns a string as the input output type and assumes that the data received by the web service will have been serialized to a string using JSX Such web services can be seamlessly handled by Triana but will be difficult for third party users to use It is recommended that standard types are used whenever possible and that the tools xsd_string xsd_double etc are appended to the start of the workflow subsect
6. web services that require complex data types use the dynamic web service type generator and viewer or generate static type classes and create custom tools The input to a web service that requires a complex type can be automatically gen erated using the WSTypeGen tool which resides in the Common WebServices toolbox Similarly the complex output from a web service can be viewed us ing the WSTypeViewer tool which is also found in the Common WebServices toolbox To use these two tools simply connect them to the web service task as shown in Figure 3 5 The act of connecting them to the web service will cause a form for inputting viewing the complex type to be dynamically gen erated This form can be accessed by either double clicking on the WSType 14 i WSTypeViewer _GetindustryNewsResponse getGetindustryNewsResult ArrayOfBusinessShortNews getBusinessShortNews BusinessShortNews getType java lang String File Edit Run Tools Services Options Window Help Heb 50XBBaXMmgOo Cc DBOry DHF AQ C Auto commit ox Cancel Apply WSTypeGen E r Figure 3 5 Generating viewing complex data types using WSTypeGen and WSTypeViewer C Timer Q CA WebServices y wstypecen y wsTypeviewer Gen WSTypeViewer task or by right clicking and selecting Properties from the pop up list Although WSTypeGen and WSTypeViewer are useful f
7. A C triana Windows setenv TRIANA home user triana unix tcsh export TRIANA home user triana unix bash Step 3 Build Triana Run the Triana build script buildTriana whichis located in the triana bin directory e g from the command prompt C triana bin buildTriana bat Windows home user triana bin buildTriana unix Step 4 Run Triana Run Triana using the triana script located in the triana bin directory e g from the command prompt C triana bin triana bat Windows home user triana bin triana unix 2 2 CVS Access This section describes the steps in correctly checking out the source code for the core Triana and Triana toolboxes from the cvs repository and building from the source code If you don t know how to use a CVS client or don t have a CVS account then it is recommended that you follow the instructions in section 2 1 2 2 1 Conventions Note These instructions assume you have the necessary user accounts and passwords It is aimed at command line cvs users WinCVS or similar users should be able to follow the instructions by using the repository and module names within their particular CVS Client e Text written this font should be typed as command line input Com mands should be entered without line breaks unless explicitly instructed This includes line breaks due to book formatting e Text written in this font and surrounded by lt
8. Triana User Guide The Triana Team Preface Preface stuff to go here Contents 1 Overview 1 1 Introduction 2 Getting Started 3 2 6 Complex Data Types 3 2 7 Deploying Web Services OM dle A Ot Pee eh Ge ART aad Gaia O ANOS MD Raa ke a 4 Applications and Case Studies 11 2 1 Download Installation and Configuration 2 2 CVS ACCESS ic a aa AO OE a a a 2 2 1 Conventions 0 00 00 0 eee ee eee 2 2 2 CVSRoot and PasswordS 2 2 3 A Word About Directory Structure 22A Easy Install sa ach Bnet da Kans Aa ea bee aS 220 Developerlastall assesses tye ge sin gS a Sat Fa gg SE a a 2 2 6 Other Install se fw acces Bde aa 2 37 Workflow BASICS AA AA as RG cE Be 2 3 1 Simple Workflow Example 2 9 2 Group Toolse pe A ES A aes 3 Distributed Computing with Triana Dil OVERVIEW tios o a A Beak ee Be a Bids Web Servic s conos cr A RO OR BB 3 2 1 Web Service Configuration 358 aan dh Gn ahh Ga ia 3 2 2 Discovering Web Services gt iii ae Eg St a eS 3 2 3 Importing Web Services 04 on Road a aces 3 2 4 Conncecting Web SERVICES je alge A eg 3 2 5 Bible Translation Example o o 4 1 Data Analysis with Triana ese paa oie ala ale a Sale 18 4 2 Audio Processing with Triana o o 18 5 Extending Triana 19 5 1 Writing your own tools 44 32 ea ote ee he ee 19 5 1 1 Using the Tool Wizard 3 ar aa ae at ae ea 19
9. and inquiry access see Section 3 2 1 This includes configuring the trust key store if required Secondly Triana launcher services must be run on the machine s that will host the deployed services To do this Triana should be installed on those machines and the following command executed from the command line TrianaService ws A web service can be created from either a single task or a group of tasks see Section 2 3 2 To deploy the task group task as a web service right click on the task and select Create Service This will cause a dialog to appear with a list of the locations where the web service can be hosted as shown in Figure 3 6 This list will include the available launcher services see above along with a Local Service option Creating a local service means that the web service is hosted within the local Triana as opposed to on a remote site Note that it can take a while for Triana to discover the available launcher services from UDDI they automatically appear in the list once discovered Create Service PSD DER Service Hosts Service Options Local Service Web Service v Advertise Service har 251 40 117 Web Service Create Cancel Figure 3 6 Dialog for deploying a task group task as a web service Once a host has been chosen Triana will attempt to deploy a web service on that host While this process is taking place the task in the workflow will appear with red stripes The
10. de in a sepa rate subdirectory Here I ve created a directory called toolboxes_other this is because Triana assumes that a toolbox contains packages so GEO for instance is the top level package for the GEO tools When Triana attempts to locate tools it uses the following path toolbox tool packagel toolname e g project toolboxes SignalProc Input Wave or project toolboxes_other GEO Algorithms SaturationMon The build and run instructions are almost the same as for the easy install e Set the TRIANA environment variable to point to the triana directory e Either edit the build file build xml in the main Triana home directory and set the appropriate toolbox location variables in the User Editable section or the preferred method add a new file called build properties to the Triana home directory with the properties and their values the contents of my build properties file can be seen in figure 2 1 e Run the buildTriana script javac flag debug on javac flag deprecation on triana geo tools toolboxes_other GEO triana gravity tools toolboxes_other GravityFromTheGroundUp triana griphyn tools toolboxes_other GriPhyN Figure 2 1 example build properties file Note Unlike the standard installation Triana will not automatically pick up the toolboxes when it is started so you will have to add those within Triana from the menu Tools Edit Tool Box Paths In my case I
11. e configured such as proxy addresses and security Information on these properties may be found on the WSPeer website www wspeer org 3 2 2 Discovering Web Services Once that a UDDI repository has been configured web services can be discov ered very simply using the Services Discover Services menu option This option displays a dialog prompting for the name of the service to search for This can either be the exact name or can include as a wildcard character For example C will search for all web services beginning with the letter C When a web service is discovered tools representing each of the operations on that web service are inserted into the Web Services package in the tool tree alongside the existing locally available tools as shown in Figure 3 2 11 3 2 3 Importing Web Services If a web service is not listed in a UDDI repository then it can be imported directly into Triana from its WSDL description This is done through selecting the Services Import Service menu option which causes a dialog requesting the service location to be displayed This service location is the full http address of the WSDL document specifying the web service to be imported The web service at the service location will be imported into the the Web Services package in the tool tree 3 2 4 Conncecting Web Services Once a web service has been discovered imported and appears in the user s tool tree it can be instantiated by draggin
12. ed as long as their output input type is compatible with the type required by the web service or alternatively the output from one web service can be directly piped to another We look at handling complex data types in Section 3 2 6 A workflow containing web services is executed as for a standard Triana work flow i e by pressing the run button 3 2 5 Bible Translation Example In this section we demonstrate the creation of a simple bible translation workflow using third party web services This example uses the XMethods UDDI repository so the following UDDI inquiry and publish addresses should be specified in the configuration see Section 3 2 1 Inquiry http uddi xmethods net inquire Publish https uddi xmethods net publish The two web services we wish to use are BabelFish an interface to AltaVista s Babelfish service and BibleVerses a web service for extracting verses from the bible The easiest way to import these web services is using the Services Disover Services menu option and then specifying B in the Discover Service dialog this queries the UDDI for all tools beginning with B Once the BabelFish and BibleVerses web services have been discovered they will appear as tools in the Web Services toolbox on the tool tree Each of these services should be dragged onto the workspace along with local StringGen and StringViewer tools to create the workflow shown in Figure 3 4 StringGen and StringViewer
13. ed mechanism for doing this is to cause the current thread to sleep interrupting the thread on the parameter being updated package UserGuide import triana unit Unit An example unit that pauses for a parameter to be updated public class PauseExample extends Unit parameter data type definitions private String someValue private reference to the current thread private Thread currentThread flags private boolean stopped private boolean selecteddone Called whenever there is data for the unit to process public void process throws Exception java lang Object input java lang Object getInputAtNode 0 stopped false selecteddone false 20 Insert main algorithm for PauseExample currentThread Thread currentThread while selecteddone stopped try Thread sleep Long MAX_VALUE catch InterruptedException except output I m finished This is called when the network is forcably stopped by the user This should be over ridde with the desired tasks lt p gt The current thread needs to be interupted in the case of the user halting the execution public void stopping super stoppingO stopped true currentThread interruptO RK Called when the unit is created Initialises the unit s properties and parameters public void init super initQ Initialise node properties setDefaultInputNodes 1 setMi
14. g the tool onto the main workspace in the same way locally available tools are instantiated Web services tasks appear in red on the workspace Each input node on an instantiated web service task represents an element of the input message for that operation and each output node represents an output message element Information on the required input output types for a web service is displayed when the mouse is hovered over the task File Edit Run Tools Services Options Window Help O088 O8GBx ac Double C input Legacy di 3 Figure 3 3 Using StringGen and StringViewer to provide input to and display the output from a temperature conversion web service Locally available tools can be used to provide the input to and display the output from web services Two useful local tools are Common String StringGen lFor example an web service interface to Altavista s BabelFish language is located at http www xmethods net sd 2001 BabelFishService wsdl 12 and Common String String Viewer which are used to generate string input and display string output respectively These tools can also be used to input output standard numerical data types int double etc as Triana automatically converts to from the required type In Figure 3 3 we show StringGen and StringViewer being used as input and output for a temperature conversion service Other local tools can also be us
15. gt prompt cvs d pserver lt username gt trianacode trianatools checkout P toolboxes Note The rest of the Triana modules from CVS are project permissions to access prompt cd toolboxes prompt cvs d pserver lt username gt trianacode trianatools checkout P toolboxes dev prompt cvs d pserver lt username gt trianacode geotools login Logging in to username trianacode org CVS password lt userpassword gt prompt cvs d pserver lt username gt trianacode geotools checkout P GEO prompt cvs d pserver lt username gt trianacode gravity login Logging in to username trianacode org CVS password lt userpassword gt prompt cvs d pserver lt username gt trianacode org home cvsroot org home cvsroot org home cvsroot org home cvsroot optional and depend on org home cvsroot org home cvsroot org home cvsroot org home cvsroot org home cvsroot gravity checkout P GravityFromTheGroundUp prompt cvs d pserver lt username gt trianacode org home cvsroot griphyntools login Logging in to username trianacode org CVS password lt userpassword gt prompt cvs d pserver lt username gt trianacode org home cvsroot griphyntools checkout P GriPhyN After those CVS commands you should have a directory structure like this triana bin toolboxes Audio Other standard toolboxes toolboxes dev GEO GravityFromTheG
16. here are two standard ways to structure a Triana distribution from CVS de pendant on whether you expect to be making regular changes to the source code under your control and or you want to do frequent updates for the latest version from CVS Or you just want to check out the latest version and build it once CVS allows checking modules out inside other modules which will give the same structure as the packaged version of Triana but it will complain if an update or commit is attempted in the source tree where there is a foreign module lower down the tree 2 2 4 Easy Install These instructions will checkout and install Triana to the same structure as the packaged release version It is fine for most users however if you expect to use CVS for more than updating small numbers of files it is suggested you use the other set of instructions This install will put all of the various toolboxes inside the Triana source tree and they will need to be removed to perform a cvs update on the core Triana code and then checked back out again From the command line prompt cvs d pserver lt username gt trianacode triana login Logging in to username trianacode org CVS password lt userpassword gt prompt cvs d pserver lt username gt trianacode triana checkout P triana prompt cd triana prompt cvs d pserver lt username gt trianacode trianatools login Logging in to username trianacode org CVS password lt userpassword
17. ion being distributed to ensure the correct standard type is used as illustrated in Figure 3 7 These tools can be found in the Common WebServices toolbox 3 3 P2PS 3 4 GAT 17 Chapter 4 Applications and Case Studies 4 1 Data Analysis with Triana 4 2 Audio Processing with Triana 18 Chapter 5 Extending Triana 5 1 Writing your own tools 5 1 1 Using the Tool Wizard 5 2 Advanced Tool Techniques In this section we look at some more advanced techniques that a tool developer may wish to use 5 2 1 Showing and Hiding a Unit s Parameter Panel Problem You want to simulate the user double clicking on a task to display the unit parameter panel Solution Call the method public void showParameterPanel to display the unit s parameter panel and public void showParameterPanel to hide the panel again These methods are inherited from the Unit superclass Discussion 19 5 2 2 Pausing Unit Execution Problem You want to pause the execution of your unit programmatically until some event happens Solution Pause the thread that is running your unit and interrupt on your desired event to resume processing Discussion Say for instance that you wish to pause the execution of your unit between the point in the main process method where the unit gets input from its input node and the point where it outputs the result The execution should halt until a particular parameter has been updated The preferr
18. nimumInputNodes 1 setMaximumInputNodes 1 setDefaultOutputNodes 1 setMinimumOutputNodes Q setMaximumOutputNodes Integer MAX_VALUE Initialise parameter update policy and output policy setParameterUpdatePolicy PROCESS_UPDATE setOutputPolicy CLONE_MULTIPLE_OUTPUT Initialise pop up description and help file location setPopUpDescription An example unit that pauses for a parameter to be updated setHelpFileLocation PauseExample html1 21 Define initial value and type of parameters defineParameter someValue USER _ACCESSIBLE Initialise GUI builder interface String guilines guilines Choose one title someValue Choice choice1 choice2 n setGUIBuilderV2Info guilines rk Called when the unit is reset Restores the unit s variables to values specified by the parameters public void reset Set unit variables to the values specified by the parameters someValue String getParameter someValue KK Called when the unit is disposed of public void dispose Insert code to clean up PauseExample e g close open files par Called a parameters is updated e g by the GUI public void parameterUpdate String paramname Object value Code to update local variables if paramname equals someValue someValue String value selecteddone true if currentThread null currentThread interrupt
19. ools Once a web service has been discovered or imported see Sections 3 2 2 and 3 2 3 it appears as a tool in the tool tree alongside the other tools and can be connected into a Triana workflow in exactly the same manner of other tools As well as discovery and importing web services Triana allows the user to deploy a workflow subsection as a web service for other users including other Triana users to access We discuss this more in Section 3 2 7 Web Service Config Basic Advanced HTTP Port 4802 UDDI Repositories xmethods Remove Figure 3 1 Web Service Configuration Dialog 3 2 1 Web Service Configuration Web service configuration can be done using the Services gt Configure menu op tion and the selecting Configure next to the web service option It should be noted that Triana automatically loads the last used web service configuration and therefore this configuration step needs only be done if you are changing the web service options e g using a different UDDI repository It should also be noted that once web services features e g discovery have been utilized the configuration cannot be changed within the current running Triana This will be indicated by a disabled Configure option The web service configuration dialog see Figure 3 1 is split into two panels Basic and Advanced The Basic panel enables the web service HTTP port and the UDDI repository to be set The HTTP po
20. or testing web services that use complex types for more long term solutions it is generally required that static classes are generated for the complex types Static type classes can easily be generated using a utility such as Apache s WSDL2Java Utilities such as WSDL2Java parse the WSDL description of the web service and generate a set of Java classes for the web service and the types used within that service It is easiest if these classes are created in the same location as the tools that will access them same Java base directory Once static classes have been created for the complex types custom Triana tools for populating the types with data or converting between types must be created These tools should be able to access the complex type classes in the same way as for any Java class We describe creating custom Triana tools in section 5 1 3 2 7 Deploying Web Services As well as using external web services Triana provides the mechanism for deploying user workflows as fully functions web services These deployed web services can either be used within a local Triana workflow allowing some of 3See http ws apache org axis java user guide html 15 the processing to be handled by a remote resource or by third party users It should be noted that third party users do not have to use Triana to access these web services In order to deploy web services Triana must first be configured with a UDDI to which you have both publish
21. rk return an array of the types accepted by each input node For node indexes not covered th E types specified by getInputTypes are assumed public String getNodeInputTypes return new String 0 0 22 rk return an array of the input types accepted by nodes not covered by getNodeInputTypes public String getInputTypesO return new String java lang Object rk return an array of the types output by each output node For node indexes not covered the E types specified by getOutputTypes are assumed public String getNode0utputTypesO return new String 0 0 rk return an array of the input types output by nodes not covered by getNodeOutputTypes public String getOutputTypes return new String java lang Object 5 3 Triana as a Workflow Editor 23 Chapter 6 Demos
22. roundUp GriPhyN The toolbox structure is the import thing there will be extra directories under triana not mentioned here Build and Run To build set an environment variable for your system TRIANA for Unix like systems or 4TRIANA for Windows to point the top level triana directory Run the build script buildTriana for Unix or buildTriana bat for Windows prompt TRIANA bin buildTriana Run the start script triana or triana bat prompt TRIANA bin triana 2 2 5 Developer Install If you are intending to write or modify any code within the various CVS modules or you just want to regularly update the modules from CVS Then we suggest that you keep all the CVS modules in their own separate directory stuctures The Ant build file is written to be able to build from default either the previous Thttp ant apache org structure or a directory structure where all the cvs modules are at the same level in the file system For instance my directory structure looks like this project triana project toolboxes project toolboxes dev project toolboxes_other project toolboxes_other GEO project toolboxes_other GravityFromTheGroundUp project toolboxes_other GriPhyN So from a sensible starting directory run the CVS commands from section 2 2 4 with the cd commands so that the Triana core and default toolboxes modules from cvs reside in your current directory Note The GEO Gravity and Griphyn toolboxes should really resi
23. rt is the port used by services created within Triana see Section 3 2 7 only If using this feature then this port must be open on the local firewall otherwise users will not be able to access the services For simply invoking external web services not port need to be opened The UDDI repository is used by Triana to discover services see Section 3 2 2 By default the XMethods www xmethods net is set but additional repositories can be added Note that when adding a UDDI repository only the inquiry address is required the publish address is only required if deploying services within Triana and a username password are only needed if required by the UDDI instance To publish in some UDDI repositories trust stores are required If this is the case 10 nu Packages default 5 E Triana Tools E audio ZA cI Common c Demos A Editing cI GEO CI GriPhyN C ImageProc E math C SignalProc EF web Services Ci BabelFish BabelFish Barnes and Noble Price Quote 7 BAX Global Tracking Service Q Bible verses read_bible C bBiblewWebservice rd EEFI PPP Figure 3 2 Web Service tools in the Tool Tree then the location of the trust store file should be specified in the config xml which is located in the wspeer admin directory Dummy trust store files can be found in the triana system directory these work for some UDDI in stances The advanced panel allows additional properties to b
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