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Triana User Guide - VL

1. 3 webservices D wstypecen Ly wsTypeviewer Figure 3 6 Generating viewing complex data types using WSTypeGen and WSTypeViewer 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 6 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 Gen WSTypeViewer task or by right clicking and selecting Properties from the pop up list Although WSTypeGen and WSTypeViewer are useful for testing web services that use complex types for more long term solutions it is generally required 36 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 ba
2. gt NS Auto commit samplingRate Figure 2 15 Parameter List Interface user has selected the frequency output parameter for the Wave task Adding an input parameter is exactly the same process using the In Params tab Note As in the case of changing the number of input and output nodes Access to parameters is constrained by the unit programmer If a parameter does not appear in the list then it has not been made externally accessible See chapter 4 22 Node Editor Shortcuts There is a short cut for increasing and decreasing the number of input and output data nodes for any task on a main Triana window If you hover the mouse over the a task icon and the Show Node Increase Decrease Icons setting is set see page 26 then you should see and symbols flash on Clicking on the left hand side symbols will increase or decrease the number of input nodes clicking on the right hand side will do the same for output nodes Note As with the Node Editor long hand method of changing the number of nodes this is only enabled where the unit programmer has specified it For many tasks it does not make sense to allow multiple input nodes for instance 2 5 2 An Example with Parameters In this tutorial we will create the following network the Wave tasks can be found in SignalProc Input and the Grapher is in SignalProc Output The connection between the two Wave tasks is a parameter connecti
3. Note that these values can be changed later either in the wizard or in the generated code 59 E Unit Wizard Parameters String aparam someval boolean anotherparar false Remove Update Policy Update at start of process w Cancel Back Next Figure 4 5 Parameter Panel in the Unit Wizard Parameter Panel The third panel the Unit Wizard shown in Figure 4 5 allows the parameters used by the unit to be specified Parameters are used to represent steer and store the internal state of the unit As the state of parameters is automatically shared between the unit and its graphical interface by Triana they are the method of choice for communications between the unit and its graphical interface also referred to as its parameter panel When adding a parameter the following information is required Parameter Name The name of the parameter also used as the variable name for the parameter in the Java code This should not include spaces or other punctuation characters except underscore Default Value The default value assigned to the parameter Data Type The data type of the parameter in the Java code Note that all parameters specified in the Unit Wizard are stored internally as strings and automatically converted into the required data type within the Java code Parameter Type The type of the parameter User Accessible indicates it can be viewed steered by the user for examp
4. Triana will attempt to deploy a P2PS service on that host as shown in Figure 3 9 While this process is taking place the task in the workflow will appear with purple stripes The task becoming completely 40 purple indicates that the deployment has been successful and that the P2PS service is ready to be used P2PS services deployed using Triana can be used either within Triana or by third party users Unlike Web Services there is not a standard set of data types defined for P2PS All data sent to and received from P2PS services deployed using Triana is serialized using JSX This serialization should be seamless to Triana users and is only a consideration for third party software using Triana deployed services 3 3 3 Discovering P2PS Services Existing P2PS services can be discovered very simply using the Services gt Discover Services menu option This option displays a dialog prompting for the name of the service to search for With P2PS this search name has match exactly ignoring case the service name required When a P2PS service is discovered a tool representing the operation provided by that service will appear in the tool tree alongside existing locally available tools The P2PS service tool will appear in the same package as the original task used to create the service however it will be displayed with a remote service icon shown in Figure 2 3 3 3 4 Connecting P2PS Services Once a P2PS service has been discovered imp
5. build file is written to be able to build from default either the previous structure or a directory structure where all the cvs modules are at the same level Thttp ant apache org 52 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 4 1 5 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 reside 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 U
6. given that both invocations are done via the GAP Interface there is a lot of commonality between the processes We outline job submission via the GridLab GAT in Section 3 4 this covers using GRMS see www globus org 2see www gridlab org 30 GRAM and Local adaptors 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 tools 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 3 2 1 Web Service Configuration Web service configuration can be done
7. rubber banding is the term given to dragging the mouse on a screen area which creates a thin box line around all of the items within the given area 14 Deleting Tasks You can delete tasks by selecting the tasks you wish to delete and then choose the Delete option from either the window s popup menu right click on one of the tool icons or the Delete option on the Edit menu Alternatively to delete any single task use the Task s popup window right click on the Task s icon and select the Delete option Moving Tasks You can move multiple tasks by selecting the tasks you wish to move and then whilst holding down the control or command key drag the tasks to where you want them to be on the window 2 3 Your First Workflow This section will demonstrate how to create and run the simple taskgraph shown in figure 2 6 gt ef s DINA um mix p Bx ACD Algorithms C Converters CI DataParam Filtering o input C Output C Exporter C GraceGraph Figure 2 6 Simple Taskgraph Lets take a closer look on how we make this connection by creating this network step by step 1 In the tool tree navigate to the SignalProc toolbox open that toolbox by double clicking the toolbox or using the open branch control by the side of the toolbox you should see all the sub toolboxes within it Now navigate to the Input toolbox and open that to reveal the tools 15 2 Now select the Wave ta
8. utilize different configuration is required Currently the available adaptors for job submission are GRAM GRMS and local the configuration they require is as follows GRAM Grid proxy initialized with valid Grid credential e g using grid proxy init in Globus COG Kit Contact your local Grid administrator concerning acquiring a Grid certificate GRMS Grid proxy initialized with valid Grid credential same as GRAM Local No configuration required The currently available adaptors for file transfer are GridFTP FTP HTTP and local the configuration they require is as follows GridFTP Grid proxy initialized with valid Grid credential same as GRAM job submission FTP Need to specify username and password in GAT configuration HTTP No configuration required See www globus org 43 Local No configuration required 3 4 3 Job Submission Job submission in a Triana workflow is represented by a special Job component a default version of which can be found in the Common toolbox Dragging the default Job component into a workflow creates an empty job submission task which by default is medium blue Right clicking on this task and the selecting Job Properties allows the submission details to be set Job Input Files Output Files Host Name bouscat cs cf ac uk Executable bin date Arguments Figure 3 11 Job Properties Dialog The main panel of the Job Properties
9. Illustrations for each of these file transfer operations are shown in figure 3 13 46 File tasks can be instantiated by dragging a file component either the default file component in the Common toolbox ora custom file saved into the toolboxes onto the workspace Once instantiated the file represented by the file task can be set through right clicking on the task and selecting Set File The URI of any file that can be handled by available GAT Adaptors see Section 3 4 2 can be set For example temp myfile dat Local file in temp directory relative to running directory temp myfile dat Local file in temp directory relative to root directory file temp myfile dat Same as temp myfile dat file temp myfile dat Same as temp myfile dat file bouscat cs cf ac uk temp myfile dat File on remote machine in temp di rectory relative to user home on remote machine file bouscat cs cf ac uk temp myfile dat File on remote machine in temp di rectory relative to root directory on remote machine file bouscat cs cf ac uk temp myfile dat File on remote machine in temp di rectory relative to root directory on remote machine ftp bouscat cs cf ac uk temp myfile dat FTP accessible file on remote ma chine http bouscat cs cf ac uk temp myfile dat HTTP accessible file on remote ma chine gsiftp bouscat cs cf ac uk temp myfile dat GSI FTP accessible file on remote machine As can be seen from som
10. Users horme spxrnss fphysics working coolboxes Volumes Users home spxmss TrianaV3Resources CroupTaols Volurnes Users home spxmss TrianaV3Resources Data Volumes Users home spxmss TrianaV3Resources Remote Add e Remove Default Volumes Users fhorme spxmss physics working toolboxes Data fvolumes Users home spxmss Trlanav3Resources Data Remote Volumes Users fhome spxmss TrianaV3Resources Remote User Volumes Users home spxmss TrianaV3 Resources CraupToals Figure 4 2 Edit Toolbox Paths different purpose The list of toolbox roots is presented in the top panel on the dialog with Add and Remove buttons which add or remove toolbox roots from that list Note There is no way to edit an existing toolbox root it should be removed and a new one added The four fields below the list labelled Default Data Remote and User and the four default toolboxes Default is the standard toolbox root where Triana stores all of the normal in cluded tools Data is a specific toolbox root for data tools such as files Remote is the toolbox root where Triana stores the component definition files for any remote tools such as P2PS services or web services User is the toolbox root that Triana uses to store user specific tools such as new group tools by default Note Apart from the default toolbox root which will normally reside inside the Triana home directory all of the other three toolbox roots are stored in a s
11. Versions 1 4 2 Home bin javac Classpath Y Validate External Tool Locations Restore Defaults z Figure 2 19 Options Window external tools HTML Help View The tool used to display HTML and help files within Triana The defaultis the internal HTML renderer this can be changed by typing the path to a browser in the text field or pressing the browse button and navigating to the executable HTML Editor The tool used to edit HTML and help files The default is the built in text editor this can be changed by typing or browsing to the path of another text editor Code Editor The tool used to edit unit source code The default is the built in text editor this can be changed by typing or browsing to the path of another text editor Javac Compiler The Java compiler used to compile unit source code within Triana The default should be the system Javac compiler this can be changed to a different compiler by the standard method Validate External Tool Locations A check box that when selected will check that any path in the external tool fields is a valid location The path must point to a real program This should be left checked unless there is a specific reason why not i e you have deliberately added a non existent compiler If an invalid path is detected it must be corrected before the settings can be saved unless the box is unchecked 27 Classpath A button which brings up the Select Path window see
12. a Sh GS ae Sk Filter Toolbox by Data Types i cee gat Sow Siete ken Sin Simple Taskgraph 2 e ir ane inca wie whe eke eke Instantiated Wave Tool elas ae Be ae Swe es Instantiated Wave and Graph Tool o o o Grapher Interface ta adidas Grapher Inteffac a pianos deis raras New Group BOX o eN New Gro p BOX sls n aa Si ny AE Te BALE Oe AAA New Group Tool Parameter Window 4 Node Editor GR a elena A en ad Parameter List Interface Sii a ae ASA ESA RA eS Parameter Connection 0000 eee ee eee Parameter Node std Ll ae Pd GS G RS GS Options Window general settings o Options Window external tools Selecting the Unit Classpath J a act a Ok ah aa ae oe Distributed Component Middleware within Triana Web Service Configuration Dialog Web Service tools in the Tool Tree a Using StringGen and StringViewer to provide input to and dis play the output from a temperature conversion web service A simple bible translation workflow Generating viewing complex data types using WSTypeGen and Waly DEN jewer a d sew oe Re dean a sS alee ee EG ES Dialog for deploying a task group task as a web service 111 30 32 33 34 35 36 38 3 8 Using xsd tools to ensure standard input output XML types are used when deploying a web Service oo o 38 3 9 Dialog for deployi
13. automating repetitive tasks such as per forming a find and replace on all the text files in a particular directory or continuously monitoring the spectrum of data that comes from an exper iment that runs for days or even years If you run an experiment Triana can help you save the cost of buying extra expensive oscilloscopes or spec trum analyzers just let your laptop or lab PC do the job If you maintain a web site you will find you can automate many of your tedious updating tasks If you are a teacher you can simplify the maintenance of student records and the grading of papers If you regularly create reports Triana will allow you to feed updated data directly into the finished document no matter how it is formatted e Triana is a wonderful assistant in the classroom or teaching laboratory It can help you to make demonstrations of analysis techniques to generate simulated experimental data to display graphs of complicated functions e If the tools supplied with Triana do not do what you need Triana contains a wizard that helps you to create new ones with parameter windows Or you can use tools that are available on another web site directly over the Internet without having to copy them to your computer e Triana includes many features to ensure that your programs should work as you want them to It checks data types and tells you if you have con nected up tools that are not compatible It gives you clear error messages if probl
14. be input or output from every task within Triana Triana auto matically detects all the parameters which a task usesand makes them available to the user For example let s demonstrate this by creating a network in which one Wave task controls another Wave task s frequency Note In Triana parameters are output after the process function has been run i e output after the data from the task and parameters are input before the process function has been run This means that you can send a parameter from a calculation in your process function of one task and the receiving task will receive this before it receives its data to process This is extremely useful for example for re constructing data sets when you need to know how beforehand how many you will want to concatenate 2 5 1 The Node Editor The Node editor in Triana is the mechanism by which the user can change the input and outputs to and from a task subject to constraints placed by the task designer see chapter 4 The editor is displayed by using the selecting the Node Editor option from a task s pop up menu page 12 The user interface consists of three three tabbed windows which can be see in figure 2 14 The first tab figure 2 14 a allows the user to change the number a Wave Node Editor e Wave Node Editor Nodes In Pz ms Nodes in Params Out Params Input Nodes 0 1 Output Nodes Add Remove lt None gt
15. configured within P2PS such as the transport protocols used and rendezvous policies however discussion of these are beyond the scope of this manual More information can be found at www p2psimplified org 3 3 2 Deploying P2PS Services As with web services see Section 3 2 7 individual group tasks within a Triana workflow can be deployed as P2PS services running on a remote machine The mechanism to do this is exactly the same a for web services Before deployment first Triana launcher services must be started and configured on each remote machine that will host a P2PS service This is done by installing Triana and the running the command TrianaService p2ps To deploy an individual group task right click on the task and select Create Service This will cause a dialog to appear listing the locations where the remote service can be hosted This list will include the locations where Triana launcher services are available plus a Local Service option The Local Service option indicates that the remote service will be hosted within the current running Triana Note that it can take a while for Triana to discover the available launcher services they automatically appear in the list once discovered Create Service SubString Service Hosts Service Options GRIDMONSTER P2PS v Advertise Service Local Service P2PS Figure 3 9 Dialog for deploying a task group task as a P2PS service Once a host has been chosen
16. dialog shown in Figure 3 11 allows the following submission properties to be set Host Name Host name of the machine the job will execute on Leave blank if running on the local machine or delegating to a Grid resource broker Executable The job executable URI e g bin date Arguments The arguments for the job if required To launch a basic job simply set the host name executable and arguments in the Job Properties dialog and then run the Triana workflow as normal The job will be submitted to the appropriate resource manager GRAM GRMS Local etc and executed on the specified host As well as detailing the job to be executed the Job Properties dialog also allows the pre staged input and post staged output files for the job to be specified 44 Job Input Files Output Files Input Node Mapping lt STDIN gt paramtile dat Add Remove Move Up Move Down Figure 3 12 Inputs Panel in the Job Properties Dialog This is done using the Inputs Panel and the Outputs Panel in the Job Properties dialog The Inputs Panel in the Job Properties Dialog see Figure 3 12 lists the files that are pre staged in the job execution directory before the job is run This list also represents the mapping between the input nodes on the job submission task and the pre staged files e g if the first item on the list is param txt then the file at node 1 is pre staged in the running directory as
17. enter Genesis 1 1 7 in the input dialog then this input 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 StringGenl1 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 Online documentation for BabelFish and BibleVerses can be found at www xmethods net 35 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 StringViewer double click on StringView view the result 3 2 6 Complex Data Types In Triana there are two ways to handle 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 mel WSTypeViewer _GetindustryNewsResponse getGetindustryNewsResult ArrayOfBusinessShortNews getBusinessShortNews BusinessShortNews getType java lang String File Edit Run Tools Services Options Window Help Demi DXHEAX AGOL DEGeJ 2E AA jan Packages default
18. group in a new main Triana window Page 18 Properties Display the parameter panel interface Control Properties Display the control properties dialog Ungroup Return this group to its constituent parts Page 18 Create Service Create a service from the selected tasks Run Script Run a script on the selected tasks Cut Cut the selected tasks to the clipboard Page 14 Copy Copy the selected tasks to the clipboard Page 14 Delete Cut the selected tasks Page 14 Paste Into Paste the selected tasks into the tool tree Page 14 Rename Rename the selected unit Table 2 7 Main Window Group Tool Menu Menu Item Description Group Editor Resolve Group Nodes Display the group editor dialog Page 18 Checks for unconnected nodes in a group Save Saves the current workflow Select All Selects all tasks in the window Page 14 Paste Paste the tasks in the clipboard to the current win dow Page 14 Table 2 8 Main Window Background Menu 13 Editing Workflows A workflow on a main Triana window is not fixed Just as if it were a document in a text editor the workflow the connections and the components within it can all be edited Cut Copy and Paste commands all work and connections can be deleted and redrawn Selecting Tasks Clicking on the task once with the mouse in the main Triana window will highlight the particular icon This means that it is selected Mul tiple tasks can be selected by
19. in A A A A 42 3 4 1 Example GAT Worfklow as 42 Oa GAT Config ratior inc eni usu aera e it a in 43 3 4 3 JOD Submission AAA A 44 A STAN E AAA AA S 46 Extending Triana 48 A EVS ACCESS a ia a Gnd Arete 48 All Conventions ia ve e Ae U ve Q 49 4 1 2 CVSRoot and PasswordS 49 4 1 3 Tagged Stable and Unstable Versions 49 4 1 4 A Word About Directory Structure 49 41 5 Easy Install ua yA A 50 41 6 Developer Install es 4 a aa maa aris as 52 4 1 7 Other Install ln A A A ARA 54 42 Writing Your Own 10015 es aaa da 54 4 2 1 Toolbox Structure AA A A b a St ta a 54 4 2 2 Creating a New Toolbox o oo o 55 4 2 3 Using th Umit Wizard ARAS A A 57 4 2 4 Compiling Units Generating Tool XML 63 43 Advanced Tool Techniques a A A a dt 64 4 3 1 Showing and Hiding a Unit s Parameter Panel 64 4 3 2 Pausing Unit Execution o 64 44 Trouble Shooting ir a rara 68 4 4 1 Triana Resource Directory oo 68 ii List of Figures 2 1 2 2 2 3 2 4 25 2 6 2 7 2 8 2 9 2 10 2 11 2 12 2 13 2 14 2 15 2 16 2 17 2 18 2 19 2 20 3 1 3 2 3 3 3 4 3 5 3 6 3 7 Main Triana User Interface 5 424 404 4 4 ae ara al de Hw ee a ae Toolbox WINDOW srice na a See y 50 a EER SE OEE DOR Sew Tool Tree ICONS 4 24042 a t ao ow a Howe a cs UNO Ge ae go Sorting by Sub packages poke Bq ed
20. menus for File Job and List tools that are discussed in chapter 3 2 2 2 Main Menus and Tool Bars You can use Menus and Toolbar to give Triana instructions about what you want to do The Tool Bar is a collection of frequently used commands or options that appear as two rows of tools The Main Menu The main menu system outlined in table 2 3 displays a list of commands Menu Group Description File This is a standard menu group and most of the commands are provided in the Toolbar Edit This menu group common commands like for selecting grouping and ungrouping tasks Run Contains start stop and reset functions for constructed work flows Tools This menu group allows you to make you own tools and also allows you to compile and generate XML file of you new tools Services If Triana is running in a distributed mode see chapter 3 then this menu provides the functions for discovering and creating remote services Options Allows for configuration of Triana options see section 2 6 such as auto connect if you select this your tasks dragged on the main triana window will be automatically connected by the cable Window This adjusts the view of the main Triana windows or workspaces Cascade or tile open Triana windows so that you can view them all Help Under this menu group youcan find comprehensive guidance for Triana It includes reference to Triana s class packages you can also search for usage and f
21. 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 gt should be replaced by the users appropriate details e Textin this font signifies the unix command line prompt the text following it will be the command to type 4 1 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 4 1 3 Tagged Stable and Unstable Versions Please see the web site http www trianacode org for the current branch tag names in the repositories If you don t know what a tag is please see a good text book such as the CVS Book 4 1 4 A Word About Directory Structure For administration reasons Triana is split into a number of different packages which are st
22. 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 griphyntools login 51 org home cvsroot Logging in to username trianacode org CVS password lt userpassword gt prompt cvs d pserver lt username gt 0Otrianacode 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 GravityFromTheGroundUp 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 4 1 6 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
23. param txt Instead of the actual pre staged file name the tag lt STDIN gt indicates the file is piped to the standard input for the job The tag lt PRE_STAGED gt indicates that the input file is pre staged under its original name The Outputs Panel in the Job Properties Dialog is exactly the same as the Inputs Panel except that it specifies the files that are post staged after job execution and their mapping to the job task output nodes As with the Inputs Panel the actual name of the file in the job execution directory can be specified or the tags lt STDIN gt and lt STDERR gt can be used to specify the post staging of the standard input and standard error respectively The tag lt POST_STAGED gt indicates the name of the file connected to the relevant output node is post staged under its original name The number of input output nodes on a job submission task is automatically set equal to the number of pre staged and post staged files Connecting file components to these input and output nodes specifies the source location of the pre post staged files This can be seen in the simple example shown in Figure 3 10 In this example InFile is connected to the input node of MyJob indicating that InFile is pre staged before job execution and OutFile is connected to the output node of MyJob indicating that OutFile is post staged after job 45 execution We discuss file transfer using the GridLab GAT further in the next section 3 4 4
24. stopping super stoppingO stopped true synchronized this 4 unitThread notifyAll 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 selectedString selectedString String value System out println selectedString selectedString We need to check that the value is not an empty string as Triana updates parameters at intialisation time and we don t want that to trigger here if CselectedString equals stringSelected true synchronized this 4 unitThread notifyAl1Q 67 Symptom Solution No tools in the toolbok tree remove the Triana resource files and restart See page 68 Table 4 1 Trouble Shooting Symptoms 4 4 Trouble Shooting 4 4 1 Triana Resource Directory Triana stores its settings in a special directory which can be found in the user home directory the location of user home is specific to your operating system and system user name but typically on linux or unix based systems it will be designated by the symbol so typing cd at the command line should take you to your home directory On windows the user home directory is typically found under C Documents Settings lt username gt Under the user home directory there is a special hidden directory created by Triana called TrianaV3Resources This cont
25. the web service can be hosted as shown in Figure 3 7 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 5See http ws apache org axis java user guide html 37 Create Service PSD DER Service Hosts Service Options Local Service Web Service v Advertise Service h 31 251 40 117 Weh Service Create Cancel Figure 3 7 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 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 File Edit Run Tools Services Options Window Help De ms I ASOM 3 Systemout C Timer Cl WebServices D WSTypeGen Bi WSTypeViewer D xsd_boolean Q xsd_double C xsa_int xed_string File a Job Demos C Editing JAN Packages detaut lt untities2 DEnb
26. File Transfer As with job submission files in a Triana workflow are represented by a special File component A default version of the file component can be found in the Common toolbox by default instances of this component are green The file transfer operation associated with a file task instance depends on where it is connected into the workflow For example File Transfer from file to to file local in File Read in file local out File Write out file File Pre Stage pre file lA File Post Stage post file Figure 3 13 File Transfer Operations e Connection between two file tasks indicates a file transfer from the left file to the right file e Connection from a file task to a local task indicates a file read operation with the input data being processed by the local task e Connection from a local task to a file task indicates a file write operation using the output data from the local task e Connection from a file task to a job submission task indicates pre staging the file before job execution The mapping between the file task and the file in the job execution directory is specified in Inputs Panel of the Job Properties dialog see Section 3 4 3 e Connection from a job submission task to a file task indicates post staging the file after job execution The mapping between the file in the job exe cution directory and the file task is specified in Outputs Panel of the Job Properties dialog see Section 3 4 3
27. Mac OS X on the tool or toolbox icon in the toolbox window The menus vary dependant upon the item chosen e All tools and toolboxes have a common set of editing functions in the menu see table 2 1 these are explained in more detail in the section on editing toolboxes on page Menu Item Description Cut Cut the selected tools to the clipboard Copy Copy the selected tools to the clipboard Paste Paste the tools in the clipboard to the current toolbox Delete Cut the selected tasks Rename Rename the selected task Table 2 1 Common Contextual Tool Menu Items e The pop up menu for a single tool has in addition to the common editing functions the following menu items in table 2 2 see section 4 2 for a detailed description Menu Item Description Edit Tool Description Edit the tool tip shown when the mouse is over this tool Edit Source Edit the source code for this tool in the default text editor Edit HTML Help Edit the help file in the default editor Edit XML Definition Editthe XML tool definition file in the default editor Compile Bring up the compile wizard for this tool Help Show the help for this tool Table 2 2 Contextual Tool Menu Items e Group tool menus are similar to a single tool menu except that the Edit Source menu item is removed and instead there is a Open menu item that will open the group in a new main Triana window e There are some specialist
28. Triana User Guide The Triana Team Contents 1 Overview TA bala yojo ao sa ea soa dia a dea s X S a A ae ee a 2 Getting Started 2 1 Download Installation and Configuration 2 2 The Triana User Interface 2 2 1 The Toolbox Window 2 2 2 Main Menus and Tool Bars 2 2 3 The Main Triana Window 2 3 Your First Workflow 0000000 eee nee 24 Grouping Tasks AA A EA ARA REA 2 5 Using Parameters Within Triana 251 Fhe Node EOS AS RR RS eo 2 5 2 An Example with Parameters aoaaa aaa 2 6 Configuring Triana Options See See eae 2 6 1 Options Configuration Window 2 7 Getting Ei A a eae Gara a ek nk Cy S usa 3 Distributed Computing with Triana 3 1 OVerView a 3 22 Web SONY ICES sa x IE LAMA AAA AS 3 2 1 Web Service Configuration_ o 3 2 2 Discovering Web Services AA Gage 3 2 3 Importing Web Services css al Hans Ro aad a4 3 224 Conncecting Web Services Laa aa 3 225 Bible Translation Example 4 3 2 6 Complex Data Types al ky soak es 3 2 7 Deploying Web Services how ae ate ew ae 9 9 EA air an ta O a EG Ela SS EE EN OED EES 3 3 1 P2PS Configuration aoe a 3 3 2 Deploying P2PS Services e a a a See 40 3 3 3 Discovering P2PS Services a e Wee Be ee A 41 3 3 4 Connecting P2PS Services ada ica a o 41 3 4 ridha SAT
29. Zoom Out 11 taskgraph run 17 text editor 27 tool directories 54 filters 7 main window context menu 9 12 programming 54 searching for 7 wizard 57 tool bars 11 tool tips 26 toolbox new 55 new root 55 root 55 searching 7 structure 54 Triana TRIANA TRIANA 4 compiling 4 download 4 environment variable 4 run 4 Triana Data Types 7 Triana resource directory 68 trouble shooting 68 Ungroup 11 70
30. _ Auto commit OK Cancel Apply _ Auto commit OK Cancel Apply a editing data nodes b editing output parameters Figure 2 14 Node Editor of input and output nodes for the task In this case we can see that for the 21 Wave Node Editor changing the number of input nodes has been disabled This constraint has been set by the writer of the Wave tool The user can change the number of outputs by selecting the desired value from the drop down list Once Apply or OK has been pressed then the number of outputs on the task will be changed to reflect the new number Note In Triana if the number of output nodes from a task is increased this means that when the task outputs its data multiple copies of the data object are sent One copy from each output node The second and third tabs the third is shown in figure 2 14 b allow the user to control a task s input and output parameters By default no task parameters are output from or used as input to another task However all of the parameters that the task programmer has used in the user interface for instance are available to use as parameters To add a parameter as an output to the task select the Out Params tab press the Add button and choose one of the listed parameters See figure 2 15 Here the Te Wave Node Editor Nodes in Params Out Params aad KA Wave phase intensity phaseRet time paramUpdateP olicy z lt None
31. a workflow subsections as standalone services running on remote machines Unlike Web Services where much of the benefit comes from utilizing existing remote services the lightweight and dynamic nature of P2PS means the ability to deploy workflow subsections as remote services is particularly beneficial For example this mechanism can be used to distribute processing units to nodes in a cluster in a high throughput task farming application We discuss deploying P2PS services further in Section 3 3 2 We also outline discovering existing P2PS services and connecting them into Triana workflows in Sections 3 3 3 and 3 3 4 However first we describe configuring P2PS peers Section 3 3 1 3 3 1 P2PS Configuration To configure P2PS select the Services gt Configure menu option and then the Configure option next to P2PS Note that once P2PS has been used within the current running Triana it cannot be reconfigured and this option will be disabled For discovering and communicating with services within your local subnet the default configuration should be sufficient For bridging between multiple subnets a rendezvous connection is required The simplest way to do this is to enable Triana as a rendezvous peer and then have at least one service in the other subnet s enabled as a rendezvous peer pointing to Triana s local rendezvous port see the Discovery Panel in the P2PS Configuration Dialog 39 There are multiple different options that can be
32. able 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 TRIANA 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 which is 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 The Triana User Interface The Triana User Interface figure 2 1 consists of a number of main compo nents H Triana File Edit Tools Options Window Help KEL Ruo ee ona Packages cf Ing x Ci Output DisplayDoc D FileShow E WriteDoc C ImageProc output ImageMapViewer E Imageview m Gaussian Ly Movieview E write GIF Cf SignalProc C output Exporter GraceGrapher Histogrammer C 86TGrapher y Tool Tree Expanded Figure 2 1 Main Triana User Interface 2 2 1 The Toolbox Window The Toolbox Window allows you to explore the Triana toolboxes and navigate through the tool
33. ains all of the settings that Triana stores in various files If you have upgraded Triana or it is not behaving as expected for instance no tools or toolboxes are showing up in the toolbox tree delete the whole directory Next time Triana is started it will recreate the directory with the default settings 68 Index TrianaV3Resources 68 auto commit 17 auto connect 26 build 4 classpath 28 compiler 27 compiling 4 compound components 18 Copy 11 creating a toolbox 55 Cut 11 CVS 48 data types 7 Delete 11 edit nodes 21 toolbox root 56 editing 14 extended tool tips 26 external tools 26 filtering tools 7 Find 11 Flush 11 general options 26 Group 11 grouping 18 Help 11 69 html browser 27 menu main window tool menu 9 12 menus 10 New 11 Node Editor 21 node editor short cuts 23 Open 11 Options 11 options amp settings 25 output node increase number 21 parameter 20 auto commit 17 update policy 65 parameter panel 64 Paste 11 pausing units programatically 64 Print 11 Reset 11 restore defaults 28 restore previous 26 root dir 55 rubber banding 14 Run 11 run 4 17 Run Recorded 11 save unit group tools 18 grouping 18 Save Save As 11 parameter 20 searching pausing 64 toolboxes 7 selecting 14 Select All 11 selecting tasks 14 workflow short keys 11 editing 14 Show Properties 11 Foon tat lap 11
34. ameters to be set automatically and immediately this may have unexpected results for some workflows Clicking the OK button applies all parameter changes and closes the parameter panel 17 Freyuency E Amplitude Peak E Phase 0 1 0 phaseRet J Samples 512 Sampling Rate 8000 0 Time of First Sample 0 0 Type of Wave Sinusoid Wave w D Auto commit OK Cancel Apply Figure 2 10 Grapher Interface 2 4 Grouping Tasks In Triana tasks can be grouped and then saved to toolbox files for later use Grouped tasks are flexible because they appear as any other Triana task and can be used in the same way Therefore grouped tasks can be used to build new tasks from existing components without needing to write any java code Let us group the tasks from the network that was created in section 2 3 page 15 Your First Workflow To demonstrate how we do this we shall convert the taskgraph in figure 2 6 page 15 into a group task called WaveView Lets take a closer look on how we do this step by step 1 First Step is to select the tasks that are to be grouped There are 3 ways different ways to select a Groups of tasks can be selected by rubber banding the tasks Click on the back ground of the main Triana window above and left of the tasks and drag a rubber banding area over the tasks When the tasks are selected their colour turns slightly darker b B
35. bject for job submission purposes Script a special type of group tool that can act on other tools List a representation of a list of objects Service a proxy component to a remote service such as a web service Searching The combined search control at the top of the toolbox window has multiple functions In text search mode typing part or all of a component s name and hitting enter will search all of the toolbox paths for matches and display any matches in place of the normal tool tree The search control is also a drop down list with six items which are all tool filters for displaying a filtered view of the toolboxes All Packages default returns the tool tree view to its default Sub Packages shows all the sub packages of all the Triana toolboxes in alphabetical order as shown in figure 2 4 a When clicked on a particular sub package it points to the corresponding toolboxes main packages that contains this sub package For example in the figure 2 4 b we can see that the Input sub package points to all the toolboxes that contain Input sub package such as the Input sub package of the Audio toolbox package All Tools expands all toolboxes and sub toolboxes so that all the tools or components are shown Input Tools is a special form of Sub Packages filter that shows all of the tools that are contained in any sub toolbox called Input This is a fast way of finding all tools that are capable of generating data for the star
36. box hierarchies It is easy to view the toolbox contents simply by double clicking the toolbox name or the corresponding pointers Contextual menus are available by right clicking on toolboxes or tools and a search entry allows for easy location of tools The Triana Toolbox Window figure 2 2 consists 5 of a tree component with branches representing toolboxes and sub toolboxes leaf nodes representing tools or components ecu Packages v N J Triana Toolboxes C Audio Cf input IN ImportGSM E LoadSound C Common Ci Input E ConstGen C Count IN DBExplore IN DBExplore2 3 Deserialize Ey Import2Co y SequenceBuffe Tunelmnon E lv Tool Tree Expanded Figure 2 2 Toolbox Window There are a number of different icons that represent different types of tools these are can be seen in figure 2 3 2 iconlist _ 1 Tool 2 Group Tool X 3 Broken Tool 4 File 3 5 Job Q 6 Script 7 List 8 Service Figure 2 3 Tool Tree Icons The icons represent different tools with toolboxes the top folder icon repre sents a toolbox 1 2 3 Standard tool Group tool a number of other tools combined and saved as a new group Broken tool a tool that cannot be instantiated on a main window Typically because it has not been compiled File a special tool that represents a file object either locally or remotely 6 5 6 YA 8 Job a special tool for representing a job o
37. d 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 preferred mechanism for doing this is to cause the current thread to sleep interrupting the thread on the parameter being updated Note An important thing to remember is that the parameter update policy must be set in the unit set up to be update immediately as opposed to the default behaviour of updating on the execution of the process method Without this change to the default behaviour the execution will hang package UserGuide import triana unit Unit This unit pops up its user interface and pauses execution until something has been selected author Matthew Shields created 23 Feb 2005 public class PopUpAndPause extends Unit parameter data type definitions private String selectedString Flag set when a user selects string boolean stringSelected Flag used by a user initiated stop boolean stopped Called whenever there is data for the unit to process 65 public void process throws Exception set the flags to false stringSelected false stopped false display the units parameter pane
38. e of the examples above it is valid to either express the protocol used to access the file explicitly e g HTTP FTP or to leave it to the GAT to determine which protocol to use e g when file scheme is specified 47 Chapter 4 Extending Triana Triana has been developed with extensibility in mind From relatively simple extensions such as writing your first unit to major extensions such as building alternative workflow language readers and writers or new GAP bindings Triana has been designed to be extended This chapter deals with some of the possible extensions to Triana The content here is often more technical from a programming perspective than the rest of this manual A understanding of some technical matter such as the Java programming language is a prerequisite This chapter is not intended to be a Java programming guide there are many fine resources for that 41 CVS Access If you intend to do anything more than simple unit programming in Triana it is recommended that you use a developers version of the system from our CVS repository 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 48 4 1 1 Conventions Note These instructions assume you have the
39. ed 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 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 be 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 32 nu Packages default 5 E Triana Tools E Audio cI Common c Demos Editing C ceo CI GriPhyN C ImageProc E Math C SignalProc EI web Services 1 BabelFish BabelFish Barnes and Noble Price Quote CJ BAX Global Tracking Service 9 Bible verses read_bible C BiblewWebservice p p 0 9 9 9 JAN Figure 3 3 Web Service tools in the Tool Tree C will search for all web se
40. elp main menu 28 Chapter 3 Distributed Computing with Triana In the previous chapters the majority of discussion has concerned creating work flows using local Triana units units where the processing is done on the same machine as the Triana application However unless the local machine happens to be a massive super computer such an approach is very limiting in terms of the computing power available to workflows In an era of service orientated computing such an approach also prevents workflows from employing any of the distributed services that are increasingly becoming available In this chapter we look at the facilities for utilizing distributed resources within Triana workflows We give an overview of TrianaSs architecture relating to distributed computing in Section 3 1 in particular noting the differences between the grid oriented components and service oriented components In sections that follow sections we outline the current distributed computing bindings within Triana namely Web Services Section 3 2 P2PS Section 3 3 and the GridLab GAT Section 3 4 3 1 Overview Distributed components within Triana can be split into two categories which we refer to as grid oriented components and service oriented components Service Oriented Service oriented components such as web services and P2PS services are network accessible components that exist on remote 29 MELO d GRAM eat x Figure 3 1 Dist
41. ems arise during the run and offers advice on how to avoid the situation You can easily insert display units to monitor intermediate re sults and track down more subtle errors Triana traps serious errors so the program will not crash at worst you need only restart the calculation Triana is being developed by scientists at Cardiff University in the UK They are working within the GEO600 gravitational wave experiment a major physics collaboration between scientists from Germany Britain and other countries GEO600 will generate many terabytes of numerical data each year and Triana is designed to make it possible for scientists in the project to examine this data in a simple and versatile way Triana is in use within GEO600 and in other major centers of research in the USA and Europe The release version of Triana will take the same principles of easy operation and versatility and extend them to a variety of types image sound text and numerical data But you don t have to be a rocket scientist to use Triana Like the internet email the web and web browsers Triana is another tool initially created for scientists that has very much wider use Triana opens programming to people who don t know a programming language 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 vari
42. en in figure 2 17 Help rulo DWAJA STA 680 CI Converters C DataParam Demos Filtering 9 E Input O ascilimporter Y DO Framebata f C importer Q LiveData 3 LoadFrame D Makematrix C Newimporter O Wave T Tool Tree Expanded Figure 2 17 Parameter Node 5 Now do the same for the Wave task but in this case add an input parameter node Go to the second tab In Params of the Wavel Node Editor click on Add select frequency and click ok Note Choosingfrequency as an input node parameter in the Wavel task means that whatever we plug into this node will be controlling Wavel s frequency There is no type checking mechanism on parameters 24 6 Now make a connection between the output node of Wave and the input node of Wavel by dragging a cable between the nodes Add a SGT Grapher task in SignalProc Output toolbox and connect it to the output from Wavel You should now have the workflow we first looked at in figure 2 16 7 Now show both parameter windows for Wave and Wavel by double clicking the task s icons and then press the run the workflow Move the scroller for the frequency in Wave task thereby changing its frequency and when you click on apply you will notice the scroller for Wavel s frequency also changes Wave is remotely controlling Wavel s frequency Now when you run the workflow again you will notice that the frequency on the graph di
43. ervice is displayed when the mouse is hovered over the task File Edit Run Tools Services Options Window Help Demi DX BBR BG oe bEOeT DEF AG Legacy o Logic juffer 4 omms El P y au onto 2 ey u CI input E Figure 3 4 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 and Common String StringViewer 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 4 we show StringGen and StringViewer being used as input and output for a temperature conversion service Other local tools can also be used 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 work flow using th
44. figure 2 20 This window allows the user to configure the classpath used with the compiler inside Triana to compile a unit It is only used by users wanting to compile their own units see chapter 4 It provides the ability to add or remove and change the order of specific items on the classpath There are options to automatically add all tool box paths which will add every item on every classpath for every tool box to the list and an item to retain the classpath for future This saves the classpath when Triana has finished ene Select Path No sihe siphysics working tri F Add all wot box paths M Retain classpath for future Figure 2 20 Selecting the Unit Classpath Note See the section on writing your own tools for more information on units and classpaths specifically this classpath is for compilation only For the run time classpath it is necessary to add any required libraries to the Triana class path Restore Defaults A button that will restore all the Triana options to their factory settings Selecting OK will save all settings and close the window returning to the normal Triana user interface 2 7 Getting Help Triana units are self documenting You can access help on a particular Triana task by selecting the task in either the tool box window or a main Triana window and selecting Help by pressing the F1 function key selecting from the contextual pop up menu selecting the tool bar button or selecting Help from the H
45. he parameter panel Note that these values can be changed later either in the wizard or in the generated code GUI Panel The fourth panel the Unit Wizard shown in Figure 4 6 allows the graphical user interface for a unit to be specified The three main categories available are No Interface No user interface GUI Builder Interface Uses the Triana GUI Builder to define an interface for updating the unit s parameters We discuss this further below Custom Interface Specifies a Java class to act as the parameter panel for the unit This class must extend ParmaterPanel in triana gui panels If required template Java code for the panel class can also be generated when the unit code is generated 61 H Unit Wizard Tool Definition Complete Select Finish to Generate Code Tool Name MyUnit Tool Box Path C projectttoolboxes Unit Package UserGuide Author lan Wang v Generate Tool Placeholder UserGuide MyUnit The following directories amp files will be created CuprojectitoolboxesWserGuidet CiprojectitoolboxesWiserGuideWMyUnit xral C projectitoolboxes UserGuide classes C project toolboxes UserGuide help C projectitoolboxes UserGuidethelp MyUnit html CuprojectitoolboxesWiserGuidetsrci Cuprojectitoolboxes1JserGuideisrciMyUnit java Cancel Back Finish Figure 4 7 Final Panel in the Unit Wizard If GUI Builder interface is selected an additional panel appears allowing GUI components
46. holding down the control key command on OS X and selecting the tasks or by rubber banding the required tasks You can do a number of things with selected tasks for example e they can be deleted e they can be moved e they can be copied and pasted into the workspace for multiple repetition of particular group of tasks e they can be copied and pasted into the tool tree for creating stored copies of the task and its current parameters e they can be grouped into a composite task group task Copying Tasks You can copy tasks by selecting the tasks you wish to copy and then choose the Copy option from either the main Triana windows popup menu right click on one of the tool icons or the Copy option on the Edit menu TIP if you select several tasks for copying from the Main Triana window then the tasks will get copied but NOT the connections If you wish to copy a selection of tasks along with the connections then make a group out of the tasks first and then copy the group Pasting Tasks Once a copy operation has taken place selecting Paste will paste a copy of the tasks to the current window The Paste option can be found either in the window s popup menu right click on one of the tool icons or by the Paste option on the Edit menu If the tools are pasted into the tool tree a stored version of the tool with the current parameters will be created This new tool will appear in the tool tree and can be reused at a later date
47. ind this that at tempts to connect to the correct task according to placement on the window Automatically save and restore the working windows Any main Triana windows with workflows will be saved at shutdown and re stored the next time Triana is started Display a short tool tip when the mouse is over Auto Connect Restore Previous At Startup Show Tool Tips a tool or task either in the toolbox window or on a main window Show Extended Tool Tive Show a more detailed tool tip includes package information directory and more Show Node Increase Decrease Show or hide the Node Editor short cuts Icons Convert Output of All Units Triana s built in data types use float by default to Doubles this option forces them to use double instead See chapter 4 Table 2 9 General Options External Tools The external tools options which can be seen in the second tab of the Triana Options window figure 2 19 has a series of text fields with browse buttons and some additional controls For most users the defaults set here should be suitable and there is no need to change them If you are using Triana to develop tasks then some of these settings may be of interest 26 rece Triana Options General External Tools Web Services Config HTML Help Viewer Default Help Viewer HTML Editor Default Editor Code Editor Default Editor fa Javac Compiler System Library Framenorks JavaVM framework
48. ird 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 34 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 File Edit Run Tools Services Options Window Help C bankvalidate StringGen1 C Barcode Generator CT Barnes and Noble Price Basic Telecom Rate Inf TIBAN Global Tracking S TI BGTrans A CJ BGZip Figure 3 5 A simple bible translation workflow 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 5 StringGen and StringViewer 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
49. l Package Tool File Figure 4 8 Compile Unit Generate Tool XML Dialog 4 2 4 Compiling Units Generating Tool XML Once a Java unit has been created see Section 4 2 3 it needs to be compiled before it can be used within Triana Also in order for the unit to appear in the Triana tool tree an XML tool representing the unit must also be generated Both compilation and tool XML generation can be done using the Tools Compile Unit Generate Tool XML menu option Alternatively to recompile an existing tool right click on that tool in the tool tree and select Compile In Figure 4 8 we show the dialog for compiling Triana tools The available options in this dialog include Unit Name The name of the unit as specified in the Unit Wizard Unit Package The package of the unit as specified in the Unit Wizard Using the browse button next the unit package field allows the Java source for a unit to be selected the unit name and unit package will automatically be set Toolbox The base toolbox for the unit see Section 4 2 1 Compile Source Selects whether the source code for the unit is compiled The Javac compiler classpath and arguments can be set Generate Tool XML Selects whether a XML tool definition of the unit is gen erated The name package and file for the generated tool can be set Compile Graphical Interface Selects whether the parameter panel source for the unit is compiled This only applies to custom parame
50. l interface showParameterPanel while stopped stringSelected synchronized this try 4 this waitQ catch InterruptedException e output selectedString eK Called when the unit is created Initialises the unit s properties and parameters public void init super initQ Initialise node properties setDefaultInputNodes Q setMinimumInputNodes Q setMaximumInputNodes 0 setDefaultOutputNodes 1 setMinimumOutputNodes 1 setMaximumOutputNodes Integer MAX_VALUE Initialise parameter update policy and output policy IMPORTANT this must be changed for the unit to restart it s thread setParameterUpdatePolicy IMMEDIATE_UPDATE setOutputPolicy CLONE_MULTIPLE_OUTPUT Initialise pop up description and help file location setPopUpDescription This unit pops up its user interface and pauses setHelpFileLocation PopUpAndPause html Define initial value and type of parameters defineParameter selectedString USER_ACCESSIBLE 66 Initialise GUI builder interface String guilines guilines Select a string title selectedString Choice guilines Mary Had A Little Lamb n setGUIBuilderV2Info guilines This is called when the network is forcably stopped by the user This should be over ridden with the desired tasks lt p gt We need to override this method to quit our paused thread public void
51. le via the parameter panel or parameter input output nodes Internal indicates the parameter is not visible to the user and Transient indicates the parameter is not visible to the user and is not stored when the tool is saved In addition to the parameters the parameter panel also allows the parameter update policy to be specified The parameter update policy states when param eters updated by the user are informed to the Java unit The available options are 60 Unit Wizard O No Interface Component Text Field X 8 GUI Builder Interface Default Value someval aparam Text Field anotherparam Check Box Title Param Show Hidden Parameters w Move Up Move Down Custom Interface Panel Class Generate Template Preview GUI Cancel Back Next Figure 4 6 GUI Panel in the Unit Wizard Update at start of process The updates are informed to the Java unit before the process method is called but no while it is executing This is the default policy as it prevents unexpected parameter changes during processing Update immediately The updates are informed to the Java unit immediately the parameter is changed even if in the middle of processing This option is required by steerable units Do not update The updates are never informed to the Java unit Any update mechanism has to be implemented explicitly using TaskListeners Select Next to accept the values specified in t
52. ly Run this unit in continuous mode Auto Save History Automatically save the history for the selected unit Save History Save the history for the selected unit Create Service Create a service from the selected unit Run Script Run a script on the selected unit Cut Cut the selected tasks to the clipboard Page 14 Copy Copy the selected tasks to the clipboard Page 14 Delete Cut the selected tasks Page 14 Paste Into Paste the tasks in the clipboard to the current window Page 14 Rename Rename the selected unit Help Display the help file for the selected task Page 28 Table 2 5 Main Window Tool Menu e Clicking on multiple selected tools section 2 4 will show a similar menu but with some additional items added and many of the previous ones removed table 2 6 e Clicking on a group tool section 2 4 will show a similar menu but with some additional items added and some previous ones removed table 2 7 e Clicking on the window background will display the final menu table 2 8 12 Menu Item Description Group Turn the selected tasks into a new group task Page 18 Cut Cut the selected tasks to the clipboard Page 14 Copy Copy the selected tasks to the clipboard Page 14 Paste Into Paste the tasks into the tool tree Page 14 Delete Cut the selected tasks Page 14 Table 2 6 Main Window Multiple Tool Menu Menu Item Description View Group Display the contents of this
53. mputer these may flash on and off almost too quickly to see 6 Display the SGTGrapher parameter panel user interface either by double clicking the tool in the main Triana window or using the contextual menu on the tool and selecting the properties item The contextual menu is a pop up menu that is accessed by right clicking on Windows or Linux operating systems and Command Clicking on Apple OS X see section 2 2 3 The interface for SGTGrapher should look like figure 2 9 Reset Zoom Snapshot Print Imearx v mear Y y xAuto Scale V yAuto Scale E W Figure 2 9 Grapher Interface 7 The form of the graph can be changed by changing the input parameter in the Wave task Display the parameter panel interface by double clicking or using the Properties contextual menu on the Wave icon in the main Triana window You should see the panel in figure 2 10 8 Change the frequency to 800 hertz and click apply Then click on the run button and view the wave type in the SGTGrapher display by repeating steps 5 and 6 You can view the graph display change as you change the frequency by moving the scroller clicking apply and thenrun again Note It is important that the Apply button is pressed after parameter values have been changed or the changes will not be set An alternative is to select the Auto Commit check box at the bottom of a parameter panel Checking this option forces changes to par
54. n Zoom Out these buttons change the size of the task graph in the main Triana window making everything smaller or larger for easier viewing Table 2 4 Tool Bar Commands 2 2 3 The Main Triana Window The Main Triana Window is a workspace for constructing programs by dragging and dropping the tools from the toolboxes Tasks are the components that can be graphically connected to create a particular data flow algorithm The connection between tasks is made by dragging a cable from the output node right hand short cut keys are platform specific keyboard combinations that can be accessed without using the menu system Cut Copy and Paste are good example that use the standard keys for the operating system control C for copy on Windows 11 side of the sending task to the input node left hand side of the receiving task Once a network has been created it can be executed Main Triana Window Contextual Menus Like most user interface components in Triana the main window for constructing workflows has contextual pop up menus These are accessed by right clicking control clicking on Mac OS X on the window The menus vary dependant on where the mouse is clicked e Clicking on a tool icon will display the contextual tool menu contents in table 2 5 Menu Item Description Properties Display the parameter panel interface Node Editor Display the node editor Page 21 Run Continuous
55. ncel Back Next Figure 4 4 Data Type Panel in the Unit Wizard Data Type The data type input output This can be any standard java type e g java lang String Triana type e g triana types SampleSet or any other type that is on the Triana classpath In addition to the data types the data type panel also allows the data output policy to be set This is the policy that is used when the general output O method is called by the unit as opposed to the specific outputAtNode method The available output policy options are Copy output pass by reference A reference to the data is output on each node no cloning is performed Any changes later tasks make to the data will affect all other tasks that received the reference This policy should only be used if the effect is desired Clone output on additional nodes A reference to the data is output on the first node but clones of the data are output on all other nodes if possible This is the default policy as changes later tasks make to the data will not affect other tasks as they received a different version of the data Clone output on additional nodes Clones of the data are output on all nodes if possible This policy is required if the task outputting the data holds on to the data for future update With this policy these updates will not affect other tasks as every task received a clone of the data Select Next to accept the values specified in the data type panel
56. ng a task group task as a P2PS service 40 3 10 Example GAT workflow 2 eaten OA EA 42 3 11 Job Properties Dialog aaa a laid ad 44 3 12 Inputs Panel in the Job Properties Dialog 45 3 13 File Transfer Operations s nia TS e 46 4 1 example build properties Ole e GG 54 42 Edit Toolbox Paths ssena a dd a dR aa ala uw cg A 56 4 3 Unit Panel in the Unit Wizard 57 4 4 Data Type Panel in the Unit Wizard 59 4 5 Parameter Panel in the Unit Wizard 60 4 6 GUI Panel in the Unit Wizard 61 4 7 Final Panel in the Unit Wizard 62 4 8 Compile Unit Generate Tool XML Dialog 63 lv List of Tables 2 1 2 2 2 3 2 4 2 5 2 6 27 2 8 2 9 4 1 Common Contextual Tool Menu Items oaoa aaa 9 Contextual Tool Menu Items 9 Menu Commands omic a AA AA 10 Tool Bar Commands 11 Main Window Tool Menu 12 Main Window Multiple Tool Menu o o o 13 Main Window Group Tool Menu co 13 Main Window Background Menu ooo o 13 General OPUS A ARS A AS 26 Trouble Shooting Symptoms oo o o 68 Chapter 1 Overview 1 1 Introduction Triana is a graphical environment that allows you to create powerful computer programs and to use them with a minimum of effort and no programming Using Triana you
57. ng for tool files and then builds up the tree from leaf node tool back to toolbox root A tool box directory contains an XML component definition file for each tool a src directory that contains any source code files for the tool a help directory that contains any help files and an optional 1ib directory that typically holds shared library objects for specific platforms All of the directory structure and files can be created by Triana and for most users that is how they should be created In section 4 2 2 we will discuss how to create a new toolbox and in section 4 2 3 we will populate that toolbox with a new tool 4 2 2 Creating a New Toolbox There are a number of ways to create a new toolbox but first so that we don t disturb the existing tools and toolboxes within Triana we will create a new toolbox root The new toolbox root will be used to hold all of our new toolboxes and tools that way they can be kept separate from the existing stable tools if we need to update the Triana version at a later date To change or add toolbox roots to Triana select the Tools main menu item and then the Edit Tool Box Paths item You should see the window in figure 4 2 The paths will obviously look slightly different to this depending on you set up and operating system the one shown is a unix system In the default setting shown here there are already four toolbox roots set and each of these has a 55 i 4 e e Edit Tool Box Paths Volumes
58. ntained task s panels in a tabbed interface Select each tab to see the user interface for each task This can be seen in figure 2 13 WA New Group SGTGrapher Wave Reset Zoom Snapshot Print tinearX linear Y v v xAuto Scale v yAuto Scale Auto commit OK Cancel apy Figure 2 13 New Group Tool Parameter Window 2 5 Using Parameters Within Triana Note This section assumes that you have read and understood section 2 3 on creating and running your first workflow Triana makes a distinction between parameters and data Most components and workflows in Triana are data driven with producer components generating data objects that fow through communication channels to the consumer component next along in the workflow A parameter is a special type of data message that is normally used for communication between a task and its parameter panel In a distributed computing setting the user interface for a component may not be running on the same computer as the task so the communication between them in Triana is decoupled and based around messages Parameters can also be used by users to pass settings or information that are not strictly a generated data results from one component to another In chapter 4 we will look at parameters in more detail and how they can be used by 20 unit programmers This section will cover the use of parameters from a users perspective Parameters can
59. on see figure 2 16 The first Wave task is outputting a parameter and the second Wavel task is receiving this parameter In this case the parameter is the frequency of the waveform DOR 9 E SignalProe Algorithms C Converters C3 DataParam Demos o Filtering Input 9 C3 output D Exporter C GraceGrapher C Histogrammer 4 CO soTorapher _ Tool Tree Expanded Figure 2 16 Parameter Connection Let s take a closer look on how we make this connection by creating this network step by step 23 1 Instantiate two instances of the SignalProc Input Wave tool onto a new main window by either dragging the tool from the toolbox twice or dragging one and then copy and pasting See pages 15 and 14 for more information 2 Select the first of the two Wave tasks and bring up the Node Editor by selecting the option from the pop up menu see the previous section on page 21 3 In the first tab Nodes set the output node count to 0 We don t need to output any data from this task for this example 4 Change to the third tab Out Params Click on Add button this will allow you to choose the parameter which will be output from the first parameter output node on the Wave task Select the frequency parameter and click OK This will added a parameter node to the output of the Wave task Parameter nodes are recognised by a white circle in the centre of the node as can be se
60. ored in various CVS repositories Some of these are project specific 49 and not publicso don tassume 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 There 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 4 1 5 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
61. orted and appears in the user s tool tree it can be instantiated by dragging the tool onto the main workspace in the same way locally available tools are instantiated P2PS services tasks appear as purple on the workspace P2PS service tasks can be connected to local tasks and other remote service tasks in exactly the same way as standard Triana tasks A workflow containing P2PS services is executed as for a standard Triana work flow i e by pressing the run button 41 3 4 GridLab GAT The GridLab GAT isa generic and flexible API for accessing Grid services such as job submission and file movement It has an adaptor based pluggable archi tecture see Figure 3 1 that allows different service bindings to be utilized For example a GRAM adaptor allows job submission using Globus GRAM while a GRMS adaptor allows job submission using GridLab GRMS New adaptors can be developed and plugged in without changing application using the GAT i e Triana Triana uses the GridLab GAT to allow job submission with a workflow and also to transfer input files to and output files from a remote job We give an example GAT workflow involving staging files and running a remote job in Section 3 4 1 and then descriptions of job submission and file transfer in Sections 3 4 3 and 3 4 4 respectively We outline configuring the GridLab GAT in Section 3 4 2 File Edit Run Tools Services Options Window Help De mil GXBBX agom lan Packages defa
62. pecial hidden directory in the users home directory called TrianaV3Resources This directory is explained in more detail in the trouble shooting section on page 68 Now to add a new toolbox root all we need to do is to select the Add button and use the file browser to navigate to a suitable empty directory or create a new directory Select OK and the new path has been added to the list of tool box roots We are now ready to create a new tool and toolbox structure within that 56 18 Unit Wizard Unit Name MyUnit Unit Package UserGuide Tool Box Path C projectitoolboxes Author lan Wang PopUp Description A demo unit for the user guide Date 15 Mar 2005 Help File MyUnit html Include Copyright Default Input Nodes 1 w Enable Resize fi Minimum Input Nodes Maximum Input Nodes Default Output Nodes 1 w Enable Resize wi Minimum Output Nodes 0 Y Maximum Output Nodes Uniimted vv Figure 4 3 Unit Panel in the Unit Wizard root path To do that we will use the Tool Wizard explained in the next section section 4 2 3 4 2 3 Using the Unit Wizard The Unit Wizard provides a simple GUI for generating skeleton Triana unit code Once generated only the process method requires implementation in order to produce a Triana unit Note that this unit must then be compiled and the tool XML file generated before it can be used within Triana We discuss compiling tools and genera
63. ributed Component Middleware within Triana computing resources These components can be discovered by Triana and then invoked from within a Triana workflow Grid Oriented Grid oriented components represent jobs launched by Triana on a remote machine using a grid resource manager e g GRAM or GRMS Unlike service components these jobs do not have network ac cessible interfaces so communication is only available via input output files Triana uses different interfaces to access these two categories of distributed com ponent For service oriented components the misnamed GAP Interface Grid Application Prototype Interface is used while for grid oriented components the GridLab GAT Grid Application Toolkit API is used Both these interfaces have multiple bindings which allow different service grid middleware to be em ployed without amending the Triana application code as shown in Figure ref fig distarch For service oriented components web services and P2PS services can currently be invoked while for grid oriented components job submission can currently be done using GRMS GRAM or the local adaptor Both the GAP Interface and the Gridlab GAT allow new bindings to be plugged in when they become available For example when a Condor GAT adaptor becomes available Triana will automatically be able to utilize Condor job submission We outline the process for invoking web services in Section 3 2 and for P2PS services in Section 3 3 however
64. ring up the popup menu of the main Triana window by clicking once on the empty space of the main Triana window with the right mouse button And choose Select All option c Select Edit from the Menu bar and choose Select All option 2 Group the selected tasks either by selecting a Edit option of the menu bar and choose the Group option 18 b Press the Group tasks button in the tool bar c Use the contextual menu on one of the selected tools by right click ing or command clicking on the tool icon and selecting the Group option A New Group box will appear where you can enter any name for the new group See figure 2 11 Fe New Group 3 Group Name New Group Figure 2 11 New Group Box 3 Enter the name WaveView and click OK A new main Triana window will be created containing our new group See figure 2 12 The name of the Figure 2 12 New Group Box New Group is now changed to WaveView Another window is showing the tasks which were grouped to make the new task WaveView 19 Note You can close the WaveView window showing the individual tasks to reopen it select the WaveView task and right click the mouse and choose View Group 4 Run the new group task by making sure its main Triana window is the front most and running in the normal manner To see the result double click or use the contextual menu on WaveView to bring up the parameter panel The panel for group tasks presents each of the co
65. rvices 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 3 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 dragging the tool onto the main workspace in the same way locally available tools are instantiated Web services tasks appear in red on the workspace 3For example an web service interface to Altavista s BabelFish language is located at http www xmethods net sd 2001 BabelFishService wsdl 33 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 s
66. se 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 4 2 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 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 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 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
67. ser 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 4 1 e Run the buildTriana script 53 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 4 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 select the directories project toolboxes project toolboxes dev project toolboxes_other 4 1 7 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 4 2 Writing Your Own Tools Writing tools in Triana can be s
68. simply assemble your program from a set of building blocks that you drag into a work space window and connect up using your mouse With a click of the mouse the program will perform whatever operations you want You can tell Triana to execute your program just once or continuously as long as data is available to it Since Triana is written in pure Java it will run on almost any computer and you can share your work with colleagues who work on different kinds of computers Triana is a revolutionary new way to expand the number of things you can do on your computer It allows you to create serious and complex programs without dealing with programming languages compilers debuggers and error codes e Use Triana on a wide variety of data numerical data either taken from an experiment or generated by Triana audio data images even text files e Triana comes with a wide variety of built in tools There is an extensive signal analysis toolkit an image manipulation toolkit a desk top publish ing toolkit and many more Most Triana tools will show you a parameter window so you can adjust the way they work Parameters can typically be changed dynamically without interrupting the flow of data e Triana will display your data either in a text editor window or ina versatile graph display window The grapher will display several curves at once and will allow you to zoom in on interesting features and mark them e Triana is particularly good at
69. sk and drag it from toolbok tree window and drop it on the left hand side of the main Triana window After dropping the wave task in the Triana workspace it should look like figure 2 7 Qe wo OU sada OXAR ASD L SignalProc Algorithms C Converters CI DataParam o CI Filtering CI input FrameData D Importer HER y Makematrix Y Wave Figure 2 7 Instantiated Wave Tool Note you can move the tasks around the main Triana window in exactly the same way i e by dragging them to the new location 3 Similarly put the SGTGrapher task a graph displayer on the main Triana window This task can be found in the Output toolbox within the SignalProc toolbox Henceforwards written as SignalProc Output You should see the main window look as figure 2 8 HER File Edit Tools Options Window DAP aso DTA EE ae 8 ath 9 E SignalProc Algorithms C Converters C DataParam o Filtering 3 input Figure 2 8 Instantiated Wave and Graph Tool 16 4 Now connect the Wave task and the SGTGrapher task by dragging the cable from the output node of the Wave task and join it to the input node of the SGTGrapher Which will give you the complete workflow shown in the first figure figure 2 6 5 Press the Run tool bar button or the menu item Run under the Run menu You should see small blue execution indicators flash on and then off each of the tasks If you have a very fast co
70. splay will also change accordingly 2 6 Configuring Triana Options Triana is highly configurable and remembers settings from session to session Window placement window size and zoom level see page 11 are saved when Triana quits and are recalled when Triana is restarted In addition to these automatic configurations some settings can be manually set Under the Options main menu item there are two items The first Debug Window displays the message logging window for Triana For most users this can be ignored unless you are curious it displays logging and error messages and is used mainly by tool programmers for debugging See chapter 4 The second item Triana Options displays the options configuration window 2 6 1 Options Configuration Window rece Triana Options General External Tools Web Services Config C Auto Connect 7 Restore Previous At Startup Y Show Tool Tips y Show Extended Tool Tips m Show Node Increase Decrease Icons C Convert Output of All Units to Doubles Figure 2 18 Options Window general settings 25 The Triana Options window consists of three tabbed panes General Options The general options settings which can be seen on the first tab of the Triana Options window figure 2 18 has a set of On Off check box settings Option Description Automatically connects a new task dropped on a main window to a task already on the window There is a smart algorithm beh
71. t Triana copyright is included in the generated skeletion Input Nodes Allows the default number of input nodes to be specified If resize is selected then the range of acceptable input nodes can be specified otherwise the number is fixed at the default Output Nodes Allows the default number of output nodes to be specified If resize is selected then the range of acceptable output nodes can be specified otherwise the number is fixed at the default Select Next to accept the values specified in the Unit Panel Note that these values can be changed later either in the wizard or in the generated code Data Type Panel The second panel the Unit Wizard shown in Figure 4 4 allows the data types which are input output by the unit to be specified This information allows type checking between units to be done at connection time When an input output type is added two pieces of information are required Node The index of the node the type is input output on where 0 is the first node 1 is the second and so on The value All Nodes indicates that the data type applies to any node The value Other Nodes indicates that the data type applies to nodes after those that have data types explicitly set 58 i Unit Wizard Input Types All java lang String Output Types 0 java lang String 1 java lang Integer Add Remove Output Policy Clone output on additional nodes w Ca
72. t of a workflow Output Tools is the corresponding filter that displays only tools from Output toolboxes These are the tools that are designed to display or output the results of a workflow Data Type Tools when selected gives you a popup menu as shown in figure 2 5 below In this menu select the Triana Data Types by which to filter the toolbox view Select the required data types from the menu and press the Ok button Triana will filter the tools which contains those selected data types Select All Tools to view the tree 7 Sort by Sub Package x Triana Toolboxes 3 Algorithms 3 Calculator 1 comms Converters DataPararn Cf Filtering 3 Functions Cf Network Output C Parameter Cf Processing 3 Statistics Tool Tree Expanded a Sub packages Sort by Sub Package C Triana Toolboxes o EJ Algorithms 3 Calculator C comms 3 Converters 3 DataParam Filtering 3 Functions 3 GalaxySim C Input EJ Audio Ci Importosm C LoadSound s Common CT Editing ImageProc 3 SignalProc _ Tool Tree Expanded b Expanded Figure 2 4 Sorting by Sub packages Untitled Select Data Types and Input Output Cor o Figure 2 5 Filter Toolbox by Data Types Toolbox Contextual Menus The contextual menus for tools and toolboxes are accessed by right clicking control clicking on
73. tarted very easily The only prerequisite is a little understanding of the Java programming language working with files and direc tories in the operating system of your choice and the desire to experiment 4 2 1 Toolbox Structure Toolboxes in Triana are as you might expect just a series of directories and files within a set structure However the relationship between the underlying file structure and the tree representation in the toolbox window is not necessarily 54 that simple The logical tree view and the physical file view of the toolbox structure does not have to be the same although it often is Toolbox structure starts with a toolbox root directory The toolbox root is the directory that Triana looks in recursively for toolboxes Triana can and in fact does have more than one toolbox root they are a useful way of com partmentalising different groups of tools If you are using the default Triana download then your default toolbox root will be TRIANA toolboxes for unix or TRIANA toolboxes for windows See the next section 4 2 2 for more information about adding or changing toolbox roots Underneath the toolbox root are packages represented by directories containing other directories and toolboxes represented by directories containing tools The whole process is recursive so package hierarchies can be to any depth and a toolbox can contain sub packages as well as tools Triana searches the directory structure looki
74. ter panels see Section 4 2 3 Select OK to compile the unit This process can take a while as the javac compiler 63 must be invoked unless only generating tool XML A debug window appears showing the output from the compiler Note that if the graphical interface is also being compiled the two debug windows will appear 4 3 Advanced Tool Techniques In this section we look at some more advanced techniques that a tool developer may wish to use Where source code is listed only the important code or code modified from template code is listed For full listings look at the tool source code listings in the UserGuide toolbox in Triana 4 3 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 Inside the process method for your unit call the showParameterPanel method Called whenever there is data for the unit to process public void process throws Exception display the units parameter panel interface showParameterPanel 4 3 2 Pausing Unit Execution Problem 64 You want to pause the execution of your unit programmatically until some event happens Solution Pause the threa
75. ting tool XML is Section 4 2 4 The Unit Wizard is located in Tools New Unit menu When selected this brings up the unit wizard window which has a number of panels that need be com pleted before the skeleton code can be generated In the next sections we look at the options on each of these panels Unit Panel The first panel in the Unit Wizard shown in Figure 4 3 has a number of fields allowing basic information about the unit to be specified This information is as follows Unit Name The name of the Java class that is generated and also the default name for the tool tasks representing this unit When a tool task is renamed 57 this does not change the name of the underlying Java unit Unit Package The package of the Java class that is generated and also the default package for the tool representing this unit When a tool is moved to a different package this does not change the package of the underlying Java unit Tool Box Path The base toolbox directory where the unit code will be gener ated see Section 4 2 1 Author The name s of the unit author s PopUp Description A brief pop up description of the units function This description is displayed when the mouse of hovered over the unit Date The date of creation Help File The html file which is displayed when the user requests help on this unit A skeleton help file is generated at the same time as the unit code Include Copyright Whether the defaul
76. to be associated with each of the unit parameters as specified in Sec tion 4 2 3 A number of standard components are available including TextField CheckBox Choice ScrollBar and File Chooser a TextField with Browse button The Preview GUI button at the bottom of this panel allows the defined interface to be previewed Select Next to accept the values specified in the GUI panel Note that these values can be changed later either in the wizard or in the generated code Final Panel The final panel the Unit Wizard shown in Figure 4 7 shows information on the unit and which files and directories will be created when the unit code is generated The Generate Tool Placeholder option indicates whether a dummy tool in the tool tree representing the unit will be created Once the process method has been implemented right clicking on this dummy tool and selecting Compile will compile the actual tool Select Finish to generate the tool specified in the Unit Wizard The Java source files for the unit html help and parameter panel if specified will be created in the specified toolbox 62 i Compile Unit Generate Tool XML UtName myuet e Unit Package UserGuide kad ToolBox Ciprojecttcoboxes Vi Compile Source Compiler Ci2sck1 42 O7binjavecexe we Classpath C orojecttrianaiclasses C wrojecttrianalibigattemisec jar C ord Arguments v Generate Tool XML Tool Name StingGen Too
77. ult C output ed Processing 3 Script CI Stream C String C Timer C WebServices File vob 3 Demos O TA Fak Figure 3 10 Example GAT workflow 3 4 1 Example GAT Worfklow In Figure reffig gatexample we show an simple example workflow for running a Grid job and transferring files to from thatjob This example workflow involves the following steps e Input generated by StringGen is written to the file InFile see www gridlab org 42 e InFile is pre staged at the location where MyJob is to be run e MyJob is run e OutFile is post staged from the location where MyJob was run e OutFile is read and the output is viewed in String Viewer The job MyJob run in this example could be any command line application and the input output data InFile OutFile can be any type of data For example MyJob could be a heavyweight numerical solver InFile the parameter file spec ifying the parameters of the solver and OutFile the results from the solver Courtesy of using the GridLab GAT this example workflow is the same regard less of whether MyJob is executed on the local machine or a remote grid resource such as a super computer We discuss submitting jobs to grid resources further in Section 3 4 3 3 4 2 GAT Configuration The architecture of the GridLab Gat allows different adaptors to be plugged in for job submission file transfer and depending on the binding you intend to
78. unctions of all the Triana tools via find tools command and other tutorials to get started with Triana Table 2 3 Menu Commands Some of the commands have images which indicate that they can be accessed 10 from the tool bar and short cut keys which can be accessed anywhere Many of the commands available from the menu can be also called with the help of popup menus directly from the main Triana Window see section 2 2 3 The Tool Bars The main toolbar contains buttons with images hovering the mouse over a tool bar item will display its function The buttons are grouped by functionality and are outlined in table 2 4 looking left to right and top to bottom Group Description File group New Open Save Save As these buttons work with taskgraphs to enable work to be saved to file and opened again Edit group Copy Cut Paste Select All Delete these buttons enable editing of tools in a taskgraph Help group Find Print Options Help these buttons enable help searching screen shot printing options and help functions Run group Run Run Recorded Stop Reset Flush these buttons enable the execution and halting of the front most Triana Main Window Task group Show Properties Group Ungroup Show properties displays the parameter panel user interface for the tool in the main Triana window group and ungroup combine all selected tools into a compound tool and back again Zoom group Zoom I
79. 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 50 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 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
80. 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 2 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 port 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 31 Web Service Config Basic Advanced HTTP Port 4802 UDDI Repositories xmethods Remove Figure 3 2 Web Service Configuration Dialog 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 requir
81. ute Gre Distribute Group NULL Ag xsd_string H SubString xsd_string1 Figure 3 8 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 38 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 subsection being distributed to ensure the correct standard type is used as illustrated in Figure 3 8 These tools can be found in the Common WebServices toolbox 3 3 P2PS P2PS Peer to Peer Simplified is a lightweight peer to peer infrastructure for dynamic service discovery and pipe based communication As alongside web services P2PS is one of the bindings to the GAP Interface see Section 3 1 it can be used within Triana to discovery and communicate with remote services It can also be used to dynamically deploy Trian

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