Generic Kepler Actors – USER MANUAL The SPA Actors
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1. curvature algorithm Retums degreeEnvelope points within the lat long bounding an ESRI ascii grid file FileReader box from Utep gravity table DatabaseQuery Interpolate gravityGrid Jinn Expression OpenDBConnection Extracting gravity points from Utep gravily database and interpolating them on the gna A C Maaglating betwen itd coordine systems lt using minimum curvature aigon ProjMet2Dets _ UtepGravityOB ascii grid ROADNet Actors The ROADNet project http roadnet ucsd edu involves the creation of a universal network to carry multidomain sensor data from the field to the lab where it can be easily archived and easily manipulated by scientists The infrastructure of the ROADNet project uses a package called Antelope developed by Boulder Real Time Technologies http www brtt com that provides relational databases via a library called Datascope as well as network data concentrators called Orbs object ring buffers An ORB in the ROADN et sense is completely distinct from an ORB in the CORBA sense Antelope ORBs act as sources and sinks for real time data such as waveforms and events Some actors have been created to allow Kepler to participate in systems based on Antelope Currently there are just a few actors for accessing Antelope ORBs In the future we will have actors to access Datascope databases as well but first we need to invent the mechanism for accessing them r2. to read both ascii and binary file formats BinaryFileReader output tngger gt ME cr Figure21 The GUI for the BinaryFileReader actor Inputs trigger unknown a trigger to invoke the actor Outputs Output byte endOfFile Boolean Parameters FileOrURL FileParameter BinaryFileWriter Writes a sequence of byte arrays into a file and eventually outputs the file path The actor is capable of writing both ascii and binary contents BinaryFile Writer mot AB pene Figure22 The GUI for the BinaryFileWriter actor Inputs input byte Outputs filePath string Parameters FileOrURL FileParameter Database Query The DatabaseQuery actor takes as input a database connection reference an SQL query and a result type parameter indication of the query result type XML record string or noMetadata outputs columns with no attributes information and the broadcast rate whether to output the complete result set as a single token or as a sequence of tokens each row individually DatahbaseQuery result query Figure23 The GUI for the DatabaseQuery actor Inputs dbcon DBConnectionType query string Outputs result XML string record string noMetadata Parameters OutputType choice outputEachRowSeparately boolean OpenDBConnection A database connection actor Receives database connection information from the user either by selecting a connection link from a database driver repository or by providing th
3. C Program Files Internet Explorer IEXPLORE EXE command lt infile gt outfile e g SHOME myprog lt inputFile in gt outputFile out command gt outfile e g C cygwin bin dir exe gt dirTemp txt command lt infile e g usr local bin myprog lt inputFile txt command arg1 argn gt outfile e g C cygwin bin perl exe c project kepler test workflows example pl gt c project kepler test workflows example out command arg argn e g usr bin perl HOME perl_code example p1 This actor will be extended to allow for the following commands command arg argn lt infile gt outfile command command 2 This type of commands need to be able to give the output of all the commands instead of only the last one Currently only the output of the last command is broadcasted A parameter to switch this on and off will be added Email Given the configuration parameters for the host SMTP server to and from addressed the Email actor sends the data that is linked to its messageBody multi port see Figure4 as an output notification email from Kepler Email messagebody ai Figure4 The GUI for the Email actor An example usage of the Email actor can be found at KEPLER workflows test emailTest xml FileFetcher Given a Globus authentication certificate and a separated list see Figure5 of the full paths of files the FileFetcher actor copies the files to the localhost destination direc
4. Generic Kepler Actors USER MANUAL Please contact the author s for the usage of the domain specific actors when necessary The Kepler actors folder is found under the Actor Library Currently there is a folder for each individual or project effort Below is a description of the generic actors categorized by the folder names The SPA Actors BrowserUI Given a file path or URL including a CGI based form this actor can be used for injecting user control and input It can also be used for efficient output of legacy applications anywhere in a workflow via the user s local web browser The BrowserUI actor uses the default browser in the user s computer Browserl amiCuiput hleaOQrRe l name i B ROWS E R value Figurel The GUI for the BrowserUI actor When not configured as a result of the CGI form execution the actor just outputs the name value pairs in XML format and as separate arrays The actor can be configured using the configuration interface to allow for automatic CGI form generation The configuration is made through a text file that imply specifies the name and type of the output ports that the user wants to configure the actor for Please refer to BrowserUIConfigureTest xml under KEPLER workflows test for more information on the configuration of this actor Command Line Given a command string and optionally one or few of arguments switches input and output files the CommandLine actor generates a command a
5. TTransformer and CommandLine components of Kepler and combines them with some domain specific knowledge using XSL scripts see Figure 19 Please refer to http www sdsc edu altintas ieee_manish_apr30_04 doc for more information on this effort SDF Director PreparelnputFiles 01Files The Computational Chemistry Prototyping Environment PrepareExpenment StanExperiment outfileHandle output Display arguments intileHandle ingger input ile Lis Y Authors Celine Amoreira Kim Baldridge Yohann Potier Wibke Sudholt University of Zurich lkay Altintas Adam Birnbaum Yang Zhao San Diego Supercomputer Center Figure19 Computational Chemistry Prototyping Environment The generic components of the Kepler project are applicable to all scientific domains as well as non scientific application domains Figure20 illustrates an example workflow that utilizes the Globus Grid based components and their usage SDF Director Globus Proxy FileStager RunJobGridClient Cai Globus ExtrCoordsGamessOut QutoutEsracter Results C FileFetcher amp Figure20 An example Grid based workflow Please refer to the test workflows under your Kepler directory for interesting test level applications utilizing these actors The GEON Actors BinaryFileReader Reads a file or a URL and outputs its content as a sequence of byte arrays The actor extends the Ptolemy FileReader and can be used
6. bDetautResource ertuna Add Remove Restore Defaults Preferences Help Cancel Figure26 SRBConnection parameters SRBQueryMD Queries the SRB metadata from a specific location with user defined conditions The conditions are generated ass follows SRBCreateQueryInterface Creates an html interface for querying the SRB metadata Will be replaced with a jsp page within a Kepler server SRBCreateQueryConditions Creates conditions for querying the SRB metadata from a user xml string conditions returned by the BrowserUI actor Inputs SRBFileSystem object srbFilePath string Collection path to begin querying from conditions string att op val Outputs output string Matching files paths existCode string Exit status of the operation SRBDisconnect Disconnects from the SRB File system once it gets an confirmation that all actors accessing the specified file system have terminated SRBFileSystem 2BDisconnect inggery Figure27 The GUI for the SRBConnect actor SGet Accepts a reference to the SRB files system a local directory and an aray of SRB remote file paths Downloads the SRB files to the local drive Outputs the local file paths and an exit status Inputs SRBFileSystem object filesToGet string Paths to the SRB files to fetch localDir string Where to fetch the files on the local drive Outputs fetchedFiles string Paths to the local location existCode string Exit status o
7. chParam Here are the methods of th F7 parameters for WebService x searchParam A searchSimple A wsdlUrl http xml nig ac jpwsdl Blast wsdl v methodName searchParam ena pe userName Select WSDL file or URL Sa password from the list Ete name nat ino Emse wee ce Figure14 An example instantiation of the WebService actor The WSDL is parsed to get the input output and binding information It dynamically generates ports for each input and output of the operation This customization happens at the configuration time of a model When the actor is fired at run time it gets the binding information and creates a call object to run the model Using this call object it invokes the web service and broadcasts the response to the output ports Figure15 below shows two different instantiation of the actor for the Blast and DDBJ web services provided by the DDBJ Example applications and test can be found under the workflows section of your Kepler directory WebSenice WebSenaice Figure15 The GUI for the WebService actor WebServiceHarvester Kepler provides a Web Service Harvester capability for importing web services from a repository This feature was developed for conveniently plugging in a whole set of possibly related services The web services to import can be searched on a web page or in a UDDI repository Once imported the web services are saved as actors These actors can be reused in different scientific wo
8. d dataset ResidualMapWebSernice AddSubtract BrowserLl miO Envelopa j p p Residualk an create Lert z nama p MohoWebSenic ae z eee BROWSER Palus SOF Director A i MohoDataService_readSelectionDatg radSelectionDataRequm Matrix Add color schema max lat meter subtract to display a map al Modeler Merging between three heterogenous sources of gravity at Extracting gridded Moho E and Sedimentary depths p Gravity fe E eR realon P 7I Moder depths to create a synthetic gravity model observation e lain 9481115471799 SedimentWebService Then comparing the synthetic gravity model with e lonMin 2667923 1142702 fin ster observed gravity model Eventually translating the j SedimentDataServine_readSplectionDatg wadSelectionDataRetum x s laiMax latMin 533330 0 paciai met differnce into a residual map and displaying on a browser lonMax lonMin 533330 0 ee z Ahora env latMinMet latMin lon MinMet lonMin latMasMiei laiMax lonMakMet lonha Efrat Jaeger Dogan Seber and Bertram Ludaescher GEON project latMetToDeg function latMetdouble latMet 180 1 PI radius Using proj ection functions to longMetToDeg function longMetdouble translate lationg coordinates inside observed gravity model latMetToDeg longMet 0 8660254 from meters to degrees radius 6370956 f lat latin latMetToDeg Surfacing the query response using a minimum Querying for lat long elevation
9. d with a registeration query The dataset is registered within the system according to user response Datasets registration model SDF Director url http igeon01 sdsc edu 6060 omi jsp dataset detail jsp id This workflow is used to annotate datasets a0 and register with GEONsearch workbench nediet eitea anklaga Display i DataRegistration_getinformat pans Ji dataset url gt ftpv dotnetsdsc edu mapdata efratlutz MUST SET PASSWORD BEFORE EXECUTING DataRegistration_register Expression BrowserDisplay Arpt p f A regigerRe A f registration form sanhatadata DataRegistration_register Fo Tr id N MUST SET PASSWORD BEFORE EXECUTING formURL file C Projects keplerfib testdata geon shapefile reg form html url SKEPLER Aibitestdata geon shapefile reg form htm Authors Efrat Jaeger Kai Lin and Bertram Ludaescher GEON project Generating datasets on the fly and registering with the GEON workbench PN Director gt This workflow is used to extract gravity lat long poir from a remote Gracie database generate a shapefile dataset and register Nuthin the GEON workbenth z registerDapaset Booleanswitch CreateDataset Te MUST SET REGISTRATION SERVICE MUST SBTUTEP GRAVITY DATABASE wee t PASSWORD PRIOR TO EXECUTION y PASSWORD PRIOR TO EXECUTION Rie Author f Efyat Jaeger Kai Lin Ashraf Memon Ghoulam Memon gnd Bertram L
10. e database URL user name and password The actor returns a reference to the database connection wrapped as a database connection token The connection can then be propagated to all actors accessing the specified database QpenDBConnection Figure24 The GUI for the DatabaseConnect actor Outputs dbcon DBConnectionType Parameters driverName string databaseURL string username string password string SRBAddMD Adds user defined metadata to an SRB dataset or collection Accepts a reference to the SRB files system an SRB remote file directory path and a list of attribute value pairs Inputs SRBFileSystem object srbFilePath string conditions string att val Outputs existCode string Exit status of the operation SRBConnect Connects to the SRB and returns a reference to the SRB file system The user needs to specify the following connection parameters srbHost srbPort srbUserName srbPasswd srbHomeCollection srbMdasDomainHome and srbDefaultResource The connection reference can then be propagated to all actors accessing the SRB workspace This actor will create a different connection object to each connected channel to allow paralel operations SRAConnect SRBFileSystem Figure25 The GUI for the SRBConnect actor Edit parameters for SRBConnect x oo 2 stbHost lnpsdscetu erbPort Bear srbUserhame ser srbPass wed asswa srbHometolection Jnomeusersdsc srbhidasDomainHome Beses sr
11. e remote location existCode string Exit status of the operation SRBAddMD Adds user defined metadata to an SRB data collection Accepts a reference to the SRB files system an SRB remote file directory path and a list of attribute value pairs Inputs SRBFileSystem object srbFilePath string conditions string att val Outputs existCode string Exit status of the operation SRBReader Accepts a reference to the SRB files system and a file name reads the file from the SRB and outputs its content as a sequence of bytes arrays SRBReader SRBFilesystem output SRE d MF Figure28 The GUI for the SRBReader actor Inputs SRBFileSystem object SRBFileName string Outputs output byte SRB Writer Accepts a reference to the SRB files system an SRB remote file name and a sequence of bytes array as input The SRBWriter actor writes the byte arrays to the remote file on the SRB and sends a trigger once it is done ORBWriter SRBFilesystem input ingger SbFileaName Figure29 The GUI for the SRBWriter actor Inputs SRBFileSystem object Input byte SRBFileName string Outputs trigger boolean LoggingActor This actor records workflow execution results from desired actors Its input is type polymorphic it accepts output token of anytype from its connected ports The actor logs the executed workflow The workflow description can be either moml or relational For each token consumed the actor record
12. emotely For an essay describing ORBs in abstract but technical terms see http splorg org people tobin kb orb orb html OrbWaveformSource This actor connects to an ORB and requests waveform packets with sourcenames matching a configurable pattern The packets are unstuffed into waveform data and the samples from this waveform data are send to the actor s output port as integer tokens Multiplexed packets which contain more than one channel of waveform data are demultiplexed onto the corresponding channels of the connected Ptolemy relation Use the multiplexor actor to access a specific channel Inputs none Outputs output integer the actual sample values times double the timestamps for each sample value bugs waveform data is more or less meaningless before it is adjusted according to the calibration curve of the instrument that generated it There is currently no mechanism to do this although it is a high priority to implement one demos see OrbModel xml for a live demonstration OrbWaveformSink This actor accepts waveform samples on its input port These are buffered until enough samples to form a packet are available with the number of samples per packet a settable parameter Then the samples are packed up into an OrbPacket and sent to an ORB inputs input integer the actual sample values times double timestamps for each sample outputs none bugs can only write GEN format packets since tha
13. f the operation SRBGetMD Returns the metadata for an SRB dataset or collection Accepts a reference to the SRB files system and an SRB remote file directory path Will be extended with an option to obtain metadata recursively Inputs SRBFileSystem object srbFilePath string Outputs Output string The metadata existCode string Exit status of the operation SGetPhysicalLocation Returns the physical location of a logical SRB path This remote location cannot be accessed through windows Inputs SRBFileSystem object logicalPath string Logical path to SRB file Outputs physicalPath string Paths to the local location existCode string Exit status of the operation SProxy Executes a proxy command Currently supported command list directory copy move remove replicate create directory remove directory change mode The actor accepts a reference to the SRB files system and a desired command with its input ports Outputs the command result along with an exit status Commands description List directory Lists a remote directory content Inputs path string Remote paths to list Output listedFiles string Arrays of the contained files paths exitCode string Option outputEachFileSeparately Whether to broadcast each file path sepearately or the whole list at once Copy Move Copys or moves files to a new path Returns the new file paths recursively copies mo
14. ge formats or network protocols are used to communicate More information on WSDL and realted standard can be found at http www w3 org TR wsdl Edit parameters for WebService X Q weed http Jxml nig ac jp AvsdlDDB wy scl methodMame qetMLEntry Userhdame CT password DO O has Trigger T Add Remove Restore Defaults Preferences Help Cancel Figure13 The parameters for specialization of the WebService actor The user can instantiate the generic web service actor by providing the WSDL URL and choosing the desired web service operation The actor then automatically specializes itself and adds ports with the inputs and outputs as described by the WSDL The so instantiated actor acts as a proxy for the web service being executed and links to the other actors through its ports Kepler Grid enabled scientific workflows Ke pler Welcome to the KEPLER Ptolemy based workflow tool You can select from one of the E S a lol x File Yiew Edit Graph Debug Help Z z Bl Z gt 1 O gt m aoln Ol F Pause CT StringConcat Blast web service of DDBJ C stringConst VEDOEMICE UserinteractiveShell 0 WebService WebServiceUsingy C WSHarvester GEON amp di WebSenice 4 y H D GIs FOR THE GEOSCIENCES HJ web services v o sinks Commut Ptolemy I HHI io Fa fi 5 Operation name display con uration Double click and a configure Blast_sear
15. ice DatabaseQuery smlResult getMapimageForxXMLStn pgeForXMLStringWithEnvelops MUST SET DB PASSWORD PRIOR TOEXECUTION Envelope Lat Long bounding box xmin 125 361 ymin 30 09 xmax 115 523 ymax 4 Browserul xmiOutput hame Remove begin and end tags from the element string StringLength Extract the array s xmitoken elements and translate them into strings Const Accepts xmlToken and xpath expression tag Lert and returns an array of iao StringIndexC xmlToken elements tll Ps The ExtractURL subworkflows demonstrates components based programming It uses actors for string manipulation The XML string is first translated into an XMLToken Than an XPath actor is used to extract the desired tag element here the value tag hold the image URL The XPath actors returns an array of XMLTokens thus and ArrayToElements actor is used to extract each token The tokens are translated into strings and the the begin and end tags are removed to return the image URL Datasets Registration Model The following workflow is used to register annotated datasets within the GEON workbench It uses the BrowserUI to facilitate user annotation input This annotation is translated into DLESE ADN ADEPT DLESE NASA metadata annotation format A registration web service is used which accepts the dataset URL and the annotation and registers the dataset within the GEON SRB
16. ires for any set of different inputs The details of this workflow can be reached at http kbi sdsc edu Sci DAC SDM piw specification ppt The workflow can be reached and executed from KEPLER workflows bio PIW xml Another domain that utilized the Kepler SPA actors is computational chemistry The goal of this effort is to develop workflow tools specific to computational chemistry Due to the current explosion of the corresponding experimental data there is a huge need for computational models which combine various scientific methods system sizes and time scales on one hand and allow all this to be done in a high throughput manner on the other hand However researchers in different fields often face the same problems Their calculations need considerable computing power that fortunately nowadays can be provided by supercomputers and or clusters which although may need to be accessed remotely or via a grid making connectivity and bookkeeping pretentious The application programs applied are typically developed by groups of scientists over many years and are highly specific and optimized but difficult to adapt Each program nearly always has its own proprietary input and output formats often mixing data and keywords making communication between different application codes difficult and ineffective As a first example of this type of workflows we have developed the Nimrod G based Gamess execution workflow This workflow utilizes the XSL
17. logist to integrate State Geologic Maps using rock and geologic age ontologies This model demonstrates the use of distributed processes within a workflow The details of this workflow can be reached from the SDSIC presentation at http kbi sdsc edu Sci DAC SDM SDSIC Integrated ppt eae Geological Map Information Integration Workflow A subworkflow to map the output schema of the ontology service to the input schema of the query service Java based transformer to generate the expressions for different states CreateExpressionFromQuery UtahQuernExpresson DataMapper OntologyData_rewriteQuery SOT isi _ BA ZONBUIUCTYE XDE SS OF 8 C seen NevadaQueryExpresgon m The client request for m generating integrated This service handles semantic RewrittenQuery Pee a a t _ map of geological discrepancies across source ear formationsin XML format datasets resolves a standard HE a geologic concept to the specifies ImageAssemblyRequest concept at the dataset bah ot _ a t BrowserDisplay imageAssemblyService_ execute ma i epresent a combinatidn Accepts the query for alecting ents image files o atial data and retums the URL ate files This web to the result of the query selection h t f of ImageQueryServiice_getExtract Utah IdahoDisplay op weary maha additional mapping UtahQueryExpression of producing pap demand as ia or files that can e client i CreateReques
18. nd executes it using the java Runtime class CommandLine arguments oulhileHandle outpul inhlaHandale exitlode Figure2 The GUI for the CommandLine actor As illustrated in Figurel the CommandLine actor has the following ports arguments Input Arguments are independent values or references passed to a function command or program by the caller The arguments can be basic string constants or can be passed into the port from other actors They can involve the command switches that are attached to the argument values They are listed in the order they were attached to the port when the command is being generated infileHandle Input This port is used if the file accepts an input file instead of a list of arguments trigger Input This is an optional port that is useful if the execution of a command should be after the successful execution of another actor The output of the previous actor should be linked to the trigger port of the depending actor for scheduling purposes It can be hidden if not used by turning off the hasTrigger radio button by selecting the configure box outfileHandle Output An output file can be used to store the results of the execution ibstead of the standard output The handle is the full path of the output file that is browsed given by the output file parameter that can be changed updated by double clicking on the actor or selecting configure right click context menu output Output The
19. put output RecordToken bugs 1 because this actor translates an arbitrary object into a record it cannot provide any information to the Ptolemy type system about what fields will be present in the resulting records This makes its intended use with RecordDisassembler impossible 2 currently all fields in the generated records contain ObjectTokens However it would make sense to turn java lang String s into StringTokens and similar for all of Java s simple types int double etc 3 As implemented it will probably die if it encounteres a primitive type eg double instead of Double 4 It is almost completely untested
20. ridFTP actor can be thought of as a combination of the FileStager and the FileFetcher actors without having to copy to from localhost The actor has a choice style selection of available hosts for ease of use If you would like to set a new source or destination hostname please click on the Preferences button on the Configure window for the actor and select Line as the style for the parameter you would like to edit type into Edit parameters for GridFTPUpdated f X s sourceHostnarme griddle adac edu Full path to source file Browse DestinationHosthame griddle sdec edu kd Full path to destination tile FRUE Add Remove Restore Defaults Preferences Help Cancel Figure9 The configuration parameters for the GridFTP based file transfer actor The GridFTP actor is under a major revision The documentation for the actor will be finalized after the revision is complete Pause This actor is used for putting an expected pause in the workflow specification to allow for execution to pause until the outputs until that time are reviewed and the workflow is paused This actor is mainly useful for long running jobs gt gt Figure10 The GUI for the Pause Run JobGridClient Given a Globus grid proxy certificate a list of input files passed from previous actors and a parameter specified host and program information this actor generates the RSL string for a Globus job It then executes the job and o
21. rkflows The WebService actor is currently under rebuild More information on the new features and usage of the actor will be given in this manual after the finalization of this actor Please refer to the WebServiceHarvesterTest xml under your EPLER workflows test directory for an example usage of the actor XSLTTrans former Given an xml stream as input XSLTTransformer is used for for linking almost but not quite fitting output port and input port data formats together The actor produces an html stream that can be viewed or queried using the BrowserUI actor see Figure Aol Actor amilin htmlOut ASLT Figurel6 The GUI for XSLTTransformer The configuration window for the XSLTTransformer actor can be viewed by double clicking on the actor or by selecting Configure from the right click context menu The window displays a GUI for browsing the XSL script which will be used to perform the transformation Edit parameters for XSLTActor X a5 2 XSLT File Path E Add Remove Restore Defaults Preferences Help Cancel Figure17 The configuration of the XSL path parameter Scientific Workflow Example The current web service components of the Kepler SPA system have been used in various scientific domains including molecular biology geosciences chemistry and ecology One example is the Geological Map Information Integration Workflow depicted in Figure18 This workflow was designed by a geo
22. s its producer the time stamp and its content The user may select to record the information into a file or forward it to the next actor Logging Actor CI Figure30 The GUI for the Logging actor Inputs input polymorphic Outputs output string Parameters workflow description type MoML or Relational operation Forward information or save to a file fileName The file name to which to write Scientific Workflow Example Generating Dataset on the Fly The following workflow utilizes Kepler s generic actors It connects to a remote database Gravity DB at UTEP and queries for gravity points returned in XML format It then uses a web service for generating a dataset shapefile from the queried points Prior to invoking the web service an XSLT actor is used to translate the query response to the web service expected XML format The web service returns an XML string that contains URLs to the created shapefile and a static image of the dataset which is displayed using a web browser UTEPdatabaseUsername geon OpenDBConnection UTEPdatabasePassword query Select latdd Jondd completeba elevation freeair fram GRAVITY TABLE where latdd between latMin and latMax and londd between longMin and longMax latMin 34 9 longMin 120 latMax 35 longMax 179 the fly rkflow is used to extract gravity lat long point from a remote Hatabase and generate shapefiles using a web serv
23. standard output of the command Broadcasts only if no outfile is selected exitcode Output A true false output that shows if the command was executed successfully All the ports of the CommandLine actor are optional depending on the usage of the actor Edit parameters for CommandLine x T command e Please type your command here OUT pUtF ile BOE outpUtLineByLine has Trigger B Add Remove Restore Defaults Preferences Help Cancel Figure3 The parameters for the CommandLine actor The parameters of the CommandLine actor see Figure2 are also used for generating the command as well as formatting the output and available ports Command The main part of the command that all the arguments and infile are attached to The full path to the command should be specified even if the command is in the PATH environment variable OutputFile Used for browsing typing the path of the output file that will be used instead of the standard output The path of the selected file will be output from the outfileHandle output port of the actor outputLineByLine Formats the standard output of the actor if no outfile is selected When selected the output output port will broadcast one token for each line in the standard output hasTrigger Activates the trigger input port of the actor when selected In the current version of the actor the following command types are supported command e g
24. t s all that com brtt antelope supports at the moment OrbPacketObjectSource This actor connects to an ORB and receives all packets corresponding to the given sourcename specification The Java Antelope interface provides these packets as OrbPacket objects and this actor provides these OrbPacket objects directly to Ptolemy wrapped up in ObjectTokens Additionally this actor will accept OrbPacket objects at its input port again wrapped in ObjectTokens and these will be sent to the Orb inputs input ObjectToken OrbPacket orb packets to be sent to the orbserver outputs output ObjectToken OrbPacket orb packets reaped from the orbserver bugs should be renamed since it s both a source and a sink ObjectToRecord ObjectToken provides a convenient mechanism for transporting arbitrary Java objects in Ptolemy However it is inconvenient to manipulate these objects in any way since they are essentially opaque objects from the point of view of Ptolemy However Java objects are very similar in structure to Ptolemy s RecordTokens both are essentially mappings between names and values Given an ObjectToken this actor constructs a RecordToken containing a field for every field in the object contained in the ObjectToken with the record field containing an ObjectToken wrapping the object pointed to by the corresponding field in the object This is accomplished using Java s introspection mechanism inputs input ObjectToken Object out
25. tFromResult i request PataMapper composite actor A Java based transformer to i a k a sub workflow i map multiple output schemas of the query service to the input schema of the assembly svice Figure18 Geological Map Information Integration Workflow The application workflows show how to employ Kepler s web service components to compose distributed scientific workflows Since web services are often not designed to fit data transformations between the outputs of previous steps and inputs of subsequent steps are usually required For this purpose specialized data transformation actors e g XSLT XQuery have been implemented User interaction and workflow output are performed via a browser actor Please open to KEPLER workflows geo geonMapHierarchical xml under Kepler to execute this workflow Another example of the Kepler SPA powered workflows is the Promoter Identification Workflow which had been a running application in different forms for 3 years It is a production workflow being used by a biologist to identify likely transcription factor binding sites in a series of genes The process of identifying these sites in a single gene involves a series of tasks such that performing the same series manually for each of a few dozen genes can be quite a repetitive and time consuming process The PIW workflow solves that problem by allowing the biologist to create the workflow once and run it as many times as he or she des
26. tory specifed by a configuration parameter see Figure6 FileFeteher cearntcate ry faichedFiles filesT iel FETCHER Figure5 The GUI for the FileFetcher actor The actor outputs a delimited list of full paths of the fetched files An example application for this actor can be found at KEPLER workflows test FileFetcherTest xml Edit parameters for FileFetcher X c 4 SourceHostname griddle dsc edu DestinationDirectoryPath Add Remove Restore Defaults Preferences Help Cancel Figure6 The configuration parameters for the FileFetcher FileStager Given a Globus authentication certificate and a separated list see Figure7 of the full paths of local files the GridFTP based FileStager actor copies the given files from their localhost paths to a remote destination directory specified by a configuration parameter see Figure8 Filestager cenificate dagedFiles filesT oF utia a Figure7 The GUI for the FileStager actor Edit parameters for FileStager X T DestinstionHostname griddle sdec edu DestinationDirectoryPath Add Remove Restore Defaults Preferences Help Cancel Figure8 The configuration parameters for the FileStager GridF TP Given a Globus grid proxy certificate and a set of configuration parameters see Figure9 this actor copies a file from any remote Globus source or local directory to any remote Globus host or local directory The G
27. udaescher GEON project Generating datasets on the fly SDF Director This workflow is used to extract gravity lat long point from a remote oracle database and generate shapefiles using a web service layer PeO XSLTActor QueryingGravityOB bgLay rs WebSenice AIT ageForXMLStringWithEnvelops getMapimageForXMLStringWithd Parameters for querying UTEP gravity DB to generate the dataset UTEPdatabaseUsername geon UTEPdatabasePassword query select latdd londd completeba elevation freeair from GRAVITY_TABLE where latdd between latMin and latMax Wowra and londd between longMin and longMax ExtractTags xmiOutput gister water es 3 SQR name b Bio fecal eronsen pi e longMin 120 longMax 119 Display ea ShpURE nvelope ExtractElementContent min 125 361 ymin 30 09 x P Extracting both the image and shapefile URLs from the web service xml response Converting the Extract URL composite actor into a class and using instances of tt instanceOfEmtractElementContent_valueTag Expression display StringToXML instanceOfExtractElementContent_shpurlTag shpURL Gravity Modeling Design Workflow The following workflow is used to compare between synthetic and observed gravity models see images below for more details Gravity Modeling Design Workflow ee 1h loge ascii gi
28. utputs the results and separated list of the output file paths see Figures 11 amp 12 RunJobGridClient certificate oulputFiles inputFiles MCE roel Figurel1 The GUI for the RunJobGridClient Edit parameters for RunJobGridClient l x 2 Globushost griddle sdsc edu Program nare CN Program version CT GIUEWE NAME Murmber of processors Add Remove Restore Defaults Preferences Help Cancel Figure12 The configuration parameters for the RunJobGridClient StringConst Given a string or a browsed file path this actor outputs a string just once This actor is used mainly in providing constant input to any actor in a workflow WebService The WebService actor as indicated in Figure13 provides the user with a plug in interface to execute any WSDL defined web service Given a URL for the WSDL of a web service and an operation name that is included in the WSDL this actor customizes itself to execute this web service operation WSDL is an XML format for describing network services as a set of endpoints operating on messages containing either document oriented or procedure oriented information The operations and messages are described abstractly and then bound to a concrete network protocol and message format to define an endpoint Related concrete endpoints are combined into abstract endpoints services WSDL is extensible to allow description of endpoints and their messages regardless of what messa
29. ves directories Inputs path string Original remote file paths newPath string Location to copy move Output copiedFiles movedFiles string Arrays of the new file paths Remove Remove directory Removes files directories Non empty directories are recursively removed by remove r Inputs path string Remote file paths Option r recursively removes files forward output an array of the removed files parent directory paths Create directory Creates new directories Returns the new directory path Inputs path string New directories paths Output dirPath Created directories paths Replicate Replicates a file directory to a new resource Inputs path string The files to be replicated newPath string The resource to replicate to Output newResource string The files new resource Change mode Changes the permissions of a file or a directory Inputs path string Files paths permission string userName string To grant permission to mdasDomain string The metadata domain Output exitPath string The files paths SPut Accepts a reference to the SRB files system an SRB remote location and an aray of local file paths Uploads the local files to the SRB location Outputs the remote file paths and an exit status Inputs SRBFileSystem object filesToPut string Paths to the files to upload remoteDir string Where to upload the files Outputs uploadedFiles string Paths to th
30. workspace The web service return a handle id to the registered dataset Using the returned id it is possible to validate the registration process either by quering a getInformation service which returns the metadata for the dataset or by viewing its path URL on a web browser to display the dataset information The registered dataset can later be searched using the GEONSsearch mechanism and used within the GEON workbench Datasets registration model Joven irector e url http fgeon01 sdsc edu 6060 omi jsp dataset detail jsp id This workflow is used to annotate datasets a and register with GEONsearch workbench Bete pee ae Sete ate Display DataRegistration getinformatjog getinto dataset url A BEFORE EXECUTING DataRegistration_register a j rows e isp ay BrowserU Expression registration form URL Ni a E DataRegistration_register ragigerte NI gt formURL pelleeue 6 MUST SET PASSWORD BEFORE EXECUTING formURL file C Projects keplerilibites tdata geon shapefile reg form html Authors un SKEPLERAib ites tdata geon shapefile reg fonm hitmi Efrat Jaeger Kai Lin and Bertram Ludaescher GEON project Registrating Datasets Generated on the Fly The following workflow is a combination of the above two models It allows user triggered registration of datasets generated on the fly The dataset image is displayed on a web browser using the BrowserUI actor and the user is prompte
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