NetKarma Cytoscape Visualization Plug-In Manual
Contents
1. Wasterer decir LinkOut b E fe SN e 0 ChmeNeghbon 000 Play Merwe Wtiriggeredih MWersDerieedErom E SIL Mode Abate Bromenr Edge Attribute Browser Network Attribute Browser Waseme tn Cytaecape 200 R ight clie 4 drag te ZOOM Middle click drag 15 PAN Figure 6 8 1 4 Right click on node E the neighbors of the node selected in step 3 F e Edit View Select ugins Help Tools eua aaa ua EU Karma T T E Instructions Drag and Drope A node shape onto ihe network view e An edge shape onis the source node then click nn the target nnde Double click m To nde neces and edges specified in SF feemar CTRL click m On empty space ip create anode a On a node to begin an Ls S LLL f node Abbe Brown Foe Attribute Browser Network Attribusr Browser Wacome t Cyteseape 2 100 Right click drag te ZOOM Middie click drag to PAN Figure 6 8 1 5 Cluster nodes Repeat step 4 until you got an abstract graph showing only the smaller set of nodes you wish to visualize 21 o Cytascapre Desktop Mru Sess 1 S2bH QQ0 a Eg Karma Seadh eter Mapper Etor Tnstructinns M B Node Atile Brass doe Ate Browser Netwerk Abtribute Browser Wacom 1n Cytsecape 2 I0 Right click drag to 200W Middie click drag tn PAN Figure 6 8 1 6 Create abstract graph 6 8 2 Navigate between graph and sub graphs Once you have create2. jm Y 7 3 Cytosrape Desktop New Session T Edit View Select Layout Plugins Help Tools aaa Oonk Karma He E ia metere Les peng Desktop Graph oprni i Network pe Editor ajej Instructions Drag and Drnp o node shape ono the nebwork view amp Aa edge shape ono the aures nade then clei nn the inrger rede Double click To add nodes and edges specihed in SF format CTRL click n dee space to cree P e eem edge and specify the Data Panel BOKI ig Il ede Attribute Browser Edo6 Xttribute browser Network Ati Aaght click crag be DSM Middla click drag be PAN Figure 6 8 3 1 A provenance graph before applying Compress Process 23 JE Cytascape Desktop New Session NN gins Help Tools File Edit View Select Layout PI BH Aana E ac metere SD ger Karma sc I1 aph epmurnedilsed xrnd rented p e space to create Visual Mapping Bypass vim On anode to begn an Nested Network Y edge and specify the Web Services Pl source rode Than chek es is red on the largat node lo Hide lade finish the edge LinkOut k h DER FTO History Lead Detail Inte ves err E Compress Processes f Compress Artdacts Expert OPM wasContrellediy Cluster Neyhbors Play Movie wersDeriveedErom pi s Mowe Attribute Browser Edge Attribute Browser Hebwork Attribute Browser Walsoma bo Gyinscage 2 iL D F ght clic
3. File Ede View Select Layout Plugins Help Took ILE LLEILE Karma B Tg Network vutapper Editor Filters e HANGE wi Anode shape ento the network views m An edge shape onto the source node then click on the target node Double click To 800 nodes and edges specified in SF format On empty apace fo create node On a node to begin an edge and pecify the source node Then click evi the Target node ta Tirisn re enge Specily Identifier io Cysacape 260 Right click dr ie ZOOM AR jo FAH Figure 6 7 2 The hierarchy graph after sorting 6 8 Creating an abstract view For some experiments the complexity of the provenance relationships can result in very complicated graphs This section introduces features of the NetKarma visualization plug in that can be sued to abstract out some of this complexity to allow you to visualize specific aspects of the provenance graph 6 8 1 Clustering neighbor nodes To deal with graphs with a large number of artifact nodes the NetKarma visualization plug in supports extracting an abstract view by clustering neighboring nodes As an example Figure 6 8 1 1 shows a graph that has a larger number of artifact nodes generated by a small number of process nodes On a node te begin an edge ard specify the Figure 6 8 1 1 A graph with large number of artifact nodes 19 You can creat
4. attribute element is added to the set of process attributes in your configuration file attribute attributeName workflowID attributeName lt importName gt import workflowID importName attribute Then the workflowID attributeName would match the property since workflowID is a substring of the property s URI Since the value element within that property also contains a child element the value of that element urn tool gush peng virtual machine 12345 1296341651 would be added as an annotation for that node in the visualization and the label for that annotation would be importWorkflowID Properties for artifact nodes within the provenance graph differ from properties for process nodes in that multiple property values can be contained within a nested block element within a property For artifact nodes in addition to searching for the attributeName in the URI of a property the visualization plug in looks inside the block element of a property to compare the tags for child elements within the block to the attributeNames specified for artifact attributes in the configuration file As an example if your provenance graph contains the following property element for an artifact node v I property uri urn tool gush peng virtual machine 15555 1292253699 Block_3 artifact content gt lt v1 value gt lt content gt dataBlocks xmlns ns http ww w dataandsearch org karma 2010 08 7 block object
5. artir a __ _ ip paeen SOOT a On empty apace Do create anode d On a node lo begin an edge nnd speeify te E BONE 8 m node atribute grosser Ede Rute oer Network rule Bra PAN eligi ie DOOM Middle aligi arag bo Figure 6 3 2 Double click on edge 6 4 Play movie If you right click on any node you can choose to play a movie displaying the provenance for the whole graph based on the order of the timestep or time attributes of the nodes 15 Ed Cyt 3 TE View Layout yout Plugins Help Tools foe on Ie tie reer Cone Ir tructons Orag and Drop T node shape onio the nelvecerk wien m An edge shape onin thie secures nee then chi on the target node Double click E To add nodes and edges specthed in SF format CTRL click E On empty apace bo create Process 17 anode On a node to begin an Visual Mapping Bypass edge nnd speeify te K a sournes node Then thi Nevhed Mebeork en the tanget node to Use Web Services nah me edge Hide Node 5necify Identifier FI LinkOut wasGeneratedby Data Provenance History Load Deta inte empress Processes Patilact empress Arti vers onbicliedBy ic Dg 7 Export OPM Cluster Neighbors Ces if Play M F amer i F tone Set time interval oe ode Attribute Growser Edge Abtribube Browser Hebreork Attribule Browser weisse to Cytmec z amp b e a ag es DOGM Middla alick drag ta PAM Figure
6. jar 4 Configuring the Plug in Properties 4 1 Updating the configuration files to connect NetKarma provenance retrieval and visualization plug ins to NetKarma service The following describes how to configure the provenance retrieval and visualization plug ins and connect them to a running NetKarma service You have two options Axis2 webservice or RabbitMQ messaging system to connect to a NetKarma server and all of the configuration information is stored in the file karmaQueryConfig txt This configuration file is used and managed by both NetKarma provenance retrieval plug in and the visualization plug in The configuration file will be loaded at the startup of either plug in and the configuration settings will be displayed in the configuration panel You can choose which option you want to use in the configuration panel and modify the default configurations You can directly modify the contents of the karmaQueryConfig txt file or make configuration changes through the configuration panel in Cytoscape To set up the configuration for connecting via the Axis2 webservice There is only one property the needs to be set when using the Axis2 server axis2 serviceURL enter the URL to the NetKarma v3 1 2 webservice To set up the configuration for connecting via RabbitMQ messaging system There are several properties that must be set to connect using the RabbtiMQ server messaging username username of RabbitMQ messaging passw
7. the tnnget node to finish the edge p Kum Right alig dreg pa ZOOM cce ab E B BEB es Karma Lt ph npmmnelifirz md Wwa ATIF AU Con onde rro km bac Visual Mapping Bypass Nested Network Use Web Services Hide Mode LinkOut Data Provenance History Load Detail Info Compress Processes Compress Artifacts Expert OPM Cluster Neighbors Play Mowie F v e ere Figure 6 8 3 5 Applying Compress Artifact 25 Saaga alB a Fy 35 Gok Karma gt B RISE aon empty pace bo Cres a node Oa anode lb begin an edge nnd speeiby fe Data Parn esu aligi i DOOM Middle alioi drag bx PAN Figure 6 8 3 6 The provenance graph after applying Compress Artifact l Wieloome to Cyinscare 23 0 26
8. 6 4 1 Display provenance as a movie You can also configure the time interval milliseconds between the appearances of two nodes in the movie WIE rie Edit View Select Layout Plugins Help Tools l susaus TESTE Karma TB Sy Figure 6 4 2 Configuring the time interval 6 5 Save as XML To save the provenance graph displayed in Cytoscape as an XML file based on the Open Provenance Model OPM right click on any node and select the menu item Export OPM You will be prompted for the location to save the XML file The graph s structure will be based on the OPM v1 1 Open Provenance Model http openprovenance org 16 Hle EO View Select Layout Phugns Help Took aaraa sansa Karma L amp prm wamaoper E Nebveork We Eile Process 6 ERUPITCTE Karma HB oy wamecper E Hebwork Mass Eds Figure 6 5 2 Choose the location to save the xml file 6 6 Get data provenance history Right clicking on any artifact will display an option for Data Provenance History Selecting that option will display a new graph that includes all of the nodes involved in the generation of the selected artifact This method utilizes a background communication with the NetKarma server 17 eG aagaals Control Panel E Lame s Metwnrk VitMapper Editor 4 p I
9. G sse U SES Mi PE Rbn SEKERES ETNEN sS cR RSV Ee AME 19 6 8 2 Navigate between graph and SUD 2raphs ceccccssecccessecceeececenececeeceeeenceeeescessuecensneeetes 22 6 8 3 Compress ProPBsS ATCIDI OE seiren Doadanc uui dendum bod uM a EM EEG dedaabedtannuaddeaniicblacinbeteeannasts 23 1 Introduction We have developed two plug ins to Cytoscape to visualize and navigate provenance information contained in the NetKarma provenance system The NetKarma provenance retrieval plug in is used to retrieve provenance graphs from a remote NetKarma server to your local machine In the Cytoscape tool this plug in is run by clicking on the blue Karma icon in the Cytoscape tool bar after the plug in is installed The second plug in is the NetKarma visualization plug in which allows you to visualize and manipulate graphs downloaded using the retrieval plug in The NetKarma visualization plug in is displayed as an orange Geni icon in the Cytoscape toolbar Visualization of provenance data is useful for manipulating very large provenance graphs for displaying different views and for interactivity This can help a user to navigate their experiment information with a mental map of what is going on in the experiment to compare different experiment runs quantitatively and to do model selection with an effective collaboration between the user and the discovery system NetKarma is a standalone system that can be added to existing cyberinfrastructure for p
10. ID urn output stdout objectID objectName stdout objectName lt objectValue gt Hello World object Value object ype BLOCK objectType block lt dataBlocks gt lt content gt lt v1 value gt v property And the ImportAttributes section of your configuration file contains the following artifact attribute definitions attribute attributeName objectID attributeName importName artifactID importName attribute attribute lt attributeName gt objectName lt attributeName gt lt importName gt artifactName lt importName gt lt attribute gt Then your provenance graph would contain two annotations for this node in the visualization an annotation labeled artifactID with the value urn output stdout and an annotation labeled artifactName with the value stdout The configuration file also contains a visualAttributes section that allows you to specify which attributes of the process and artifact nodes should used to label the nodes when visualized The attributes to be used for process nodes and artifact nodes are listed separately within processLabel and artifactLabel elements within the configuration file Each of these elements contains one or more attributeName elements that specify a prioritized list of the attributes to be used to label the nodes As an example if your configuration file contains the following artifactLabel element lt arti
11. NetKarma Provenance Retrieval and Visualization Plug in For Cytoscape User Manual V1 1 0 August 21 2011 NetKarma DATA TO INSIGHT CENTER INDIANA UNIVERSITY Pervasive Technology Institute Copyright 2011 The Trustees of Indiana University This document contains instructions for using the NetKarma provenance retrieval and visualization plug in version 1 1 0 which provides core capability to retrieve provenance information from a NetKarma provenance system and visualize the returned graph NetKarma provenance retrieval and visualization plug in is licensed under Apache License Version 2 0 the License http www apache org licenses LICENSE 2 0 The code is copyrighted and copyright owned by The Trustees of Indiana University NetKarma provenance retrieval and visualization plug in is a product of the Data to Insight Center at Indiana University See http pti iu edu d2i provenance for more information Contents mmr 01066 VLG o NR mem 4 2 Software LIC CNOCTICIOS asa ciosstaecencvorendesnacsdassoatecaiaiverbateneerainep Pales uade aes anaoa aaea aa inona 4 2 1 Do A om 0a 81 1 6 os Loc ene eee E ee eee 4 2 2 DnstalldHorn de pede n6 lS e E essa deett med espcdiesa fs sb ties tad ncM subo bu esed ras ud a E Se ER UNUS 5 SNMP Sogl 5 3 1 Deploying under Mac Lanux U nix OW wiscsiccessacaseaconoieenonscusesnsterstatnnbaneondsnensauessenscaaisesnaseudeseezanenenee 5 3 2 Deploying u
12. an edge nnd aperify the ES H t3 ID He oR source nade Then ckek nn thr wget noir in hnesh th edge Specify Tien amp fler Add on Ed iios i Fie name ts cuta ml open Webwork Fies ol type sl Bee oni Canoni Packed a Nail Add a Nested febres 1 m Node atribute Dosser Edge Altribule Browser Nebwork Attribute Browser Welcome in Cyirezape 2 6 0 Righi nlipk drag in DOGM Miridig nlizk drag in PAM Figure 6 1 3 Select the NetKarma provenance XML file 4 Load the NetKarma provenance graph 12 File Edit View Select Leyout Plugins Help Tools v The sample OPM graph crested for file C Usert peng Desktop Graph_opmamiits cut am i Ce Node Attribute Browser Edge Attribute Browser Network Attribute Browser click drag 10 ZOOM Middle clik drag to PAN Figure 6 1 4 Load the NetKarma provenance graph The initial graph will look like this your graph may differ depending on your experiment s a e Cytoscape Desktop New Section Fie Edit Veew Select Layout Plugins Help Took Saaana s aig Karma FB Node Attribute Browser Edge Attribute Browser Network Attribute Browser g inc MA y 5e PAN Figure 6 1 5 Initial m 6 2 Applying layout algorithms to the NetKarma provenance graph Different layouts for the provenance graph are available from the Cytoscape Layout Cytoscape Layouts menu 13 a Goss eyo Seale Align and Distribut
13. d an abstract view you can navigate between that parent abstract view and the sub graph for any collapsed node 1 Double click on any abstract node will show the view of the collapsed sub graph nn rw 5 22 DnR Ege Karma 0 T 8 Made Atinbute Gromer Edge Abribube Browser Network Attribute Browser Riahi alick drag io ZOG Middig olick drag ip FAM Figure 6 8 2 1 The sub graph 2 You can go back to the parent graph by clicking on the item in the network panel on the left hand side of the screen 22 re Edit View aa Layout Help Tools E CEPIT By rg A cos Karma ia eak Liners peng DeskbopGraph_opmamiiis_ouldaml Mode Alribule Bremer Edge Attribute Browser Hetwork Attribuse Browser Welcome in Cyteicapa 2 10 H ighi click a drag te 200m Middla click drag 15 PAN Figure 6 8 2 2 The parent graph 6 8 3 Compress Process Artifact Right clicking on any node in the graph you will see menu options for Compress Process and Compress Artifact Clicking on Compress Process the Cytoscape visualization plug in will eliminate all of the Process nodes that link to two artifact nodes with the outgoing edge represents the relationship used and the incoming edge represents the relationship wasGeneratedBy The process node will be replaced by a new edge between these two artifact nodes that represents the relationship wasDerivedFrom
14. e Desktop release test 220ml Sellim yFiles F GENIOPMLaycut Cytescapelayouts F Attribute Circle Layout JGraph Layouts Edqe Wrighted Spring Ervbedded Edge Weighted Force Directed BioLayout Spring Embedded Hierarchical Layout Circular Lmycaut inverted Self Organizing Map Layout Group Attributes Layeut Grid Layout Force Directed Layout Degree Sorbed Circle Layout Node Attribute Browser Edge Attribute Brewer Network Browser high g 12004 kaiaia dri 35 PAH Figure 6 2 1 Do hierarchy layout 1 For US if you select the hierarchy layout the graph will appear as shown in Figure 6 2 2 Cl eperera Dei New Sen File Edi Vemw Select Layout Plugins Hes dp Took Node Attribute Browser REESE Browser g in OON Misch deg 15 PAH Figure 6 2 2 Hierarchical layout c of graph 6 3 Navigating the NetKarma provenance graph 1 Double click on any node to see its attributes 14 28828 ap URN eme e L B To add nodes and edges specihed in SF tonne CTRL click E On empty apace bo creme a node On a node lo begin an Figure 6 3 1 Double click on workflow node 2 Double click on any edge to see its attributes File Edit View Select Layout Plugins Help Tools aaaoaesauumEPDEe Karma BS conto Pane Is Network virManper Edtor a Ir tructons Orag and Drop CENE ERIS E To add nodes and edges specified in SF format M dei rename Pec E
15. e an abstract view for this type of graph using the following 5 step process 1 Select the iuit nodes on the lower left side of the graph in Figure 6 8 1 2 A EE Mew Sans jm x File Edit View Select Layout Plus 5 Help Tools eua ea TEO sl Karma MB aa Eu a A node shape onto the neharork view a oAncdge shape cies the soured nada then click nn ihe target node Danalie click To odd nodes and edges specified in ZI format CTRL click amp On empty space to create anode a Cn a node to begin an edge and specify the source rusdi Then click nn the target node tn finish the edge wasenerntedBy Data Panal SOE Right click drag be TOM Middle click drag ia FAH Figure 6 8 1 2 Select processes 2 Click zoom selected region icon from the toolbar highlighted magnifying glass icon the Figure 6 8 1 3 EET Ba Kama T ul bed und Dro Dn node do begin an pige mma specify the soume node Then ciek on the target node t9 Spec Idenster E DE pm O i Process 12 Process 15 Process 17 Process 18 l ghi alick drag in ZOOM Middle olink drag in FAN Figure 6 8 1 3 Zoom into process region 3 Right click on one of the nodes with a large out degree a significant number of edges 20 5 eua aaa ua Bayer Karma LI es api E Lu mel i eub Process 12 Visusl Mapping Bypass Mested Hetan Use Web Services
16. e connection parameters 11 A Cytosrape Tiesktap Mew Sez a aoe a m LE eG Oe sy E ge Karma Control Panel E fg Network vaMapper EI H amp bwork N Ed gt gt Inge an OPH Graph from xmi fie vet umitalion Anes i Rebbe J Axis Config Rabbibmq contig Laer Durst peeved quest Feces 156 5515 hoslperb 5672 virtusibost Data Pant BORE ID enchangename kame hange qena kama uue rnutingke y Karmakey Curent Session nebwork attribuses wil be lost Do vou want te connue CK Cancel Neve Attribute Browser Edge Attribute Browser Network Attribute Browser Viele bo Cyl 2 3 D Rishsi cl ich deas bo IDOM Mishdla click drag bs PAN Figure 6 1 2 Configure the connection to Karma Server 3 Select the NetKarma provenance XML file 3 Cynscape Desi Control Panel Tel Ig Network vaMapper Latta L Instructions Drag and Drape B A node shape oto the nehwerk view m An eige shape ents ther snuree node then skk on the target node Lookin Graph epm xmi d ema B irl D new nut1 ml Bl new out5 xml Double click Bl new dutl Bl bi cutani Bl tn_culz aml Deskten D ts cout ar D ts cout arl m E To 800 nodes and edges specified in Sa cea CTRL rlick S On empty space 1o create anode Dika Panel Ona node io begin
17. e graphs we generally recommend retrieving without annotations since the NetKarma visualization plug in will load the annotations On Demand while navigating the provenance graph Note 2 While retrieving the XML file Cytoscape will appear to be blocked but will continue to work right after the file 1s retrieved successfully Please be patient while waiting for a graph to be downloaded 6 Using the NetKarma Visualization Plug in 6 1 Load the NetKarma provenance XML file 1 Click on the GENI toolbar Uo c E 8000000000 E EJ Q Gi FX ea iga E3 8 en Ies oe Karma um Conal Panel t Hebat Widener je Mebreark Pao GOL Rabbitrmg coalfeg current Sessiondall rsetearkabtribules wil be kak Do yes vean ta continue Ut Linc Figure 6 1 1 Click on the GENI icon in the toolbar Select whether to import the provenance xml with annotations or without annotations When you import provenance without annotations the NetKarma visualization plug in will set up a background connection to the NetKarma server and load both annotations and the registry level information On Demand when you select any node in the provenance graph during navigation the NetKarma visualization will retrieve more information for 1t 2 If you choose to import provenance without annotations you also need to choose which connection method you want to use for the background connection and configure th
18. em administrator for obtaining access 2 2 Installation dependencies The NetKarma provenance retrieval and visualization plug in v1 0 0 has been tested with the following software packages on which it has a dependency These packages will need to be installed before using the visualization plug in 1 Java Development Kit JDK v5 or v6 http java sun com 2 Cytoscape v2 8 1 http www cytoscape org 3 Deploying Plug in Download the plug in package as a zip file from http pti 1u edu d2i provenance_karma 3 1 Deploying under Mac Linux Unix OS 1 Unzip the plug in package unzip NetKarmaVisPlugin zip 2 Copy the jar files into the plug ins directory under Cytoscape_v2 8 1 Install the NetKarma visualization plug in cp NetKarmaVisPlugin KarmaGraph jar cytoscape 2 8 1 plugins Install the NetKarma provenance retrieval plug in cp NetKarmaVisPlugin KarmaRetrieval jar cytoscape 2 8 1 plugins 3 Copy the configuration files into the plug ins directory under Cytoscape_v2 8 1 Create a new directory named config under cytoscape s plugins directory mkdir cytoscape 2 8 1 plugins config Deploy the configuration file for the NetKarma visualization plug in cp NetKarmaVisPlugin config pluginConfig xml cytoscape 2 8 1 plugins config Deploy the configuration file for the NetKarma provenance retrieval plug in cp NetKarmaVisPlugin config karmaQueryConfig txt cytoscape 2 8 1 plugins config 4 After you finish i
19. factLabel gt attributeName objectValue attributeName lt attributeName gt ID lt attributeName gt lt artifactLabel gt Then for each artifact node if it has an objectValue attribute the value of that attribute will be used as the label for that artifact in the visualization If an artifact does not have an objectValue attribute then the ID attribute will be used to label that node 5 Using the NetKarma Provenance Retrieval Plug in 1 Run Cytoscape and click on the Karma icon in the toolbar Ch Cytosrane Desktop Mew Ge eG eu Control Panel t Metveork vieMapper Ei Hebwork Hg Eu E E ig LN De eg geni Karma E e KBrma Server Con aursbon 7 led Axis Config Serve IRL tip melkarma tes Gab greed S080 axi 7 fuer vices Varmaser vice Rabbibmg contig He oe Curent Sessor al rebyrorkfathibes vell be ket Do you mant bo continue Necks Abide Browser Edge AFtribute Browser Neberek Atteib re Brenner Figure 5 1 Click on NetKarma toolbar If you have not already edited the configuration file or wish to use different settings choose the connection method you want to use and configure its connection parameters Choosing Axis2 the Service URL in the Axis2 Config panel needs to be configured choosing Rabbitmq all parameters in the Rabiitmg config panel need to be configured 2 When you are satisfied with your configuration settings click the OK butt
20. k drag 65 ZOOM Middla click 4 drag b PAN File Edit View Plugins Hep Tools CORALE wstDernoedE nom TIT hi click dag bo TOOM Figure 6 8 3 2 Applying Compress Process 0 By oi Karma ede Attribute Browser Middla click drag be PAH Figure 6 8 3 3 The provenance graph after applying Compress Process Clicking on Compress Artifact the Cytoscape visualization plug in will eliminate all of the artifact nodes that link two Process nodes where the outgoing edge represents the relationship wasGeneratedBy and the incoming edge represents the relationship used The artifact will be replaced by a new edge between these two Process nodes that represents the relationship wasTriggeredBy 24 JG Cytoscape D File Edit View Select Layout Plugir To add nodes and edges apecitied in SF format CTRL elicks E On empty apace to create stop New Session d Data Paral E m node attrbute rens Middle ig PAM E an Figure 6 8 3 4 A provenance meN before applying Compress Artifact File Edit View Select Layout Plugins Help p Tools Tm o Drag and Drop 9 made shape ono e To add nodes and edges specihed in SF format CTRL elicks d Cn empty space to Create a node a Coa node lo begin an edge nnd specify te apurar nade Then chi en
21. nder Windows OS save tonccsncevcataainsetemetdedtaneecue whe tentuseceoscancendetanecaneseetandsascajennihetenseectases 6 4 Contouring the Flup m Properties snes ccncacsevestacencnetsencenenducestiacnctemesacteneinannn EERE ERATE ERE 6 4 1 Updating the configuration files to connect NetKarma provenance retrieval and visualization Pae ON E SC e E E E 6 4 2 The configuration file for the NetKarma visualization PlUQ 11 cee cceeeeeeeeeeeteeeeeeeeeeees 7 5 Using the NetKarma Provenance Retrieval Plug in esseeeesseeseseeeeeeeeeeeene nennen nennen nenne 9 6 Using the NetKarma Visualization Plug in eseeseesessseesseeeeeeeeeeeee nennen nnne 11 6 1 Load the NetKarma provenance XML file 00 0 0 eeeeeeeeeeeeeeeeeeeeeeeeeeaaaaaaaaaaaaaaaaaaaaaaaaeeeeeeenes 11 6 2 Applying layout algorithms to the NetKarma provenance graph seen 13 6 3 Navigating the NetKarma provenance graph essseseeeeeeeeeeee enne eene nennen 14 UU MEBUu xui Mc E 15 6 5 sp c Qu c 16 660 Gel dati provenance DIstOfy asoesetecoeme reper Ete diva ut EIE E EEA EUREN Or quiu REEE aa 17 6 7 ba HOLEN RR 18 6 8 OF AU am SERA CU VIO V iocos etc set ec sia tub OMM vai des cbe eget mI EIU PER eres eases 19 6 8 1 Clusterime neighbor THOGXGBS i destiss id petes ut PSEEbPYa E CDeagErR
22. nstalling the two plug ins the plugins directory under Cytoscape_v2 8 1 will look like Cytoscape_v2 8 1 HOME DIRECTORY plugins KarmaGraph jar KarmaRetrieval jar config karmaQueryConfig txt pluginConfig xml 3 2 Deploying under Windows OS 1 Unzip the plugin package unzip NetKarmaVisPlugin zip 2 Copy the jar files into the plugins directory under Cytoscape_v2 8 1 Install the NetKarma visualization plug in copy NetKarmaVisPlugin KarmaGraph jar C Program files cytoscape 2 8 1 plugins Install the NetKarma provenance retrieval plug in copy NetKarmaVisPlugin KarmaRetrieval jar C Program files cytoscape 2 8 1 plugins 3 Copy the configuration files into the plugins directory under Cytoscape_v2 8 1 Create a new directory named config under cytoscape s plugins directory mkdir C Program files cytoscape 2 8 1 plugins config Deploy the configuration file for the NetKarma visualization plug in copy NetKarmaVisPlugin config pluginConfig xml C Program files cytoscape 2 8 1 plugins config Deploy the configuration file for the Karma provenance retrieval plug in copy NetKarmaVisPlugin config karmaQueryConfig txt C Program files cytoscape 2 8 1 plugins config 4 After you finish installing the two plug ins the plugins directory under Cytoscape_v2 8 1 will look like Cytoscape_v2 8 1 HOME DIRECTORY plugins KarmaGraph jar KarmaRetrieval
23. on and a new dialog window will appear which prompts you for the workflowID MC oop eae ee eue Ea de Br E oe Karma P antral Fanal zn Te Hebvak yumaa ETT Me break Hes ER Data Panel i ilBn fo SE Bj Hade Attribute Brewer Edge attribute reyeser Network atinbute Prosmsr alcune io Cytecapa 2 B0 Rigpe drag 12 DOOM Middiesciec diag 12 PAH Figure 5 2 Enter the workflow ID Enter the workflowID of the graph you want to retrieve and select whether you want the annotations included in the graph or not Press the OK button to continue 3 After the plug in has retrieved the NetKarma provenance XML you will be prompted to choose the name and location to store that XML file sktap Mes IT SH Gee Ha on or amp oem Karma Contre Panel pray Tg network VisMapper ei r Ve bwork H aum WS Computer s i e mz its coy READER D revert tems a RECOWERW E e DVD Dres F Data Panel im Liao D Heo ad Fie names teat Save Flies of type ami files omi T Cancel Niekam bs Cuizeccem T 3 D Right click deas bo ZOOM Middla click dra bs PAM Figure 5 3 Save the OPM XML file Note 1 The time required to retrieve the graph varies depending on the size and complexity of the XML file Retrieving a graph without annotations can significantly reduce the time required For large 10 provenanc
24. ord password of RabbitMQ messaging hostname hostname or IP address messaging hostport port 4 2 The configuration file for the NetKarma visualization plug in The pluginConfig xml file defines which properties of process and artifact nodes in the provenance eraph will be added as annotations to their respective types of nodes in the visualization To identify node properties that should be added as annotations an attribute element is added to the process or artifact section within the importAttributes element within the configuration file Each attribute element contains attributeName and importName child elements When visualizing the graph node properties are checked to see if the URI for the property contains the substring specified as the attributeName of an attribute in the configuration file If the substring is found in the URI then the value of the child element within the value element is added as an annotation to the respective node in the visualization The description for that annotation will be the value specified for the importName As an example if a process node in your provenance graph has the following property element v I property uri urn tool gush peng virtual machine 12345 129634165 1 Process_1 process entity workflowID vI value lt workflowID gt urn tool gush peng virtual machine 12345 129634165 1 lt workflowID gt lt v1 value gt v property And the following
25. r tructons Drag and Drop 4 node shape onto the L Pg Pr d ees Karma WED Do Cpl 28 0 E alice i DOOM Middla oliog drag bx PAN Figure 6 6 1 Get data provenance history Note This functionality works best when the NetKarma visualization plug in is connected to NetKarma using the Axis2 webservice instead of the RabbitMQ 6 7 X axis sort You can display the nodes using a layered format based on the order of the time attribute by selecting the OPM X sort option from the Layout GENI OPMLayout menu tage Le kbs Pd B Cylascape Deskbop Mew sermar File Edel Veew Select Layout Plugins Help Toci z a Seale Insincere Drag and Drop Setinggi i yfiles F m Anode shape m An edge node men Double click To amp 33inodes and edges soecified in SF format GENI OPMLayput AM Un empty space to create a node On a node to begin an edge and specify the source node Then click an Eve argel node Bo finish fe edge Spexily Identifier E aime dean s Wes Triggeredity Mio ierberdErom used Wialbura to Cytescapa 2 52 Cytescape Layouts Graph Layouts Pighi click drag io IDOM H k Nede Attribute rosse Edge AErBute Browse Hebvork urbt Iowa Middlie ciech diag do FAH B By nE 7 Karma Align and Distribute Figure 6 7 1 Select the X sort algorithm 18
26. urposes of collection and representation of provenance data The NetKarma query plug in aims to provide a GUI component that queries provenance information of scientific experiments from the NetKarma provenance repository The NetKarma server is accessible via either a webservice API or RabbitMQ enterprise bus and our provenance retrieval plug in supports both access methods Cytoscape http www cytoscape org is an open source software platform for complex network analysis and visualization We use Cytoscape because of its support for detail and overlaying visualizations with additional annotations We developed our visualization tool as a plug in that can generate the provenance graph visualization directly from the NetKarma provenance information using an XML and provide control of the navigation process 2 Software Dependencies 2 1 Service dependencies The NetKarma plug ins retrieve provenance as graphs from the NetKarma provenance server To use the Cytoscape plug ins you will need to either setup a NetKarma server or process a log file using an established NetKarma service such the Data to Insight Center s NetKarma service on the GRNOC server To set up a NetKarma server please refer to the NetKarma Provenance System user guide at http pti iu edu d2i provenance karma If an instance of the NetKarma service either hosted as a web service or as a standalone service using the RabbitMQ messaging bus already exists contact your syst
Download Pdf Manuals
Related Search