2/12/11. Addendum (different syntax, similar ideas): XML, JSON, Motivation: Why Scientific Workflows? Scientific Workflows
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1 Addendum (different syntax, similar ideas): XML, JSON, Python (a) Python (b) w/ dickonaries XML (a): "meta schema" JSON syntax LISP Source: h:p://en.wikipedia.org/wiki/json XML (b): "direct" schema Source: h:p://en.wikipedia.org/wiki/json PHP array inikalizers Motivation: Why Scientific Workflows? ScienKsts open need to integrate exiskng and new programs into larger computa(onal pipelines via "master programs" Some common challenges: Heterogeneity of component programs compute resources (desktop, cluster, cloud) data formats Need to: Organize and manage output data (files, folders, databases) Track and report how results were obtained (lineage) Backward tracing of product to its "ingredients" (data sources, params,..) Concurrently execute programs (scalability) Scientific Workflows Capture how a scienkst works with data and analykcal tools data access, transformakon, analysis, visualizakon dataflow oriented (~ scripkng + dataflow) ScienKfic workflow (wf) benefits: wf automa(on wf & component reuse wf design, documenta(on wf archival, sharing built in concurrency (task, pipeline parallelism) built in provenance support distributed & parallel exec: Grid & cluster support 3 4 Example: Phylogenetic Analysis Pipeline Provenance of Data: Data Lineage Advantage of using a workflow system: automatic tracking of data lineage 5 6 1
2 Using R in Kepler Ports each actor has a set of named input and output ports data tokens are produced or consumed through ports ports are typed (more on this later) relations Parameters parameters act as special stakc ports parameter values used to configure actor used by actor across invocakons Dataflow ConnecKons actor communicakon channels directed (hyper) edges connect output ports with input ports merge step + distribute step workflow variable Sub workflows / Composite Actors composite actors wrap sub workflows like actors, have input and output ports hierarchical workflows (arbitrary neskng levels) Parameter variables internal variables for a workflow open used to configure workflow default seangs used within actors (expressions, actor parameter ports) 2
3 Kepler User Interface Tool Bar Quick Search Workflow Canvas Directors coordinate the execukon of workflows schedules the invocakon of actors actors decoupled from parkcular director (ideally) large number of different directors available Actor Libraries Thumbnail Navigation viewing adding ports running add relation The Run Window alternakve way to run a workflow to view: Window > RunKme Window shows display output, set parameters, etc. Creating a simple XPath workflow Important: Set firingcountlimit parameter on Const to 1 Remove enforcearraylength opkon on ArrayToSequence 3
4 Opening and running a demo workflow Example Actors: Importing Data Read from local file or URL outputs each line as a string addikonal actors split columns, etc See File Reader, File to Array, Read from tabular data based on R read table outputs R data frames EML Data Source integrated into data tab (EcoGrid) data described using EML metadata various opkons for outpukng tabular data (port per column, array per row, etc) File > Open File > geang started DB query actor provides access to remove databases Example Actors: Generic Actors Expression language actor fairly extensive scripkng language integrates port types see Help > DocumentaKon > Ptolemy DocumentaKon expression evaluator: Tools > Expression Evaluator Command line execukon actor execute shell command number of variants R expression actor execute R scripts Web services call external web services configure with WSDL URL and operakon Example Actors: Visualizing Results Textual representakon of data Useful for observing data at any point in a workflow XY Plo:er plots x and y double values one of many plot actors Timed Plo:er works with CT domain plots double values over Kme ImageJ image display and processing system developed by NIH Built in macro language R visualizakon Vast assortment of graphics available through R Some as built in actors, others through R actor Kepler Actor Library The actor library comes with a number of default actors Support for adding new actors and libraries workflows and actors described via XML files (View > XML Tree) KAR archives web repository (library.kepler project.org) local library addikons Adds actor to local library under the selected categories and w/ the new name Designing Workflows via Composites Empty composite actors can be used to prototype and specify abstract workflows 1. Drag composite actors to canvas 2. Rename them 3. Add ports 4. Add port types 5. Add comments (annotations) 6. Add director 7. Drill-down to composites 4
5 Actor Port Types Ports have data types in Kepler Many data/token types: ints (5), doubles (5.5), etc. strings ( hello world ) arrays ( {1,2,3,4}) records (e.g., {a=1, b= foo, c=5.5}) matrices ([1,2;3,4]) objects (e.g., plain old Java objects) General (supertype of all types) Unknown (subtype of all types) Kepler performs type checking / type inference To make sure there are no type errors before a workflow is run To make sure actors behave during runkme Can lead to headaches when wrikng / designing workflows 5
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