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(ATS6-PLAT04) Query service

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The Query Service is the new platform solution for querying a variety of data sources. The goal of Query Service is that administrators can configure a metadata description of the data source that can …

The Query Service is the new platform solution for querying a variety of data sources. The goal of Query Service is that administrators can configure a metadata description of the data source that can then be used by end users without detailed knowledge of the underlying data source. This session explains how to configure Query Service data sources and use them with the RESTful API or component collection.

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  • 1. (ATS6-PLAT04) Query ServiceJon HurleySenior ManagerPlatform R&DJon.Hurley@accelrys.com
  • 2. The information on the roadmap and future software development efforts areintended to outline general product direction and should not be relied on in makinga purchasing decision.
  • 3. • Introduction• Administrator– Installation– Configuring data sources• Application Developer– RESTful API• Protocol Author– Pipeline Pilot Component Collection• ConclusionContent
  • 4. Accelrys Query ServiceAccelrysQueryServicesShareableAd-hoc &persistentPublic Data• Literature• Patents• Competitive IntelExperimentalData Repositories• Unified Registration• LIMS• ELN - ExperimentsLegacy Data• Inventory• Summary Data Warehouse• Team Data MartsSimulations Data• Molecular & Biologics Design• ADMET• Formulations DesignsUnstructuredData• Documents• ReportsOffice & SharePointWebInsightRegistrationBreaking down the scientific data silos, increasing access across the value chainCorporateExternal
  • 5. • Three (sometimes four) kinds of people involved– Admin• Manages applications• Defines data sources• Knows all about SQL, etc.– Protocol author• Provides scientific analysis• Does not do programming per se• Calculations, graphing, etc.– End user• Generates Information within applications (e.g. Insight)• Uses provided templates and GUIs– Sometimes: Application developer• Implements access to protocols in custom applicationsPersonas
  • 6. Use an existingdata source(ACD,Notebook, etc.)Access yourdata:integration andaggregationDatatransformation:pivot, calculate,web servicesDynamic accessto data: selfaware datasourcesData Sources: from OOTB to custom dynamic DSOut-of-the-boxGraphicaltoolAdvancedconfigurationProgramming
  • 7. Administrator• Installation• Configuring Data Sources
  • 8. • AQS is part of the AEP Core– Nothing else required to run• Everything installed with 9.0– Query Service– Data Source Builder• Data Source Builder included– .NET Client– Used by Query Service Administrators– Needs to be installed from the AEP home pageInstallation Facts
  • 9. Download Data Source Builder from Home Page
  • 10. • QueryService/Administer Permission– Required to• Start Data Source Builder• Execute any administrative task from the interface– Given by Default to QueryService/Administrators group– Defined by default as Platform/Administrators• QueryService/Logon Permission– Required to• Execute any Query Service call– Given by Default to QueryService/Users group– Defined by default as Platform/EveryoneAdministration: Permissions
  • 11. • In the AEP Administration Portal– Configure relational data source (RDS)– Assign access rights• In Data Source Builder– Configure Integrating Data Source (IDS)– Configure Aggregating Data Source (ADS)– Test, debug & optimize themData Source Configuration
  • 12. Data Source Administration Page
  • 13. 13Integrating Data SourceLink relationships graphicallyAttach calculators & web servicesDynamic data sources based onmetadata & user selectionPublish to scientistsPivot data on the flyPick the tables you want
  • 14. Integrating Data Source – resultScientists are just exposedto information they need &when they need itBrowse bymoleculeBrowse byDocument…or Target…orFormulation
  • 15. • An Integrating Data Source (IDS) is created using Data SourceBuilder• Same interface as for Isentris• Start by dragging a RDS• Drag table or views– Same or different schema• Define linking fields• Fine tune properties• Test itData Source configuration IDS
  • 16. RWB Example IDS in Data Source Builder
  • 17. DemoData Source Builder• View and simple edit of an IDS
  • 18. • Aggregating Data Sources (ADS)• Searching in parallel a set of IDS• Must have similar contentAggregation
  • 19. • An Aggregating Data Source (ADS) is created using DataSource Builder• Same interface as for Isentris• Start by dragging similar IDS• Select common parts• Rename parents & fields as necessaryData Source configuration ADS
  • 20. Application Developer• RESTful API
  • 21. Any Application accessing Restful web service API• Released by Accelrys– Data Source Builder– Query Service Component collection• Customer/Services extensions– Web Browser (+ add-on for POST)– C#/Java/JavaScript REST Client appsQuery Service Clients
  • 22. • URL = AEP platform base URL– + /auth/queryservice/– + resource + modifier + parameters• Authentication done by the platform• Re-directed to AQS Tomcat• Documentation:– Query Service Developer Guide– Chapter 4: Query Service REST ResourcesBasics
  • 23. • http://{server:port}/auth/queryservice/datasources• http://{server:port}/auth/queryservice/datasources/{dataSourceName}/metadata?rootNames=*&rootnamesonly=false&format=xml• After a search:• http://{server:port}/auth/queryservice/queries/{activeQueryId}/metadata• http://{server:port}/auth/queryservice/queries/{activeQueryId}?nextpage=true&format=json&pagesize=5GET examples (any browser)
  • 24. • URL:http://{server:port}/auth/queryservice/queries?format=xml&datasource=inventory_ids• Body:select cdbregno, molname from molecules where cdbregno < 100• UQL query can be copied from Data Source BuilderPOST examples
  • 25. Protocol Author• Pipeline Pilot Component Collection
  • 26. Pipeline Pilot Components
  • 27. Query Service Example Protocol
  • 28. • Main Components– Generate Query Results– Generate Query Results for Each Data• Composite components that– Define the query– Execute the query– Return the results• If you create protocols that process all data to completion– These are the only components you needComponent Collection
  • 29. • Generate Query Results– Define a single query with the Query Builder UI• Either provide all query values in the UI or through componentparameter values– Executes the query and returns all the results from the query• Generate Query Results for Each Data– Same as above but runs the same query once for each inputdata recordComposite Components
  • 30. DemoExample ‘03 Query RWB with Multiple Corporate ID Values’• Simple example using Generate Query Results
  • 31. • Utility Components– Data Source utilities• Information about data sources– Query Components• Define and execute queries• Asynchronous support for running query and retrieving subset of results– HitList Components• * Prototypes *• Manage hit lists as cache files• These are more advanced components– Used by Insight and other ‘interactive’ clientsComponent Collection
  • 32. DemoExample ‘02 Query RWB Using Biological Results’• More sophisticated example using many AQScomponents
  • 33. • Streamlined RESTful API– Consistent with Component Collection• Initial Component Collection– Will extend with next release of InsightSummary
  • 34. • Some sample use cases for Query ServiceAppendix
  • 35. Appendix• Additional information, use cases for Query Service
  • 36. • A RESTful web service API– Authorization through the AEP platform– Runs in the platform Tomcat server– All end points accessible as GET/POST/DELETE– Functionality taken from Isentris Data Source Service• A collection of PP Components– Replaces the LMQS collection– Calls the Query Service Restful APIWhat is AQS?
  • 37. • Are supported as well• Cannot create RDS file in Data Source Builder any more• Must be copied from Isentris into AEP folder {AEPinstall}webqueryservicedsfiles• Only for public IDS (no access rights)– Not associated to an AEP data sourceLegacy Isentris RDS
  • 38. QS Folders in AEP
  • 39. • (Single) Structure based searching of ACD deployed asPP and Web Port protocol• Goal is to create a protocol to be used by my chemists that master PPand a web port app for the chemists that don’t• As a protocol author I want to configure a generic query: Compoundscontaining a particular SS, mw between x and y, alogp between x and y• I want to create a protocol that allows someone to draw a substructureand specify mw and alogp boundaries as protocol parameters• I want to avoid having to do any programming but my expectation is thatI can visually construct this query• I want to deploy this as a simple web port app: query structure sketcher+ MW + alogp parameterUser Story # 1
  • 40. • (Multiple) Structure based searching of ACD deployedas PP and Web Port protocol• Goal is to create a protocol to be used by my chemists that master PP and a web port app for the chemiststhat don‘t• As a protocol author I want to configure a generic query: Compounds containing a particular SS, mwbetween x and y, alogp between x and y• I want to create a protocol that allows someone to pipe in different substructures and specify mw andalogp boundaries as protocol parameters• For each substructure passed in it should search ACD and return results• I want to avoid having to do any programming but my expectation is that I can visually construct this query• I want to deploy this as a simple web port app: source (SD) file + MW + alogp parameter•Variant 1: Additionally add constraint for one "child" field, for example limit for a given supplierVariant 2: Replace SSS by a similarity search with fixed similarity valuesUser Story # 2
  • 41. • (Multiple) Name based searching of ACD deployed as PPand Web Port protocol• Goal is to create a protocol to be used by my chemists that master PP and a web port app for the chemiststhat don‘t• As a protocol author I want to configure a generic query: Compounds with a name containing a particularstring, quantity in a given range and price below a given value• I want to create a protocol that allows someone to pipe in different names and specify quantity between xand y and price limit boundaries as protocol parameters• For each name passed in it should search ACD (molnames contains the submitted string or synonymscontains the submitted string) and return results• I want to avoid having to do any programming but my expectation is that I can visually construct this query• I want to deploy this as a simple web port app: source for names + quantity and price parametersUser Story # 3
  • 42. • Reaction searching over Notebook deployed as PP and Web Portprotocol• Goal is to create a protocol to be used by my chemists that master PP and a web port appfor the chemists that don’t• As a protocol author I want to configure a generic query: Reactions implementing aparticular transform, with yield more than a given threshold. I want to the display toinclude the reference to the Notebook experiment done.• I want to create a protocol that allows someone to draw a reaction transform and specifyminimum yield value as protocol parameters• I want to avoid having to do any programming but my expectation is that I can visuallyconstruct this query• I want to deploy this as a simple web port app: query structure sketcher + minimum yieldparameterUser Story #4
  • 43. • Activity searching over RWB deployed as PP and Web Portprotocol• Goal is to create a protocol to be used by my scientists that master PP and a web portapp for the chemists that don’t• As a protocol author I want to configure a generic query: Compounds with a particularSS, activity larger than a given value for the CDK2 assay and smaller than a given value forthe PKCa assay.• I want to create a protocol that allows someone to draw a substructure and specifyminimum result value for CDK2 and maximum value for PKCa as protocol parameters• I want to avoid having to do any programming but my expectation is that I can visuallyconstruct this query• I want to deploy this as a simple web port app: query structure sketcher + minimumCDK2 and maximum PKCA parametersUser Story #5