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Query Service Administration Guide ADMINISTRATION GUIDE BIOVIA QUERY SERVICE 9.5.200 Copyright Notice ©2015 Dassault Systèmes. All rights reserved. 3DEXPERIENCE, the Compass icon and the 3DS logo, CATIA, SOLIDWORKS, ENOVIA, DELMIA, SIMULIA, GEOVIA, EXALEAD, 3D VIA, BIOVIA and NETVIBES are commercial trademarks or registered trademarks of Dassault Systèmes or its subsidiaries in the U.S. and/or other countries. All other trademarks are owned by their respective owners. Use of any Dassault Systèmes or its subsidiaries trademarks is subject to their express written approval. Acknowledgments and References To print photographs or files of computational results (figures and/or data) obtained using BIOVIA software, acknowledge the source in an appropriate format. For example: "Computational results obtained using software programs from Dassault Systèmes BIOVIA. The ab initio calculations were performed with the DMol3 program, and graphical displays generated with BIOVIA Query Service." BIOVIA may grant permission to republish or reprint its copyrighted materials. Requests should be submitted to BIOVIA Support, either through electronic mail to [email protected], or in writing to: BIOVIA Support 5005 Wateridge Vista Drive, San Diego, CA 92121 USA Contents Chapter 1: Introduction 1 Creating an ADS 19 Purpose of the BIOVIA Query Service 1 Using the template IDS XML configuration Query Service 1 files 20 Client applications 1 Setting up a data source using existing Isentris data source files 20 The Query Service RESTful API 1 Creating a data source XML file manually 21 Key features of the Query Service 2 Configuring an IDS to support retrieval of Conventions 2 molecules as Pipeline Pilot Chemistry Additional information 2 instead of CHIME strings 23 Chapter 2: System Requirements 3 Configuring Query Service in the Software requirements (Data Source Builder) 3 Administration Portal 23 Required software 3 Configuring the Query Service catalog 24 Required software settings 3 Editing the Catalog.xml file 24 Optional software 3 Checking the Query Service catalog 25 Supported Registration databases 3 Chapter 5: Optional Configuration Tasks 26 Modifying the definition of the automatic Chapter 3: Overview for Administrators 4 structure search 26 Query Service concepts 4 Example 26 REpresentational State Transfer (REST) 4 Modifying exact structure "query type" Data sources 4 searches 28 Data Source Builder 5 To modify the XML file 28 Query 5 Enabling matching of total charge in Active query 5 substructure mapping of pi systems 29 Hitlist 5 To modify the XML file 29 Catalog 5 Setting up custom JAR files and configuration files 30 Metadata 5 Setting properties for shared data sources 30 Sharing data sources 6 Chapter 6: Setting Up the Query Service Closed data sources 6 Examples 32 The lifetime of a recordset 6 Setting up example protocols with the Managing lists and temporary tables 7 Research Workbench (RWB) database 32 Configuration 7 Setting up example protocols with the ACD Important files and folders 8 database 32 Setting permissions for using Web Port to run Chapter 4: Required Configuration 9 example protocols 32 Host name and port name 9 Chapter 7: Troubleshooting 34 Configuring Query Service permissions 9 Using the Query Service log file 34 Managing permissions 11 Using the Tomcat log file on Windows 34 Configuring Query Service data sources 12 Using the Tomcat log file on Linux 35 Adding and configuring relational data sources in the Pipeline Pilot Administration Using the monitor REST endpoints 36 Portal 12 Examples 36 Using the Template_rel.xml file 17 Appendix A: Installing the RWB Database 37 Using Oracle proxy accounts 17 Tables 38 Editing a relational data source 17 Views 38 Deleting a relational data source 18 Appendix B: Spanning multiple Oracle Installing Data Source Builder 18 instances 40 Creating an IDS 18 About spanning multiple Oracle instances 40 IDS workflow summary 19 IDS over Oracle materialized views 40 Advantages 40 Disadvantage 40 IDS standard data source connector 41 Advantage 41 Disadvantage 41 IDS DBLink data source connector 41 Advantage 41 Disadvantage 41 IDS INCursor data source connector 41 Advantage 42 Disadvantages 42 When to use 42 Examples 42 IDS over Oracle view of DBLinked table 43 Advantage 43 Disadvantages 43 Chapter 1: Introduction The BIOVIA Query Service is a Web service that provides client and Web applications with integrated access to corporate scientific data sources. It is supplied with BIOVIA Pipeline Pilot Server. The Query Service is an HTTP-based service implemented using a REpresentational State Transfer (REST) interface. To learn more about the REST interface, see the BIOVIA Query Service Developer’s Guide. This guide is designed for BIOVIA Pipeline Pilot Server and database administrators familiar with Oracle administration concepts and BIOVIA Pipeline Pilot developers familiar with objects in a database. Purpose of the BIOVIA Query Service Traditional scientific database systems load data into individual schemas, each system having its own client application. As the availability of external data grows, or companies merge systems, the number of database systems and platforms multiplies, and more systems are introduced to handle the increase in data. The complexity of the infrastructure increases, and data becomes difficult to manage and access across multiple systems and platforms. The Query Service solves the problem of searching across multiple data sources, by mapping the metadata of each data source to descriptive field aliases. Queries are built using these field aliases, and can be mapped onto any data source for which a corresponding mapping is provided. This method eliminates the need to migrate data or modify database schemas, and provides the flexibility to modify data sources. Query Service queries are written using the Unified Query Language (UQL). UQL has a similar syntax to the widely-used Structured Query Language (SQL). An XML query format is also available. The Query Service is compatible with Oracle databases. Query Service Client applications The client application of the Query Service can be any of the following: Pipeline Pilot Client. Access to Query Service data sources is provided by a comprehensive set of Pipeline Pilot components. A web-based application that sends RESTful HTTP requests to the Query Service and converts the response data to HTML for display on web pages. A custom client with an HTTP back end, that presents the data retrieved from the Query Service to the user in any format desired. The Query Service RESTful API The Query Service exposes a RESTful API that client applications can use to perform the following tasks: Get the metadata of a data source to determine what data can be queried Execute cataloged (i.e. stored) and ad hoc queries Combine record sets (i.e. sets of full records) or search results Introduction | Page 1 The Query Service can provide responses in various formats, including XML (the default format), XDfile, SDfile, JavaScript Object Notation (JSON), and several character-delimited formats. For more details about available response formats, see the Query Service Developer's Guide. Key features of the Query Service The following features are available: A full set of Pipeline Pilot components that provide access to all the main features of the Query Service API in a highly visual and user-friendly way. An extended RESTful API that provides client applications with greater flexibility in querying data sources. Simpler configuration of data sources using the Data Source Builder application. It is no longer necessary to edit data source configuration XML files directly. Conventions These are the conventions in this guide: References to functions, paths, and file names are presented in this font. For clarity and readability in paragraphs and tables, the font may also appear in bold. All code input and output snippets are presented in this font on a gray background. You must follow the order in a numbered list. A bulleted list has no order. Note: In this guide, {PPS installation directory} is used to represent the root folder of the BIOVIA Pipeline Pilot Server installation. On 32-bit Windows this is typically C:/Program Files/BIOVIA/PPS On 64-bit Windows this is typically C:/Program Files/BIOVIA/PPS For 32-bit installations on 64-bit Windows this is typically C:/Program Files (x86)/BIOVIA/PPS Additional information For additional information about the Query Service, see the following documentation: Query Service Developer's Guide Integrating Data Source (IDS) Guide Aggregating Data Source (ADS) Guide For more information about the Query Service and other BIOVIA software products, visit: https://community.3dsbiovia.com Page 2 | BIOVIA Query Service • Administration Guide Chapter 2: System Requirements The following requirements are specific to Query Service, and these requirements are in addition to BIOVIA Pipeline Pilot Server system requirements. Software requirements (Data Source Builder) You can use Data Source Builder to create integrating data sources and test the Query Service. Data Source Builder is available for download from the BIOVIA Pipeline Pilot Server Home page. Before using Data Source Builder, install and configure the software described below. Required software Software Version(s) Comments Microsoft .NET Framework 4.0 or 3.5 Required to run the Data Source Builder installer. Required software settings Software Version(s) Comments Apache Tomcat Virtual Standard The Query Service runs within the Apache Memory Tomcat virtual machine. There is
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