Don Hurst, Zymogenetics Sarmad Pirzada, Hybrid Data Systems

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1 Use of selected Third Party XML Tools in Conjunction with the Importing, Exporting and Manipulation of XML Files within the SAS System WUSS, 2007 Don Hurst, Zymogenetics Sarmad Pirzada, Hybrid Data Systems

2 Disclaimer The material contained in this presentation represents the opinions of the presenters and should not be construed as reflecting ZymoGenetics position or opinion. 2

3 XML into SAS 1. Getting an XML files into SAS 2. SAS and non-sas tools for manipulating XML files a. XML Mapper b. Altova XML Spy c. oxygen XML Editor d. Exchanger XML Lite V3.2 editor e. W3C Validation checker 3

4 XML Terms XML: Extensible Markup Language New method of for web applications and data transfer standard for creating XML tags for transferring and interpreting business files TAG: <subjnum< subjnum>2008</ >2008</subjnum> DTD: Data type definition collection of tags parent child relationship 4

5 SGML XML Relation 5

6 What Does XML Look Like? <?xml version="1.0" encoding="iso "?>  <note> <to> ove </to> <from> Jani </from> <heading> Reminder </heading> <body> Don't forget me this weekend! </body> </note> 6

7 Another XML Example <?xml version="1.0" encoding="iso "?> <breakfast_menu> <food> <name>belgian Waffles</name> <price>$5.95 $5.95</price> <description>two two of our famous Belgian Waffles with plenty of real maple syrup</description> <calories> </calories> </food > </breakfast_menu breakfast_menu> 7

8 Every XML File Should Have There is a beginning and end container tag There is a hierarchy of items within the food segments Every segment and field begins and ends with a tag It should be well-formed 8

9 XML Error (Internet Explorer) The XML page cannot be displayed Cannot view XML input using XSL style sheet. Please correct the error and then click the Refresh button, or try again later. End tag 'Ffrom' Ffrom' ' does not match the start tag 'from'. Error processing resource ' ml/note_error.xml <from> Jani </Ffrom from> ^ 9

10 Correcting the XML Error Several methods: Note pad and redisplaying in IE W3C consortium tools 3d party XML editing tools 10

11 Representing a Hierarchy in SAS Visual perspective of the hierarchical XML file structure small part of XML SAS datasets are rows/columns, e.g. observations/variables Defaults that exist when an XML file is read into SAS 3 levels can be handled without extensive mapping 11

12 An Example <?xml version="1.0" encoding="windows- 1252"?> <TABLE> <DEMOG> <SUBJID> 200 </SUBJID> <AGE> 58 </AGE> <SEX> Female </SEX> <RACE> Asian </RACE> <BIRTHDA> </BIRTHDA> </DEMOG> </TABLE> 12

13 How do I get that XML file into SAS? libname in1 xml Y:\subject.xml' ; proc copy indd=in1 outdd=work ; run; 13

14 What does it look like in SAS (Proc Print)? Demographics DEMOG XML file represented in SAS Obs BIRTHDA RACE SEX AGE SUBJID Asian Female Black Female Other Male Why is the Y left off of the BIRTHDAY variable name? 14

15 Role of Schema/Mapping XML schema tells machines how to carry out rules defined in the schema, define the data structure, content, shared vocabularies and semantics of XML documents. Business rules often dictate complex hierarchical relationships that are beyond the default capabilities of the SAS/XML engine SAS XML Mapper was created for such a purpose on mapping the XML document into SAS 15

16 XML Mapper Overview XML Mapper is a tool provided by the SAS Institute for telling SAS how to read and represent an XML file into SAS XML Mapper has been widely written about and will be briefly covered here. 16

17 SAS XML Mapper Mapper is a Graphical User Interface (GUI) written in Java Allows the user to generate XML Map by drop and drag Also can show sample SAS code, table views, and contents. 17

18 What XML Mapper looks like XML Window Map Window Source Window 18

19 XML Mapper with ODM XML XML Window Map Window Source Window 19

20 XML Mapper with Manufacturer XML XML Window Map Window Source Window 20

21 XML Mapper Shortcomings It sometimes will abort with an error without any warning. Its validation of a well formed XML structure is not necessarily the same as other 3 rd party tools, e.g. XMLspy, oxygen, etc. Map creation is very iterative and the resulting map when used in a SAS program can be frustrating. 21

22 How to Get SAS Mapper Comes with the SAS Foundation cd s Or, download from support.sas.com under base software It can be run as a standalone after unzipping into a folder by clicking on sas.sxle.atlas,, an executable jar. Meant, however, to be a plug-in into the SAS products of the programs. 22

23 Other Non-Sas 3rd Party Tools Altova s XML Spy Generally good for non-pharma XML files Heavily used in the Financial/Manufacturing sectors There were some problems validating an Pharma XML file conforming to CDISC and W3C standards Used MSXML engine and was not W3C compliant Just recently changed 23

24 What Altova XML Spy looks like 24

25 XML Spy Validation Portion (Validation Error) Unable to show schema:c:\program Files\Altova Altova\XMLSpy2007\Examples\Indus trystandards\patents Patents\application- example.xml XML Schema has to begin with a <schema> element in namespace ' Error location: patent-application application- publication 25

26 <oxygen/>(r) XML Editor 26

27 <oxygen/>(r) XML Editor (Validation Error) systemid: C:\Program Files\Oxygen XML Editor 8.2\samples\svg\sales.xmlDescription: There is no schema or DTD associated with the document. You can create an association either with the Associate Schema action or configuring in the Options the Preferences/Editor/Default Schema Association list, or by creating a Validation Scenario. 27

28 XML Exchanger Lite V3.2 28

29 XML Exchanger Lite 3.2 (Validation of Schema) [Xerces-J J 2.7.1] Checking "converted.xsd" converted.xsd" for Well-formedness... Well-formed Document. 29

30 Validation Checker 30

31 ODM XML file to be Validated 31

32 SAS System and XML (summary) SAS System The XML In requires a XML document & schema for SAS to properly parse the document Business Rules XML In XML Out 32

33 Common SAS /XML Flow Validated XML document (xml file + schema) Industry specific business rules Mapper file for bringing validated XML documents into SAS Industry specific XML validation with schema rules in accord with W3C 33

34 Concluding Remarks Manipulate XML file data within the SAS system in accordance to a set of business rules Depends upon the Industry group and application Desired output affects the manipulation of the SAS representation of the XML data. 34

35 Concluding Remarks (continued) SAS and representative non-sas tools are available to facilitate XML file handling XML Mapper Altova xmlspy editor oxygen XML editor Exchanger XML Lite V3.2 editor W3C Validation checker 35

36 References and Further Reading SAS XML Libname Engine 9.1.3, User s s Guide, SAS Institute, Cary, NC, USA SAS Implementing CDISC data models in the SAS Metadata Server Yeh,, Shi-Tao. Using XML Mapper to Create an XML Map. NESUG18 Proceedings. Cisternas,, M., (2004): Reading and Writing XML files from SAS, Proceedings of the 29 th SAS Users Group International Conference, Paper 119. Pirzada, Sarmad. Moving XML Files within SAS and Maintaining Segment Hierarchy. PNWSUG, Zender, Cymthia L. Creating a Tagset Template for the SAS XML Libname Engine. TT-24, SAS Conference Proceedings: PharmaSUG 2007June 3-6, , Denver, Colorado. 36

37 References and Further Reading (continued) support.sas.com

38 Acknowledgements SAS is a registered trademark of SAS Institute, Inc. in the USA and other countries. Other brand and product names are registered trademarks or trademarks in their respective companies. indicates USA registration. 38

39 Questions? Don Hurst, Sarmad Pirzada, 39

CDISC Variable Mapping and Control Terminology Implementation Made Easy

PharmaSUG2011 - Paper CD11 CDISC Variable Mapping and Control Terminology Implementation Made Easy Balaji Ayyappan, Ockham Group, Cary, NC Manohar Sure, Ockham Group, Cary, NC ABSTRACT: CDISC SDTM (Study