Using stylesheets to render Define.xml

Transcription

1 Using stylesheets to render Define.xml d Wise Technologies Mike Molter Senior Life Sciences Consultant

2 Agenda Introduction Dfi Define.xml Major components Required links Stylesheets What is a stylesheet? The XSLT language

3 HTML through a web browser HTML Draw a table HTML Draw a table row Draw a table cell

4 XML vs. HTML similarities Both are contained din plain li text files Share a similar file structure and element rules Files made up of elements Start and end tags (<tag name>, </tag name>) Start tags may contain attributes <tag name attribute name1= name1= attribute value1 value1 > > Elements may contain textual content <tag name>element content</tag name> Elements may contain properly nested elements <tag name> <child element>content</child element> </tag name>

5 Purposes XML vs. HTML differences HTML Display One set of pre defined HTML elements for all web browsers, each element serving a unique aspect of this purpose Content is consumed by viewing it

6 Purposes HTML XML vs. HTML differences Display One set of pre defined HTML elements for all web browsers, each element serving a unique aspect of this purpose Content is consumed by viewing it XML Transport and storage Content is consumed by extracting it No pre defined tags, different applications define different tags

7 XML <BugsBunny> Whats up doc</bugsbunny> <ElmerFudd season= Wabbit > <DumbDuck>Daffy</DumbDuck> <PorkyPig catchphrase= Thats all folks /> </ElmerFudd>

8 XML in the clinical world ODM Storage mechanism for operational data Define an extension of ODM for metadata

9 Define.pdf Define.xml see examples

10 Define.xml Components Information (study, document, model) Annotated CRFs Supplemental Docs Computational Methods Data sets Variable Definitions Value level metadata Controlled Terminology

11 Define.xml Structure <?xml version="1.0" encoding="iso "?> <?xml stylesheet type="text/xsl" href="define1 0 0.xsl"?> <ODM attributes> <study OID= study oid value > <GlobalVariables> 3 elements with content </GlobalVariables> <MetaDataVersion attributes> Lots of elements </MetaDataVersion > </study> </ODM>

12 <MetaDataVersion> Define.xml Structure <AnnotatedCRF> (acrfs) <SupplementalDoc> (additional documentation) <def:leaf> (links for acrfs and supplemental docs) <ItemGroupDef> (one per data set) <ItemRef> (one per variable in the data set) <ItemDef> (one per unique definition of a variable) <CodeList> (one per unique codelist) <def:valuelistdef> (one per unique list of values) <def:computationmethod> dfc hd (one per unique algorithm)

13 <MetaDataVersion attributes> Define.xml Structure acrfs <def:annotatedcrf> <def:documentref leafid= Tweety > </def:annotatedcrf> <def:leaf ID= Tweety > <def:title>annotated Case Report Form</def:title> </def:leaf>

14 Define.xml Structure Other documents <def:supplementaldoc> dfs ld <def:documentref leafid= Sylvester > <def:documentref leafid= FoghornLeghorn > g </def:supplementaldoc> <def:leaf ID= Sylvester > > <def:title>reviewers Guide</def:title> </def:leaf> <def:leaf ID= FoghornLeghorn > <def:title>statistical Analysis Plan</def:title> </def:leaf>

15 Define.xml Structure Data sets <ItemGroupDef OID= AE Name= AE def:label= Adverse Events def:structure= One record peradverse event persubject def:domainkeys= USUBJID, AETERM, AESEQ def:class= Events several other attributes > <ItemRef ItemOID= domain OrderNumber= 1 Mandatory= Yes Role= Identifier /> one ItemRef per variable in the data set </ItemGroupDef> one ItemGroupDef per data set

16 Define.xml Structure Variable definitions <ItemDef OID= domain Name= DOMAIN DataType= text Origin= Assigned def:label= Domain Abbreviation Length= 2 > </ItemDef> one ItemDef per unique variable definition

17 Define.xml Data set to Variable Link Dt Data set Dfiiti Definitions Variable Definitions Dfiiti AE <ItemGroupDef OID= AE <ItemRef ItemOID= roadrunner USUBJID DM <ItemGroupDef OID= DM <ItemRef ItemOID= roadrunner <ItemDef OID= roadrunner EG <ItemGroupDef OID= EG <ItemRef ItemOID= roadrunner

18 Define.xml Structure Variable definitions <ItemDef OID= lbblfl Name= LBBLFL DataType= text Origin= Derived def:label= Lab Baseline Flag Length= 1 > <CodeListRef CodeListOID= YN /> </ItemDef> one ItemDef per unique variable definition

19 Define.xml Structure CodeList definitions <CodeList OID= YN Name= Yes/No DataType= text > <CodeListItem CodedValue= Y > Y> <Decode> <TranslatedText xml:lang= en >Yes</TranslatedText> </Decode> </CodeListItem> <CodeListItem CodedValue= N > <Decode> <TranslatedText xml:lang= en >No</TranslatedText> </Decode> </CodeListItem> </CodeList>

20 Define.xml Variable to CodeList Link Variable Definitions CodelistDefinitions LBDRVFL <ItemDef Name = LBDRVFL <CodeListRef CodeListOID= WileyCoyote /> YESNO <CodeList OID= WileyCoyote EGBLFL <ItemDef Name = EGBLFL <CodeListRef CodeListOID= WileyCoyote />

21 Define.xml Structure Variable definitions <ItemDef OID= VSTESTCD Name= VSTESTCD DataType= text Origin= Assigned def:label= Vital Signs Test Code Length= 8 > <def:valuelistref ValueListOID= VSTESTCD /> </ItemDef> one ItemDef per unique variable definition

22 Define.xml Structure Value List definitions <def:valuelistdef OID= VSTESTCD <ItemRef ItemOID= HEIGHT /> one ItemRef for each value of VSTESTCD </def:valuelistdef> <ItemDef OID= HEIGHT Name= HEIGHT DataType= float Oii Origin= CRF CRFPage 4 def:label= Subject height at baseline Length= 4 > one ItemDef for each value of VSTESTCD

23 Define.xml Variable to Value List Link Variable Definitions Value Level Definitions EGTESTCD <ItemDef Name = EGTESTCD <def:valuelistref Vl ValueListOID= YosemiteSam /> LitOID Y it EGTESTCD <def:valuelistdef OID= YosemiteSam <ItemRef ItemOID= HRMEAN <ItemRefItemOID= PRMIN Value Definitions HRMEAN <ItemDef OID= HRMEAN PRMIN <ItemDef OID= PRMIN

24 Define.xml Structure Variable definitions <ItemDef OID= AESTDY Name= AESTDY DataType= integer Origin= Derived def:label= Study Day of AE start date Length= 2 h def:computationmethodoid= STDY > </ItemDef> one ItemDef per unique variable definition

25 Define.xml Structure Algorithm definitions <def:computationmethod OID= STDY > Date less informed consent date. Add 1 if negative. </def:computationmethod>

26 Variable Definitions Define.xml Variable to Algorithm Link Method Definitions AESTDY <ItemDef Name = AESTDY def:computationmethodoid= STDY VSDY STDY <def:computationmethod OID= STDY > Date less informed consent date. Add 1 if negative. </def:computationmethod > <ItemDef Name = VSDY def:computationmethodoid= STDY LBDY <ItemDef Name = LBDY def:computationmethodoid= STDY

27 Data set definitions Define.xml Linking Method, Value List, Terminology definitions Variable definitions

28 XSLT Stylesheets An XSLT Stylesheet is an XML based file that provides rules (templates) for creating output based on an input XML file An XSLT processor is a piece of software that reads the input XML and creates output according to the rules in the stylesheet Web browsers have built in XSLT processors that allow output HTML to be viewed like web pages.

29 <?xml version= 1.0?> <xsl:stylesheet attributes > XSLT Stylesheets <xsl:template match= XPATH element name 1 > template rule </xsl:template> <xsl:template match= XPATH element name 2 > template t rule </xsl:template> more templates </xsl:stylesheet>

30 XSLT Stylesheets XPath expressions hl help to identify if locations in the XML document being read <xsl:template match= /ODM/Study/GlobalVariables > <xsl:template match= /ODM/Study/MetaDataVersion > <xsl:template l match= / > h / (identifies ifi the root element) Think of Unix or Windows paths. Can be absolute or relative

31 XSLT Stylesheets Template rules provide a template for producing output when the processor is processing the element identified in the match attribute. They normally contain a combination of the following: Output options text conditionally produced text iteratively ti produced dtextt capture data from input document Other tools variable creation

32 %macro test (j=) ; data %if &n=1 %then x ; %else y ; ; set %do i=1 %to &j ; z&i %end ; ; run ;

33 Example 1: Rendering Define.xml with an Empty Stylesheet <?xml version= 1.0 > <xsl:stylesheet version= 1.0 namespace attributes > </xsl:stylesheet> <ODM attributes <Study OID="1234"> <GlobalVariables> <StudyName>1234</StudyName> <StudyDescription>1234 Data Definition</StudyDescription> <ProtocolName>1234</ProtocolName>

34 Example 2: Rendering Define.xml with Hello World! <?xml version= 1.0?> <xsl:stylesheet version= 1.0 namespace attributes > <xsl:template match= / > HELLO WORLD! </xsl:template> </xsl:stylesheet>

35 Rendering Define.xml with metadata tables Define.xml Structure <ODM attributes> <study OID= study oid value > <GlobalVariables> 3 elements with content </GlobalVariables> <MetaDataVersion attributes> Lots of elements </MetaDataVersion > </study> </ODM> HTML result of transformation <html> <head> <title>content</title> </head> <body> Datasets TOC table Data Definitions Dfiiti (one table per dataset) </body> </html>

36 THE PLAN (overall) <html> <head> <title>content</title> / </head> <body> Datasets TOC table Data Definitions (one table per dataset) </body> </html> <xsl:template match= / > Used to generate high level elements <xsl:template match="/odm:odm/odm:study/odm:me tadataversion"> Used to generate the details of the <body> element <xsl:template match="/odm:odm/odm:study/odm:glo balvariables"/> Used to generate nothing. Absolutely nothing.

37 HTML text to generate: <html> <head> <title> Study 1234, Data Definitions </title> <ODM attributes XSLT used to output above HTML: <xsl:template l match= / > h / <Study OID="1234"> <html> <head> <title>study <xsl:value of select= /ODM/Study/GlobalVariables/StudyName />, Data Definitions </title> </head> <body> <xsl:apply templates/> </body> </html> </xsl:template> <GlobalVariables> <StudyName>1234</StudyName>

38 <xsl:template match="/odm:odm/odm:study/odm:globalvariables"/> No content, no child elements <xsl:template match="/odm:odm/odm:study/odm:metadataversion">

39 Generating the TOC HTML text to generate (first row): <table attributes> <tr> <th colspan= 6 other attributes> Datasets for Study 1234 </th> </tr> XSLT used to output above HTML: <xsl:template match= odm:odm/odm:study/ods:metadataversion > <table attributes> <tr> <th colspan= 6 other attributes> Datasets for Study <xsl:value of select= /ODM/Study/GlobalVariables/StudyName /> /> </th> </tr>

40 Generating the TOC HTML text to generate (second row): <tr align='center'> <th align='center' valign='bottom'>dataset</th> <th align='center' valign='bottom'>description</th> <th align='center' valign='bottom'>structure</th> <th align='center' valign='bottom'>purpose</th> <th align='center' valign='bottom'>keys</th> <th align='center' valign='bottom'>location</th> </tr>

41 Generating the TOC HTML text to generate (data rows): <tr align= left valign= top > <td>dm</td> <td><a href= #DM >Demographics</a></td> <td>special Purpose-One record per event per subject</td> <ItemGroupDef OID= DM <tr align= left l valign= top > Name= DM <td>te</td> <td><a href= #TE >Trial def:label= Demographics Elements</a></td> <td>trial Design-One Record Per Element</td> etc def:structure= SpecialPurpose One Special record per event per subject

42 Generating the TOC (still in the MetadataVersion template...) <xsl:for each select=. /ItemGroupDef > ef <xsl:call template name= ItemGroupDef /> </xsl:for each>

43 Generating the TOC (still in the MetadataVersion template...) <xsl:template name= ItemGroupDef > <td><xsl:value of /></td> /td <td> <a> <xsl:attribute name="href"> #<xsl:value of </xsl:attribute> <xsl:value of l select="@def:label"/> df bl"/ </a> </td>

44 Generate acrf link HTML text to generate: <p align= left > Annotated Case Report Forms ( <a href= blankcrf.pdf > blankcrf.pdf</a> ) </p>

45 Generate acrf link <def:annotatedcrf> <def:documentref leafid= Tweety > </def:annotatedcrf> <def:leaf ID= Tweety > <def:title>annotated Case Report Form</def:title> </def:leaf> The Plan Check for existence of acrfs. If found... Iterate through each instance of def:documentref Store value of leafid attribute in variable Use variable to find corresponding def:leaf element Extract information and generate HTML

46 Data Definition Tables <ItemGroupDef OID= DM other attributes <ItemRef fitemoid= STUDYID attributes t /> <ItemRef ItemOID= DOMAIN attributes /> one ItemRef per domain variable <ItemGroupDef OID= TE other attributes <ItemRef ItemOID= STUDYID attributes /> <ItemRef ItemOID= ETCD attributes /> one ItemRef per domain variable <ItemDef OID="STUDYID" etc. Name="STUDYID" DataType="text" Length="8" Origin="CRF Page" Comment="Demographics CRF Page 4" def:label="study IDENTIFIER"> </ItemDef>

47 Data Definition Tables <ItemGroupDef OID= DM other attributes <ItemRef ItemOID= STUDYID attributes /> <ItemRef ItemOID= DOMAIN attributes /> one ItemRef per domain variable <ItemGroupDef OID= TE other attributes <ItemRef ItemOID= STUDYID attributes /> <ItemRef ItemOID= ETCD attributes /> one ItemRef per domain variable etc. The Plan Create target for TOC hyperlinks Iterate through each instance of ItemGroupDef Within each ItemGroupDef, iterate through each ItemRef Store value of ItemOID attribute in variable Use variable to find corresponding ItemDefelement Extract information and generate HTML

48 Data Definition Tables hyperlinks From variable names to value level metadata From Controlled Term column to terminology list From Origin to PDF pages From Role to Role terminology list From Comment to computational algorithm

49 Contact Me Name: Mike Molter Company: Website: d Wise Technologies wise.com mmolter@d wise.com Phone: