Commit 3486cc4d authored by R.W.Majeed's avatar R.W.Majeed

example finished

parent c1258ed5
......@@ -11,7 +11,6 @@ import org.w3c.dom.Element;
import de.sekmi.histream.export.FactClassAnnotator;
import de.sekmi.histream.impl.ObservationImplJAXBTest;
import de.sekmi.histream.xml.XMLUtils;
public class TestFactClassAnnotator {
......
<?xml version="1.0" encoding="UTF-8"?>
<export xmlns="http://sekmi.de/ns/histream/export"
xmlns:eav="http://sekmi.de/histream/ns/eav-data">
<export xmlns="http://sekmi.de/ns/histream/export">
<!--
the export is a three step process:
......@@ -29,65 +28,37 @@ to construct table data.
<patient>
<column header="pid" xpath="@id"/>
<column header="birthdate" xpath="eav:birthdate"/>
<column header="gender" xpath="eav:gender"/>
<column header="birthdate" xpath="birthdate"/>
<column header="gender" xpath="gender"/>
</patient>
<visit>
<!-- context for XPath expressions is each visit node -->
<!-- XMLNS for XPath is assumed to be http://sekmi.de/histream/ns/eav-data -->
<column header="pid" xpath="../@id"/>
<column header="visit" xpath="@id"/>
<!-- concepts for the visit table must occur only once
per visit and may not repeat -->
<column header="start" xpath="eav:start"/>
<column header="start" xpath="start"/>
<!-- What is better? -->
<!-- (a) First column, then concepts with value -->
<column header="diagnostik_labort_ts" na="NULL" xpath="facts/fact[@class='d_lab']/@start">
<concept code="LOINC:26436-6"/>
<concept code="LOINC:26436-6:NEG"/>
<value type="script">
<eval>fact.conceptId.substring(6)</eval>
</value>
</column>
<column header="diagnostik_labort_ts" xpath="facts/fact[@class='d_lab']/@start"/>
<column header="diagnostik_labort" xpath="facts/fact[@class='d_lab']/@concept"/>
<!-- (b) first concepts then columns with value -->
<group>
<concept code="LOINC:26436-6"/>
<concept code="LOINC:26436-6:NEG"/>
<column header="lab_ts" type="attribute">
<attribute>start</attribute>
</column>
<column header="diagnostik_labort_ts" xpath="facts/fact[@class='d_lab']/@start"/>
<column header="diagnostik_labort" xpath="facts/fact[@class='d_lab']/modifier[@code='OPB' or @code='PB']/@code"/>
<!-- We want this:
6:NEG -> not tested
6/mod=OPB -> tested non pathological
6/mod=PB -> tested pathological
-->
<column header="lab_ergebnis" type="attribute">
<modifier>PB</modifier>
<attribute>start</attribute>
</column>
</group>
</visit>
<table id="diagnosen">
<!-- makes more sense for fact tables to specify
the list of concepts first. -->
<concept wildcard="ICD10:*"/>
<concept code="ICD9:123"/>
<column header="pid" type="patient-ref"/>
<column header="visit" type="visit-ref"/>
<column header="start" type="attribute">
<attribute>start</attribute>
</column>
<column header="primary" type="attribute" na="nein">
<modifier>fuehrend</modifier>
<!-- if a modifier element is provided, the property
will use the context of that modifier -->
<constant-value>ja</constant-value>
</column>
<column header="text" type="attribute">
<modifier>originalText</modifier>
<property>value</property>
</column>
<!-- reference sequence from patient -->
<column header="seq1" type="sequence">
<sequence ref="seq1"/>
</column>
<!-- export separate table for repeating elements -->
<table id="diag" class="diag">
<!-- context for XPath expressions is each fact node -->
<column header="pid" xpath="patient-ref"/>
<column header="visit" xpath="visit-ref"/>
<column header="start" type="@start"/>
<column header="code" type="@concept"/>
<column header="primary" xpath="modifier[@code='fuehrend']/@code"/>
</table>
</export>
\ No newline at end of file
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