ShExGenerator Tests included from working branch
This commit is contained in:
dksharma
parent
b248d00ee7
commit
e6ca865d68
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@ -5,7 +5,7 @@
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<parent>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>org.hl7.fhir.core</artifactId>
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<version>5.6.99-SNAPSHOT</version>
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<version>5.6.94-SNAPSHOT</version>
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<relativePath>../pom.xml</relativePath>
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</parent>
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@ -50,6 +50,13 @@
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<optional>true</optional>
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</dependency>
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<!-- ShEx -->
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<dependency>
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<groupId>es.weso</groupId>
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<artifactId>shexs_2.12</artifactId>
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<version>0.2.31</version>
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</dependency>
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<!-- JSON Parsers -->
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<dependency>
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<groupId>com.google.code.gson</groupId>
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@ -0,0 +1,168 @@
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package org.hl7.fhir.r5.test;
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import org.hl7.fhir.r5.model.StructureDefinition;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.List;
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public class ShexGeneratorTestUtils {
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public class resDef {
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public String name;
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public String url;
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public String info;
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public resDef(String _name, String _url, String _info){
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this.name = _name;
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this.url = _url;
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this.info = _info;
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}
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@Override
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public String toString() {
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return " " + name + "[ " + url + " ] ";
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}
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}
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public enum RESOURCE_CATEGORY{
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LOGICAL_NAMES, STRUCTURE_DEFINITIONS, EXTENSIONS, PROFILES, ALL
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}
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public List<resDef> getSDs(List<StructureDefinition> sds, RESOURCE_CATEGORY cat) {
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List<resDef> selSDs = new ArrayList<resDef>();
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sds.forEach((StructureDefinition sd) -> {
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switch(cat) {
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case STRUCTURE_DEFINITIONS:
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if (sd.getType().trim().equals(sd.getName().trim()))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
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break;
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case LOGICAL_NAMES:
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if (sd.getBaseDefinition() == null)
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
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break;
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case EXTENSIONS:
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if ("Extension".equals(sd.getType()))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
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break;
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case PROFILES:
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if (!((sd.getBaseDefinition() == null) ||
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("Extension".equals(sd.getType())) ||
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(sd.getType().trim().equals(sd.getName().trim()))))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
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break;
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default:
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
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}
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});
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Collections.sort(selSDs, new Comparator<resDef>() {
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@Override
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public int compare(resDef o1, resDef o2) {
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return o1.name.compareTo(o2.name);
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}
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});
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return selSDs;
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}
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public static List<String> getMetaStructureDefinitionsToSkip(){
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List<String> skipSDs = new ArrayList<String>();
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/ActivityDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/AdministrableProductDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/ChargeItemDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/ClinicalUseDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/CodeSystem");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/ConceptMap");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/CompartmentDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/CompartmentDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/DeviceDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/ElementDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/EventDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/GraphDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/GuidanceResponse");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/Library");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/ManufacturedItemDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/Measure");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/MeasureReport");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/MedicinalProductDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/MessageDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/NamingSystem");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/ObservationDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/OperationDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/PackagedProductDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/ParameterDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/PlanDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/SearchParameter");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/SpecimenDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/StructureDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/SubstanceDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/Task");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/TerminologyCapabilities");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/TriggerDefinition");
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skipSDs.add("http://hl7.org/fhir/StructureDefinition/ValueSet");
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return skipSDs;
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}
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/**
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* This method prepares selected extensions to test the policy in which ShEx Generator
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* only translates selected resource extensions
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* @return List<String> List of selected resource extensions for testing
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*/
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public static List<String> getSelectedExtensions(){
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List<String> selectedExtesnsions = new ArrayList<String>();
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selectedExtesnsions.add("http://fhir-registry.smarthealthit.org/StructureDefinition/capabilities");
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selectedExtesnsions.add("http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris");
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return selectedExtesnsions;
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}
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public static String getSDInfo(StructureDefinition sd) {
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if (sd != null) {
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String kind = " ";
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try {
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kind = sd.getKind().name();
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} catch (Exception e) {
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System.out.println("Kind is null");
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}
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String name = " ";
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try {
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name = sd.getName();
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} catch (Exception e) {
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System.out.println("Name is null");
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}
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String type = " ";
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try {
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type = sd.getType();
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} catch (Exception e) {
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System.out.println("Type is null");
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}
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String derv = " ";
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try {
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derv = sd.getDerivation().name();
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} catch (Exception e) {
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System.out.println("Derivation is null");
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}
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String url = " ";
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try {
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url = sd.getUrl();
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} catch (Exception e) {
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System.out.println("URL is null");
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}
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String base = " ";
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try {
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base = sd.getBaseDefinition();
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} catch (Exception e) {
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System.out.println("Base is null");
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}
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return kind + "\t" + name + "\t" + type + "\t" + derv + "\t" + url + "\t" + base;
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}
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return "";
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}
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public static void printList(String title, List<ShexGeneratorTestUtils.resDef> items) {
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System.out.println("************************************************************************");
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System.out.println("Printing " + title);
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System.out.println("************************************************************************");
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items.forEach((resDef item) -> {
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System.out.println(item.name + " [" + item.url + "]");
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});
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}
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}
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@ -4,18 +4,37 @@ import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.nio.file.FileSystems;
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import java.nio.file.Path;
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import java.util.ArrayList;
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import java.util.List;
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import es.weso.shex.Schema;
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import es.weso.shex.validator.ShExsValidator;
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import es.weso.shex.validator.ShExsValidatorBuilder;
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import org.apache.commons.lang3.StringUtils;
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import org.fhir.ucum.UcumException;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
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import org.hl7.fhir.r5.conformance.ShExGenerator;
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import org.hl7.fhir.r5.conformance.ShExGenerator.HTMLLinkPolicy;
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import org.hl7.fhir.r5.context.IWorkerContext;
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import org.hl7.fhir.r5.model.StructureDefinition;
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import org.hl7.fhir.r5.test.utils.TestingUtilities;
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import org.hl7.fhir.utilities.TextFile;
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import org.junit.Assert;
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import org.junit.Ignore;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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import static org.hl7.fhir.r5.test.ShexGeneratorTestUtils.printList;
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public class ShexGeneratorTests {
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public static List<String> selectedExtesnsions = new ArrayList<String>();
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public ShExGenerator shexGenerator;
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@BeforeAll
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public static void setup() {
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}
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private void doTest(String name) throws FileNotFoundException, IOException, FHIRException, UcumException {
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StructureDefinition sd = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
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@ -24,8 +43,9 @@ public class ShexGeneratorTests {
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}
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Path outPath = FileSystems.getDefault().getPath(System.getProperty("java.io.tmpdir"), name.toLowerCase() + ".shex");
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TextFile.stringToFile(new ShExGenerator(TestingUtilities.getSharedWorkerContext()).generate(HTMLLinkPolicy.NONE, sd), outPath.toString());
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}
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//this.doTestThis(name.toLowerCase(), name, false, ShExGenerator.ConstraintTranslationPolicy.ALL, false, false);
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}
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@Test
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public void testId() throws FHIRException, IOException, UcumException {
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doTest("id");
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@ -75,4 +95,188 @@ public class ShexGeneratorTests {
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public void testSignature() throws FHIRException, IOException, UcumException {
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doTest("Signature");
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}
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private void doTestThis(String shortName, String name, boolean useSelectedExtensions, ShExGenerator.ConstraintTranslationPolicy policy, boolean debugMode, boolean validateShEx) {
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IWorkerContext ctx = TestingUtilities.getSharedWorkerContext();
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StructureDefinition sd = ctx.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
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if (sd == null) {
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throw new FHIRException("StructuredDefinition for " + name + " was null");
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}
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//Path outPath = FileSystems.getDefault().getPath(System.getProperty("java.io.tmpdir"), name.toLowerCase() + ".shex");
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Path outPath = FileSystems.getDefault().getPath(System.getProperty("user.home") + "/runtime_environments/ShExSchemas", shortName + ".shex");
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try {
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this.shexGenerator = new ShExGenerator(ctx);
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this.shexGenerator.debugMode = debugMode;
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this.shexGenerator.constraintPolicy = policy;
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// ShEx Generator skips resources which are at Meta level of FHIR Resource definitions
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this.shexGenerator.setExcludedStructureDefinitionUrls(
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ShexGeneratorTestUtils.getMetaStructureDefinitionsToSkip());
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// when ShEx translates only selected resource extensions
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if (useSelectedExtensions) {
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List<StructureDefinition> selExtns = new ArrayList<StructureDefinition>();
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for (String eUrl : ShexGeneratorTestUtils.getSelectedExtensions()) {
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StructureDefinition esd = ctx.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(eUrl, null));
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if (esd != null)
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selExtns.add(esd);
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}
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this.shexGenerator.setSelectedExtension(selExtns);
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}
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String schema = this.shexGenerator.generate(HTMLLinkPolicy.NONE, sd);
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if (!schema.isEmpty()) {
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if (validateShEx) {
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try {
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ShExsValidator validator = ShExsValidatorBuilder.fromStringSync(schema, "ShexC");
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Schema sch = validator.schema();
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Assert.assertNotNull(sch);
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System.out.println("VALIDATION PASSED for ShEx Schema " + sd.getName());
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} catch (Exception e) {
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System.out.println("VALIDATION FAILED for ShEx Schema " + sd.getName());
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//System.out.println("\t\t\tMessage: " + e.getMessage());
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}
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}
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TextFile.stringToFile(schema, outPath.toString());
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}
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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}
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@Ignore
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public void doTestAll() throws FileNotFoundException, IOException, FHIRException, UcumException {
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List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
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processSDList(
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ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
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sds, // List of Structure Definitions
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false, //Process all extensions
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ShExGenerator.ConstraintTranslationPolicy.ALL
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// Process all types of constraints, do not skip
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);
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}
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@Ignore
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public void doTestGenericExtensionsOnlyPolicy() throws FileNotFoundException, IOException, FHIRException, UcumException {
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List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
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processSDList(
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ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
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sds, // List of Structure Definitions
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false, //Process all extensions
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ShExGenerator.ConstraintTranslationPolicy.GENERIC_ONLY
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// Process generic constraints only, ignore constraints of type 'context of use'
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);
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}
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@Ignore
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public void doTestContextOfUseExtensionsOnlyPolicy() throws FileNotFoundException, IOException, FHIRException, UcumException {
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List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
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processSDList(
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ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
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sds, // List of Structure Definitions
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false, //Process all extensions
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ShExGenerator.ConstraintTranslationPolicy.CONTEXT_OF_USE_ONLY
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// Process constraints only where context of use found, skip otherwise
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);
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}
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@Ignore
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public void doTestSelectedExtensions() throws FileNotFoundException, IOException, FHIRException, UcumException {
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List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
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processSDList(
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ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
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sds, // List of Structure Definitions
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true, //Process only given/selected extensions, ignore other extensions
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ShExGenerator.ConstraintTranslationPolicy.ALL // Process all type of constraints
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);
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}
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@Ignore
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public void testStructureDefinitionsOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
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List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
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processSDList(
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ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITIONS, // Processing All kinds of Structure Definitions
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sds, // List of Structure Definitions
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false, //Process only given/selected extensions, ignore other extensions
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ShExGenerator.ConstraintTranslationPolicy.ALL // Process all type of constraints
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);
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}
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@Ignore
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public void testExtensionsOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
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List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
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processSDList(
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ShexGeneratorTestUtils.RESOURCE_CATEGORY.EXTENSIONS, // Processing All kinds of Structure Definitions
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sds, // List of Structure Definitions
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false, //Process only given/selected extensions, ignore other extensions
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ShExGenerator.ConstraintTranslationPolicy.ALL // Process all type of constraints
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);
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}
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@Ignore
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public void testLogicalNamesOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
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List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
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processSDList(
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ShexGeneratorTestUtils.RESOURCE_CATEGORY.LOGICAL_NAMES, // Processing All kinds of Structure Definitions
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sds, // List of Structure Definitions
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false, //Process only given/selected extensions, ignore other extensions
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ShExGenerator.ConstraintTranslationPolicy.ALL // Process all type of constraints
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);
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}
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@Ignore
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public void testProfilesOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
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List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
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processSDList(
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ShexGeneratorTestUtils.RESOURCE_CATEGORY.PROFILES, // Processing All kinds of Structure Definitions
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sds, // List of Structure Definitions
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false, //Process only given/selected extensions, ignore other extensions
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ShExGenerator.ConstraintTranslationPolicy.ALL // Process all type of constraints
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);
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}
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private void processSDList(ShexGeneratorTestUtils.RESOURCE_CATEGORY cat,
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List<StructureDefinition> sds,
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boolean useSelectedExtensions,
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ShExGenerator.ConstraintTranslationPolicy policy) {
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if ((sds == null) || (sds.isEmpty())) {
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throw new FHIRException("No StructuredDefinition found!");
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}
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ShexGeneratorTestUtils shexTestUtils = new ShexGeneratorTestUtils();
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List<ShexGeneratorTestUtils.resDef> sdDefs = shexTestUtils.getSDs(sds, cat);
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printList(cat.toString(), sdDefs);
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System.out.println("************************************************************************");
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System.out.println("Processing " + cat);
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System.out.println("************************************************************************");
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sdDefs.forEach((ShexGeneratorTestUtils.resDef resDef) -> {
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String name = resDef.url;
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if (resDef.url.indexOf("/") != -1) {
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String els[] = resDef.url.split("/");
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name = els[els.length - 1];
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}
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System.out.println("******************** " + resDef + " *********************");
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doTestThis(name, resDef.url, useSelectedExtensions, policy, true, true);
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});
|
||||
|
||||
System.out.println("************************ END PROCESSING ******************************");
|
||||
|
||||
System.out.println("************************************************************************");
|
||||
List<String> skipped = this.shexGenerator.getExcludedStructureDefinitionUrls();
|
||||
System.out.println("Total Items processed: " + sds.size());
|
||||
System.out.println("************************************************************************");
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue