Merge pull request #1144 from hapifhir/do-20230227-fhircat-shex-fix
Fix for build failures in #1120
This commit is contained in:
Grahame Grieve
GitHub
commit
94de728553
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@ -50,6 +50,14 @@
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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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<optional>true</optional>
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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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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,221 @@
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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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/**
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* ShexGeneratorTestUtils
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*
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* This class provides auxiliary methos to perform testing of
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* Shape Expressions (ShEx) translation of various FHIR Resources.
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*
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* Author: Deepak Sharma
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*/
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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 RESOURCE_CATEGORY kind;
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public resDef(String _name, String _url, String _info, RESOURCE_CATEGORY _kind){
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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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this.kind = _kind;
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}
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@Override
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public String toString() {
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return " " + name + " (Kind: " + kind + " ) [ " + url + " ]";
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}
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}
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public enum RESOURCE_CATEGORY{
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LOGICAL_NAME, STRUCTURE_DEFINITION, EXTENSION, PROFILE, ALL, META_OR_EXAMPLE_OR_OTHER_IGNORE
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}
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/**
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* Filters Structure Definitions from a given list of
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* mixed types of StructureDefinitons based on resource categories
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* @param sds List of StructureDefiniton of any resource type
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* @param cat Resource category filter criteria (inclusive)
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* @return List of resDef with just Structure Definition's name, url and description.
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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_DEFINITION:
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if (getCategory(sd).equals(RESOURCE_CATEGORY.STRUCTURE_DEFINITION))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), RESOURCE_CATEGORY.STRUCTURE_DEFINITION));
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break;
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case LOGICAL_NAME:
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if (getCategory(sd).equals(RESOURCE_CATEGORY.LOGICAL_NAME))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), RESOURCE_CATEGORY.LOGICAL_NAME));
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break;
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case EXTENSION:
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if (getCategory(sd).equals(RESOURCE_CATEGORY.EXTENSION))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), RESOURCE_CATEGORY.EXTENSION));
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break;
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case PROFILE:
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if (getCategory(sd).equals(RESOURCE_CATEGORY.PROFILE))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), RESOURCE_CATEGORY.PROFILE));
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break;
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default:
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), getCategory(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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private RESOURCE_CATEGORY getCategory(StructureDefinition sd) {
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if ("Extension".equals(sd.getType()))
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return RESOURCE_CATEGORY.EXTENSION;
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if (sd.getBaseDefinition() == null)
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return RESOURCE_CATEGORY.LOGICAL_NAME;
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if (sd.getType().trim().equals(sd.getName().trim()))
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return RESOURCE_CATEGORY.STRUCTURE_DEFINITION;
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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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return RESOURCE_CATEGORY.PROFILE;
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return RESOURCE_CATEGORY.META_OR_EXAMPLE_OR_OTHER_IGNORE;
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}
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/**
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* This method is used in testing only - during Resource Constraint translation to ShEx constructs.
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* It can be used by future developers to avoid unnecessary processing of constraints
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* that belong to these Meta Level Resources of FHIR. This list was created by FHIRCat
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* Project group for testing (fhircat.org). It does not skip these SDs for the build.
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* @return List of StructureDefinitions at meta Level
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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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/**
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* Structure Definition Information for debug/printing purpose during testing.
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* @param sd Structure Definition
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* @return String representation of basic SD Information
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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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/**
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* Utility Print method to print interim resDef object for debug/testing purpose.
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* @param title title of resDef types (Resources, Extensions, profiles, etc.)
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* @param items List of resDef objects
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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 + " \t[" + item.url + "]\t" + item.info);
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});
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}
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}
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@ -4,75 +4,421 @@ 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.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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public class ShexGeneratorTests {
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import static org.hl7.fhir.r5.test.ShexGeneratorTestUtils.printList;
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private void doTest(String name) throws FileNotFoundException, IOException, FHIRException, UcumException {
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public class ShexGeneratorTests {
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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, ShexGeneratorTestUtils.RESOURCE_CATEGORY cat) throws FileNotFoundException, IOException, FHIRException, UcumException {
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// ------- Comment following for debugging/testing
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StructureDefinition sd = TestingUtilities.getSharedWorkerContext().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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TextFile.stringToFile(new ShExGenerator(TestingUtilities.getSharedWorkerContext()).generate(HTMLLinkPolicy.NONE, sd), outPath.toString());
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// For Testing Schema Processing and Constraint Mapping related Development
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// If you un-comment the following lines, please comment all other lines in this method.
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// Test with processing constraints flag
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// ----------------- Uncomment following to testing/Debugging -----
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// boolean processConstraints = false;
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// this.doTestSingleSD(name.toLowerCase(), cat, name,
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// false, ShExGenerator.ConstraintTranslationPolicy.ALL,
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// true, true, false, processConstraints);
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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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doTest("id", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
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}
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@Test
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public void testUri() throws FHIRException, IOException, UcumException {
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doTest("uri");
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doTest("uri", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
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}
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@Test
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public void testPatient() throws FHIRException, IOException, UcumException {
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doTest("Patient", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
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}
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@Test
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public void testObservation() throws FHIRException, IOException, UcumException {
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doTest("Observation");
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doTest("Observation", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
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}
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@Test
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public void testRef() throws FHIRException, IOException, UcumException {
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doTest("Reference");
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doTest("Reference", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
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}
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@Test
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public void testAccount() throws FHIRException, IOException, UcumException {
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doTest("Account");
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doTest("Account", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
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}
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@Test
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public void testAppointment() throws FHIRException, IOException, UcumException {
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doTest("Appointment", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
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}
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@Test
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public void testBundle() throws FHIRException, IOException, UcumException {
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doTest("Bundle", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
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}
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@Test
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public void testAge() throws FHIRException, IOException, UcumException {
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doTest("Age", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
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}
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@Test
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public void testMedicationRequest() throws FHIRException, IOException, UcumException {
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doTest("MedicationRequest");
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doTest("MedicationRequest", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
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}
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@Test
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public void testAllergyIntolerance() throws FHIRException, IOException, UcumException {
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doTest("AllergyIntolerance");
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doTest("AllergyIntolerance", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
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}
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@Test
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public void testCoding() throws FHIRException, IOException, UcumException {
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doTest("Coding");
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doTest("Coding", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
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}
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@Test
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public void testTiming() throws FHIRException, IOException, UcumException {
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doTest("Timing");
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doTest("Timing", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
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}
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@Test
|
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public void testSignature() throws FHIRException, IOException, UcumException {
|
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doTest("Signature");
|
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doTest("Signature", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
|
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}
|
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|
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@Test
|
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public void testCapabilityStatement() throws FHIRException, IOException, UcumException {
|
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doTest("CapabilityStatement", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
|
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}
|
||||
|
||||
@Test
|
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public void testElement() throws FHIRException, IOException, UcumException {
|
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doTest("Element", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
|
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}
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||||
|
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@Ignore
|
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public void doTestAllSingleSDMode() throws FileNotFoundException, IOException, FHIRException, UcumException {
|
||||
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
|
||||
|
||||
processSDList(
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
|
||||
sds, // List of Structure Definitions
|
||||
false, //Process all extensions
|
||||
// Process all types of constraints, do not skip
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL,
|
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// BatchMode - All Shex Schemas in one single file
|
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false,
|
||||
// process constraints or not
|
||||
false
|
||||
);
|
||||
}
|
||||
|
||||
@Ignore
|
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public void doTestAllBatchMode() throws FileNotFoundException, IOException, FHIRException, UcumException {
|
||||
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
|
||||
|
||||
processSDList(
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
|
||||
sds, // List of Structure Definitions
|
||||
false, //Process all extensions
|
||||
// Process all types of constraints, do not skip
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL,
|
||||
// BatchMode - All Shex Schemas in one single file
|
||||
true,
|
||||
// process constraints or not
|
||||
true
|
||||
);
|
||||
}
|
||||
|
||||
@Ignore
|
||||
public void doTestGenericExtensionsOnlyPolicy() throws FileNotFoundException, IOException, FHIRException, UcumException {
|
||||
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
|
||||
|
||||
processSDList(
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
|
||||
sds, // List of Structure Definitions
|
||||
false, //Process all extensions
|
||||
ShExGenerator.ConstraintTranslationPolicy.GENERIC_ONLY,
|
||||
// Process generic constraints only, ignore constraints of type 'context of use'
|
||||
false,
|
||||
// process constraints or not
|
||||
true
|
||||
);
|
||||
|
||||
}
|
||||
|
||||
@Ignore
|
||||
public void doTestContextOfUseExtensionsOnlyPolicy() throws FileNotFoundException, IOException, FHIRException, UcumException {
|
||||
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
|
||||
|
||||
processSDList(
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
|
||||
sds, // List of Structure Definitions
|
||||
false, //Process all extensions
|
||||
ShExGenerator.ConstraintTranslationPolicy.CONTEXT_OF_USE_ONLY,
|
||||
// Process constraints only where context of use found, skip otherwise
|
||||
false,
|
||||
// process constraints or not
|
||||
true
|
||||
);
|
||||
}
|
||||
|
||||
@Ignore
|
||||
public void doTestSelectedExtensions() throws FileNotFoundException, IOException, FHIRException, UcumException {
|
||||
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
|
||||
|
||||
processSDList(
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
|
||||
sds, // List of Structure Definitions
|
||||
true, //Process only given/selected extensions, ignore other extensions
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
|
||||
false,
|
||||
// process constraints or not
|
||||
true
|
||||
);
|
||||
}
|
||||
|
||||
@Ignore
|
||||
public void testStructureDefinitionsOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
|
||||
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
|
||||
|
||||
processSDList(
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION, // Processing All kinds of Structure Definitions
|
||||
sds, // List of Structure Definitions
|
||||
false, //Process only given/selected extensions, ignore other extensions
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
|
||||
false,
|
||||
// process constraints or not
|
||||
true
|
||||
);
|
||||
}
|
||||
|
||||
@Ignore
|
||||
public void testExtensionsOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
|
||||
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
|
||||
|
||||
processSDList(
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.EXTENSION, // Processing All kinds of Structure Definitions
|
||||
sds, // List of Structure Definitions
|
||||
false, //Process only given/selected extensions, ignore other extensions
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
|
||||
false,
|
||||
// process constraints or not
|
||||
true
|
||||
);
|
||||
}
|
||||
|
||||
@Ignore
|
||||
public void testLogicalNamesOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
|
||||
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
|
||||
|
||||
processSDList(
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.LOGICAL_NAME, // Processing All kinds of Structure Definitions
|
||||
sds, // List of Structure Definitions
|
||||
false, //Process only given/selected extensions, ignore other extensions
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
|
||||
false,
|
||||
// process constraints or not
|
||||
true
|
||||
);
|
||||
}
|
||||
|
||||
@Ignore
|
||||
public void testProfilesOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
|
||||
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
|
||||
processSDList(
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.PROFILE, // Processing All kinds of Structure Definitions
|
||||
sds, // List of Structure Definitions
|
||||
false, //Process only given/selected extensions, ignore other extensions
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
|
||||
false,
|
||||
// process constraints or not
|
||||
true
|
||||
);
|
||||
}
|
||||
|
||||
private void processSDList(ShexGeneratorTestUtils.RESOURCE_CATEGORY cat,
|
||||
List<StructureDefinition> sds,
|
||||
boolean useSelectedExtensions,
|
||||
ShExGenerator.ConstraintTranslationPolicy policy,
|
||||
boolean batchMode, boolean processConstraints) {
|
||||
if ((sds == null) || (sds.isEmpty())) {
|
||||
throw new FHIRException("No StructuredDefinition found!");
|
||||
}
|
||||
|
||||
ShexGeneratorTestUtils shexTestUtils = new ShexGeneratorTestUtils();
|
||||
List<ShexGeneratorTestUtils.resDef> sdDefs = shexTestUtils.getSDs(sds, cat);
|
||||
|
||||
printList(cat.toString(), sdDefs);
|
||||
System.out.println("************************************************************************");
|
||||
System.out.println("Processing " + cat);
|
||||
System.out.println("************************************************************************");
|
||||
|
||||
if (!batchMode) {
|
||||
sdDefs.forEach((ShexGeneratorTestUtils.resDef resDef) -> {
|
||||
String name = resDef.url;
|
||||
if (resDef.url.indexOf("/") != -1) {
|
||||
String els[] = resDef.url.split("/");
|
||||
name = els[els.length - 1];
|
||||
}
|
||||
System.out.println("******************** " + resDef + " *********************");
|
||||
doTestSingleSD(name, resDef.kind, resDef.url, useSelectedExtensions, policy, true, true, false, processConstraints);
|
||||
});
|
||||
} else {
|
||||
doTestBatchSD(sds, useSelectedExtensions, policy, true, true, false, processConstraints);
|
||||
}
|
||||
|
||||
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("************************************************************************");
|
||||
}
|
||||
|
||||
private void doTestSingleSD(String shortName, ShexGeneratorTestUtils.RESOURCE_CATEGORY cat,
|
||||
String name, boolean useSelectedExtensions,
|
||||
ShExGenerator.ConstraintTranslationPolicy policy,
|
||||
boolean debugMode, boolean validateShEx,
|
||||
boolean excludeMetaSDs, boolean processConstraints) {
|
||||
IWorkerContext ctx = TestingUtilities.getSharedWorkerContext();
|
||||
StructureDefinition sd = ctx.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
|
||||
if (sd == null) {
|
||||
throw new FHIRException("StructuredDefinition for " + name + "(Kind:" + cat + ") was null");
|
||||
}
|
||||
//Path outPath = FileSystems.getDefault().getPath(System.getProperty("java.io.tmpdir"), name.toLowerCase() + ".shex");
|
||||
Path outPath = FileSystems.getDefault().getPath(System.getProperty("user.home") + "/runtime_environments/ShExSchemas", shortName + ".shex");
|
||||
try {
|
||||
this.shexGenerator = new ShExGenerator(ctx);
|
||||
|
||||
this.shexGenerator.debugMode = debugMode;
|
||||
this.shexGenerator.processConstraints = processConstraints;
|
||||
this.shexGenerator.constraintPolicy = policy;
|
||||
|
||||
if (excludeMetaSDs) {
|
||||
// ShEx Generator skips resources which are at Meta level of FHIR Resource definitions
|
||||
this.shexGenerator.setExcludedStructureDefinitionUrls(
|
||||
ShexGeneratorTestUtils.getMetaStructureDefinitionsToSkip());
|
||||
}
|
||||
|
||||
// when ShEx translates only selected resource extensions
|
||||
if (useSelectedExtensions) {
|
||||
List<StructureDefinition> selExtns = new ArrayList<StructureDefinition>();
|
||||
for (String eUrl : ShexGeneratorTestUtils.getSelectedExtensions()) {
|
||||
StructureDefinition esd = ctx.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(eUrl, null));
|
||||
if (esd != null)
|
||||
selExtns.add(esd);
|
||||
}
|
||||
this.shexGenerator.setSelectedExtension(selExtns);
|
||||
}
|
||||
|
||||
String schema = this.shexGenerator.generate(HTMLLinkPolicy.NONE, sd);
|
||||
if (!schema.isEmpty()) {
|
||||
|
||||
if (validateShEx) {
|
||||
try {
|
||||
ShExsValidator validator = ShExsValidatorBuilder.fromStringSync(schema, "ShexC");
|
||||
Schema sch = validator.schema();
|
||||
|
||||
Assert.assertNotNull(sch);
|
||||
|
||||
System.out.println("VALIDATION PASSED for ShEx Schema " + sd.getName() + " (Kind:" + cat + ")");
|
||||
} catch (Exception e) {
|
||||
System.out.println("VALIDATION FAILED for ShEx Schema " + sd.getName() + " (Kind:" + cat + ")");
|
||||
e.printStackTrace();
|
||||
}
|
||||
}
|
||||
TextFile.stringToFile(schema, outPath.toString());
|
||||
}
|
||||
} catch (IOException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
private void doTestBatchSD(List<StructureDefinition> sds, boolean useSelectedExtensions,
|
||||
ShExGenerator.ConstraintTranslationPolicy policy, boolean debugMode,
|
||||
boolean validateShEx, boolean excludeMetaSDs, boolean processConstraints) {
|
||||
IWorkerContext ctx = TestingUtilities.getSharedWorkerContext();
|
||||
//Path outPath = FileSystems.getDefault().getPath(System.getProperty("java.io.tmpdir"), name.toLowerCase() + ".shex");
|
||||
Path outPath = FileSystems.getDefault().getPath(System.getProperty("user.home") + "/runtime_environments/ShExSchemas", "ShEx.shex");
|
||||
try {
|
||||
this.shexGenerator = new ShExGenerator(ctx);
|
||||
|
||||
this.shexGenerator.debugMode = debugMode;
|
||||
this.shexGenerator.processConstraints = processConstraints;
|
||||
this.shexGenerator.constraintPolicy = policy;
|
||||
|
||||
if (excludeMetaSDs) {
|
||||
// ShEx Generator skips resources which are at Meta level of FHIR Resource definitions
|
||||
this.shexGenerator.setExcludedStructureDefinitionUrls(
|
||||
ShexGeneratorTestUtils.getMetaStructureDefinitionsToSkip());
|
||||
}
|
||||
|
||||
// when ShEx translates only selected resource extensions
|
||||
if (useSelectedExtensions) {
|
||||
List<StructureDefinition> selExtns = new ArrayList<StructureDefinition>();
|
||||
for (String eUrl : ShexGeneratorTestUtils.getSelectedExtensions()) {
|
||||
StructureDefinition esd = ctx.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(eUrl, null));
|
||||
if (esd != null)
|
||||
selExtns.add(esd);
|
||||
}
|
||||
this.shexGenerator.setSelectedExtension(selExtns);
|
||||
}
|
||||
|
||||
String schema = this.shexGenerator.generate(HTMLLinkPolicy.NONE, sds);
|
||||
if (!schema.isEmpty()) {
|
||||
if (validateShEx) {
|
||||
try {
|
||||
ShExsValidator validator = ShExsValidatorBuilder.fromStringSync(schema, "ShexC");
|
||||
Schema sch = validator.schema();
|
||||
|
||||
Assert.assertNotNull(sch);
|
||||
System.out.println("VALIDATION PASSED for ShEx Schema ALL SHEX STRUCTURES");
|
||||
} catch (Exception e) {
|
||||
System.out.println("VALIDATION FAILED for ShEx Schema ALL SHEX STRUCTURES");
|
||||
e.printStackTrace();
|
||||
}
|
||||
}
|
||||
TextFile.stringToFile(schema, outPath.toString());
|
||||
}
|
||||
} catch (IOException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue