ShExGenerator Tests included from working branch

org.hl7.fhir.r5/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>5.6.99-SNAPSHOT</version>
+		<version>5.6.94-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -50,6 +50,13 @@
 			<optional>true</optional>
 		</dependency>
 
+		<!-- ShEx -->
+		<dependency>
+			<groupId>es.weso</groupId>
+			<artifactId>shexs_2.12</artifactId>
+			<version>0.2.31</version>
+		</dependency>
+
 		<!-- JSON Parsers -->
 		<dependency>
 			<groupId>com.google.code.gson</groupId>

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ShexGeneratorTestUtils.java

@@ -0,0 +1,168 @@
+package org.hl7.fhir.r5.test;
+
+import org.hl7.fhir.r5.model.StructureDefinition;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+public class ShexGeneratorTestUtils {
+  public class resDef {
+    public String name;
+    public String url;
+    public String info;
+
+    public resDef(String _name, String _url, String _info){
+      this.name = _name;
+      this.url = _url;
+      this.info = _info;
+    }
+
+    @Override
+    public String toString() {
+      return " " + name + "[ " + url + " ] ";
+    }
+  }
+
+  public enum RESOURCE_CATEGORY{
+    LOGICAL_NAMES, STRUCTURE_DEFINITIONS, EXTENSIONS, PROFILES, ALL
+  }
+  public List<resDef> getSDs(List<StructureDefinition> sds, RESOURCE_CATEGORY cat) {
+    List<resDef> selSDs = new ArrayList<resDef>();
+    sds.forEach((StructureDefinition sd) -> {
+      switch(cat) {
+        case STRUCTURE_DEFINITIONS:
+          if (sd.getType().trim().equals(sd.getName().trim()))
+              selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
+          break;
+        case LOGICAL_NAMES:
+          if (sd.getBaseDefinition() == null)
+            selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
+          break;
+        case EXTENSIONS:
+          if ("Extension".equals(sd.getType()))
+            selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
+          break;
+        case PROFILES:
+          if (!((sd.getBaseDefinition() == null) ||
+              ("Extension".equals(sd.getType())) ||
+              (sd.getType().trim().equals(sd.getName().trim()))))
+            selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
+          break;
+        default:
+          selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
+      }
+    });
+
+    Collections.sort(selSDs, new Comparator<resDef>() {
+      @Override
+      public int compare(resDef o1, resDef o2) {
+        return o1.name.compareTo(o2.name);
+      }
+    });
+
+    return selSDs;
+  }
+  public static List<String> getMetaStructureDefinitionsToSkip(){
+    List<String> skipSDs = new ArrayList<String>();
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/ActivityDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/AdministrableProductDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/ChargeItemDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/ClinicalUseDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/CodeSystem");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/ConceptMap");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/CompartmentDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/CompartmentDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/DeviceDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/ElementDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/EventDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/GraphDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/GuidanceResponse");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/Library");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/ManufacturedItemDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/Measure");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/MeasureReport");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/MedicinalProductDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/MessageDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/NamingSystem");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/ObservationDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/OperationDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/PackagedProductDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/ParameterDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/PlanDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/SearchParameter");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/SpecimenDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/StructureDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/SubstanceDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/Task");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/TerminologyCapabilities");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/TriggerDefinition");
+    skipSDs.add("http://hl7.org/fhir/StructureDefinition/ValueSet");
+    return skipSDs;
+  }
+
+  /**
+   * This method prepares selected extensions to test the policy in which ShEx Generator
+   * only translates selected resource extensions
+   * @return List<String> List of selected resource extensions for testing
+   */
+  public static List<String> getSelectedExtensions(){
+    List<String> selectedExtesnsions = new ArrayList<String>();
+    selectedExtesnsions.add("http://fhir-registry.smarthealthit.org/StructureDefinition/capabilities");
+    selectedExtesnsions.add("http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris");
+    return selectedExtesnsions;
+  }
+
+  public static String getSDInfo(StructureDefinition sd) {
+    if (sd != null) {
+      String kind = " ";
+      try {
+        kind = sd.getKind().name();
+      } catch (Exception e) {
+        System.out.println("Kind is null");
+      }
+      String name = " ";
+      try {
+        name = sd.getName();
+      } catch (Exception e) {
+        System.out.println("Name is null");
+      }
+      String type = " ";
+      try {
+        type = sd.getType();
+      } catch (Exception e) {
+        System.out.println("Type is null");
+      }
+      String derv = " ";
+      try {
+        derv = sd.getDerivation().name();
+      } catch (Exception e) {
+        System.out.println("Derivation is null");
+      }
+      String url = " ";
+      try {
+        url = sd.getUrl();
+      } catch (Exception e) {
+        System.out.println("URL is null");
+      }
+      String base = " ";
+      try {
+        base = sd.getBaseDefinition();
+      } catch (Exception e) {
+        System.out.println("Base is null");
+      }
+      return kind + "\t" + name + "\t" + type + "\t" + derv + "\t" + url + "\t" + base;
+    }
+    return "";
+  }
+
+  public static void printList(String title, List<ShexGeneratorTestUtils.resDef> items) {
+    System.out.println("************************************************************************");
+    System.out.println("Printing " + title);
+    System.out.println("************************************************************************");
+    items.forEach((resDef item) -> {
+      System.out.println(item.name + " [" + item.url + "]");
+    });
+  }
+}

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ShexGeneratorTests.java

@@ -4,18 +4,37 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.nio.file.FileSystems;
 import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.List;
 
+import es.weso.shex.Schema;
+import es.weso.shex.validator.ShExsValidator;
+import es.weso.shex.validator.ShExsValidatorBuilder;
+import org.apache.commons.lang3.StringUtils;
 import org.fhir.ucum.UcumException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
 import org.hl7.fhir.r5.conformance.ShExGenerator;
 import org.hl7.fhir.r5.conformance.ShExGenerator.HTMLLinkPolicy;
+import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.utilities.TextFile;
+import org.junit.Assert;
+import org.junit.Ignore;
+import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
 
+import static org.hl7.fhir.r5.test.ShexGeneratorTestUtils.printList;
+
 public class ShexGeneratorTests {
+  public static List<String> selectedExtesnsions = new ArrayList<String>();
+
+  public ShExGenerator shexGenerator;
+
+  @BeforeAll
+  public static void setup() {
+  }
 
   private void doTest(String name) throws FileNotFoundException, IOException, FHIRException, UcumException {
     StructureDefinition sd = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
@@ -24,8 +43,9 @@ public class ShexGeneratorTests {
     }
     Path outPath = FileSystems.getDefault().getPath(System.getProperty("java.io.tmpdir"), name.toLowerCase() + ".shex");
     TextFile.stringToFile(new ShExGenerator(TestingUtilities.getSharedWorkerContext()).generate(HTMLLinkPolicy.NONE, sd), outPath.toString());
-  }
 
+    //this.doTestThis(name.toLowerCase(), name, false, ShExGenerator.ConstraintTranslationPolicy.ALL, false, false);
+  }
   @Test
   public void testId() throws FHIRException, IOException, UcumException {
     doTest("id");
@@ -75,4 +95,188 @@ public class ShexGeneratorTests {
   public void testSignature() throws FHIRException, IOException, UcumException {
     doTest("Signature");
   }
+
+  private void doTestThis(String shortName, String name, boolean useSelectedExtensions, ShExGenerator.ConstraintTranslationPolicy policy, boolean debugMode, boolean validateShEx) {
+    IWorkerContext ctx = TestingUtilities.getSharedWorkerContext();
+    StructureDefinition sd = ctx.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
+    if (sd == null) {
+      throw new FHIRException("StructuredDefinition for " + name + " 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.constraintPolicy = policy;
+
+      // 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());
+          } catch (Exception e) {
+            System.out.println("VALIDATION FAILED for ShEx Schema " + sd.getName());
+            //System.out.println("\t\t\tMessage: " + e.getMessage());
+          }
+        }
+        TextFile.stringToFile(schema, outPath.toString());
+      }
+    } catch (IOException e) {
+      throw new RuntimeException(e);
+    }
+  }
+
+    @Ignore
+    public void doTestAll() 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.ALL
+        // Process all types of constraints, do not skip
+      );
+    }
+
+    @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'
+      );
+
+    }
+
+    @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
+      );
+    }
+
+    @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
+      );
+    }
+
+  @Ignore
+  public void testStructureDefinitionsOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
+    List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
+
+    processSDList(
+      ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITIONS, // 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
+    );
+  }
+
+  @Ignore
+  public void testExtensionsOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
+    List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
+
+    processSDList(
+      ShexGeneratorTestUtils.RESOURCE_CATEGORY.EXTENSIONS, // 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
+    );
+  }
+
+  @Ignore
+  public void testLogicalNamesOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
+    List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
+
+    processSDList(
+      ShexGeneratorTestUtils.RESOURCE_CATEGORY.LOGICAL_NAMES, // 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
+    );
+  }
+
+  @Ignore
+  public void testProfilesOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
+    List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
+    processSDList(
+      ShexGeneratorTestUtils.RESOURCE_CATEGORY.PROFILES, // 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
+    );
+  }
+
+  private void processSDList(ShexGeneratorTestUtils.RESOURCE_CATEGORY cat,
+                             List<StructureDefinition> sds,
+                           boolean useSelectedExtensions,
+                           ShExGenerator.ConstraintTranslationPolicy policy) {
+    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("************************************************************************");
+
+    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 + " *********************");
+      doTestThis(name, resDef.url, useSelectedExtensions, policy, true, true);
+    });
+
+    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("************************************************************************");
+  }
 }