Merge remote-tracking branch 'origin/master'

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/client/FHIRToolingClient.java

@@ -171,10 +171,13 @@ public class FHIRToolingClient {
   public TerminologyCapabilities getTerminologyCapabilities() {
     TerminologyCapabilities capabilities = null;
 
-      capabilities =  getCapabilities(resourceAddress.resolveMetadataTxCaps(),
+    try {
+      capabilities = getCapabilities(resourceAddress.resolveMetadataTxCaps(),
         "TerminologyCapabilities",
         "Error fetching the server's terminology capabilities");
-
+    } catch (ClassCastException e) {
+      throw new FHIRException("Unexpected response format for Terminology Capability metadata", e);
+    }
     return capabilities;
   }
 

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/utils/client/FHIRToolingClientTest.java

@@ -32,8 +32,7 @@ import okhttp3.Headers;
 import okhttp3.Request;
 import okhttp3.internal.http2.Header;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.*;
 import static org.mockito.Mockito.times;
 
 class FHIRToolingClientTest {
@@ -162,6 +161,20 @@ class FHIRToolingClientTest {
     checkHeaders(argumentCaptorValue);
   }
 
+  @Test
+  void getTerminologyCapabilitiesNotSupported() throws IOException {
+    Mockito.when(mockClient.issueGetResourceRequest(Mockito.any(URI.class), Mockito.anyString(),
+        Mockito.any(Headers.class), Mockito.eq("TerminologyCapabilities"), Mockito.anyLong()))
+      .thenReturn(new ResourceRequest<>(new CapabilityStatement(), 200, "location"));
+
+    ArgumentCaptor<Headers> headersArgumentCaptor = ArgumentCaptor.forClass(Headers.class);
+    toolingClient.setClientHeaders(getHeaders());
+    Exception exception = assertThrows(FHIRException.class, () -> {
+      toolingClient.getTerminologyCapabilities();
+    });
+    assertEquals(exception.getCause().getClass(), ClassCastException.class);
+  }
+
   @Test
   void getTerminologyCapabilitiesFailsForJSON() throws IOException {
     Mockito.when(mockClient.issueGetResourceRequest(Mockito.any(URI.class), Mockito.anyString(),

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/DurationUtil.java

@@ -0,0 +1,29 @@
+package org.hl7.fhir.utilities;
+
+import java.util.concurrent.TimeUnit;
+
+public class DurationUtil {
+  public static String presentDuration(long duration) {
+    duration = duration / 1000000;
+    String res = "";    // ;
+    long days       = TimeUnit.MILLISECONDS.toDays(duration);
+    long hours      = TimeUnit.MILLISECONDS.toHours(duration) -
+        TimeUnit.DAYS.toHours(TimeUnit.MILLISECONDS.toDays(duration));
+    long minutes    = TimeUnit.MILLISECONDS.toMinutes(duration) -
+        TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(duration));
+    long seconds    = TimeUnit.MILLISECONDS.toSeconds(duration) -
+        TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(duration));
+    long millis     = TimeUnit.MILLISECONDS.toMillis(duration) -
+        TimeUnit.SECONDS.toMillis(TimeUnit.MILLISECONDS.toSeconds(duration));
+
+    if (days > 0)
+      res = String.format("%dd %02d:%02d:%02d.%03d", days, hours, minutes, seconds, millis);
+    else if (hours > 0)
+      res = String.format("%02d:%02d:%02d.%03d", hours, minutes, seconds, millis);
+    else //
+      res = String.format("%02d:%02d.%03d", minutes, seconds, millis);
+//    else
+//      res = String.format("%02d.%04d", seconds, millis);
+    return res;
+  }
+}

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/TimeTracker.java

@@ -1,11 +1,7 @@
 package org.hl7.fhir.utilities;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
-
-import org.hl7.fhir.utilities.TimeTracker.Counter;
 
 public class TimeTracker {
 
@@ -72,29 +68,29 @@ public class TimeTracker {
     CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
     for (Counter c : records) {
       if (c.count == 1) {
-        b.append(c.name+": "+Utilities.presentDuration(c.length));
+        b.append(c.name+": "+ DurationUtil.presentDuration(c.length));
       }
     }
     for (Counter c : records) {
       if (c.count > 1) {
-        b.append(c.name+": "+Utilities.presentDuration(c.length)+" (#"+c.count+")");
+        b.append(c.name+": "+ DurationUtil.presentDuration(c.length)+" (#"+c.count+")");
       }
     }
     return "Times: "+b.toString();
   }
   
   public String clock() {
-    return Utilities.presentDuration(System.nanoTime() - globalStart);
+    return DurationUtil.presentDuration(System.nanoTime() - globalStart);
   }
 
   public String instant() {
-    return Utilities.presentDuration(System.nanoTime() - globalStart);
+    return DurationUtil.presentDuration(System.nanoTime() - globalStart);
   }
 
   public String milestone() {
     long start = milestone == 0 ? globalStart : milestone ;
     milestone = System.nanoTime();
-    return Utilities.presentDuration(milestone - start);
+    return DurationUtil.presentDuration(milestone - start);
   }
 
 }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java

@@ -22,14 +22,12 @@ import java.nio.file.StandardCopyOption;
 import java.time.Duration;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Calendar;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Set;
 import java.util.UUID;
-import java.util.concurrent.TimeUnit;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 
@@ -92,7 +90,7 @@ public class Utilities {
    *
    * @param word the word that is to be pluralized.
    * @return the pluralized form of the word, or the word itself if it could not be pluralized
-   * @see #singularize(Object)
+   * @see Inflector#singularize(Object)
    */
   public static String pluralizeMe(String word) {
     Inflector inf = new Inflector();
@@ -1423,30 +1421,6 @@ public class Utilities {
 
     return byteArrays;
   }
-  
-  public static String presentDuration(long duration) {
-    duration = duration / 1000000;
-    String res = "";    // ;
-    long days       = TimeUnit.MILLISECONDS.toDays(duration);
-    long hours      = TimeUnit.MILLISECONDS.toHours(duration) -
-        TimeUnit.DAYS.toHours(TimeUnit.MILLISECONDS.toDays(duration));
-    long minutes    = TimeUnit.MILLISECONDS.toMinutes(duration) -
-        TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(duration));
-    long seconds    = TimeUnit.MILLISECONDS.toSeconds(duration) -
-        TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(duration));
-    long millis     = TimeUnit.MILLISECONDS.toMillis(duration) -
-        TimeUnit.SECONDS.toMillis(TimeUnit.MILLISECONDS.toSeconds(duration));
-
-    if (days > 0)
-      res = String.format("%dd %02d:%02d:%02d.%04d", days, hours, minutes, seconds, millis);
-    else if (hours > 0)
-      res = String.format("%02d:%02d:%02d.%04d", hours, minutes, seconds, millis);
-    else //
-      res = String.format("%02d:%02d.%04d", minutes, seconds, millis);
-//    else
-//      res = String.format("%02d.%04d", seconds, millis);
-    return res;
-  }
 
   public static void unzip(InputStream zip, Path target) throws IOException {
     try (ZipInputStream zis = new ZipInputStream(zip)) {

org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/DurationUtilTest.java

@@ -0,0 +1,44 @@
+package org.hl7.fhir.utilities;
+
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+import org.xml.sax.SAXException;
+
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.IOException;
+import java.time.Duration;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Stream;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+
+public class DurationUtilTest {
+
+
+  public static Stream<Arguments> data() throws ParserConfigurationException, SAXException, IOException {
+    List<Arguments> objects = new ArrayList<>();
+    objects.add(Arguments.of("PT0.001S", "00:00.001"));
+    objects.add(Arguments.of("PT0.012S", "00:00.012"));
+    objects.add(Arguments.of("PT0.123S", "00:00.123"));
+    objects.add(Arguments.of("PT0.999S", "00:00.999"));
+    objects.add(Arguments.of("PT1.001S", "00:01.001"));
+    objects.add(Arguments.of("PT1M1.001S", "01:01.001"));
+    objects.add(Arguments.of("PT59M1.001S", "59:01.001"));
+    objects.add(Arguments.of("PT1H1M1.001S", "01:01:01.001"));
+    objects.add(Arguments.of("PT23H1M1.001S", "23:01:01.001"));
+    objects.add(Arguments.of("P1DT23H1M1.001S", "1d 23:01:01.001"));
+    objects.add(Arguments.of("P12DT23H1M1.001S", "12d 23:01:01.001"));
+    return objects.stream();
+  }
+
+  @ParameterizedTest
+  @MethodSource("data")
+  public void testPresentDuration(String iso8601String, String expectedPresentation) {
+    assertEquals(expectedPresentation, DurationUtil.presentDuration(Duration.parse(iso8601String).toNanos()));
+  }
+
+
+}

org.hl7.fhir.validation/src/main/resources/help.txt

@@ -13,6 +13,9 @@ schematron checking is performed, then some additional checks are performed.
 If requested, instances will also be verified against the appropriate schema W3C
 XML Schema, JSON schema or ShEx, as appropriate
 
+Default Usage
+=============
+
 Usage: java -jar [validator].jar (parameters)
 
 The following parameters are supported:
@@ -111,9 +114,11 @@ proxy
 
 Parameters can appear in any order
 
-Alternatively, you can use the validator to execute a transformation as
-described by a structure map. To do this, you must provide some additional
-parameters:
+Transforms
+==========
+
+You can use the validator to execute a transformation as described by a
+structure map. To do this, you must provide some additional parameters:
 
  -transform [map]
 
@@ -124,24 +129,33 @@ Any other dependency maps have to be loaded through an -ig reference
 -transform uses the parameters -defn, -txserver, -ig (at least one with the map
 files), and -output
 
-Alternatively, you can use the validator to generate narrative for a resource.
-To do this, you must provide a specific parameter:
+Narratives
+==========
+
+You can use the validator to generate narrative for a resource. To do this, you
+must provide a specific parameter:
 
  -narrative
 
 -narrative requires the parameters -defn, -txserver, -source, and -output. ig
 and profile may be used
 
-Alternatively, you can use the validator to convert a resource or logical model.
-To do this, you must provide a specific parameter:
+Conversion
+==========
+
+You can use the validator to convert a resource or logical model. To do this,
+you must provide a specific parameter:
 
  -convert
 
 -convert requires the parameters -source and -output. ig may be used to provide
 a logical model
 
-Alternatively, you can use the validator to evaluate a FHIRPath expression on a
-resource or logical model. To do this, you must provide a specific parameter:
+FHIRPath
+========
+
+You can use the validator to evaluate a FHIRPath expression on a resource or
+logical model. To do this, you must provide a specific parameter:
 
  -fhirpath [FHIRPath]
 
@@ -150,10 +164,41 @@ resource or logical model. To do this, you must provide a specific parameter:
 -fhirpath requires the parameters -source. ig may be used to provide a logical
 model
 
-Finally, you can use the validator to generate a snapshot for a profile.
-To do this, you must provide a specific parameter:
+Snapshots
+=========
+
+You can use the validator to generate a snapshot for a profile. To do this, you
+must provide a specific parameter:
 
  -snapshot
 
 -snapshot requires the parameters -defn, -txserver, -source, and -output. ig may
-be used to provide necessary base profiles
+be used to provide necessary base profiles
+
+Tests
+=====
+
+The validator can be run in test mode, which executes all JUnit tests for the
+FHIR core library against a set of test cases in a local directory. To do this,
+you must provide a specific parameter with a directory value:
+
+ -test [directory]
+
+The directory must follow the same conventions as the reference test cases found
+at https://github.com/FHIR/fhir-test-cases. This mode must also be executed with
+the Java property java.locale.providers set to COMPAT as below:
+
+  java -Djava.locale.providers=COMPAT -jar validator_cli.jar -tests
+  ./my/path/to/fhir-test-cases
+
+This parameter is compatible with -txCache, -test-modules, and
+-test-classname-filter parameters.
+
+The following test-specific parameters can be used to limit which tests are run:
+-test-modules [module-names] A comma delimited list of Java module names for
+    which to run JUnit tests. By default, all modules are used to run tests.
+    Example: -test-modules org.hl7.fhir.dstu2,org.hl7.fhir.dstu2016may
+
+-test-classname-filter [regex] A regex filter applied to test Java class names
+    for selecting which JUnit tests to run. By default, all tests are run.
+    Example: -test-classname-filter .*ShexGeneratorTests