Merge pull request #385 from hapifhir/gg-v522

5.2. cumulative release

RELEASE_NOTES.md

@@ -1 +1,8 @@
-* fix for issue 383
+Validator Changes:
+* no effective changes
+
+Other Code Changes:
+* fix bug converting type mode in Structure Map
+* fix bug converting Timing.when (issue 383)
+* fix bug doing date time comparisons with seconds in FHIRPath
+* Add support for instance-name and instance-description extensions

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv40_50/StructureMap40_50.java

@@ -3,6 +3,7 @@ package org.hl7.fhir.convertors.conv40_50;
 
 import org.hl7.fhir.convertors.VersionConvertor_40_50;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupTypeMode;
 
 import java.util.stream.Collectors;
 
@@ -220,8 +221,11 @@ public class StructureMap40_50 extends VersionConvertor_40_50 {
             tgt.setNameElement(convertId(src.getNameElement()));
         if (src.hasExtends())
             tgt.setExtendsElement(convertId(src.getExtendsElement()));
-        if (src.hasTypeMode())
+        if (src.hasTypeMode()) {
             tgt.setTypeModeElement(convertStructureMapGroupTypeMode(src.getTypeModeElement()));
+        } else {
+          tgt.setTypeMode(StructureMapGroupTypeMode.NONE);          
+        }
         if (src.hasDocumentation())
             tgt.setDocumentationElement(convertString(src.getDocumentationElement()));
         for (org.hl7.fhir.r5.model.StructureMap.StructureMapGroupInputComponent t : src.getInput()) tgt.addInput(convertStructureMapGroupInputComponent(t));

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java

@@ -812,6 +812,10 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
     return loadedPackages.contains(id+"#"+ver);
   }
 
+  public boolean hasPackage(String idAndver) {
+    return loadedPackages.contains(idAndver);
+  }
+
   public void setClock(TimeTracker tt) {
     clock = tt;
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/BaseDateTimeType.java

@@ -899,16 +899,12 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
       lowRight = lowRight - (14 * DateUtils.MILLIS_PER_HOUR);
       highRight = highRight + (14 * DateUtils.MILLIS_PER_HOUR);
     }
-    System.out.print("["+((lowLeft / 1000) - 130000000)+"-"+((highLeft / 1000)  - 130000000)+"] vs ["+((lowRight / 1000) - 130000000)+"-"+((highRight / 1000) - 130000000)+"] = ");
     if (highRight < lowLeft) {
-      System.out.println("false");
       return false;
     }
     if (highLeft < lowRight) {
-      System.out.println("false");
       return false;
     }
-    System.out.println("true");
     return true;
   }
 
@@ -1000,6 +996,14 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
         return def;
       }
 
+      if (left.getSecond() < right.getSecond()) {
+        return -1;
+      } else if (left.getSecond() > right.getSecond()) {
+        return 1;
+      } else if (left.getPrecision() == TemporalPrecisionEnum.SECOND && right.getPrecision() == TemporalPrecisionEnum.SECOND) {
+        return 0;
+      }
+
       if (left.getSecondsMilli() < right.getSecondsMilli()) {
         return -1;
       } else if (left.getSecondsMilli() > right.getSecondsMilli()) {

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java

@@ -523,7 +523,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
       InputStream stream = fetchFromUrlSpecific(Utilities.pathURL("http://build.fhir.org", id + ".tgz"), false);
       return new InputStreamWithSrc(stream, Utilities.pathURL("http://build.fhir.org", id + ".tgz"), "current");
     } else {
-      throw new FHIRException("The package '" + id + "' has not entry on the current build server");
+      throw new FHIRException("The package '" + id + "' has no entry on the current build server");
     }
   }
 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java

@@ -1087,6 +1087,12 @@ public class NpmPackage {
         return false;
       }
     }
+    if (Utilities.existsInList(name(), "fhir.test.data.r2", "fhir.test.data.r3", "fhir.test.data.r4", "fhir.tx.support.r2", "fhir.tx.support.r3", "fhir.tx.support.r4", "us.nlm.vsac")) {
+      return true;
+    }
+    if (JSONUtil.bool(npm, "lazy-load")) {
+      return true;
+    }
     if (!hasFile("other", "spec.internals")) {
       return false;
     }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlParser.java

@@ -55,6 +55,7 @@ import org.xmlpull.v1.XmlPullParserException;
 
 public class XhtmlParser {
   public static final String XHTML_NS = "http://www.w3.org/1999/xhtml";
+  private static final char END_OF_CHARS = (char) -1;
 
   public class NSMap {
     private Map<String, String> nslist = new HashMap<String, String>();
@@ -515,7 +516,7 @@ private boolean elementIsOk(String name) throws FHIRFormatError  {
   private void parseElementInner(XhtmlNode node, List<XhtmlNode> parents, NSMap nsm, boolean escaping) throws FHIRFormatError, IOException 
   {
     StringBuilder s = new StringBuilder();
-    while (peekChar() != '\0' && !parents.contains(unwindPoint) && !(node == unwindPoint))
+    while (peekChar() != END_OF_CHARS && !parents.contains(unwindPoint) && !(node == unwindPoint))
     {
       if (peekChar() == '<')
       {
@@ -606,7 +607,7 @@ private boolean elementIsOk(String name) throws FHIRFormatError  {
   {
     while (Character.isWhitespace(peekChar()))
       readChar();
-    while (peekChar() != '>' && peekChar() != '/' && peekChar() != '\0')
+    while (peekChar() != '>' && peekChar() != '/' && peekChar() != END_OF_CHARS)
     {
       String name = readName();
       if (name.length() == 0)
@@ -630,7 +631,7 @@ private boolean elementIsOk(String name) throws FHIRFormatError  {
         if (peekChar() == '"' || peekChar() == '\'')
           node.getAttributes().put(name, parseAttributeValue(readChar()));
         else
-          node.getAttributes().put(name, parseAttributeValue('\0'));
+          node.getAttributes().put(name, parseAttributeValue(END_OF_CHARS));
       }
       while (Character.isWhitespace(peekChar()))
         readChar();
@@ -640,7 +641,7 @@ private boolean elementIsOk(String name) throws FHIRFormatError  {
   private String parseAttributeValue(char term) throws IOException, FHIRFormatError 
   {
     StringBuilder b = new StringBuilder();
-    while (peekChar() != '\0' && peekChar() != '>' && (term != '\0' || peekChar() != '/') && peekChar() != term)
+    while (peekChar() != END_OF_CHARS && peekChar() != '>' && (term != END_OF_CHARS || peekChar() != '/') && peekChar() != term)
     {
       if (peekChar() == '&')
       {
@@ -704,15 +705,15 @@ private boolean elementIsOk(String name) throws FHIRFormatError  {
     if (cache.length() > 0)
       return cache.charAt(0);
     else if (!rdr.ready())
-      return '\0';
+      return END_OF_CHARS;
     else
     {
-      char c = (char)rdr.read();
+      int i = rdr.read();
-      if (c == (char)-1)
+      if (i == -1)       {
-      {
         cache = "";
-        return '\0';
+        return END_OF_CHARS;
       }
+      char c = (char) i;
       cache =  Character.toString(c);
       return c;
     }
@@ -727,7 +728,7 @@ private boolean elementIsOk(String name) throws FHIRFormatError  {
       cache = cache.length() == 1 ? "" : cache.substring(1);
     }
     else if (!rdr.ready())
-      c = '\0';
+      c = END_OF_CHARS;
     else
       c = (char)rdr.read();
     if (c == '\r' || c == '\n') {
@@ -744,9 +745,9 @@ private boolean elementIsOk(String name) throws FHIRFormatError  {
   private String readToTagEnd() throws IOException, FHIRFormatError 
   {
     StringBuilder s = new StringBuilder();
-    while (peekChar() != '>' && peekChar() != '\0')
+    while (peekChar() != '>' && peekChar() != END_OF_CHARS)
       s.append(readChar());
-    if (peekChar() != '\0')
+    if (peekChar() != END_OF_CHARS)
     {
       readChar();
       skipWhiteSpace();
@@ -765,7 +766,7 @@ private boolean elementIsOk(String name) throws FHIRFormatError  {
       if (c == '>') {
         done = true;
         readChar();
-      } else if (c != '\0')
+      } else if (c != END_OF_CHARS)
         s.append(readChar());
       else if (mustBeWellFormed)
         throw new FHIRFormatError("Unexpected termination of html source"+descLoc());
@@ -814,12 +815,12 @@ private boolean elementIsOk(String name) throws FHIRFormatError  {
       } else if (c == '[' && s.toString().startsWith("DOCTYPE ")) {
         doctypeEntities = true;
         s.append(readChar());
-      } else if (c != '\0')
+      } else if (c != END_OF_CHARS)
         s.append(readChar());
       else if (mustBeWellFormed)
         throw new FHIRFormatError("Unexpected termination of html source"+descLoc());
     }
-    if (peekChar() != '\0')
+    if (peekChar() != END_OF_CHARS)
     {
       readChar();
       skipWhiteSpace();

org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/XhtmlNodeTest.java

@@ -1,6 +1,8 @@
 package org.hl7.fhir.utilities.tests;
 
+import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
+import org.hl7.fhir.utilities.xhtml.XhtmlParser;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
@@ -88,4 +90,9 @@ public class XhtmlNodeTest {
     ObjectOutputStream oout = new ObjectOutputStream(bout);
     oout.writeObject(node);
   }
+  
+  @Test
+  public void testParseBadChars() throws FHIRFormatError, IOException {
+    XhtmlNode x = new XhtmlParser().parse(BaseTestingUtilities.loadTestResource("xhtml", "bad-chars.html"), "div");
+  }
 }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java

@@ -1007,7 +1007,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
   }
 
   public void loadIg(String src, boolean recursive) throws IOException, FHIRException {
-    NpmPackage npm = src.matches(FilesystemPackageCacheManager.PACKAGE_VERSION_REGEX_OPT) ? pcm.loadPackage(src, null) : null;
+    NpmPackage npm = src.matches(FilesystemPackageCacheManager.PACKAGE_VERSION_REGEX_OPT) && !new File(src).exists() ? pcm.loadPackage(src, null) : null;
     if (npm != null) {
       for (String s : npm.dependencies()) {
         if (!context.getLoadedPackages().contains(s)) {

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java

@@ -52,6 +52,7 @@ import org.hl7.fhir.r5.utils.IResourceValidator.ReferenceValidationPolicy;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
+import org.hl7.fhir.utilities.json.JSONUtil;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@@ -81,8 +82,9 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
 
     Map<String, JsonObject> examples = new HashMap<String, JsonObject>();
     manifest = (JsonObject) new com.google.gson.JsonParser().parse(contents);
-    for (Entry<String, JsonElement> e : manifest.getAsJsonObject("test-cases").entrySet()) {
+    for (JsonElement e : manifest.getAsJsonArray("test-cases")) {
-      examples.put(e.getKey(), e.getValue().getAsJsonObject());
+      JsonObject o = (JsonObject) e;
+      examples.put(JSONUtil.str(o, "name"), o);
     }
 
     List<String> names = new ArrayList<String>(examples.size());
@@ -154,7 +156,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
     if (content.has("use-test") && !content.get("use-test").getAsBoolean())
       return;
 
-    String testCaseContent = TestingUtilities.loadTestResource("validator", name);
+    String testCaseContent = TestingUtilities.loadTestResource("validator", JSONUtil.str(content, "file"));
     InstanceValidator val = vCurr.getValidator();
     val.setWantCheckSnapshotUnchanged(true);
     val.getContext().setClientRetryCount(4);
@@ -226,7 +228,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
     if (content.has("logical")==false) {
       val.setAssumeValidRestReferences(content.has("assumeValidRestReferences") ? content.get("assumeValidRestReferences").getAsBoolean() : false);
       System.out.println(String.format("Start Validating (%d to set up)", (System.nanoTime() - setup) / 1000000));
-      if (name.endsWith(".json"))
+      if (JSONUtil.str(content, "file").endsWith(".json"))
         val.validate(null, errors, IOUtils.toInputStream(testCaseContent, Charsets.UTF_8), FhirFormat.JSON);
       else
         val.validate(null, errors, IOUtils.toInputStream(testCaseContent, Charsets.UTF_8), FhirFormat.XML);
@@ -258,7 +260,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
       val.getContext().cacheResource(sd);
       val.setAssumeValidRestReferences(profile.has("assumeValidRestReferences") ? profile.get("assumeValidRestReferences").getAsBoolean() : false);
       List<ValidationMessage> errorsProfile = new ArrayList<ValidationMessage>();
-      if (name.endsWith(".json"))
+      if (JSONUtil.str(content, "file").endsWith(".json"))
         val.validate(null, errorsProfile, IOUtils.toInputStream(testCaseContent, Charsets.UTF_8), FhirFormat.JSON, asSdList(sd));
       else
         val.validate(null, errorsProfile, IOUtils.toInputStream(testCaseContent, Charsets.UTF_8), FhirFormat.XML, asSdList(sd));

pom.xml

@@ -19,7 +19,7 @@
 
     <properties>
         <hapi_fhir_version>5.1.0</hapi_fhir_version>
-        <validator_test_case_version>1.1.50</validator_test_case_version>
+        <validator_test_case_version>1.1.51-SNAPSHOT</validator_test_case_version>
         <junit_jupiter_version>5.6.2</junit_jupiter_version>
         <maven_surefire_version>3.0.0-M4</maven_surefire_version>
         <jacoco_version>0.8.5</jacoco_version>