Merge remote-tracking branch 'origin/master'

org.hl7.fhir.convertors/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>5.6.116-SNAPSHOT</version>
+        <version>5.6.117-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.dstu2/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>5.6.116-SNAPSHOT</version>
+		<version>5.6.117-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.dstu2016may/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>5.6.116-SNAPSHOT</version>
+		<version>5.6.117-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.dstu3/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>5.6.116-SNAPSHOT</version>
+        <version>5.6.117-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.r4/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>5.6.116-SNAPSHOT</version>
+		<version>5.6.117-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.r4b/.classpath

@@ -19,7 +19,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-17">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>

org.hl7.fhir.r4b/.project

@@ -17,6 +17,7 @@
 		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.pde.PluginNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 	</natures>

org.hl7.fhir.r4b/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>5.6.116-SNAPSHOT</version>
+		<version>5.6.117-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.r5/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>5.6.116-SNAPSHOT</version>
+		<version>5.6.117-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/FmlParser.java

@@ -108,10 +108,18 @@ public class FmlParser extends ParserBase {
         parseGroup(result, lexer);
       }
     } catch (FHIRLexerException e) {
+      if (policy == ValidationPolicy.NONE) {
+        throw e;
+      } else {
         logError("2023-02-24", e.getLocation().getLine(), e.getLocation().getColumn(), "??", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
+      }
     } catch (Exception e) {
+      if (policy == ValidationPolicy.NONE) {
+        throw e;
+      } else {
         logError("2023-02-24", -1, -1, "?", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
       }
+    }
     result.setIgnorePropertyOrder(true);
     return result;
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/CodeSystemUtilities.java

@@ -698,5 +698,15 @@ public class CodeSystemUtilities {
     }
     return list;
   }
+
+  public static boolean checkDisplay(CodeSystem cs, ConceptDefinitionComponent cd, String display) {
+    List<String> displays = getDisplays(cs, cd);
+    for (String s : displays) {
+      if (s.equalsIgnoreCase(display)) {
+        return true;
+      }
+    }
+    return false;
+  }
 }
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/TestingUtilities.java

@@ -93,7 +93,7 @@ public class TestingUtilities extends BaseTestingUtilities {
         fcontext.loadFromPackage(utg, new TestPackageLoader(Utilities.strings("CodeSystem", "ValueSet")));
       } 
       if (!fcontext.hasPackage("hl7.fhir.uv.extensions", null)) {
-        NpmPackage ext = pcm.loadPackage("hl7.fhir.uv.extensions", "current");
+        NpmPackage ext = pcm.loadPackage("hl7.fhir.uv.extensions", "1.0.0");
         System.out.println("Loading Extensions: "+ext.name()+"#"+ext.version());
         fcontext.loadFromPackage(ext, new TestPackageLoader(Utilities.strings("CodeSystem", "ValueSet", "StructureDefinition")));
       } 

org.hl7.fhir.report/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>5.6.116-SNAPSHOT</version>
+        <version>5.6.117-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.utilities/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>5.6.116-SNAPSHOT</version>
+        <version>5.6.117-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

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

@@ -0,0 +1,202 @@
+package org.hl7.fhir.utilities;
+
+import lombok.AccessLevel;
+import lombok.AllArgsConstructor;
+import lombok.With;
+
+import java.io.File;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+@AllArgsConstructor(access = AccessLevel.PRIVATE)
+public class PathBuilder {
+
+  /**
+   * By default, the normalized built path must be a child of the first entry of the buildPath arguments. If a
+   * different parent is desired, this can be set via <code>withRequiredTarget</code>
+   */
+  @With
+  private final String requiredTarget;
+
+  /**
+   * By default, the first entry of the buildPath argument cannot be null or an empty string. Setting this to false will
+   * disable this check.
+   */
+  @With
+  private final boolean requireNonNullNonEmptyFirstEntry;
+
+  /**
+   * By default, the first entry of the buildPath argument cannot be a root directory (<code>"/", "C:\", etc. </code>. Setting this to false will disable this check.
+   */
+  @With
+  private final boolean requireNonRootFirstEntry;
+
+  /**
+   * By default, the normalized built path must be a child of the first entry of the buildPath arguments. Setting this
+   * to false will disable this check.
+   */
+  @With
+  private final boolean requirePathIsChildOfTarget;
+
+  /**
+   * Returns an instance of PathBuilder with all checks enabled (recommended).
+   *
+   * @return
+   */
+  public static PathBuilder getPathBuilder() {
+    return new PathBuilder(null, true, true, true);
+  }
+
+  /**
+   * <p>Builds a path from the passed argument strings. This path will be compatible with the local filesystem.
+   * </p>
+   *
+   * <p>
+   * If the args contain variables enclosed in square brackets (<code>[ ]</code>), they will be replaced with values in
+   * the built path. There are several built-in variables available, listed below. Any text between square brackets that
+   * does not match these will be replaced by a matching System environment variable if one is available.
+   * </p>
+   *
+   * <p>
+   * Built-in variables include:
+   * <ul>
+   *  <li><i>[tmp]</i> An available temp directory (Java Temp directory, <code>c:\\temp, $TMPDIR, %TEMP%</code>, etc.) </li>
+   *  <li><i>[user]</i> The OS user directory (~, user.home, etc) </li>
+   * </ul>
+   * </p>
+   *
+   * <p>
+   * This method will run several checks by default to ensure that the built path does not point to unintended areas of
+   * the filesystem. If these checks are violated, a RuntimeException will be thrown. If needed in special cases, the
+   * behavior of these checks can be modified via the linked fluent constructor methods below.
+   * </p>
+   *
+   * @param args entries with which to construct the filesystem path
+   * @throws RuntimeException
+   * @return a local filesystem path
+   *
+   * @see this#withRequiredTarget(String)
+   * @see this#withRequireNonNullNonEmptyFirstEntry(boolean)
+   * @see this#withRequireNonRootFirstEntry(boolean)
+   * @see this#withRequirePathIsChildOfTarget(boolean)
+   */
+  public String buildPath(String... args) {
+
+    checkNonNullNonEmptyFirstEntry(args);
+    checkNonRootFirstEntry(args);
+
+    StringBuilder stringBuilder = new StringBuilder();
+    boolean argIsNotEmptyOrNull = false;
+
+    boolean first = true;
+    for (String arg : args) {
+      if (first && arg == null)
+        continue;
+      first = false;
+      if (!argIsNotEmptyOrNull)
+        argIsNotEmptyOrNull = !Utilities.noString(arg);
+      else if (!stringBuilder.toString().endsWith(File.separator))
+        stringBuilder.append(File.separator);
+      String a = arg;
+      if (stringBuilder.length() == 0) {
+        a = replaceVariables(a);
+      }
+      a = a.replace("\\", File.separator);
+      a = a.replace("/", File.separator);
+      if (stringBuilder.length() > 0 && a.startsWith(File.separator))
+        a = a.substring(File.separator.length());
+
+      while (a.startsWith(".." + File.separator)) {
+        if (stringBuilder.length() == 0) {
+          stringBuilder = new StringBuilder(Paths.get(".").toAbsolutePath().normalize().toString());
+        } else {
+          String p = stringBuilder.toString().substring(0, stringBuilder.length() - 1);
+          if (!p.contains(File.separator)) {
+            stringBuilder = new StringBuilder();
+          } else {
+            stringBuilder = new StringBuilder(p.substring(0, p.lastIndexOf(File.separator)) + File.separator);
+          }
+        }
+        a = a.substring(3);
+      }
+      if ("..".equals(a)) {
+        int i = stringBuilder.substring(0, stringBuilder.length() - 1).lastIndexOf(File.separator);
+        stringBuilder = new StringBuilder(stringBuilder.substring(0, i + 1));
+      } else
+        stringBuilder.append(a);
+    }
+    checkPathIsChildOfTarget(stringBuilder.toString(), args);
+    return stringBuilder.toString();
+  }
+
+  private void checkPathIsChildOfTarget(String path, String[] args) {
+    if (!requirePathIsChildOfTarget) {
+      return;
+    }
+
+    final String target = requiredTarget != null
+      ? requiredTarget
+      : args[0];
+
+    if (!Path.of(path).normalize().startsWith(Path.of(replaceVariables(target)).normalize())) {
+      throw new RuntimeException("Computed path does not start with first element: " + String.join(", ", args));
+    }
+  }
+
+  private void checkNonRootFirstEntry(String[] args) {
+    if (!requireNonRootFirstEntry) {
+      return;
+    }
+    if (isPathRoot(args[0])) {
+      throw new RuntimeException("First entry cannot be root: " + args[0]);
+    }
+  }
+
+  private void checkNonNullNonEmptyFirstEntry(String[] args) {
+    if (!requireNonNullNonEmptyFirstEntry) {
+      return;
+    }
+    if (args[0] == null || Utilities.noString(args[0].trim())) {
+      throw new RuntimeException("First entry cannot be null or empty");
+    }
+  }
+
+
+  private String replaceVariables(String a) {
+    if ("[tmp]".equals(a)) {
+      if (hasCTempDir()) {
+        return Utilities.C_TEMP_DIR;
+      } else if (ToolGlobalSettings.hasTempPath()) {
+        return ToolGlobalSettings.getTempPath();
+      } else {
+        return System.getProperty("java.io.tmpdir");
+      }
+    } else if ("[user]".equals(a)) {
+      return System.getProperty("user.home");
+    } else if (a.startsWith("[") && a.endsWith("]")) {
+      String ev = System.getenv(a.replace("[", "").replace("]", ""));
+      if (ev != null) {
+        return ev;
+      } else {
+        return "null";
+      }
+    }
+    return a;
+  }
+
+  protected static boolean hasCTempDir() {
+    if (!System.getProperty("os.name").toLowerCase().contains("win")) {
+      return false;
+    }
+    File tmp = new File(Utilities.C_TEMP_DIR);
+    return tmp.exists() && tmp.isDirectory() && tmp.canWrite();
+  }
+
+  protected static boolean isPathRoot(String pathString) {
+    boolean actual;
+    Path path = Path.of(pathString);
+    Path normalizedPath = path.normalize();
+    actual = normalizedPath.equals(path.getRoot());
+    return actual;
+  }
+}

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

@@ -613,47 +613,22 @@ public class Utilities {
     return s.toString();
   }
 
-  private static boolean isPathRoot(String pathString) {
-    boolean actual;
-    Path path = Path.of(pathString);
-    Path normalizedPath = path.normalize();
-    actual = normalizedPath.equals(path.getRoot());
-    return actual;
-  }
-
   /**
    * Composes a path string using by concatenating the passed arguments.
-   * Variables such as [tmp] and [user] are replaced.
    *
-   * In order to prevent unintentional access to areas of the file system
+   * This method enables all checks for unintended path locations.
-   * outside of the first entry, this method will throw exceptions in situations
-   * where the constructed path is at a higher level than the first entry, or
-   * where the first entry is null or empty.
    *
    * @param args
    * @return
    * @throws IOException
+   * @see PathBuilder#buildPath(String...)
    */
   public static String path(String... args) throws IOException {
-    if (args[0] == null || noString(args[0].trim())) {
+    return PathBuilder.getPathBuilder().buildPath(args);
-      throw new RuntimeException("First entry cannot be null or empty");
-    }
-
-    if (isPathRoot(args[0])) {
-      throw new RuntimeException("First entry cannot be root: " + args[0]);
-    }
-
-    String output = uncheckedPath(args);
-
-    if (!Path.of(output.toString()).normalize().startsWith(Path.of(replaceVariables(args[0])).normalize())) {
-     throw new RuntimeException("Computed path does not start with first element: " + String.join(", ", args));
-    }
-    return output.toString();
   }
 
   /**
    * Composes a path string using by concatenating the passed arguments.
-   * Variables such as [tmp] and [user] are replaced.
    *
    * This method does not check for unintentional access to areas of the file
    * system outside of the first entry. ONLY USE THIS METHOD IN CASES WHERE YOU
@@ -662,83 +637,18 @@ public class Utilities {
    * @param args
    * @return
    * @throws IOException
+   *
+   * @see PathBuilder#buildPath(String...)
    */
+  @Deprecated
   public static String uncheckedPath(String... args) {
-    StringBuilder s = new StringBuilder();
+    return PathBuilder.getPathBuilder()
-    boolean argIsNotEmptyOrNull = false;
+      .withRequireNonRootFirstEntry(false)
-
+      .withRequireNonNullNonEmptyFirstEntry(false)
-    boolean first = true;
+      .withRequirePathIsChildOfTarget(false)
-    for (String arg : args) {
+      .buildPath(args);
-      if (first && arg == null)
-        continue;
-      first = false;
-      if (!argIsNotEmptyOrNull)
-        argIsNotEmptyOrNull = !noString(arg);
-      else if (!s.toString().endsWith(File.separator))
-        s.append(File.separator);
-      String a = arg;
-      if (s.length() == 0) {
-        a = replaceVariables(a);
-      }
-      a = a.replace("\\", File.separator);
-      a = a.replace("/", File.separator);
-      if (s.length() > 0 && a.startsWith(File.separator))
-        a = a.substring(File.separator.length());
-
-      while (a.startsWith(".." + File.separator)) {
-        if (s.length() == 0) {
-          s = new StringBuilder(Paths.get(".").toAbsolutePath().normalize().toString());
-        } else {
-          String p = s.toString().substring(0, s.length() - 1);
-          if (!p.contains(File.separator)) {
-            s = new StringBuilder();
-          } else {
-            s = new StringBuilder(p.substring(0, p.lastIndexOf(File.separator)) + File.separator);
-          }
-        }
-        a = a.substring(3);
-      }
-      if ("..".equals(a)) {
-        int i = s.substring(0, s.length() - 1).lastIndexOf(File.separator);
-        s = new StringBuilder(s.substring(0, i + 1));
-      } else
-        s.append(a);
-    }
-//    if (!Path.of(s.toString()).normalize().startsWith(Path.of(replaceVariables(args[0])).normalize())) {
-//     throw new RuntimeException("Computed path '"+s.toString()+"' normalised to '"+Path.of(s.toString()).normalize()+"' does not start with first element: " + String.join(", ", args));
-//    }
-    return s.toString();
   }
 
-  private static String replaceVariables(String a) {
-    if ("[tmp]".equals(a)) {
-      if (hasCTempDir()) {
-        return C_TEMP_DIR;
-      } else if (ToolGlobalSettings.hasTempPath()) {
-        return ToolGlobalSettings.getTempPath();
-      } else {
-        return System.getProperty("java.io.tmpdir");
-      }
-    } else if ("[user]".equals(a)) {
-      return System.getProperty("user.home");
-    } else if (a.startsWith("[") && a.endsWith("]")) {
-      String ev = System.getenv(a.replace("[", "").replace("]", ""));
-      if (ev != null) {
-        return ev;
-      } else {
-        return "null";
-      }
-    }
-    return a;
-  }
-
-  private static boolean hasCTempDir() {
-    if (!System.getProperty("os.name").toLowerCase().contains("win")) {
-      return false;
-    }
-    File tmp = new File(C_TEMP_DIR);
-    return tmp.exists() && tmp.isDirectory() && tmp.canWrite();
-  }
 
   public static String pathURL(String... args) {
     StringBuilder s = new StringBuilder();

org.hl7.fhir.validation.cli/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>5.6.116-SNAPSHOT</version>
+        <version>5.6.117-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.validation/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>5.6.116-SNAPSHOT</version>
+        <version>5.6.117-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/ConceptMapValidator.java

@@ -157,8 +157,7 @@ public class ConceptMapValidator  extends BaseValidator {
       if (warningOrError(srcCS.getContent() == CodeSystemContentMode.COMPLETE, errors, "2023-03-05", IssueType.REQUIRED, code.line(), code.col(), stack.push(code, -1, null, null).getLiteralPath(), cd != null, I18nConstants.CONCEPTMAP_GROUP_SOURCE_CODE_INVALID, c, srcCS.getVersionedUrl())) {
         Element display = src.getNamedChild("display");
         if (display != null) {
-          List<String> displays = CodeSystemUtilities.getDisplays(srcCS, cd);
+          warning(errors, "2023-03-05", IssueType.REQUIRED, code.line(), code.col(), stack.push(code, -1, null, null).getLiteralPath(), CodeSystemUtilities.checkDisplay(srcCS, cd, display.getValue()), I18nConstants.CONCEPTMAP_GROUP_SOURCE_DISPLAY_INVALID, display.getValue(), CodeSystemUtilities.getDisplays(srcCS, cd));
-          ok = rule(errors, "2023-03-05", IssueType.REQUIRED, code.line(), code.col(), stack.push(code, -1, null, null).getLiteralPath(), displays.contains(display.getValue()), I18nConstants.CONCEPTMAP_GROUP_SOURCE_DISPLAY_INVALID, display.getValue(), displays) && ok;
         }
       } else {
         ok = false;
@@ -184,8 +183,7 @@ public class ConceptMapValidator  extends BaseValidator {
       if (warningOrError(tgtCS.getContent() == CodeSystemContentMode.COMPLETE, errors, "2023-03-05", IssueType.REQUIRED, code.line(), code.col(), stack.push(code, -1, null, null).getLiteralPath(), cd != null, I18nConstants.CONCEPTMAP_GROUP_TARGET_CODE_INVALID, c, tgtCS.getVersionedUrl())) {
         Element display = tgt.getNamedChild("display");
         if (display != null) {          
-          List<String> displays = CodeSystemUtilities.getDisplays(tgtCS, cd);
+          warning(errors, "2023-03-05", IssueType.REQUIRED, code.line(), code.col(), stack.push(code, -1, null, null).getLiteralPath(), CodeSystemUtilities.checkDisplay(tgtCS, cd, display.getValue()), I18nConstants.CONCEPTMAP_GROUP_TARGET_DISPLAY_INVALID, display.getValue(), CodeSystemUtilities.getDisplays(tgtCS, cd));
-          ok = rule(errors, "2023-03-05", IssueType.REQUIRED, code.line(), code.col(), stack.push(code, -1, null, null).getLiteralPath(), displays.contains(display.getValue()), I18nConstants.CONCEPTMAP_GROUP_TARGET_DISPLAY_INVALID, display.getValue(), displays) && ok;
         }
       } else {
         ok = false;

pom.xml

@@ -14,7 +14,7 @@
     HAPI FHIR
     -->
     <artifactId>org.hl7.fhir.core</artifactId>
-    <version>5.6.116-SNAPSHOT</version>
+    <version>5.6.117-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <properties>