Merge remote-tracking branch 'origin/master'

hapifhir · Aug 22, 2023 · 7a7a85f · 7a7a85f
2 parents 53a9829 + 2ab5919
commit 7a7a85f
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Showing 13 changed files with 100 additions and 28 deletions.
diff --git a/org.hl7.fhir.convertors/pom.xml b/org.hl7.fhir.convertors/pom.xml
@@ -78,10 +78,19 @@
         <dependency>
             <groupId>org.fhir</groupId>
             <artifactId>ucum</artifactId>
-            <version>1.0.3</version>
             <optional>true</optional>
         </dependency>
 
+        <dependency>
+            <groupId>xpp3</groupId>
+            <artifactId>xpp3</artifactId>
+            <optional>true</optional>
+        </dependency>
+        <dependency>
+            <groupId>xpp3</groupId>
+            <artifactId>xpp3_xpath</artifactId>
+            <optional>true</optional>
+        </dependency>
         <!-- HTTP Client -->
         <dependency>
           <groupId>org.apache.httpcomponents</groupId>

diff --git a/org.hl7.fhir.dstu2/pom.xml b/org.hl7.fhir.dstu2/pom.xml
@@ -32,7 +32,6 @@
         <dependency>
             <groupId>org.fhir</groupId>
             <artifactId>ucum</artifactId>
-            <version>1.0.3</version>
             <optional>true</optional>
         </dependency>
 

diff --git a/org.hl7.fhir.dstu2016may/pom.xml b/org.hl7.fhir.dstu2016may/pom.xml
@@ -32,22 +32,7 @@
         <dependency>
             <groupId>org.fhir</groupId>
             <artifactId>ucum</artifactId>
-            <version>1.0.3</version>
             <optional>true</optional>
-            <exclusions>
-                <exclusion>
-                    <groupId>xpp3</groupId>
-                    <artifactId>xpp3</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>xpp3</groupId>
-                    <artifactId>xpp3_xpath</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>xpp3</groupId>
-                    <artifactId>xpp3_min</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
 
         <!-- XML Parsers -->

diff --git a/org.hl7.fhir.dstu3/pom.xml b/org.hl7.fhir.dstu3/pom.xml
@@ -32,7 +32,6 @@
         <dependency>
             <groupId>org.fhir</groupId>
             <artifactId>ucum</artifactId>
-            <version>1.0.3</version>
             <optional>true</optional>
         </dependency>
 

diff --git a/org.hl7.fhir.r4/pom.xml b/org.hl7.fhir.r4/pom.xml
@@ -39,7 +39,6 @@
 		<dependency>
 			<groupId>org.fhir</groupId>
 			<artifactId>ucum</artifactId>
-			<version>1.0.3</version>
 			<optional>true</optional>
 		</dependency>
 

diff --git a/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/ParametersBuilder.java b/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/ParametersBuilder.java
@@ -0,0 +1,68 @@
+package org.hl7.fhir.r4.utils;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Set;
+import java.util.HashSet;
+
+import org.hl7.fhir.r4.formats.IParser.OutputStyle;
+import org.hl7.fhir.r4.formats.JsonParser;
+import org.hl7.fhir.r4.model.Resource;
+import org.hl7.fhir.r4.model.MetadataResource;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.utilities.TextFile;
+
+/**
+ * Used to take an overload dump from tx.fhir.org and turn it into a parameters resource
+ * 
+ * @author grahamegrieve
+ *
+ */
+public class ParametersBuilder {
+
+  public static void main(String[] args) throws FileNotFoundException, IOException {
+    new ParametersBuilder(args[0], args[1]).process(args[2]);
+  }
+
+
+
+  private String folder;
+  private String baseId;
+
+  protected ParametersBuilder(String folder, String baseId) {
+    super();
+    this.folder = folder;
+    this.baseId = baseId;
+  }
+
+  private void process(String output) throws FileNotFoundException, IOException {
+    Parameters p = new Parameters();
+    Set<String> ids = new HashSet<>();
+    for (File f : new File(folder).listFiles()) {
+      if (f.getName().startsWith(baseId)) {
+        if (f.getName().startsWith(baseId)) {
+          byte[] cnt = TextFile.fileToBytes(f);
+          cnt = shaveZeros(cnt); // bug in tx.fhir.org
+          MetadataResource r = (MetadataResource) new JsonParser().parse(cnt);
+          if (!ids.contains(r.getUrl()+"|"+r.getVersion())) {
+            ids.add(r.getUrl()+"|"+r.getVersion());
+            p.addParameter().setName("tx-resource").setResource(r);
+          }
+        }
+      }
+    }
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(output), p);
+  }
+
+  private byte[] shaveZeros(byte[] cnt) {
+    for (int i = 0; i < cnt.length; i++) {
+      if (cnt[i] == 0) {
+        return Arrays.copyOf(cnt, i-1);
+      }
+    }
+    return cnt;
+  }
+}
diff --git a/org.hl7.fhir.r4b/pom.xml b/org.hl7.fhir.r4b/pom.xml
@@ -38,7 +38,6 @@
 		<dependency>
 			<groupId>org.fhir</groupId>
 			<artifactId>ucum</artifactId>
-			<version>1.0.3</version>
 			<optional>true</optional>
 		</dependency>
 

diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
@@ -1499,7 +1499,7 @@ private boolean addDependentResources(Parameters pin, ConceptSetComponent inc, R
     boolean cache = false;
     for (CanonicalType c : inc.getValueSet()) {
       ValueSet vs = fetchResource(ValueSet.class, c.getValue(), src);
-      if (vs != null) {
+      if (vs != null && !hasCanonicalResource(pin, "tx-resource", vs.getVUrl())) {
         pin.addParameter().setName("tx-resource").setResource(vs);
         if (tcc.isTxCaching() && tcc.getCacheId() == null || !tcc.getCached().contains(vs.getVUrl())) {
           tcc.getCached().add(vs.getVUrl());
@@ -1509,7 +1509,7 @@ private boolean addDependentResources(Parameters pin, ConceptSetComponent inc, R
       }
     }
     CodeSystem cs = fetchResource(CodeSystem.class, inc.getSystem(), src);
-    if (cs != null && (cs.getContent() == CodeSystemContentMode.COMPLETE || cs.getContent() == CodeSystemContentMode.FRAGMENT)) {
+    if (cs != null && !hasCanonicalResource(pin, "tx-resource", cs.getVUrl()) && (cs.getContent() == CodeSystemContentMode.COMPLETE || cs.getContent() == CodeSystemContentMode.FRAGMENT)) {
       pin.addParameter().setName("tx-resource").setResource(cs);
       if (tcc.isTxCaching() && tcc.getCacheId() == null || !tcc.getCached().contains(cs.getVUrl())) {
         tcc.getCached().add(cs.getVUrl());
@@ -1520,6 +1520,16 @@ private boolean addDependentResources(Parameters pin, ConceptSetComponent inc, R
     return cache;
   }
 
+  private boolean hasCanonicalResource(Parameters pin, String name, String vUrl) {
+    for (ParametersParameterComponent p : pin.getParameter()) {
+      if (name.equals(p.getName()) && p.hasResource() &&
+          p.getResource() instanceof CanonicalResource && vUrl.equals(((CanonicalResource) p.getResource()).getVUrl())) {
+        return true;
+      }
+    }
+    return false;
+  }
+
   public ValidationResult processValidationResult(Parameters pOut, String vs) {
     boolean ok = false;
     String message = "No Message returned";

diff --git a/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/PathBuilder.java b/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/PathBuilder.java
@@ -150,7 +150,7 @@ private void checkNonRootFirstEntry(String[] args) {
       return;
     }
     if (isPathRoot(args[0])) {
-      throw new RuntimeException("First entry cannot be root: " + args[0]);
+      throw new RuntimeException("First entry in file path cannot be root: " + args[0]+", full path = "+String.join(", ", args));
     }
   }
 
@@ -159,7 +159,7 @@ private void checkNonNullNonEmptyFirstEntry(String[] args) {
       return;
     }
     if (args[0] == null || Utilities.noString(args[0].trim())) {
-      throw new RuntimeException("First path entry cannot be null or empty");
+      throw new RuntimeException("First entry in file path cannot be null or empty, full path = "+String.join(", ", args));
     }
   }
 

diff --git a/org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/UtilitiesTest.java b/org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/UtilitiesTest.java
@@ -293,7 +293,7 @@ private static void testCantStartWithRoot(String[] pathStrings) {
     RuntimeException thrown = Assertions.assertThrows(RuntimeException.class, () -> {
       Utilities.path(pathStrings);
     });
-    assertTrue(thrown.getMessage().endsWith(pathStrings[0]));
+    assertTrue(thrown.getMessage().endsWith(pathStrings[0]+", full path = "+String.join(", ", pathStrings)));
   }
 
   public static Stream<Arguments> macAndLinuxNonFirstElementStartPaths() {
@@ -384,7 +384,7 @@ public void testNullOrEmptyFirstPathEntryFails(String[] pathsStrings) {
     RuntimeException thrown = Assertions.assertThrows(RuntimeException.class, () -> {
       Utilities.path(pathsStrings);
     });
-    assertEquals("First path entry cannot be null or empty",thrown.getMessage());
+    assertEquals("First entry in file path cannot be null or empty, full path = "+String.join(", ", pathsStrings),thrown.getMessage());
   }
 
   @Test

diff --git a/org.hl7.fhir.validation.cli/pom.xml b/org.hl7.fhir.validation.cli/pom.xml
@@ -286,7 +286,6 @@
         <dependency>
             <groupId>org.fhir</groupId>
             <artifactId>ucum</artifactId>
-            <version>1.0.3</version>
         </dependency>
         <dependency>
             <groupId>xpp3</groupId>

diff --git a/org.hl7.fhir.validation/pom.xml b/org.hl7.fhir.validation/pom.xml
@@ -120,7 +120,7 @@
         <dependency>
             <groupId>org.fhir</groupId>
             <artifactId>ucum</artifactId>
-            <version>1.0.3</version>
+            <optional>true</optional>
         </dependency>
 
         <!-- CQL-to-ELM -->

diff --git a/pom.xml b/pom.xml
@@ -164,6 +164,11 @@
                 <artifactId>Saxon-HE</artifactId>
                 <version>${saxon_he_version}</version>
             </dependency>
+            <dependency>
+                <groupId>org.fhir</groupId>
+                <artifactId>ucum</artifactId>
+                <version>1.0.8</version>
+            </dependency>
 
             <dependency>
                 <groupId>mysql</groupId>