Advances hapi versions and skips xhtml fields (#1240)

google · Nov 15, 2024 · d42c792 · d42c792
1 parent f0d0a6c
commit d42c792
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Showing 7 changed files with 27 additions and 6 deletions.
diff --git a/bunsen/bunsen-avro/src/main/java/com/cerner/bunsen/avro/AvroConverter.java b/bunsen/bunsen-avro/src/main/java/com/cerner/bunsen/avro/AvroConverter.java
@@ -20,7 +20,7 @@
 import org.apache.avro.Schema;
 import org.apache.avro.Schema.Field;
 import org.apache.avro.generic.IndexedRecord;
-import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.collections4.CollectionUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
 /** Converter to change HAPI objects into Avro structures and vice versa. */

diff --git a/.../bunsen-avro/src/main/java/com/cerner/bunsen/avro/converters/DefinitionToAvroVisitor.java b/.../bunsen-avro/src/main/java/com/cerner/bunsen/avro/converters/DefinitionToAvroVisitor.java
@@ -140,6 +140,8 @@ public Schema getDataType() {
           .put("time", STRING_CONVERTER)
           .put("string", STRING_CONVERTER)
           .put("oid", STRING_CONVERTER)
+          // Note `xhtml` types are currently skipped because of:
+          // https://github.com/google/fhir-data-pipes/issues/1014
           .put("xhtml", STRING_CONVERTER)
           .put("decimal", DOUBLE_CONVERTER)
           .put("integer", INTEGER_CONVERTER)

diff --git a/bunsen/bunsen-core/src/main/java/com/cerner/bunsen/definitions/PrimitiveConverter.java b/bunsen/bunsen-core/src/main/java/com/cerner/bunsen/definitions/PrimitiveConverter.java
@@ -63,7 +63,13 @@ protected Object fromHapi(IPrimitiveType primitive) {
 
   @Override
   public Object fromHapi(Object input) {
-
+    // TODO: remove this hack! It is added to address this bug:
+    // https://github.com/google/fhir-data-pipes/issues/1014
+    // with root cause being:
+    // https://github.com/hapifhir/org.hl7.fhir.core/issues/1800
+    if (!(input instanceof IPrimitiveType)) {
+      return "";
+    }
     return fromHapi((IPrimitiveType) input);
   }
 

diff --git a/bunsen/bunsen-core/src/main/java/com/cerner/bunsen/definitions/StructureDefinitions.java b/bunsen/bunsen-core/src/main/java/com/cerner/bunsen/definitions/StructureDefinitions.java
@@ -36,6 +36,8 @@ public abstract class StructureDefinitions {
           .add("time")
           .add("string")
           .add("oid")
+          // Note `xhtml` types are currently skipped because of:
+          // https://github.com/google/fhir-data-pipes/issues/1014
           .add("xhtml")
           .add("decimal")
           .add("integer")

diff --git a/bunsen/pom.xml b/bunsen/pom.xml
@@ -25,7 +25,7 @@
 
   <properties>
     <compile.source>11</compile.source>
-    <hapi.fhir.version>7.2.2</hapi.fhir.version>
+    <hapi.fhir.version>7.4.5</hapi.fhir.version>
     <avro.version>1.12.0</avro.version>
     <junit.version>4.13.2</junit.version>
     <hamcrest.version>3.0</hamcrest.version>
@@ -90,6 +90,12 @@
       <artifactId>jackson-core</artifactId>
       <version>2.18.1</version>
     </dependency>
+
+    <dependency>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-collections4</artifactId>
+      <version>4.4</version>
+    </dependency>
   </dependencies>
 
   <build>

diff --git a/pipelines/common/src/test/java/com/google/fhir/analytics/view/SQLonFHIRv2Test.java b/pipelines/common/src/test/java/com/google/fhir/analytics/view/SQLonFHIRv2Test.java
@@ -55,7 +55,6 @@
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.hl7.fhir.r4.utils.FHIRLexer.FHIRLexerException;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.mockito.junit.MockitoJUnitRunner;
@@ -144,7 +143,7 @@ public void runAllTests() throws IOException {
                 String.format(
                     "Number of rows does not match %d vs %d", totalRows, expectedRows.getNumRows()),
                 totalRows == expectedRows.getNumRows());
-          } catch (ViewApplicationException | ViewDefinitionException | FHIRLexerException e) {
+          } catch (ViewApplicationException | ViewDefinitionException e) {
             assertThat(
                 "View exceptions were thrown while none was expected!", expectedRows == null);
           }

diff --git a/pipelines/pom.xml b/pipelines/pom.xml
@@ -45,7 +45,7 @@
     <junit.version>4.13.2</junit.version>
     <slf4j.version>2.0.16</slf4j.version>
     <logback.version>1.5.12</logback.version>
-    <hapi.fhir.version>7.2.2</hapi.fhir.version>
+    <hapi.fhir.version>7.4.5</hapi.fhir.version>
     <hamcrest.version>3.0</hamcrest.version>
     <mockito.version>5.2.0</mockito.version>
     <jcommander.version>1.82</jcommander.version>
@@ -233,6 +233,12 @@
       <artifactId>jackson-core</artifactId>
       <version>2.18.1</version>
     </dependency>
+
+    <dependency>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-collections4</artifactId>
+      <version>4.4</version>
+    </dependency>
   </dependencies>
 
   <build>