This is an automated email from the ASF dual-hosted git repository.
mattyb149 pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/nifi.git
The following commit(s) were added to refs/heads/main by this push:
new e966336e89 NIFI-11029 Added Standard XML parsing to
ExtractCCDAAttributes
e966336e89 is described below
commit e966336e8966cf0cbbd12a2c4f2d73a7ceb75cd8
Author: exceptionfactory <[email protected]>
AuthorDate: Fri Jan 6 13:18:56 2023 -0600
NIFI-11029 Added Standard XML parsing to ExtractCCDAAttributes
- Added DeprecationNotice to ExtractCCDAAttributes
Signed-off-by: Matthew Burgess <[email protected]>
This closes #6828
---
.../nifi-ccda-bundle/nifi-ccda-processors/pom.xml | 5 ++++
.../processors/ccda/ExtractCCDAAttributes.java | 10 ++++++-
.../processors/ccda/TestExtractCCDAAttributes.java | 32 +++++++++++++---------
3 files changed, 33 insertions(+), 14 deletions(-)
diff --git a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/pom.xml
b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/pom.xml
index 09aa3ef074..a69f811823 100644
--- a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/pom.xml
+++ b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/pom.xml
@@ -35,6 +35,11 @@
<artifactId>nifi-utils</artifactId>
<version>1.20.0-SNAPSHOT</version>
</dependency>
+ <dependency>
+ <groupId>org.apache.nifi</groupId>
+ <artifactId>nifi-xml-processing</artifactId>
+ <version>1.20.0-SNAPSHOT</version>
+ </dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
diff --git
a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/java/org/apache/nifi/processors/ccda/ExtractCCDAAttributes.java
b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/java/org/apache/nifi/processors/ccda/ExtractCCDAAttributes.java
index 24e339e5ad..ac52406bbd 100644
---
a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/java/org/apache/nifi/processors/ccda/ExtractCCDAAttributes.java
+++
b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/java/org/apache/nifi/processors/ccda/ExtractCCDAAttributes.java
@@ -41,6 +41,7 @@ import
org.apache.nifi.annotation.behavior.InputRequirement.Requirement;
import org.apache.nifi.annotation.behavior.SideEffectFree;
import org.apache.nifi.annotation.behavior.SupportsBatching;
import org.apache.nifi.annotation.documentation.CapabilityDescription;
+import org.apache.nifi.annotation.documentation.DeprecationNotice;
import org.apache.nifi.annotation.documentation.Tags;
import org.apache.nifi.annotation.lifecycle.OnScheduled;
import org.apache.nifi.components.PropertyDescriptor;
@@ -53,6 +54,7 @@ import org.apache.nifi.processor.Relationship;
import org.apache.nifi.processor.exception.ProcessException;
import org.apache.nifi.processor.util.StandardValidators;
import org.apache.nifi.util.StopWatch;
+import org.apache.nifi.xml.processing.parsers.StandardDocumentProvider;
import org.eclipse.emf.common.util.Diagnostic;
import org.openhealthtools.mdht.uml.cda.CDAPackage;
import org.openhealthtools.mdht.uml.cda.ClinicalDocument;
@@ -62,7 +64,9 @@ import org.openhealthtools.mdht.uml.cda.hitsp.HITSPPackage;
import org.openhealthtools.mdht.uml.cda.ihe.IHEPackage;
import org.openhealthtools.mdht.uml.cda.util.CDAUtil;
import org.openhealthtools.mdht.uml.cda.util.CDAUtil.ValidationHandler;
+import org.w3c.dom.Document;
+@DeprecationNotice(reason = "Parsing XML elements to FlowFile attributes is
not recommend and should be replaced with record-oriented handling")
@SideEffectFree
@SupportsBatching
@InputRequirement(Requirement.INPUT_REQUIRED)
@@ -284,7 +288,11 @@ public class ExtractCCDAAttributes extends
AbstractProcessor {
ClinicalDocument cd = null;
try {
- cd = CDAUtil.load(inputStream); // load CDA document
+ final StandardDocumentProvider documentProvider = new
StandardDocumentProvider();
+ documentProvider.setNamespaceAware(true);
+ final Document document = documentProvider.parse(inputStream);
+
+ cd = CDAUtil.load(document); // load CDA document
if (!skipValidation && !CDAUtil.validate(cd, new
CDAValidationHandler())) { //optional validation
getLogger().error("Failed to validate CDA document");
throw new ProcessException("Failed to validate CDA document");
diff --git
a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/test/java/org/apache/nifi/processors/ccda/TestExtractCCDAAttributes.java
b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/test/java/org/apache/nifi/processors/ccda/TestExtractCCDAAttributes.java
index 68e0fca20f..27620a6cdc 100644
---
a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/test/java/org/apache/nifi/processors/ccda/TestExtractCCDAAttributes.java
+++
b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/test/java/org/apache/nifi/processors/ccda/TestExtractCCDAAttributes.java
@@ -19,7 +19,6 @@ package org.apache.nifi.processors.ccda;
import org.apache.nifi.util.MockFlowFile;
import org.apache.nifi.util.TestRunner;
import org.apache.nifi.util.TestRunners;
-import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.openhealthtools.mdht.uml.cda.consol.ConsolFactory;
@@ -33,20 +32,17 @@ import
org.openhealthtools.mdht.uml.cda.consol.VitalSignsOrganizer;
import org.openhealthtools.mdht.uml.cda.consol.VitalSignsSection;
import org.openhealthtools.mdht.uml.cda.util.CDAUtil;
-import java.io.IOException;
import java.io.StringWriter;
-import java.util.HashMap;
+import java.util.LinkedHashMap;
import java.util.Map;
-
public class TestExtractCCDAAttributes {
- private TestRunner runner;
+ private static final String INVALID_DOCTYPE = "<!DOCTYPE invalid [<!ENTITY
entity SYSTEM 'file:///file-not-found'> %entity;]>";
- @BeforeAll
- public static void setup() {
- System.setProperty("org.slf4j.simpleLogger.log.org.apache.nifi",
"INFO");
- }
+ private static final String INVALID_DOCUMENT = String.format("<?xml
version=\"1.0\" encoding=\"UTF-8\" ?>%s<ClinicalDocument
xmlns=\"urn:hl7-org:v3\" />", INVALID_DOCTYPE);
+
+ private TestRunner runner;
@BeforeEach
public void init() {
@@ -55,7 +51,7 @@ public class TestExtractCCDAAttributes {
@Test
public void testProcessor() throws Exception {
- Map<String, String> expectedAttributes = new HashMap<String, String>();
+ Map<String, String> expectedAttributes = new LinkedHashMap<>();
expectedAttributes.put("code.code", "34133-9");
expectedAttributes.put("code.codeSystem", "2.16.840.1.113883.6.1");
expectedAttributes.put("code.codeSystemName", "LOINC");
@@ -110,11 +106,21 @@ public class TestExtractCCDAAttributes {
StringWriter writer = new StringWriter();
CDAUtil.save(doc, writer);
- runTests(writer.toString(), expectedAttributes, true, true);
+ runTests(writer.toString(), expectedAttributes);
+ }
+
+ @Test
+ public void testRunInvalidDocument() {
+ runner.enqueue(INVALID_DOCUMENT);
+
+ runner.run();
+
+
runner.assertAllFlowFilesTransferred(ExtractCCDAAttributes.REL_FAILURE);
}
- private void runTests(final String content, Map<String, String>
expectedAttributes, final boolean skipValidation, final boolean prettyPrinting)
throws IOException{
- runner.setProperty(ExtractCCDAAttributes.SKIP_VALIDATION,
String.valueOf(skipValidation));
+
+ private void runTests(final String content, final Map<String, String>
expectedAttributes) {
+ runner.setProperty(ExtractCCDAAttributes.SKIP_VALIDATION,
Boolean.TRUE.toString());
runner.enqueue(content);
