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NIFI-3147 Build processor to parse CCDA into attributes 

This closes #1312

Signed-off-by: Joey Frazee <jfrazee@apache.org>
This commit is contained in:
kedarchitale 2016-12-09 15:45:19 +05:30 committed by Joey Frazee
parent 83fa24b68f
commit 457df93dd6
14 changed files with 1086 additions and 31 deletions
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63
nifi-assembly/NOTICE
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@ -27,7 +27,7 @@ The following binary components are provided under the Apache Software License v
(ASLv2) Apache Commons Collections
The following NOTICE information applies:
Apache Commons Collections
Copyright 2001-2013 The Apache Software Foundation
Copyright 2001-2013 The Apache Software Foundation
(ASLv2) Apache Commons Compress
The following NOTICE information applies:
@ -88,7 +88,7 @@ The following binary components are provided under the Apache Software License v
Copyright (c) 2005, Graph Builder
(ASLv2) Jasypt
The following NOTICE information applies:
The following NOTICE information applies:
Copyright (c) 2007-2010, The JASYPT team (http://www.jasypt.org)
(ASLv2) Apache Commons Codec
@ -135,26 +135,26 @@ The following binary components are provided under the Apache Software License v
(ASLv2) Twitter4J
The following NOTICE information applies:
Copyright 2007 Yusuke Yamamoto
Twitter4J includes software from JSON.org to parse JSON response from the Twitter API.
You can see the license term at http://www.JSON.org/license.html
Copyright (c) 2002 JSON.org
Permission is hereby granted, free of charge, to any person obtaining a copy of this
software and associated documentation files (the "Software"), to deal in the Software
without restriction, including without limitation the rights to use, copy, modify,
merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
Permission is hereby granted, free of charge, to any person obtaining a copy of this
software and associated documentation files (the "Software"), to deal in the Software
without restriction, including without limitation the rights to use, copy, modify,
merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to the following
conditions:
The above copyright notice and this permission notice shall be included in all
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
The Software shall be used for Good, not Evil.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF
CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE
@ -300,7 +300,7 @@ The following binary components are provided under the Apache Software License v
- software copyright (c) 1999-2002, Lotus Development Corporation., http://www.lotus.com.
- software copyright (c) 2001-2002, Sun Microsystems., http://www.sun.com.
- software copyright (c) 2003, IBM Corporation., http://www.ibm.com.
- voluntary contributions made by Ovidiu Predescu (ovidiu@cup.hp.com) on behalf of the
- voluntary contributions made by Ovidiu Predescu (ovidiu@cup.hp.com) on behalf of the
Apache Software Foundation and was originally developed at Hewlett Packard Company.
(ASLv2) Apache XML Commons XML APIs
@ -402,20 +402,20 @@ The following binary components are provided under the Apache Software License v
from the Minpack package
Minpack Copyright Notice (1999) University of Chicago. All rights reserved
===============================================================================
The GraggBulirschStoerIntegrator class in package
org.apache.commons.math3.ode.nonstiff includes software translated
from the odex Fortran routine developed by E. Hairer and G. Wanner.
Original source copyright:
Copyright (c) 2004, Ernst Hairer
===============================================================================
The EigenDecompositionImpl class in package
org.apache.commons.math3.linear includes software translated
from some LAPACK Fortran routines. Original source copyright:
Copyright (c) 1992-2008 The University of Tennessee. All rights reserved.
===============================================================================
The MersenneTwister class in package org.apache.commons.math3.random
includes software translated from the 2002-01-26 version of
the Mersenne-Twister generator written in C by Makoto Matsumoto and Takuji
@ -423,19 +423,19 @@ The following binary components are provided under the Apache Software License v
Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
All rights reserved
===============================================================================
The LocalizedFormatsTest class in the unit tests is an adapted version of
the OrekitMessagesTest class from the orekit library distributed under the
terms of the Apache 2 licence. Original source copyright:
Copyright 2010 CS Systèmes d'Information
===============================================================================
The HermiteInterpolator class and its corresponding test have been imported from
the orekit library distributed under the terms of the Apache 2 licence. Original
source copyright:
Copyright 2010-2012 CS Systèmes d'Information
===============================================================================
The creation of the package "o.a.c.m.analysis.integration.gauss" was inspired
by an original code donated by Sébastien Brisard.
===============================================================================
@ -484,13 +484,13 @@ The following binary components are provided under the Apache Software License v
The following NOTICE information applies:
This product includes software developed by Google
Snappy: http://code.google.com/p/snappy/ (New BSD License)
This product includes software developed by Apache
PureJavaCrc32C from apache-hadoop-common http://hadoop.apache.org/
(Apache 2.0 license)
This library containd statically linked libstdc++. This inclusion is allowed by
"GCC RUntime Library Exception"
This library containd statically linked libstdc++. This inclusion is allowed by
"GCC RUntime Library Exception"
http://gcc.gnu.org/onlinedocs/libstdc++/manual/license.html
(ASLv2) ApacheDS
@ -531,8 +531,8 @@ The following binary components are provided under the Apache Software License v
original software and related information is available
at http://mx4j.sourceforge.net.
Java compilation software for JSP pages is provided by Eclipse,
which is open source software. The orginal software and
Java compilation software for JSP pages is provided by Eclipse,
which is open source software. The orginal software and
related infomation is available at
http://www.eclipse.org.
@ -579,13 +579,13 @@ The following binary components are provided under the Apache Software License v
as the Unicode Character Database. See http://unicode.org/copyright.html for more
details.
Brics Automaton (under core/src/java/org/apache/lucene/util/automaton) is
Brics Automaton (under core/src/java/org/apache/lucene/util/automaton) is
BSD-licensed, created by Anders Møller. See http://www.brics.dk/automaton/
The levenshtein automata tables (under core/src/java/org/apache/lucene/util/automaton) were
automatically generated with the moman/finenight FSA library, created by
Jean-Philippe Barrette-LaPierre. This library is available under an MIT license,
see http://sites.google.com/site/rrettesite/moman and
see http://sites.google.com/site/rrettesite/moman and
http://bitbucket.org/jpbarrette/moman/overview/
The class org.apache.lucene.util.WeakIdentityMap was derived from
@ -639,7 +639,7 @@ The following binary components are provided under the Apache Software License v
analysis/common/src/java/org/apache/lucene/analysis/ru/RussianLightStemmer.java
analysis/common/src/java/org/apache/lucene/analysis/sv/SwedishLightStemmer.java
The Stempel analyzer (stempel) includes BSD-licensed software developed
The Stempel analyzer (stempel) includes BSD-licensed software developed
by the Egothor project http://egothor.sf.net/, created by Leo Galambos, Martin Kvapil,
and Edmond Nolan.
@ -651,8 +651,8 @@ The following binary components are provided under the Apache Software License v
The SmartChineseAnalyzer source code (smartcn) was
provided by Xiaoping Gao and copyright 2009 by www.imdict.net.
WordBreakTestUnicode_*.java (under modules/analysis/common/src/test/)
is derived from Unicode data such as the Unicode Character Database.
WordBreakTestUnicode_*.java (under modules/analysis/common/src/test/)
is derived from Unicode data such as the Unicode Character Database.
See http://unicode.org/copyright.html for more details.
The Morfologik analyzer (morfologik) includes BSD-licensed software
@ -768,7 +768,7 @@ The following binary components are provided under the Apache Software License v
(ASLv2) Apache Geronimo
The following NOTICE information applies:
Apache Geronimo
Apache Geronimo
Copyright 2003-2008 The Apache Software Foundation
(ASLv2) Swagger Core
@ -817,7 +817,7 @@ The following binary components are provided under the Apache Software License v
The following NOTICE information applies:
JOAuth
Copyright 2010-2013 Twitter, Inc
(ASLv2) Hosebird Client
The following NOTICE information applies:
Hosebird Client (hbc)
@ -854,7 +854,7 @@ The following binary components are provided under the Apache Software License v
The following NOTICE information applies:
Apache Commons DBCP
Copyright 2001-2015 The Apache Software Foundation.
(ASLv2) Apache Commons Pool
The following NOTICE information applies:
Apache Commons Pool
@ -863,7 +863,7 @@ The following binary components are provided under the Apache Software License v
(ASLv2) Apache Derby
The following NOTICE information applies:
Apache Derby
Copyright 2004-2014 Apache, Apache DB, Apache Derby, Apache Torque, Apache JDO, Apache DDLUtils,
Copyright 2004-2014 Apache, Apache DB, Apache Derby, Apache Torque, Apache JDO, Apache DDLUtils,
the Derby hat logo, the Apache JDO logo, and the Apache feather logo are trademarks of The Apache Software Foundation.
(ASLv2) Apache Directory Server
@ -907,7 +907,7 @@ The following binary components are provided under the Apache Software License v
Portions of this software were originally based on the following:
- software copyright (c) 1999, IBM Corporation., http://www.ibm.com.
- software copyright (c) 1999, Sun Microsystems., http://www.sun.com.
- voluntary contributions made by Paul Eng on behalf of the
- voluntary contributions made by Paul Eng on behalf of the
Apache Software Foundation that were originally developed at iClick, Inc.,
software copyright (c) 1999.
@ -1277,6 +1277,7 @@ Eclipse Public License 1.0
The following binary components are provided under the Eclipse Public License 1.0. See project link for details.
(EPL 1.0) Model-Driven Health Tools ( org.openehealth.ipf.oht.mdht ) https://projects.eclipse.org/proposals/model-driven-health-tools
(EPL 1.0) AspectJ Weaver (org.aspectj:aspectjweaver:jar:1.8.5 - http://www.eclipse.org/aspectj/)
(EPL 1.0) AspectJ Runtime (org.aspectj:aspectjrt:jar:1.8.0 - http://www.eclipse.org/aspectj/)
(EPL 1.0)(MPL 2.0) H2 Database (com.h2database:h2:jar:1.3.176 - http://www.h2database.com/html/license.html)

5
nifi-assembly/pom.xml
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@ -258,6 +258,11 @@ language governing permissions and limitations under the License. -->
<artifactId>nifi-hl7-nar</artifactId>
<type>nar</type>
</dependency>
<dependency>
<groupId>org.apache.nifi</groupId>
<artifactId>nifi-ccda-nar</artifactId>
<type>nar</type>
</dependency>
<dependency>
<groupId>org.apache.nifi</groupId>
<artifactId>nifi-language-translation-nar</artifactId>

39
nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/pom.xml Normal file
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@ -0,0 +1,39 @@
<?xml version="1.0" encoding="UTF-8"?>
<!--
Licensed to the Apache Software Foundation (ASF) under one or more
contributor license agreements. See the NOTICE file distributed with
this work for additional information regarding copyright ownership.
The ASF licenses this file to You under the Apache License, Version 2.0
(the "License"); you may not use this file except in compliance with
the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
-->
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.apache.nifi</groupId>
<artifactId>nifi-ccda-bundle</artifactId>
<version>1.2.0-SNAPSHOT</version>
</parent>
<artifactId>nifi-ccda-nar</artifactId>
<packaging>nar</packaging>
<properties>
<maven.javadoc.skip>true</maven.javadoc.skip>
<source.skip>true</source.skip>
</properties>
<dependencies>
<dependency>
<groupId>org.apache.nifi</groupId>
<artifactId>nifi-ccda-processors</artifactId>
</dependency>
</dependencies>
</project>

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nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/src/main/resources/META-INF/LICENSE Normal file
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@ -0,0 +1,209 @@
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nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/src/main/resources/META-INF/NOTICE Normal file
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@ -0,0 +1,37 @@
nifi-ccda-nar
Copyright 2015-2016 The Apache Software Foundation
This product includes software developed at
The Apache Software Foundation (http://www.apache.org/).
******************
Apache Software License v2
******************
The following binary components are provided under the Apache Software License v2
(ASLv2) Apache Commons JEXL
The following NOTICE information applies:
Apache Commons JEXL
Copyright 2001-2015 The Apache Software Foundation
This product includes software developed at
The Apache Software Foundation (http://www.apache.org/).
(ASLv2) Apache Commons Lang
The following NOTICE information applies:
Apache Commons Lang
Copyright 2001-2015 The Apache Software Foundation
This product includes software from the Spring Framework,
under the Apache License 2.0 (see: StringUtils.containsWhitespace())
*****************
Eclipse Public License - v 1.0
*****************
The following binary components are provided under the Eclipse Public License v1.1.
(EPLv1) Model-Driven Health Tools (MDHT)
The following NOTICE information applies:
Copyright (c) 2011, 2012 Sean Muir and others. (http://www.eclipse.org/legal/epl-v10.html)

78
nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/pom.xml Normal file
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@ -0,0 +1,78 @@
<?xml version="1.0" encoding="UTF-8"?>
<!--
Licensed to the Apache Software Foundation (ASF) under one or more
contributor license agreements. See the NOTICE file distributed with
this work for additional information regarding copyright ownership.
The ASF licenses this file to You under the Apache License, Version 2.0
(the "License"); you may not use this file except in compliance with
the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
-->
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.apache.nifi</groupId>
<artifactId>nifi-ccda-bundle</artifactId>
<version>1.2.0-SNAPSHOT</version>
</parent>
<artifactId>nifi-ccda-processors</artifactId>
<packaging>jar</packaging>
<dependencies>
<dependency>
<groupId>org.apache.nifi</groupId>
<artifactId>nifi-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.nifi</groupId>
<artifactId>nifi-processor-utils</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-jexl3</artifactId>
<version>3.0</version>
</dependency>
<dependency>
<groupId>org.openehealth.ipf.oht.mdht</groupId>
<artifactId>ipf-oht-mdht-uml-cda</artifactId>
<version>1.2.0.201212201425</version>
</dependency>
<dependency>
<groupId>org.openehealth.ipf.oht.mdht</groupId>
<artifactId>ipf-oht-mdht-uml-cda-ccd</artifactId>
<version>1.2.0.201212201425</version>
</dependency>
<dependency>
<groupId>org.openehealth.ipf.oht.mdht</groupId>
<artifactId>ipf-oht-mdht-uml-cda-hitsp</artifactId>
<version>1.2.0.201212201425</version>
</dependency>
<dependency>
<groupId>org.openehealth.ipf.oht.mdht</groupId>
<artifactId>ipf-oht-mdht-uml-cda-consol</artifactId>
<version>1.2.0.201212201425</version>
</dependency>
<dependency>
<groupId>org.apache.nifi</groupId>
<artifactId>nifi-mock</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
</project>

339
nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/java/org/apache/nifi/processors/ccda/ExtractCCDAAttributes.java Normal file
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@ -0,0 +1,339 @@
/*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.apache.nifi.processors.ccda;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Properties;
import java.util.Set;
import java.util.TreeMap;
import java.util.concurrent.TimeUnit;
import org.apache.commons.jexl3.JexlBuilder;
import org.apache.commons.jexl3.JexlContext;
import org.apache.commons.jexl3.JexlEngine;
import org.apache.commons.jexl3.JexlExpression;
import org.apache.commons.jexl3.MapContext;
import org.apache.commons.lang3.StringUtils;
import org.apache.nifi.annotation.behavior.InputRequirement;
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.Tags;
import org.apache.nifi.annotation.lifecycle.OnScheduled;
import org.apache.nifi.components.PropertyDescriptor;
import org.apache.nifi.flowfile.FlowFile;
import org.apache.nifi.processor.AbstractProcessor;
import org.apache.nifi.processor.ProcessContext;
import org.apache.nifi.processor.ProcessSession;
import org.apache.nifi.processor.ProcessorInitializationContext;
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.eclipse.emf.common.util.Diagnostic;
import org.openhealthtools.mdht.uml.cda.CDAPackage;
import org.openhealthtools.mdht.uml.cda.ClinicalDocument;
import org.openhealthtools.mdht.uml.cda.ccd.CCDPackage;
import org.openhealthtools.mdht.uml.cda.consol.ConsolPackage;
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;
@SideEffectFree
@SupportsBatching
@InputRequirement(Requirement.INPUT_REQUIRED)
@Tags({"CCDA", "healthcare", "extract", "attributes"})
@CapabilityDescription("Extracts information from an Consolidated CDA formatted FlowFile and provides individual attributes "
+ "as FlowFile attributes. The attributes are named as <Parent> <dot> <Key>. "
+ "If the Parent is repeating, the naming will be <Parent> <underscore> <Parent Index> <dot> <Key>. "
+ "For example, section.act_07.observation.name=Essential hypertension")
public class ExtractCCDAAttributes extends AbstractProcessor {
private static final char FIELD_SEPARATOR = '@';
private static final char KEY_VALUE_SEPARATOR = '#';
private Map<String, Map<String, String>> processMap = new LinkedHashMap<String, Map<String, String>>(); // stores mapping data for Parser
private JexlEngine jexl = null; // JEXL Engine to execute code for mapping
private JexlContext jexlCtx = null; // JEXL Context to hold element being processed
private List<PropertyDescriptor> properties;
private Set<Relationship> relationships;
/**
* SKIP_VALIDATION - Indicates whether to validate the CDA document after loading.
* if true and the document is not valid, then ProcessException will be thrown
*/
public static final PropertyDescriptor SKIP_VALIDATION = new PropertyDescriptor.Builder().name("skip-validation")
.displayName("Skip Validation").description("Whether or not to validate CDA message values").required(true)
.allowableValues("true", "false").defaultValue("true").addValidator(StandardValidators.BOOLEAN_VALIDATOR)
.build();
/**
* REL_SUCCESS - Value to be returned in case the processor succeeds
*/
public static final Relationship REL_SUCCESS = new Relationship.Builder()
.name("success")
.description("A FlowFile is routed to this relationship if it is properly parsed as CDA and its contents extracted as attributes.")
.build();
/**
* REL_FAILURE - Value to be returned in case the processor fails
*/
public static final Relationship REL_FAILURE = new Relationship.Builder()
.name("failure")
.description("A FlowFile is routed to this relationship if it cannot be parsed as CDA or its contents extracted as attributes.")
.build();
@Override
protected List<PropertyDescriptor> getSupportedPropertyDescriptors() {
return properties;
}
@Override
public Set<Relationship> getRelationships() {
return relationships;
}
@Override
protected void init(final ProcessorInitializationContext context) {
final Set<Relationship> _relationships = new HashSet<>();
_relationships.add(REL_SUCCESS);
_relationships.add(REL_FAILURE);
this.relationships = Collections.unmodifiableSet(_relationships);
final List<PropertyDescriptor> _properties = new ArrayList<>();
_properties.add(SKIP_VALIDATION);
this.properties = Collections.unmodifiableList(_properties);
}
@OnScheduled
public void onScheduled(final ProcessContext context) throws IOException {
getLogger().debug("Loading packages");
final StopWatch stopWatch = new StopWatch(true);
// Load required MDHT packages
System.setProperty( "org.eclipse.emf.ecore.EPackage.Registry.INSTANCE",
"org.eclipse.emf.ecore.impl.EPackageRegistryImpl" );
CDAPackage.eINSTANCE.eClass();
HITSPPackage.eINSTANCE.eClass();
CCDPackage.eINSTANCE.eClass();
ConsolPackage.eINSTANCE.eClass();
IHEPackage.eINSTANCE.eClass();
stopWatch.stop();
getLogger().debug("Loaded packages in {}", new Object[] {stopWatch.getDuration(TimeUnit.MILLISECONDS)});
// Initialize JEXL
jexl = new JexlBuilder().cache(1024).debug(false).silent(true).strict(false).create();
jexlCtx = new MapContext();
getLogger().debug("Loading mappings");
loadMappings(); // Load CDA mappings for parser
}
@Override
public void onTrigger(final ProcessContext context, final ProcessSession session) {
Map<String, String> attributes = new TreeMap<String, String>(); // stores CDA attributes
getLogger().info("Processing CCDA");
FlowFile flowFile = session.get();
if ( flowFile == null ) {
return;
}
if(processMap.isEmpty()) {
getLogger().error("Process Mapping is not loaded");
session.transfer(flowFile, REL_FAILURE);
return;
}
final Boolean skipValidation = context.getProperty(SKIP_VALIDATION).asBoolean();
final StopWatch stopWatch = new StopWatch(true);
ClinicalDocument cd = null;
try {
cd = loadDocument(session.read(flowFile), skipValidation); // Load and optionally validate CDA document
} catch (ProcessException e) {
session.transfer(flowFile, REL_FAILURE);
return;
}
getLogger().debug("Loaded document for {} in {}", new Object[] {flowFile, stopWatch.getElapsed(TimeUnit.MILLISECONDS)});
getLogger().debug("Processing elements");
processElement(null, cd, attributes); // Process CDA element using mapping data
flowFile = session.putAllAttributes(flowFile, attributes);
stopWatch.stop();
getLogger().debug("Successfully processed {} in {}", new Object[] {flowFile, stopWatch.getDuration(TimeUnit.MILLISECONDS)});
if(getLogger().isDebugEnabled()){
for (Entry<String, String> entry : attributes.entrySet()) {
getLogger().debug("Attribute: {}={}", new Object[] {entry.getKey(), entry.getValue()});
}
}
session.transfer(flowFile, REL_SUCCESS);
}
/**
* Process elements children based on the parser mapping.
* Any String values are added to attributes
* For List, the processList method is called to iterate and process
* For an Object this method is called recursively
* While adding to the attributes the key is prefixed by parent
* @param parent parent key for this element, used as a prefix for attribute key
* @param element element to be processed
* @param attributes map of attributes to populate
* @return map of processed data, value can contain String or Map of Strings
*/
protected Map<String, Object> processElement(String parent, Object element, Map<String, String> attributes) {
final StopWatch stopWatch = new StopWatch(true);
Map<String, Object> map = new LinkedHashMap<String, Object>();
String name = element.getClass().getName();
Map<String, String> jexlMap = processMap.get(name); // get JEXL mappings for this element
if (jexlMap == null) {
getLogger().warn("Missing mapping for element " + name);
return null;
}
for (Entry<String, String> entry : jexlMap.entrySet()) { // evaluate JEXL for each child element
jexlCtx.set("element", element);
JexlExpression jexlExpr = jexl.createExpression(entry.getValue());
Object value = jexlExpr.evaluate(jexlCtx);
String key = entry.getKey();
String prefix = parent != null ? parent + "." + key : key;
addElement(map, prefix, key, value, attributes);
}
stopWatch.stop();
getLogger().debug("Processed {} in {}", new Object[] {name, stopWatch.getDuration(TimeUnit.MILLISECONDS)});
return map;
}
/**
* Adds element to the attribute list based on the type
* @param map object map
* @param prefix parent key as prefix
* @param key element key
* @param value element value
*/
protected Map<String, String> addElement(Map<String, Object> map, String prefix, String key, Object value, Map<String, String> attributes) {
// if the value is a String, add it to final attribute list
// else process it further until we have a String representation
if (value instanceof String) {
if(value != null && !((String) value).isEmpty()) {
map.put(key, value);
attributes.put(prefix, (String) value);
}
} else if (value instanceof List) {
if(value != null && !((List) value).isEmpty()) {
map.put(key, processList(prefix, (List) value, attributes));
}
} else if (value != null) { // process element further
map.put(key, processElement(prefix, value, attributes));
}
return attributes;
}
/**
* Iterate through the list and calls processElement to process each element
* @param key key used while calling processElement
* @param value value is the individual Object being processed
* @param attributes map of attributes to populate
* @return list of elements
*/
protected List<Object> processList(String key, List value, Map<String, String> attributes) {
List<Object> items = new ArrayList<Object>();
String keyFormat = value.size() > 1 ? "%s_%02d" : "%s";
for (Object item : value) { // iterate over all elements and process each element
items.add(processElement(String.format(keyFormat, key, items.size() + 1), item, attributes));
}
return items;
}
protected ClinicalDocument loadDocument(InputStream inputStream, Boolean skipValidation) {
ClinicalDocument cd = null;
try {
cd = CDAUtil.load(inputStream); // 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");
}
} catch (Exception e) {
getLogger().error("Failed to load CDA document", e);
throw new ProcessException("Failed to load CDA document", e);
}
return cd;
}
protected void loadMappings() {
ClassLoader classloader = Thread.currentThread().getContextClassLoader();
Properties mappings = new Properties();
try (InputStream is = classloader.getResourceAsStream("mapping.properties")){
mappings.load(is);
// each child element is key#value and multiple elements are separated by @
for (String property : mappings.stringPropertyNames()) {
String[] variables = StringUtils.split(mappings.getProperty(property), FIELD_SEPARATOR);
Map<String, String> map = new LinkedHashMap<String, String>();
for (String variable : variables) {
String[] keyvalue = StringUtils.split(variable, KEY_VALUE_SEPARATOR);
map.put(keyvalue[0], keyvalue[1]);
}
processMap.put(property, map);
}
} catch (IOException e) {
getLogger().error("Failed to load mappings", e);
throw new ProcessException("Failed to load mappings", e);
}
}
protected class CDAValidationHandler implements ValidationHandler {
@Override
public void handleError(Diagnostic diagnostic) {
getLogger().error(new StringBuilder("ERROR: ").append(diagnostic.getMessage()).toString());
}
@Override
public void handleWarning(Diagnostic diagnostic) {
getLogger().warn(new StringBuilder("WARNING: ").append(diagnostic.getMessage()).toString());
}
@Override
public void handleInfo(Diagnostic diagnostic) {
getLogger().info(new StringBuilder("INFO: ").append(diagnostic.getMessage()).toString());
}
}
}

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# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use this file except in compliance with
# the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
org.apache.nifi.processors.ccda.ExtractCCDAAttributes

63
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<!DOCTYPE html>
<html lang="en">
<!--
Licensed to the Apache Software Foundation (ASF) under one or more
contributor license agreements. See the NOTICE file distributed with
this work for additional information regarding copyright ownership.
The ASF licenses this file to You under the Apache License, Version 2.0
(the "License"); you may not use this file except in compliance with
the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
-->
<head>
<meta charset="utf-8" />
<title>ExtractCCDAAttributes</title>
<link rel="stylesheet" href="../../css/component-usage.css" type="text/css" />
</head>
<body>
<!-- Processor Documentation ================================================== -->
<h2>Apache NiFi C-CDA Processor</h2>
<p>
C-CDA Processor Bundle provides parser for Consolidated-CDA documents</br>
This processor parses C-CDA and sets attributes as FlowFile attributes. The attributes are named as &lt;Parent&gt; &lt;dot&gt; &lt;Key&gt;.</br>
If the Parent is repeating, the naming will be &lt;Parent&gt; &lt;underscore&gt; &lt;Parent Index&gt; &lt;dot&gt; &lt;Key&gt;.</br>
</p>
<h3>Example Attribute Output</h3>
<p>
<pre><code>
problemSection.act.observation.problemStatus.code.code=33999-4
problemSection.act.observation.problemStatus.code.codeSystem=2.16.840.1.113883.6.1
problemSection.act.observation.problemStatus.code.codeSystemName=LOINC
problemSection.act.observation.problemStatus.code.displayName=Status
problemSection.act.observation.problemStatus.statusCode.code=completed
problemSection.act.observation.statusCode.code=completed
</code></pre>
</p>
<h3>Example Parser Mapping</h3>
<p>
This processor is driven by a mapping file which specifies the element relationships. For example
<pre><code>
org.openhealthtools.mdht.uml.cda.consol.impl.ProblemObservationImpl=id#element.ids\
@values#element.values[0]\
@statusCode#element.statusCode\
@effectiveTime#element.effectiveTime\
@negation#element.negationInd\
@problemStatus#element.problemStatus
org.openhealthtools.mdht.uml.cda.consol.impl.ProblemStatusImpl=id#element.id\
@code#element.code\
@values#element.values[0]\
@statusCode#element.statusCode
</code></pre>
</p>
<h3>References</h3>
<p>
These mappings are defined as per the implementation guide&mdash;<a href="http://www.hl7.org/documentcenter/public/standards/dstu/CDAR2_IG_IHE_CONSOL_DSTU_R1dot1_2012JUL.zip">HL7 Implementation Guide for CDA&reg; Release 2</a></br>
</p>
</body>
</html>

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# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use this file except in compliance with
# the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# Consolidated CCD
org.openhealthtools.mdht.uml.cda.consol.impl.ContinuityOfCareDocumentImpl=id#element.id\
@code#element.code\
@title#element.title.text\
@effectiveTime#element.effectiveTime.value\
@problemSection#element.problemSection\
@vitalSignsSection#element.vitalSignsSectionEntriesOptional
org.openhealthtools.mdht.uml.cda.consol.impl.ProblemSectionImpl=id#element.id\
@code#element.code\
@title#element.title.text\
@act#element.problemConcerns
org.openhealthtools.mdht.uml.cda.consol.impl.ProblemConcernActImpl=id#element.ids\
@code#element.code\
@statusCode#element.statusCode\
@effectiveTime#element.effectiveTime\
@observation#element.observations
org.openhealthtools.mdht.uml.cda.consol.impl.ProblemObservationImpl=id#element.ids\
@values#element.values[0]\
@statusCode#element.statusCode\
@effectiveTime#element.effectiveTime\
@negation#element.negationInd\
@problemStatus#element.problemStatus
org.openhealthtools.mdht.uml.cda.consol.impl.ProblemStatusImpl=id#element.id\
@code#element.code\
@values#element.values[0]\
@statusCode#element.statusCode
org.openhealthtools.mdht.uml.cda.consol.impl.VitalSignsSectionImpl=ids#element.ids\
@code#element.code\
@title#element.title.text\
@organizer#element.vitalSignsOrganizers
org.openhealthtools.mdht.uml.cda.consol.impl.VitalSignsSectionEntriesOptionalImpl=organizer#element.vitalSignsOrganizers
org.openhealthtools.mdht.uml.cda.consol.impl.VitalSignsOrganizerImpl=ids#element.ids\
@code#element.code\
@statusCode#element.statusCode\
@effectiveTime#element.effectiveTime\
@observations#element.vitalSignObservations
org.openhealthtools.mdht.uml.cda.consol.impl.VitalSignObservationImpl=ids#element.ids\
@code#element.code\
@text#element.text\
@statusCode#element.statusCode\
@effectiveTime#element.effectiveTime\
@values#element.values
# HL7 Datatypes
org.openhealthtools.mdht.uml.hl7.datatypes.impl.CEImpl=code#element.code\
@codeSystem#element.codeSystem\
@codeSystemName#element.codeSystemName\
@displayName#element.displayName\
@originalText#element.originalText\
@translations#element.translations
org.openhealthtools.mdht.uml.hl7.datatypes.impl.CSImpl=code#element.code\
@codeSystem#element.codeSystem\
@codeSystemName#element.codeSystemName\
@displayName#element.displayName\
@originalText#element.originalText\
@translations#element.translations
org.openhealthtools.mdht.uml.hl7.datatypes.impl.CDImpl=code#element.code\
@codeSystem#element.codeSystem\
@codeSystemName#element.codeSystemName\
@displayName#element.displayName\
@originalText#element.originalText\
@translations#element.translations
org.openhealthtools.mdht.uml.hl7.datatypes.impl.IVL_TSImpl=low#element.low != null? element.low.value: null\
@high#element.high != null? element.high.value: null\
@center#element.center != null? element.center.value: null\
@value#element.value
org.openhealthtools.mdht.uml.hl7.datatypes.impl.IIImpl=extension#element.extension\
@root#element.root
org.openhealthtools.mdht.uml.hl7.datatypes.impl.PQImpl=unit#element.unit\
@value#element.value.toPlainString()
org.openhealthtools.mdht.uml.hl7.datatypes.impl.EDImpl=reference#element.reference\
@text#element.mixed
org.openhealthtools.mdht.uml.hl7.datatypes.impl.TELImpl=value#element.value
org.eclipse.emf.ecore.impl.EStructuralFeatureImpl$SimpleFeatureMapEntry=value#element.value.trim()
org.eclipse.emf.ecore.impl.EStructuralFeatureImpl$ContainmentUpdatingFeatureMapEntry=value#element.value.trim()

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/*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.apache.nifi.processors.ccda;
import java.io.IOException;
import java.io.StringWriter;
import java.util.HashMap;
import java.util.Map;
import org.apache.nifi.util.MockFlowFile;
import org.apache.nifi.util.TestRunner;
import org.apache.nifi.util.TestRunners;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import org.openhealthtools.mdht.uml.cda.consol.ConsolFactory;
import org.openhealthtools.mdht.uml.cda.consol.ContinuityOfCareDocument;
import org.openhealthtools.mdht.uml.cda.consol.ProblemConcernAct;
import org.openhealthtools.mdht.uml.cda.consol.ProblemObservation;
import org.openhealthtools.mdht.uml.cda.consol.ProblemSection;
import org.openhealthtools.mdht.uml.cda.consol.ProblemStatus;
import org.openhealthtools.mdht.uml.cda.consol.VitalSignObservation;
import org.openhealthtools.mdht.uml.cda.consol.VitalSignsOrganizer;
import org.openhealthtools.mdht.uml.cda.consol.VitalSignsSection;
import org.openhealthtools.mdht.uml.cda.util.CDAUtil;
public class TestExtractCCDAAttributes {
private TestRunner runner;
@BeforeClass
public static void setup() {
System.setProperty("org.slf4j.simpleLogger.log.org.apache.nifi", "INFO");
}
@Before
public void init() {
runner = TestRunners.newTestRunner(ExtractCCDAAttributes.class);
}
@Test
public void testProcessor() throws Exception {
Map<String, String> expectedAttributes = new HashMap<String, String>();
expectedAttributes.put("code.code", "34133-9");
expectedAttributes.put("code.codeSystem", "2.16.840.1.113883.6.1");
expectedAttributes.put("code.codeSystemName", "LOINC");
expectedAttributes.put("code.displayName", "Summarization of Episode Note");
expectedAttributes.put("problemSection.code.code", "11450-4");
expectedAttributes.put("problemSection.code.codeSystem", "2.16.840.1.113883.6.1");
expectedAttributes.put("problemSection.code.codeSystemName", "LOINC");
expectedAttributes.put("problemSection.code.displayName", "Problem List");
expectedAttributes.put("problemSection.act.code.code", "CONC");
expectedAttributes.put("problemSection.act.code.codeSystem", "2.16.840.1.113883.5.6");
expectedAttributes.put("problemSection.act.code.codeSystemName", "HL7ActClass");
expectedAttributes.put("problemSection.act.code.displayName", "Concern");
expectedAttributes.put("problemSection.act.observation.problemStatus.code.code", "33999-4");
expectedAttributes.put("problemSection.act.observation.problemStatus.code.codeSystem", "2.16.840.1.113883.6.1");
expectedAttributes.put("problemSection.act.observation.problemStatus.code.codeSystemName", "LOINC");
expectedAttributes.put("problemSection.act.observation.problemStatus.code.displayName", "Status");
expectedAttributes.put("problemSection.act.observation.problemStatus.statusCode.code", "completed");
expectedAttributes.put("problemSection.act.observation.statusCode.code", "completed");
expectedAttributes.put("vitalSignsSection.code.code", "8716-3");
expectedAttributes.put("vitalSignsSection.code.codeSystem", "2.16.840.1.113883.6.1");
expectedAttributes.put("vitalSignsSection.code.codeSystemName", "LOINC");
expectedAttributes.put("vitalSignsSection.code.displayName", "Vital Signs");
expectedAttributes.put("vitalSignsSection.organizer.code.code", "46680005");
expectedAttributes.put("vitalSignsSection.organizer.code.codeSystem", "2.16.840.1.113883.6.96");
expectedAttributes.put("vitalSignsSection.organizer.code.codeSystemName", "SNOMEDCT");
expectedAttributes.put("vitalSignsSection.organizer.code.displayName", "Vital signs");
expectedAttributes.put("vitalSignsSection.organizer.statusCode.code", "completed");
expectedAttributes.put("vitalSignsSection.organizer.observations.code.codeSystem", "2.16.840.1.113883.6.1");
expectedAttributes.put("vitalSignsSection.organizer.observations.code.codeSystemName", "LOINC");
expectedAttributes.put("vitalSignsSection.organizer.observations.statusCode.code", "completed");
ContinuityOfCareDocument doc = ConsolFactory.eINSTANCE.createContinuityOfCareDocument().init();
ProblemConcernAct problemAct = ConsolFactory.eINSTANCE.createProblemConcernAct().init();
ProblemObservation problemObservation = ConsolFactory.eINSTANCE.createProblemObservation().init();
ProblemStatus problemStatus = ConsolFactory.eINSTANCE.createProblemStatus().init();
ProblemSection problemSection = ConsolFactory.eINSTANCE.createProblemSection().init();
doc.addSection(problemSection);
problemSection.addAct(problemAct);
problemAct.addObservation(problemObservation);
problemObservation.addObservation(problemStatus);
VitalSignsOrganizer vitalSignsOrganizer = ConsolFactory.eINSTANCE.createVitalSignsOrganizer().init();
VitalSignObservation vitalSignObservation = ConsolFactory.eINSTANCE.createVitalSignObservation().init();
VitalSignsSection vitalSignsSection = ConsolFactory.eINSTANCE.createVitalSignsSection().init();
doc.addSection(vitalSignsSection);
vitalSignsSection.addOrganizer(vitalSignsOrganizer);
vitalSignsOrganizer.addObservation(vitalSignObservation);
StringWriter writer = new StringWriter();
CDAUtil.save(doc, writer);
runTests(writer.toString(), expectedAttributes, true, true);
}
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));
runner.enqueue(content);
runner.run();
runner.assertAllFlowFilesTransferred(ExtractCCDAAttributes.REL_SUCCESS, 1);
final MockFlowFile flowFile = runner.getFlowFilesForRelationship(ExtractCCDAAttributes.REL_SUCCESS).get(0);
for (final Map.Entry<String, String> entry : expectedAttributes.entrySet()) {
flowFile.assertAttributeEquals(entry.getKey(), entry.getValue());
}
}
}

43
nifi-nar-bundles/nifi-ccda-bundle/pom.xml Normal file
View File

@ -0,0 +1,43 @@
<?xml version="1.0" encoding="UTF-8"?>
<!--
Licensed to the Apache Software Foundation (ASF) under one or more
contributor license agreements. See the NOTICE file distributed with
this work for additional information regarding copyright ownership.
The ASF licenses this file to You under the Apache License, Version 2.0
(the "License"); you may not use this file except in compliance with
the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
-->
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.apache.nifi</groupId>
<artifactId>nifi-nar-bundles</artifactId>
<version>1.2.0-SNAPSHOT</version>
</parent>
<artifactId>nifi-ccda-bundle</artifactId>
<packaging>pom</packaging>
<modules>
<module>nifi-ccda-processors</module>
<module>nifi-ccda-nar</module>
</modules>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.apache.nifi</groupId>
<artifactId>nifi-ccda-processors</artifactId>
<version>1.2.0-SNAPSHOT</version>
</dependency>
</dependencies>
</dependencyManagement>
</project>

1
nifi-nar-bundles/pom.xml
View File

@ -39,6 +39,7 @@
<module>nifi-social-media-bundle</module>
<module>nifi-enrich-bundle</module>
<module>nifi-hl7-bundle</module>
<module>nifi-ccda-bundle</module>
<module>nifi-language-translation-bundle</module>
<module>nifi-mongodb-bundle</module>
<module>nifi-flume-bundle</module>

6
pom.xml
View File

@ -1066,6 +1066,12 @@ language governing permissions and limitations under the License. -->
<version>1.2.0-SNAPSHOT</version>
<type>nar</type>
</dependency>
<dependency>
<groupId>org.apache.nifi</groupId>
<artifactId>nifi-ccda-nar</artifactId>
<version>1.2.0-SNAPSHOT</version>
<type>nar</type>
</dependency>
<dependency>
<groupId>org.apache.nifi</groupId>
<artifactId>nifi-language-translation-nar</artifactId>