Apache
/
nifi
mirror of https://github.com/apache/nifi.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
nifi-assembly/NOTICE
View File

@ -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. 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 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) 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) (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
View File

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

39
nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/pom.xml Normal file
View File

@ -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>

209
nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/src/main/resources/META-INF/LICENSE Normal file
View File

@ -0,0 +1,209 @@
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
1. Definitions.
"License" shall mean the terms and conditions for use, reproduction,
and distribution as defined by Sections 1 through 9 of this document.
"Licensor" shall mean the copyright owner or entity authorized by
the copyright owner that is granting the License.
"Legal Entity" shall mean the union of the acting entity and all
other entities that control, are controlled by, or are under common
control with that entity. For the purposes of this definition,
"control" means (i) the power, direct or indirect, to cause the
direction or management of such entity, whether by contract or
otherwise, or (ii) ownership of fifty percent (50%) or more of the
outstanding shares, or (iii) beneficial ownership of such entity.
"You" (or "Your") shall mean an individual or Legal Entity
exercising permissions granted by this License.
"Source" form shall mean the preferred form for making modifications,
including but not limited to software source code, documentation
source, and configuration files.
"Object" form shall mean any form resulting from mechanical
transformation or translation of a Source form, including but
not limited to compiled object code, generated documentation,
and conversions to other media types.
"Work" shall mean the work of authorship, whether in Source or
Object form, made available under the License, as indicated by a
copyright notice that is included in or attached to the work
(an example is provided in the Appendix below).
"Derivative Works" shall mean any work, whether in Source or Object
form, that is based on (or derived from) the Work and for which the
editorial revisions, annotations, elaborations, or other modifications
represent, as a whole, an original work of authorship. For the purposes
of this License, Derivative Works shall not include works that remain
separable from, or merely link (or bind by name) to the interfaces of,
the Work and Derivative Works thereof.
"Contribution" shall mean any work of authorship, including
the original version of the Work and any modifications or additions
to that Work or Derivative Works thereof, that is intentionally
submitted to Licensor for inclusion in the Work by the copyright owner
or by an individual or Legal Entity authorized to submit on behalf of
the copyright owner. For the purposes of this definition, "submitted"
means any form of electronic, verbal, or written communication sent
to the Licensor or its representatives, including but not limited to
communication on electronic mailing lists, source code control systems,
and issue tracking systems that are managed by, or on behalf of, the
Licensor for the purpose of discussing and improving the Work, but
excluding communication that is conspicuously marked or otherwise
designated in writing by the copyright owner as "Not a Contribution."
"Contributor" shall mean Licensor and any individual or Legal Entity
on behalf of whom a Contribution has been received by Licensor and
subsequently incorporated within the Work.
2. Grant of Copyright License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
copyright license to reproduce, prepare Derivative Works of,
publicly display, publicly perform, sublicense, and distribute the
Work and such Derivative Works in Source or Object form.
3. Grant of Patent License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
(except as stated in this section) patent license to make, have made,
use, offer to sell, sell, import, and otherwise transfer the Work,
where such license applies only to those patent claims licensable
by such Contributor that are necessarily infringed by their
Contribution(s) alone or by combination of their Contribution(s)
with the Work to which such Contribution(s) was submitted. If You
institute patent litigation against any entity (including a
cross-claim or counterclaim in a lawsuit) alleging that the Work
or a Contribution incorporated within the Work constitutes direct
or contributory patent infringement, then any patent licenses
granted to You under this License for that Work shall terminate
as of the date such litigation is filed.
4. Redistribution. You may reproduce and distribute copies of the
Work or Derivative Works thereof in any medium, with or without
modifications, and in Source or Object form, provided that You
meet the following conditions:
(a) You must give any other recipients of the Work or
Derivative Works a copy of this License; and
(b) You must cause any modified files to carry prominent notices
stating that You changed the files; and
(c) You must retain, in the Source form of any Derivative Works
that You distribute, all copyright, patent, trademark, and
attribution notices from the Source form of the Work,
excluding those notices that do not pertain to any part of
the Derivative Works; and
(d) If the Work includes a "NOTICE" text file as part of its
distribution, then any Derivative Works that You distribute must
include a readable copy of the attribution notices contained
within such NOTICE file, excluding those notices that do not
pertain to any part of the Derivative Works, in at least one
of the following places: within a NOTICE text file distributed
as part of the Derivative Works; within the Source form or
documentation, if provided along with the Derivative Works; or,
within a display generated by the Derivative Works, if and
wherever such third-party notices normally appear. The contents
of the NOTICE file are for informational purposes only and
do not modify the License. You may add Your own attribution
notices within Derivative Works that You distribute, alongside
or as an addendum to the NOTICE text from the Work, provided
that such additional attribution notices cannot be construed
as modifying the License.
You may add Your own copyright statement to Your modifications and
may provide additional or different license terms and conditions
for use, reproduction, or distribution of Your modifications, or
for any such Derivative Works as a whole, provided Your use,
reproduction, and distribution of the Work otherwise complies with
the conditions stated in this License.
5. Submission of Contributions. Unless You explicitly state otherwise,
any Contribution intentionally submitted for inclusion in the Work
by You to the Licensor shall be under the terms and conditions of
this License, without any additional terms or conditions.
Notwithstanding the above, nothing herein shall supersede or modify
the terms of any separate license agreement you may have executed
with Licensor regarding such Contributions.
6. Trademarks. This License does not grant permission to use the trade
names, trademarks, service marks, or product names of the Licensor,
except as required for reasonable and customary use in describing the
origin of the Work and reproducing the content of the NOTICE file.
7. Disclaimer of Warranty. Unless required by applicable law or
agreed to in writing, Licensor provides the Work (and each
Contributor provides its Contributions) on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
implied, including, without limitation, any warranties or conditions
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
PARTICULAR PURPOSE. You are solely responsible for determining the
appropriateness of using or redistributing the Work and assume any
risks associated with Your exercise of permissions under this License.
8. Limitation of Liability. In no event and under no legal theory,
whether in tort (including negligence), contract, or otherwise,
unless required by applicable law (such as deliberate and grossly
negligent acts) or agreed to in writing, shall any Contributor be
liable to You for damages, including any direct, indirect, special,
incidental, or consequential damages of any character arising as a
result of this License or out of the use or inability to use the
Work (including but not limited to damages for loss of goodwill,
work stoppage, computer failure or malfunction, or any and all
other commercial damages or losses), even if such Contributor
has been advised of the possibility of such damages.
9. Accepting Warranty or Additional Liability. While redistributing
the Work or Derivative Works thereof, You may choose to offer,
and charge a fee for, acceptance of support, warranty, indemnity,
or other liability obligations and/or rights consistent with this
License. However, in accepting such obligations, You may act only
on Your own behalf and on Your sole responsibility, not on behalf
of any other Contributor, and only if You agree to indemnify,
defend, and hold each Contributor harmless for any liability
incurred by, or claims asserted against, such Contributor by reason
of your accepting any such warranty or additional liability.
END OF TERMS AND CONDITIONS
APPENDIX: How to apply the Apache License to your work.
To apply the Apache License to your work, attach the following
boilerplate notice, with the fields enclosed by brackets "[]"
replaced with your own identifying information. (Don't include
the brackets!) The text should be enclosed in the appropriate
comment syntax for the file format. We also recommend that a
file or class name and description of purpose be included on the
same "printed page" as the copyright notice for easier
identification within third-party archives.
Copyright [yyyy] [name of copyright owner]
Licensed 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.
APACHE NIFI SUBCOMPONENTS:
The Apache NiFi project contains subcomponents with separate copyright
notices and license terms. Your use of the source code for the these
subcomponents is subject to the terms and conditions of the following
licenses.

37
nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/src/main/resources/META-INF/NOTICE Normal file
View File

@ -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
View File

@ -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
View File

@ -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());
}
}
}

15
nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/META-INF/services/org.apache.nifi.processor.Processor Normal file
View File

@ -0,0 +1,15 @@
# 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
nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/docs/org.apache.nifi.processors.ccda.ExtractCCDAAttributes/additionalDetails.html Normal file
View File

@ -0,0 +1,63 @@
<!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>

89
nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/mapping.properties Normal file
View File

@ -0,0 +1,89 @@
# 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()

130
nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/test/java/org/apache/nifi/processors/ccda/TestExtractCCDAAttributes.java Normal file
View File

@ -0,0 +1,130 @@
/*
* 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-social-media-bundle</module>
<module>nifi-enrich-bundle</module> <module>nifi-enrich-bundle</module>
<module>nifi-hl7-bundle</module> <module>nifi-hl7-bundle</module>
<module>nifi-ccda-bundle</module>
<module>nifi-language-translation-bundle</module> <module>nifi-language-translation-bundle</module>
<module>nifi-mongodb-bundle</module> <module>nifi-mongodb-bundle</module>
<module>nifi-flume-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> <version>1.2.0-SNAPSHOT</version>
<type>nar</type> <type>nar</type>
</dependency> </dependency>
<dependency>
<groupId>org.apache.nifi</groupId>
<artifactId>nifi-ccda-nar</artifactId>
<version>1.2.0-SNAPSHOT</version>
<type>nar</type>
</dependency>
<dependency> <dependency>
<groupId>org.apache.nifi</groupId> <groupId>org.apache.nifi</groupId>
<artifactId>nifi-language-translation-nar</artifactId> <artifactId>nifi-language-translation-nar</artifactId>