Repository: nifi Updated Branches: refs/heads/master 83fa24b68 -> 457df93dd
NIFI-3147 Build processor to parse CCDA into attributes This closes #1312 Signed-off-by: Joey Frazee <[email protected]> Project: http://git-wip-us.apache.org/repos/asf/nifi/repo Commit: http://git-wip-us.apache.org/repos/asf/nifi/commit/457df93d Tree: http://git-wip-us.apache.org/repos/asf/nifi/tree/457df93d Diff: http://git-wip-us.apache.org/repos/asf/nifi/diff/457df93d Branch: refs/heads/master Commit: 457df93dd6b0dccbe0dd437234aee53b76f010b4 Parents: 83fa24b Author: kedarchitale <[email protected]> Authored: Fri Dec 9 15:45:19 2016 +0530 Committer: Joey Frazee <[email protected]> Committed: Wed Mar 29 20:30:57 2017 +0000 ---------------------------------------------------------------------- nifi-assembly/NOTICE | 63 ++-- nifi-assembly/pom.xml | 5 + .../nifi-ccda-bundle/nifi-ccda-nar/pom.xml | 39 +++ .../src/main/resources/META-INF/LICENSE | 209 ++++++++++++ .../src/main/resources/META-INF/NOTICE | 37 ++ .../nifi-ccda-processors/pom.xml | 78 +++++ .../processors/ccda/ExtractCCDAAttributes.java | 339 +++++++++++++++++++ .../org.apache.nifi.processor.Processor | 15 + .../additionalDetails.html | 63 ++++ .../src/main/resources/mapping.properties | 89 +++++ .../ccda/TestExtractCCDAAttributes.java | 130 +++++++ nifi-nar-bundles/nifi-ccda-bundle/pom.xml | 43 +++ nifi-nar-bundles/pom.xml | 1 + pom.xml | 6 + 14 files changed, 1086 insertions(+), 31 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/nifi-assembly/NOTICE ---------------------------------------------------------------------- diff --git a/nifi-assembly/NOTICE b/nifi-assembly/NOTICE index 3821269..e5db477 100644 --- a/nifi-assembly/NOTICE +++ b/nifi-assembly/NOTICE @@ -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 ([email protected]) on behalf of the + - voluntary contributions made by Ovidiu Predescu ([email protected]) 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) http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/nifi-assembly/pom.xml ---------------------------------------------------------------------- diff --git a/nifi-assembly/pom.xml b/nifi-assembly/pom.xml index 0a810f6..7751666 100755 --- a/nifi-assembly/pom.xml +++ b/nifi-assembly/pom.xml @@ -260,6 +260,11 @@ language governing permissions and limitations under the License. --> </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> <type>nar</type> </dependency> http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/pom.xml ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/pom.xml b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/pom.xml new file mode 100644 index 0000000..41ddb5c --- /dev/null +++ b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/pom.xml @@ -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> http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/src/main/resources/META-INF/LICENSE ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/src/main/resources/META-INF/LICENSE b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/src/main/resources/META-INF/LICENSE new file mode 100644 index 0000000..6effaa8 --- /dev/null +++ b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/src/main/resources/META-INF/LICENSE @@ -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. 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Your use of the source code for the these +subcomponents is subject to the terms and conditions of the following +licenses. \ No newline at end of file http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/src/main/resources/META-INF/NOTICE ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/src/main/resources/META-INF/NOTICE b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/src/main/resources/META-INF/NOTICE new file mode 100644 index 0000000..0d1fb59 --- /dev/null +++ b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-nar/src/main/resources/META-INF/NOTICE @@ -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) + http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/pom.xml ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/pom.xml b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/pom.xml new file mode 100644 index 0000000..d3022e7 --- /dev/null +++ b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/pom.xml @@ -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> http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/java/org/apache/nifi/processors/ccda/ExtractCCDAAttributes.java ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/java/org/apache/nifi/processors/ccda/ExtractCCDAAttributes.java b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/java/org/apache/nifi/processors/ccda/ExtractCCDAAttributes.java new file mode 100644 index 0000000..24e339e --- /dev/null +++ b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/java/org/apache/nifi/processors/ccda/ExtractCCDAAttributes.java @@ -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()); + } + } + +} http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/META-INF/services/org.apache.nifi.processor.Processor ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/META-INF/services/org.apache.nifi.processor.Processor b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/META-INF/services/org.apache.nifi.processor.Processor new file mode 100644 index 0000000..b88018d --- /dev/null +++ b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/META-INF/services/org.apache.nifi.processor.Processor @@ -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 \ No newline at end of file http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/docs/org.apache.nifi.processors.ccda.ExtractCCDAAttributes/additionalDetails.html ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/docs/org.apache.nifi.processors.ccda.ExtractCCDAAttributes/additionalDetails.html b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/docs/org.apache.nifi.processors.ccda.ExtractCCDAAttributes/additionalDetails.html new file mode 100644 index 0000000..999078a --- /dev/null +++ b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/docs/org.apache.nifi.processors.ccda.ExtractCCDAAttributes/additionalDetails.html @@ -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 <Parent> <dot> <Key>.</br> + If the Parent is repeating, the naming will be <Parent> <underscore> <Parent Index> <dot> <Key>.</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—<a href="http://www.hl7.org/documentcenter/public/standards/dstu/CDAR2_IG_IHE_CONSOL_DSTU_R1dot1_2012JUL.zip";>HL7 Implementation Guide for CDA® Release 2</a></br> + </p> + </body> +</html> http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/mapping.properties ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/mapping.properties b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/mapping.properties new file mode 100644 index 0000000..c2fbc97 --- /dev/null +++ b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/resources/mapping.properties @@ -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() \ No newline at end of file http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/test/java/org/apache/nifi/processors/ccda/TestExtractCCDAAttributes.java ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/test/java/org/apache/nifi/processors/ccda/TestExtractCCDAAttributes.java b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/test/java/org/apache/nifi/processors/ccda/TestExtractCCDAAttributes.java new file mode 100644 index 0000000..aafb0c8 --- /dev/null +++ b/nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/test/java/org/apache/nifi/processors/ccda/TestExtractCCDAAttributes.java @@ -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()); + } + + } +} http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/nifi-nar-bundles/nifi-ccda-bundle/pom.xml ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-ccda-bundle/pom.xml b/nifi-nar-bundles/nifi-ccda-bundle/pom.xml new file mode 100644 index 0000000..d5dc2ca --- /dev/null +++ b/nifi-nar-bundles/nifi-ccda-bundle/pom.xml @@ -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> http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/nifi-nar-bundles/pom.xml ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/pom.xml b/nifi-nar-bundles/pom.xml index 2a30231..ea50bbc 100755 --- a/nifi-nar-bundles/pom.xml +++ b/nifi-nar-bundles/pom.xml @@ -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> http://git-wip-us.apache.org/repos/asf/nifi/blob/457df93d/pom.xml ---------------------------------------------------------------------- diff --git a/pom.xml b/pom.xml index 78664da..e621efa 100644 --- a/pom.xml +++ b/pom.xml @@ -1068,6 +1068,12 @@ language governing permissions and limitations under the License. --> </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> <version>1.2.0-SNAPSHOT</version> <type>nar</type>
