Github user jfrazee commented on a diff in the pull request: https://github.com/apache/nifi/pull/1312#discussion_r102508342 --- Diff: nifi-nar-bundles/nifi-ccda-bundle/nifi-ccda-processors/src/main/java/org/apache/nifi/processors/ccda/ExtractCCDAAttributes.java --- @@ -0,0 +1,383 @@ +/* + * 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.io.OutputStream; +import java.util.ArrayList; +import java.util.HashMap; +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 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.components.PropertyDescriptor; +import org.apache.nifi.flowfile.FlowFile; +import org.apache.nifi.flowfile.attributes.CoreAttributes; +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.io.OutputStreamCallback; +import org.apache.nifi.processor.util.StandardValidators; +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; + +import com.google.gson.Gson; +import com.google.gson.GsonBuilder; + +@SideEffectFree +@SupportsBatching +@InputRequirement(Requirement.INPUT_REQUIRED) +@Tags({"CCDA", "healthcare", "extract", "JSON", "attributes"}) +@CapabilityDescription("Extracts information from an Consolidated CDA formatted FlowFile and provides JSON as FlowFile content " + + "and 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 String APPLICATION_JSON = "application/json"; + 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 List<String> timingStats = new ArrayList<String>(); // stores timing statistics + private Map<String, String> attributes = new TreeMap<String, String>(); // stores CDA attributes + 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(); + + /** + * PRETTY_PRINTING - Choice of whether generated JSON in the FileFlow content is + * pretty printed with new line and tabs or just a continuous string of characters + */ + public static final PropertyDescriptor PRETTY_PRINTING = new PropertyDescriptor.Builder().name("pretty-printing") + .displayName("Pretty Printing").description("Whether or not to Pretty Print JSON output").required(true) + .allowableValues("true", "false").defaultValue("false").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 content stored in FlowFile") + .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 parse CDA and store content to FlowFile.") + .build(); + + @Override + protected List<PropertyDescriptor> getSupportedPropertyDescriptors() { + return properties; + } + + @Override + public Set<Relationship> getRelationships() { + return relationships; + } + + @Override + protected void init(final ProcessorInitializationContext context) { + getLogger().info("Loading packages"); + + relationships = new HashSet<>(); + relationships.add(REL_SUCCESS); + relationships.add(REL_FAILURE); + + properties = new ArrayList<>(); + properties.add(SKIP_VALIDATION); + properties.add(PRETTY_PRINTING); + + long start = System.currentTimeMillis(); + + // 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(); + timingStats.add(String.format("Loaded packages in %d ms", System.currentTimeMillis() - start)); + + // Initialize JEXL + jexl = new JexlBuilder().cache(1024).debug(false).silent(true).strict(false).create(); + jexlCtx = new MapContext(); + + getLogger().info("Loading mappings"); + loadMappings(); // Load CDA mappings for parser + + } + + @Override + public void onTrigger(final ProcessContext context, final ProcessSession session) { + 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 Boolean prettyPrinting = context.getProperty(PRETTY_PRINTING).asBoolean(); + + long start = System.currentTimeMillis(), total = start; + + ClinicalDocument cd = loadDocument(session.read(flowFile), skipValidation); // Load and optionally validate CDA document + + start = System.currentTimeMillis(); + getLogger().info("Processing elements"); + Map<String, Object> elements = processElement(null, cd); // Process CDA element using mapping data + + start = System.currentTimeMillis(); + getLogger().info("Generating JSON"); + + // Initialize GSON with optional pretty printing + Gson gson = prettyPrinting ? new GsonBuilder().setPrettyPrinting().create() : new GsonBuilder().create(); + String json = gson.toJson(elements); + timingStats.add(String.format("JSON created in %d ms", System.currentTimeMillis() - start)); + timingStats.add(String.format("CCDA Processed in %d ms", System.currentTimeMillis() - total)); + + logDetails(json); + + flowFile = session.write(flowFile, new OutputStreamCallback() { + + @Override + public void process(OutputStream output) throws IOException { + output.write(json.getBytes("UTF-8")); + } + }); + flowFile = session.putAttribute(flowFile, CoreAttributes.MIME_TYPE.key(), APPLICATION_JSON); + flowFile = session.putAllAttributes(flowFile, attributes); + + session.transfer(flowFile, REL_SUCCESS); + + } + + /** + * Process elements children based on the parser mapping. + * Any String values are added to attributes and JSON map + * 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 + * @return Map of processed data, value can contain String or Map of Strings + */ + protected Map<String, Object> processElement(String parent, Object element) { + long start = System.currentTimeMillis(); + + Map<String, Object> map = new LinkedHashMap<String, Object>(); + String name = element.getClass().getName(); + Map<String, String> jexlMap = (HashMap<String, String>) processMap.get(name); // get JEXL mappings for this element + getLogger().debug("Processing " + name); + + if (jexlMap == null) { + getLogger().info("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); + } + timingStats.add(String.format("Processed %s in %d ms", name, System.currentTimeMillis() - start)); + return map; + } + + /** + * Adds element to the JSON map and attribute list based on the type + * @param map JSON map + * @param prefix parent key as prefix + * @param key element key + * @param value element value + */ + protected void addElement(Map<String, Object> map, String prefix, String key, Object value) { + // 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)); + } + } else if (value != null) { // process element further + map.put(key, processElement(prefix, value)); + } + } + + /** + * 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 + * @return list of elements + */ + protected List<Object> processList(String key, List value) { + 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)); + } + return items; + } + + protected ClinicalDocument loadDocument(InputStream inputStream, Boolean skipValidation) { + long start = System.currentTimeMillis(); + ClinicalDocument cd = null; + + try { + getLogger().info("Loading document"); --- End diff -- This should be a debug() or trace() since it's going to get called for every onTrigger().
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