| /* |
| * 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.hl7; |
| |
| import java.io.IOException; |
| import java.io.InputStream; |
| import java.nio.charset.Charset; |
| import java.util.ArrayList; |
| import java.util.HashSet; |
| import java.util.List; |
| import java.util.Map; |
| import java.util.Set; |
| import java.util.TreeMap; |
| |
| import org.apache.commons.lang3.StringUtils; |
| import org.apache.commons.lang3.text.WordUtils; |
| |
| 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.processor.AbstractProcessor; |
| import org.apache.nifi.processor.ProcessContext; |
| import org.apache.nifi.processor.ProcessSession; |
| import org.apache.nifi.processor.Relationship; |
| import org.apache.nifi.processor.exception.ProcessException; |
| import org.apache.nifi.processor.io.InputStreamCallback; |
| import org.apache.nifi.processor.util.StandardValidators; |
| import org.apache.nifi.stream.io.StreamUtils; |
| |
| import ca.uhn.hl7v2.DefaultHapiContext; |
| import ca.uhn.hl7v2.HL7Exception; |
| import ca.uhn.hl7v2.HapiContext; |
| import ca.uhn.hl7v2.model.Composite; |
| import ca.uhn.hl7v2.model.Group; |
| import ca.uhn.hl7v2.model.Message; |
| import ca.uhn.hl7v2.model.Segment; |
| import ca.uhn.hl7v2.model.Structure; |
| import ca.uhn.hl7v2.model.Type; |
| import ca.uhn.hl7v2.model.Visitable; |
| import ca.uhn.hl7v2.parser.CanonicalModelClassFactory; |
| import ca.uhn.hl7v2.parser.DefaultEscaping; |
| import ca.uhn.hl7v2.parser.EncodingCharacters; |
| import ca.uhn.hl7v2.parser.Escaping; |
| import ca.uhn.hl7v2.parser.PipeParser; |
| import ca.uhn.hl7v2.validation.ValidationContext; |
| import ca.uhn.hl7v2.validation.impl.ValidationContextFactory; |
| |
| @SideEffectFree |
| @SupportsBatching |
| @InputRequirement(Requirement.INPUT_REQUIRED) |
| @Tags({"HL7", "health level 7", "healthcare", "extract", "attributes"}) |
| @CapabilityDescription("Extracts information from an HL7 (Health Level 7) formatted FlowFile and adds the information as FlowFile Attributes. " |
| + "The attributes are named as <Segment Name> <dot> <Field Index>. If the segment is repeating, the naming will be " |
| + "<Segment Name> <underscore> <Segment Index> <dot> <Field Index>. For example, we may have an attribute named \"MHS.12\" with " |
| + "a value of \"2.1\" and an attribute named \"OBX_11.3\" with a value of \"93000^CPT4\".") |
| public class ExtractHL7Attributes extends AbstractProcessor { |
| |
| private static final EncodingCharacters HL7_ENCODING = EncodingCharacters.defaultInstance(); |
| |
| private static final Escaping HL7_ESCAPING = new DefaultEscaping(); |
| |
| public static final PropertyDescriptor CHARACTER_SET = new PropertyDescriptor.Builder() |
| .name("Character Encoding") |
| .displayName("Character Encoding") |
| .description("The Character Encoding that is used to encode the HL7 data") |
| .required(true) |
| .expressionLanguageSupported(true) |
| .addValidator(StandardValidators.CHARACTER_SET_VALIDATOR) |
| .defaultValue("UTF-8") |
| .build(); |
| |
| public static final PropertyDescriptor USE_SEGMENT_NAMES = new PropertyDescriptor.Builder() |
| .name("use-segment-names") |
| .displayName("Use Segment Names") |
| .description("Whether or not to use HL7 segment names in attributes") |
| .required(true) |
| .allowableValues("true", "false") |
| .defaultValue("false") |
| .addValidator(StandardValidators.BOOLEAN_VALIDATOR) |
| .build(); |
| |
| public static final PropertyDescriptor PARSE_SEGMENT_FIELDS = new PropertyDescriptor.Builder() |
| .name("parse-segment-fields") |
| .displayName("Parse Segment Fields") |
| .description("Whether or not to parse HL7 segment fields into attributes") |
| .required(true) |
| .allowableValues("true", "false") |
| .defaultValue("false") |
| .addValidator(StandardValidators.BOOLEAN_VALIDATOR) |
| .build(); |
| |
| public static final PropertyDescriptor SKIP_VALIDATION = new PropertyDescriptor.Builder() |
| .name("skip-validation") |
| .displayName("Skip Validation") |
| .description("Whether or not to validate HL7 message values") |
| .required(true) |
| .allowableValues("true", "false") |
| .defaultValue("true") |
| .addValidator(StandardValidators.BOOLEAN_VALIDATOR) |
| .build(); |
| |
| public static final PropertyDescriptor HL7_INPUT_VERSION = new PropertyDescriptor.Builder() |
| .name("hl7-input-version") |
| .displayName("HL7 Input Version") |
| .description("The HL7 version to use for parsing and validation") |
| .required(true) |
| .allowableValues("autodetect", "2.2", "2.3", "2.3.1", "2.4", "2.5", "2.5.1", "2.6") |
| .defaultValue("autodetect") |
| .addValidator(StandardValidators.NON_EMPTY_VALIDATOR) |
| .build(); |
| |
| 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 HL7 and its attributes extracted") |
| .build(); |
| |
| public static final Relationship REL_FAILURE = new Relationship.Builder() |
| .name("failure") |
| .description("A FlowFile is routed to this relationship if it cannot be mapped to FlowFile Attributes. This would happen if the FlowFile does not contain valid HL7 data") |
| .build(); |
| |
| @Override |
| protected List<PropertyDescriptor> getSupportedPropertyDescriptors() { |
| final List<PropertyDescriptor> properties = new ArrayList<>(); |
| properties.add(CHARACTER_SET); |
| properties.add(USE_SEGMENT_NAMES); |
| properties.add(PARSE_SEGMENT_FIELDS); |
| properties.add(SKIP_VALIDATION); |
| properties.add(HL7_INPUT_VERSION); |
| return properties; |
| } |
| |
| @Override |
| public Set<Relationship> getRelationships() { |
| final Set<Relationship> relationships = new HashSet<>(); |
| relationships.add(REL_SUCCESS); |
| relationships.add(REL_FAILURE); |
| return relationships; |
| } |
| |
| @Override |
| public void onTrigger(final ProcessContext context, final ProcessSession session) throws ProcessException { |
| FlowFile flowFile = session.get(); |
| if (flowFile == null) { |
| return; |
| } |
| |
| final Charset charset = Charset.forName(context.getProperty(CHARACTER_SET).evaluateAttributeExpressions(flowFile).getValue()); |
| final Boolean useSegmentNames = context.getProperty(USE_SEGMENT_NAMES).asBoolean(); |
| final Boolean parseSegmentFields = context.getProperty(PARSE_SEGMENT_FIELDS).asBoolean(); |
| final Boolean skipValidation = context.getProperty(SKIP_VALIDATION).asBoolean(); |
| final String inputVersion = context.getProperty(HL7_INPUT_VERSION).getValue(); |
| |
| final byte[] buffer = new byte[(int) flowFile.getSize()]; |
| session.read(flowFile, new InputStreamCallback() { |
| @Override |
| public void process(final InputStream in) throws IOException { |
| StreamUtils.fillBuffer(in, buffer); |
| } |
| }); |
| |
| @SuppressWarnings("resource") |
| final HapiContext hapiContext = new DefaultHapiContext(); |
| if (!inputVersion.equals("autodetect")) { |
| hapiContext.setModelClassFactory(new CanonicalModelClassFactory(inputVersion)); |
| } |
| if (skipValidation) { |
| hapiContext.setValidationContext((ValidationContext) ValidationContextFactory.noValidation()); |
| } |
| |
| final PipeParser parser = hapiContext.getPipeParser(); |
| final String hl7Text = new String(buffer, charset); |
| try { |
| final Message message = parser.parse(hl7Text); |
| final Map<String, String> attributes = getAttributes(message, useSegmentNames, parseSegmentFields); |
| flowFile = session.putAllAttributes(flowFile, attributes); |
| getLogger().debug("Added the following attributes for {}: {}", new Object[]{flowFile, attributes}); |
| } catch (final HL7Exception e) { |
| getLogger().error("Failed to extract attributes from {} due to {}", new Object[]{flowFile, e}); |
| session.transfer(flowFile, REL_FAILURE); |
| return; |
| } |
| |
| session.transfer(flowFile, REL_SUCCESS); |
| } |
| |
| public static Map<String, String> getAttributes(final Group group, final boolean useNames, final boolean parseFields) throws HL7Exception { |
| final Map<String, String> attributes = new TreeMap<>(); |
| if (!isEmpty(group)) { |
| for (final Map.Entry<String, Segment> segmentEntry : getAllSegments(group).entrySet()) { |
| final String segmentKey = segmentEntry.getKey(); |
| final Segment segment = segmentEntry.getValue(); |
| final Map<String, Type> fields = getAllFields(segmentKey, segment, useNames); |
| for (final Map.Entry<String, Type> fieldEntry : fields.entrySet()) { |
| final String fieldKey = fieldEntry.getKey(); |
| final Type field = fieldEntry.getValue(); |
| // These maybe should used the escaped values, but that would |
| // change the existing non-broken behavior of the processor |
| if (parseFields && (field instanceof Composite) && !isTimestamp(field)) { |
| for (final Map.Entry<String, Type> componentEntry : getAllComponents(fieldKey, field).entrySet()) { |
| final String componentKey = componentEntry.getKey(); |
| final Type component = componentEntry.getValue(); |
| final String componentValue = HL7_ESCAPING.unescape(component.encode(), HL7_ENCODING); |
| if (!StringUtils.isEmpty(componentValue)) { |
| attributes.put(componentKey, componentValue); |
| } |
| } |
| } else { |
| final String fieldValue = HL7_ESCAPING.unescape(field.encode(), HL7_ENCODING); |
| if (!StringUtils.isEmpty(fieldValue)) { |
| attributes.put(fieldKey, fieldValue); |
| } |
| } |
| |
| } |
| } |
| } |
| return attributes; |
| } |
| |
| private static Map<String, Segment> getAllSegments(final Group group) throws HL7Exception { |
| final Map<String, Segment> segments = new TreeMap<>(); |
| addSegments(group, segments); |
| return segments; |
| } |
| |
| private static void addSegments(final Group group, final Map<String, Segment> segments) throws HL7Exception { |
| if (!isEmpty(group)) { |
| for (final String name : group.getNames()) { |
| for (final Structure structure : group.getAll(name)) { |
| if (group.isGroup(name) && structure instanceof Group) { |
| addSegments((Group) structure, segments); |
| } else if (structure instanceof Segment) { |
| addSegments((Segment) structure, segments); |
| } |
| } |
| } |
| } |
| } |
| |
| private static void addSegments(final Segment segment, final Map<String, Segment> segments) throws HL7Exception { |
| if (!isEmpty(segment)) { |
| final StringBuilder sb = new StringBuilder().append(segment.getName()); |
| if (isRepeating(segment)) { |
| final Type field = segment.getField(1, 0); |
| if (!isEmpty(field)) { |
| final String fieldValue = field.encode(); |
| final int segmentIndex = StringUtils.isEmpty(fieldValue) ? 1 : Integer.parseInt(fieldValue); |
| sb.append("_").append(segmentIndex); |
| } |
| } |
| final String segmentKey = sb.toString(); |
| segments.put(segmentKey, segment); |
| } |
| } |
| |
| private static Map<String, Type> getAllFields(final String segmentKey, final Segment segment, final boolean useNames) throws HL7Exception { |
| final Map<String, Type> fields = new TreeMap<>(); |
| final String[] segmentNames = segment.getNames(); |
| for (int i = 1; i <= segment.numFields(); i++) { |
| final Type field = segment.getField(i, 0); |
| if (!isEmpty(field)) { |
| final String fieldName; |
| if (useNames) { |
| fieldName = WordUtils.capitalize(segmentNames[i-1]).replaceAll("\\W+", ""); |
| } else { |
| fieldName = String.valueOf(i); |
| } |
| |
| final String fieldKey = new StringBuilder() |
| .append(segmentKey) |
| .append(".") |
| .append(fieldName) |
| .toString(); |
| |
| fields.put(fieldKey, field); |
| } |
| } |
| return fields; |
| } |
| |
| private static Map<String, Type> getAllComponents(final String fieldKey, final Type field) throws HL7Exception { |
| final Map<String, Type> components = new TreeMap<>(); |
| if (!isEmpty(field) && (field instanceof Composite)) { |
| final Type[] types = ((Composite) field).getComponents(); |
| for (int i = 0; i < types.length; i++) { |
| final Type type = types[i]; |
| if (!isEmpty(type)) { |
| String fieldName = field.getName(); |
| if (fieldName.equals("CM_MSG")) { |
| fieldName = "CM"; |
| } |
| final String typeKey = new StringBuilder() |
| .append(fieldKey) |
| .append(".") |
| .append(fieldName) |
| .append(".") |
| .append(i+1) |
| .toString(); |
| components.put(typeKey, type); |
| } |
| } |
| } |
| return components; |
| } |
| |
| private static boolean isTimestamp(final Type field) throws HL7Exception { |
| if (isEmpty(field)) { |
| return false; |
| } |
| final String fieldName = field.getName(); |
| return (fieldName.equals("TS") || fieldName.equals("DT") || fieldName.equals("TM")); |
| } |
| |
| private static boolean isRepeating(final Segment segment) throws HL7Exception { |
| if (isEmpty(segment)) { |
| return false; |
| } |
| |
| final Group parent = segment.getParent(); |
| final Group grandparent = parent.getParent(); |
| if (parent == grandparent) { |
| return false; |
| } |
| |
| return grandparent.isRepeating(parent.getName()); |
| } |
| |
| private static boolean isEmpty(final Visitable visitable) throws HL7Exception { |
| return (visitable == null || visitable.isEmpty()); |
| } |
| } |