org.apache.nifi.processors.hl7.ExtractHL7Attributes.java Source code

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/*
 * Licensed to the Apache Software Foundation (ASF) under one or more
 * contributor license agreements.  See the NOTICE file distributed with
 * this work for additional information regarding copyright ownership.
 * The ASF licenses this file to You under the Apache License, Version 2.0
 * (the "License"); you may not use this file except in compliance with
 * the License.  You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package org.apache.nifi.processors.hl7;

import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import org.apache.commons.beanutils.PropertyUtils;
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,
                                useNames).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, new HashMap<String, Integer>());
        return Collections.unmodifiableMap(segments);
    }

    private static void addSegments(final Group group, final Map<String, Segment> segments,
            final Map<String, Integer> segmentIndexes) 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, segmentIndexes);
                    } else if (structure instanceof Segment) {
                        addSegments((Segment) structure, segments, segmentIndexes);
                    }
                }
                segmentIndexes.put(name, segmentIndexes.getOrDefault(name, 1) + 1);
            }
        }
    }

    private static void addSegments(final Segment segment, final Map<String, Segment> segments,
            final Map<String, Integer> segmentIndexes) throws HL7Exception {
        if (!isEmpty(segment)) {
            final String segmentName = segment.getName();
            final StringBuilder sb = new StringBuilder().append(segmentName);
            if (isRepeating(segment)) {
                final int segmentIndex = segmentIndexes.getOrDefault(segmentName, 1);
                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,
            final boolean useNames) throws HL7Exception {
        final Map<String, Type> components = new TreeMap<>();
        if (!isEmpty(field) && (field instanceof Composite)) {
            if (useNames) {
                final Pattern p = Pattern.compile("^(cm_msg|[a-z][a-z][a-z]?)([0-9]+)_(\\w+)$");
                try {
                    final java.beans.PropertyDescriptor[] properties = PropertyUtils.getPropertyDescriptors(field);
                    for (final java.beans.PropertyDescriptor property : properties) {
                        final String propertyName = property.getName();
                        final Matcher matcher = p.matcher(propertyName);
                        if (matcher.find()) {
                            final Type type = (Type) PropertyUtils.getProperty(field, propertyName);
                            if (!isEmpty(type)) {
                                final String componentName = matcher.group(3);
                                final String typeKey = new StringBuilder().append(fieldKey).append(".")
                                        .append(componentName).toString();
                                components.put(typeKey, type);
                            }
                        }
                    }
                } catch (Exception e) {
                    throw new RuntimeException(e.getMessage(), e);
                }
            } else {
                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());
    }
}