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io.github.linuxforhealth.hl7.parsing.HL7DataExtractor Maven / Gradle / Ivy
/*
* (C) Copyright IBM Corp. 2020, 2021
*
* SPDX-License-Identifier: Apache-2.0
*/
package io.github.linuxforhealth.hl7.parsing;
import java.util.ArrayList;
import java.util.List;
import java.util.function.Predicate;
import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.base.Preconditions;
import com.google.common.collect.Lists;
import ca.uhn.hl7v2.HL7Exception;
import ca.uhn.hl7v2.model.Composite;
import ca.uhn.hl7v2.model.Group;
import ca.uhn.hl7v2.model.Message;
import ca.uhn.hl7v2.model.Primitive;
import ca.uhn.hl7v2.model.Segment;
import ca.uhn.hl7v2.model.Structure;
import ca.uhn.hl7v2.model.Type;
import ca.uhn.hl7v2.model.Unmodifiable;
import ca.uhn.hl7v2.model.Variable;
import ca.uhn.hl7v2.model.v26.segment.MSH;
import ca.uhn.hl7v2.util.Terser;
import io.github.linuxforhealth.hl7.parsing.result.Hl7ParsingStringResult;
import io.github.linuxforhealth.hl7.parsing.result.Hl7ParsingStructureResult;
import io.github.linuxforhealth.hl7.parsing.result.Hl7ParsingTypeResult;
import io.github.linuxforhealth.hl7.parsing.result.ParsingResult;
public class HL7DataExtractor {
private static final String CANNOT_EXTRACT_VALUE_FOR_REP_REASON = "Cannot extract value for {} rep {}";
private static final String SEGMENT_CANNOT_BE_NULL_OR_EMPTY = "segment cannot be null or empty";
private static final String REP_CANNOT_BE_NEGATIVE = "rep cannot be negative";
private static final Logger LOGGER = LoggerFactory.getLogger(HL7DataExtractor.class);
private final Message message;
public HL7DataExtractor(Message message) {
this.message = message;
}
private static Predicate isEmpty() {
return (Structure p) -> {
try {
return p == null || p.isEmpty();
} catch (HL7Exception e) {
return true;
}
};
}
public ParsingResult getStructure(String group, int groupRep, String segment,
int rep) {
try {
ParsingResult parsingResult = null;
Preconditions.checkArgument(StringUtils.isNotBlank(group), "group cannot be null or empty");
Preconditions.checkArgument(StringUtils.isNotBlank(segment), SEGMENT_CANNOT_BE_NULL_OR_EMPTY);
Preconditions.checkArgument(groupRep >= 0, "groupRep should be greater than or equal to 0");
Preconditions.checkArgument(rep >= 0, "Segment rep cannot be less than 0");
Structure groupStr = message.get(group, groupRep);
if (groupStr instanceof Group) {
Group gp = (Group) groupStr;
Structure s = gp.get(segment, rep);
if (s != null && !s.isEmpty()) {
parsingResult = new Hl7ParsingStructureResult(s);
} else {
parsingResult = new Hl7ParsingStructureResult(new ArrayList<>());
}
} else {
parsingResult = new Hl7ParsingStructureResult(new ArrayList<>());
}
return parsingResult;
} catch (HL7Exception | IllegalArgumentException | ArrayIndexOutOfBoundsException e) {
String spec = group + " " + groupRep + " " + segment;
LOGGER.warn(CANNOT_EXTRACT_VALUE_FOR_REP_REASON, spec, rep);
return new Hl7ParsingStructureResult(new ArrayList<>());
}
}
public ParsingResult getAllStructures(String group, int groupRep, String segment) {
try {
ParsingResult parsingResult = null;
Preconditions.checkArgument(StringUtils.isNotBlank(group), "group cannot be null or empty");
Preconditions.checkArgument(StringUtils.isNotBlank(segment), SEGMENT_CANNOT_BE_NULL_OR_EMPTY);
Preconditions.checkArgument(groupRep >= 0, "groupRep should be greater than or equal to 0");
Structure groupStr = message.get(group, groupRep);
if (groupStr instanceof Group) {
Group gp = (Group) groupStr;
Structure[] s = gp.getAll(segment);
List list = Lists.newArrayList(s);
list.removeIf(isEmpty());
parsingResult = new Hl7ParsingStructureResult(Lists.newArrayList(list));
} else {
parsingResult = new Hl7ParsingStructureResult(new ArrayList<>());
}
return parsingResult;
} catch (HL7Exception | IllegalArgumentException | ArrayIndexOutOfBoundsException e) {
String spec = group + " " + groupRep + " " + segment;
LOGGER.warn("Cannot extract value for {} ", spec);
return new Hl7ParsingStructureResult(new ArrayList<>());
}
}
public boolean doesSegmentExists(String spec) {
try {
Preconditions.checkArgument(StringUtils.isNotBlank(spec),
"Not a valid string to extract from Message");
Message unmodifiableMessage = Unmodifiable.unmodifiableMessage(message);
Structure s = unmodifiableMessage.get(spec);
return s != null;
} catch (IllegalArgumentException | HL7Exception | ArrayIndexOutOfBoundsException e) {
LOGGER.warn("Cannot extract value for {} ", spec);
return false;
}
}
public boolean doesSegmentExists(String spec, int rep) {
try {
Preconditions.checkArgument(StringUtils.isNotBlank(spec),
"Not a valid string to extract from Terser");
Preconditions.checkArgument(rep >= 0, "Segment rep cannot be less than 0");
Message unmodifiableMessage = Unmodifiable.unmodifiableMessage(message);
Structure s = unmodifiableMessage.get(spec, rep);
return s != null;
} catch (IllegalArgumentException | HL7Exception | ArrayIndexOutOfBoundsException e) {
LOGGER.warn(CANNOT_EXTRACT_VALUE_FOR_REP_REASON, spec, rep);
return false;
}
}
public ParsingResult getStructure(String structure, int rep) {
try {
ParsingResult parsingResult = null;
if (doesSegmentExists(structure, rep)) {
Preconditions.checkArgument(StringUtils.isNotBlank(structure),
"Not a valid string to extract from Hl7");
Preconditions.checkArgument(rep >= 0, REP_CANNOT_BE_NEGATIVE);
parsingResult = new Hl7ParsingStructureResult(message.get(structure, rep));
} else {
parsingResult = new Hl7ParsingStructureResult(new ArrayList<>());
}
return parsingResult;
} catch (HL7Exception | IllegalArgumentException | ArrayIndexOutOfBoundsException e) {
LOGGER.warn(CANNOT_EXTRACT_VALUE_FOR_REP_REASON, structure, rep);
return new Hl7ParsingStructureResult(new ArrayList<>());
}
}
public ParsingResult getAllStructures(String structure) {
try {
ParsingResult parsingResult = null;
if (doesSegmentExists(structure)) {
Preconditions.checkArgument(StringUtils.isNotBlank(structure),
"Not a valid string to extract from Hl7");
Structure[] strs = message.getAll(structure);
parsingResult = new Hl7ParsingStructureResult(Lists.newArrayList(strs));
} else {
parsingResult = new Hl7ParsingStructureResult(new ArrayList<>());
}
return parsingResult;
} catch (HL7Exception | IllegalArgumentException | ArrayIndexOutOfBoundsException e) {
LOGGER.warn("Cannot extract value for {} ", structure);
return new Hl7ParsingStructureResult(new ArrayList<>());
}
}
public ParsingResult getType(Segment segment, int field, int rep) {
try {
Preconditions.checkArgument(segment != null, "segment cannot be null");
Preconditions.checkArgument(field >= 1, "field cannot be negative");
Preconditions.checkArgument(rep >= 0, REP_CANNOT_BE_NEGATIVE);
return new Hl7ParsingTypeResult(segment.getField(field, rep));
} catch (HL7Exception | IllegalArgumentException | ArrayIndexOutOfBoundsException e) {
LOGGER.warn("Cannot extract value for {} rep {} field {} ", segment, rep, field);
return new Hl7ParsingTypeResult(new ArrayList<>());
}
}
public ParsingResult getTypes(Segment segment, int field) {
try {
Preconditions.checkArgument(segment != null, "segment cannot be null");
Preconditions.checkArgument(field >= 1, "field cannot be negative");
Type[] fields = segment.getField(field);
return new Hl7ParsingTypeResult(Lists.newArrayList(fields));
} catch (HL7Exception | IllegalArgumentException | ArrayIndexOutOfBoundsException e) {
LOGGER.warn("Cannot extract value for segment {} field {} ", segment, field);
return new Hl7ParsingTypeResult(new ArrayList<>());
}
}
public ParsingResult getComponent(Type inputType, int component) {
try {
Preconditions.checkArgument(inputType != null, "type!=null");
ParsingResult result;
Type type = inputType;
if (inputType instanceof Variable) {
type = ((Variable) inputType).getData();
}
if (type instanceof Composite) {
Type value = ((Composite) type).getComponent(component - 1);
if (value != null && !value.isEmpty()) {
result = new Hl7ParsingTypeResult(((Composite) type).getComponent(component - 1));
} else {
result = new Hl7ParsingTypeResult(new ArrayList<>());
}
} else {
result = new Hl7ParsingTypeResult(type);
}
return result;
} catch (IllegalArgumentException | HL7Exception | ArrayIndexOutOfBoundsException e) {
LOGGER.warn("Cannot extract value for type {} component {} ", inputType, component);
return new Hl7ParsingTypeResult(new ArrayList<>());
}
}
public ParsingResult getComponent(Type inputType, int component, int subComponent) {
try {
Preconditions.checkArgument(inputType != null, "inputType!=null");
ParsingResult result;
Type type = inputType;
if (inputType instanceof Variable) {
type = ((Variable) inputType).getData();
}
Primitive prim = Terser.getPrimitive(type, component, subComponent);
if (prim != null && !prim.isEmpty()) {
result = new Hl7ParsingTypeResult(prim);
} else {
result = new Hl7ParsingTypeResult(new ArrayList<>());
}
return result;
} catch (IllegalArgumentException | HL7Exception | ArrayIndexOutOfBoundsException e) {
LOGGER.warn("Cannot extract value for type {} component {},subComponent {} ",
inputType, component, subComponent);
return new Hl7ParsingTypeResult(new ArrayList<>());
}
}
private Terser getTerser() {
Message unmodifiableMessage = Unmodifiable.unmodifiableMessage(message);
return new Terser(unmodifiableMessage);
}
public static String getMessageType(Message message) {
try {
MSH msh = (MSH) message.get("MSH");
return msh.getMessageType().getMsg1_MessageCode().getValue() + "_"
+ msh.getMessageType().getMsg2_TriggerEvent().getValue();
} catch (HL7Exception e) {
LOGGER.warn("Cannot extract actual message type.");
}
return null;
}
public String getMessageType() {
return getMessageType(message);
}
/**
*
* @param segment Segment to evaluate
* @param field Field of segment
* @return {@link ParsingResult}
*/
public ParsingResult get(String segment, String field) {
Preconditions.checkArgument(StringUtils.isNotBlank(segment), "segment cannot be blank");
Preconditions.checkArgument(StringUtils.isNotBlank(field), "field cannot be blank");
try {
return new Hl7ParsingStringResult(getTerser().get("/" + segment + "-" + field));
} catch (HL7Exception | IllegalArgumentException | ArrayIndexOutOfBoundsException e) {
LOGGER.warn("Cannot extract value for Segment {} field {}, reason {}", segment, field,
e.getMessage());
return new Hl7ParsingStringResult(null);
}
}
public String getMessageId() {
try {
return getTerser().get("/MSH-10");
} catch (HL7Exception | IllegalArgumentException e) {
LOGGER.warn("Cannot extract message control id.");
return null;
}
}
public ParsingResult getAllStructures(Structure struct, String segment) {
try {
ParsingResult parsingResult = null;
Preconditions.checkArgument(struct != null, "struct cannot be null ");
Preconditions.checkArgument(StringUtils.isNotBlank(segment), SEGMENT_CANNOT_BE_NULL_OR_EMPTY);
if (struct instanceof Group) {
Group gp = (Group) struct;
Structure[] s = gp.getAll(segment);
List list = Lists.newArrayList(s);
list.removeIf(isEmpty());
parsingResult = new Hl7ParsingStructureResult(list);
} else {
parsingResult = new Hl7ParsingStructureResult(new ArrayList<>());
}
return parsingResult;
} catch (HL7Exception | IllegalArgumentException | ArrayIndexOutOfBoundsException e) {
LOGGER.warn("Cannot extract value for Structure {} Segment {} ", struct, segment);
return new Hl7ParsingStructureResult(new ArrayList<>());
}
}
}
