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io.cdap.directives.parser.HL7Parser Maven / Gradle / Ivy
/*
* Copyright © 2017-2019 Cask Data, Inc.
*
* Licensed 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 io.cdap.directives.parser;
import ca.uhn.hl7v2.DefaultHapiContext;
import ca.uhn.hl7v2.HL7Exception;
import ca.uhn.hl7v2.HapiContext;
import ca.uhn.hl7v2.Location;
import ca.uhn.hl7v2.model.Composite;
import ca.uhn.hl7v2.model.Field;
import ca.uhn.hl7v2.model.Group;
import ca.uhn.hl7v2.model.Message;
import ca.uhn.hl7v2.model.MessageVisitor;
import ca.uhn.hl7v2.model.MessageVisitors;
import ca.uhn.hl7v2.model.Primitive;
import ca.uhn.hl7v2.model.Segment;
import ca.uhn.hl7v2.parser.GenericModelClassFactory;
import ca.uhn.hl7v2.parser.ModelClassFactory;
import ca.uhn.hl7v2.parser.Parser;
import ca.uhn.hl7v2.parser.PipeParser;
import ca.uhn.hl7v2.validation.impl.NoValidation;
import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import io.cdap.cdap.api.annotation.Description;
import io.cdap.cdap.api.annotation.Name;
import io.cdap.cdap.api.annotation.Plugin;
import io.cdap.wrangler.api.Arguments;
import io.cdap.wrangler.api.Directive;
import io.cdap.wrangler.api.DirectiveExecutionException;
import io.cdap.wrangler.api.DirectiveParseException;
import io.cdap.wrangler.api.ExecutorContext;
import io.cdap.wrangler.api.Optional;
import io.cdap.wrangler.api.Row;
import io.cdap.wrangler.api.annotations.Categories;
import io.cdap.wrangler.api.lineage.Lineage;
import io.cdap.wrangler.api.lineage.Many;
import io.cdap.wrangler.api.lineage.Mutation;
import io.cdap.wrangler.api.parser.ColumnName;
import io.cdap.wrangler.api.parser.Numeric;
import io.cdap.wrangler.api.parser.TokenType;
import io.cdap.wrangler.api.parser.UsageDefinition;
import java.util.List;
/**
* A step for parsing the HL7 Message.
*/
@Plugin(type = Directive.TYPE)
@Name("parse-as-hl7")
@Categories(categories = { "parser", "hl7"})
@Description("Parses for Health Level 7 Version 2 (HL7 V2) messages; indicates at which point " +
"JSON object enumeration terminates.")
public class HL7Parser implements Directive, Lineage {
public static final String NAME = "parse-as-hl7";
private String column;
private HapiContext context;
private Parser parser;
private int depth;
@Override
public UsageDefinition define() {
UsageDefinition.Builder builder = UsageDefinition.builder(NAME);
builder.define("column", TokenType.COLUMN_NAME);
builder.define("depth", TokenType.NUMERIC, Optional.TRUE);
return builder.build();
}
@Override
public void initialize(Arguments args) throws DirectiveParseException {
this.column = ((ColumnName) args.value("column")).value();
if (args.contains("depth")) {
this.depth = ((Numeric) args.value("depth")).value().intValue();
} else {
this.depth = Integer.MAX_VALUE;
}
context = new DefaultHapiContext();
context.setValidationContext(new NoValidation());
ModelClassFactory modelClassFactory = new GenericModelClassFactory();
parser = new PipeParser(modelClassFactory);
parser.getParserConfiguration().setAllowUnknownVersions(true);
}
@Override
public void destroy() {
// no-op
}
@Override
public Mutation lineage() {
return Mutation.builder()
.readable("Parsed column '%s' as HL7 record", column)
.all(Many.columns(column), Many.columns(column))
.build();
}
@Override
public List execute(List rows, ExecutorContext context) throws DirectiveExecutionException {
for (Row row : rows) {
try {
int idx = row.find(column);
if (idx != -1) {
Object object = row.getValue(idx);
if (object == null) {
throw new DirectiveExecutionException(
NAME, String.format("Column '%s' has null value. It should be a non-null 'String'.", column)
);
}
// Handling the first parsing on HL7 message
if (object instanceof String) {
Message message = parser.parse((String) object);
HL7MessageVisitor visitor = new HL7MessageVisitor(row, column + "_hl7", depth);
MessageVisitors.visit(message,
MessageVisitors.visitPopulatedElements(visitor)).getDelegate();
} else {
throw new DirectiveExecutionException(
NAME, String.format("Column '%s' has invalid type '%s'. It should be of type 'String'.",
column, object.getClass().getSimpleName())
);
}
}
} catch (HL7Exception e) {
throw new DirectiveExecutionException(NAME, e.getMessage(), e);
}
}
return rows;
}
/**
* HL7 Message Visitor.
*/
private final class HL7MessageVisitor implements MessageVisitor {
private final Row row;
private final String column;
private final int depth;
private JsonObject segments = new JsonObject();
private JsonObject segmentObject = new JsonObject();
private JsonObject compositeObject = new JsonObject();
private boolean inComposite = false;
HL7MessageVisitor(Row row, String column, int depth) {
this.row = row;
this.column = column;
this.depth = depth;
}
@Override
public boolean start(Message message) {
return true;
}
@Override
public boolean end(Message message) {
JsParser.jsonFlatten(segments, column, 1, depth, row);
return true;
}
@Override
public boolean start(Group group, Location location) {
return true;
}
@Override
public boolean end(Group group, Location location) {
return true;
}
@Override
public boolean start(Segment segment, Location location) {
segmentObject = new JsonObject();
return true;
}
@Override
public boolean end(Segment segment, Location location) {
if (!segments.has(segment.getName())) {
segments.add(segment.getName(), segmentObject);
} else {
Object object = segments.get(segment.getName());
if (!(object instanceof JsonArray)) {
JsonObject o = (JsonObject) segments.get(segment.getName());
JsonArray a = new JsonArray();
a.add(o);
a.add(segmentObject);
segments.add(segment.getName(), a);
}
}
return true;
}
@Override
public boolean start(Field field, Location location) {
return true;
}
@Override
public boolean end(Field field, Location location) {
return true;
}
@Override
public boolean start(Composite composite, Location location) {
inComposite = true;
compositeObject = new JsonObject();
return true;
}
@Override
public boolean end(Composite composite, Location location) {
segmentObject.add(Integer.toString(location.getField()), compositeObject);
inComposite = false;
return true;
}
@Override
public boolean visit(Primitive primitive, Location location) {
if (inComposite) {
compositeObject.addProperty(Integer.toString(location.getComponent()), primitive.getValue());
} else {
String fieldComponent = String.format("%d_%d", location.getField(), location.getComponent());
if (location.getComponent() < 0) {
fieldComponent = String.format("%d", location.getField());
}
segmentObject.addProperty(fieldComponent, primitive.getValue());
}
return true;
}
}
}
