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FhirConverter.java
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FhirConverter.java
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/*
* Copyright 2020-2022 Google LLC
*
* 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 org.openmrs.analytics;
import com.google.common.annotations.VisibleForTesting;
import io.debezium.data.Envelope.Operation;
import java.io.IOException;
import java.sql.SQLException;
import java.time.Instant;
import java.time.ZoneOffset;
import java.time.ZonedDateTime;
import java.time.format.DateTimeFormatter;
import java.util.Map;
import org.apache.camel.Exchange;
import org.apache.camel.Message;
import org.apache.camel.Processor;
import org.apache.camel.component.debezium.DebeziumConstants;
import org.hl7.fhir.r4.model.Resource;
import org.openmrs.analytics.model.DatabaseConfiguration;
import org.openmrs.analytics.model.EventConfiguration;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
// A Debezium events to FHIR URI mapper
public class FhirConverter implements Processor {
private static final Logger log = LoggerFactory.getLogger(FhirConverter.class);
private final OpenmrsUtil openmrsUtil;
private final FhirStoreUtil fhirStoreUtil;
private final ParquetUtil parquetUtil;
private final DatabaseConfiguration databaseConfiguration;
private final UuidUtil uuidUtil;
private final StatusServer statusServer;
@VisibleForTesting
FhirConverter() {
this.openmrsUtil = null;
this.fhirStoreUtil = null;
this.parquetUtil = null;
this.databaseConfiguration = null;
this.uuidUtil = null;
this.statusServer = null;
}
public FhirConverter(
OpenmrsUtil openmrsUtil,
FhirStoreUtil fhirStoreUtil,
ParquetUtil parquetUtil,
String configFileName,
UuidUtil uuidUtil,
StatusServer statusServer)
throws IOException {
// TODO add option for switching to Parquet-file outputs.
this.openmrsUtil = openmrsUtil;
this.fhirStoreUtil = fhirStoreUtil;
this.parquetUtil = parquetUtil;
this.databaseConfiguration = DatabaseConfiguration.createConfigFromFile(configFileName);
this.uuidUtil = uuidUtil;
this.statusServer = statusServer;
}
@VisibleForTesting
void updateLastResourceTime(String fhirResource, Message message) {
Long messageTime = message.getHeader(DebeziumConstants.HEADER_TIMESTAMP, Long.class);
if (messageTime != null) {
String messageTimeStr =
ZonedDateTime.ofInstant(Instant.ofEpochMilli(messageTime), ZoneOffset.UTC)
.format(DateTimeFormatter.ISO_OFFSET_DATE_TIME);
statusServer.setVar("last_" + fhirResource, messageTimeStr);
}
}
public void process(Exchange exchange) throws SQLException {
Message message = exchange.getMessage();
final Map payload = message.getBody(Map.class);
final Map sourceMetadata =
message.getHeader(DebeziumConstants.HEADER_SOURCE_METADATA, Map.class);
String operation = message.getHeader(DebeziumConstants.HEADER_OPERATION, String.class);
// for malformed event, return null
if (sourceMetadata == null || payload == null || operation == null) {
return;
}
if (!operation.equals(Operation.CREATE.code()) && !operation.equals(Operation.UPDATE.code())) {
log.debug("Skipping non create/update operation " + message.getHeaders());
return;
}
final String table = sourceMetadata.get("table").toString();
log.debug("Processing Table --> " + table);
final EventConfiguration config = databaseConfiguration.getEventConfigurations().get(table);
if (config == null || !config.getLinkTemplates().containsKey("fhir")) {
log.trace("Skipping unmapped data ..." + table);
return;
}
if (!config.isEnabled()) {
log.trace("Skipping disabled events ..." + table);
return;
}
String uuid = "";
if (payload.get("uuid") != null) {
uuid = payload.get("uuid").toString();
} else {
if (config.getParentTable() == null) {
log.error(String.format("No parentTable in %s ignoring payload %s ", table, payload));
return;
}
uuid =
uuidUtil.getUuid(
config.getParentTable(),
config.getParentForeignKey(),
payload.get(config.getChildPrimaryKey()).toString());
}
final String fhirUrl = config.getLinkTemplates().get("fhir").replace("{uuid}", uuid);
log.info("Fetching FHIR resource at " + fhirUrl);
Resource resource = openmrsUtil.fetchFhirResource(fhirUrl);
if (resource == null) {
// TODO: check how this can be signalled to Camel to be retried.
return;
}
final String fhirResource =
config.getLinkTemplates().get("fhir").replace("/{uuid}", "").replaceAll("/", "");
updateLastResourceTime(fhirResource, message);
if (!parquetUtil.getParquetPath().isEmpty()) {
try {
parquetUtil.write(resource);
} catch (IOException e) {
log.error(String.format("Cannot create ParquetWriter Exception: %s", e));
}
}
if (!fhirStoreUtil.getSinkUrl().isEmpty()) {
fhirStoreUtil.uploadResource(resource);
}
}
}