Consolidate changes to Command Line Tool and add/improve tests.
This commit is contained in:
ianmarshall
parent
a302d26eb1
commit
83e673e725
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@ -173,7 +173,6 @@ public abstract class BaseApp {
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commands.add(new ExportConceptMapToCsvCommand());
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commands.add(new ImportCsvToConceptMapCommand());
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commands.add(new HapiFlywayMigrateDatabaseCommand());
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commands.add(new RunJpaServerWithElasticsearchCommand());
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return commands;
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}
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@ -1,250 +0,0 @@
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package ca.uhn.fhir.cli;
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/*-
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* #%L
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* HAPI FHIR - Command Line Client - API
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* %%
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* Copyright (C) 2014 - 2020 University Health Network
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.jpa.demo.*;
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import org.apache.commons.cli.CommandLine;
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import org.apache.commons.cli.Options;
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import org.apache.commons.cli.ParseException;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.time.DateUtils;
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import org.eclipse.jetty.server.Server;
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import org.eclipse.jetty.webapp.WebAppContext;
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import org.springframework.web.context.ContextLoader;
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import org.springframework.web.context.ContextLoaderListener;
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import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
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import javax.servlet.ServletContextEvent;
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import javax.servlet.ServletContextListener;
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import java.io.*;
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import java.net.SocketException;
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public class RunJpaServerWithElasticsearchCommand extends BaseCommand {
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private static final String OPTION_DISABLE_REFERENTIAL_INTEGRITY = "disable-referential-integrity";
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private static final String OPTION_LOWMEM = "lowmem";
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private static final String OPTION_ALLOW_EXTERNAL_REFS = "allow-external-refs";
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private static final String OPTION_REUSE_SEARCH_RESULTS_MILLIS = "reuse-search-results-milliseconds";
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private static final String OPTION_EXTERNAL_ELASTICSEARCH = "external-elasticsearch";
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private static final int DEFAULT_PORT = 8080;
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private static final String OPTION_P = "p";
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// TODO: Don't use qualified names for loggers in HAPI CLI.
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RunJpaServerWithElasticsearchCommand.class);
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public static final String RUN_SERVER_COMMAND_ELASTICSEARCH = "run-server-elasticsearch";
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private int myPort;
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private Server myServer;
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@Override
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public String getCommandName() {
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return RUN_SERVER_COMMAND_ELASTICSEARCH;
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}
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@Override
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public Options getOptions() {
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Options options = new Options();
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addFhirVersionOption(options);
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options.addOption(OPTION_P, "port", true, "The port to listen on (default is " + DEFAULT_PORT + ")");
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options.addOption(null, OPTION_LOWMEM, false, "If this flag is set, the server will operate in low memory mode (some features disabled)");
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options.addOption(null, OPTION_ALLOW_EXTERNAL_REFS, false, "If this flag is set, the server will allow resources to be persisted contaning external resource references");
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options.addOption(null, OPTION_DISABLE_REFERENTIAL_INTEGRITY, false, "If this flag is set, the server will not enforce referential integrity");
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options.addOption(null, OPTION_EXTERNAL_ELASTICSEARCH, false, "If this flag is set, the server will attempt to use an external elasticsearch instance listening on port 9301");
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addOptionalOption(options, "u", "url", "Url", "If this option is set, specifies the JDBC URL to use for the database connection");
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Long defaultReuseSearchResults = DaoConfig.DEFAULT_REUSE_CACHED_SEARCH_RESULTS_FOR_MILLIS;
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String defaultReuseSearchResultsStr = defaultReuseSearchResults == null ? "off" : String.valueOf(defaultReuseSearchResults);
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options.addOption(null, OPTION_REUSE_SEARCH_RESULTS_MILLIS, true, "The time in milliseconds within which the same results will be returned for multiple identical searches, or \"off\" (default is " + defaultReuseSearchResultsStr + ")");
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return options;
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}
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private int parseOptionInteger(CommandLine theCommandLine, String opt, int defaultPort) throws ParseException {
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try {
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return Integer.parseInt(theCommandLine.getOptionValue(opt, Integer.toString(defaultPort)));
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} catch (NumberFormatException e) {
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throw new ParseException("Invalid value '" + theCommandLine.getOptionValue(opt) + "' (must be numeric)");
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}
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}
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@Override
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public void run(CommandLine theCommandLine) throws ParseException {
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parseFhirContext(theCommandLine);
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myPort = parseOptionInteger(theCommandLine, OPTION_P, DEFAULT_PORT);
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if (theCommandLine.hasOption(OPTION_LOWMEM)) {
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ourLog.info("Running in low memory mode, some features disabled");
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System.setProperty(OPTION_LOWMEM, OPTION_LOWMEM);
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}
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if (theCommandLine.hasOption(OPTION_ALLOW_EXTERNAL_REFS)) {
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ourLog.info("Server is configured to allow external references");
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ContextPostgreSQLHolder.setAllowExternalRefs(true);
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}
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if (theCommandLine.hasOption(OPTION_DISABLE_REFERENTIAL_INTEGRITY)) {
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ourLog.info("Server is configured to not enforce referential integrity");
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ContextPostgreSQLHolder.setDisableReferentialIntegrity(true);
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}
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if (theCommandLine.hasOption(OPTION_EXTERNAL_ELASTICSEARCH)) {
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ourLog.info("Server is configured to use external elasticsearch");
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ContextPostgreSQLHolder.setExternalElasticsearch(true);
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}
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ContextPostgreSQLHolder.setDatabaseUrl(theCommandLine.getOptionValue("u"));
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String reuseSearchResults = theCommandLine.getOptionValue(OPTION_REUSE_SEARCH_RESULTS_MILLIS);
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if (reuseSearchResults != null) {
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if (reuseSearchResults.equals("off")) {
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ourLog.info("Server is configured to not reuse search results");
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ContextPostgreSQLHolder.setReuseCachedSearchResultsForMillis(null);
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} else {
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try {
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long reuseSearchResultsMillis = Long.parseLong(reuseSearchResults);
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if (reuseSearchResultsMillis < 0) {
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throw new NumberFormatException("expected a positive integer");
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}
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ourLog.info("Server is configured to reuse search results for " + String.valueOf(reuseSearchResultsMillis) + " milliseconds");
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ContextPostgreSQLHolder.setReuseCachedSearchResultsForMillis(reuseSearchResultsMillis);
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} catch (NumberFormatException e) {
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throw new ParseException("Invalid value '" + reuseSearchResults + "' (must be a positive integer)");
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}
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}
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}
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ContextPostgreSQLHolder.setCtx(getFhirContext());
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ourLog.info("Preparing HAPI FHIR JPA server on port {}", myPort);
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File tempWarFile;
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try {
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tempWarFile = File.createTempFile("hapi-fhir", ".war");
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tempWarFile.deleteOnExit();
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InputStream inStream = RunJpaServerWithElasticsearchCommand.class.getResourceAsStream("/hapi-fhir-cli-jpaserver.war");
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OutputStream outStream = new BufferedOutputStream(new FileOutputStream(tempWarFile, false));
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IOUtils.copy(inStream, outStream);
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} catch (IOException e) {
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ourLog.error("Failed to create temporary file", e);
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return;
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}
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final ContextLoaderListener cll = new ContextLoaderListener();
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ourLog.info("Starting HAPI FHIR JPA server in {} mode", ContextPostgreSQLHolder.getCtx().getVersion().getVersion());
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WebAppContext root = new WebAppContext();
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root.setAllowDuplicateFragmentNames(true);
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root.setWar(tempWarFile.getAbsolutePath());
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root.setParentLoaderPriority(true);
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root.setContextPath("/");
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root.addEventListener(new ServletContextListener() {
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@Override
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public void contextInitialized(ServletContextEvent theSce) {
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theSce.getServletContext().setInitParameter(ContextLoader.CONTEXT_CLASS_PARAM, AnnotationConfigWebApplicationContext.class.getName());
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switch (ContextPostgreSQLHolder.getCtx().getVersion().getVersion()) {
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case DSTU2:
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theSce.getServletContext().setInitParameter(ContextLoader.CONFIG_LOCATION_PARAM, FhirServerConfig.class.getName());
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break;
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case DSTU3:
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theSce.getServletContext().setInitParameter(ContextLoader.CONFIG_LOCATION_PARAM, FhirServerConfigDstu3.class.getName());
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break;
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case R4:
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theSce.getServletContext().setInitParameter(ContextLoader.CONFIG_LOCATION_PARAM, FhirServerElasticsearchConfigR4.class.getName());
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break;
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case DSTU2_1:
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case DSTU2_HL7ORG:
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break;
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}
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cll.contextInitialized(theSce);
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}
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@Override
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public void contextDestroyed(ServletContextEvent theSce) {
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cll.contextDestroyed(theSce);
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}
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});
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String path = ContextPostgreSQLHolder.getPath();
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root.addServlet("ca.uhn.fhir.jpa.demo.JpaServerDemo", path + "*");
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myServer = new Server(myPort);
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myServer.setHandler(root);
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try {
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myServer.start();
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} catch (SocketException e) {
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throw new CommandFailureException("Server failed to start on port " + myPort + " because of the following error \"" + e.toString() + "\". Note that you can use the '-p' option to specify an alternate port.");
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} catch (Exception e) {
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ourLog.error("Server failed to start", e);
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throw new CommandFailureException("Server failed to start", e);
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}
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ourLog.info("Server started on port {}", myPort);
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ourLog.info("Web Testing UI : http://localhost:{}/", myPort);
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ourLog.info("Server Base URL: http://localhost:{}{}", myPort, path);
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// Never quit.. We'll let the user ctrl-C their way out.
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loopForever();
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}
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@SuppressWarnings("InfiniteLoopStatement")
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private void loopForever() {
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while (true) {
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try {
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Thread.sleep(DateUtils.MILLIS_PER_MINUTE);
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} catch (InterruptedException theE) {
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// ignore
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}
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}
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}
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public static void main(String[] theArgs) {
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Server server = new Server(22);
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String path = "../hapi-fhir-cli-jpaserver";
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WebAppContext webAppContext = new WebAppContext();
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webAppContext.setContextPath("/");
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webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
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webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-example");
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webAppContext.setParentLoaderPriority(true);
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server.setHandler(webAppContext);
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try {
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server.start();
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} catch (Exception e) {
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e.printStackTrace();
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}
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ourLog.info("Started");
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}
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@Override
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public String getCommandDescription() {
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return "Start a FHIR server which can be used for testing";
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}
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}
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@ -21,12 +21,8 @@ package ca.uhn.fhir.cli;
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*/
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.jpa.demo.ContextHolder;
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import ca.uhn.fhir.jpa.demo.FhirServerConfig;
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import ca.uhn.fhir.jpa.demo.FhirServerConfigDstu3;
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import ca.uhn.fhir.jpa.demo.FhirServerConfigR4;
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import ca.uhn.fhir.jpa.demo.*;
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import org.apache.commons.cli.CommandLine;
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import org.apache.commons.cli.OptionGroup;
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import org.apache.commons.cli.Options;
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import org.apache.commons.cli.ParseException;
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import org.apache.commons.io.IOUtils;
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@ -48,8 +44,10 @@ public class RunServerCommand extends BaseCommand {
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private static final String OPTION_LOWMEM = "lowmem";
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private static final String OPTION_ALLOW_EXTERNAL_REFS = "allow-external-refs";
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private static final String OPTION_REUSE_SEARCH_RESULTS_MILLIS = "reuse-search-results-milliseconds";
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private static final String OPTION_EXTERNAL_ELASTICSEARCH = "external-elasticsearch";
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private static final int DEFAULT_PORT = 8080;
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private static final String OPTION_P = "p";
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private static final String OPTION_POSTGRES = "postgresql";
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// TODO: Don't use qualified names for loggers in HAPI CLI.
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RunServerCommand.class);
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@ -71,8 +69,12 @@ public class RunServerCommand extends BaseCommand {
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options.addOption(null, OPTION_LOWMEM, false, "If this flag is set, the server will operate in low memory mode (some features disabled)");
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options.addOption(null, OPTION_ALLOW_EXTERNAL_REFS, false, "If this flag is set, the server will allow resources to be persisted contaning external resource references");
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options.addOption(null, OPTION_DISABLE_REFERENTIAL_INTEGRITY, false, "If this flag is set, the server will not enforce referential integrity");
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options.addOption(null, OPTION_EXTERNAL_ELASTICSEARCH, false, "If this flag is set, the server will attempt to use a local elasticsearch server listening on port 9301");
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options.addOption(null, OPTION_POSTGRES, false, "If this flag is set, the server will attempt to use a local postgresql DB instance listening on port 5432");
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addOptionalOption(options, "u", "url", "Url", "If this option is set, specifies the JDBC URL to use for the database connection");
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addOptionalOption(options, "d", "default-size", "PageSize", "If this option is set, specifies the default page size for number of query results");
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addOptionalOption(options, "m", "max-size", "MaxSize", "If this option is set, specifies the maximum result set size for queries");
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Long defaultReuseSearchResults = DaoConfig.DEFAULT_REUSE_CACHED_SEARCH_RESULTS_FOR_MILLIS;
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String defaultReuseSearchResultsStr = defaultReuseSearchResults == null ? "off" : String.valueOf(defaultReuseSearchResults);
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@ -109,7 +111,28 @@ public class RunServerCommand extends BaseCommand {
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ContextHolder.setDisableReferentialIntegrity(true);
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}
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ContextHolder.setDatabaseUrl(theCommandLine.getOptionValue("u"));
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if (theCommandLine.hasOption(OPTION_EXTERNAL_ELASTICSEARCH)) {
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ourLog.info("Server is configured to use external elasticsearch");
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ContextHolder.setExternalElasticsearch(true);
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}
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ContextHolder.setDatabaseUrl(theCommandLine.getOptionValue("u"));
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if (theCommandLine.hasOption(OPTION_POSTGRES)) {
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ourLog.info("Server is configured to use PostgreSQL database");
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ContextHolder.setPostgreSql(true);
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}
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String defaultPageSize = theCommandLine.getOptionValue("d");
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String maxPageSize = theCommandLine.getOptionValue("m");
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if (defaultPageSize != null) {
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ContextHolder.setDefaultPageSize(Integer.valueOf(defaultPageSize));
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if (maxPageSize != null) {
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ContextHolder.setMaxPageSize(Integer.valueOf(maxPageSize));
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} else {
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ContextHolder.setMaxPageSize(Integer.valueOf(defaultPageSize));
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}
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}
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String reuseSearchResults = theCommandLine.getOptionValue(OPTION_REUSE_SEARCH_RESULTS_MILLIS);
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if (reuseSearchResults != null) {
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@ -183,10 +183,10 @@
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</overlays>
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<webXml>src/main/webapp/WEB-INF/web.xml</webXml>
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<attachClasses>true</attachClasses>
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<excludes>
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<packagingExcludes>
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WEB-INF/lib/Saxon-HE-*,
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WEB-INF/lib/hapi-*
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</excludes>
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</packagingExcludes>
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</configuration>
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</plugin>
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@ -20,23 +20,34 @@ package ca.uhn.fhir.jpa.demo;
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* #L%
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*/
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import ca.uhn.fhir.context.ConfigurationException;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.jpa.model.entity.ModelConfig;
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import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
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import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
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import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
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import org.apache.commons.dbcp2.BasicDataSource;
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import org.apache.commons.lang3.time.DateUtils;
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import org.hibernate.dialect.H2Dialect;
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import org.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus;
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import org.hibernate.search.elasticsearch.cfg.IndexSchemaManagementStrategy;
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import org.springframework.context.annotation.Bean;
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import org.springframework.context.annotation.Configuration;
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import pl.allegro.tech.embeddedelasticsearch.EmbeddedElastic;
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import pl.allegro.tech.embeddedelasticsearch.PopularProperties;
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import javax.annotation.PreDestroy;
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import javax.sql.DataSource;
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import java.io.IOException;
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import java.util.Properties;
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import java.util.UUID;
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import java.util.concurrent.TimeUnit;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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@SuppressWarnings("Duplicates")
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// TODO: Merge this with new CommonPostgreSQLConfig or find way to avoid conflicts with it.
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//@Configuration
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@Configuration
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public class CommonConfig {
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/**
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@ -65,6 +76,42 @@ public class CommonConfig {
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*/
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@Bean(destroyMethod = "close")
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public DataSource dataSource() {
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if (ContextHolder.isPostGreSql()) {
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return getPostgreSqlDataSource();
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} else {
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return getH2DataSource();
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}
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}
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/**
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* The following method creates a PostgreSQL database connection. The 'url' property value of "jdbc:postgresql://localhost:5432/hapi" indicates that the server should save resources in a
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* PostgreSQL database named "hapi".
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*
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* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
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*/
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private DataSource getPostgreSqlDataSource() {
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String dbUrl = "jdbc:postgresql://localhost:5432/hapi";
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String dbUsername = "hapi";
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String dbPassword = "HapiFHIR";
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if (isNotBlank(ContextHolder.getDatabaseUrl())) {
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dbUrl = ContextHolder.getDatabaseUrl();
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}
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BasicDataSource retVal = new BasicDataSource();
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retVal.setDriverClassName("org.postgresql.Driver");
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retVal.setUrl(dbUrl);
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retVal.setUsername(dbUsername);
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retVal.setPassword(dbPassword);
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return retVal;
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}
|
||||
|
||||
/**
|
||||
* The following method creates an H2 database connection. The 'url' property value of "jdbc:h2:file:target./jpaserver_h2_files" indicates that the server should save resources in a
|
||||
* directory called "jpaserver_h2_files".
|
||||
*
|
||||
* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
|
||||
*/
|
||||
private DataSource getH2DataSource() {
|
||||
String url = "jdbc:h2:file:./target/jpaserver_h2_files";
|
||||
if (isNotBlank(ContextHolder.getDatabaseUrl())) {
|
||||
url = ContextHolder.getDatabaseUrl();
|
||||
|
|
@ -80,6 +127,14 @@ public class CommonConfig {
|
|||
|
||||
@Bean
|
||||
public Properties jpaProperties() {
|
||||
if (ContextHolder.isPostGreSql()) {
|
||||
return getPostGreSqlJpaProperties();
|
||||
} else {
|
||||
return getH2JpaProperties();
|
||||
}
|
||||
}
|
||||
|
||||
private Properties getH2JpaProperties() {
|
||||
Properties extraProperties = new Properties();
|
||||
extraProperties.put("hibernate.dialect", H2Dialect.class.getName());
|
||||
extraProperties.put("hibernate.format_sql", "true");
|
||||
|
|
@ -99,8 +154,105 @@ public class CommonConfig {
|
|||
if (System.getProperty("lowmem") != null) {
|
||||
extraProperties.put("hibernate.search.autoregister_listeners", "false");
|
||||
}
|
||||
|
||||
return extraProperties;
|
||||
|
||||
return configureElasticearch(extraProperties);
|
||||
}
|
||||
|
||||
private Properties getPostGreSqlJpaProperties() {
|
||||
|
||||
Properties extraProperties = new Properties();
|
||||
extraProperties.put("hibernate.dialect", org.hibernate.dialect.PostgreSQL94Dialect.class.getName());
|
||||
extraProperties.put("hibernate.format_sql", "false");
|
||||
extraProperties.put("hibernate.show_sql", "false");
|
||||
extraProperties.put("hibernate.hbm2ddl.auto", "update");
|
||||
extraProperties.put("hibernate.jdbc.batch_size", "20");
|
||||
extraProperties.put("hibernate.cache.use_query_cache", "false");
|
||||
extraProperties.put("hibernate.cache.use_second_level_cache", "false");
|
||||
extraProperties.put("hibernate.cache.use_structured_entries", "false");
|
||||
extraProperties.put("hibernate.cache.use_minimal_puts", "false");
|
||||
extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
|
||||
extraProperties.put("hibernate.search.default.directory_provider", "local-heap");
|
||||
extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
|
||||
extraProperties.put("hibernate.search.default.worker.execution", "sync");
|
||||
|
||||
if (System.getProperty("lowmem") != null) {
|
||||
extraProperties.put("hibernate.search.autoregister_listeners", "false");
|
||||
}
|
||||
|
||||
return configureElasticearch(extraProperties);
|
||||
}
|
||||
|
||||
private Properties configureElasticearch(Properties theExtraProperties) {
|
||||
|
||||
String elasticsearchHost = "localhost";
|
||||
String elasticsearchUserId = "";
|
||||
String elasticsearchPassword = "";
|
||||
Integer elasticsearchPort;
|
||||
|
||||
if(ContextHolder.isExternalElasticsearch()) {
|
||||
elasticsearchUserId = "elastic";
|
||||
elasticsearchPassword = "changeme";
|
||||
elasticsearchPort = 9301;
|
||||
} else {
|
||||
elasticsearchPort = embeddedElasticSearch().getHttpPort();
|
||||
}
|
||||
|
||||
new ElasticsearchHibernatePropertiesBuilder()
|
||||
.setDebugRefreshAfterWrite(true)
|
||||
.setDebugPrettyPrintJsonLog(true)
|
||||
.setIndexSchemaManagementStrategy(IndexSchemaManagementStrategy.CREATE)
|
||||
.setIndexManagementWaitTimeoutMillis(10000)
|
||||
.setRequiredIndexStatus(ElasticsearchIndexStatus.YELLOW)
|
||||
.setRestUrl("http://" + elasticsearchHost + ":" + elasticsearchPort)
|
||||
.setUsername(elasticsearchUserId)
|
||||
.setPassword(elasticsearchPassword)
|
||||
.apply(theExtraProperties);
|
||||
|
||||
return theExtraProperties;
|
||||
|
||||
}
|
||||
|
||||
@Bean()
|
||||
public ElasticsearchSvcImpl myElasticsearchSvc() throws IOException {
|
||||
String elasticsearchHost = "localhost";
|
||||
String elasticsearchUserId = "";
|
||||
String elasticsearchPassword = "";
|
||||
Integer elasticsearchPort;
|
||||
|
||||
if(ContextHolder.isExternalElasticsearch()) {
|
||||
elasticsearchUserId = "elastic";
|
||||
elasticsearchPassword = "changeme";
|
||||
elasticsearchPort = 9301;
|
||||
} else {
|
||||
elasticsearchPort = embeddedElasticSearch().getHttpPort();
|
||||
}
|
||||
return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUserId, elasticsearchPassword);
|
||||
}
|
||||
|
||||
@Bean
|
||||
public EmbeddedElastic embeddedElasticSearch() {
|
||||
String ELASTIC_VERSION = "6.5.4";
|
||||
|
||||
EmbeddedElastic embeddedElastic;
|
||||
try {
|
||||
embeddedElastic = EmbeddedElastic.builder()
|
||||
.withElasticVersion(ELASTIC_VERSION)
|
||||
.withSetting(PopularProperties.TRANSPORT_TCP_PORT, 0)
|
||||
.withSetting(PopularProperties.HTTP_PORT, 0)
|
||||
.withSetting(PopularProperties.CLUSTER_NAME, UUID.randomUUID())
|
||||
.withStartTimeout(60, TimeUnit.SECONDS)
|
||||
.build()
|
||||
.start();
|
||||
} catch (IOException | InterruptedException e) {
|
||||
throw new ConfigurationException(e);
|
||||
}
|
||||
|
||||
return embeddedElastic;
|
||||
}
|
||||
|
||||
@PreDestroy
|
||||
public void stop() {
|
||||
embeddedElasticSearch().stop();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,180 +0,0 @@
|
|||
package ca.uhn.fhir.jpa.demo;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR - Command Line Client - Server WAR
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2020 University Health Network
|
||||
* %%
|
||||
* 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.
|
||||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.context.ConfigurationException;
|
||||
import ca.uhn.fhir.jpa.dao.DaoConfig;
|
||||
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
|
||||
import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
|
||||
import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
|
||||
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
|
||||
import org.apache.commons.dbcp2.BasicDataSource;
|
||||
import org.apache.commons.lang3.time.DateUtils;
|
||||
import org.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus;
|
||||
import org.hibernate.search.elasticsearch.cfg.IndexSchemaManagementStrategy;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
import pl.allegro.tech.embeddedelasticsearch.EmbeddedElastic;
|
||||
import pl.allegro.tech.embeddedelasticsearch.PopularProperties;
|
||||
|
||||
import javax.annotation.PreDestroy;
|
||||
import javax.sql.DataSource;
|
||||
import java.io.IOException;
|
||||
import java.util.Properties;
|
||||
import java.util.UUID;
|
||||
import java.util.concurrent.TimeUnit;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
|
||||
@SuppressWarnings("Duplicates")
|
||||
@Configuration
|
||||
public class CommonPostgreSQLConfig {
|
||||
|
||||
static String elasticsearchHost = "localhost";
|
||||
static String elasticsearchUserId = "";
|
||||
static String elasticsearchPassword = "";
|
||||
static Integer elasticsearchPort;
|
||||
|
||||
/**
|
||||
* Configure FHIR properties around the the JPA server via this bean
|
||||
*/
|
||||
@Bean
|
||||
public DaoConfig daoConfig() {
|
||||
DaoConfig retVal = new DaoConfig();
|
||||
retVal.setSubscriptionEnabled(true);
|
||||
retVal.setSubscriptionPollDelay(5000);
|
||||
retVal.setSubscriptionPurgeInactiveAfterMillis(DateUtils.MILLIS_PER_HOUR);
|
||||
retVal.setAllowMultipleDelete(true);
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Bean
|
||||
public ModelConfig modelConfig() {
|
||||
return daoConfig().getModelConfig();
|
||||
}
|
||||
|
||||
/**
|
||||
* The following bean configures the database connection. The 'url' property value of "jdbc:postgresql://localhost:5432/hapi" indicates that the server should save resources in a
|
||||
* PostgreSQL database named "hapi".
|
||||
*
|
||||
* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
|
||||
*/
|
||||
@Bean(destroyMethod = "close")
|
||||
public DataSource dataSource() {
|
||||
String dbUrl = "jdbc:postgresql://localhost:5432/hapi";
|
||||
String dbUsername = "hapi";
|
||||
String dbPassword = "HapiFHIR";
|
||||
if (isNotBlank(ContextPostgreSQLHolder.getDatabaseUrl())) {
|
||||
dbUrl = ContextPostgreSQLHolder.getDatabaseUrl();
|
||||
}
|
||||
|
||||
BasicDataSource retVal = new BasicDataSource();
|
||||
retVal.setDriverClassName("org.postgresql.Driver");
|
||||
retVal.setUrl(dbUrl);
|
||||
retVal.setUsername(dbUsername);
|
||||
retVal.setPassword(dbPassword);
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Bean
|
||||
public Properties jpaProperties() {
|
||||
|
||||
if(ContextPostgreSQLHolder.isExternalElasticsearch()) {
|
||||
elasticsearchUserId = "elastic";
|
||||
elasticsearchPassword = "changeme";
|
||||
elasticsearchPort = 9301;
|
||||
} else {
|
||||
elasticsearchPort = embeddedElasticSearch().getHttpPort();
|
||||
}
|
||||
|
||||
Properties extraProperties = new Properties();
|
||||
extraProperties.put("hibernate.dialect", org.hibernate.dialect.PostgreSQL94Dialect.class.getName());
|
||||
extraProperties.put("hibernate.format_sql", "false");
|
||||
extraProperties.put("hibernate.show_sql", "false");
|
||||
extraProperties.put("hibernate.hbm2ddl.auto", "update");
|
||||
extraProperties.put("hibernate.jdbc.batch_size", "20");
|
||||
extraProperties.put("hibernate.cache.use_query_cache", "false");
|
||||
extraProperties.put("hibernate.cache.use_second_level_cache", "false");
|
||||
extraProperties.put("hibernate.cache.use_structured_entries", "false");
|
||||
extraProperties.put("hibernate.cache.use_minimal_puts", "false");
|
||||
extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
|
||||
extraProperties.put("hibernate.search.default.directory_provider", "local-heap");
|
||||
extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
|
||||
extraProperties.put("hibernate.search.default.worker.execution", "sync");
|
||||
|
||||
if (System.getProperty("lowmem") != null) {
|
||||
extraProperties.put("hibernate.search.autoregister_listeners", "false");
|
||||
}
|
||||
|
||||
new ElasticsearchHibernatePropertiesBuilder()
|
||||
.setDebugRefreshAfterWrite(true)
|
||||
.setDebugPrettyPrintJsonLog(true)
|
||||
.setIndexSchemaManagementStrategy(IndexSchemaManagementStrategy.CREATE)
|
||||
.setIndexManagementWaitTimeoutMillis(10000)
|
||||
.setRequiredIndexStatus(ElasticsearchIndexStatus.YELLOW)
|
||||
.setRestUrl("http://" + elasticsearchHost + ":" + elasticsearchPort)
|
||||
.setUsername(elasticsearchUserId)
|
||||
.setPassword(elasticsearchPassword)
|
||||
.apply(extraProperties);
|
||||
|
||||
// extraProperties.setProperty("hibernate.search.default.elasticsearch.refresh_after_write", "true");
|
||||
return extraProperties;
|
||||
}
|
||||
|
||||
@Bean()
|
||||
public ElasticsearchSvcImpl myElasticsearchSvc() throws IOException {
|
||||
if(ContextPostgreSQLHolder.isExternalElasticsearch()) {
|
||||
elasticsearchUserId = "elastic";
|
||||
elasticsearchPassword = "changeme";
|
||||
elasticsearchPort = 9301;
|
||||
} else {
|
||||
elasticsearchPort = embeddedElasticSearch().getHttpPort();
|
||||
}
|
||||
return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUserId, elasticsearchPassword);
|
||||
}
|
||||
|
||||
@Bean
|
||||
public EmbeddedElastic embeddedElasticSearch() {
|
||||
String ELASTIC_VERSION = "6.5.4";
|
||||
|
||||
EmbeddedElastic embeddedElastic;
|
||||
try {
|
||||
embeddedElastic = EmbeddedElastic.builder()
|
||||
.withElasticVersion(ELASTIC_VERSION)
|
||||
.withSetting(PopularProperties.TRANSPORT_TCP_PORT, 0)
|
||||
.withSetting(PopularProperties.HTTP_PORT, 0)
|
||||
.withSetting(PopularProperties.CLUSTER_NAME, UUID.randomUUID())
|
||||
.withStartTimeout(60, TimeUnit.SECONDS)
|
||||
.build()
|
||||
.start();
|
||||
} catch (IOException | InterruptedException e) {
|
||||
throw new ConfigurationException(e);
|
||||
}
|
||||
|
||||
return embeddedElastic;
|
||||
}
|
||||
|
||||
@PreDestroy
|
||||
public void stop() {
|
||||
embeddedElasticSearch().stop();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -33,6 +33,10 @@ public class ContextHolder {
|
|||
private static String ourPath;
|
||||
private static Long ourReuseSearchResultsMillis;
|
||||
private static String ourDatabaseUrl;
|
||||
private static boolean myExternalElasticsearch = false;
|
||||
private static boolean myPostGreSql = false;
|
||||
private static Integer myDefaultPageSize = 10;
|
||||
private static Integer myMaxPageSize = 50;
|
||||
|
||||
static {
|
||||
ourReuseSearchResultsMillis = DaoConfig.DEFAULT_REUSE_CACHED_SEARCH_RESULTS_FOR_MILLIS;
|
||||
|
|
@ -100,4 +104,37 @@ public class ContextHolder {
|
|||
public static void setDatabaseUrl(String theDatabaseUrl) {
|
||||
ourDatabaseUrl = theDatabaseUrl;
|
||||
}
|
||||
|
||||
public static void setExternalElasticsearch(Boolean theExternalElasticsearch) {
|
||||
myExternalElasticsearch = theExternalElasticsearch;
|
||||
}
|
||||
|
||||
public static Boolean isExternalElasticsearch() {
|
||||
return myExternalElasticsearch;
|
||||
}
|
||||
|
||||
public static void setPostgreSql(boolean thePostGreSql) {
|
||||
myPostGreSql = thePostGreSql;
|
||||
}
|
||||
|
||||
public static boolean isPostGreSql() {
|
||||
return myPostGreSql;
|
||||
}
|
||||
|
||||
public static void setDefaultPageSize(Integer theDefaultPageSize) {
|
||||
myDefaultPageSize = theDefaultPageSize;
|
||||
}
|
||||
|
||||
public static Integer getDefaultPageSize() {
|
||||
return myDefaultPageSize;
|
||||
}
|
||||
|
||||
public static void setMaxPageSize(Integer theMaxPageSize) {
|
||||
myMaxPageSize = theMaxPageSize;
|
||||
}
|
||||
|
||||
public static Integer getMaxPageSize() {
|
||||
return myMaxPageSize;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,89 +0,0 @@
|
|||
package ca.uhn.fhir.jpa.demo;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR - Command Line Client - Server WAR
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2020 University Health Network
|
||||
* %%
|
||||
* 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.
|
||||
* #L%
|
||||
*/
|
||||
|
||||
public class ContextPostgreSQLHolder extends ContextHolder {
|
||||
|
||||
// private static String myDbUsername;
|
||||
// private static String myDbPassword;
|
||||
private static boolean myExternalElasticsearch = false;
|
||||
// private static String myElasticsearchHost;
|
||||
// private static Integer myElasticsearchPort;
|
||||
// private static String myElasticsearchUsername;
|
||||
// private static String myElasticsearchPassword;
|
||||
|
||||
/* public static void setDbUsername(String theDbUsername) {
|
||||
myDbUsername = theDbUsername;
|
||||
}
|
||||
|
||||
public static String getDbUsername() {
|
||||
return myDbUsername;
|
||||
}
|
||||
|
||||
public static void setDbPassword(String theDbPassword) {
|
||||
myDbPassword = theDbPassword;
|
||||
}
|
||||
|
||||
public static String getDbPassword() {
|
||||
return myDbPassword;
|
||||
}
|
||||
*/
|
||||
public static void setExternalElasticsearch(Boolean theExternalElasticsearch) {
|
||||
myExternalElasticsearch = theExternalElasticsearch;
|
||||
}
|
||||
|
||||
public static Boolean isExternalElasticsearch() {
|
||||
return myExternalElasticsearch;
|
||||
}
|
||||
/*
|
||||
public static void setElasticsearchHost(String theElasticsearchHost) {
|
||||
myElasticsearchHost = theElasticsearchHost;
|
||||
}
|
||||
|
||||
public static String getElasticsearchHost() {
|
||||
return myElasticsearchHost;
|
||||
}
|
||||
|
||||
public static void setElasticsearchPort(Integer theElasticsearchPort) {
|
||||
myElasticsearchPort = theElasticsearchPort;
|
||||
}
|
||||
|
||||
public static Integer getElasticsearchPort() {
|
||||
return myElasticsearchPort;
|
||||
}
|
||||
|
||||
public static void setElasticsearchUsername(String theElasticsearchUsername) {
|
||||
myElasticsearchUsername = theElasticsearchUsername;
|
||||
}
|
||||
|
||||
public static String getElasticsearchUsername() {
|
||||
return myElasticsearchUsername;
|
||||
}
|
||||
|
||||
public static void setElasticsearchPassword(String theElasticsearchPassword) {
|
||||
myElasticsearchPassword = theElasticsearchPassword;
|
||||
}
|
||||
|
||||
public static String getElasticsearchPassword() {
|
||||
return myElasticsearchPassword;
|
||||
}
|
||||
*/
|
||||
}
|
||||
|
|
@ -1,107 +0,0 @@
|
|||
package ca.uhn.fhir.jpa.demo;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR - Command Line Client - Server WAR
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2020 University Health Network
|
||||
* %%
|
||||
* 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.
|
||||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
|
||||
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorR4;
|
||||
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
|
||||
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
|
||||
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
|
||||
import org.springframework.beans.factory.annotation.Autowire;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.beans.factory.annotation.Qualifier;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
import org.springframework.context.annotation.Import;
|
||||
import org.springframework.orm.jpa.JpaTransactionManager;
|
||||
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
|
||||
import org.springframework.transaction.annotation.EnableTransactionManagement;
|
||||
|
||||
import javax.persistence.EntityManagerFactory;
|
||||
import javax.sql.DataSource;
|
||||
import java.util.Properties;
|
||||
|
||||
/**
|
||||
* This class isn't used by default by the example, but
|
||||
* you can use it as a config if you want to support DSTU3
|
||||
* instead of DSTU2 in your server.
|
||||
* <p>
|
||||
* See https://github.com/jamesagnew/hapi-fhir/issues/278
|
||||
*/
|
||||
@Configuration
|
||||
@EnableTransactionManagement()
|
||||
@Import(CommonPostgreSQLConfig.class)
|
||||
public class FhirServerElasticsearchConfigR4 extends BaseJavaConfigR4 {
|
||||
|
||||
@Autowired
|
||||
private DataSource myDataSource;
|
||||
@Autowired()
|
||||
@Qualifier("jpaProperties")
|
||||
private Properties myJpaProperties;
|
||||
|
||||
@Override
|
||||
@Bean
|
||||
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
|
||||
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
|
||||
retVal.setPersistenceUnitName("HAPI_PU");
|
||||
retVal.setDataSource(myDataSource);
|
||||
retVal.setJpaProperties(myJpaProperties);
|
||||
return retVal;
|
||||
}
|
||||
|
||||
/**
|
||||
* Do some fancy logging to create a nice access log that has details about each incoming request.
|
||||
* @return
|
||||
*/
|
||||
public LoggingInterceptor loggingInterceptor() {
|
||||
LoggingInterceptor retVal = new LoggingInterceptor();
|
||||
retVal.setLoggerName("fhirtest.access");
|
||||
retVal.setMessageFormat(
|
||||
"Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
|
||||
retVal.setLogExceptions(true);
|
||||
retVal.setErrorMessageFormat("ERROR - ${requestVerb} ${requestUrl}");
|
||||
return retVal;
|
||||
}
|
||||
|
||||
/**
|
||||
* This interceptor adds some pretty syntax highlighting in responses when a browser is detected
|
||||
* @return
|
||||
*/
|
||||
@Bean(autowire = Autowire.BY_TYPE)
|
||||
public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
|
||||
ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Bean(autowire = Autowire.BY_TYPE)
|
||||
public IServerInterceptor subscriptionSecurityInterceptor() {
|
||||
SubscriptionsRequireManualActivationInterceptorR4 retVal = new SubscriptionsRequireManualActivationInterceptorR4();
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Bean
|
||||
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
|
||||
JpaTransactionManager retVal = new JpaTransactionManager();
|
||||
retVal.setEntityManagerFactory(entityManagerFactory);
|
||||
return retVal;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -160,7 +160,8 @@ public class JpaServerDemo extends RestfulServer {
|
|||
/*
|
||||
* This is a simple paging strategy that keeps the last 10 searches in memory
|
||||
*/
|
||||
setPagingProvider(new FifoMemoryPagingProvider(10));
|
||||
// TODO: Make this configurable via the ContextHolder
|
||||
setPagingProvider(new FifoMemoryPagingProvider(10).setDefaultPageSize(ContextHolder.getDefaultPageSize()).setMaximumPageSize(ContextHolder.getMaxPageSize()));
|
||||
|
||||
// Register a CORS filter
|
||||
CorsInterceptor corsInterceptor = new CorsInterceptor();
|
||||
|
|
|
|||
|
|
@ -58,6 +58,10 @@ public class FhirResourceDaoObservationR4 extends BaseHapiFhirResourceDao<Observ
|
|||
|
||||
@Override
|
||||
public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {
|
||||
if (!isPagingProviderDatabaseBacked(theRequestDetails)) {
|
||||
theSearchParameterMap.setLoadSynchronous(true);
|
||||
}
|
||||
|
||||
return mySearchCoordinatorSvc.registerSearch(this, theSearchParameterMap, getResourceName(), new CacheControlDirective().parse(theRequestDetails.getHeaders(Constants.HEADER_CACHE_CONTROL)), theRequestDetails);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -199,7 +199,7 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
|
|||
@Override
|
||||
public List<ResourcePersistentId> executeLastN(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails, IdHelperService theIdHelperService) {
|
||||
Integer myMaxObservationsPerCode = 1;
|
||||
String[] maxCountParams = theRequestDetails.getParameters().get("map");
|
||||
String[] maxCountParams = theRequestDetails.getParameters().get("max");
|
||||
if (maxCountParams != null && maxCountParams.length > 0) {
|
||||
myMaxObservationsPerCode = Integer.valueOf(maxCountParams[0]);
|
||||
}
|
||||
|
|
@ -237,6 +237,7 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
|
|||
compositeAggSubjectSources.add(subjectValuesBuilder);
|
||||
CompositeAggregationBuilder compositeAggregationSubjectBuilder = new CompositeAggregationBuilder("group_by_subject", compositeAggSubjectSources);
|
||||
compositeAggregationSubjectBuilder.subAggregation(observationCodeAggregationBuilder);
|
||||
compositeAggregationSubjectBuilder.size(theMaximumResultSetSize);
|
||||
|
||||
return compositeAggregationSubjectBuilder;
|
||||
}
|
||||
|
|
@ -286,7 +287,8 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
|
|||
List<ParsedComposite.ParsedBucket> subjectBuckets = aggregatedSubjects.getBuckets();
|
||||
List<ResourcePersistentId> myObservationIds = new ArrayList<>();
|
||||
for(ParsedComposite.ParsedBucket subjectBucket : subjectBuckets) {
|
||||
Aggregations observationCodeAggregations = subjectBucket.getAggregations();ParsedTerms aggregatedObservationCodes = observationCodeAggregations.get("group_by_code");
|
||||
Aggregations observationCodeAggregations = subjectBucket.getAggregations();
|
||||
ParsedTerms aggregatedObservationCodes = observationCodeAggregations.get("group_by_code");
|
||||
List<? extends Terms.Bucket> observationCodeBuckets = aggregatedObservationCodes.getBuckets();
|
||||
for (Terms.Bucket observationCodeBucket : observationCodeBuckets) {
|
||||
Aggregations topHitObservationCodes = observationCodeBucket.getAggregations();
|
||||
|
|
|
|||
|
|
@ -116,6 +116,7 @@ public class IntegratedObservationIndexedSearchParamLastNTest {
|
|||
myObservation.setCategory(categoryConcepts);
|
||||
|
||||
// Create CodeableConcept for Code with three codings.
|
||||
// TODO: Temporarily limit this to two codings until we sort out how to manage multiple codings
|
||||
String observationCodeText = "Test Codeable Concept Field for Code";
|
||||
CodeableConcept codeableConceptField = new CodeableConcept().setText(observationCodeText);
|
||||
codeableConceptField.addCoding(new Coding("http://mycodes.org/fhir/observation-code", "test-code", "test-code display"));
|
||||
|
|
@ -224,7 +225,7 @@ public class IntegratedObservationIndexedSearchParamLastNTest {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testSampleBundle() {
|
||||
public void testSampleBundleInTransaction() throws IOException {
|
||||
FhirContext myFhirCtx = FhirContext.forR4();
|
||||
|
||||
PathMatchingResourcePatternResolver provider = new PathMatchingResourcePatternResolver();
|
||||
|
|
@ -274,6 +275,23 @@ public class IntegratedObservationIndexedSearchParamLastNTest {
|
|||
}
|
||||
);
|
||||
|
||||
SearchParameterMap searchParameterMap = new SearchParameterMap();
|
||||
|
||||
// execute Observation ID search - Composite Aggregation
|
||||
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationAllFieldsCompositeSearchRequest(1000, searchParameterMap, 1);
|
||||
SearchResponse responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
|
||||
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
|
||||
|
||||
assertEquals(20, observationIdsOnly.size());
|
||||
ObservationJson observationIdOnly = observationIdsOnly.get(0);
|
||||
|
||||
searchRequestIdsOnly = elasticsearchSvc.buildObservationAllFieldsCompositeSearchRequest(1000, searchParameterMap, 3);
|
||||
responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
|
||||
observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
|
||||
|
||||
assertEquals(38, observationIdsOnly.size());
|
||||
observationIdOnly = observationIdsOnly.get(0);
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,150 @@
|
|||
package ca.uhn.fhir.jpa.dao.r4;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.interceptor.executor.InterceptorService;
|
||||
import ca.uhn.fhir.jpa.dao.*;
|
||||
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl.Suggestion;
|
||||
import ca.uhn.fhir.jpa.dao.lastn.config.TestIntegratedObservationIndexSearchConfig;
|
||||
import ca.uhn.fhir.jpa.model.util.JpaConstants;
|
||||
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
|
||||
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||
import ca.uhn.fhir.rest.api.Constants;
|
||||
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
||||
import ca.uhn.fhir.rest.param.*;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import ca.uhn.fhir.util.BundleUtil;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import org.hl7.fhir.instance.model.api.IBaseBundle;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.*;
|
||||
import org.hl7.fhir.r4.model.Observation.ObservationStatus;
|
||||
import org.junit.AfterClass;
|
||||
import org.junit.Before;
|
||||
import org.junit.Ignore;
|
||||
import org.junit.Test;
|
||||
import org.junit.runner.RunWith;
|
||||
import org.mockito.Answers;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.MockitoAnnotations;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.beans.factory.annotation.Qualifier;
|
||||
import org.springframework.test.context.ContextConfiguration;
|
||||
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
|
||||
import org.springframework.transaction.PlatformTransactionManager;
|
||||
|
||||
import javax.servlet.http.HttpServletRequest;
|
||||
import java.util.*;
|
||||
|
||||
import static org.hamcrest.Matchers.*;
|
||||
import static org.junit.Assert.*;
|
||||
import static org.mockito.ArgumentMatchers.eq;
|
||||
import static org.mockito.Mockito.mock;
|
||||
import static org.mockito.Mockito.when;
|
||||
|
||||
@RunWith(SpringJUnit4ClassRunner.class)
|
||||
@ContextConfiguration(classes = { TestIntegratedObservationIndexSearchConfig.class })
|
||||
public class FhirResourceDaoR4LastNTest extends BaseJpaTest {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4LastNTest.class);
|
||||
|
||||
@Autowired
|
||||
@Qualifier("myPatientDaoR4")
|
||||
protected IFhirResourceDaoPatient<Patient> myPatientDao;
|
||||
|
||||
@Autowired
|
||||
@Qualifier("myObservationDaoR4")
|
||||
protected IFhirResourceDaoObservation<Observation> myObservationDao;
|
||||
|
||||
@Autowired
|
||||
protected DaoConfig myDaoConfig;
|
||||
|
||||
@Autowired
|
||||
protected FhirContext myFhirCtx;
|
||||
|
||||
@Autowired
|
||||
protected PlatformTransactionManager myPlatformTransactionManager;
|
||||
|
||||
@Override
|
||||
protected FhirContext getContext() {
|
||||
return myFhirCtx;
|
||||
}
|
||||
|
||||
@Override
|
||||
protected PlatformTransactionManager getTxManager() {
|
||||
return myPlatformTransactionManager;
|
||||
}
|
||||
|
||||
@Before
|
||||
public void beforeDisableResultReuse() {
|
||||
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
|
||||
}
|
||||
|
||||
private ServletRequestDetails mockSrd() {
|
||||
return mySrd;
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testLastN() {
|
||||
Patient pt = new Patient();
|
||||
pt.addName().setFamily("Lastn").addGiven("Arthur");
|
||||
IIdType ptId = myPatientDao.create(pt, mockSrd()).getId().toUnqualifiedVersionless();
|
||||
|
||||
Map<String, String[]> requestParameters = new HashMap<>();
|
||||
String[] maxParam = new String[1];
|
||||
maxParam[0] = "1";
|
||||
requestParameters.put("max", maxParam);
|
||||
when(mySrd.getParameters()).thenReturn(requestParameters);
|
||||
|
||||
Map<IIdType, CodeableConcept> observationIds = new HashMap<>();
|
||||
for(int observationIdx = 0 ; observationIdx < 20 ; observationIdx++) {
|
||||
Calendar observationDate = new GregorianCalendar();
|
||||
String idxSuffix = String.valueOf(observationIdx);
|
||||
|
||||
Observation obs = new Observation();
|
||||
obs.getText().setDivAsString("<div>OBSTEXT0_" + idxSuffix + "</div>");
|
||||
obs.getSubject().setReferenceElement(ptId);
|
||||
obs.getCode().addCoding().setCode("CODE_" + idxSuffix).setSystem("http://mycode.com");
|
||||
obs.setValue(new StringType("obsvalue0_" + idxSuffix));
|
||||
observationDate.add(Calendar.HOUR, -2);
|
||||
Date effectiveDtm = observationDate.getTime();
|
||||
obs.setEffective(new DateTimeType(effectiveDtm));
|
||||
observationIds.put(myObservationDao.create(obs, mockSrd()).getId().toUnqualifiedVersionless(), obs.getCode());
|
||||
|
||||
obs = new Observation();
|
||||
obs.getText().setDivAsString("<div>OBSTEXT1_" + idxSuffix + "</div>");
|
||||
obs.getSubject().setReferenceElement(ptId);
|
||||
obs.getCode().addCoding().setCode("CODE_" + idxSuffix).setSystem("http://mycode.com");
|
||||
obs.setValue(new StringType("obsvalue1_" + idxSuffix));
|
||||
observationDate.add(Calendar.HOUR, -1);
|
||||
effectiveDtm = observationDate.getTime();
|
||||
obs.setEffective(new DateTimeType(effectiveDtm));
|
||||
observationIds.put(myObservationDao.create(obs, mockSrd()).getId().toUnqualifiedVersionless(), obs.getCode());
|
||||
|
||||
obs = new Observation();
|
||||
obs.getText().setDivAsString("<div>OBSTEXT2_" + idxSuffix + "</div>");
|
||||
obs.getSubject().setReferenceElement(ptId);
|
||||
obs.getCode().addCoding().setCode("CODE_" + idxSuffix).setSystem("http://mycode.com");
|
||||
obs.setValue(new StringType("obsvalue2_" + idxSuffix));
|
||||
observationDate.add(Calendar.HOUR, -0);
|
||||
effectiveDtm = observationDate.getTime();
|
||||
obs.setEffective(new DateTimeType(effectiveDtm));
|
||||
observationIds.put(myObservationDao.create(obs, mockSrd()).getId().toUnqualifiedVersionless(), obs.getCode());
|
||||
}
|
||||
|
||||
HttpServletRequest request;
|
||||
List<String> actual;
|
||||
SearchParameterMap params = new SearchParameterMap();
|
||||
params.setLastN(true);
|
||||
actual = toUnqualifiedVersionlessIdValues(myObservationDao.observationsLastN(params, mockSrd(),null));
|
||||
|
||||
assertEquals(20, actual.size());
|
||||
|
||||
}
|
||||
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -68,7 +68,7 @@ public class LastNElasticsearchSvcMultipleObservationsTest {
|
|||
|
||||
validateQueryResponse(observationIdsOnly);
|
||||
|
||||
// execute Observation ID search (Terms Aggregation) last 3 observations for each patient
|
||||
// execute Observation ID search (Composite Aggregation) last 3 observations for each patient
|
||||
searchRequestIdsOnly = elasticsearchSvc.buildObservationCompositeSearchRequest(1000, null, 3);
|
||||
responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
|
||||
observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
|
||||
|
|
@ -153,9 +153,9 @@ public class LastNElasticsearchSvcMultipleObservationsTest {
|
|||
TokenParam codeParam = new TokenParam("http://mycodes.org/fhir/observation-code", "test-code-1");
|
||||
searchParameterMap.add("code", codeParam);
|
||||
|
||||
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationTermsSearchRequest(1000, searchParameterMap, 100);
|
||||
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationCompositeSearchRequest(1000, searchParameterMap, 100);
|
||||
SearchResponse responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
|
||||
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationTermsResults(responseIds);
|
||||
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
|
||||
|
||||
assertEquals(10, observationIdsOnly.size());
|
||||
|
||||
|
|
@ -172,9 +172,9 @@ public class LastNElasticsearchSvcMultipleObservationsTest {
|
|||
TokenParam codeParam = new TokenParam("test-code-1");
|
||||
searchParameterMap.add("code", codeParam);
|
||||
|
||||
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationTermsSearchRequest(1000, searchParameterMap, 100);
|
||||
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationCompositeSearchRequest(1000, searchParameterMap, 100);
|
||||
SearchResponse responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
|
||||
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationTermsResults(responseIds);
|
||||
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
|
||||
|
||||
assertEquals(5, observationIdsOnly.size());
|
||||
|
||||
|
|
@ -191,9 +191,9 @@ public class LastNElasticsearchSvcMultipleObservationsTest {
|
|||
TokenParam codeParam = new TokenParam("http://mycodes.org/fhir/observation-code", null);
|
||||
searchParameterMap.add("code", codeParam);
|
||||
|
||||
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationTermsSearchRequest(1000, searchParameterMap, 100);
|
||||
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationCompositeSearchRequest(1000, searchParameterMap, 100);
|
||||
SearchResponse responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
|
||||
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationTermsResults(responseIds);
|
||||
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
|
||||
|
||||
assertEquals(10, observationIdsOnly.size());
|
||||
}
|
||||
|
|
@ -210,9 +210,9 @@ public class LastNElasticsearchSvcMultipleObservationsTest {
|
|||
codeParam.setModifier(TokenParamModifier.TEXT);
|
||||
searchParameterMap.add("code", codeParam);
|
||||
|
||||
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationTermsSearchRequest(1000, searchParameterMap, 100);
|
||||
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationCompositeSearchRequest(1000, searchParameterMap, 100);
|
||||
SearchResponse responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
|
||||
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationTermsResults(responseIds);
|
||||
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
|
||||
|
||||
assertEquals(5, observationIdsOnly.size());
|
||||
|
||||
|
|
@ -223,16 +223,18 @@ public class LastNElasticsearchSvcMultipleObservationsTest {
|
|||
String codeableConceptId1 = UUID.randomUUID().toString();
|
||||
CodeableConcept codeableConceptField1 = new CodeableConcept().setText("Test Codeable Concept Field for First Code");
|
||||
codeableConceptField1.addCoding(new Coding("http://mycodes.org/fhir/observation-code", "test-code-1", "test-code-1 display"));
|
||||
codeableConceptField1.addCoding(new Coding("http://myalternatecodes.org/fhir/observation-code", "test-alt-code-1", "test-alt-code-1 display"));
|
||||
codeableConceptField1.addCoding(new Coding("http://mysecondaltcodes.org/fhir/observation-code", "test-second-alt-code-1", "test-second-alt-code-1 display"));
|
||||
// TODO: uncomment the following once there is a solution to supporting multiple codings for Observation Code
|
||||
// codeableConceptField1.addCoding(new Coding("http://myalternatecodes.org/fhir/observation-code", "test-alt-code-1", "test-alt-code-1 display"));
|
||||
// codeableConceptField1.addCoding(new Coding("http://mysecondaltcodes.org/fhir/observation-code", "test-second-alt-code-1", "test-second-alt-code-1 display"));
|
||||
CodeJson codeJson1 = new CodeJson(codeableConceptField1, codeableConceptId1);
|
||||
String codeJson1Document = ourMapperNonPrettyPrint.writeValueAsString(codeJson1);
|
||||
|
||||
String codeableConceptId2 = UUID.randomUUID().toString();
|
||||
CodeableConcept codeableConceptField2 = new CodeableConcept().setText("Test Codeable Concept Field for Second Code");
|
||||
codeableConceptField2.addCoding(new Coding("http://mycodes.org/fhir/observation-code", "test-code-2", "test-code-2 display"));
|
||||
codeableConceptField2.addCoding(new Coding("http://myalternatecodes.org/fhir/observation-code", "test-alt-code-2", "test-alt-code-2 display"));
|
||||
codeableConceptField2.addCoding(new Coding("http://mysecondaltcodes.org/fhir/observation-code", "test-second-alt-code-2", "test-second-alt-code-2 display"));
|
||||
// TODO: uncomment the following once there is a solution to supporting multiple codings for Observation Code
|
||||
// codeableConceptField2.addCoding(new Coding("http://myalternatecodes.org/fhir/observation-code", "test-alt-code-2", "test-alt-code-2 display"));
|
||||
// codeableConceptField2.addCoding(new Coding("http://mysecondaltcodes.org/fhir/observation-code", "test-second-alt-code-2", "test-second-alt-code-2 display"));
|
||||
CodeJson codeJson2 = new CodeJson(codeableConceptField2, codeableConceptId2);
|
||||
String codeJson2Document = ourMapperNonPrettyPrint.writeValueAsString(codeJson2);
|
||||
|
||||
|
|
|
|||
|
|
@ -285,28 +285,36 @@ public class LastNElasticsearchSvcSingleObservationTest {
|
|||
assertEquals(OBSERVATIONCODETEXT, persistedCodeConceptText);
|
||||
|
||||
List<String> persistedCodeCodingSystems = persistedObservationCode.getCoding_system();
|
||||
assertEquals(3,persistedCodeCodingSystems.size());
|
||||
// TODO: Temporary changes until find a solution for addressing Observation Code with multiple codings.
|
||||
// assertEquals(3,persistedCodeCodingSystems.size());
|
||||
assertEquals(1,persistedCodeCodingSystems.size());
|
||||
assertEquals(CODEFIRSTCODINGSYSTEM, persistedCodeCodingSystems.get(0));
|
||||
assertEquals(CODESECONDCODINGSYSTEM, persistedCodeCodingSystems.get(1));
|
||||
assertEquals(CODETHIRDCODINGSYSTEM, persistedCodeCodingSystems.get(2));
|
||||
// assertEquals(CODESECONDCODINGSYSTEM, persistedCodeCodingSystems.get(1));
|
||||
// assertEquals(CODETHIRDCODINGSYSTEM, persistedCodeCodingSystems.get(2));
|
||||
|
||||
List<String> persistedCodeCodingCodes = persistedObservationCode.getCoding_code();
|
||||
assertEquals(3, persistedCodeCodingCodes.size());
|
||||
// TODO: Temporary changes until find a solution for addressing Observation Code with multiple codings.
|
||||
// assertEquals(3, persistedCodeCodingCodes.size());
|
||||
assertEquals(1, persistedCodeCodingCodes.size());
|
||||
assertEquals(CODEFIRSTCODINGCODE, persistedCodeCodingCodes.get(0));
|
||||
assertEquals(CODESECONDCODINGCODE, persistedCodeCodingCodes.get(1));
|
||||
assertEquals(CODETHIRDCODINGCODE, persistedCodeCodingCodes.get(2));
|
||||
// assertEquals(CODESECONDCODINGCODE, persistedCodeCodingCodes.get(1));
|
||||
// assertEquals(CODETHIRDCODINGCODE, persistedCodeCodingCodes.get(2));
|
||||
|
||||
List<String> persistedCodeCodingDisplays = persistedObservationCode.getCoding_display();
|
||||
assertEquals(3, persistedCodeCodingDisplays.size());
|
||||
// TODO: Temporary changes until find a solution for addressing Observation Code with multiple codings.
|
||||
// assertEquals(3, persistedCodeCodingDisplays.size());
|
||||
assertEquals(1, persistedCodeCodingDisplays.size());
|
||||
assertEquals(CODEFIRSTCODINGDISPLAY, persistedCodeCodingDisplays.get(0));
|
||||
assertEquals(CODESECONDCODINGDISPLAY, persistedCodeCodingDisplays.get(1));
|
||||
assertEquals(CODETHIRDCODINGDISPLAY, persistedCodeCodingDisplays.get(2));
|
||||
// assertEquals(CODESECONDCODINGDISPLAY, persistedCodeCodingDisplays.get(1));
|
||||
// assertEquals(CODETHIRDCODINGDISPLAY, persistedCodeCodingDisplays.get(2));
|
||||
|
||||
List<String> persistedCodeCodingCodeSystemHashes = persistedObservationCode.getCoding_code_system_hash();
|
||||
assertEquals(3, persistedCodeCodingCodeSystemHashes.size());
|
||||
// TODO: Temporary changes until find a solution for addressing Observation Code with multiple codings.
|
||||
// assertEquals(3, persistedCodeCodingCodeSystemHashes.size());
|
||||
assertEquals(1, persistedCodeCodingCodeSystemHashes.size());
|
||||
assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE)), persistedCodeCodingCodeSystemHashes.get(0));
|
||||
assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODESECONDCODINGSYSTEM, CODESECONDCODINGCODE)), persistedCodeCodingCodeSystemHashes.get(1));
|
||||
assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODETHIRDCODINGSYSTEM, CODETHIRDCODINGCODE)), persistedCodeCodingCodeSystemHashes.get(2));
|
||||
// assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODESECONDCODINGSYSTEM, CODESECONDCODINGCODE)), persistedCodeCodingCodeSystemHashes.get(1));
|
||||
// assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODETHIRDCODINGSYSTEM, CODETHIRDCODINGCODE)), persistedCodeCodingCodeSystemHashes.get(2));
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -349,8 +357,9 @@ public class LastNElasticsearchSvcSingleObservationTest {
|
|||
indexedObservation.setCode_concept_id(OBSERVATIONSINGLECODEID);
|
||||
CodeableConcept codeableConceptField = new CodeableConcept().setText(OBSERVATIONCODETEXT);
|
||||
codeableConceptField.addCoding(new Coding(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE, CODEFIRSTCODINGDISPLAY));
|
||||
codeableConceptField.addCoding(new Coding(CODESECONDCODINGSYSTEM, CODESECONDCODINGCODE, CODESECONDCODINGDISPLAY));
|
||||
codeableConceptField.addCoding(new Coding(CODETHIRDCODINGSYSTEM, CODETHIRDCODINGCODE, CODETHIRDCODINGDISPLAY));
|
||||
// TODO: Temporary changes until find a solution for addressing Observation Code with multiple codings.
|
||||
// codeableConceptField.addCoding(new Coding(CODESECONDCODINGSYSTEM, CODESECONDCODINGCODE, CODESECONDCODINGDISPLAY));
|
||||
// codeableConceptField.addCoding(new Coding(CODETHIRDCODINGSYSTEM, CODETHIRDCODINGCODE, CODETHIRDCODINGDISPLAY));
|
||||
indexedObservation.setCode(codeableConceptField);
|
||||
|
||||
String observationDocument = ourMapperNonPrettyPrint.writeValueAsString(indexedObservation);
|
||||
|
|
|
|||
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Reference in New Issue