Merge branch 'master' into 2973-CLI_option_help_fails
This commit is contained in:
katie_smilecdr
commit
ab3af7af2a
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@ -31,12 +31,11 @@ In addition, the Elasticsearch client service, `ElasticsearchSvcImpl` will need
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```java
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@Bean()
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public ElasticsearchSvcImpl elasticsearchSvc() {
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String elasticsearchHost = "localhost";
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String elasticsearchUserId = "elastic";
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String elasticsearchHost = "localhost:9200";
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String elasticsearchUsername = "elastic";
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String elasticsearchPassword = "changeme";
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int elasticsearchPort = 9301;
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return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUserId, elasticsearchPassword);
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return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchUsername, elasticsearchPassword);
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}
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```
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@ -1087,7 +1087,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
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ourLog.trace("Performing count");
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ISearchBuilder sb = newSearchBuilder();
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Iterator<Long> countIterator = sb.createCountQuery(myParams, mySearch.getUuid(), myRequest, myRequestPartitionId);
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Long count = countIterator.hasNext() ? countIterator.next() : 0;
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Long count = countIterator.hasNext() ? countIterator.next() : 0L;
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ourLog.trace("Got count {}", count);
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TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
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@ -37,6 +37,7 @@ import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchIndexSettings
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import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
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import org.slf4j.Logger;
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import javax.annotation.Nullable;
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import java.io.IOException;
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import java.util.Arrays;
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import java.util.Properties;
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@ -49,13 +50,13 @@ import static org.slf4j.LoggerFactory.getLogger;
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* FHIR JPA server. This class also injects a starter template into the ES cluster.
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*/
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public class ElasticsearchHibernatePropertiesBuilder {
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private static final Logger ourLog = getLogger(ElasticsearchHibernatePropertiesBuilder.class);
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private static final Logger ourLog = getLogger(ElasticsearchHibernatePropertiesBuilder.class);
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private IndexStatus myRequiredIndexStatus = IndexStatus.YELLOW.YELLOW;
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private IndexStatus myRequiredIndexStatus = IndexStatus.YELLOW;
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private SchemaManagementStrategyName myIndexSchemaManagementStrategy = SchemaManagementStrategyName.CREATE;
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private String myRestUrl;
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private String myHosts;
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private String myUsername;
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private String myPassword;
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private long myIndexManagementWaitTimeoutMillis = 10000L;
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@ -77,11 +78,8 @@ public class ElasticsearchHibernatePropertiesBuilder {
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// the below properties are used for ElasticSearch integration
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theProperties.put(BackendSettings.backendKey(BackendSettings.TYPE), "elasticsearch");
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theProperties.put(BackendSettings.backendKey(ElasticsearchIndexSettings.ANALYSIS_CONFIGURER), HapiElasticsearchAnalysisConfigurer.class.getName());
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theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.HOSTS), myRestUrl);
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theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.HOSTS), myHosts);
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theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.PROTOCOL), myProtocol);
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if (StringUtils.isNotBlank(myUsername)) {
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@ -102,8 +100,7 @@ public class ElasticsearchHibernatePropertiesBuilder {
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//This tells elasticsearch to use our custom index naming strategy.
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theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.LAYOUT_STRATEGY), IndexNamePrefixLayoutStrategy.class.getName());
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injectStartupTemplate(myProtocol, myRestUrl, myUsername, myPassword);
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injectStartupTemplate(myProtocol, myHosts, myUsername, myPassword);
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}
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public ElasticsearchHibernatePropertiesBuilder setRequiredIndexStatus(IndexStatus theRequiredIndexStatus) {
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@ -111,11 +108,8 @@ public class ElasticsearchHibernatePropertiesBuilder {
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return this;
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}
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public ElasticsearchHibernatePropertiesBuilder setRestUrl(String theRestUrl) {
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if (theRestUrl.contains("://")) {
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throw new ConfigurationException("Elasticsearch URL cannot include a protocol, that is a separate property. Remove http:// or https:// from this URL.");
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}
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myRestUrl = theRestUrl;
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public ElasticsearchHibernatePropertiesBuilder setHosts(String hosts) {
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myHosts = hosts;
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return this;
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}
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@ -150,18 +144,13 @@ public class ElasticsearchHibernatePropertiesBuilder {
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* TODO GGG HS: In HS6.1, we should have a native way of performing index settings manipulation at bootstrap time, so this should
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* eventually be removed in favour of whatever solution they come up with.
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*/
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void injectStartupTemplate(String theProtocol, String theHostAndPort, String theUsername, String thePassword) {
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void injectStartupTemplate(String theProtocol, String theHosts, @Nullable String theUsername, @Nullable String thePassword) {
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PutIndexTemplateRequest ngramTemplate = new PutIndexTemplateRequest("ngram-template")
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.patterns(Arrays.asList("*resourcetable-*", "*termconcept-*"))
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.settings(Settings.builder().put("index.max_ngram_diff", 50));
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int colonIndex = theHostAndPort.indexOf(":");
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String host = theHostAndPort.substring(0, colonIndex);
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Integer port = Integer.valueOf(theHostAndPort.substring(colonIndex + 1));
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String qualifiedHost = theProtocol + "://" + host;
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try {
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RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(qualifiedHost, port, theUsername, thePassword);
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RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(theProtocol, theHosts, theUsername, thePassword);
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ourLog.info("Adding starter template for large ngram diffs");
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AcknowledgedResponse acknowledgedResponse = elasticsearchHighLevelRestClient.indices().putTemplate(ngramTemplate, RequestOptions.DEFAULT);
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assert acknowledgedResponse.isAcknowledged();
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@ -20,6 +20,8 @@ package ca.uhn.fhir.jpa.search.lastn;
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* #L%
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*/
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import ca.uhn.fhir.context.ConfigurationException;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.http.Header;
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import org.apache.http.HttpHost;
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import org.apache.http.auth.AuthScope;
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@ -27,45 +29,51 @@ import org.apache.http.auth.UsernamePasswordCredentials;
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import org.apache.http.client.CredentialsProvider;
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import org.apache.http.impl.client.BasicCredentialsProvider;
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import org.apache.http.message.BasicHeader;
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import org.elasticsearch.client.Node;
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import org.elasticsearch.client.RestClient;
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import org.elasticsearch.client.RestClientBuilder;
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import org.elasticsearch.client.RestHighLevelClient;
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import javax.annotation.Nullable;
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import java.util.Arrays;
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import java.util.List;
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import java.util.stream.Collectors;
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public class ElasticsearchRestClientFactory {
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private static String determineScheme(String theHostname) {
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int schemeIdx = theHostname.indexOf("://");
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if (schemeIdx > 0) {
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return theHostname.substring(0, schemeIdx);
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} else {
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return "http";
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static public RestHighLevelClient createElasticsearchHighLevelRestClient(
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String protocol, String hosts, @Nullable String theUsername, @Nullable String thePassword) {
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if (hosts.contains("://")) {
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throw new ConfigurationException("Elasticsearch URLs cannot include a protocol, that is a separate property. Remove http:// or https:// from this URL.");
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}
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}
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private static String stripHostOfScheme(String theHostname) {
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int schemeIdx = theHostname.indexOf("://");
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if (schemeIdx > 0) {
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return theHostname.substring(schemeIdx + 3);
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} else {
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return theHostname;
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String[] hostArray = hosts.split(",");
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List<Node> clientNodes = Arrays.stream(hostArray)
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.map(String::trim)
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.filter(s -> s.contains(":"))
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.map(h -> {
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int colonIndex = h.indexOf(":");
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String host = h.substring(0, colonIndex);
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int port = Integer.parseInt(h.substring(colonIndex + 1));
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return new Node(new HttpHost(host, port, protocol));
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})
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.collect(Collectors.toList());
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if (hostArray.length != clientNodes.size()) {
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throw new ConfigurationException("Elasticsearch URLs have to contain ':' as a host:port separator. Example: localhost:9200,localhost:9201,localhost:9202");
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}
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RestClientBuilder clientBuilder = RestClient.builder(clientNodes.toArray(new Node[0]));
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if (StringUtils.isNotBlank(theUsername) && StringUtils.isNotBlank(thePassword)) {
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final CredentialsProvider credentialsProvider = new BasicCredentialsProvider();
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credentialsProvider.setCredentials(AuthScope.ANY, new UsernamePasswordCredentials(theUsername, thePassword));
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clientBuilder.setHttpClientConfigCallback(httpClientBuilder -> httpClientBuilder
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.setDefaultCredentialsProvider(credentialsProvider));
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}
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Header[] defaultHeaders = new Header[]{new BasicHeader("Content-Type", "application/json")};
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clientBuilder.setDefaultHeaders(defaultHeaders);
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return new RestHighLevelClient(clientBuilder);
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}
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static public RestHighLevelClient createElasticsearchHighLevelRestClient(String theHostname, int thePort, String theUsername, String thePassword) {
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final CredentialsProvider credentialsProvider =
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new BasicCredentialsProvider();
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credentialsProvider.setCredentials(AuthScope.ANY,
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new UsernamePasswordCredentials(theUsername, thePassword));
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RestClientBuilder clientBuilder = RestClient.builder(
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new HttpHost(stripHostOfScheme(theHostname), thePort, determineScheme(theHostname)))
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.setHttpClientConfigCallback(httpClientBuilder -> httpClientBuilder
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.setDefaultCredentialsProvider(credentialsProvider));
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Header[] defaultHeaders = new Header[]{new BasicHeader("Content-Type", "application/json")};
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clientBuilder.setDefaultHeaders(defaultHeaders);
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return new RestHighLevelClient(clientBuilder);
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}
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}
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@ -68,11 +68,11 @@ import org.elasticsearch.search.aggregations.bucket.terms.ParsedTerms;
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import org.elasticsearch.search.aggregations.bucket.terms.Terms;
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import org.elasticsearch.search.aggregations.bucket.terms.TermsAggregationBuilder;
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import org.elasticsearch.search.aggregations.metrics.ParsedTopHits;
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import org.elasticsearch.search.aggregations.support.ValueType;
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import org.elasticsearch.search.builder.SearchSourceBuilder;
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import org.elasticsearch.search.sort.SortOrder;
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import org.springframework.beans.factory.annotation.Autowired;
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import javax.annotation.Nullable;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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@ -125,13 +125,13 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
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private PartitionSettings myPartitionSettings;
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//This constructor used to inject a dummy partitionsettings in test.
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public ElasticsearchSvcImpl(PartitionSettings thePartitionSetings, String theHostname, int thePort, String theUsername, String thePassword) {
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this(theHostname, thePort, theUsername, thePassword);
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public ElasticsearchSvcImpl(PartitionSettings thePartitionSetings, String theHostname, @Nullable String theUsername, @Nullable String thePassword) {
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this(theHostname, theUsername, thePassword);
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this.myPartitionSettings = thePartitionSetings;
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}
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public ElasticsearchSvcImpl(String theHostname, int thePort, String theUsername, String thePassword) {
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myRestHighLevelClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(theHostname, thePort, theUsername, thePassword);
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public ElasticsearchSvcImpl(String theHostname, @Nullable String theUsername, @Nullable String thePassword) {
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myRestHighLevelClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient("http", theHostname, theUsername, thePassword);
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try {
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createObservationIndexIfMissing();
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@ -128,7 +128,7 @@ public class ElasticsearchWithPrefixConfig {
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.settings(Settings.builder().put("index.max_ngram_diff", 50));
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try {
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RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient("http://" + host, httpPort, "", "");
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RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient("http", host + ":" + httpPort, "", "");
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AcknowledgedResponse acknowledgedResponse = elasticsearchHighLevelRestClient.indices().putTemplate(ngramTemplate, RequestOptions.DEFAULT);
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assert acknowledgedResponse.isAcknowledged();
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} catch (IOException theE) {
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@ -41,7 +41,7 @@ public class TestR4ConfigWithElasticSearch extends TestR4Config {
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.setIndexSchemaManagementStrategy(SchemaManagementStrategyName.CREATE)
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.setIndexManagementWaitTimeoutMillis(10000)
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.setRequiredIndexStatus(IndexStatus.YELLOW)
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.setRestUrl(host+ ":" + httpPort)
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.setHosts(host + ":" + httpPort)
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.setProtocol("http")
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.setUsername("")
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.setPassword("")
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@ -21,7 +21,7 @@ public class TestR4ConfigWithElasticsearchClient extends TestR4ConfigWithElastic
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public ElasticsearchSvcImpl myElasticsearchSvc() {
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int elasticsearchPort = elasticContainer().getMappedPort(9200);
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String host = elasticContainer().getHost();
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return new ElasticsearchSvcImpl(host, elasticsearchPort, "", "");
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return new ElasticsearchSvcImpl(host + ":" + elasticsearchPort, null, null);
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}
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@PreDestroy
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@ -33,7 +33,7 @@ public class ElasticsearchPrefixTest {
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public void test() throws IOException {
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//Given
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RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(
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"http://" + elasticsearchContainer.getHost(), elasticsearchContainer.getMappedPort(9200), "", "");
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"http", elasticsearchContainer.getHost() + ":" + elasticsearchContainer.getMappedPort(9200), "", "");
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//When
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RestClient lowLevelClient = elasticsearchHighLevelRestClient.getLowLevelClient();
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@ -23,17 +23,11 @@ class ElasticsearchHibernatePropertiesBuilderTest {
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ElasticsearchHibernatePropertiesBuilder myPropertiesBuilder = spy(ElasticsearchHibernatePropertiesBuilder.class);
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@BeforeEach
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public void prepMocks() {
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//ensures we don't try to reach out to a real ES server on apply.
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doNothing().when(myPropertiesBuilder).injectStartupTemplate(any(), any(), any(), any());
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}
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@Test
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public void testRestUrlCannotContainProtocol() {
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public void testHostsCannotContainProtocol() {
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String host = "localhost:9200";
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String protocolHost = "https://" + host;
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String failureMessage = "Elasticsearch URL cannot include a protocol, that is a separate property. Remove http:// or https:// from this URL.";
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String failureMessage = "Elasticsearch URLs cannot include a protocol, that is a separate property. Remove http:// or https:// from this URL.";
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myPropertiesBuilder
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.setProtocol("https")
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@ -42,19 +36,42 @@ class ElasticsearchHibernatePropertiesBuilderTest {
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//SUT
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try {
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myPropertiesBuilder.setRestUrl(protocolHost);
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myPropertiesBuilder.setHosts(protocolHost)
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.apply(new Properties());
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fail();
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} catch (ConfigurationException e ) {
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assertThat(e.getMessage(), is(equalTo(failureMessage)));
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}
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doNothing().when(myPropertiesBuilder).injectStartupTemplate(any(), any(), any(), any());
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Properties properties = new Properties();
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myPropertiesBuilder
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.setRestUrl(host)
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.setHosts(host)
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.apply(properties);
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assertThat(properties.getProperty(BackendSettings.backendKey(ElasticsearchBackendSettings.HOSTS)), is(equalTo(host)));
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}
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@Test
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public void testHostsValueValidation() {
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String host = "localhost_9200,localhost:9201,localhost:9202";
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String failureMessage = "Elasticsearch URLs have to contain ':' as a host:port separator. Example: localhost:9200,localhost:9201,localhost:9202";
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myPropertiesBuilder
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.setProtocol("https")
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.setHosts(host)
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.setUsername("whatever")
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.setPassword("whatever");
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//SUT
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try {
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myPropertiesBuilder
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.apply(new Properties());
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fail();
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} catch (ConfigurationException e ) {
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assertThat(e.getMessage(), is(equalTo(failureMessage)));
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}
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}
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}
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@ -68,7 +68,7 @@ public class LastNElasticsearchSvcMultipleObservationsIT {
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public void before() throws IOException {
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PartitionSettings partitionSettings = new PartitionSettings();
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partitionSettings.setPartitioningEnabled(false);
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elasticsearchSvc = new ElasticsearchSvcImpl(partitionSettings, elasticsearchContainer.getHost(), elasticsearchContainer.getMappedPort(9200), "", "");
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elasticsearchSvc = new ElasticsearchSvcImpl(partitionSettings, elasticsearchContainer.getHost() + ":" + elasticsearchContainer.getMappedPort(9200), null, null);
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if (!indexLoaded) {
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createMultiplePatientsAndObservations();
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|
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@ -97,7 +97,7 @@ public class LastNElasticsearchSvcSingleObservationIT {
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public void before() {
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PartitionSettings partitionSettings = new PartitionSettings();
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partitionSettings.setPartitioningEnabled(false);
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elasticsearchSvc = new ElasticsearchSvcImpl(partitionSettings, elasticsearchContainer.getHost(), elasticsearchContainer.getMappedPort(9200), "", "");
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elasticsearchSvc = new ElasticsearchSvcImpl(partitionSettings, elasticsearchContainer.getHost() + ":" + elasticsearchContainer.getMappedPort(9200), "", "");
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}
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@AfterEach
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|
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