Merge pull request #198 from samply/release/7.8.0

Release/7.8.0
samply · Sep 9, 2022 · a117409 · a117409
2 parents 0c1cfc2 + 6a86ade
commit a117409
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
+## [7.8.0 - 2022-08-08]
+### Added
+- create sublist for cql results
+- changed NumberDisguiser to LaplaceMechanism
+- init resources for directory sync
+
 ## [7.7.2 - 2022-07-27]
 ### Fixed
 - Translate German remaining sentences for English version of main site

diff --git a/pom.xml b/pom.xml
@@ -11,7 +11,7 @@
   </parent>
 
   <artifactId>share-client</artifactId>
-  <version>7.7.2</version>
+  <version>7.8.0</version>
   <packaging>war</packaging>
 
   <name>Connector</name>
@@ -64,10 +64,10 @@
     <jsf-renderer.version>2.0.0</jsf-renderer.version>
     <common-mailing.version>3.0.0</common-mailing.version>
     <common-http.version>7.4.4</common-http.version>
-    <common-ldmclient.centraxx.version>6.2.0</common-ldmclient.centraxx.version>
+    <common-ldmclient.centraxx.version>6.2.1</common-ldmclient.centraxx.version>
     <common-ldmclient.samplystore.biobank.version>3.0.0
     </common-ldmclient.samplystore.biobank.version>
-    <common-ldmclient.cql.version>2.0.0</common-ldmclient.cql.version>
+    <common-ldmclient.cql.version>2.1.1</common-ldmclient.cql.version>
     <converter.dktk.patient.version>2.4.0</converter.dktk.patient.version>
     <project-directory-client.version>1.3.0</project-directory-client.version>
 
@@ -98,7 +98,7 @@
     <twbs-pagination.version>1.4.1</twbs-pagination.version>
     <jqplot.version>1.0.9.d96a669-1</jqplot.version>
     <hapi.version>5.7.2</hapi.version>
-    <directory-sync.version>0.1.1</directory-sync.version>
+    <directory-sync.version>0.2.0</directory-sync.version>
     <togglz.version>2.8.0</togglz.version>
     <swagger-ui.version>4.1.3</swagger-ui.version>
     <microprofile-openapi-api.version>3.0</microprofile-openapi-api.version>
@@ -119,7 +119,6 @@
     <commons-io.version>2.11.0</commons-io.version>
     <log4j.version>2.17.2</log4j.version>
     <slf4j.version>1.7.36</slf4j.version>
-
     <protobuf-java.version>3.19.4</protobuf-java.version>
     <maven-resources-plugin.version>3.2.0</maven-resources-plugin.version>
     <json-smart.version>1.3.3</json-smart.version>

diff --git a/src/main/java/de/samply/share/client/control/ApplicationBean.java b/src/main/java/de/samply/share/client/control/ApplicationBean.java
@@ -2,6 +2,9 @@
 
 import static org.omnifaces.util.Faces.getServletContext;
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
 import com.google.common.base.Splitter;
 import de.dth.mdr.validator.MdrConnection;
 import de.dth.mdr.validator.MdrValidator;
@@ -14,6 +17,10 @@
 import de.samply.common.mdrclient.MdrInvalidResponseException;
 import de.samply.config.util.FileFinderUtil;
 import de.samply.config.util.JaxbUtil;
+import de.samply.directory_sync.Sync;
+import de.samply.directory_sync.directory.DirectoryApi;
+import de.samply.directory_sync.fhir.FhirApi;
+import de.samply.directory_sync.fhir.FhirReporting;
 import de.samply.project.directory.client.DktkProjectDirectory;
 import de.samply.project.directory.client.DktkProjectDirectoryParameters;
 import de.samply.project.directory.client.ProjectDirectory;
@@ -83,6 +90,7 @@
 import de.samply.share.common.utils.Constants;
 import de.samply.share.common.utils.ProjectInfo;
 import de.samply.web.mdrfaces.MdrContext;
+import io.vavr.control.Either;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -103,6 +111,7 @@
 import javax.faces.bean.ManagedBean;
 import javax.faces.context.FacesContext;
 import javax.faces.validator.ValidatorException;
+import javax.security.auth.login.CredentialNotFoundException;
 import javax.servlet.ServletContext;
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
@@ -111,7 +120,9 @@
 import org.apache.commons.configuration.ConfigurationException;
 import org.apache.http.HttpHeaders;
 import org.apache.http.client.CredentialsProvider;
+import org.apache.http.impl.client.HttpClients;
 import org.flywaydb.core.api.FlywayException;
+import org.hl7.fhir.r4.model.OperationOutcome;
 import org.quartz.CronExpression;
 import org.quartz.CronScheduleBuilder;
 import org.quartz.CronTrigger;
@@ -179,6 +190,7 @@ public class ApplicationBean implements Serializable {
   private ConnectCheckResult patientListAvailability = new ConnectCheckResult();
   private ConnectCheckResult projectPseudonAvailability = new ConnectCheckResult();
   private static Crypt crypt;
+  private FhirContext ctx = FhirContext.forR4();
 
 
   public static Locale getLocale() {
@@ -278,7 +290,7 @@ private static void loadCommonConfig() {
     } catch (UnmarshalException ue) {
       throw new RuntimeException("Unable to unmarshal config file");
     } catch (SAXException | JAXBException | ParserConfigurationException e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
     }
   }
 
@@ -301,7 +313,7 @@ private static void loadUrls() {
     } catch (UnmarshalException ue) {
       throw new RuntimeException("Unable to unmarshal common_urls file", ue);
     } catch (SAXException | JAXBException | ParserConfigurationException e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
     }
   }
 
@@ -324,7 +336,7 @@ private static void loadOperator() {
     } catch (UnmarshalException ue) {
       throw new RuntimeException("Unable to unmarshal common_operator file");
     } catch (SAXException | JAXBException | ParserConfigurationException e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
     }
   }
 
@@ -347,7 +359,7 @@ private static void loadBridgeheadInfo() {
     } catch (UnmarshalException ue) {
       throw new RuntimeException("Unable to unmarshal bridgehead_info file", ue);
     } catch (SAXException | JAXBException | ParserConfigurationException e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
     }
   }
 
@@ -370,7 +382,7 @@ private static void loadCtsInfo() {
     } catch (UnmarshalException ue) {
       throw new RuntimeException("Unable to unmarshal CTS file", ue);
     } catch (SAXException | JAXBException | ParserConfigurationException e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
     }
   }
 
@@ -927,6 +939,15 @@ public void init() {
       logger.info("initializing crypt...");
       initCrypt();
     }
+    if (featureManager.getFeatureState(ClientFeature.BBMRI_DIRECTORY_SYNC).isEnabled()) {
+      IGenericClient client = ctx
+          .newRestfulGenericClient(ApplicationBean.getUrlsForDirectory().getLdmUrl());
+      client.registerInterceptor(new LoggingInterceptor(true));
+      FhirApi fhirApi = new FhirApi(client);
+      FhirReporting fhirReporting = new FhirReporting(ctx, fhirApi);
+      Sync sync = new Sync(fhirApi, fhirReporting, null, null);
+      sync.initResources();
+    }
     logger.info("Application Bean initialized");
 
   }
@@ -1068,6 +1089,26 @@ public void updateLocalComponentInfo() {
     }
   }
 
+  private Either<OperationOutcome, DirectoryApi> createDirectoryApi()
+      throws CredentialNotFoundException {
+    List<Credentials> credentialsList = CredentialsUtil
+        .getCredentialsByTarget(TargetType.TT_DIRECTORY);
+    if (credentialsList.size() < 1) {
+      throw new CredentialNotFoundException("No directory credentials found");
+    }
+    Credentials credentials = credentialsList.get(0);
+    return DirectoryApi.createWithLogin(HttpClients.createDefault(),
+        ApplicationBean.getUrlsForDirectory().getDirectoryUrl(), credentials.getUsername(),
+        credentials.getPasscode());
+  }
+
+  private FhirApi createFhirApi() {
+    IGenericClient client = ctx
+        .newRestfulGenericClient(ApplicationBean.getUrlsForDirectory().getLdmUrl());
+    client.registerInterceptor(new LoggingInterceptor(true));
+    return new FhirApi(client);
+  }
+
   private void setComponentInfoViewModel(IcomponentBasicInfoConnector basicInfoConnector,
       ConnectCheckResult connectCheckResult) {
     try {

diff --git a/src/main/java/de/samply/share/client/control/InquiryBean.java b/src/main/java/de/samply/share/client/control/InquiryBean.java
@@ -151,7 +151,7 @@ private static TreeModel<Container> resultPageToTree(Result queryResultPage) {
           try {
             containerTmp = Converter.convertCcpContainerToCommonContainer(patientContainer);
           } catch (JAXBException e) {
-            logger.error(e.getMessage(),e);
+            logger.error(e.getMessage(), e);
           }
           containerTree = visitContainerNode(containerTree, containerTmp);
 
@@ -173,7 +173,7 @@ private static TreeModel<Container> resultPageToTree(Result queryResultPage) {
           try {
             containerTmp = Converter.convertOsseContainerToCommonContainer(patientContainer);
           } catch (JAXBException e) {
-            logger.error(e.getMessage(),e);
+            logger.error(e.getMessage(), e);
           }
 
           containerTree = visitContainerNode(containerTree, containerTmp);
@@ -598,7 +598,6 @@ public void loadSelectedInquiry() {
   }
 
 
-
   /**
    * Generate the query criteria tree from the criteria string in common namespace.
    *
@@ -785,6 +784,19 @@ private void buildPatientPageTree(Result queryResultPage) {
     patientPageTree = resultPageToTree(queryResultPage);
   }
 
+  /**
+   * Load the sublist results.
+   * @return sublist results
+   */
+  public List<String> loadSubListUrls() {
+    List<InquiryResult> inquiryResultList = InquiryResultUtil.fetchLastTwoInquiryResult(
+        latestInquiryDetails.getId(), false);
+    List<String> locations = new ArrayList<>();
+    locations.add(inquiryResultList.get(0).getLocation());
+    locations.add(inquiryResultList.get(1).getLocation());
+    return locations;
+  }
+
   /**
    * Send a reply back to the broker. Currently only supports the size. TODO: Add support for other
    * reply types TODO: Add success/error message
@@ -808,7 +820,7 @@ public String reply() {
                   .getLocation());
               brokerConnector.reply(latestInquiryDetails, queryResult);
             } catch (LdmConnectorException e) {
-              logger.error(e.getMessage(),e);
+              logger.error(e.getMessage(), e);
             }
           } else if (ApplicationUtils.isLanguageCql()) {
             CqlResult queryResult = new CqlResultFactory(latestInquiryDetails).createCqlResult();
@@ -885,7 +897,7 @@ public void handleDocumentUpload(AjaxBehaviorEvent event) {
       newDocument = null;
       Ajax.oncomplete(RESET_FILEINPUT, CREATE_EVENTHANDLERS);
     } catch (IOException e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
       logger.error("Document upload failed.");
     }
   }
@@ -955,7 +967,7 @@ private void reloadPage() {
     try {
       reloadPageWithoutExceptionManagement();
     } catch (IOException e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
     }
   }
 
@@ -1003,7 +1015,7 @@ private void generateExportFileWithoutManagementException(
     Integer timeout = ConfigurationUtil
         .getConfigurationElementValueAsInteger(EnumConfiguration.EXPORT_TIMEOUT_IN_MINUTES);
     ExportFileGenerator exportFileGenerator =
-        new ExportFileGenerator(latestInquiryResult, ldmConnector, inquiry,selectedInquiryContact,
+        new ExportFileGenerator(latestInquiryResult, ldmConnector, inquiry, selectedInquiryContact,
             validationHandling, timeout);
 
     ByteArrayOutputStream bos = exportFileGenerator.generateExport();

diff --git a/src/main/java/de/samply/share/client/job/CheckInquiryStatusJobCql.java b/src/main/java/de/samply/share/client/job/CheckInquiryStatusJobCql.java
@@ -1,14 +1,19 @@
 package de.samply.share.client.job;
 
+import de.samply.common.ldmclient.LdmClientException;
 import de.samply.share.client.job.util.CqlResultFactory;
 import de.samply.share.client.model.db.enums.InquiryStatusType;
 import de.samply.share.client.model.db.enums.QueryLanguageType;
 import de.samply.share.client.model.db.tables.pojos.InquiryCriteria;
+import de.samply.share.client.model.db.tables.pojos.InquiryResult;
 import de.samply.share.client.util.connector.BrokerConnector;
 import de.samply.share.client.util.connector.LdmConnectorCql;
 import de.samply.share.client.util.connector.exception.BrokerConnectorException;
 import de.samply.share.client.util.db.InquiryCriteriaUtil;
+import de.samply.share.client.util.db.InquiryResultUtil;
 import de.samply.share.model.cql.CqlResult;
+import java.net.URI;
+import java.net.URISyntaxException;
 import java.util.function.Consumer;
 import org.quartz.DisallowConcurrentExecution;
 import org.quartz.JobExecutionContext;
@@ -45,18 +50,37 @@ InquiryCriteria getInquiryCriteria() {
 
   void handleInquiryStatusReady() {
     inquiryDetails.setStatus(InquiryStatusType.IS_PARTIALLY_READY);
-
+    createSublist();
     CheckInquiryStatusReadyForMultipleCriteriaJobCql.spawnNewJob(inquiryDetails);
   }
 
+  private void createSublist() {
+    try {
+      String location = ldmConnector.createSubjectList(new URI(inquiryResult.getLocation()));
+      InquiryResult inquiryResultSubList = new InquiryResult();
+      inquiryResultSubList.setInquiryCriteriaId(inquiryResult.getInquiryCriteriaId());
+      inquiryResultSubList.setInquiryDetailsId(inquiryResult.getInquiryDetailsId());
+      inquiryResultSubList.setSize(inquiryResult.getSize());
+      inquiryResultSubList.setStatisticsOnly(false);
+      inquiryResultSubList.setIsError(false);
+      inquiryResultSubList.setNotificationSent(false);
+      inquiryResultSubList.setLocation(location);
+      InquiryResultUtil.insertInquiryResult(inquiryResultSubList);
+    } catch (LdmClientException | URISyntaxException e) {
+      logger.error(e.getMessage());
+    }
+
+  }
+
+
   @Override
   Consumer<BrokerConnector> getProcessReplyRuleMethod() {
     return brokerConnector -> {
       try {
         CqlResult queryResult = new CqlResultFactory(inquiryDetails).createCqlResult();
         brokerConnector.reply(inquiryDetails, queryResult);
       } catch (BrokerConnectorException e) {
-        logger.error(e.getMessage(),e);
+        logger.error(e.getMessage(), e);
         handleBrokerConnectorException(e);
       }
     };

diff --git a/src/main/java/de/samply/share/client/job/util/CqlResultFactory.java b/src/main/java/de/samply/share/client/job/util/CqlResultFactory.java
@@ -37,7 +37,7 @@ public CqlResult createCqlResult() {
 
     for (InquiryCriteria inquiryCriteria : inquiryCriteriaList) {
       InquiryResult inquiryResult = InquiryResultUtil
-          .fetchLatestInquiryResultForInquiryCriteriaById(inquiryCriteria.getId());
+          .fetchLatestInquiryResultForInquiryCriteriaById(inquiryCriteria.getId(), true);
       if (InquiryCriteriaEntityType.PATIENT.getName().equals(inquiryCriteria.getEntityType())) {
         queryResult.setNumberOfPatients(inquiryResult.getSize());
         List<Stratification> stratifications = readStratifications(inquiryResult);
@@ -61,7 +61,7 @@ private List<Stratification> readStratifications(InquiryResult inquiryResult) {
           .readValue(inquiryResult.getStratifications(), new TypeReference<List<Stratification>>() {
           });
     } catch (IOException e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
       return new ArrayList<>();
     }
   }

diff --git a/src/main/java/de/samply/share/client/messages/messages_de.properties b/src/main/java/de/samply/share/client/messages/messages_de.properties
@@ -232,7 +232,7 @@ si_subject=Ihre Anfrage
 si_institution=Institution
 si_criteria=Suchkriterien
 si_executeInquiry=Anfrage erneut ausf\u00FChren
-si_matchingResults=Passende Datens\u00E4tze ({0})
+si_matchingResults=Passende Datens\u00E4tze
 si_exportResults=Exportieren
 si_details=Details der Anfrage
 si_events=Verlauf

diff --git a/src/main/java/de/samply/share/client/rest/Connector.java b/src/main/java/de/samply/share/client/rest/Connector.java
@@ -458,7 +458,7 @@ private InquiryLine fetchLatestInquiryResultForInquiryDetailsById_WithoutManagem
       InquiryLine inquiryLine, InquiryDetails inquiryDetails) {
     List<InquiryResult> inquiryResultList = new ArrayList<>();
     if (ApplicationUtils.isLanguageCql()) {
-      inquiryResultList = InquiryResultUtil.fetchLastTwoInquiryResult(inquiryDetails.getId());
+      inquiryResultList = InquiryResultUtil.fetchLastTwoInquiryResult(inquiryDetails.getId(), true);
     } else if (ApplicationUtils.isLanguageQuery()) {
       inquiryResultList.add(
           InquiryResultUtil.fetchLatestInquiryResultForInquiryDetailsById(inquiryDetails.getId()));
@@ -501,7 +501,7 @@ private String getSizeOfInquiryResult(InquiryResult inquiryResult, String defaul
       return inquiryResult.getSize().toString();
 
     } catch (Exception e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
       return Messages.getString(defaultErrorMessage);
     }
 
@@ -544,7 +544,7 @@ private String getBrokerName(Inquiry inquiry) {
       return brokerName;
 
     } catch (Exception e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
       return UNKNOWN;
     }