WIP: Scheduled export/gsrs file for CT US

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/ClinicalTrialDataSourceConfig.java

@@ -57,7 +57,7 @@ public class ClinicalTrialDataSourceConfig extends GSRSDataSourceConfig  {
     protected static final String NAME_DATA_SOURCE = PERSIST_UNIT + "DataSource";
     public static final String NAME_ENTITY_MANAGER = PERSIST_UNIT + "EntityManager";
     protected static final String NAME_DATA_SOURCE_PROPERTIES = PERSIST_UNIT + "DataSourceProperties";
-    protected static final String NAME_TRANSACTION_MANAGER = PERSIST_UNIT + "TransactionManager";
+    public static final String NAME_TRANSACTION_MANAGER = PERSIST_UNIT + "TransactionManager";
 
 
 

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/base/models/ClinicalTrialBase.java

@@ -25,7 +25,7 @@
 @Backup
 // (taking out of EventListners annotation for now and until substance indexing issue resolved)
 // BackupEntityProcessorListener.class
-@EntityListeners({AuditingEntityListener.class, GsrsEntityProcessorListener.class, IndexerEntityListener.class})
+@EntityListeners({AuditingEntityListener.class, GsrsEntityProcessorListener.class, IndexerEntityListener.class, BackupEntityProcessorListener.class})
 public abstract class ClinicalTrialBase extends
         AbstractGsrsTablePerClassEntity
                 implements FetchableEntity, ForceUpdateDirtyMakerMixin {

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/base/repositories/ClinicalTrialBaseRepository.java

@@ -6,8 +6,6 @@
 import gsrs.repository.GsrsRepository;
 import org.springframework.data.repository.NoRepositoryBean;
 import org.springframework.stereotype.Repository;
-import org.springframework.stereotype.Service;
-
 
 @Repository
 @NoRepositoryBean

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/us/exporters/JsonExporter.java

@@ -0,0 +1,37 @@
+package gov.hhs.gsrs.clinicaltrial.us.exporters;
+
+import com.fasterxml.jackson.databind.ObjectWriter;
+import gov.hhs.gsrs.clinicaltrial.us.models.ClinicalTrialUS;
+import ix.core.controllers.EntityFactory;
+import ix.ginas.exporters.Exporter;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.util.Objects;
+
+public class JsonExporter implements Exporter<ClinicalTrialUS> {
+private final BufferedWriter out;
+
+private static final String LEADING_HEADER= "\t\t";
+private final ObjectWriter writer =  EntityFactory.EntityMapper.FULL_ENTITY_MAPPER().writer();
+
+public JsonExporter(OutputStream out) throws IOException{
+Objects.requireNonNull(out);
+this.out = new BufferedWriter(new OutputStreamWriter(out));
+}
+@Override
+public void export(ClinicalTrialUS obj) throws IOException {
+out.write(LEADING_HEADER);
+//need to write as a string because the json writer
+//will sometimes close the writer depending on which implementation it is...
+out.write(writer.writeValueAsString(obj));
+out.newLine();
+}
+
+@Override
+public void close() throws IOException {
+out.close();
+}
+}

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/us/exporters/JsonExporterFactory.java

@@ -0,0 +1,48 @@
+package gov.hhs.gsrs.clinicaltrial.us.exporters;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+import gov.hhs.gsrs.clinicaltrial.us.models.ClinicalTrialUS;
+import ix.ginas.exporters.Exporter;
+import ix.ginas.exporters.ExporterFactory;
+import ix.ginas.exporters.OutputFormat;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.Collections;
+import java.util.Set;
+import java.util.zip.GZIPOutputStream;
+
+public class JsonExporterFactory implements ExporterFactory {
+
+OutputFormat format = new OutputFormat("gsrs", "GSRS bulk, gzipped JSON (.gsrs)");
+
+@Override
+public boolean supports(Parameters params) {
+return params.getFormat().equals(format);
+}
+
+@Override
+public Set<OutputFormat> getSupportedFormats() {
+return Collections.singleton(format);
+}
+
+@Override
+public Exporter<ClinicalTrialUS> createNewExporter(OutputStream out, Parameters params) throws IOException {
+// if(params.shouldCompress()) {
+return new JsonExporter(new GZIPOutputStream(out));
+//        }
+//        return new JsonExporter(out);
+}
+
+@Override
+public JsonNode getSchema() {
+ObjectNode parameters = JsonNodeFactory.instance.objectNode();
+parameters.put("excludedCollections", "String[]");
+parameters.put("recordLimit", Integer.class.getName());
+return generateSchemaNode("JSON Exporter Parameters", parameters);
+}
+
+
+}
+

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/us/repositories/ClinicalTrialUSRepository.java

@@ -1,16 +1,26 @@
 package gov.hhs.gsrs.clinicaltrial.us.repositories;
 
-import gov.hhs.gsrs.clinicaltrial.ClinicalTrialDataSourceConfig;
 import gov.hhs.gsrs.clinicaltrial.us.models.ClinicalTrialUS;
 import gov.hhs.gsrs.clinicaltrial.base.repositories.ClinicalTrialBaseRepository;
+import org.springframework.data.jpa.repository.Query;
 import org.springframework.stereotype.Repository;
-import org.springframework.stereotype.Service;
-
-import javax.persistence.PersistenceContext;
 import org.springframework.transaction.annotation.Transactional;
 
+import java.util.List;
+import java.util.stream.Stream;
+
 @Repository
 @Transactional
-public interface ClinicalTrialUSRepository extends ClinicalTrialBaseRepository<ClinicalTrialUS> { }
+public interface ClinicalTrialUSRepository extends ClinicalTrialBaseRepository<ClinicalTrialUS> {
+
+    @Query("select t from ClinicalTrialUS t")
+    public Stream<ClinicalTrialUS> streamAll();
+
+    @Query("select t.trialNumber from ClinicalTrialUS t")
+    List<String> getAllIds();
+
+
+
+}
 
 

gsrs-module-clinical-trials-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/clinicaltrial/us/tasks/ClinicalTrialUSRebackupTaskInitializer.java

@@ -0,0 +1,45 @@
+package gov.hhs.gsrs.clinicaltrial.us.tasks;
+
+
+import gsrs.scheduledTasks.ScheduledTaskInitializer;
+import gsrs.scheduledTasks.SchedulerPlugin;
+import gsrs.services.BackupService;
+import gsrs.springUtils.StaticContextAccessor;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.data.jpa.repository.JpaRepository;
+
+public class ClinicalTrialUSRebackupTaskInitializer extends ScheduledTaskInitializer {
+@Autowired
+private BackupService backupService;
+
+private String description;
+
+private Class<? extends JpaRepository> repositoryClass;
+
+public void setDescription(String description) {
+this.description = description;
+}
+
+public Class<? extends JpaRepository> getRepositoryClass() {
+return repositoryClass;
+}
+
+public void setRepositoryClass(Class<? extends JpaRepository> repositoryClass) {
+this.repositoryClass = repositoryClass;
+}
+
+@Override
+public String getDescription() {
+return description;
+}
+
+
+@Override
+public void run(SchedulerPlugin.JobStats stats, SchedulerPlugin.TaskListener l){
+backupService.reBackupAllEntitiesOfType(StaticContextAccessor.getBean(repositoryClass),
+PageRequest.of(0, 200), taskProgress -> {
+l.message(taskProgress.getCurrentCount() + "  of " + taskProgress.getTotalCount());
+});
+}
+}