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DwayneJengSageDwayneJengSage
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Merge pull request #672 from DwayneJengSage/dev3
DHP-1071 CSV Storage API
2 parents e23516f + 38b5870 commit 073ee51

25 files changed

+1831
-3
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‎src/main/java/org/sagebionetworks/bridge/config/SpringConfig.java‎

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import org.sagebionetworks.bridge.hibernate.HibernateAccountSecret;
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import org.sagebionetworks.bridge.hibernate.HibernateEnrollment;
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import org.sagebionetworks.bridge.hibernate.HibernateHelper;
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import org.sagebionetworks.bridge.hibernate.HibernateUploadTableRow;
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import org.sagebionetworks.bridge.hibernate.MySQLHibernatePersistenceExceptionConverter;
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import org.sagebionetworks.bridge.hibernate.HibernateSharedModuleMetadata;
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import org.sagebionetworks.bridge.hibernate.HibernateStudy;
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MetadataSources metadataSources = new MetadataSources(reg);
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metadataSources.addAnnotatedClass(HibernateAccount.class);
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metadataSources.addAnnotatedClass(HibernateStudy.class);
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metadataSources.addAnnotatedClass(HibernateUploadTableRow.class);
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metadataSources.addAnnotatedClass(HibernateEnrollment.class);
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metadataSources.addAnnotatedClass(HibernateSharedModuleMetadata.class);
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metadataSources.addAnnotatedClass(HibernateAccountSecret.class);

‎src/main/java/org/sagebionetworks/bridge/dao/UploadTableRowDao.java‎

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package org.sagebionetworks.bridge.dao;
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import java.util.Optional;
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import org.sagebionetworks.bridge.models.PagedResourceList;
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import org.sagebionetworks.bridge.upload.UploadTableRow;
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import org.sagebionetworks.bridge.upload.UploadTableRowQuery;
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/** DAO to interact with upload table rows. */
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public interface UploadTableRowDao {
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/** Delete a single upload table row. */
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void deleteUploadTableRow(String appId, String studyId, String recordId);
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/** Get a single upload table row. */
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Optional<UploadTableRow> getUploadTableRow(String appId, String studyId, String recordId);
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/** Query for upload table rows. */
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PagedResourceList<UploadTableRow> queryUploadTableRows(UploadTableRowQuery query);
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/** Create a new upload table row, or overwrite it if the row already exists. */
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void saveUploadTableRow(UploadTableRow row);
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}

‎src/main/java/org/sagebionetworks/bridge/hibernate/HibernateUploadTableRow.java‎

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package org.sagebionetworks.bridge.hibernate;
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import java.util.HashMap;
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import java.util.Map;
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import javax.persistence.Convert;
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import javax.persistence.Entity;
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import javax.persistence.Id;
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import javax.persistence.IdClass;
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import javax.persistence.Table;
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import org.joda.time.DateTime;
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import org.sagebionetworks.bridge.json.BridgeTypeName;
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import org.sagebionetworks.bridge.upload.UploadTableRow;
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/** Hibernate implementation of UploadTableRow. */
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@BridgeTypeName("UploadTableRow")
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@Entity
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@IdClass(HibernateUploadTableRowId.class)
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@Table(name = "UploadTableRows")
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public class HibernateUploadTableRow implements UploadTableRow {
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private String appId;
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private String studyId;
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private String recordId;
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private String assessmentGuid;
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private DateTime createdOn;
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private boolean testData;
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private String healthCode;
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private Integer participantVersion;
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private Map<String, String> metadata = new HashMap<>();
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private Map<String, String> data = new HashMap<>();
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@Id
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@Override
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public String getAppId() {
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return appId;
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}
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@Override
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public void setAppId(String appId) {
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this.appId = appId;
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}
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@Id
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@Override
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public String getStudyId() {
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return studyId;
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}
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@Override
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public void setStudyId(String studyId) {
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this.studyId = studyId;
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}
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@Id
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@Override
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public String getRecordId() {
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return recordId;
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}
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@Override
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public void setRecordId(String recordId) {
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this.recordId = recordId;
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}
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@Override
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public String getAssessmentGuid() {
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return assessmentGuid;
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}
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@Override
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public void setAssessmentGuid(String assessmentGuid) {
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this.assessmentGuid = assessmentGuid;
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}
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@Convert(converter = DateTimeToLongAttributeConverter.class)
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@Override
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public DateTime getCreatedOn() {
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return createdOn;
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}
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@Override
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public void setCreatedOn(DateTime createdOn) {
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this.createdOn = createdOn;
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}
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@Override
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public boolean isTestData() {
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return testData;
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}
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@Override
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public void setTestData(boolean testData) {
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this.testData = testData;
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}
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@Override
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public String getHealthCode() {
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return healthCode;
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}
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@Override
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public void setHealthCode(String healthCode) {
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this.healthCode = healthCode;
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}
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@Override
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public Integer getParticipantVersion() {
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return participantVersion;
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}
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@Override
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public void setParticipantVersion(Integer participantVersion) {
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this.participantVersion = participantVersion;
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}
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@Convert(converter = StringMapConverter.class)
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@Override
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public Map<String, String> getMetadata() {
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return metadata;
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}
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@Override
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public void setMetadata(Map<String, String> metadata) {
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this.metadata = metadata != null ? metadata : new HashMap<>();
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}
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@Convert(converter = StringMapConverter.class)
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@Override
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public Map<String, String> getData() {
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return data;
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}
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@Override
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public void setData(Map<String, String> data) {
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this.data = data != null ? data : new HashMap<>();
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}
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}

‎src/main/java/org/sagebionetworks/bridge/hibernate/HibernateUploadTableRowDao.java‎

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package org.sagebionetworks.bridge.hibernate;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Optional;
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import javax.annotation.Resource;
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import org.springframework.stereotype.Component;
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import org.sagebionetworks.bridge.BridgeConstants;
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import org.sagebionetworks.bridge.dao.UploadTableRowDao;
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import org.sagebionetworks.bridge.models.PagedResourceList;
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import org.sagebionetworks.bridge.upload.UploadTableRow;
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import org.sagebionetworks.bridge.upload.UploadTableRowQuery;
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/** Hibernate implementation of UploadTableRowDao. */
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@Component
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public class HibernateUploadTableRowDao implements UploadTableRowDao {
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private HibernateHelper hibernateHelper;
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@Resource(name = "basicHibernateHelper")
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public final void setHibernateHelper(HibernateHelper hibernateHelper) {
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this.hibernateHelper = hibernateHelper;
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}
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@Override
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public void deleteUploadTableRow(String appId, String studyId, String recordId) {
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HibernateUploadTableRowId id = new HibernateUploadTableRowId(appId, studyId, recordId);
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hibernateHelper.deleteById(HibernateUploadTableRow.class, id);
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}
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@Override
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public Optional<UploadTableRow> getUploadTableRow(String appId, String studyId, String recordId) {
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HibernateUploadTableRowId id = new HibernateUploadTableRowId(appId, studyId, recordId);
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UploadTableRow row = hibernateHelper.getById(HibernateUploadTableRow.class, id);
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return Optional.ofNullable(row);
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}
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@Override
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public PagedResourceList<UploadTableRow> queryUploadTableRows(UploadTableRowQuery query) {
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QueryBuilder builder = new QueryBuilder();
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builder.append("FROM HibernateUploadTableRow");
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// appId and studyId are always required. (This is validated in the service.)
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builder.append("WHERE appId = :appId AND studyId = :studyId");
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builder.getParameters().put("appId", query.getAppId());
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builder.getParameters().put("studyId", query.getStudyId());
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// Filter by assessment.
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if (query.getAssessmentGuid() != null) {
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builder.append("AND assessmentGuid = :assessmentGuid");
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builder.getParameters().put("assessmentGuid", query.getAssessmentGuid());
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}
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// Filter by date range.
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if (query.getStartTime() != null) {
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builder.append("AND createdOn >= :startDate");
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builder.getParameters().put("startDate", query.getStartTime());
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}
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if (query.getEndTime() != null) {
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builder.append("AND createdOn < :endDate");
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builder.getParameters().put("endDate", query.getEndTime());
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}
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// Include test data?
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if (!query.getIncludeTestData()) {
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builder.append("AND testData = 0");
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}
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// Get total.
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int total = hibernateHelper.queryCount("SELECT COUNT(DISTINCT recordId) " + builder.getQuery(),
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builder.getParameters());
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// Start and count.
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Integer start = query.getStart();
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if (start == null) {
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start = 0;
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}
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Integer pageSize = query.getPageSize();
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if (pageSize == null) {
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pageSize = BridgeConstants.API_DEFAULT_PAGE_SIZE;
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}
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// Query.
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List<HibernateUploadTableRow> hibernateList = hibernateHelper.queryGet(builder.getQuery(),
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builder.getParameters(), start, pageSize, HibernateUploadTableRow.class);
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// Because of Java generic typing issues, we need to convert this to a non-Hibernate UploadTableRow.
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List<UploadTableRow> list = new ArrayList<>(hibernateList);
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return new PagedResourceList<>(list, total)
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.withRequestParam("assessmentGuid", query.getAssessmentGuid())
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.withRequestParam("startTime", query.getStartTime())
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.withRequestParam("endTime", query.getEndTime())
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.withRequestParam("includeTestData", query.getIncludeTestData())
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.withRequestParam("start", start)
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.withRequestParam("pageSize", pageSize);
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}
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@Override
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public void saveUploadTableRow(UploadTableRow row) {
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hibernateHelper.saveOrUpdate(row);
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}
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}

‎src/main/java/org/sagebionetworks/bridge/hibernate/HibernateUploadTableRowId.java‎

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package org.sagebionetworks.bridge.hibernate;
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import java.io.Serializable;
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/**
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* Represents the composite key for UploadTableRow, which is appId, studyId, and recordId. Default constructor and
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* setters are required by Hibernate.
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*/
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@SuppressWarnings("serial")
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public class HibernateUploadTableRowId implements Serializable {
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private String appId;
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private String studyId;
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private String recordId;
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public HibernateUploadTableRowId() {
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}
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public HibernateUploadTableRowId(String appId, String studyId, String recordId) {
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this.appId = appId;
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this.studyId = studyId;
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this.recordId = recordId;
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}
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public String getAppId() {
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return appId;
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}
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public void setAppId(String appId) {
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this.appId = appId;
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}
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public String getStudyId() {
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return studyId;
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}
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public void setStudyId(String studyId) {
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this.studyId = studyId;
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}
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public String getRecordId() {
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return recordId;
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}
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public void setRecordId(String recordId) {
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this.recordId = recordId;
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}
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}

‎src/main/java/org/sagebionetworks/bridge/hibernate/StringMapConverter.java‎

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package org.sagebionetworks.bridge.hibernate;
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import java.util.Map;
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import javax.persistence.Converter;
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import com.fasterxml.jackson.core.type.TypeReference;
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/** Hibernate converter that serializes a string map to JSON for storage in SQL. */
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@Converter
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public class StringMapConverter extends BaseJsonAttributeConverter<Map<String, String>> {
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static final TypeReference<Map<String, String>> TYPE_REFERENCE = new TypeReference<Map<String, String>>() {};
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@Override
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public String convertToDatabaseColumn(Map<String, String> map) {
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return serialize(map);
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}
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@Override
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public Map<String, String> convertToEntityAttribute(String value) {
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return deserialize(value, TYPE_REFERENCE);
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}
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}

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