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PLFM-9656 #1

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42 changes: 38 additions & 4 deletions ...jdomodels/src/main/java/org/sagebionetworks/repo/model/dbo/dao/dataaccess/DBORequest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_ACCESS_REQUIREMENT_ID;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_CREATED_BY;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_CREATED_ON;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_EDUC_ENVELOPE_ID;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_ETAG;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_ID;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_MODIFIED_BY;
Expand All @@ -16,12 +17,12 @@
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.Arrays;
import java.util.LinkedList;
import java.util.List;

import org.sagebionetworks.repo.model.dbo.FieldColumn;
import org.sagebionetworks.repo.model.dbo.MigratableDatabaseObject;
import org.sagebionetworks.repo.model.dbo.TableMapping;
import org.sagebionetworks.repo.model.dbo.migration.BasicMigratableTableTranslation;
import org.sagebionetworks.repo.model.dbo.migration.MigratableTableTranslation;
import org.sagebionetworks.repo.model.migration.MigrationType;

Expand All @@ -36,7 +37,8 @@ public class DBORequest implements MigratableDatabaseObject<DBORequest, DBOReque
new FieldColumn("modifiedBy", COL_DATA_ACCESS_REQUEST_MODIFIED_BY),
new FieldColumn("modifiedOn", COL_DATA_ACCESS_REQUEST_MODIFIED_ON),
new FieldColumn("etag", COL_DATA_ACCESS_REQUEST_ETAG).withIsEtag(true),
new FieldColumn("requestSerialized", COL_DATA_ACCESS_REQUEST_REQUEST_SERIALIZED).withHasFileHandleRef(true)
new FieldColumn("requestSerialized", COL_DATA_ACCESS_REQUEST_REQUEST_SERIALIZED).withHasFileHandleRef(true),
new FieldColumn("eDucEnvelopeId", COL_DATA_ACCESS_REQUEST_EDUC_ENVELOPE_ID)
};

private Long id;
Expand All @@ -48,6 +50,7 @@ public class DBORequest implements MigratableDatabaseObject<DBORequest, DBOReque
private Long modifiedOn;
private String etag;
private byte[] requestSerialized;
private String eDucEnvelopeId;

@Override
public String toString() {
Expand Down Expand Up @@ -199,6 +202,14 @@ public void setRequestSerialized(byte[] requestSerialized) {
this.requestSerialized = requestSerialized;
}

public String getEDucEnvelopeId() {
return eDucEnvelopeId;
}

public void setEDucEnvelopeId(String eDucEnvelopeId) {
this.eDucEnvelopeId = eDucEnvelopeId;
}

@Override
public TableMapping<DBORequest> getTableMapping() {
return new TableMapping<DBORequest>(){
Expand All @@ -216,6 +227,7 @@ public DBORequest mapRow(ResultSet rs, int rowNum) throws SQLException {
dbo.setEtag(rs.getString(COL_DATA_ACCESS_REQUEST_ETAG));
Blob blob = rs.getBlob(COL_DATA_ACCESS_REQUEST_REQUEST_SERIALIZED);
dbo.setRequestSerialized(blob.getBytes(1, (int) blob.length()));
dbo.setEDucEnvelopeId(rs.getString(COL_DATA_ACCESS_REQUEST_EDUC_ENVELOPE_ID));
return dbo;
}

Expand Down Expand Up @@ -249,7 +261,27 @@ public MigrationType getMigratableTableType() {

@Override
public MigratableTableTranslation<DBORequest, DBORequest> getTranslator() {
return new BasicMigratableTableTranslation<DBORequest>();
return new MigratableTableTranslation<DBORequest, DBORequest>() {
@Override
public DBORequest createDatabaseObjectFromBackup(DBORequest backup) {
if (backup.getEDucEnvelopeId() == null && backup.getRequestSerialized() != null) {
try {
var dto = RequestUtils.readSerializedField(backup.getRequestSerialized());
if (dto.getEDucSignatureEnvelopeId() != null) {
backup.setEDucEnvelopeId(dto.getEDucSignatureEnvelopeId());
}
} catch (Exception e) {
// If deserialization fails during migration, skip populating the column
}
}
return backup;
}

@Override
public DBORequest createBackupFromDatabaseObject(DBORequest dbo) {
return dbo;
}
};
}

@Override
Expand All @@ -264,7 +296,9 @@ public Class<? extends DBORequest> getDatabaseObjectClass() {

@Override
public List<MigratableDatabaseObject<?, ?>> getSecondaryTypes() {
return null;
List<MigratableDatabaseObject<?, ?>> list = new LinkedList<>();
list.add(new DBORequestUser());
return list;
}

}
146 changes: 125 additions & 21 deletions ...ls/src/main/java/org/sagebionetworks/repo/model/dbo/dao/dataaccess/DBORequestDAOImpl.java
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Original file line number Diff line number Diff line change
@@ -1,14 +1,38 @@
package org.sagebionetworks.repo.model.dbo.dao.dataaccess;

import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_ACCESS_REQUIREMENT_NAME;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_ACCESS_REQUIREMENT_ID;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_CREATED_BY;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_EDUC_ENVELOPE_ID;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_ID;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_MODIFIED_ON;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_USER_REQUEST_ID;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_REQUEST_USER_USER_ID;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_SUBMISSION_DATA_ACCESS_REQUEST_ID;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_SUBMISSION_ID;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_SUBMISSION_STATUS_CREATED_ON;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_SUBMISSION_STATUS_MODIFIED_ON;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_SUBMISSION_STATUS_STATE;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.COL_DATA_ACCESS_SUBMISSION_STATUS_SUBMISSION_ID;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.TABLE_ACCESS_REQUIREMENT;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.TABLE_DATA_ACCESS_REQUEST;

import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.TABLE_DATA_ACCESS_REQUEST_USER;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.TABLE_DATA_ACCESS_SUBMISSION;
import static org.sagebionetworks.repo.model.query.jdo.SqlConstants.TABLE_DATA_ACCESS_SUBMISSION_STATUS;

import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Date;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.UUID;

import org.sagebionetworks.ids.IdGenerator;
import org.sagebionetworks.ids.IdType;
import org.sagebionetworks.repo.model.dataaccess.AccessType;
import org.sagebionetworks.repo.model.dataaccess.AccessorChange;
import org.sagebionetworks.repo.model.dataaccess.PrincipalInvestigator;
import org.sagebionetworks.repo.model.dataaccess.Request;
import org.sagebionetworks.repo.model.dataaccess.RequestInterface;
import org.sagebionetworks.repo.model.dbo.DBOBasicDao;
Expand All @@ -22,7 +46,7 @@
import org.springframework.stereotype.Repository;

@Repository
public class DBORequestDAOImpl implements RequestDAO{
public class DBORequestDAOImpl implements RequestDAO {

public static final String DATA_ACCESS_REQUEST_DOES_NOT_EXIST = "Data access request: '%s' does not exist";

Expand All @@ -35,26 +59,62 @@ public class DBORequestDAOImpl implements RequestDAO{
@Autowired
private IdGenerator idGenerator;

public static final String SQL_DELETE = "DELETE FROM "+TABLE_DATA_ACCESS_REQUEST
+ " WHERE "+COL_DATA_ACCESS_REQUEST_ID+" = ?";
public static final String SQL_DELETE = "DELETE FROM " + TABLE_DATA_ACCESS_REQUEST
+ " WHERE " + COL_DATA_ACCESS_REQUEST_ID + " = ?";

public static final String SQL_GET = "SELECT *"
+ " FROM "+TABLE_DATA_ACCESS_REQUEST
+ " WHERE "+COL_DATA_ACCESS_REQUEST_ACCESS_REQUIREMENT_ID+" = ?"
+ " AND "+COL_DATA_ACCESS_REQUEST_CREATED_BY+" = ?";
+ " FROM " + TABLE_DATA_ACCESS_REQUEST
+ " WHERE " + COL_DATA_ACCESS_REQUEST_ACCESS_REQUIREMENT_ID + " = ?"
+ " AND " + COL_DATA_ACCESS_REQUEST_CREATED_BY + " = ?";

public static final String SQL_GET_BY_ID = "SELECT *"
+ " FROM "+TABLE_DATA_ACCESS_REQUEST
+ " WHERE "+COL_DATA_ACCESS_REQUEST_ID+" = ?";

public static final String SQL_GET_AR_ID_BY_ID = "SELECT " + COL_DATA_ACCESS_REQUEST_ACCESS_REQUIREMENT_ID
+ " FROM "+TABLE_DATA_ACCESS_REQUEST
+ " WHERE "+COL_DATA_ACCESS_REQUEST_ID+" = ?";
+ " FROM " + TABLE_DATA_ACCESS_REQUEST
+ " WHERE " + COL_DATA_ACCESS_REQUEST_ID + " = ?";

public static final String SQL_GET_FOR_UPDATE = SQL_GET_BY_ID+" FOR UPDATE";
public static final String SQL_GET_AR_ID_BY_ID = "SELECT " + COL_DATA_ACCESS_REQUEST_ACCESS_REQUIREMENT_ID
+ " FROM " + TABLE_DATA_ACCESS_REQUEST
+ " WHERE " + COL_DATA_ACCESS_REQUEST_ID + " = ?";

public static final String SQL_GET_FOR_UPDATE = SQL_GET_BY_ID + " FOR UPDATE";

private static final String SQL_DELETE_REQUEST_USERS = "DELETE FROM " + TABLE_DATA_ACCESS_REQUEST_USER
+ " WHERE " + COL_DATA_ACCESS_REQUEST_USER_REQUEST_ID + " = ?";

private static final String SQL_GET_USER_REQUESTS =
"SELECT r." + COL_DATA_ACCESS_REQUEST_ID + " AS REQUEST_ID"
+ ", r." + COL_DATA_ACCESS_REQUEST_ACCESS_REQUIREMENT_ID + " AS ACCESS_REQUIREMENT_ID"
+ ", ar." + COL_ACCESS_REQUIREMENT_NAME + " AS ACCESS_REQUIREMENT_NAME"
+ ", ss." + COL_DATA_ACCESS_SUBMISSION_STATUS_STATE + " AS SUBMISSION_STATUS"
+ ", r." + COL_DATA_ACCESS_REQUEST_EDUC_ENVELOPE_ID + " IS NOT NULL AS IS_EDUC"
+ ", r." + COL_DATA_ACCESS_REQUEST_EDUC_ENVELOPE_ID + " AS ENVELOPE_ID"
+ ", ss." + COL_DATA_ACCESS_SUBMISSION_STATUS_CREATED_ON + " AS SUBMITTED_ON"
+ ", ss." + COL_DATA_ACCESS_SUBMISSION_STATUS_MODIFIED_ON + " AS MODIFIED_ON"
+ " FROM " + TABLE_DATA_ACCESS_REQUEST + " r"
+ " JOIN " + TABLE_DATA_ACCESS_REQUEST_USER + " ru ON r." + COL_DATA_ACCESS_REQUEST_ID + " = ru." + COL_DATA_ACCESS_REQUEST_USER_REQUEST_ID
+ " JOIN " + TABLE_ACCESS_REQUIREMENT + " ar ON r." + COL_DATA_ACCESS_REQUEST_ACCESS_REQUIREMENT_ID + " = ar.ID"
+ " LEFT JOIN " + TABLE_DATA_ACCESS_SUBMISSION + " s ON s." + COL_DATA_ACCESS_SUBMISSION_DATA_ACCESS_REQUEST_ID + " = r." + COL_DATA_ACCESS_REQUEST_ID
+ " LEFT JOIN " + TABLE_DATA_ACCESS_SUBMISSION_STATUS + " ss ON ss." + COL_DATA_ACCESS_SUBMISSION_STATUS_SUBMISSION_ID + " = s." + COL_DATA_ACCESS_SUBMISSION_ID
+ " WHERE ru." + COL_DATA_ACCESS_REQUEST_USER_USER_ID + " = ?"
+ " ORDER BY r." + COL_DATA_ACCESS_REQUEST_MODIFIED_ON + " DESC"
+ " LIMIT ? OFFSET ?";

private static final RowMapper<DBORequest> MAPPER = new DBORequest().getTableMapping();

private static final RowMapper<RequestUserInfo> USER_REQUEST_MAPPER = (ResultSet rs, int rowNum) -> {
RequestUserInfo info = new RequestUserInfo();
info.setRequestId(String.valueOf(rs.getLong("REQUEST_ID")));
info.setAccessRequirementId(String.valueOf(rs.getLong("ACCESS_REQUIREMENT_ID")));
info.setAccessRequirementName(rs.getString("ACCESS_REQUIREMENT_NAME"));
info.setSubmissionStatus(rs.getString("SUBMISSION_STATUS"));
info.setIsEDuc(rs.getBoolean("IS_EDUC"));
info.setEnvelopeId(rs.getString("ENVELOPE_ID"));
long submittedOn = rs.getLong("SUBMITTED_ON");
info.setSubmittedOn(rs.wasNull() ? null : new Date(submittedOn));
long modifiedOn = rs.getLong("MODIFIED_ON");
info.setModifiedOn(rs.wasNull() ? null : new Date(modifiedOn));
return info;
};

@WriteTransaction
@Override
public Request create(Request toCreate) {
Expand All @@ -63,6 +123,7 @@ public Request create(Request toCreate) {
DBORequest dbo = new DBORequest();
RequestUtils.copyDtoToDbo(toCreate, dbo);
basicDao.createNew(dbo);
populateRequestUsers(toCreate);
return (Request) getUserOwnCurrentRequest(toCreate.getAccessRequirementId(), toCreate.getCreatedBy());
}

Expand All @@ -71,8 +132,7 @@ public RequestInterface getUserOwnCurrentRequest(String accessRequirementId, Str
throws NotFoundException {
try {
DBORequest dbo = jdbcTemplate.queryForObject(SQL_GET, MAPPER, accessRequirementId, userId);
RequestInterface dto = RequestUtils.copyDboToDto(dbo);
return dto;
return RequestUtils.copyDboToDto(dbo);
} catch (EmptyResultDataAccessException e) {
throw new NotFoundException(String.format("Data access request does not exist for access requirement: '%s' and user id: '%s'", accessRequirementId, userId));
}
Expand All @@ -85,6 +145,7 @@ public RequestInterface update(RequestInterface toUpdate) throws NotFoundExcepti
RequestUtils.copyDtoToDbo(toUpdate, dbo);
dbo.setEtag(UUID.randomUUID().toString());
basicDao.update(dbo);
populateRequestUsers(toUpdate);
return getUserOwnCurrentRequest(toUpdate.getAccessRequirementId(), toUpdate.getCreatedBy());
}

Expand All @@ -98,8 +159,7 @@ public void delete(String id) {
public RequestInterface getForUpdate(String id) {
try {
DBORequest dbo = jdbcTemplate.queryForObject(SQL_GET_FOR_UPDATE, MAPPER, id);
RequestInterface dto = RequestUtils.copyDboToDto(dbo);
return dto;
return RequestUtils.copyDboToDto(dbo);
} catch (EmptyResultDataAccessException e) {
throw new NotFoundException(String.format(DATA_ACCESS_REQUEST_DOES_NOT_EXIST, id));
}
Expand All @@ -109,13 +169,12 @@ public RequestInterface getForUpdate(String id) {
public RequestInterface get(String id) {
try {
DBORequest dbo = jdbcTemplate.queryForObject(SQL_GET_BY_ID, MAPPER, id);
RequestInterface dto = RequestUtils.copyDboToDto(dbo);
return dto;
return RequestUtils.copyDboToDto(dbo);
} catch (EmptyResultDataAccessException e) {
throw new NotFoundException(String.format(DATA_ACCESS_REQUEST_DOES_NOT_EXIST, id));
}
}

@Override
public String getAccessRequirementId(String requestId) {
try {
Expand All @@ -125,9 +184,54 @@ public String getAccessRequirementId(String requestId) {
}
}

@Override
public List<RequestUserInfo> getUserRequests(Long userId, long limit, long offset) {
return jdbcTemplate.query(SQL_GET_USER_REQUESTS, USER_REQUEST_MAPPER, userId, limit, offset);
}

@Override
public void truncateAll() {
jdbcTemplate.update("DELETE FROM " + TABLE_DATA_ACCESS_REQUEST);
}

private void populateRequestUsers(RequestInterface request) {
Long requestId = Long.parseLong(request.getId());
jdbcTemplate.update(SQL_DELETE_REQUEST_USERS, requestId);

List<DBORequestUser> users = buildRequestUsers(request);
if (!users.isEmpty()) {
basicDao.createBatch(users);
}
}

List<DBORequestUser> buildRequestUsers(RequestInterface request) {
Long requestId = Long.parseLong(request.getId());
LinkedHashSet<Long> userIds = new LinkedHashSet<>();

userIds.add(Long.parseLong(request.getCreatedBy()));

PrincipalInvestigator pi = request.getPrincipalInvestigator();
if (pi != null && pi.getUserId() != null) {
userIds.add(Long.parseLong(pi.getUserId()));
}

List<AccessorChange> accessorChanges = request.getAccessorChanges();
if (accessorChanges != null) {
for (AccessorChange change : accessorChanges) {
if (AccessType.GAIN_ACCESS.equals(change.getType())
|| AccessType.RENEW_ACCESS.equals(change.getType())) {
userIds.add(Long.parseLong(change.getUserId()));
}
}
}

List<DBORequestUser> result = new ArrayList<>(userIds.size());
for (Long userId : userIds) {
DBORequestUser dbo = new DBORequestUser();
dbo.setRequestId(requestId);
dbo.setUserId(userId);
result.add(dbo);
}
return result;
}
}
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