Examples with ParticipantCohortStatus org.pmiops.workbench.db.model.ParticipantCohortStatus used on opensource projects

Example 21 with ParticipantCohortStatus

use of org.pmiops.workbench.db.model.ParticipantCohortStatus in project workbench by all-of-us.

the class CohortReviewController method createParticipantCohortStatusesList.

/**
 * Helper method that builds a list of {@link ParticipantCohortStatus} from BigQuery results.
 *
 * @param cohortReviewId
 * @param result
 * @param rm
 * @return
 */
private List<ParticipantCohortStatus> createParticipantCohortStatusesList(Long cohortReviewId, QueryResult result, Map<String, Integer> rm) {
    List<ParticipantCohortStatus> participantCohortStatuses = new ArrayList<>();
    for (List<FieldValue> row : result.iterateAll()) {
        String birthDateTimeString = bigQueryService.getString(row, rm.get("birth_datetime"));
        if (birthDateTimeString == null) {
            throw new BigQueryException(500, "birth_datetime is null at position: " + rm.get("birth_datetime"));
        }
        java.util.Date birthDate = Date.from(Instant.ofEpochMilli(Double.valueOf(birthDateTimeString).longValue() * 1000));
        participantCohortStatuses.add(new ParticipantCohortStatus().participantKey(new ParticipantCohortStatusKey(cohortReviewId, bigQueryService.getLong(row, rm.get("person_id")))).status(CohortStatus.NOT_REVIEWED).birthDate(new java.sql.Date(birthDate.getTime())).genderConceptId(bigQueryService.getLong(row, rm.get("gender_concept_id"))).raceConceptId(bigQueryService.getLong(row, rm.get("race_concept_id"))).ethnicityConceptId(bigQueryService.getLong(row, rm.get("ethnicity_concept_id"))));
    }
    return participantCohortStatuses;
}

Example 22 with ParticipantCohortStatus

use of org.pmiops.workbench.db.model.ParticipantCohortStatus in project workbench by all-of-us.

the class CohortMaterializationServiceTest method makeStatus.

private ParticipantCohortStatus makeStatus(long cohortReviewId, long participantId, CohortStatus status) {
    ParticipantCohortStatusKey key = new ParticipantCohortStatusKey();
    key.setCohortReviewId(cohortReviewId);
    key.setParticipantId(participantId);
    ParticipantCohortStatus result = new ParticipantCohortStatus();
    result.setStatus(status);
    result.setParticipantKey(key);
    return result;
}

Example 23 with ParticipantCohortStatus

use of org.pmiops.workbench.db.model.ParticipantCohortStatus in project workbench by all-of-us.

the class ParticipantCohortStatusDaoImpl method saveParticipantCohortStatusesCustom.

@Override
public void saveParticipantCohortStatusesCustom(List<ParticipantCohortStatus> participantCohortStatuses) {
    Statement statement = null;
    Connection connection = null;
    int index = 0;
    String sqlStatement = INSERT_SQL_TEMPLATE;
    try {
        connection = jdbcTemplate.getDataSource().getConnection();
        statement = connection.createStatement();
        connection.setAutoCommit(false);
        for (ParticipantCohortStatus pcs : participantCohortStatuses) {
            String birthDate = pcs.getBirthDate() == null ? "NULL" : "'" + pcs.getBirthDate().toString() + "'";
            String nextSql = String.format(NEXT_INSERT, birthDate, pcs.getEthnicityConceptId(), pcs.getGenderConceptId(), pcs.getRaceConceptId(), // this represents NOT_REVIEWED
            3, pcs.getParticipantKey().getCohortReviewId(), pcs.getParticipantKey().getParticipantId());
            sqlStatement = sqlStatement.equals(INSERT_SQL_TEMPLATE) ? sqlStatement + nextSql : sqlStatement + ", " + nextSql;
            if (++index % BATCH_SIZE == 0) {
                statement.execute(sqlStatement);
                sqlStatement = INSERT_SQL_TEMPLATE;
            }
        }
        if (!sqlStatement.equals(INSERT_SQL_TEMPLATE)) {
            statement.execute(sqlStatement);
        }
        connection.commit();
    } catch (SQLException ex) {
        log.log(Level.INFO, "SQLException: " + ex.getMessage());
        rollback(connection);
        throw new RuntimeException("SQLException: " + ex.getMessage(), ex);
    } finally {
        turnOnAutoCommit(connection);
        close(statement);
        close(connection);
    }
}