Example usage for java.sql SQLException fillInStackTrace

List of usage examples for java.sql SQLException fillInStackTrace

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Introduction

In this page you can find the example usage for java.sql SQLException fillInStackTrace.

Prototype

public synchronized Throwable fillInStackTrace()

Source Link

Document

Fills in the execution stack trace.

Usage

From source file:uk.nhs.cfh.dsp.snomed.dao.impl.SnomedConceptDatabaseDAO.java

/**
 * Initialise statements.//from w  w  w  .  ja v a  2 s .c  om
 */
public synchronized void initialiseStatements() {
    // create prepared statements
    try {
        getConceptWithIDStatement = connection
                .prepareStatement("" + "SELECT DISTINCT FULLYSPECIFIEDNAME, ISPRIMITIVE, CONCEPTSTATUS,"
                        + "CTV3ID, SNOMEDID, SOURCE FROM SNOMED.CONCEPT " + "WHERE CONCEPTID = ? ");

        // descriptions
        getDescriptionsForConceptIDStatement = connection.prepareStatement(
                "" + "SELECT DISTINCT  DESCRIPTIONID, DESCRIPTIONSTATUS, TERM, INITIALCAPITALSTATUS, "
                        + "DESCRIPTIONTYPE, LANGUAGECODE, SOURCE FROM SNOMED.TERM " + "WHERE CONCEPTID = ? ");

        // relationships
        getRelationshipsForConceptIDStatement = connection
                .prepareStatement("" + "SELECT DISTINCT RELATIONSHIPID, CONCEPTID1, RELATIONSHIPTYPE, "
                        + "CONCEPTID2, CHARACTERISTICTYPE, REFINABILITY, RELATIONSHIPGROUP, SOURCE "
                        + "FROM SNOMED.REL WHERE CONCEPTID1 = ?");

        getChildRelationshipsForConceptIDStatement = connection
                .prepareStatement("" + "SELECT DISTINCT CONCEPTID1 "
                        + "FROM SNOMED.REL WHERE RELATIONSHIPTYPE = '116680003' AND CONCEPTID2 = ?");

        // get concepts like statement
        getConceptsLikeStatement = connection.prepareStatement(
                "" + "SELECT DISTINCT CONCEPTID FROM SNOMED.CONCEPT " + "WHERE FULLYSPECIFIEDNAME LIKE ? ");

        // get ancestors statement
        getAncestorsStatement = connection.prepareStatement(
                "" + "SELECT SUPERTYPEID FROM SNOMED.TRANSITIVECLOSURE " + "WHERE SUBTYPEID = ?");

        // get descendants
        getDescendantsStatement = connection.prepareStatement(
                "" + "SELECT SUBTYPEID FROM SNOMED.TRANSITIVECLOSURE " + "WHERE SUPERTYPEID = ?");

        // get replacements
        getReplacementConceptStatement = connection
                .prepareStatement("" + "SELECT CONCEPTID2 FROM SNOMED.REL WHERE CONCEPTID1 = ? AND "
                        + "RELATIONHSIPTYPE IN ('168666000', '370124000')");

        // get preferred term
        getPreferredTermStatement = connection.prepareStatement(
                "" + "SELECT TERM FROM SNOMED.TERM WHERE DESCRIPTIONTYPE = 1 AND CONCEPTID = ?");

    } catch (SQLException e) {
        logger.warn("SQL error encountered while initialising statements.\n" + "Nested exception is : "
                + e.fillInStackTrace());
    }
}

From source file:uk.nhs.cfh.dsp.snomed.dao.impl.SnomedConceptDatabaseDAO.java

public synchronized TerminologyConcept getTerminologyConcept(String conceptID) throws ConceptNotFoundException {

    String conceptLabel = "";
    boolean isPrimitive = true;
    String source = "";
    int conceptStatus = 0;
    String ctv3ID = "";
    String snomedID = "";
    // set value in prepared statement
    try {//from  w  ww  .  j  a  v a2 s  .  co m
        // strip all non digit numbers from concept id
        conceptID = conceptID.replaceAll("[^\\d]", "");
        getConceptWithIDStatement.setString(1, conceptID);
        ResultSet rs = getConceptWithIDStatement.executeQuery();
        while (rs.next()) {
            conceptLabel = rs.getString(1);
            int isPrim = rs.getInt(2);
            conceptStatus = rs.getInt(3);
            ctv3ID = rs.getString(4);
            snomedID = rs.getString(5);
            if (isPrim == 0) {
                isPrimitive = false;
            }
            source = rs.getString(6);
        }

        // close result set
        rs.close();

    } catch (SQLException e) {
        logger.warn("SQL Error encountered while checking for concept with id : " + conceptID
                + "\nNested exception is : " + e.fillInStackTrace());
    } catch (Exception e) {
        logger.warn("A variable most likely returned a null value unexpectedly." + "\nNested exception is : "
                + e.fillInStackTrace());
    }

    // create terminology concept
    if ("".equalsIgnoreCase(conceptLabel)) {
        throw new ConceptNotFoundException(conceptID);
    } else {
        SnomedConcept concept = new SnomedConceptImpl(conceptID, conceptLabel);
        // add primitve status
        concept.setPrimitive(isPrimitive);
        concept.setSource(source);
        // use utility function of ComponentStatus to get value
        concept.setStatus(ComponentStatus.valueOf(conceptStatus));
        concept.setCtv3ID(ctv3ID);
        concept.setSnomedID(snomedID);
        // set concept type
        concept.setType(getConceptType(conceptID));

        try {
            // set descriptions
            setDescriptions(concept);

            // set relationships
            setRelationships(concept);

        } catch (SQLException e) {
            logger.warn("SQL Exception while querying database. Nested exception is : " + e.fillInStackTrace());
        } catch (Exception e) {
            logger.warn("A variable most likely returned a null value unexpectedly."
                    + "\nNested exception is : " + e.fillInStackTrace());
        }

        return concept;
    }
}

From source file:uk.nhs.cfh.dsp.snomed.dao.impl.SnomedConceptDatabaseDAO.java

public synchronized TerminologyConcept getCurrentConceptForConcept(String conceptId)
        throws ConceptNotFoundException {

    if (conceptId != null) {
        // replace value in getReplacementConceptStatement
        try {//from   ww  w. j a v  a2  s  .  c  om
            getReplacementConceptStatement.setString(1, conceptId);
            ResultSet rs = getReplacementConceptStatement.executeQuery();
            Set<String> replacements = new HashSet<String>();
            while (rs.next()) {
                replacements.add(rs.getString(1));
            }

            // close result set
            rs.close();
            List<String> concepts = new ArrayList<String>(replacements);

            if (replacements.size() > 1) {
                logger.warn("More than one matching replacement concept found. Returning the first "
                        + "concept found. The following is a list of all matching replacements : "
                        + replacements);
                return getTerminologyConcept(concepts.get(0));
            } else if (replacements.size() == 0) {
                logger.warn("No replacement concept found for concept with ID : " + conceptId);
                return null;
            } else {
                return getTerminologyConcept(concepts.get(0));
            }
        } catch (SQLException e) {
            logger.warn(e.fillInStackTrace());
            return null;
        }
    } else {
        throw new IllegalArgumentException("Concept ID passed can not be null.");
    }
}

From source file:uk.nhs.cfh.dsp.snomed.dao.impl.SnomedConceptDatabaseDAO.java

/**
 * Gets the concept type.//ww  w. j  a va  2s  . c  om
 *
 * @param conceptId the concept id
 * @return the concept type
 */
protected synchronized ConceptType getConceptType(String conceptId) {

    ConceptType type = ConceptType.UNKNOWN;
    // we create a sorted concept type list, because we need to check in a specific order
    List<ConceptType> types = new ArrayList<ConceptType>();
    types.add(ConceptType.DISEASE);
    types.add(ConceptType.FINDING);
    types.add(ConceptType.FINDING_WEC);
    types.add(ConceptType.OBSERVABLE_ENTITY);
    types.add(ConceptType.BODY_STRUCTURE);
    types.add(ConceptType.PHARMACEUTICAL_OR_BIOLOGICAL_PRODUCT);
    types.add(ConceptType.EVENT);
    types.add(ConceptType.SURGICAL_PROCEDURE);
    types.add(ConceptType.PROCEDURE);
    types.add(ConceptType.PROCEDURE_WEC);
    types.add(ConceptType.SPECIMEN);
    types.add(ConceptType.DRUG_DEVICE_COMBO_PRODUCT);
    types.add(ConceptType.SITUATION_WEC);

    try {
        PreparedStatement ps = connection.prepareStatement("SELECT COUNT(SUBTYPEID) FROM "
                + "SNOMED.TRANSITIVECLOSURE WHERE SUBTYPEID = ? AND  SUPERTYPEID= ?");
        ps.setString(1, conceptId);
        // change supertype and check result
        int result = 0;
        for (ConceptType ct : types) {
            ps.setString(2, ct.getID());
            // execute statement and check result
            ResultSet rs = ps.executeQuery();
            while (rs.next()) {
                result = rs.getInt(1);
            }

            // close result set
            rs.close();
            if (result == 1) {
                // close ps
                ps.close();
                return ct;
            }
        }

    } catch (SQLException e) {
        logger.warn("Error querying transitive closure table. Nested exception is : " + e.fillInStackTrace());
    }

    return type;
}

From source file:uk.nhs.cfh.dsp.snomed.dao.impl.SnomedConceptDatabaseDAO.java

/**
 * Sets the data source./* w  w w . j  a  v a2s.  c  om*/
 *
 * @param dataSource the new data source
 */
public synchronized void setDataSource(DataSource dataSource) {
    if (dataSource != null) {
        try {
            this.connection = dataSource.getConnection();
            initialiseStatements();
        } catch (SQLException e) {
            logger.warn("Error obtaining connection from data source. " + "Nested exception is : "
                    + e.fillInStackTrace());
        }
    }
}

From source file:uk.nhs.cfh.dsp.snomed.expression.comparator.impl.AbstractExpressionComparator.java

/**
 * Instantiates a new abstract expression comparator.
 *
 * @param dataSource the data source//from  w  w  w .j  a  va  2 s  . co  m
 * @param terminologyConceptDAO the terminology concept dao
 */
protected AbstractExpressionComparator(DataSource dataSource, TerminologyConceptDAO terminologyConceptDAO) {
    try {
        this.connection = dataSource.getConnection();
        initialiseStatements();
    } catch (SQLException e) {
        logger.warn("Error obtaining connection from data source. " + "Nested exception is : "
                + e.fillInStackTrace());
    }
    this.terminologyConceptDAO = terminologyConceptDAO;
}

From source file:uk.nhs.cfh.dsp.snomed.expression.comparator.impl.AbstractExpressionComparator.java

/**
 * Initialise statements./*from  w w  w.  ja  v  a2  s .c  o  m*/
 */
protected void initialiseStatements() {

    try {
        checkAncestorsStatement = connection
                .prepareStatement("" + "SELECT COUNT(SUPERTYPEID) FROM SNOMED.TRANSITIVECLOSURE WHERE "
                        + "SUPERTYPEID = ? AND SUBTYPEID = ?");
        checkDescendantsStatement = connection
                .prepareStatement("" + "SELECT COUNT(SUBTYPEID) FROM SNOMED.TRANSITIVECLOSURE WHERE "
                        + "SUBTYPEID = ? AND SUPERTYPEID = ?");
        checkStatusStatement = connection
                .prepareStatement("" + "SELECT CONCEPTSTATUS FROM SNOMED.CONCEPT WHERE CONCEPTID = ?");
    } catch (SQLException e) {
        logger.warn(e.fillInStackTrace());
    }

}

From source file:uk.nhs.cfh.dsp.snomed.expression.comparator.impl.AbstractExpressionComparator.java

/**
 * Sets the data source./*  w ww .  j  av a  2 s .co m*/
 *
 * @param dataSource the new data source
 */
public synchronized void setDataSource(DataSource dataSource) {
    try {
        this.connection = dataSource.getConnection();
        initialiseStatements();
    } catch (SQLException e) {
        logger.warn("Error obtaining connection from data source. " + "Nested exception is : "
                + e.fillInStackTrace());
    }
}

From source file:uk.nhs.cfh.dsp.snomed.expression.comparator.impl.AbstractExpressionComparator.java

/**
 * Checks if is active concept.// w  w  w . jav  a  2 s .  co  m
 *
 * @param conceptId the concept id
 * @return true, if is active concept
 */
private boolean isActiveConcept(String conceptId) {

    boolean isActive = false;
    // set value in checkStatusStatement
    try {
        int status = 0;
        checkStatusStatement.setString(1, conceptId);
        ResultSet rs = checkStatusStatement.executeQuery();
        while (rs.next()) {
            status = rs.getInt(1);
        }

        if (status == 0 || status == 6 || status == 11) {
            isActive = true;
        }
    } catch (SQLException e) {
        logger.warn(e.fillInStackTrace());
    }

    return isActive;
}

From source file:uk.nhs.cfh.dsp.snomed.hierarchyprovider.impl.AbstractHierarchyProvider.java

/**
* Instantiates a new hierarchy provider impl.
*
* @param dataSource the data source/*from ww  w  .ja v a 2 s  .c  o m*/
*/
public AbstractHierarchyProvider(DataSource dataSource) {
    try {
        this.connection = dataSource.getConnection();
        initialiseStatements();
    } catch (SQLException e) {
        logger.warn("Error obtaining connection from data source. " + "Nested exception is : "
                + e.fillInStackTrace());
    }
}