Example usage for org.apache.commons.validator GenericValidator isBlankOrNull

List of usage examples for org.apache.commons.validator GenericValidator isBlankOrNull

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Introduction

In this page you can find the example usage for org.apache.commons.validator GenericValidator isBlankOrNull.

Prototype

public static boolean isBlankOrNull(String value)

Source Link

Document

Checks if the field isn't null and length of the field is greater than zero not including whitespace.

Usage

From source file:us.mn.state.health.lims.analysisexchange.daoimpl.AnalysisExchangeDAOImpl.java

@SuppressWarnings("unchecked")
public AnalysisExchange getAnalysisExchangeByInternalAnalysisId(String internalAnalysisId)
        throws LIMSRuntimeException {
    AnalysisExchange result = null;/*from w  ww  . ja va  2s. co  m*/
    if (!GenericValidator.isBlankOrNull(internalAnalysisId)) {
        try {
            String sql = "from AnalysisExchange ae where ae.internalAnalysisId = :internalAnalysisId";

            org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql);
            query.setInteger("internalAnalysisId", Integer.parseInt(internalAnalysisId));
            List<AnalysisExchange> list = query.list();
            if (list.size() > 0) {
                result = list.get(0);
            }
            //closeSession();

        } catch (Exception e) {
            handleException(e, "getAnalysisExchangeByInternalAnalysisId");
            LogEvent.logError("AnalysisExchangeDAOImpl", "getAnalysisExchangeByInternalAnalysisId()",
                    e.toString());
        }
    }

    return result;
}

From source file:us.mn.state.health.lims.analyzerimport.action.AnalyzerImportServlet.java

@Override
protected void doPost(HttpServletRequest request, HttpServletResponse response)
        throws ServletException, IOException {

    String password = null;//from w ww. j  ava  2s  . com
    String user = null;
    AnalyzerReader reader = null;
    boolean fileRead = false;

    InputStream stream = null;

    try {
        ServletFileUpload upload = new ServletFileUpload();

        FileItemIterator iterator = upload.getItemIterator(request);
        while (iterator.hasNext()) {
            FileItemStream item = iterator.next();
            stream = item.openStream();

            String name = null;

            if (item.isFormField()) {

                if (PASSWORD.equals(item.getFieldName())) {
                    password = streamToString(stream);
                } else if (USER.equals(item.getFieldName())) {
                    user = streamToString(stream);
                }

            } else {

                name = item.getName();

                reader = AnalyzerReaderFactory.getReaderFor(name);

                if (reader != null) {
                    fileRead = reader.readStream(new InputStreamReader(stream));
                }
            }

            stream.close();
        }
    } catch (Exception ex) {
        throw new ServletException(ex);
    } finally {
        if (stream != null) {
            try {
                stream.close();
            } catch (IOException e) {
                //   LOG.warning(e.toString());
            }
        }
    }

    if (GenericValidator.isBlankOrNull(user) || GenericValidator.isBlankOrNull(password)) {
        response.getWriter().print("missing user");
        response.setStatus(HttpServletResponse.SC_PARTIAL_CONTENT);
        return;
    }

    if (!userValid(user, password)) {
        response.getWriter().print("invalid user/password");
        response.setStatus(HttpServletResponse.SC_FORBIDDEN);
        return;
    }

    if (fileRead) {
        boolean successful = reader.insertAnalyzerData(systemUserId);

        if (successful) {
            response.getWriter().print("success");
            response.setStatus(HttpServletResponse.SC_OK);
            return;
        } else {
            response.getWriter().print(reader.getError());
            response.setStatus(HttpServletResponse.SC_INTERNAL_SERVER_ERROR);
        }

    } else {
        response.getWriter().print(reader.getError());
        response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
        return;
    }

}

From source file:us.mn.state.health.lims.analyzerimport.action.AnalyzerTestNameUpdateAction.java

private void validateAnalyzerAndTestName(String analyzerId, String analyzerTestName, String testId,
        ActionMessages errors) {/*from   ww w .  j  av a2  s . co  m*/
    //This is not very efficient but this is a very low usage action
    if (GenericValidator.isBlankOrNull(analyzerId) || GenericValidator.isBlankOrNull(analyzerTestName)
            || GenericValidator.isBlankOrNull(testId)) {
        errors.add(ActionErrors.GLOBAL_MESSAGE, new ActionError("error.all.required"));
        return;
    }

    AnalyzerTestMappingDAO mappingDAO = new AnalyzerTestMappingDAOImpl();
    List<AnalyzerTestMapping> testMappingList = mappingDAO.getAllAnalyzerTestMappings();

    for (AnalyzerTestMapping testMapping : testMappingList) {
        if (analyzerId.equals(testMapping.getAnalyzerId())
                && analyzerTestName.equals(testMapping.getAnalyzerTestName())) {
            errors.add(ActionErrors.GLOBAL_MESSAGE, new ActionError("error.analyzer.test.name.duplicate"));
        }
    }
}

From source file:us.mn.state.health.lims.analyzerimport.analyzerreaders.CobasC311Reader.java

private AnalyzerResults createAnalyzerResult(String analyzerTestName, String[] fields, int index,
        String accessionNumber, Timestamp orderTimeStamp) {

    if (fields.length <= index) {
        return null;
    }//from   w  w w . j av a  2s  .c  o m

    String result = fields[index].trim();

    if (GenericValidator.isBlankOrNull(result)) {
        return null;
    }

    AnalyzerResults analyzerResults = new AnalyzerResults();

    MappedTestName mappedName = AnalyzerTestNameCache.instance().getMappedTest(AnalyzerTestNameCache.COBAS_C311,
            analyzerTestName);

    if (mappedName == null) {
        mappedName = AnalyzerTestNameCache.instance().getEmptyMappedTestName(AnalyzerTestNameCache.COBAS_C311,
                analyzerTestName);
    }

    analyzerResults.setAnalyzerId(mappedName.getAnalyzerId());
    analyzerResults.setResult(adjustResult(analyzerTestName, result));
    analyzerResults.setCompleteDate(orderTimeStamp);
    analyzerResults.setTestId(mappedName.getTestId());
    analyzerResults.setIsControl(
            accessionNumber.length() < 9 || !VALID_PREFIXES.contains(accessionNumber.subSequence(0, 3)));
    analyzerResults.setTestName(mappedName.getOpenElisTestName());
    analyzerResults.setResultType("N");

    analyzerResults.setAccessionNumber(accessionNumber);

    return analyzerResults;
}

From source file:us.mn.state.health.lims.analyzerimport.analyzerreaders.CobasReader.java

public boolean insert(List<String> lines, String currentUserId) {
    boolean successful = true;

    if (lines == null) {
        return true;
    }/*from w  w w .ja  v  a  2  s  . c  o m*/

    if (GenericValidator.isBlankOrNull(currentUserId)) {
        return false;
    }

    List<AnalyzerResults> results = new ArrayList<AnalyzerResults>();
    List<AnalyzerResults> notMatchedResults = new ArrayList<AnalyzerResults>();

    Map<String, AnalyzerResults[]> accessionToResultMap = new HashMap<String, AnalyzerResults[]>();
    List<String> accessionOrder = new ArrayList<String>();

    for (String line : lines) {
        createAnalyzerResultFromLine(line, accessionToResultMap, accessionOrder, notMatchedResults);
    }

    for (String accessionNumber : accessionOrder) {

        AnalyzerResults[] resultSet = accessionToResultMap.get(accessionNumber);

        for (int i = 0; i < 4; i++) {
            if (resultSet[i] != null) {
                addValueToResults(results, resultSet[i]);
            }
        }

        for (AnalyzerResults analyzerResult : notMatchedResults) {
            addValueToResults(results, analyzerResult);
        }
    }

    if (results.size() > 0) {

        Transaction tx = HibernateProxy.beginTransaction();

        try {
            persistResults(results, currentUserId);
            tx.commit();
        } catch (LIMSRuntimeException lre) {
            tx.rollback();
            successful = false;
        } finally {
            HibernateProxy.closeSession();
        }
    }

    return successful;
}

From source file:us.mn.state.health.lims.analyzerimport.analyzerreaders.EvolisReader.java

private void addAnalyzerResultFromLine(List<AnalyzerResults> results, String line) {
    line = line.replace("\"", "").replace(DELIMITER, ":");
    String[] fields = line.split(":");

    String analyzerAccessionNumber = fields[Id];

    if (fields.length == 7 && !GenericValidator.isBlankOrNull(analyzerAccessionNumber)
            && analyzerAccessionNumber.length() > 6 && fields[assay].length() > 5) {

        MappedTestName mappedName = AnalyzerTestNameCache.instance().getMappedTest(AnalyzerTestNameCache.EVOLIS,
                fields[assay]);//from   w ww .ja va2 s .c  o m
        AnalyzerResults analyzerResults = new AnalyzerResults();
        analyzerResults.setAnalyzerId(mappedName.getAnalyzerId());
        analyzerResults.setResult(getDictioanryValueForResult(fields[result]));
        analyzerResults.setResultType("D");
        analyzerResults.setCompleteDate(new Timestamp(new Date().getTime()));
        analyzerResults.setTestId(mappedName.getTestId());
        analyzerResults.setAccessionNumber(analyzerAccessionNumber);
        analyzerResults.setTestName(mappedName.getOpenElisTestName());
        analyzerResults.setIsControl(false);
        results.add(analyzerResults);

        AnalyzerResults resultFromDB = readerUtil.createAnalyzerResultFromDB(analyzerResults);
        if (resultFromDB != null) {
            results.add(resultFromDB);
        }

    }
}

From source file:us.mn.state.health.lims.analyzerimport.analyzerreaders.FacscaliburReader.java

private void addAnalyzerResultFromLine(List<AnalyzerResults> results, String line) {
    String[] fields = line.split(DELIMITER);

    AnalyzerReaderUtil readerUtil = new AnalyzerReaderUtil();
    String analyzerAccessionNumber = fields[Sample_ID];

    String date = fields[Collection_Date];

    for (int i = 0; i < testNameIndex.length; i++) {
        if (!GenericValidator.isBlankOrNull(testNameIndex[i])) {
            MappedTestName mappedName = AnalyzerTestNameCache.instance()
                    .getMappedTest(AnalyzerTestNameCache.FACSCALIBUR, testNameIndex[i]);

            if (mappedName == null) {
                mappedName = AnalyzerTestNameCache.instance()
                        .getEmptyMappedTestName(AnalyzerTestNameCache.FACSCALIBUR, testNameIndex[i]);
            }/*from   www.  ja  v  a 2  s.c  o m*/

            AnalyzerResults analyzerResults = new AnalyzerResults();

            analyzerResults.setAnalyzerId(mappedName.getAnalyzerId());

            String result = fields[i];

            analyzerResults.setResult(result);
            analyzerResults.setUnits(unitsIndex[i]);
            String dateTime = date;
            Timestamp timestamp = getTimestampFromDate(dateTime);
            analyzerResults.setCompleteDate(timestamp);
            analyzerResults.setTestId(mappedName.getTestId());
            analyzerResults.setAccessionNumber(analyzerAccessionNumber);
            analyzerResults.setTestName(mappedName.getOpenElisTestName());

            if (analyzerAccessionNumber != null) {
                analyzerResults.setIsControl(analyzerAccessionNumber.startsWith(CONTROL_ACCESSION_PREFIX));
            } else {
                analyzerResults.setIsControl(false);
            }

            results.add(analyzerResults);

            AnalyzerResults resultFromDB = readerUtil.createAnalyzerResultFromDB(analyzerResults);
            if (resultFromDB != null) {
                results.add(resultFromDB);
            }
        }
    }
}

From source file:us.mn.state.health.lims.analyzerimport.analyzerreaders.FACSCantoReader.java

private void addAnalyzerResultFromLine(List<AnalyzerResults> results, String line) {
    String[] fields = StringUtil.separateCSVWithMixedEmbededQuotes(line);

    //This insures that the row has not been truncated
    if (fields.length < maxViewedIndex) {
        return;/*www  . jav  a 2 s . com*/
    }

    AnalyzerReaderUtil readerUtil = new AnalyzerReaderUtil();
    String analyzerAccessionNumber = fields[Sample_ID].replace("\"", "");
    analyzerAccessionNumber = StringUtil.strip(analyzerAccessionNumber, " ");

    String date = fields[Date_Analyzed].replace("\"", "");

    //this is sort of dumb, we have the indexes we are interested in
    for (int i = 0; i < testNameIndex.length; i++) {
        if (!GenericValidator.isBlankOrNull(testNameIndex[i])) {
            MappedTestName mappedName = AnalyzerTestNameCache.instance()
                    .getMappedTest(AnalyzerTestNameCache.FACSCANTO, testNameIndex[i].replace("\"", ""));

            if (mappedName == null) {
                mappedName = AnalyzerTestNameCache.instance().getEmptyMappedTestName(
                        AnalyzerTestNameCache.FACSCANTO, testNameIndex[i].replace("\"", ""));
            }

            AnalyzerResults analyzerResults = new AnalyzerResults();

            analyzerResults.setAnalyzerId(mappedName.getAnalyzerId());

            String result = fields[i].replace("\"", "");
            result = roundTwoDigits(result);
            analyzerResults.setResult(result);
            analyzerResults.setUnits(unitsIndex[i]);

            analyzerResults.setCompleteDate(
                    DateUtil.convertStringDateToTimestampWithPatternNoLocale(date, DATE_PATTERN));
            //analyzerResults.setCompleteTime(DateUtil.convertStringDateToTimestamp(date));
            analyzerResults.setTestId(mappedName.getTestId());
            analyzerResults.setAccessionNumber(analyzerAccessionNumber);
            analyzerResults.setTestName(mappedName.getOpenElisTestName());

            if (analyzerAccessionNumber != null) {
                analyzerResults.setIsControl(analyzerAccessionNumber.startsWith(CONTROL_ACCESSION_PREFIX));
            } else {
                analyzerResults.setIsControl(false);
            }

            results.add(analyzerResults);

            AnalyzerResults resultFromDB = readerUtil.createAnalyzerResultFromDB(analyzerResults);
            if (resultFromDB != null) {
                results.add(resultFromDB);
            }
        }
    }
}

From source file:us.mn.state.health.lims.analyzerimport.analyzerreaders.SysmexReader.java

private void addAnalyzerResultFromLine(List<AnalyzerResults> results, String line) {
    String[] fields = line.split(DELIMITER);

    AnalyzerReaderUtil readerUtil = new AnalyzerReaderUtil();
    String analyzerAccessionNumber = fields[ACCESSION];
    Timestamp timestamp = DateUtil.convertStringDateToTimestampWithPattern(fields[DATE] + " " + fields[TIME],
            DATE_PATTERN);//from  www  . j a v a2 s  .  c  om

    List<AnalyzerResults> readOnlyResults = new ArrayList<AnalyzerResults>();

    //the reason for the indirection is to get the order of tests correct
    for (int i = 0; i < orderedTestIndexs.length; i++) {
        int testIndex = orderedTestIndexs[i];

        if (!GenericValidator.isBlankOrNull(testNameIndex[testIndex])) {
            MappedTestName mappedName = AnalyzerTestNameCache.instance()
                    .getMappedTest(AnalyzerTestNameCache.SYSMEX_XT2000_NAME, testNameIndex[testIndex]);

            if (mappedName == null) {
                mappedName = AnalyzerTestNameCache.instance().getEmptyMappedTestName(
                        AnalyzerTestNameCache.SYSMEX_XT2000_NAME, testNameIndex[testIndex]);
            }

            AnalyzerResults analyzerResults = new AnalyzerResults();

            analyzerResults.setAnalyzerId(mappedName.getAnalyzerId());

            double result = Double.NaN;

            try {
                result = Double.parseDouble(fields[testIndex]) / scaleIndex[testIndex];
            } catch (NumberFormatException nfe) {
                //no-op -- defaults to NAN
            }

            analyzerResults.setResult(String.valueOf(result));
            analyzerResults.setUnits(unitsIndex[testIndex]);
            analyzerResults.setCompleteDate(timestamp);
            analyzerResults.setTestId(mappedName.getTestId());
            analyzerResults.setAccessionNumber(analyzerAccessionNumber);
            analyzerResults.setTestName(mappedName.getOpenElisTestName());
            analyzerResults.setReadOnly(readOnlyIndex[testIndex]);

            if (analyzerAccessionNumber != null) {
                analyzerResults.setIsControl(analyzerAccessionNumber.startsWith(CONTROL_ACCESSION_PREFIX));
            } else {
                analyzerResults.setIsControl(false);
            }

            if (analyzerResults.isReadOnly()) {
                readOnlyResults.add(analyzerResults);
            } else {
                results.add(analyzerResults);
            }

            AnalyzerResults resultFromDB = readerUtil.createAnalyzerResultFromDB(analyzerResults);
            if (resultFromDB != null) {
                results.add(resultFromDB);
            }
        }
    }

    results.addAll(readOnlyResults);
}

From source file:us.mn.state.health.lims.analyzerimport.valueholder.AnalyzerTestMapping.java

public String getUniqueIdentifyer() {
    if (GenericValidator.isBlankOrNull(uniqueIdentifyer)) {
        uniqueIdentifyer = getAnalyzerId() + "-" + getAnalyzerTestName();
    }//from   w  w w  .j a v  a 2  s .c  o m

    return uniqueIdentifyer;
}