Java tutorial
/** * Exhibit A - UIRF Open-source Based Public Software License. * * The contents of this file are subject to the UIRF Open-source Based Public * Software License(the "License"); you may not use this file except in * compliance with the License. You may obtain a copy of the License at * openelis.uhl.uiowa.edu * * Software distributed under the License is distributed on an "AS IS" basis, * WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for * the specific language governing rights and limitations under the License. * * The Original Code is OpenELIS code. * * The Initial Developer of the Original Code is The University of Iowa. * Portions created by The University of Iowa are Copyright 2006-2008. All * Rights Reserved. * * Contributor(s): ______________________________________. * * Alternatively, the contents of this file marked "Separately-Licensed" may be * used under the terms of a UIRF Software license ("UIRF Software License"), in * which case the provisions of a UIRF Software License are applicable instead * of those above. */ package org.openelis.scriptlet.ms.firstInteg; import static org.openelis.scriptlet.ms.Constants.*; import java.util.ArrayList; import java.util.HashMap; import java.util.logging.Level; import org.openelis.constants.Messages; import org.openelis.domain.AnalysisQaEventViewDO; import org.openelis.domain.AnalysisViewDO; import org.openelis.domain.AnalyteParameterViewDO; import org.openelis.domain.Constants; import org.openelis.domain.DictionaryDO; import org.openelis.domain.QaEventDO; import org.openelis.domain.ResultViewDO; import org.openelis.manager.AnalyteParameterManager1; import org.openelis.manager.SampleManager1; import org.openelis.manager.TestManager; import org.openelis.meta.SampleMeta; import org.openelis.scriptlet.SampleSO; import org.openelis.scriptlet.SampleSO.Action_Before; import org.openelis.scriptlet.ms.Constants.Interpretation; import org.openelis.scriptlet.ms.ScriptletProxy; import org.openelis.scriptlet.ms.Util; import org.openelis.scriptlet.ms.firstTri.Compute; import org.openelis.scriptlet.ms.firstTri.Test; import org.openelis.ui.common.DataBaseUtil; import org.openelis.ui.common.Datetime; import org.openelis.ui.common.FormErrorCaution; import org.openelis.ui.common.FormErrorException; import org.openelis.ui.common.NotFoundException; import org.openelis.ui.common.data.QueryData; import org.openelis.ui.scriptlet.ScriptletInt; import org.openelis.ui.scriptlet.ScriptletObject.Status; import org.openelis.utilcommon.ResultFormatter; import org.openelis.utilcommon.ResultHelper; import com.google.gwt.i18n.shared.DateTimeFormat; import com.google.gwt.i18n.shared.DefaultDateTimeFormatInfo; /** * The scriptlet for "ms 1st integ (Sample 1 Maternal Integrated Screen)" test. * It uses a compute engine to calculate the MoMs for various tests such as NT * and risks and interpretations for various disorders such as Downs. The * computations are done based on patient information and results entered by the * analyst. If the results are overridden, the MoMs, risks and interpretations * are blanked. The computations are done as soon as the user changes any of the * values or on completing/releasing the analysis. */ public class Scriptlet implements ScriptletInt<SampleSO> { private ScriptletProxy proxy; private Integer analysisId; private Compute compute; private ArrayList<String> changes; private HashMap<String, HashMap<String, ResultViewDO>> resultMap; private AnalyteParameterManager1 testParamManager, provParamManager; private static DateTimeFormat dateFormatter; private static boolean initialized; private static Integer YES, NO, UNIT_MM, UNIT_POUNDS, UNIT_YEARS, INT_POSITIVE, INT_NEGATIVE, INT_UNKNOWN, ACTION_US_DIAG, ACTION_NO_ACTION, ACTION_RISK_NOT_CALC; private static String YES_STR; private static final String INTEGRATE_TEST_NAME = "ms integrate", METHOD_NAME = "eia"; private enum Risk { NT, DOWNS, T18 } public Scriptlet(ScriptletProxy proxy, Integer analysisId) { this.proxy = proxy; this.analysisId = analysisId; proxy.log(Level.FINE, "Initializing MS1stIntegScriptlet1", null); try { if (!initialized) { initialized = true; YES = proxy.getDictionaryBySystemName("yes").getId(); UNIT_MM = proxy.getDictionaryBySystemName("millimeters").getId(); UNIT_POUNDS = proxy.getDictionaryBySystemName("pounds_local").getId(); UNIT_YEARS = proxy.getDictionaryBySystemName("years_local").getId(); INT_POSITIVE = proxy.getDictionaryBySystemName("positive").getId(); INT_NEGATIVE = proxy.getDictionaryBySystemName("negative").getId(); INT_UNKNOWN = proxy.getDictionaryBySystemName("unknown").getId(); ACTION_US_DIAG = proxy.getDictionaryBySystemName("ms_rec_action_us_diag").getId(); ACTION_NO_ACTION = proxy.getDictionaryBySystemName("ms_rec_action_no_action").getId(); ACTION_RISK_NOT_CALC = proxy.getDictionaryBySystemName("ms_rec_action_risk_not_calc").getId(); YES_STR = YES.toString(); /* * the formatter that converts from string to date */ dateFormatter = new DateTimeFormat(Messages.get().datePattern(), new DefaultDateTimeFormatInfo()) { }; } proxy.log(Level.FINE, "Initialized MS1stIntegScriptlet1", null); } catch (Exception e) { initialized = false; proxy.log(Level.SEVERE, "Failed to initialize dictionary constants", e); } } @Override public SampleSO run(SampleSO data) { Integer accession; ArrayList<Integer> accList; SampleManager1 sm; AnalysisViewDO ana; ResultViewDO res; ArrayList<SampleManager1> sms; proxy.log(Level.FINE, "In MS1stIntegScriptlet1.run", null); changes = data.getChanges(); sm = data.getManager(); ana = (AnalysisViewDO) sm.getObject(Constants.uid().getAnalysis(analysisId)); if (ana == null || Constants.dictionary().ANALYSIS_CANCELLED.equals(ana.getStatusId()) || changes.size() == 0) return data; accession = sm.getSample().getAccessionNumber(); /* * manage result changed, the risks needing to be recomputed, the * analysis getting completed or released, a qa event added/removed or * collection date, patient's birth date or patient's race changed */ if (data.getActionBefore().contains(Action_Before.RESULT)) { res = (ResultViewDO) sm.getObject(data.getUid()); if (!analysisId.equals(res.getAnalysisId())) return data; } else if (data.getActionBefore().contains(Action_Before.COMPLETE) || data.getActionBefore().contains(Action_Before.RELEASE) || changes.contains(SampleMeta.getAnalysisStartedDate())) { ana = (AnalysisViewDO) sm.getObject(data.getUid()); if (!analysisId.equals(ana.getId())) return data; } else if (data.getActionBefore().contains(Action_Before.UNRELEASE)) { ana = (AnalysisViewDO) sm.getObject(data.getUid()); if (!analysisId.equals(ana.getId())) return data; /* * don't let the analysis be unreleased if a released 2nd tri * integrate analysis has this sample as its 1st tri sample */ try { sms = fetchSecondTriSamples(sm); if (sms != null && sms.size() > 0) { accList = new ArrayList<Integer>(); for (SampleManager1 sm1 : sms) accList.add(sm1.getSample().getAccessionNumber()); data.setStatus(Status.FAILED); data.addException( new FormErrorException(Messages.get().analysis_cantUnreleaseMS1stIntegException( accession, ana.getTestName(), ana.getMethodName(), INTEGRATE_TEST_NAME, METHOD_NAME, DataBaseUtil.concatWithSeparator(accList, ", ")))); } } catch (NotFoundException e) { // ignore } catch (Exception e) { data.setStatus(Status.FAILED); data.addException(new FormErrorException( DataBaseUtil.concatWithSeparator(Messages.get().sample_accessionAnalysisPrefix(accession, ana.getTestName(), ana.getMethodName()), " ", e.getMessage()))); } } else if (!data.getActionBefore().contains(Action_Before.QA) && !data.getActionBefore().contains(Action_Before.PATIENT) && !data.getActionBefore().contains(Action_Before.RECOMPUTE) && !data.getActionBefore().contains(Action_Before.ANALYSIS) && !changes.contains(SampleMeta.getCollectionDate()) && !changes.contains(SampleMeta.getReceivedDate()) && !changes.contains(SampleMeta.getClinicalPatientBirthDate()) && !changes.contains(SampleMeta.getClinicalPatientRaceId())) { return data; } /* * check for released here because the analysis would be released even * on getting unreleased (see the block for UNRELEASE) */ if (Constants.dictionary().ANALYSIS_RELEASED.equals(ana.getStatusId())) return data; /* * patient must be present for doing computations; it may not be present * if, for example, this test is added to a PT sample */ if (sm.getSampleClinical() == null || sm.getSampleClinical().getPatientId() == null) { /* * for display */ if (accession == null) accession = 0; data.setStatus(Status.FAILED); data.addException(new FormErrorException(Messages.get().analysis_patientRequiredForComputeException( accession, ana.getTestName(), ana.getMethodName()))); return data; } setRisks(data, ana); return data; } /** * Fetches the sample(s) where the patient is the same as the passed sample * and where it has been set as the 1st trimester sample on a released 2nd * trimester integrated analysis */ private ArrayList<SampleManager1> fetchSecondTriSamples(SampleManager1 sm) throws Exception { QueryData field; ArrayList<QueryData> fields; fields = new ArrayList<QueryData>(); field = new QueryData(); field.setKey(SampleMeta.getResultAnalyteExternalId()); field.setType(QueryData.Type.STRING); field.setQuery("accession_1st_tri"); fields.add(field); field = new QueryData(); field.setKey(SampleMeta.getResultValue()); field.setType(QueryData.Type.STRING); field.setQuery(sm.getSample().getAccessionNumber().toString()); fields.add(field); return Util.fetchRelatedSamples(INTEGRATE_TEST_NAME, METHOD_NAME, sm, fields, proxy); } /** * Initializes the map containing the ResultViewDOs for various analytes; * calculates/copies result values based on sample and patient fields such * as birth date or race; sets values in the compute engine from results; * sets the values computed by the engine in results and formats them */ private void setRisks(SampleSO data, AnalysisViewDO ana) { Integer accession; Exception lastEx; proxy.log(Level.FINE, "In MS1stIntegScriptlet1.setRisks", null); try { initializeResultMap(data, ana); setBirthDate(data, ana); setMaternalWeight(data, ana); setRaceBlack(data, ana); setComputeValues(data, ana); compute.compute(); setResultValues(data, ana); formatValues(data, ana); setUnits(data, ana); addRemoveQaEvents(data, ana); /* * if the compute engine encountered an error, make it available to * be shown to the user; add the accession number to the error * message because the engine doesn't know that information */ lastEx = compute.getLastException(); if (lastEx != null) { accession = data.getManager().getSample().getAccessionNumber(); /* * for display */ if (accession == null) accession = 0; data.setStatus(Status.FAILED); data.addException(new FormErrorException( DataBaseUtil.concatWithSeparator(Messages.get().sample_accessionAnalysisPrefix(accession, ana.getTestName(), ana.getMethodName()), " ", lastEx.getMessage()))); } } catch (Exception e) { data.setStatus(Status.FAILED); data.addException(e); } } /** * Initialize a hash map where the key is the external id of a row analyte * and the value is another hash map containing the ResultViewDOs for all * analytes in the row; the key in the second map is the external id of a * row or column analyte and the value is the ResultVIewDO for that analyte; * these maps are used to quickly lookup ResultViewDOs for getting or * setting their value */ private void initializeResultMap(SampleSO data, AnalysisViewDO ana) throws Exception { int i, j; ResultViewDO res; SampleManager1 sm; HashMap<String, ResultViewDO> map; proxy.log(Level.FINE, "Creating hashmap of results", null); sm = data.getManager(); resultMap = new HashMap<String, HashMap<String, ResultViewDO>>(); map = null; for (i = 0; i < sm.result.count(ana); i++) { for (j = 0; j < sm.result.count(ana, i); j++) { res = sm.result.get(ana, i, j); if ("N".equals(res.getIsColumn())) { map = resultMap.get(res.getAnalyteExternalId()); if (map == null) { map = new HashMap<String, ResultViewDO>(); resultMap.put(res.getAnalyteExternalId(), map); } } map.put(res.getAnalyteExternalId(), res); } } } /** * Sets the birth date value from the egg donor's age or from patient's * birth date */ private void setBirthDate(SampleSO data, AnalysisViewDO ana) throws Exception { ResultViewDO res, resAge, resBirth; ResultFormatter rf; TestManager tm; SampleManager1 sm; Datetime bd; proxy.log(Level.FINE, "Setting birth date from either the egg's age or from patient's birth date", null); sm = data.getManager(); resBirth = getResult("birth"); tm = (TestManager) data.getCache().get(Constants.uid().getTest(ana.getTestId())); rf = tm.getFormatter(); /* * find out if egg's age was changed or egg donor was changed from "Yes" * to "No" or vice-versa */ if (data.getActionBefore().contains(Action_Before.RESULT)) { res = (ResultViewDO) sm.getObject(data.getUid()); if ("eggs_age".equals(res.getAnalyteExternalId()) || "egg_donor".equals(res.getAnalyteExternalId())) { /* * if it's an egg donor, compute and set birth date from egg's * age; otherwise wipe egg's age; set birth date value as either * the computed value or the patient's birth date */ resAge = getResult("eggs_age"); if (YES_STR.equals(getValue("egg_donor"))) { bd = Util.getBirthDate(getDoubleValue(resAge, sm, ana, false), proxy, data, ana); } else { bd = null; setValue(resAge, null, rf, false, data, ana); } setValue(resBirth, bd, rf, false, data, ana); } } if (resBirth.getValue() == null && sm.getSampleClinical().getPatient().getBirthDate() != null) { bd = sm.getSampleClinical().getPatient().getBirthDate(); setValue(resBirth, bd, rf, false, data, ana); } /* * if the result value for birth date doesn't match the patient's birth * date, add a caution to inform the user */ if (DataBaseUtil.isDifferentYD(getDateValue(resBirth), sm.getSampleClinical().getPatient().getBirthDate())) addResultNotMatchCaution(resBirth.getAnalyte(), data, ana); } /** * Validates the maternal weight entered and converts it to lbs from kgs if * it contains "k" */ private void setMaternalWeight(SampleSO data, AnalysisViewDO ana) throws Exception { double multiplier; String value; Double weight; ResultViewDO res; TestManager tm; /* * do something only if a result was changed, that result was maternal * weight and its value is not null */ if (data.getActionBefore().contains(Action_Before.RESULT)) { res = (ResultViewDO) data.getManager().getObject(data.getUid()); value = res.getValue(); if ("mat_weight".equals(res.getAnalyteExternalId()) && value != null) { proxy.log(Level.FINE, "Formatting and resetting maternal weight", null); /* * convert from kgs to lbs if weight contains "k" or "kg" */ tm = (TestManager) data.getCache().get(Constants.uid().getTest(ana.getTestId())); try { multiplier = 1.0; if (value.endsWith("k")) { value = value.substring(0, value.length() - 1); multiplier = 2.204; } else if (value.endsWith("kg")) { value = value.substring(0, value.length() - 2); multiplier = 2.204; } weight = new Double(value) * multiplier; setValue(res, weight, tm.getFormatter(), false, data, ana); } catch (NumberFormatException e) { throw getValueInvalidException(res, data.getManager(), ana); } } } } /** * Sets the value of "Maternal Race Black" to "Yes" if the patient's race is * black even if it's mixed race; otherwise sets the value to "No" */ private void setRaceBlack(SampleSO data, AnalysisViewDO ana) throws Exception { boolean raceblack; Integer value, raceId; DictionaryDO dict; ResultViewDO res; TestManager tm; /* * race is black if the system name contains a "b" e.g. "race_b" or * "race_wb", otherwise not; change 'maternal race black' if either the * patient's race was changed or if the analyte's value is not set */ raceId = data.getManager().getSampleClinical().getPatient().getRaceId(); raceblack = false; res = getResult("mat_race_black"); if (raceId != null) { dict = proxy.getDictionaryById(raceId); raceblack = dict.getSystemName() != null && dict.getSystemName().contains("b"); } if (changes.contains(SampleMeta.getClinicalPatientRaceId()) && res.getValue() == null) { proxy.log(Level.FINE, "Setting 'maternal race black' from the sample", null); value = raceblack ? YES : NO; tm = (TestManager) data.getCache().get(Constants.uid().getTest(ana.getTestId())); setValue(res, value, tm.getFormatter(), true, data, ana); } /* * if the result value for 'maternal race black' isn't consistent with * the patient, add a caution to inform the user */ value = getIntegerValue(res, data.getManager(), ana); if ((!raceblack && YES.equals(value)) || (raceblack && !YES.equals(value))) addResultNotMatchCaution(res.getAnalyte(), data, ana); } /** * Set values in the compute engine from the passed sample, analysis, * results of specific analytes and analyte parameters */ private void setComputeValues(SampleSO data, AnalysisViewDO ana) throws Exception { SampleManager1 sm; ResultViewDO res; HashMap<Integer, AnalyteParameterViewDO> provParamMap, testParamMap; proxy.log(Level.FINE, "Setting values in the compute engine", null); /* * set sample/analysis level info */ sm = data.getManager(); compute = new Compute(); compute.setIsOverridden(sm.qaEvent.hasType(Constants.dictionary().QAEVENT_OVERRIDE) || sm.qaEvent.hasType(ana, Constants.dictionary().QAEVENT_OVERRIDE)); compute.setIsIntegrated(true); compute.setEnteredDate(sm.getSample().getEnteredDate()); compute.setCollectionDate(sm.getSample().getCollectionDate()); /* * set patient info */ compute.setBirthDate(getDateValue(getValue("birth"))); compute.setUltrasoundDate(getDateValue(getValue("ultrasound"))); compute.setWeight(getDoubleValue(getResult("mat_weight"), sm, ana, false)); compute.setCRL(getIntegerValue(getResult("crl"), sm, ana)); /* * if the sonographer was changed or if this analysis is getting * completed, released or risks need to be recomputed, get the * sonographer's analyte parameters; they provide p-values for "NT" */ try { if (data.getActionBefore().contains(Action_Before.RESULT)) { res = (ResultViewDO) sm.getObject(data.getUid()); if ("sonographer".equals(res.getAnalyteExternalId())) provParamManager = getSonographerParams(sm, ana); } if (provParamManager == null || data.getActionBefore().contains(Action_Before.COMPLETE) || data.getActionBefore().contains(Action_Before.RELEASE)) { provParamManager = getSonographerParams(sm, ana); } } catch (NotFoundException e) { /* * analyte parameters were not found; if this exception is not * handled here, an error with the message "null" is shown, which is * not very helpful; a more descriptive error will be added later if * some computation(s) can't be done because of missing p-values */ } provParamMap = Util.getParameters(provParamManager, data, ana, null); /* * get this test's analyte parameters; they provide p-values for * analytes other than "NT" e.g. "HCG" */ if (testParamManager == null) { try { testParamManager = proxy.fetchParameters(ana.getTestId(), Constants.table().TEST); } catch (NotFoundException e) { /* * see the comment in the previous catch block */ } } testParamMap = Util.getParameters(testParamManager, data, ana); /* * set p-values and results from the instrument for "NT" etc. */ setTestValues(compute.getNT(), "nt_mom", provParamMap, sm, ana); setTestValues(compute.getPAPPA(), "papp_a_mom", testParamMap, sm, ana); setTestValues(compute.getHCG(), "hcg_mom", testParamMap, sm, ana); } /** * Sets values such as MoMs, risks, cutoffs, interpretations etc. in the * results from the compute engine */ private void setResultValues(SampleSO data, AnalysisViewDO ana) throws Exception { Integer gestAge; Double ntResult; Datetime collected; TestManager tm; ResultFormatter rf; proxy.log(Level.FINE, "Setting values in the results from the compute engine", null); tm = (TestManager) data.getCache().get(Constants.uid().getTest(ana.getTestId())); rf = tm.getFormatter(); setValue(getResult("mat_age_at_delivery"), compute.getMothersDueAge(), rf, false, data, ana); /* * copy the NT intrument result to the reportable analyte; set MoMs */ ntResult = getDoubleValue(getResult("nt_mom", "result"), data.getManager(), ana, false); setValue(getResult("nt_measurement"), ntResult, rf, false, data, ana); setValue(getResult("nt_mom"), compute.getNT().getMom(), rf, false, data, ana); setValue(getResult("papp_a_mom"), compute.getPAPPA().getMom(), rf, false, data, ana); setValue(getResult("hcg_mom"), compute.getHCG().getMom(), rf, false, data, ana); /* * risks, screening cutoffs(limits), interpretations, recommended * actions; nt */ setInterpretation("nt_mom", compute.getInterpretationNT(), Risk.NT, rf, data, ana); setRecommendedAction("nt_mom", compute.getInterpretationNT(), rf, data, ana); /* * downs */ setRisk("downs_risk", compute.getRiskSignDowns(), compute.getRiskDowns(), rf, data, ana); setScreeningCutoff("downs_risk", compute.getLimitDowns(), rf, data, ana); setInterpretation("downs_risk", compute.getInterpretationDowns(), Risk.DOWNS, rf, data, ana); setRecommendedAction("downs_risk", compute.getInterpretationDowns(), rf, data, ana); /* * t18 */ setRisk("trisomy_18_risk", compute.getRiskSignTrisomy18(), compute.getRiskTrisomy18(), rf, data, ana); setScreeningCutoff("trisomy_18_risk", compute.getLimitTrisomy18(), rf, data, ana); setInterpretation("trisomy_18_risk", compute.getInterpretationTrisomy18(), Risk.T18, rf, data, ana); setRecommendedAction("trisomy_18_risk", compute.getInterpretationTrisomy18(), rf, data, ana); /* * gestational age in weeks and days */ gestAge = compute.getGestAge(); setValue(getResult("gest_age"), Util.getWeeksAndDays(gestAge), rf, false, data, ana); /* * the dates between which the second trimester sample must be collected */ collected = data.getManager().getSample().getCollectionDate(); setValue(getResult("coll_2nd_sample_from"), getSecondCollDate(collected, 105, gestAge), rf, false, data, ana); setValue(getResult("coll_2nd_sample_to"), getSecondCollDate(collected, 146, gestAge), rf, false, data, ana); } /** * Formats "double" values such as egg's age, MoMs and intrument results * etc. to have one or two fractional digits */ private void formatValues(SampleSO data, AnalysisViewDO ana) throws Exception { TestManager tm; proxy.log(Level.FINE, "Formatting result values", null); tm = (TestManager) data.getCache().get(Constants.uid().getTest(ana.getTestId())); /* * egg's age, weight and weeks & days have one fractional digit */ formatValue(getResult("eggs_age"), 1, tm.getFormatter(), false, data, ana); formatValue(getResult("mat_weight"), 1, tm.getFormatter(), false, data, ana); /* * test MoMs and instrument results have two fractional digit */ formatValue(getResult("nt_measurement"), 2, tm.getFormatter(), false, data, ana); formatValue(getResult("nt_mom"), 2, tm.getFormatter(), false, data, ana); formatValue(getResult("nt_mom", "result"), 2, tm.getFormatter(), true, data, ana); formatValue(getResult("papp_a_mom"), 2, tm.getFormatter(), false, data, ana); formatValue(getResult("papp_a_mom", "result"), 2, tm.getFormatter(), true, data, ana); formatValue(getResult("hcg_mom"), 2, tm.getFormatter(), false, data, ana); formatValue(getResult("hcg_mom", "result"), 2, tm.getFormatter(), true, data, ana); } /** * Sets the values in the "Unit" column for various row analytes such as * "Maternal Weight", "CRL" etc; sets the unit as null if the row analyte's * value is null */ private void setUnits(SampleSO data, AnalysisViewDO ana) throws Exception { ResultFormatter rf; TestManager tm; tm = (TestManager) data.getCache().get(Constants.uid().getTest(ana.getTestId())); rf = tm.getFormatter(); setUnit("eggs_age", UNIT_YEARS, rf, data, ana); setUnit("mat_age_at_delivery", UNIT_YEARS, rf, data, ana); setUnit("mat_weight", UNIT_POUNDS, rf, data, ana); setUnit("crl", UNIT_MM, rf, data, ana); setUnit("nt_measurement", UNIT_MM, rf, data, ana); } /** * Adds a QA event to the analysis if age at delivery < 15 years or if there * are multiple fetuses; removes a QA event if the condition for which it * was added is no longer true */ private void addRemoveQaEvents(SampleSO data, AnalysisViewDO ana) throws Exception { Double age, mom; mom = getDoubleValue(getValue("papp_a_mom"), false); if (mom != null && mom < PAPP_A_LIMIT) addQAEvent(QA_PAPP_A_MOM, data, ana); else removeQAEvent(QA_PAPP_A_MOM, data, ana); age = getDoubleValue(getValue("mat_age_at_delivery"), false); if (age != null && age < 15.0) addQAEvent(QA_LESS_THAN_15, data, ana); else removeQAEvent(QA_LESS_THAN_15, data, ana); } /** * Returns the ResultViewDO for the row analyte with the passed external id */ private ResultViewDO getResult(String rowExtId) { return getResult(rowExtId, rowExtId); } /** * Returns the ResultViewDO for a column analyte whose row analyte's * external id is the first argument and whose external id is the second * argument */ private ResultViewDO getResult(String rowExtId, String colExtId) { HashMap<String, ResultViewDO> map; map = resultMap.get(rowExtId); return map != null ? map.get(colExtId) : null; } /** * Sets the passed value in the passed result; the flag isDict means that * the value is a dictionary id and a dictionary record needs to be * obtained, because ResultHelper validates dictionary entries and not ids */ private void setValue(ResultViewDO result, Object value, ResultFormatter rf, boolean isDict, SampleSO data, AnalysisViewDO ana) throws Exception { String val; val = null; if (value != null) val = isDict ? proxy.getDictionaryById((Integer) value).getEntry() : value.toString(); if (ResultHelper.formatValue(result, val, ana.getUnitOfMeasureId(), rf)) { data.setChanges(result.getAnalyteExternalId()); data.addChangedUid(Constants.uid().getResult(result.getId())); proxy.log(Level.FINE, "Setting the value of " + result.getAnalyte() + " as: " + val, null); } } /** * Returns the value for the row analyte whose external id is the passed * value */ private String getValue(String rowExtId) { ResultViewDO res; res = getResult(rowExtId); return res != null ? res.getValue() : null; } /** * Adds a caution to inform the user that the value for passed analyte e.g. * "Race" doesn't match the patient's value; a caution is used here because * it's just a warning to the user; the sample doesn't need to go to error * status and update doesn't need to fail */ private void addResultNotMatchCaution(String analyteName, SampleSO data, AnalysisViewDO ana) throws Exception { Integer accession; /* * for display */ accession = data.getManager().getSample().getAccessionNumber(); if (accession == null) accession = 0; data.setStatus(Status.FAILED); data.addException(new FormErrorCaution(Messages.get().result_resultNotMatchPatientCaution(accession, ana.getTestName(), ana.getMethodName(), analyteName))); } /** * Returns the analyte parameters for the currently entered sonographer; * returns null if no sonographer has been entered */ private AnalyteParameterManager1 getSonographerParams(SampleManager1 sm, AnalysisViewDO ana) throws Exception { Integer dictId, provId; String sysName; DictionaryDO dict; dictId = getIntegerValue(getResult("sonographer"), sm, ana); if (dictId != null) { /* * the sonographer's dictionary entry's system name contains the id * of a provider e.g. "son_1234", where "1234" is the id; fetch the * AnalyteParameterManager1 using that id */ dict = proxy.getDictionaryById(dictId); sysName = dict.getSystemName(); if (sysName != null && sysName.startsWith("son_")) { provId = Integer.valueOf(sysName.substring(4)); return proxy.fetchParameters(provId, Constants.table().PROVIDER); } } return null; } /** * Adds a QA event with the passed name to the passed analysis if it's not * already added; throws an exception if the QA event was not found in the * system */ private void addQAEvent(String name, SampleSO data, AnalysisViewDO ana) throws Exception { Integer accession; QaEventDO qa; AnalysisQaEventViewDO aqa; SampleManager1 sm; qa = Util.getQAEvent(name, ana.getTestId(), proxy); sm = data.getManager(); accession = sm.getSample().getAccessionNumber(); if (qa == null) { /* * for display */ if (accession == null) accession = 0; throw new FormErrorException(Messages.get().analysis_qaEventNotFoundException(accession, ana.getTestName(), ana.getMethodName(), name)); } if (!sm.qaEvent.hasName(ana, name)) { proxy.log(Level.FINE, "Adding the qa event: " + name, null); aqa = sm.qaEvent.add(ana, qa); data.addChangedUid(Constants.uid().getAnalysisQAEvent(aqa.getId())); } } /** * Removes the QA event with the passed name from the passed analysis if it * was added earlier */ private void removeQAEvent(String name, SampleSO data, AnalysisViewDO ana) { int i; AnalysisQaEventViewDO aqa; SampleManager1 sm; proxy.log(Level.FINE, "Removing the qa event: " + name, null); sm = data.getManager(); for (i = 0; i < sm.qaEvent.count(ana); i++) { aqa = sm.qaEvent.get(ana, i); if (aqa.getQaEventName().equals(name)) { sm.qaEvent.remove(ana, aqa); break; } } data.addChangedUid(Constants.uid().getAnalysis(ana.getId())); data.addActionAfter(SampleSO.Action_After.QA_REMOVED); } /** * Returns the id for the row analyte whose external id is the passed value */ private Integer getAnalyteId(String rowExtId) { ResultViewDO res; res = getResult(rowExtId); return res != null ? res.getAnalyteId() : null; } /** * Returns the passed result's value converted to an Integer; returns null * if the value is null; throws an exception if the value contains any * non-numeric characters such as "<" or ">" */ private Integer getIntegerValue(ResultViewDO res, SampleManager1 sm, AnalysisViewDO ana) throws Exception { if (res != null && res.getValue() != null) { try { return new Integer(res.getValue()); } catch (NumberFormatException e) { throw getValueInvalidException(res, sm, ana); } } return null; } /** * Returns the passed results's value converted to a Datetime; returns null * if the result or value is null */ private Datetime getDateValue(ResultViewDO res) throws Exception { return res != null ? getDateValue(res.getValue()) : null; } /** * Returns the passed value converted to a Datetime; returns null if the * value is null */ private Datetime getDateValue(String value) throws Exception { if (DataBaseUtil.isEmpty(value)) return null; return Datetime.getInstance(Datetime.YEAR, Datetime.DAY, dateFormatter.parseStrict(value)); } /** * Returns the passed result's value converted to a Double; returns null if * the value is null; if the boolean flag is true, treats a value with a "<" * as valid; otherwise throws an exception if the value contains any non-numeric * characters such as "<" or ">" */ private Double getDoubleValue(ResultViewDO res, SampleManager1 sm, AnalysisViewDO ana, boolean allowLessThan) throws Exception { if (res != null) { try { return getDoubleValue(res.getValue(), allowLessThan); } catch (NumberFormatException e) { throw getValueInvalidException(res, sm, ana); } } return null; } /** * Returns the passed value converted to a Double; returns null if * the value is null; if the boolean flag is true, treats a value with a "<" * as valid; otherwise throws an exception if the value contains any non-numeric * characters such as "<" or ">" */ private Double getDoubleValue(String value, boolean allowLessThan) throws Exception { if (value != null) { value = allowLessThan ? value.replaceAll("<", "") : value; return new Double(value); } return null; } /** * Returns an exception whose message states that the passed result's value * is invalid */ private Exception getValueInvalidException(ResultViewDO res, SampleManager1 sm, AnalysisViewDO ana) { Integer accession; accession = sm.getSample().getAccessionNumber(); /* * for display */ if (accession == null) accession = 0; return new FormErrorException(Messages.get().result_valueInvalidException(accession, ana.getTestName(), ana.getMethodName(), res.getAnalyte(), res.getValue())); } /** * Sets p-values and result from the intrument for the passed test */ private void setTestValues(Test t, String analyteName, HashMap<Integer, AnalyteParameterViewDO> paramMap, SampleManager1 sm, AnalysisViewDO ana) throws Exception { AnalyteParameterViewDO ap; ap = paramMap != null ? paramMap.get(getAnalyteId(analyteName)) : null; t.setP1(getP1(ap)); t.setP2(getP2(ap)); t.setP3(getP3(ap)); t.setResult(getDoubleValue(getResult(analyteName, "result"), sm, ana, true)); } /** * Returns the begin or end date of the period during which the second * trimester sample must be collected */ private Datetime getSecondCollDate(Datetime collected, int days, Integer gestAge) { if (collected == null || gestAge == null) return null; return collected.add(days - gestAge); } /** * Sets the value in the "Unit" column for a row analyte such as * "Maternal Weight", "CRL" etc; sets the unit as null if the row analyte's * value is null */ private void setUnit(String externalId, Integer unitId, ResultFormatter rf, SampleSO data, AnalysisViewDO ana) throws Exception { Object value; ResultViewDO res; res = getResult(externalId); value = (res != null && res.getValue() != null) ? unitId : null; setValue(getResult(externalId, "unit"), value, rf, true, data, ana); } /** * Returns the passed parameter's p1 value; returns null if either the * parameter or the value is null */ private Double getP1(AnalyteParameterViewDO ap) { return ap == null || ap.getP1() == null ? null : ap.getP1(); } /** * Returns the passed parameter's p2 value; returns null if either the * parameter or the value is null */ private Double getP2(AnalyteParameterViewDO ap) { return ap == null || ap.getP2() == null ? null : ap.getP2(); } /** * Returns the passed parameter's p3 value; returns null if either the * parameter or the value is null */ private Double getP3(AnalyteParameterViewDO ap) { return ap == null || ap.getP3() == null ? null : ap.getP3(); } /** * Sets the value of the analyte with the passed external id as the risk * created from the passed risk sign and computed risk */ private void setRisk(String externalId, String riskSign, Integer risk, ResultFormatter rf, SampleSO data, AnalysisViewDO ana) throws Exception { String value; value = risk == null ? null : DataBaseUtil.concatWithSeparator(riskSign, "1:", risk); setValue(getResult(externalId), value, rf, false, data, ana); } /** * Sets the value of the analyte with the passed external id as the * screening cutoff created from the passed computed limit */ private void setScreeningCutoff(String externalId, Integer limit, ResultFormatter rf, SampleSO data, AnalysisViewDO ana) throws Exception { String value; value = limit == null ? null : DataBaseUtil.concat("1:", limit); setValue(getResult(externalId, "screen_cutoff"), value, rf, false, data, ana); } /** * Sets the value of the analyte with the passed external id as the * interpretation e.g. "Positive", based on the passed computed * interpretation e.g. "Presumptive Positive" */ private void setInterpretation(String externalId, Interpretation interp, Risk risk, ResultFormatter rf, SampleSO data, AnalysisViewDO ana) throws Exception { boolean isDict; Object value; value = null; isDict = false; if (interp != null) { switch (interp) { case NORMAL: switch (risk) { case NT: value = Messages.get().result_ntInterpretation("<"); break; case DOWNS: case T18: value = INT_NEGATIVE; isDict = true; break; } break; case PRES_POS: switch (risk) { case NT: value = Messages.get().result_ntInterpretation(">="); break; case DOWNS: case T18: value = INT_POSITIVE; isDict = true; break; } break; case UNKNOWN: value = INT_UNKNOWN; break; } } setValue(getResult(externalId, "interpretation"), value, rf, isDict, data, ana); } /** * Sets the value of the analyte with the passed external id as a * recommended action e.g. "Offer amniocentesis"; the action depends on the * passed interpretation e.g. "Positive" and a risk e.g. "Downs" */ private void setRecommendedAction(String externalId, Interpretation interp, ResultFormatter rf, SampleSO data, AnalysisViewDO ana) throws Exception { Integer value; value = null; if (interp != null) { switch (interp) { case NORMAL: value = ACTION_NO_ACTION; break; case PRES_POS: value = ACTION_US_DIAG; break; case UNKNOWN: value = ACTION_RISK_NOT_CALC; break; } } setValue(getResult(externalId, "rec_action"), value, rf, true, data, ana); } /** * Formats the passed result's value to have one or two fractional digits * based on the passed precision; the boolean flag specifies whether the * value can have a "<"; if the value has a "<" before formatting, * concatenates "<" to the formatted value */ private void formatValue(ResultViewDO res, int precision, ResultFormatter rf, boolean allowLessThan, SampleSO data, AnalysisViewDO ana) throws Exception { boolean hasLessThan; Double val; String value; value = res.getValue(); if (value == null) return; hasLessThan = value.startsWith("<"); val = getDoubleValue(res, data.getManager(), ana, allowLessThan); value = Util.format(val, precision, proxy); if (hasLessThan) value = DataBaseUtil.concat("<", value); setValue(res, value, rf, false, data, ana); } }