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Merge pull request #571 from mozzy11/2.8
add IHC report
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199 changes: 199 additions & 0 deletions
199
...n/java/org/openelisglobal/reports/action/implementation/PatientImmunoChemistryReport.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,199 @@ | ||
| package org.openelisglobal.reports.action.implementation; | ||
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| import org.openelisglobal.program.service.ImmunohistochemistrySampleService; | ||
| import org.openelisglobal.program.valueholder.immunohistochemistry.ImmunohistochemistrySample; | ||
| import org.openelisglobal.reports.action.implementation.reportBeans.ProgramSampleReportData; | ||
| import org.openelisglobal.reports.form.ReportForm; | ||
| import org.openelisglobal.result.service.ResultService; | ||
| import org.openelisglobal.result.valueholder.Result; | ||
| import org.openelisglobal.spring.util.SpringContext; | ||
| import org.openelisglobal.test.service.TestServiceImpl; | ||
| import org.openelisglobal.typeoftestresult.service.TypeOfTestResultServiceImpl; | ||
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| import java.util.ArrayList; | ||
| import java.util.Collections; | ||
| import java.util.Comparator; | ||
| import java.util.HashSet; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
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| import org.apache.commons.validator.GenericValidator; | ||
| import org.openelisglobal.analysis.valueholder.Analysis; | ||
| import org.openelisglobal.common.services.IStatusService; | ||
| import org.openelisglobal.common.services.StatusService.AnalysisStatus; | ||
| import org.openelisglobal.dictionary.valueholder.Dictionary; | ||
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| public class PatientImmunoChemistryReport extends PatientProgramReport{ | ||
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| protected ImmunohistochemistrySampleService immunohistochemistrySampleService = SpringContext.getBean(ImmunohistochemistrySampleService.class); | ||
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| private ImmunohistochemistrySample immunohistochemistrySample; | ||
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| private static Set<Integer> analysisStatusIds; | ||
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| static { | ||
| analysisStatusIds = new HashSet<>(); | ||
| analysisStatusIds.add(Integer | ||
| .parseInt(SpringContext.getBean(IStatusService.class).getStatusID(AnalysisStatus.BiologistRejected))); | ||
| analysisStatusIds.add( | ||
| Integer.parseInt(SpringContext.getBean(IStatusService.class).getStatusID(AnalysisStatus.Finalized))); | ||
| analysisStatusIds.add(Integer.parseInt( | ||
| SpringContext.getBean(IStatusService.class).getStatusID(AnalysisStatus.NonConforming_depricated))); | ||
| analysisStatusIds.add( | ||
| Integer.parseInt(SpringContext.getBean(IStatusService.class).getStatusID(AnalysisStatus.NotStarted))); | ||
| analysisStatusIds.add(Integer | ||
| .parseInt(SpringContext.getBean(IStatusService.class).getStatusID(AnalysisStatus.TechnicalAcceptance))); | ||
| analysisStatusIds.add( | ||
| Integer.parseInt(SpringContext.getBean(IStatusService.class).getStatusID(AnalysisStatus.Canceled))); | ||
| analysisStatusIds.add(Integer | ||
| .parseInt(SpringContext.getBean(IStatusService.class).getStatusID(AnalysisStatus.TechnicalRejected))); | ||
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| } | ||
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| @Override | ||
| protected String getReportName() { | ||
| return "PatientImmunoChemistryReport"; | ||
| } | ||
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| @Override | ||
| protected void setAdditionalReportItems() { | ||
| List<Analysis> analyses = analysisService.getAnalysesBySampleIdAndStatusId(sampleService.getId(sample) ,analysisStatusIds); | ||
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| List<ProgramSampleReportData.Result> resultsData = new ArrayList<>(); | ||
| analyses.forEach(analysis -> { | ||
| ProgramSampleReportData.Result resultData = new ProgramSampleReportData.Result(); | ||
| resultData.setTest(TestServiceImpl.getUserLocalizedReportingTestName(analysis.getTest())); | ||
| List<Result> resultList = analysisService.getResults(analysis); | ||
| setAppropriateResults(resultList ,resultData); | ||
| resultData.setUom(getUnitOfMeasure(analysis.getTest())); | ||
| resultsData.add(resultData); | ||
| }); | ||
| data.setResults(resultsData); | ||
| } | ||
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| @Override | ||
| protected void innitializeSample(ReportForm form) { | ||
| immunohistochemistrySample = immunohistochemistrySampleService.get(Integer.valueOf(form.getProgramSampleId())); | ||
| sample = immunohistochemistrySample.getSample(); | ||
| } | ||
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| private void setAppropriateResults(List<Result> resultList ,ProgramSampleReportData.Result resultData) { | ||
| String reportResult = ""; | ||
| if (!resultList.isEmpty()) { | ||
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| // If only one result just get it and get out | ||
| if (resultList.size() == 1) { | ||
| Result result = resultList.get(0); | ||
| if (TypeOfTestResultServiceImpl.ResultType.isDictionaryVariant(result.getResultType())) { | ||
| Dictionary dictionary = new Dictionary(); | ||
| dictionary.setId(result.getValue()); | ||
| dictionaryService.getData(dictionary); | ||
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| if (result.getAnalyte() != null && "Conclusion".equals(result.getAnalyte().getAnalyteName())) { | ||
| currentConclusion = dictionary.getId() != null ? dictionary.getLocalizedName() : ""; | ||
| } else { | ||
| reportResult = dictionary.getId() != null ? dictionary.getLocalizedName() : ""; | ||
| } | ||
| } else { | ||
| ResultService resultResultService = SpringContext.getBean(ResultService.class); | ||
| reportResult = resultResultService.getResultValue(result, true); | ||
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| } | ||
| } else { | ||
| // If multiple results it can be a quantified result, multiple | ||
| // results with quantified other results or it can be a | ||
| // conclusion | ||
| ResultService resultResultService = SpringContext.getBean(ResultService.class); | ||
| Result result = resultList.get(0); | ||
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| if (TypeOfTestResultServiceImpl.ResultType.DICTIONARY | ||
| .matches(resultResultService.getTestType(result))) { | ||
| // data.setAbnormalResult(resultResultService.isAbnormalDictionaryResult(result)); | ||
| List<Result> dictionaryResults = new ArrayList<>(); | ||
| Result quantification = null; | ||
| for (Result sibResult : resultList) { | ||
| if (TypeOfTestResultServiceImpl.ResultType.DICTIONARY.matches(sibResult.getResultType())) { | ||
| dictionaryResults.add(sibResult); | ||
| } else if (TypeOfTestResultServiceImpl.ResultType.ALPHA.matches(sibResult.getResultType()) | ||
| && sibResult.getParentResult() != null) { | ||
| quantification = sibResult; | ||
| } | ||
| } | ||
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| Dictionary dictionary = new Dictionary(); | ||
| for (Result sibResult : dictionaryResults) { | ||
| dictionary.setId(sibResult.getValue()); | ||
| dictionaryService.getData(dictionary); | ||
| if (sibResult.getAnalyte() != null | ||
| && "Conclusion".equals(sibResult.getAnalyte().getAnalyteName())) { | ||
| currentConclusion = dictionary.getId() != null ? dictionary.getLocalizedName() : ""; | ||
| } else { | ||
| reportResult = dictionary.getId() != null ? dictionary.getLocalizedName() : ""; | ||
| if (quantification != null | ||
| && quantification.getParentResult().getId().equals(sibResult.getId())) { | ||
| reportResult += ": " + quantification.getValue(true); | ||
| } | ||
| } | ||
| } | ||
| } else if (TypeOfTestResultServiceImpl.ResultType | ||
| .isMultiSelectVariant(resultResultService.getTestType(result))) { | ||
| Dictionary dictionary = new Dictionary(); | ||
| StringBuilder multiResult = new StringBuilder(); | ||
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| Collections.sort(resultList, new Comparator<Result>() { | ||
| @Override | ||
| public int compare(Result o1, Result o2) { | ||
| if (o1.getGrouping() == o2.getGrouping()) { | ||
| return Integer.parseInt(o1.getId()) - Integer.parseInt(o2.getId()); | ||
| } else { | ||
| return o1.getGrouping() - o2.getGrouping(); | ||
| } | ||
| } | ||
| }); | ||
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| Result quantifiedResult = null; | ||
| for (Result subResult : resultList) { | ||
| if (TypeOfTestResultServiceImpl.ResultType.ALPHA.matches(subResult.getResultType())) { | ||
| quantifiedResult = subResult; | ||
| resultList.remove(subResult); | ||
| break; | ||
| } | ||
| } | ||
| int currentGrouping = resultList.get(0).getGrouping(); | ||
| for (Result subResult : resultList) { | ||
| if (subResult.getGrouping() != currentGrouping) { | ||
| currentGrouping = subResult.getGrouping(); | ||
| multiResult.append("-------\n"); | ||
| } | ||
| dictionary.setId(subResult.getValue()); | ||
| dictionaryService.getData(dictionary); | ||
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| if (dictionary.getId() != null) { | ||
| multiResult.append(dictionary.getLocalizedName()); | ||
| if (quantifiedResult != null | ||
| && quantifiedResult.getParentResult().getId().equals(subResult.getId()) | ||
| && !GenericValidator.isBlankOrNull(quantifiedResult.getValue())) { | ||
| multiResult.append(": "); | ||
| multiResult.append(quantifiedResult.getValue(true)); | ||
| } | ||
| multiResult.append("\n"); | ||
| } | ||
| } | ||
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| if (multiResult.length() > 1) { | ||
| // remove last "\n" | ||
| multiResult.setLength(multiResult.length() - 1); | ||
| } | ||
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| reportResult = multiResult.toString(); | ||
| } | ||
| } | ||
| } | ||
| resultData.setResult(reportResult); | ||
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| } | ||
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| } |
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