Merge pull request #570 from mozzy11/2.8

improve cytology and pathology reports
I-TECH-UW · Oct 20, 2023 · 5a31630 · 5a31630
2 parents 0e7e5c5 + 5d1cc72
commit 5a31630
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Showing 11 changed files with 220 additions and 82 deletions.
diff --git a/src/main/java/org/openelisglobal/program/service/cytology/CytologyDisplayService.java b/src/main/java/org/openelisglobal/program/service/cytology/CytologyDisplayService.java
@@ -2,10 +2,13 @@
 
 import org.openelisglobal.program.valueholder.cytology.CytologyCaseViewDisplayItem;
 import org.openelisglobal.program.valueholder.cytology.CytologyDisplayItem;
+import org.openelisglobal.program.valueholder.cytology.CytologySample;
 
 public interface CytologyDisplayService {
 
     CytologyCaseViewDisplayItem convertToCaseDisplayItem(Integer cytologySampleId);
 
     CytologyDisplayItem convertToDisplayItem(Integer cytologySampleId); 
+
+    CytologySample getCytologySampleWithLoadedAttributes(Integer cytologySampleId);
 }
diff --git a/src/main/java/org/openelisglobal/program/service/cytology/CytologyDisplayServiceImpl.java b/src/main/java/org/openelisglobal/program/service/cytology/CytologyDisplayServiceImpl.java
@@ -145,5 +145,13 @@ public CytologyDisplayItem convertToDisplayItem(Integer cytologySampleId) {
         displayItem.setPathologySampleId(cytologySample.getId());
         return displayItem;
     }
+
+    @Override
+        @Transactional
+    public CytologySample getCytologySampleWithLoadedAttributes(Integer cytologySampleId) {
+        CytologySample cytologySample = cytologySampleService.get(cytologySampleId);
+        cytologySample.getDiagnosis().getDiagnosisResultsMaps().size();
+        return cytologySample;
+    }
 
 }
diff --git a/src/main/java/org/openelisglobal/reports/action/implementation/PatientCytologyReport.java b/src/main/java/org/openelisglobal/reports/action/implementation/PatientCytologyReport.java
@@ -1,41 +1,90 @@
 package org.openelisglobal.reports.action.implementation;
+
 import java.util.ArrayList;
 import java.util.List;
+import java.util.stream.Collectors;
 
-import org.openelisglobal.program.service.cytology.CytologySampleService;
+import org.apache.commons.lang3.StringUtils;
+import org.openelisglobal.internationalization.MessageUtil;
+import org.openelisglobal.program.service.cytology.CytologyDisplayService;
+import org.openelisglobal.program.valueholder.cytology.CytologyDiagnosis;
+import org.openelisglobal.program.valueholder.cytology.CytologyDiagnosis.CytologyDiagnosisResultType;
 import org.openelisglobal.program.valueholder.cytology.CytologySample;
+import org.openelisglobal.program.valueholder.cytology.CytologySpecimenAdequacy.SpecimenAdequancySatisfaction;
 import org.openelisglobal.reports.form.ReportForm;
 import org.openelisglobal.spring.util.SpringContext;
 
 public class PatientCytologyReport extends PatientProgramReport {
-
-    protected  CytologySampleService cytologySampleService = SpringContext.getBean(CytologySampleService.class);
+
+    protected CytologyDisplayService cytologySampleService = SpringContext.getBean(CytologyDisplayService.class);
+
     private CytologySample cytologySample;
-
+    
     @Override
     protected String getReportName() {
         return "PatientCytologyReport";
     }
-
+    
     @Override
     protected void setAdditionalReportItems() {
-        data.setSpecimenAdequacy("Dummy specimenn");
-        data.setDiagnosis("NEGATIVE DIAGNOSIS");
-
-        List<String> stringList = new ArrayList<>();
-        stringList.add("dummy diagnosis");
-        stringList.add("sample diagnosis");
-        stringList.add("example diagnosis");
-
-        data.setEpithelialCellAbnomalities(stringList);
-        data.setReactiveCellularChanges(stringList);
-        data.setOrganisms(stringList);
-        data.setOtherDiagnoses(stringList);
+        if (cytologySample.getSpecimenAdequacy() != null) {
+            data.setSpecimenAdequacy(cytologySample.getSpecimenAdequacy().getSatisfaction()
+                    .equals(SpecimenAdequancySatisfaction.SATISFACTORY_FOR_EVALUATION)
+                            ? MessageUtil.getMessage("cytology.label.satisfactory")
+                            : MessageUtil.getMessage("cytology.label.unsatisfactory"));
+
+        }
+        if (cytologySample.getDiagnosis() != null) {
+            if (cytologySample.getDiagnosis().getNegativeDiagnosis()) {
+                data.setDiagnosis(MessageUtil.getMessage("cytology.label.negative"));
+
+            } else {
+                CytologyDiagnosis cytoDiagnosis = cytologySample.getDiagnosis();
+                if (cytoDiagnosis.getDiagnosisResultsMaps() != null) {
+                    cytoDiagnosis.getDiagnosisResultsMaps().forEach(diagnosisResult -> {
+                        List<String> diagnoses = new ArrayList<>();
+
+                        if (diagnosisResult.getResultType().equals(CytologyDiagnosisResultType.DICTIONARY)) {
+                            diagnoses.addAll(diagnosisResult.getResults().stream().filter(e -> StringUtils.isNotBlank(e))
+                                    .map(e -> dictionaryService.get(e).getLocalizedName()).collect(Collectors.toList()));
+                        } else {
+                            diagnoses.add(diagnosisResult.getResults().get(0));
+                        }
+                        switch (diagnosisResult.getCategory()) {
+                            case EPITHELIAL_CELL_ABNORMALITY: {
+                                data.setEpithelialCellAbnomalities(diagnoses);
+                                break;
+                            }
+                            case NON_NEOPLASTIC_CELLULAR_VARIATIONS: {
+                                data.setNonNeoplasticCellularVariations(diagnoses);
+                                break;
+                            }
+                            case ORGANISMS: {
+                                data.setOrganisms(diagnoses);
+                                break;
+                            }
+                            case REACTIVE_CELLULAR_CHANGES: {
+                                data.setReactiveCellularChanges(diagnoses);
+                                break;
+                            }
+                            case OTHER: {
+                                data.setOtherDiagnoses(diagnoses);
+                                break;
+                            }
+                        } 
+                    });
+                }
+
+            }
+
+        }
+
     }
-
+    
     @Override
     protected void innitializeSample(ReportForm form) {
-        cytologySample = cytologySampleService.get(Integer.valueOf(form.getProgramSampleId()));
+        cytologySample = cytologySampleService
+                .getCytologySampleWithLoadedAttributes(Integer.valueOf(form.getProgramSampleId()));
         sample = cytologySample.getSample();
     }
 

diff --git a/src/main/java/org/openelisglobal/reports/action/implementation/PatientPathologyReport.java b/src/main/java/org/openelisglobal/reports/action/implementation/PatientPathologyReport.java
@@ -33,8 +33,7 @@ protected void setAdditionalReportItems() {
         List<String> codedConclusions =  pathologySample.getConclusions().stream().filter(e -> e.getType() == ConclusionType.DICTIONARY)
         .map(e -> dictionaryService.get(e.getValue()).getLocalizedName())
         .collect(Collectors.toList());
-        String commaSeparatedString = String.join(", ", codedConclusions);
-        data.setCodedConclusion(commaSeparatedString);
+        data.setCodedConclusion(codedConclusions);
     }
 
     @Override

diff --git a/...org/openelisglobal/reports/action/implementation/reportBeans/ProgramSampleReportData.java b/...org/openelisglobal/reports/action/implementation/reportBeans/ProgramSampleReportData.java
@@ -101,7 +101,7 @@ public final class ProgramSampleReportData {
 
     private String microExam;
 
-    private String codedConclusion;
+    private List<String> codedConclusion;
 
     private String textConclusion;
 
@@ -571,11 +571,11 @@ public void setMicroExam(String microExam) {
         this.microExam = microExam;
     }
 
-    public String getCodedConclusion() {
+    public List<String> getCodedConclusion() {
         return codedConclusion;
     }
 
-    public void setCodedConclusion(String codedConclusion) {
+    public void setCodedConclusion(List<String> codedConclusion) {
         this.codedConclusion = codedConclusion;
     }
 

diff --git a/src/main/resources/languages/message_en.properties b/src/main/resources/languages/message_en.properties
@@ -7823,4 +7823,8 @@ cytology.label.organisms =  Organisms
 cytology.label.otherResult =  Other Diagnosis Result 
 cytology.label.diagnosis =  Diagnosis/Impression
 cytology.label.papsmear =  PAP SMEAR REPORT
+cytology.label.negative = Negative For Intraepithelial Lesion or Malignancy
+cytology.label.satisfactory = Satisfactory for evaluation 
+cytology.label.unsatisfactory = Unsatisfactory for evaluation 
+
 
diff --git a/src/main/resources/languages/message_fr.properties b/src/main/resources/languages/message_fr.properties
@@ -6770,7 +6770,7 @@ test.validation.total.percent                                 = H\
                                                                 matologie \
                                                                 Totale %
 
-test.antimicrobialResistance  = Résistance aux antimicrobiens
+test.antimicrobialResistance  = R�sistance aux antimicrobiens
 
 testSection.Biochemistry     = Biochimie
 testSection.EID              = Virologie DNA PCR
@@ -7322,3 +7322,6 @@ cytology.label.organisms = Organismes
 cytology.label.otherResult = Autre résultat de diagnostic
 cytology.label.diagnosis = Diagnostic/Impression
 cytology.label.papsmear = Rapport du frottis de PAP
+cytology.label.negative=Négatif pour lésion intraépithéliale ou malignité
+cytology.label.satisfactory=Satisfaisant pour l'évaluation
+cytology.label.unsatisfactory=Insatisfaisant pour l'évaluation
diff --git a/src/main/resources/reports/PatientCytologyReport.jasper b/src/main/resources/reports/PatientCytologyReport.jasper