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Merge pull request #574 from mozzy11/2.8
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more Work on IHC reports
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@mozzy11
mozzy11 authored Oct 26, 2023
2 parents 281f838 + d7a9d07 commit 69c3390
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Showing 11 changed files with 629 additions and 285 deletions.
169 changes: 166 additions & 3 deletions frontend/src/components/immunohistochemistry/ImmunohistochemistryCaseView.js
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Original file line number Diff line number Diff line change
Expand Up @@ -125,6 +125,12 @@ function ImmunohistochemistryCaseView() {
herScore: "",
diagnosis: "",
molecularSubType: "",
conclusion : "",
ihcScore: "",
ihcRatio: "",
averageChrom: "",
averageHer2: "",
numberOfcancerNuclei: "",
toggled : false
},
});
Expand Down Expand Up @@ -427,7 +433,7 @@ function ImmunohistochemistryCaseView() {
}}
/>
</Column>
<Column lg={16} md={8} sm={4}>
<Column lg={16} md={8} sm={4}>
<div> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;</div>
</Column>
<Column lg={3} md={8} sm={4}>
Expand Down Expand Up @@ -477,9 +483,160 @@ function ImmunohistochemistryCaseView() {
</>
);
case "DUAL_IN_SITU_HYBRIDISATION":
return <></>;
return <>

<Column lg={16} md={8} sm={4}>
<Grid fullWidth={true} className="gridBoundary">
<Column lg={3} md={8} sm={4}>
Number of Cancer nuclei
</Column>
<Column lg={5} md={8} sm={4}>
<TextInput
id={"nuclei_" + index}
labelText=""
hideLabel={true}
value={reportParams[index]?.numberOfcancerNuclei}
onChange={(e) => {
var params = { ...reportParams };
if (!params[index]) {
params[index] = {};
}
params[index].numberOfcancerNuclei = e.target.value;
setReportParams(params);
}}
/>
</Column>
<Column lg={16} md={8} sm={4}>
<div> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;</div>
</Column>
<Column lg={3} md={8} sm={4}>
Average HER2 per nucleus
</Column>
<Column lg={5} md={8} sm={4}>
<TextInput
id={"her_" + index}
labelText=""
hideLabel={true}
value={reportParams[index]?.averageHer2}
onChange={(e) => {
var params = { ...reportParams };
if (!params[index]) {
params[index] = {};
}
params[index].averageHer2 = e.target.value;
var her2 = e.target.value;
var chrom = params[index].averageChrom;
if(chrom){
var ratio = her2/chrom ;
params[index].ihcRatio = ratio;
if (ratio >= 2.0) {
params[index].ihcScore = "AMPLIFICATION"
}else{
params[index].ihcScore = "NO_AMPLIFICATION"
}
}
setReportParams(params);
}}
/>
</Column>
<Column lg={16} md={8} sm={4}>
<div> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;</div>
</Column>
<Column lg={3} md={8} sm={4}>
Average Chromozome 17 Sinals per nucleus
</Column>
<Column lg={5} md={8} sm={4}>
<TextInput
id={"her_" + index}
labelText=""
hideLabel={true}
value={reportParams[index]?.averageChrom}
onChange={(e) => {
var params = { ...reportParams };
if (!params[index]) {
params[index] = {};
}
params[index].averageChrom = e.target.value;
var her2 = params[index].averageHer2
var chrom = e.target.value;
if(her2){
var ratio = her2/chrom ;
params[index].ihcRatio = ratio;
if (ratio >= 2.0) {
params[index].ihcScore = "AMPLIFICATION"
}else{
params[index].ihcScore = "NO_AMPLIFICATION"
}
}
setReportParams(params);
}}
/>
</Column>
<Column lg={16} md={8} sm={4}>
<div> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;</div>
</Column>
<Column lg={3} md={8} sm={4}>
Ratio of Her2/neu Signals to Chromozome 17
</Column>
<Column lg={5} md={8} sm={4}>
<TextInput
id={"her_" + index}
labelText=""
hideLabel={true}
disabled={true}
value={reportParams[index]?.ihcRatio}
/>
</Column>

<Column lg={16} md={8} sm={4}>
<div> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;</div>
</Column>
<Column lg={3} md={8} sm={4}>
IHC (Cerb2 Scoer)
</Column>
<Column lg={5} md={8} sm={4}>
<TextInput
id={"her_" + index}
labelText=""
hideLabel={true}
disabled={true}
value={reportParams[index]?.ihcScore}
/>
</Column>

</Grid>
</Column>


</>;
case "IMMUNOHISTOCHEMISTRY":
return <></>;
return <>
<Column lg={16} md={8} sm={4}>
<Grid fullWidth={true} className="gridBoundary">
<Column lg={3} md={8} sm={4}>
Conlusion
</Column>
<Column lg={13} md={8} sm={4}>
<TextArea
id={"conclusion_" + index}
labelText=""
hideLabel={true}
value={reportParams[index]?.conclusion}
onChange={(e) => {
var params = { ...reportParams };
if (!params[index]) {
params[index] = {};
}
params[index].conclusion = e.target.value;
setReportParams(params);
}}
/>
</Column>


</Grid>
</Column>
</>;
}
}

Expand Down Expand Up @@ -962,6 +1119,12 @@ function ImmunohistochemistryCaseView() {
herScore: reportParams[index]?.herScore,
diagnosis: reportParams[index]?.diagnosis,
molecularSubType: reportParams[index]?.molecularSubType,
conclusion: reportParams[index]?.conclusion,
ihcScore: reportParams[index]?.ihcScore,
ihcRatio: reportParams[index]?.ihcRatio,
averageChrom: reportParams[index]?.averageChrom,
averageHer2: reportParams[index]?.averageHer2,
numberOfcancerNuclei: reportParams[index]?.numberOfcancerNuclei,
};
postToOpenElisServerFullResponse(
"/rest/ReportPrint",
Expand Down
49 changes: 44 additions & 5 deletions ...a/org/openelisglobal/reports/action/implementation/BreastCancerHormoneReceptorReport.java
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Original file line number Diff line number Diff line change
@@ -1,14 +1,22 @@
package org.openelisglobal.reports.action.implementation;

import java.util.ArrayList;
import java.util.List;
import java.util.Locale;
import java.util.Set;

import org.openelisglobal.analysis.valueholder.Analysis;
import org.openelisglobal.program.service.ImmunohistochemistrySampleService;
import org.openelisglobal.program.valueholder.immunohistochemistry.ImmunohistochemistrySample;
import org.openelisglobal.reports.form.ReportForm;
import org.openelisglobal.result.valueholder.Result;
import org.openelisglobal.sample.valueholder.Sample;
import org.openelisglobal.spring.util.SpringContext;

import org.openelisglobal.test.valueholder.Test;

public class BreastCancerHormoneReceptorReport extends PatientProgramReport {

protected ImmunohistochemistrySampleService immunohistochemistrySampleService = SpringContext
private ImmunohistochemistrySampleService immunohistochemistrySampleService = SpringContext
.getBean(ImmunohistochemistrySampleService.class);

private ImmunohistochemistrySample immunohistochemistrySample;
Expand All @@ -20,9 +28,14 @@ protected String getReportName() {

@Override
protected void setAdditionalReportItems() {
data.setErResult("0.1");
data.setPrResult("0.2");
data.setMibResult("33");
Test erTest = testService.getActiveTestByLocalizedName("Anti-ER", Locale.ENGLISH);
data.setErResult(getResult(erTest));

Test prTest = testService.getActiveTestByLocalizedName("Anti-PR", Locale.ENGLISH);
data.setPrResult(getResult(prTest));

Test mibTest = testService.getActiveTestByLocalizedName("Anti-Ki67", Locale.ENGLISH);
data.setMibResult(getResult(mibTest));
}

@Override
Expand All @@ -47,4 +60,30 @@ protected void innitializeSample(ReportForm form) {
sample = immunohistochemistrySample.getSample();
}

private List<Analysis> getAnalysesByTestAndSampleAndStatus(Sample sample, Test test, Set<Integer> statusIdList) {
List<Integer> sampleIdList = new ArrayList<>();
sampleIdList.add(Integer.valueOf(sample.getId()));

List<Integer> testIdList = new ArrayList<>();
testIdList.add(Integer.valueOf(test.getId()));
List<Analysis> analyses = analysisService.getAnalysesBySampleIdTestIdAndStatusId(sampleIdList, testIdList,
new ArrayList<>(statusIdList));
return analyses != null ? analyses : new ArrayList<Analysis>();
}

private String getResult(Test test) {
String result = "";
if (test == null) {
return result;
}
List<Analysis> analyses = new ArrayList<>();
analyses = getAnalysesByTestAndSampleAndStatus(sample, test, analysisStatusIds);
if (!analyses.isEmpty()) {
List<Result> resultList = analysisService.getResults(analyses.get(0));
result = getAppropriateResults(resultList);
} else {
return result;
}
return result;
}
}
32 changes: 23 additions & 9 deletions .../java/org/openelisglobal/reports/action/implementation/DualInSituHybridizationReport.java
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Original file line number Diff line number Diff line change
@@ -1,24 +1,38 @@
package org.openelisglobal.reports.action.implementation;

import org.openelisglobal.internationalization.MessageUtil;
import org.openelisglobal.program.service.ImmunohistochemistrySampleService;
import org.openelisglobal.program.valueholder.immunohistochemistry.ImmunohistochemistrySample;
import org.openelisglobal.reports.form.ReportForm;
import org.openelisglobal.spring.util.SpringContext;

public class DualInSituHybridizationReport extends PatientProgramReport{

public class DualInSituHybridizationReport extends PatientProgramReport {

private ImmunohistochemistrySampleService immunohistochemistrySampleService = SpringContext
.getBean(ImmunohistochemistrySampleService.class);

private ImmunohistochemistrySample immunohistochemistrySample;

@Override
protected String getReportName() {
return "DualInSituHybridizationReport";
}

@Override
protected void setAdditionalReportItems() {
// TODO Auto-generated method stub
throw new UnsupportedOperationException("Unimplemented method 'setAdditionalReportItems'");
String reportDetails = MessageUtil.getMessage("dualInSitu.report.details", new String[] {
form.getNumberOfcancerNuclei(), form.getAverageHer2(), form.getAverageChrom(), form.getIhcRatio() });
data.setIhcReportDetails(reportDetails);
if (form.getIhcScore().equals("AMPLIFICATION")) {
data.setIhcScore(MessageUtil.getMessage("dualInSitu.label.amp"));
} else {
data.setIhcScore(MessageUtil.getMessage("dualInSitu.label.noAmp"));
}
}

@Override
protected void innitializeSample(ReportForm form) {
// TODO Auto-generated method stub
throw new UnsupportedOperationException("Unimplemented method 'innitializeSample'");
immunohistochemistrySample = immunohistochemistrySampleService.get(Integer.valueOf(form.getProgramSampleId()));
sample = immunohistochemistrySample.getSample();
}

}
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