Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

more Work on IHC reports #574

Merged
merged 2 commits into from
Oct 26, 2023
Merged

more Work on IHC reports #574

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
2d22800
more Work on IHC reports
mozzy11 Oct 26, 2023
d7a9d07
add ISH report
mozzy11 Oct 26, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
169 changes: 166 additions & 3 deletions frontend/src/components/immunohistochemistry/ImmunohistochemistryCaseView.js
View file
Open in desktop
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
View file
Open in desktop
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
View file
Open in desktop
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();
}

}
Loading
Loading