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Added "synonymDesignation" argument to GenericValueSetGenerator. Rest… #365

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merged 2 commits into from
May 11, 2022
Merged

Added "synonymDesignation" argument to GenericValueSetGenerator. Rest… #365

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616d088
Added "synonymDesignation" argument to GenericValueSetGenerator. Rest…
sliver007 May 3, 2022
6c299eb
Fixed bug in iteration of GenericValueSetGenerator that was causing i…
sliver007 May 11, 2022
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2 changes: 1 addition & 1 deletion src/main/java/org/opencds/cqf/tooling/OperationFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@ static Operation createOperation(String operationName) {
case "BundlesToBundle":
throw new NotImplementedException("BundlesToBundle");
case "BundleToResources":
throw new NotImplementedException("BundleToResources");
return new BundleToResources();
case "ExtractMatBundle":
return new ExtractMatBundleOperation();
case "GenerateMIs":
Expand Down
49 changes: 43 additions & 6 deletions src/main/java/org/opencds/cqf/tooling/terminology/GenericValueSetGenerator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@

import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Workbook;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.Enumerations;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.opencds.cqf.tooling.Operation;
Expand Down Expand Up @@ -77,6 +78,11 @@ public class GenericValueSetGenerator extends Operation {
private int systemRow = 1;
private int systemCol = 2;

private boolean hasSynonymDesignation = false;
private int synonymDesignationSheet = 1; // -synonymdesignation (-syn) = sheet#:row#:column#
private int synonymDesignationRow = 1;
private int synonymDesignationCol = 4;

private boolean hasStaticSystem = false;
private int staticSystemSheet = -1; // -staticsystem (-ss) = sheet#:row#:column#
private int staticSystemRow = -1;
Expand All @@ -94,10 +100,7 @@ public class GenericValueSetGenerator extends Operation {

private Map<Integer, org.opencds.cqf.tooling.terminology.ValueSet> codesBySystem = new HashMap<>();

@Override
public void execute(String[] args) {
setOutputPath("src/main/resources/org/opencds/cqf/tooling/terminology/output"); // default

private void processArguments(String[] args) {
for (String arg : args) {
if (arg.equals("-XlsxToValueSet")) {
continue;
Expand Down Expand Up @@ -197,6 +200,13 @@ else if (flag.equals("-outputpath") || flag.equals("-op")) {
systemRow = Integer.valueOf(sheetRowCol[1]);
systemCol = Integer.valueOf(sheetRowCol[2]);
break;
case "synonymdesignation": case "syn":
hasSynonymDesignation = true;
if (sheetRowCol == null) break;
synonymDesignationSheet = Integer.valueOf(sheetRowCol[0]);
synonymDesignationRow = Integer.valueOf(sheetRowCol[1]);
synonymDesignationCol = Integer.valueOf(sheetRowCol[2]);
break;
case "staticsystem": case "ss":
if (hasSystem) {
throw new IllegalArgumentException("Cannot have both system and staticsystem flags set");
Expand Down Expand Up @@ -255,6 +265,13 @@ else if (flag.equals("-outputpath") || flag.equals("-op")) {
if (!hasSystem && !hasStaticSystem) {
throw new IllegalArgumentException("-system or -staticsystem flag must be specified");
}
}

@Override
public void execute(String[] args) {
setOutputPath("src/main/resources/org/opencds/cqf/tooling/terminology/output"); // default

processArguments(args);

Workbook workbook = SpreadsheetHelper.getWorkbook(pathToSpreadsheet);
ValueSet vs = new ValueSet();
Expand Down Expand Up @@ -297,6 +314,7 @@ public void resolveCodeList(Workbook workbook) {
Iterator<Row> codeIterator = workbook.getSheetAt(codeSheet).rowIterator();
Iterator<Row> displayIterator = hasDisplay ? workbook.getSheetAt(displaySheet).rowIterator() : null;
Iterator<Row> systemIterator = hasSystem ? workbook.getSheetAt(systemSheet).rowIterator() : null;
Iterator<Row> synonymDesignationIterator = hasSynonymDesignation ? workbook.getSheetAt(synonymDesignationSheet).rowIterator() : null;
String system = hasStaticSystem
? SpreadsheetHelper.getCellAsString(workbook.getSheetAt(staticSystemSheet).getRow(staticSystemRow).getCell(staticSystemCol))
: null;
Expand All @@ -311,12 +329,19 @@ public void resolveCodeList(Workbook workbook) {
continue;
}

String code = SpreadsheetHelper.getCellAsString(row.getCell(codeCol));
if (code == null || code.isEmpty()) {
break;
}

if (systemIterator != null) {
system = getNextValue(systemIterator, systemRow, systemCol);
}

if (system == null) {
throw new IllegalArgumentException("System not provided");
}

try {
system = system.startsWith("http") ? system : CodeSystemLookupDictionary.getUrlFromName(system);
} catch (IllegalArgumentException e) {
Expand All @@ -333,14 +358,26 @@ public void resolveCodeList(Workbook workbook) {
codesBySystem.put(hash, new org.opencds.cqf.tooling.terminology.ValueSet().setSystem(system).setVersion(version));
}

String code = SpreadsheetHelper.getCellAsString(row.getCell(codeCol));

String display = null;
if (displayIterator != null) {
display = getNextValue(displayIterator, displayRow, displayCol);
}

String synonym = null;
if (synonymDesignationIterator != null) {
synonym = getNextValue(synonymDesignationIterator, synonymDesignationRow, synonymDesignationCol);
}

ValueSet.ConceptReferenceComponent concept = new ValueSet.ConceptReferenceComponent().setCode(code).setDisplay(display);
if (synonym != null && !synonym.isEmpty()) {
Coding synonymUseCoding = new Coding();
synonymUseCoding.setSystem("http://snomed.info/sct");
synonymUseCoding.setCode("synonym");
synonymUseCoding.setDisplay("Synonym");

ValueSet.ConceptReferenceDesignationComponent conceptDesignation = new ValueSet.ConceptReferenceDesignationComponent().setUse(synonymUseCoding).setValue(synonym);
concept.getDesignation().add(conceptDesignation);
}
codesBySystem.get(hash).addCode(concept);
}
}
Expand Down