org.opencds.cqf.terminology.distributable.DistributableValueSetGenerator Maven / Gradle / Ivy
package org.opencds.cqf.terminology.distributable;
import ca.uhn.fhir.context.FhirContext;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.ss.usermodel.Workbook;
import org.hl7.fhir.r4.model.ValueSet;
import org.opencds.cqf.Operation;
import org.opencds.cqf.terminology.SpreadsheetHelper;
import java.io.FileOutputStream;
import java.io.IOException;
import java.time.Instant;
import java.util.*;
public class DistributableValueSetGenerator extends Operation {
private FhirContext fhirContext;
public DistributableValueSetGenerator() {
this.fhirContext = FhirContext.forR4();
}
private String pathToSpreadsheet; // -pathtospreadsheet (-pts)
private String encoding = "json"; // -encoding (-e)
private final String CANONICAL_URL = "Canonical URL";
private final String COPYRIGHT = "Copyright";
private final String JURISDICTION = "Jurisdiction";
private final String PUBLISHER = "Publisher";
private final String AUTHOR_NAME = "author.name";
private final String AUTHOR_TELECOM_SYSTEM = "author.telecom.system";
private final String AUTHOR_TELECOM_VALUE = "author.telecom.value";
@Override
public void execute(String[] args) {
setOutputPath("src/main/resources/org/opencds/cqf/terminology/output");
for (String arg : args) {
if (arg.equals("-DistributableXlsxToValueSet")) continue;
String[] flagAndValue = arg.split("=");
if (flagAndValue.length < 2) {
throw new IllegalArgumentException("Invalid argument: " + arg);
}
String flag = flagAndValue[0];
String value = flagAndValue[1];
switch (flag.replace("-", "").toLowerCase()) {
case "outputpath": case "op": setOutputPath(value); break; // -outputpath (-op)
case "pathtospreadsheet": case "pts": pathToSpreadsheet = value; break;
case "encoding": case "e": encoding = value.toLowerCase(); break;
default: throw new IllegalArgumentException("Unknown flag: " + flag);
}
if (pathToSpreadsheet == null) {
throw new IllegalArgumentException("The path to the spreadsheet is required");
}
}
Workbook workbook = SpreadsheetHelper.getWorkbook(pathToSpreadsheet);
CommonMetaData commonMetaData = processCommonMetaData(workbook.getSheetAt(0));
output(resolveValueSets(commonMetaData, workbook));
}
private CommonMetaData processCommonMetaData(Sheet commonMetaDataSheet) {
CommonMetaData commonMetaData = new CommonMetaData();
Iterator rowIterator = commonMetaDataSheet.rowIterator();
boolean isCodeSystem = false;
boolean isValueSet = false;
while (rowIterator.hasNext()) {
Row row = rowIterator.next();
String cellAsString = SpreadsheetHelper.getCellAsString(row.getCell(0));
if (cellAsString == null) continue;
if (cellAsString.equals("CodeSystems")) {
isCodeSystem = true;
}
else if (cellAsString.equals("ValueSets")) {
isCodeSystem = false;
isValueSet = true;
}
else if (isCodeSystem) {
commonMetaData.addCodeSystemMeta(
SpreadsheetHelper.getCellAsString(row.getCell(0)),
SpreadsheetHelper.getCellAsString(row.getCell(1)),
SpreadsheetHelper.getCellAsString(row.getCell(2))
);
}
else if (isValueSet) {
commonMetaData.addValueSetMeta(
SpreadsheetHelper.getCellAsString(row.getCell(0)),
SpreadsheetHelper.getCellAsString(row.getCell(2)),
SpreadsheetHelper.getCellAsString(row.getCell(3))
);
}
else {
switch (cellAsString) {
case CANONICAL_URL:
commonMetaData.getOrganizationalMetaData().setCanonicalUrlBase(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case COPYRIGHT:
commonMetaData.getOrganizationalMetaData().setCopyright(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case JURISDICTION:
commonMetaData.getOrganizationalMetaData().setJurisdiction(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case PUBLISHER:
commonMetaData.getOrganizationalMetaData().setPublisher(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case AUTHOR_NAME:
commonMetaData.getOrganizationalMetaData().setAuthorName(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case AUTHOR_TELECOM_SYSTEM:
commonMetaData.getOrganizationalMetaData().setAuthorTelecomSystem(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case AUTHOR_TELECOM_VALUE:
commonMetaData.getOrganizationalMetaData().setAuthorTelecomValue(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
default:
break;
}
}
}
return commonMetaData;
}
private DistributableValueSetMeta resolveDistributableValueSetMeta(Sheet sheet) {
DistributableValueSetMeta meta = new DistributableValueSetMeta();
Iterator rowIterator = sheet.rowIterator();
while (rowIterator.hasNext()) {
Row row = rowIterator.next();
String cellString = SpreadsheetHelper.getCellAsString(row.getCell(0));
if (cellString == null) continue;
switch (cellString) {
case "id":
meta.setId(SpreadsheetHelper.getCellAsString(row.getCell(1)).toLowerCase());
break;
case "identifier":
meta.setIdentifier(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "rules-text":
meta.setRulesText(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "warning":
meta.setWarning(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "version":
meta.setVersion(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "name":
meta.setName(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "title":
meta.setTitle(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "status":
meta.setStatus(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "experimental":
meta.setExperimental(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "date":
meta.setDate(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "description":
meta.setDescription(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "purpose":
meta.setPurpose(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "purpose.ClinicalFocus":
meta.setPurposeClinicalFocus(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "purpose.DataElementScope":
meta.setPurposeDataElementScope(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "purpose.InclusionCriteria":
meta.setPurposeInclusionCriteria(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "purpose.ExclusionCriteria":
meta.setPurposeExclusionCriteria(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
case "compose":
meta.setCompose(SpreadsheetHelper.getCellAsString(row.getCell(1)));
break;
default:
break;
}
}
return meta;
}
private List resolveValueSets(CommonMetaData meta, Workbook workbook) {
List valueSets = new ArrayList<>();
DistributableValueSetMeta distributableValueSetMeta;
ValueSet vs;
for (Map.Entry entrySet : meta.getValueSetMeta().entrySet()) {
if (entrySet.getKey().isEmpty()
|| entrySet.getValue().getMetaPageName().isEmpty()
|| entrySet.getValue().getCodeListPageName().isEmpty())
{
continue;
}
distributableValueSetMeta = resolveDistributableValueSetMeta(workbook.getSheet(entrySet.getValue().getMetaPageName()));
vs = distributableValueSetMeta.populate(fhirContext);
meta.getOrganizationalMetaData().populate(vs);
resolveCodeList(meta, workbook.getSheet(entrySet.getValue().getCodeListPageName()), vs);
valueSets.add(vs);
}
return valueSets;
}
private void resolveCodeList(CommonMetaData meta, Sheet sheet, ValueSet vs) {
Iterator rowIterator = sheet.rowIterator();
Boolean active = true;
String system = null;
String version = null;
while (rowIterator.hasNext()) {
Row row = rowIterator.next();
String code = SpreadsheetHelper.getCellAsString(row.getCell(0));
if (code.equals("Code")) continue;
String description = SpreadsheetHelper.getCellAsString(row.getCell(1));
active = SpreadsheetHelper.getCellAsString(row.getCell(2)) == null ? active : Boolean.valueOf(SpreadsheetHelper.getCellAsString(row.getCell(2)));
system = SpreadsheetHelper.getCellAsString(row.getCell(3)) == null ? system : SpreadsheetHelper.getCellAsString(row.getCell(3));
if (system == null) {
throw new RuntimeException("A system must be specified in the code list");
}
version = SpreadsheetHelper.getCellAsString(row.getCell(4)) == null ? version : SpreadsheetHelper.getCellAsString(row.getCell(4));
if (!vs.hasExpansion()) {
vs.setExpansion(
new ValueSet.ValueSetExpansionComponent()
.setTimestamp(Date.from(Instant.now()))
.addContains(
new ValueSet.ValueSetExpansionContainsComponent()
.setSystem(system)
.setCode(code)
.setDisplay(description)
.setVersion(meta.getCodeSystemMeta().get(system).getVersion())
)
);
}
else {
vs.getExpansion()
.addContains(
new ValueSet.ValueSetExpansionContainsComponent()
.setSystem(system)
.setCode(code)
.setDisplay(description)
.setVersion(meta.getCodeSystemMeta().get(system).getVersion())
);
}
}
}
private void output(List valueSets) {
for (ValueSet valueSet : valueSets) {
try (FileOutputStream writer = new FileOutputStream(getOutputPath() + "/" + "valueset-" + valueSet.getId() + "." + encoding)) {
writer.write(
encoding.equals("json")
? fhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet).getBytes()
: fhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(valueSet).getBytes()
);
writer.flush();
} catch (IOException e) {
e.printStackTrace();
throw new IllegalArgumentException("Error outputting ValueSet: " + valueSet.getId());
}
}
}
}
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