org.opencds.cqf.terminology.RCKMSJurisdictionsGenerator Maven / Gradle / Ivy
package org.opencds.cqf.terminology;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import org.apache.poi.ss.usermodel.*;
import org.hl7.fhir.dstu3.model.Enumerations;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeType;
import org.opencds.cqf.Operation;
import org.apache.commons.text.WordUtils;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.*;
public class RCKMSJurisdictionsGenerator extends Operation {
private String pathToSpreadsheet; // -pathtospreadsheet (-pts)
private String encoding = "json"; // -encoding (-e)
private String phaState;
// Code sheet defaults
private int codeSheetNum = 0; // -codesheetnum (-csn)
private int codeListRow = 1; // -codelistrow (-clr)
private int idCol = 0; // -idcol (-ic)
private int nameCol = 1; // -namecol (-nc)
private int typeCol = 2; // -typecol (-tc)
private int stateCol = 3; // -statecol (-sc)
private int postalcodeCol = 4; // -postalcodecol (-pc)
@Override
public void execute(String[] args) {
setOutputPath("src/main/resources/org/opencds/cqf/terminology/output"); // default
for (String arg : args) {
if (arg.equals("-JurisdictionsXlsxToCodeSystem")) 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;
case "codesheetnum": case "csn": codeSheetNum = Integer.valueOf(value); break;
case "codelistrow": case "clr": codeListRow = Integer.valueOf(value); break;
case "idcol": case "ic": idCol = Integer.valueOf(value); break;
case "namecol": case "nc": nameCol = Integer.valueOf(value); break;
case "typecol": case "tc": typeCol = Integer.valueOf(value); break;
case "statecol": case "sc": stateCol = Integer.valueOf(value); break;
case "postalcodeCol": case "pc": postalcodeCol = Integer.valueOf(value); 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);
CodeSystem cs = new CodeSystem();
writeCodeSystem(cs, workbook);
writeCodeSystemToFile(cs, encoding);
}
private void writeCodeSystemToFile(CodeSystem cs, String encoding) {
String fileName = ("CodeSystem-ersd-jurisdictions").concat("." + encoding);
IParser parser =
encoding == null
? FhirContext.forDstu3().newJsonParser()
: encoding.toLowerCase().startsWith("j")
? FhirContext.forDstu3().newJsonParser()
: FhirContext.forDstu3().newXmlParser();
try (FileOutputStream writer = new FileOutputStream(getOutputPath() + "/" + fileName)) {
writer.write(parser.setPrettyPrint(true).encodeResourceToString(cs).getBytes());
writer.flush();
} catch (IOException e) {
e.printStackTrace();
throw new IllegalArgumentException("Error writing ValueSet to file: " + e.getMessage());
}
}
public void writeCodeSystem(CodeSystem cs, Workbook workbook) {
cs.setId("ersd-jurisdictions");
cs.setUrl("http://hl7.org/fhir/us/ecr/CodeSystem/ersd-jurisdictions");
cs.setVersion("0.1.0");
cs.setName("ERSDJurisdictions");
cs.setTitle("eRSD Jurisdictions");
cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
cs.setDescription("This code system describes jurisdictions that require public health reporting.");
cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
cs.setCaseSensitive(false);
CodeSystem.PropertyComponent propertyType = new CodeSystem.PropertyComponent();
propertyType.setCode("type");
propertyType.setUri("http://hl7.org/fhir/us/ecr/CodeSystem/ersd-jurisdiction-types");
propertyType.setDescription("Type of public health jurisdiction.");
propertyType.setType(CodeSystem.PropertyType.CODE);
cs.addProperty(propertyType);
CodeSystem.PropertyComponent propertyState = new CodeSystem.PropertyComponent();
propertyState.setCode("state");
propertyState.setUri("http://hl7.org/fhir/us/ecr/CodeSystem/ersd-jurisdiction-states");
propertyState.setDescription("Public health jurisdiction state or territory.");
propertyState.setType(CodeSystem.PropertyType.CODE);
cs.addProperty(propertyState);
CodeSystem.PropertyComponent propertyPost = new CodeSystem.PropertyComponent();
propertyPost.setCode("postalcode");
propertyPost.setUri("http://hl7.org/fhir/us/ecr/CodeSystem/ersd-jurisdiction-postalcodes");
propertyPost.setDescription("Postal code within the public health jurisdiction.");
propertyPost.setType(CodeSystem.PropertyType.CODE);
cs.addProperty(propertyPost);
CodeSystem.ConceptDefinitionComponent concept = new CodeSystem.ConceptDefinitionComponent();
CodeSystem.ConceptPropertyComponent conceptPropType;
CodeSystem.ConceptPropertyComponent conceptPropState;
CodeSystem.ConceptPropertyComponent conceptProp = new CodeSystem.ConceptPropertyComponent();
ArrayList phaCodes = new ArrayList();
Iterator i = workbook.getSheetAt(codeSheetNum).rowIterator();
while (i.hasNext()) {
Row row = i.next();
String phaId = SpreadsheetHelper.getCellAsString(row.getCell(idCol));
String pha_State = SpreadsheetHelper.getCellAsString(row.getCell(stateCol));
String phaStateArr[] = pha_State.split("_");
phaState = String.join(" ", phaStateArr);
phaState = WordUtils.capitalizeFully(phaState);
String phaZip = SpreadsheetHelper.getCellAsString(row.getCell(postalcodeCol));
if (row.getRowNum() < codeListRow) {
continue;
}
convertStateToCode();
if(!phaCodes.contains(phaId)) {
concept = new CodeSystem.ConceptDefinitionComponent();
concept.setCode(phaId.toUpperCase());
concept.setDisplay(SpreadsheetHelper.getCellAsString(row.getCell(stateCol)));
concept.setDefinition(SpreadsheetHelper.getCellAsString(row.getCell(nameCol)));
cs.addConcept(concept);
conceptPropType = new CodeSystem.ConceptPropertyComponent();
conceptPropType.setCode("type");
conceptPropType.setValue(new CodeType(SpreadsheetHelper.getCellAsString(row.getCell(typeCol))));
concept.addProperty(conceptPropType);
conceptPropState = new CodeSystem.ConceptPropertyComponent();
conceptPropState.setCode("state");
conceptPropState.setValue(new CodeType(phaState));
concept.addProperty(conceptPropState);
if (!phaZip.equals("(null)")){
conceptProp = new CodeSystem.ConceptPropertyComponent();
conceptProp.setCode("postalcode");
conceptProp.setValue(new CodeType(phaZip));
concept.addProperty(conceptProp);
}
phaCodes.add(phaId);
} else {
conceptProp = new CodeSystem.ConceptPropertyComponent();
conceptProp.setCode("postalcode");
conceptProp.setValue(new CodeType(phaZip));
concept.addProperty(conceptProp);
}
}
}
public void convertStateToCode() {
switch (phaState) {
case "Alaska": phaState = "AK"; break;
case "Alabama": phaState = "AL"; break;
case "Arkansas": phaState = "AR"; break;
case "American Samoa": phaState = "AS"; break;
case "Arizona": phaState = "AZ"; break;
case "California": phaState = "CA"; break;
case "Colorado": phaState = "CO"; break;
case "Connecticut": phaState = "CT"; break;
case "District Of Columbia": phaState = "DC"; break;
case "Delaware": phaState = "DE"; break;
case "Florida": phaState = "FL"; break;
case "Federated States Of Micronesia": phaState = "FM"; break;
case "Georgia": phaState = "GA"; break;
case "Guam": phaState = "GU"; break;
case "Hawaii": phaState = "HI"; break;
case "Iowa": phaState = "IA"; break;
case "Idaho": phaState = "ID"; break;
case "Illinois": phaState = "IL"; break;
case "Indiana": phaState = "IN"; break;
case "Kansas": phaState = "KS"; break;
case "Kentucky": phaState = "KY"; break;
case "Louisiana": phaState = "LA"; break;
case "Massachusetts": phaState = "MA"; break;
case "Maryland": phaState = "MD"; break;
case "Maine": phaState = "ME"; break;
case "Marshall Islands": phaState = "MH"; break;
case "Michigan": phaState = "MI"; break;
case "Minnesota": phaState = "MN"; break;
case "Missouri": phaState = "MO"; break;
case "Northern Mariana Islands": phaState = "MP"; break;
case "Mississippi": phaState = "MS"; break;
case "Montana": phaState = "MT"; break;
case "North Carolina": phaState = "NC"; break;
case "North Dakota": phaState = "ND"; break;
case "Nebraska": phaState = "NE"; break;
case "New Hampshire": phaState = "NH"; break;
case "New Jersey": phaState = "NJ"; break;
case "New Mexico": phaState = "NM"; break;
case "Nevada": phaState = "NV"; break;
case "New York": phaState = "NY"; break;
case "Ohio": phaState = "OH"; break;
case "Oklahoma": phaState = "OK"; break;
case "Oregon": phaState = "OR"; break;
case "Pennsylvania": phaState = "PA"; break;
case "Puerto Rico": phaState = "PR"; break;
case "Palau": phaState = "PW"; break;
case "Rhode Island": phaState = "RI"; break;
case "South Carolina": phaState = "SC"; break;
case "South Dakota": phaState = "SD"; break;
case "Tennessee": phaState = "TN"; break;
case "Texas": phaState = "TX"; break;
case "U.S. Minor Outlying Islands": phaState = "UM"; break;
case "Utah": phaState = "UT"; break;
case "Virginia": phaState = "VA"; break;
case "Virgin Islands of the U.S.": phaState = "VI"; break;
case "Virgin Islands": phaState = "VI"; break;
case "Vermont": phaState = "VT"; break;
case "Washington": phaState = "WA"; break;
case "Wisconsin": phaState = "WI"; break;
case "West Virginia": phaState = "WV"; break;
case "Wyoming": phaState = "WY"; break;
default: throw new IllegalArgumentException("Unknown State: " + phaState);
}
}
}
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