org.hl7.fhir.r5.utils.MappingSheetParser Maven / Gradle / Ivy
package org.hl7.fhir.r5.utils;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.ConceptMap;
import org.hl7.fhir.r5.model.ConceptMap.ConceptMapGroupComponent;
import org.hl7.fhir.r5.model.ConceptMap.OtherElementComponent;
import org.hl7.fhir.r5.model.ConceptMap.SourceElementComponent;
import org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent;
import org.hl7.fhir.r5.model.DateTimeType;
import org.hl7.fhir.r5.model.Enumerations.ConceptMapRelationship;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupComponent;
import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupRuleComponent;
import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupRuleDependentComponent;
import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupRuleSourceComponent;
import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupRuleTargetComponent;
import org.hl7.fhir.r5.model.StructureMap.StructureMapTransform;
import org.hl7.fhir.r5.model.UrlType;
import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.FileUtilities;
import org.hl7.fhir.utilities.MarkedToMoveToAdjunctPackage;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
@MarkedToMoveToAdjunctPackage
public class MappingSheetParser {
public class MappingRow {
private String sequence;
private String identifier;
private String name;
private String dataType;
private String cardinality;
private String condition;
private String attribute;
private String type;
private String minMax;
private String dtMapping;
private String vocabMapping;
private String derived;
private String derivedMapping;
private String comments;
public String getSequence() {
return sequence;
}
public String getIdentifier() {
return identifier;
}
public String getName() {
return name;
}
public String getDataType() {
return dataType;
}
public String getCardinality() {
return cardinality;
}
public int getCardinalityMin() {
return Integer.parseInt(cardinality.split("\\.")[0]);
}
public String getCardinalityMax() {
return cardinality.split("\\.")[2];
}
public String getCondition() {
return condition;
}
public String getAttribute() {
return attribute;
}
public String getType() {
return type;
}
public String getMinMax() {
return minMax;
}
public String getDtMapping() {
return dtMapping;
}
public String getVocabMapping() {
return vocabMapping;
}
public String getDerived() {
return derived;
}
public String getDerivedMapping() {
return derivedMapping;
}
public String getComments() {
return comments;
}
}
private List rows = new ArrayList<>();
private Map metadata = new HashMap<>();
public MappingSheetParser() {
super();
}
public void parse(InputStream stream, String name) throws FHIRException, IOException {
CSVReader csv = new CSVReader(stream);
checkHeaders1(csv, name);
checkHeaders2(csv, name);
while (csv.line()) {
processRow(csv);
}
}
private void checkHeaders1(CSVReader csv, String name) throws FHIRException, IOException {
csv.readHeaders();
csv.checkColumn(1, "HL7 v2", "Mapping Sheet "+name);
csv.checkColumn(6, "Condition (IF True)", "Mapping Sheet "+name);
csv.checkColumn(7, "HL7 FHIR", "Mapping Sheet "+name);
csv.checkColumn(14, "Comments", "Mapping Sheet "+name);
csv.checkColumn(16, "Name", "Mapping Sheet "+name);
csv.checkColumn(17, "Value", "Mapping Sheet "+name);
}
private void checkHeaders2(CSVReader csv, String name) throws FHIRException, IOException {
csv.readHeaders();
csv.checkColumn(1, "Display Sequence", "Mapping Sheet "+name);
csv.checkColumn(2, "Identifier", "Mapping Sheet "+name);
csv.checkColumn(3, "Name", "Mapping Sheet "+name);
csv.checkColumn(4, "Data Type", "Mapping Sheet "+name);
csv.checkColumn(5, "Cardinality", "Mapping Sheet "+name);
csv.checkColumn(7, "FHIR Attribute", "Mapping Sheet "+name);
csv.checkColumn(8, "Data Type", "Mapping Sheet "+name);
csv.checkColumn(9, "Cardinality", "Mapping Sheet "+name);
csv.checkColumn(10, "Data Type Mapping", "Mapping Sheet "+name);
csv.checkColumn(11, "Vocabulary Mapping\n(IS, ID, CE, CNE, CWE)", "Mapping Sheet "+name);
csv.checkColumn(12, "Derived Mapping", "Mapping Sheet "+name);
}
private void processRow(CSVReader csv) {
MappingRow mr = new MappingRow();
mr.sequence = csv.value(1);
mr.identifier = csv.value(2);
mr.name = csv.value(3);
mr.dataType = csv.value(4);
mr.cardinality = csv.value(5);
mr.condition = csv.value(6);
mr.attribute = csv.value(7);
mr.type = csv.value(8);
mr.minMax = csv.value(9);
mr.dtMapping = csv.value(10);
mr.vocabMapping = csv.value(11);
mr.derived = csv.value(12);
if (!Utilities.noString(mr.derived)) {
String[] s = mr.derived.split("\\=");
mr.derived = s[0].trim();
mr.derivedMapping = s[1].trim();
}
mr.comments = csv.value(14);
rows.add(mr);
if (!org.hl7.fhir.utilities.Utilities.noString(csv.value(16)))
metadata.put(csv.value(16), csv.value(17));
}
public List getRows() {
return rows;
}
public ConceptMap getConceptMap() throws FHIRException {
ConceptMap map = new ConceptMap();
loadMetadata(map);
if (metadata.containsKey("copyright"))
map.setCopyright(metadata.get("copyright"));
for (MappingRow row : rows) {
SourceElementComponent element = map.getGroupFirstRep().addElement();
element.setCode(row.getIdentifier());
element.setId(row.getSequence());
element.setDisplay(row.getName()+" : "+row.getDataType()+" ["+row.getCardinality()+"]");
element.addExtension(ToolingExtensions.EXT_MAPPING_NAME, new StringType(row.getName()));
element.addExtension(ToolingExtensions.EXT_MAPPING_TYPE, new StringType(row.getDataType()));
element.addExtension(ToolingExtensions.EXT_MAPPING_CARD, new StringType(row.getCardinality()));
if ("N/A".equals(row.getAttribute()))
element.setNoMap(true);
else {
element.getTargetFirstRep().setRelationship(ConceptMapRelationship.RELATEDTO);
if (row.getCondition() != null)
element.getTargetFirstRep().addDependsOn().setAttribute("http://hl7.org/fhirpath").setValue(new StringType(processCondition(row.getCondition())));
element.getTargetFirstRep().setCode(row.getAttribute());
element.getTargetFirstRep().setDisplay(row.getType()+" : ["+row.getMinMax()+"]");
element.getTargetFirstRep().addExtension(ToolingExtensions.EXT_MAPPING_TGTTYPE, new StringType(row.getType()));
element.getTargetFirstRep().addExtension(ToolingExtensions.EXT_MAPPING_TGTCARD, new StringType(row.getMinMax()));
if (row.getDerived() != null)
element.getTargetFirstRep().getProductFirstRep().setAttribute(row.getDerived()).setValue(new StringType(row.getDerivedMapping()));
if (row.getComments() != null)
element.getTargetFirstRep().setComment(row.getComments());
if (row.getDtMapping() != null)
element.getTargetFirstRep().addExtension("http://hl7.org/fhir/StructureDefinition/ConceptMap-type-mapping", new UrlType("todo#"+row.getDtMapping()));
if (row.getVocabMapping() != null)
element.getTargetFirstRep().addExtension("http://hl7.org/fhir/StructureDefinition/ConceptMap-vocab-mapping", new UrlType("todo#"+row.getVocabMapping()));
}
}
return map;
}
private String processCondition(String condition) {
if (condition.startsWith("IF ") && condition.endsWith(" IS VALUED"))
return "`"+condition.substring(4, condition.length()-10)+"`.exists()";
if (condition.startsWith("IF ") && condition.endsWith(" DOES NOT EXIST"))
return "`"+condition.substring(4, condition.length()-15)+"`.exists()";
throw new Error("not processed yet: "+condition);
}
private void loadMetadata(CanonicalResource mr) throws FHIRException {
if (metadata.containsKey("id"))
mr.setId(metadata.get("id"));
if (metadata.containsKey("url"))
mr.setUrl(metadata.get("url"));
if (metadata.containsKey("name"))
mr.setName(metadata.get("name"));
if (metadata.containsKey("title"))
mr.setTitle(metadata.get("title"));
if (metadata.containsKey("version"))
mr.setVersion(metadata.get("version"));
if (metadata.containsKey("status"))
mr.setStatus(PublicationStatus.fromCode(metadata.get("status")));
if (metadata.containsKey("date"))
mr.setDateElement(new DateTimeType(metadata.get("date")));
if (metadata.containsKey("publisher"))
mr.setPublisher(metadata.get("publisher"));
if (metadata.containsKey("description"))
mr.setDescription(metadata.get("description"));
}
public StructureMap getStructureMap() throws FHIRException {
StructureMap map = new StructureMap();
loadMetadata(map);
if (metadata.containsKey("copyright"))
map.setCopyright(metadata.get("copyright"));
StructureMapGroupComponent grp = map.addGroup();
for (MappingRow row : rows) {
StructureMapGroupRuleComponent rule = grp.addRule();
rule.setName(row.getSequence());
StructureMapGroupRuleSourceComponent src = rule.getSourceFirstRep();
src.setContext("src");
src.setElement(row.getIdentifier());
src.setMin(row.getCardinalityMin());
src.setMax(row.getCardinalityMax());
src.setType(row.getDataType());
src.addExtension(ToolingExtensions.EXT_MAPPING_NAME, new StringType(row.getName()));
if (row.getCondition() != null) {
src.setCheck(processCondition(row.getCondition()));
}
StructureMapGroupRuleTargetComponent tgt = rule.getTargetFirstRep();
tgt.setContext("tgt");
tgt.setElement(row.getAttribute());
tgt.addExtension(ToolingExtensions.EXT_MAPPING_TGTTYPE, new StringType(row.getType()));
tgt.addExtension(ToolingExtensions.EXT_MAPPING_TGTCARD, new StringType(row.getMinMax()));
if (row.getDtMapping() != null) {
src.setVariable("s");
tgt.setVariable("t");
tgt.setTransform(StructureMapTransform.CREATE);
StructureMapGroupRuleDependentComponent dep = rule.addDependent();
dep.setName(row.getDtMapping());
dep.addParameter().setValue(new IdType("s"));
dep.addParameter().setValue(new IdType("t"));
} else if (row.getVocabMapping() != null) {
tgt.setTransform(StructureMapTransform.TRANSLATE);
tgt.addParameter().setValue(new StringType(row.getVocabMapping()));
tgt.addParameter().setValue(new IdType("src"));
} else {
tgt.setTransform(StructureMapTransform.COPY);
}
rule.setDocumentation(row.getComments());
if (row.getDerived() != null) {
tgt = rule.addTarget();
tgt.setContext("tgt");
tgt.setElement(row.getDerived());
tgt.setTransform(StructureMapTransform.COPY);
tgt.addParameter().setValue(new StringType(row.getDerivedMapping()));
}
}
return map;
}
public boolean isSheet(ConceptMap cm) {
if (cm.getGroup().size() != 1)
return false;
ConceptMapGroupComponent grp = cm.getGroupFirstRep();
for (SourceElementComponent e : grp.getElement()) {
if (!e.hasExtension(ToolingExtensions.EXT_MAPPING_TYPE))
return false;
}
return true;
}
public String genSheet(ConceptMap cm) throws FHIRException {
StringBuilder b = new StringBuilder();
readConceptMap(cm);
b.append("\r\n");
addHeaderRow1(b);
addHeaderRow2(b);
for (MappingRow row : rows)
addRow(b, row);
b.append("
\r\n");
return b.toString();
}
private void addRow(StringBuilder b, MappingRow row) {
b.append(" ");
b.append(""+Utilities.escapeXml(nn(row.sequence))+" ");
b.append(""+Utilities.escapeXml(nn(row.identifier))+" ");
b.append(""+Utilities.escapeXml(nn(row.name))+" ");
b.append(""+Utilities.escapeXml(nn(row.dataType))+" ");
b.append(""+Utilities.escapeXml(nn(row.cardinality))+" ");
b.append(""+Utilities.escapeXml(nn(row.condition))+" ");
b.append(""+Utilities.escapeXml(nn(row.attribute))+" ");
b.append(""+Utilities.escapeXml(nn(row.type))+" ");
b.append(""+Utilities.escapeXml(nn(row.minMax))+" ");
b.append(""+Utilities.escapeXml(nn(row.dtMapping))+" ");
b.append(""+Utilities.escapeXml(nn(row.vocabMapping))+" ");
if (row.derived != null)
b.append(""+Utilities.escapeXml(nn(row.derived+"="+row.derivedMapping))+" ");
else
b.append(""+Utilities.escapeXml(nn(row.comments))+" ");
b.append(" \r\n");
}
private String nn(String s) {
return s == null ? "" : s;
}
private void addHeaderRow1(StringBuilder b) {
b.append(" ");
b.append("v2 ");
b.append("Condition ");
b.append("FHIR ");
b.append("Comments ");
b.append(" \r\n");
}
private void addHeaderRow2(StringBuilder b) {
b.append(" ");
b.append("Display Sequence ");
b.append("Identifier ");
b.append("Name ");
b.append("Data Type ");
b.append("Cardinality ");
b.append("FHIR Attribute ");
b.append("Data Type ");
b.append("Cardinality ");
b.append("Data Type Mapping ");
b.append("Vocabulary Mapping ");
b.append("Derived Mapping ");
b.append(" \r\n");
}
private void readConceptMap(ConceptMap cm) throws FHIRException {
for (ConceptMapGroupComponent g : cm.getGroup()) {
for (SourceElementComponent e : g.getElement()) {
if (e.hasId() && e.getTarget().size() == 1 && e.hasExtension(ToolingExtensions.EXT_MAPPING_TYPE)) {
TargetElementComponent t = e.getTargetFirstRep();
MappingRow row = new MappingRow();
row.sequence = e.getId();
row.identifier = e.getCode();
row.name = e.getExtensionString(ToolingExtensions.EXT_MAPPING_NAME);
row.dataType = e.getExtensionString(ToolingExtensions.EXT_MAPPING_TYPE);
row.cardinality = e.getExtensionString(ToolingExtensions.EXT_MAPPING_CARD);
if (e.getNoMap() == true) {
row.attribute = "N/A";
} else {
OtherElementComponent dep = getDependency(t, "http://hl7.org/fhirpath");
if (dep != null)
row.condition = dep.getValue().primitiveValue();
row.attribute = t.getCode();
row.type = t.getExtensionString(ToolingExtensions.EXT_MAPPING_TGTTYPE);
row.minMax = t.getExtensionString(ToolingExtensions.EXT_MAPPING_TGTCARD);
row.dtMapping = t.getExtensionString("http://hl7.org/fhir/StructureDefinition/ConceptMap-type-mapping");
row.vocabMapping = t.getExtensionString("http://hl7.org/fhir/StructureDefinition/ConceptMap-vocab-mapping");
if (t.getProduct().size() > 0) {
row.derived = t.getProductFirstRep().getAttribute();
row.derivedMapping = t.getProductFirstRep().getValue().primitiveValue();
}
}
row.comments = t.getComment();
rows.add(row);
}
}
}
}
private OtherElementComponent getDependency(TargetElementComponent t, String prop) {
for (OtherElementComponent dep : t.getDependsOn()) {
if (prop.equals(dep.getAttribute()))
return dep;
}
return null;
}
private static final String PFX = "\r\n";
private static final String SFX = "";
public static void main(String[] args) throws FileNotFoundException, IOException, FHIRException {
MappingSheetParser parser = new MappingSheetParser();
parser.parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "v2-pid.csv")), "v2-pid.csv");
ConceptMap cm = parser.getConceptMap();
StructureMap sm = parser.getStructureMap();
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "sm.json")), sm);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "cm.json")), cm);
FileUtilities.stringToFile(StructureMapUtilities.render(sm), Utilities.path("[tmp]", "sm.txt"));
FileUtilities.stringToFile(PFX+parser.genSheet(cm)+SFX, Utilities.path("[tmp]", "map.html"));
}
} © 2015 - 2025 Weber Informatics LLC | Privacy Policy