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Merge pull request #1396 from hapifhir/2023-08-gg-tx-tests-externals
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2023 08 gg tx tests externals
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@grahamegrieve
grahamegrieve authored Aug 19, 2023
2 parents 4766cb3 + 1248bae commit 12e38a3
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78 changes: 67 additions & 11 deletions org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/CPTImporter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,8 @@
import java.sql.SQLException;
import java.sql.Statement;
import java.util.Date;
import java.util.List;
import java.util.ArrayList;
import java.util.Scanner;

import org.hl7.fhir.exceptions.FHIRException;
Expand Down Expand Up @@ -56,19 +58,23 @@ private void doImport(String src, String version, String dst) throws FHIRExcepti
cs.setCopyright("CPT © Copyright 2019 American Medical Association. All rights reserved. AMA and CPT are registered trademarks of the American Medical Association.");
cs.addProperty().setCode("modifier").setDescription("Whether code is a modifier code").setType(PropertyType.BOOLEAN);
cs.addProperty().setCode("modified").setDescription("Whether code has been modified (all base codes are not modified)").setType(PropertyType.BOOLEAN);
cs.addProperty().setCode("orthopox").setDescription("Whether code is one of the Pathology and Laboratory and Immunization Code(s) for Orthopoxvirus").setType(PropertyType.BOOLEAN);
cs.addProperty().setCode("telemedicine").setDescription("Whether code is appropriate for use with telemedicine (and the telemedicine modifier)").setType(PropertyType.BOOLEAN);
cs.addProperty().setCode("kind").setDescription("Kind of Code (see metadata)").setType(PropertyType.CODE);

defineMetadata(cs);

System.out.println(readCodes(cs, Utilities.path(src, "LONGULT.txt"), false, null, null));
System.out.println(readCodes(cs, Utilities.path(src, "LONGUT.txt"), false, "upper", null));
System.out.println(readCodes(cs, Utilities.path(src, "MEDU.txt"), false, "med", null));
System.out.println(readCodes(cs, Utilities.path(src, "SHORTU.txt"), false, "short", null));
System.out.println(readCodes(cs, Utilities.path(src, "ConsumerDescriptor.txt"), true, "consumer", null));
System.out.println(readCodes(cs, Utilities.path(src, "ClinicianDescriptor.txt"), true, "clinician", null));
System.out.println(readCodes(cs, Utilities.path(src, "OrthopoxvirusCodes.txt"), false, null, "orthopod"));
System.out.println("LONGULT: "+readCodes(cs, Utilities.path(src, "LONGULT.txt"), false, null, null, null));
System.out.println("LONGUT: "+readCodes(cs, Utilities.path(src, "LONGUT.txt"), false, "upper", null, null));
System.out.println("MEDU: "+readCodes(cs, Utilities.path(src, "MEDU.txt"), false, "med", null, null));
System.out.println("SHORTU: "+readCodes(cs, Utilities.path(src, "SHORTU.txt"), false, "short", null, null));
System.out.println("ConsumerDescriptor: "+readCodes(cs, Utilities.path(src, "ConsumerDescriptor.txt"), true, "consumer", null, null));
System.out.println("ClinicianDescriptor: "+readCodes(cs, Utilities.path(src, "ClinicianDescriptor.txt"), true, "clinician", null, null));
System.out.println("OrthopoxvirusCodes: "+readCodes(cs, Utilities.path(src, "OrthopoxvirusCodes.txt"), false, null, null, "orthopox"));

System.out.println(processModifiers(cs, Utilities.path(src, "modifiers.csv")));
System.out.println("modifiers: "+processModifiers(cs, Utilities.path(src, "modifiers.csv")));
System.out.println("appendix P: "+processAppendixP(cs));


System.out.println("-------------------");
System.out.println(cs.getConcept().size());
Expand All @@ -87,11 +93,59 @@ private void doImport(String src, String version, String dst) throws FHIRExcepti
produceDB(Utilities.changeFileExt(dst, ".db"), cs);

cs.setContent(CodeSystemContentMode.FRAGMENT);
cs.getConcept().removeIf(cc -> !Utilities.existsInList(cc.getCode(), "metadata-kinds", "metadata-designations", "99202", "99203", "0001A", "25", "P1", "1P", "F1"));
cs.getConcept().removeIf(cc -> !Utilities.existsInList(cc.getCode(), "metadata-kinds", "metadata-designations", "99202", "99203", "0001A", "99252", "25", "P1", "1P", "F1", "95"));
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.changeFileExt(dst, "-fragment.json")), cs);
produceDB(Utilities.changeFileExt(dst, "-fragment.db"), cs);
}

private String processAppendixP(CodeSystem cs) {
List<String> tcodes = new ArrayList<>();
tcodes.add("90785");
tcodes.add("90791");
tcodes.add("90792");
tcodes.add("90832");
tcodes.add("90833");
tcodes.add("90834");
tcodes.add("90836");
tcodes.add("90837");
tcodes.add("90838");
tcodes.add("90839");
tcodes.add("90840");
tcodes.add("90845");
tcodes.add("90846");
tcodes.add("90847");
tcodes.add("92507");
tcodes.add("92508");
tcodes.add("92521");
tcodes.add("92522");
tcodes.add("92523");
tcodes.add("92524");
tcodes.add("96040");
tcodes.add("96110");
tcodes.add("96116");
tcodes.add("96160");
tcodes.add("96161");
tcodes.add("97802");
tcodes.add("97803");
tcodes.add("97804");
tcodes.add("99406");
tcodes.add("99407");
tcodes.add("99408");
tcodes.add("99409");
tcodes.add("99497");
tcodes.add("99498");

for (String c : tcodes) {
ConceptDefinitionComponent cc = CodeSystemUtilities.findCode(cs.getConcept(), c);
if (cc == null) {
throw new Error("unable to find tcode "+c);
}
cc.addProperty().setCode("telemedicine").setValue(new BooleanType(true));
}
return String.valueOf(tcodes.size());
}


private void produceDB(String path, CodeSystem cs) throws ClassNotFoundException, SQLException {
Connection con = connect(path);

Expand Down Expand Up @@ -197,7 +251,6 @@ private void defineMetadata(CodeSystem cs) {
mm(pc.addConcept()).setCode("physical-status").setDisplay("Anesthesia Physical Status Modifiers");
mm(pc.addConcept()).setCode("general").setDisplay("A general modifier");
mm(pc.addConcept()).setCode("hcpcs").setDisplay("Level II (HCPCS/National) Modifiers");
mm(pc.addConcept()).setCode("orthopox").setDisplay("");
mm(pc.addConcept()).setCode("metadata").setDisplay("A kind of code or designation");

ConceptDefinitionComponent dc = mm(cs.addConcept().setCode("metadata-designations"));
Expand Down Expand Up @@ -251,7 +304,7 @@ private int processModifiers(CodeSystem cs, String path) throws FHIRException, F
return res;
}

private int readCodes(CodeSystem cs, String path, boolean hasConceptId, String use, String type) throws IOException {
private int readCodes(CodeSystem cs, String path, boolean hasConceptId, String use, String type, String boolProp) throws IOException {
int res = 0;
FileInputStream inputStream = null;
Scanner sc = null;
Expand Down Expand Up @@ -286,6 +339,9 @@ private int readCodes(CodeSystem cs, String path, boolean hasConceptId, String u
} else if (type != null) {
cc.addProperty().setCode("kind").setValue(new CodeType(type));
}
if (boolProp != null) {
cc.addProperty().setCode(boolProp).setValue(new BooleanType(true));
}
if (use == null) {
if (cc.hasDisplay()) {
System.err.println("?");
Expand Down
133 changes: 110 additions & 23 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/CanonicalResourceComparer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,15 +9,13 @@
import java.util.Set;

import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.comparison.CanonicalResourceComparer.ChangeAnalysisState;
import org.hl7.fhir.r5.comparison.ResourceComparer.MessageCounts;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.PrimitiveType;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
Expand Down Expand Up @@ -257,53 +255,53 @@ public CanonicalResourceComparer(ComparisonSession session) {
super(session);
}

protected boolean compareMetadata(CanonicalResource left, CanonicalResource right, Map<String, StructuralMatch<String>> comp, CanonicalResourceComparison<? extends CanonicalResource> res, List<String> changes, Base parent, String version) {
protected boolean compareMetadata(CanonicalResource left, CanonicalResource right, Map<String, StructuralMatch<String>> comp, CanonicalResourceComparison<? extends CanonicalResource> res, List<String> changes, Base parent) {
var changed = false;
if (comparePrimitivesWithTracking("url", left.getUrlElement(), right.getUrlElement(), comp, IssueSeverity.ERROR, res, parent, version)) {
if (comparePrimitivesWithTracking("url", left.getUrlElement(), right.getUrlElement(), comp, IssueSeverity.ERROR, res, parent)) {
changed = true;
changes.add("url");
}
if (session.getForVersion() == null) {
if (comparePrimitivesWithTracking("version", left.getVersionElement(), right.getVersionElement(), comp, IssueSeverity.ERROR, res, parent, version)) {
if (!session.isAnnotate()) {
if (comparePrimitivesWithTracking("version", left.getVersionElement(), right.getVersionElement(), comp, IssueSeverity.ERROR, res, parent)) {
changed = true;
changes.add("version");
}
}
if (comparePrimitivesWithTracking("name", left.getNameElement(), right.getNameElement(), comp, IssueSeverity.INFORMATION, res, parent, version)) {
if (comparePrimitivesWithTracking("name", left.getNameElement(), right.getNameElement(), comp, IssueSeverity.INFORMATION, res, parent)) {
changed = true;
changes.add("name");
}
if (comparePrimitivesWithTracking("title", left.getTitleElement(), right.getTitleElement(), comp, IssueSeverity.INFORMATION, res, parent, version)) {
if (comparePrimitivesWithTracking("title", left.getTitleElement(), right.getTitleElement(), comp, IssueSeverity.INFORMATION, res, parent)) {
changed = true;
changes.add("title");
}
if (comparePrimitivesWithTracking("status", left.getStatusElement(), right.getStatusElement(), comp, IssueSeverity.INFORMATION, res, parent, version)) {
if (comparePrimitivesWithTracking("status", left.getStatusElement(), right.getStatusElement(), comp, IssueSeverity.INFORMATION, res, parent)) {
changed = true;
changes.add("status");
}
if (comparePrimitivesWithTracking("experimental", left.getExperimentalElement(), right.getExperimentalElement(), comp, IssueSeverity.WARNING, res, parent, version)) {
if (comparePrimitivesWithTracking("experimental", left.getExperimentalElement(), right.getExperimentalElement(), comp, IssueSeverity.WARNING, res, parent)) {
changed = true;
changes.add("experimental");
}
if (session.getForVersion() == null) {
if (comparePrimitivesWithTracking("date", left.getDateElement(), right.getDateElement(), comp, IssueSeverity.INFORMATION, res, parent, version)) {
if (!session.isAnnotate()) {
if (comparePrimitivesWithTracking("date", left.getDateElement(), right.getDateElement(), comp, IssueSeverity.INFORMATION, res, parent)) {
changed = true;
changes.add("date");
}
}
if (comparePrimitivesWithTracking("publisher", left.getPublisherElement(), right.getPublisherElement(), comp, IssueSeverity.INFORMATION, res, parent, version)) {
if (comparePrimitivesWithTracking("publisher", left.getPublisherElement(), right.getPublisherElement(), comp, IssueSeverity.INFORMATION, res, parent)) {
changed = true;
changes.add("publisher");
}
if (comparePrimitivesWithTracking("description", left.getDescriptionElement(), right.getDescriptionElement(), comp, IssueSeverity.NULL, res, parent, version)) {
if (comparePrimitivesWithTracking("description", left.getDescriptionElement(), right.getDescriptionElement(), comp, IssueSeverity.NULL, res, parent)) {
changed = true;
changes.add("description");
}
if (comparePrimitivesWithTracking("purpose", left.getPurposeElement(), right.getPurposeElement(), comp, IssueSeverity.NULL, res, parent, version)) {
if (comparePrimitivesWithTracking("purpose", left.getPurposeElement(), right.getPurposeElement(), comp, IssueSeverity.NULL, res, parent)) {
changed = true;
changes.add("purpose");
}
if (comparePrimitivesWithTracking("copyright", left.getCopyrightElement(), right.getCopyrightElement(), comp, IssueSeverity.INFORMATION, res, parent, version)) {
if (comparePrimitivesWithTracking("copyright", left.getCopyrightElement(), right.getCopyrightElement(), comp, IssueSeverity.INFORMATION, res, parent)) {
changed = true;
changes.add("copyright");
}
Expand Down Expand Up @@ -464,29 +462,59 @@ protected boolean comparePrimitives(String name, PrimitiveType l, PrimitiveType
}


protected boolean comparePrimitivesWithTracking(String name, List< ? extends PrimitiveType> ll, List<? extends PrimitiveType> rl, Map<String, StructuralMatch<String>> comp, IssueSeverity level, CanonicalResourceComparison<? extends CanonicalResource> res, Base parent) {
boolean def = false;

List<PrimitiveType> matchR = new ArrayList<>();
for (PrimitiveType l : ll) {
PrimitiveType r = findInList(rl, l);
if (r == null) {
session.markDeleted(parent, "element", l);
} else {
matchR.add(r);
def = comparePrimitivesWithTracking(name, l, r, comp, level, res, parent) || def;
}
}
for (PrimitiveType r : rl) {
if (!matchR.contains(r)) {
session.markAdded(r);
}
}
return def;
}

private PrimitiveType findInList(List<? extends PrimitiveType> rl, PrimitiveType l) {
for (PrimitiveType r : rl) {
if (r.equalsDeep(l)) {
return r;
}
}
return null;
}

@SuppressWarnings("rawtypes")
protected boolean comparePrimitivesWithTracking(String name, PrimitiveType l, PrimitiveType r, Map<String, StructuralMatch<String>> comp, IssueSeverity level, CanonicalResourceComparison<? extends CanonicalResource> res, Base parent, String version) {
protected boolean comparePrimitivesWithTracking(String name, PrimitiveType l, PrimitiveType r, Map<String, StructuralMatch<String>> comp, IssueSeverity level, CanonicalResourceComparison<? extends CanonicalResource> res, Base parent) {
StructuralMatch<String> match = null;
if (l.isEmpty() && r.isEmpty()) {
match = new StructuralMatch<>(null, null, null);
} else if (l.isEmpty()) {
match = new StructuralMatch<>(null, r.primitiveValue(), vmI(IssueSeverity.INFORMATION, "Added the item '"+r.primitiveValue()+"'", fhirType()+"."+name));
VersionComparisonAnnotation.markAdded(r, version);
session.markAdded(r);
} else if (r.isEmpty()) {
match = new StructuralMatch<>(l.primitiveValue(), null, vmI(IssueSeverity.INFORMATION, "Removed the item '"+l.primitiveValue()+"'", fhirType()+"."+name));
VersionComparisonAnnotation.markDeleted(parent, version, name, l);
session.markDeleted(parent, name, l);
} else if (!l.hasValue() && !r.hasValue()) {
match = new StructuralMatch<>(null, null, vmI(IssueSeverity.INFORMATION, "No Value", fhirType()+"."+name));
} else if (!l.hasValue()) {
match = new StructuralMatch<>(null, r.primitiveValue(), vmI(IssueSeverity.INFORMATION, "No Value on Left", fhirType()+"."+name));
VersionComparisonAnnotation.markAdded(r, version);
session.markAdded(r);
} else if (!r.hasValue()) {
match = new StructuralMatch<>(l.primitiveValue(), null, vmI(IssueSeverity.INFORMATION, "No Value on Right", fhirType()+"."+name));
VersionComparisonAnnotation.markDeleted(parent, version, name, l);
session.markDeleted(parent, name, l);
} else if (l.getValue().equals(r.getValue())) {
match = new StructuralMatch<>(l.primitiveValue(), r.primitiveValue(), null);
} else {
VersionComparisonAnnotation.markChanged(r, version);
session.markChanged(r, l);
match = new StructuralMatch<>(l.primitiveValue(), r.primitiveValue(), vmI(level, "Values Differ", fhirType()+"."+name));
if (level != IssueSeverity.NULL && res != null) {
res.getMessages().add(new ValidationMessage(Source.ProfileComparer, IssueType.INFORMATIONAL, fhirType()+"."+name, "Values for "+name+" differ: '"+l.primitiveValue()+"' vs '"+r.primitiveValue()+"'", level));
Expand All @@ -497,6 +525,65 @@ protected boolean comparePrimitivesWithTracking(String name, PrimitiveType l, Pr
}
return match.isDifferent();
}


protected boolean compareDataTypesWithTracking(String name, List< ? extends DataType> ll, List<? extends DataType> rl, Map<String, StructuralMatch<String>> comp, IssueSeverity level, CanonicalResourceComparison<? extends CanonicalResource> res, Base parent) {
boolean def = false;

List<DataType> matchR = new ArrayList<>();
for (DataType l : ll) {
DataType r = findInList(rl, l);
if (r == null) {
session.markDeleted(parent, "element", l);
} else {
matchR.add(r);
def = compareDataTypesWithTracking(name, l, r, comp, level, res, parent) || def;
}
}
for (DataType r : rl) {
if (!matchR.contains(r)) {
session.markAdded(r);
}
}
return def;
}

private DataType findInList(List<? extends DataType> rl, DataType l) {
for (DataType r : rl) {
if (r.equalsDeep(l)) {
return r;
}
}
return null;
}

@SuppressWarnings("rawtypes")
protected boolean compareDataTypesWithTracking(String name, DataType l, DataType r, Map<String, StructuralMatch<String>> comp, IssueSeverity level, CanonicalResourceComparison<? extends CanonicalResource> res, Base parent) {
StructuralMatch<String> match = null;
boolean le = l == null || l.isEmpty();
boolean re = r == null || r.isEmpty();
if (le && re) {
match = new StructuralMatch<>(null, null, null);
} else if (le) {
match = new StructuralMatch<>(null, r.primitiveValue(), vmI(IssueSeverity.INFORMATION, "Added the item '"+r.fhirType()+"'", fhirType()+"."+name));
session.markAdded(r);
} else if (re) {
match = new StructuralMatch<>(l.primitiveValue(), null, vmI(IssueSeverity.INFORMATION, "Removed the item '"+l.fhirType()+"'", fhirType()+"."+name));
session.markDeleted(parent, name, l);
} else if (l.equalsDeep(r)) {
match = new StructuralMatch<>(l.primitiveValue(), r.primitiveValue(), null);
} else {
session.markChanged(r, l);
match = new StructuralMatch<>(l.fhirType(), r.fhirType(), vmI(level, "Values Differ", fhirType()+"."+name));
if (level != IssueSeverity.NULL && res != null) {
res.getMessages().add(new ValidationMessage(Source.ProfileComparer, IssueType.INFORMATIONAL, fhirType()+"."+name, "Values for "+name+" differ: '"+l.fhirType()+"' vs '"+r.fhirType()+"'", level));
}
}
if (comp != null) {
comp.put(name, match);
}
return match.isDifferent();
}

protected abstract String fhirType();

Expand Down
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