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Minor correction to align with FHIR R5 RDF changes

This commit is contained in:
dksharma 2023-02-27 02:18:24 -06:00
parent 5fde3a2106
commit a593e9a60d
2 changed files with 135 additions and 89 deletions
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152
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ShExGenerator.java
View File

@ -61,7 +61,9 @@ public class ShExGenerator {
public boolean withComments = true; // include comments
public boolean completeModel = false; // doing complete build (fhir.shex)
public boolean debugMode = false;
public boolean debugMode = false; // Used for Debugging and testing the code
public boolean processConstraints = true; // set to false - to skip processing constraints
public ConstraintTranslationPolicy constraintPolicy = ConstraintTranslationPolicy.ALL;
@ -643,25 +645,27 @@ public class ShExGenerator {
isInnerType = true;
}
// Process constraints
for (ElementDefinition.ElementDefinitionConstraintComponent constraint : ed.getConstraint()) {
String sdType = sd.getType();
String cstype = constraint.getSource();
if ((!cstype.isEmpty()) && (cstype.indexOf("/") != -1)) {
String[] els = cstype.split("/");
cstype = els[els.length - 1];
}
if (processConstraints) {
// Process constraints
for (ElementDefinition.ElementDefinitionConstraintComponent constraint : ed.getConstraint()) {
String sdType = sd.getType();
String cstype = constraint.getSource();
if ((!cstype.isEmpty()) && (cstype.indexOf("/") != -1)) {
String[] els = cstype.split("/");
cstype = els[els.length - 1];
}
String id = ed.hasBase() ? ed.getBase().getPath() : ed.getPath();
String shortId = id.substring(id.lastIndexOf(".") + 1);
if ((ed.hasContentReference() && (!ed.hasType())) || (id.equals(sd.getName() + "." + shortId))) {
if ((sdType.equals(cstype)) || baseDataTypes.contains(sdType)) {
if (!isInnerType) {
debug("\n Key: " + constraint.getKey() + " SD type: " + sd.getType() + " Element: " + ed.getPath() + " Constraint Source: " + constraint.getSource() + " Constraint:" + constraint.getExpression());
String transl = translateConstraint(sd, ed, constraint);
if (transl.isEmpty() || constraintsList.contains(transl))
continue;
constraintsList.add(transl);
String id = ed.hasBase() ? ed.getBase().getPath() : ed.getPath();
String shortId = id.substring(id.lastIndexOf(".") + 1);
if ((ed.hasContentReference() && (!ed.hasType())) || (id.equals(sd.getName() + "." + shortId))) {
if ((sdType.equals(cstype)) || baseDataTypes.contains(sdType)) {
if (!isInnerType) {
debug("\n Key: " + constraint.getKey() + " SD type: " + sd.getType() + " Element: " + ed.getPath() + " Constraint Source: " + constraint.getSource() + " Constraint:" + constraint.getExpression());
String transl = translateConstraint(sd, ed, constraint);
if (transl.isEmpty() || constraintsList.contains(transl))
continue;
constraintsList.add(transl);
}
}
}
}
@ -679,24 +683,27 @@ public class ShExGenerator {
}
}
// Constraints for differential to cover constraints on SD itself without any elements of its own
for (ElementDefinition ded : sd.getDifferential().getElement()) {
// Process constraints
for (ElementDefinition.ElementDefinitionConstraintComponent dconstraint : ded.getConstraint()) {
String sdType = sd.getType();
if (processConstraints) {
// Constraints for differential to cover constraints on SD itself without any elements of its own
for (ElementDefinition ded : sd.getDifferential().getElement()) {
// Process constraints
for (ElementDefinition.ElementDefinitionConstraintComponent dconstraint : ded.getConstraint()) {
String sdType = sd.getType();
String id = ded.hasBase() ? ded.getBase().getPath() : ded.getPath();
String shortId = id.substring(id.lastIndexOf(".") + 1);
String id = ded.hasBase() ? ded.getBase().getPath() : ded.getPath();
String shortId = id.substring(id.lastIndexOf(".") + 1);
if (!isInInnerTypes(ded)) {
debug("\n Key: " + dconstraint.getKey() + " SD type: " + sd.getType() + " Element: " + ded.getPath() + " Constraint Source: " + dconstraint.getSource() + " Constraint:" + dconstraint.getExpression());
String dtransl = translateConstraint(sd, ded, dconstraint);
if (dtransl.isEmpty() || constraintsList.contains(dtransl))
continue;
constraintsList.add(dtransl);
if (!isInInnerTypes(ded)) {
debug("\n Key: " + dconstraint.getKey() + " SD type: " + sd.getType() + " Element: " + ded.getPath() + " Constraint Source: " + dconstraint.getSource() + " Constraint:" + dconstraint.getExpression());
String dtransl = translateConstraint(sd, ded, dconstraint);
if (dtransl.isEmpty() || constraintsList.contains(dtransl))
continue;
constraintsList.add(dtransl);
}
}
}
}
shape_defn.add("elements", StringUtils.join(elements, "\n"));
shape_defn.add("comment", root_comment == null? " " : "# " + root_comment);
@ -713,7 +720,12 @@ public class ShExGenerator {
if (!sd.getContext().isEmpty()) {
for (StructureDefinition.StructureDefinitionContextComponent uc : sd.getContext()) {
if (!uc.getExpression().isEmpty()) {
String toStore = uc.getExpression() ;
String toStore = uc.getExpression();
debug("CONTEXT-OF-USE FOUND: " + toStore);
if (toStore.indexOf("http") != -1) {
debug("\t\tWARNING: CONTEXT-OF-USE SKIPPED as it has 'http' in it, might be a URL, instead of '.' delimited string");
continue; // some erroneous context of use may use a URL; ignore them
}
String[] backRefs = toStore.split("\\.");
toStore = "a [fhir:" + backRefs[0] + "]";
for (int i = 1; i < backRefs.length; i++)
@ -724,7 +736,13 @@ public class ShExGenerator {
}
}
}
contextOfUseStr = "^fhir:extension { " + StringUtils.join(contextOfUse, " OR \n ") + "\n }";
if (!contextOfUse.isEmpty()) {
if (contextOfUse.size() > 1)
contextOfUseStr = "^fhir:extension { " + StringUtils.join(contextOfUse, "} OR \n {") + "}\n";
else
contextOfUseStr = "^fhir:extension { " + contextOfUse.get(0) + "}\n";
}
}
shape_defn.add("contextOfUse", contextOfUseStr);
@ -740,7 +758,8 @@ public class ShExGenerator {
private String translateConstraint(StructureDefinition sd, ElementDefinition ed, ElementDefinition.ElementDefinitionConstraintComponent constraint){
String translated = "";
if (false) {
if (constraint != null) {
//if (false) {
String ce = constraint.getExpression();
String constItem = "FHIR-SD-Path:" + ed.getPath() + " Expression: " + ce;
try {
@ -865,16 +884,16 @@ public class ShExGenerator {
}
break;
case "And":
case "Implies" :
ops = " AND ";
break;
//case "Implies" :
ops = " AND ";
break;
case "As":
case "Is":
ops = " a ";
break;
case "Xor":
ops = " XOR ";
break;
//case "Xor":
//ops = " XOR "; // Although I implemented a routine for XOR, but that needs more testing.
// break;
default:
String toStore = "UNMAPPED_OPERATOR_" + opName + " in Node type: " + node.getKind();
if (!unMappedFunctions.contains(toStore))
@ -1068,7 +1087,7 @@ public class ShExGenerator {
else{
String mT = (mainTxt != null) ? mainTxt.trim() : "";
String dR = (mT.startsWith(".") || mT.startsWith("{") || mT.startsWith("[")) ? "" : ".";
return postProcessing(funCall.replaceFirst("CALLER", "CALLER" + dR + mainTxt ), nextText) ;
return postProcessing(funCall.replaceFirst("CALLER", Matcher.quoteReplacement("CALLER" + dR + mT )), nextText) ;
}
}
@ -1115,7 +1134,8 @@ public class ShExGenerator {
qp = q.split("XOR")[1];
// because p xor q = ( p and not q) OR (not p and q)
return "(" + p + " AND NOT " + qp + ") OR ( NOT " + p + " AND " + qp + ")";
//return "(" + p + " AND NOT " + qp + ") OR ( NOT " + p + " AND " + qp + ")";
return "{" + p + "} AND NOT {" + qp + "} OR { NOT {" + p + "} AND " + qp + "} ";
}
return p + qp;
@ -1625,7 +1645,7 @@ public class ShExGenerator {
String base = id.replace("[x]", "");
for (ElementDefinition.TypeRefComponent typ : ed.getType()) {
String entry = genChoiceEntry(sd, ed, "", "", typ);
String entry = genChoiceEntry(sd, ed, base, typ);
refValues.clear();
if (typ.hasTargetProfile()) {
typ.getTargetProfile().forEach((CanonicalType tps) -> {
@ -1644,14 +1664,13 @@ public class ShExGenerator {
/**
* Generate an entry in a choice list
* @param base base identifier
* @param id base identifier
* @param typ type/discriminant
* @return ShEx fragment for choice entry
*/
private String genChoiceEntry(StructureDefinition sd,
ElementDefinition ed,
String id,
String base,
ElementDefinition.TypeRefComponent typ) {
ST shex_choice_entry = tmplt(ELEMENT_TEMPLATE);
@ -1723,26 +1742,29 @@ public class ShExGenerator {
element_reference.add("elements", StringUtils.join(elements, "\n"));
List<String> innerConstraintsList = new ArrayList<String>();
// Process constraints
for (ElementDefinition.ElementDefinitionConstraintComponent constraint : ed.getConstraint()) {
String sdType = sd.getType();
String cstype = constraint.getSource();
if ((cstype != null) && (cstype.indexOf("/") != -1)) {
String[] els = cstype.split("/");
cstype = els[els.length - 1];
}
String id = ed.hasBase() ? ed.getBase().getPath() : ed.getPath();
String shortId = id.substring(id.lastIndexOf(".") + 1);
if ((ed.hasContentReference() && (!ed.hasType())) || (id.equals(sd.getName() + "." + shortId))) {
if ((sdType.equals(cstype)) || baseDataTypes.contains(sdType)) {
//if (!isInInnerTypes(ed)) {
debug("\n (INNER ED) Key: " + constraint.getKey() + " SD type: " + sd.getType() + " Element: " + ed.getPath() + " Constraint Source: " + constraint.getSource() + " Constraint:" + constraint.getExpression());
String transl = translateConstraint(sd, ed, constraint);
if (transl.isEmpty() || innerConstraintsList.contains(transl))
continue;
innerConstraintsList.add(transl);
//}
if (processConstraints) {
// Process constraints
for (ElementDefinition.ElementDefinitionConstraintComponent constraint : ed.getConstraint()) {
String sdType = sd.getType();
String cstype = constraint.getSource();
if ((cstype != null) && (cstype.indexOf("/") != -1)) {
String[] els = cstype.split("/");
cstype = els[els.length - 1];
}
String id = ed.hasBase() ? ed.getBase().getPath() : ed.getPath();
String shortId = id.substring(id.lastIndexOf(".") + 1);
if ((ed.hasContentReference() && (!ed.hasType())) || (id.equals(sd.getName() + "." + shortId))) {
if ((sdType.equals(cstype)) || baseDataTypes.contains(sdType)) {
//if (!isInInnerTypes(ed)) {
debug("\n (INNER ED) Key: " + constraint.getKey() + " SD type: " + sd.getType() + " Element: " + ed.getPath() + " Constraint Source: " + constraint.getSource() + " Constraint:" + constraint.getExpression());
String transl = translateConstraint(sd, ed, constraint);
if (transl.isEmpty() || innerConstraintsList.contains(transl))
continue;
innerConstraintsList.add(transl);
//}
}
}
}
}

72
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ShexGeneratorTests.java
View File

@ -34,18 +34,22 @@ public class ShexGeneratorTests {
}
private void doTest(String name, ShexGeneratorTestUtils.RESOURCE_CATEGORY cat) throws FileNotFoundException, IOException, FHIRException, UcumException {
// StructureDefinition sd = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
// if (sd == null) {
// throw new FHIRException("StructuredDefinition for " + name + "was null");
// }
// Path outPath = FileSystems.getDefault().getPath(System.getProperty("java.io.tmpdir"), name.toLowerCase() + ".shex");
// TextFile.stringToFile(new ShExGenerator(TestingUtilities.getSharedWorkerContext()).generate(HTMLLinkPolicy.NONE, sd), outPath.toString());
// ------- Comment following for debugging/testing
StructureDefinition sd = TestingUtilities.getSharedWorkerContext().fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
if (sd == null) {
throw new FHIRException("StructuredDefinition for " + name + "was null");
}
Path outPath = FileSystems.getDefault().getPath(System.getProperty("java.io.tmpdir"), name.toLowerCase() + ".shex");
TextFile.stringToFile(new ShExGenerator(TestingUtilities.getSharedWorkerContext()).generate(HTMLLinkPolicy.NONE, sd), outPath.toString());
// For Testing Schema Processing and Constraint Mapping related Development
// If you un-comment the following lines, please comment all other lines in this method.
this.doTestSingleSD(name.toLowerCase(), cat, name,
false, ShExGenerator.ConstraintTranslationPolicy.ALL,
true, true, false);
// Test with processing constraints flag
// ----------------- Uncomment following to testing/Debugging -----
// boolean processConstraints = true;
// this.doTestSingleSD(name.toLowerCase(), cat, name,
// false, ShExGenerator.ConstraintTranslationPolicy.ALL,
// true, true, false, processConstraints);
}
@Test
@ -128,7 +132,7 @@ public class ShexGeneratorTests {
doTest("Element", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
@Ignore
public void doTestAllSingleSDMode() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
@ -139,11 +143,13 @@ public class ShexGeneratorTests {
// Process all types of constraints, do not skip
ShExGenerator.ConstraintTranslationPolicy.ALL,
// BatchMode - All Shex Schemas in one single file
false
false,
// process constraints or not
true
);
}
@Test
@Ignore
public void doTestAllBatchMode() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
@ -154,6 +160,8 @@ public class ShexGeneratorTests {
// Process all types of constraints, do not skip
ShExGenerator.ConstraintTranslationPolicy.ALL,
// BatchMode - All Shex Schemas in one single file
true,
// process constraints or not
true
);
}
@ -168,7 +176,9 @@ public class ShexGeneratorTests {
false, //Process all extensions
ShExGenerator.ConstraintTranslationPolicy.GENERIC_ONLY,
// Process generic constraints only, ignore constraints of type 'context of use'
false
false,
// process constraints or not
true
);
}
@ -183,7 +193,9 @@ public class ShexGeneratorTests {
false, //Process all extensions
ShExGenerator.ConstraintTranslationPolicy.CONTEXT_OF_USE_ONLY,
// Process constraints only where context of use found, skip otherwise
false
false,
// process constraints or not
true
);
}
@ -196,7 +208,9 @@ public class ShexGeneratorTests {
sds, // List of Structure Definitions
true, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
false
false,
// process constraints or not
true
);
}
@ -209,7 +223,9 @@ public class ShexGeneratorTests {
sds, // List of Structure Definitions
false, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
false
false,
// process constraints or not
true
);
}
@ -222,7 +238,9 @@ public class ShexGeneratorTests {
sds, // List of Structure Definitions
false, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
false
false,
// process constraints or not
true
);
}
@ -235,7 +253,9 @@ public class ShexGeneratorTests {
sds, // List of Structure Definitions
false, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
false
false,
// process constraints or not
true
);
}
@ -247,7 +267,9 @@ public class ShexGeneratorTests {
sds, // List of Structure Definitions
false, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
false
false,
// process constraints or not
true
);
}
@ -255,7 +277,7 @@ public class ShexGeneratorTests {
List<StructureDefinition> sds,
boolean useSelectedExtensions,
ShExGenerator.ConstraintTranslationPolicy policy,
boolean batchMode) {
boolean batchMode, boolean processConstraints) {
if ((sds == null) || (sds.isEmpty())) {
throw new FHIRException("No StructuredDefinition found!");
}
@ -276,10 +298,10 @@ public class ShexGeneratorTests {
name = els[els.length - 1];
}
System.out.println("******************** " + resDef + " *********************");
doTestSingleSD(name, resDef.kind, resDef.url, useSelectedExtensions, policy, true, true, false);
doTestSingleSD(name, resDef.kind, resDef.url, useSelectedExtensions, policy, true, true, false, processConstraints);
});
} else {
doTestBatchSD(sds, useSelectedExtensions, policy, true, true, false);
doTestBatchSD(sds, useSelectedExtensions, policy, true, true, false, processConstraints);
}
System.out.println("************************ END PROCESSING ******************************");
@ -294,7 +316,7 @@ public class ShexGeneratorTests {
String name, boolean useSelectedExtensions,
ShExGenerator.ConstraintTranslationPolicy policy,
boolean debugMode, boolean validateShEx,
boolean excludeMetaSDs) {
boolean excludeMetaSDs, boolean processConstraints) {
IWorkerContext ctx = TestingUtilities.getSharedWorkerContext();
StructureDefinition sd = ctx.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
if (sd == null) {
@ -306,6 +328,7 @@ public class ShexGeneratorTests {
this.shexGenerator = new ShExGenerator(ctx);
this.shexGenerator.debugMode = debugMode;
this.shexGenerator.processConstraints = processConstraints;
this.shexGenerator.constraintPolicy = policy;
if (excludeMetaSDs) {
@ -350,7 +373,7 @@ public class ShexGeneratorTests {
private void doTestBatchSD(List<StructureDefinition> sds, boolean useSelectedExtensions,
ShExGenerator.ConstraintTranslationPolicy policy, boolean debugMode,
boolean validateShEx, boolean excludeMetaSDs) {
boolean validateShEx, boolean excludeMetaSDs, boolean processConstraints) {
IWorkerContext ctx = TestingUtilities.getSharedWorkerContext();
//Path outPath = FileSystems.getDefault().getPath(System.getProperty("java.io.tmpdir"), name.toLowerCase() + ".shex");
Path outPath = FileSystems.getDefault().getPath(System.getProperty("user.home") + "/runtime_environments/ShExSchemas", "ShEx.shex");
@ -358,6 +381,7 @@ public class ShexGeneratorTests {
this.shexGenerator = new ShExGenerator(ctx);
this.shexGenerator.debugMode = debugMode;
this.shexGenerator.processConstraints = processConstraints;
this.shexGenerator.constraintPolicy = policy;
if (excludeMetaSDs) {