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Merge pull request #10 from fhircat/ShExGenerator_R5_2023 

Removed BASE directive, sorted value-set rendering and correct imports
This commit is contained in:
Deepak Sharma 2023-02-27 13:56:14 -06:00 committed by GitHub
parent 0748abba00 6ba6a0ae62
commit e513ca022d
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GPG Key ID: 4AEE18F83AFDEB23
3 changed files with 617 additions and 340 deletions
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org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ShExGenerator.java
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@ -32,6 +32,8 @@ package org.hl7.fhir.r5.conformance;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.ImmutablePair;
@ -59,13 +61,16 @@ 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 = false; // set to false - to skip processing constraints
public ConstraintTranslationPolicy constraintPolicy = ConstraintTranslationPolicy.ALL;
private static String SHEX_TEMPLATE = "$header$\n\n" +
"$shapeDefinitions$";
private static String SHEX_TEMPLATE =
"$header$\n" +
"$imports$\n" +
"$shapeDefinitions$";
// A header is a list of prefixes, a base declaration and a start node
private static String FHIR = "http://hl7.org/fhir/";
@ -74,8 +79,10 @@ public class ShExGenerator {
"PREFIX fhir: <$fhir$> \n" +
"PREFIX fhirvs: <$fhirvs$>\n" +
"PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> \n" +
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
"BASE <http://hl7.org/fhir/shape/>\n$start$";
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n";
//"BASE <http://hl7.org/fhir/shape/>\n";
private static String IMPORT_TEMPLATE = "IMPORT <$import$$fileExt$>\n";
// Start template for single (open) entry
private static String START_TEMPLATE = "\n\nstart=@<$id$> AND {fhir:nodeRole [fhir:treeRoot]}\n";
@ -103,7 +110,14 @@ public class ShExGenerator {
// Base DataTypes
private List<String> baseDataTypes = Arrays.asList(
"DataType",
"PrimitiveType"
"PrimitiveType",
"BackboneElement"
);
private List<String> shortIdException = Arrays.asList(
"base64Binary", "boolean",
"date", "dateTime", "decimal", "instant", "integer64",
"integer", "string", "time", "uri"
);
private List<String> mappedFunctions = Arrays.asList(
@ -128,7 +142,7 @@ public class ShExGenerator {
// Resource Definition
// an open shape of type Resource. Used when completeModel = false.
private static String RESOURCE_SHAPE_TEMPLATE =
"$comment$\n<Resource> {a .+;" +
"$comment$\n<Resource> {" +
"\n $elements$" +
"\n $contextOfUse$" +
"\n} $constraints$ \n";
@ -142,10 +156,10 @@ public class ShExGenerator {
// Resource Declaration
// a type node
// an optional treeRoot declaration (identifies the entry point)
private static String RESOURCE_DECL_TEMPLATE = "\na [fhir:$id$];$root$";
private static String RESOURCE_DECL_TEMPLATE = "\na [fhir:$id$]?;$root$";
// Root Declaration.
private static String ROOT_TEMPLATE = "\nfhir:nodeRole [fhir:treeRoot]?;";
private static String ROOT_TEMPLATE = "\nfhir:nodeRole [fhir:treeRoot]?;\n";
// Element
// a predicate, type and cardinality triple
@ -162,7 +176,7 @@ public class ShExGenerator {
private static String SIMPLE_ELEMENT_DEFN_TEMPLATE = "@<$typ$>$vsdef$";
// Value Set Element
private static String VALUESET_DEFN_TEMPLATE = " AND\n\t{fhir:value @$vsn$}";
private static String VALUESET_DEFN_TEMPLATE = " AND\n\t{fhir:v @$vsn$}";
// Fixed Value Template
private static String FIXED_VALUE_TEMPLATE = " AND\n\t{fhir:value [\"$val$\"]}";
@ -257,6 +271,8 @@ public class ShExGenerator {
// Extensions are Structure Definitions with type as "Extension".
private List<StructureDefinition> selectedExtensions;
private List<String> selectedExtensionUrls;
private List<String> imports;
private FHIRPathEngine fpe;
public ShExGenerator(IWorkerContext context) {
@ -276,6 +292,7 @@ public class ShExGenerator {
excludedSDUrls = new ArrayList<String>();
selectedExtensions = new ArrayList<StructureDefinition>();
selectedExtensionUrls = new ArrayList<String>();
imports = new ArrayList<String>();
fpe = new FHIRPathEngine(context);
}
@ -293,6 +310,7 @@ public class ShExGenerator {
references.clear();
required_value_sets.clear();
known_resources.clear();
imports.clear();
return generate(links, list);
}
@ -369,7 +387,6 @@ public class ShExGenerator {
shex_def.add("header",
tmplt(HEADER_TEMPLATE).
add("start", start_cmd).
add("fhir", FHIR).
add("fhirvs", FHIR_VS).render());
@ -380,6 +397,7 @@ public class ShExGenerator {
// We remove them. Also, it is possible for the same sd to have multiple hashes...
uniq_structures = new LinkedList<StructureDefinition>();
uniq_structure_urls = new HashSet<String>();
StringBuffer allStructures = new StringBuffer("");
for (StructureDefinition sd : structures) {
// Exclusion Criteria...
if ((excludedSDUrls != null) &&
@ -415,94 +433,140 @@ public class ShExGenerator {
}
}
boolean isShapeDefinitionEmpty = true;
for (StructureDefinition sd : uniq_structures) {
printBuildMessage(" ---- Generating ShEx for : " + sd.getName() + " [ " + sd.getUrl() + " ] ...");
String shapeDefinitionStr = genShapeDefinition(sd, true);
if (!shapeDefinitionStr.isEmpty()) {
isShapeDefinitionEmpty = false;
shapeDefinitions.append(shapeDefinitionStr);
}
else {
printBuildMessage(" ---- EMPTY/No ShEx SCHEMA generated for : " + sd.getName() + " [ " + sd.getUrl() + " ].");
} else {
printBuildMessage(" ---- WARNING! EMPTY/No ShEx SCHEMA Body generated for : " + sd.getName() + " [ " + sd.getUrl() + " ].\n" +
"This might not be an issue, if this resource is normative base or a meta resource");
shapeDefinitions.append("<" + sd.getName() + "> CLOSED {\n}");
}
}
shapeDefinitions.append(emitInnerTypes());
// There was not shape generated. return empty.
// No need to generate data types, references and valuesets
if (isShapeDefinitionEmpty) {
return "";
}
shapeDefinitions.append(emitInnerTypes());
// If data types are to be put in the same file
if(doDatatypes) {
shapeDefinitions.append("\n#---------------------- Data Types -------------------\n");
while (emittedDatatypes.size() < datatypes.size() ||
emittedInnerTypes.size() < innerTypes.size()) {
shapeDefinitions.append(emitDataTypes());
// As process data types, it may introduce some more inner types, so we repeat the call here.
shapeDefinitions.append(emitInnerTypes());
// If data types are to be put in the same file
if (doDatatypes) {
shapeDefinitions.append("\n#---------------------- Data Types -------------------\n");
while (emittedDatatypes.size() < datatypes.size() ||
emittedInnerTypes.size() < innerTypes.size()) {
shapeDefinitions.append(emitDataTypes());
// As process data types, it may introduce some more inner types, so we repeat the call here.
shapeDefinitions.append(emitInnerTypes());
}
}
}
if (oneOrMoreTypes.size() > 0) {
shapeDefinitions.append("\n#---------------------- Cardinality Types (OneOrMore) -------------------\n");
oneOrMoreTypes.forEach((String oomType) -> {
shapeDefinitions.append(getOneOrMoreType(oomType));
if (oneOrMoreTypes.size() > 0) {
shapeDefinitions.append("\n#---------------------- Cardinality Types (OneOrMore) -------------------\n");
oneOrMoreTypes.forEach((String oomType) -> {
shapeDefinitions.append(getOneOrMoreType(oomType));
});
}
if (references.size() > 0) {
shapeDefinitions.append("\n#---------------------- Reference Types -------------------\n");
for (String r : references) {
shapeDefinitions.append("\n").append(tmplt(TYPED_REFERENCE_TEMPLATE).add("refType", r).render()).append("\n");
if (!"Resource".equals(r) && !known_resources.contains(r))
shapeDefinitions.append("\n").append(tmplt(TARGET_REFERENCE_TEMPLATE).add("refType", r).render()).append("\n");
}
}
if (completeModel && known_resources.size() > 0) {
shapeDefinitions.append("\n").append(tmplt(COMPLETE_RESOURCE_TEMPLATE)
.add("resources", StringUtils.join(known_resources, "> OR\n\t@<")).render());
List<String> all_entries = new ArrayList<String>();
for (String kr : known_resources)
all_entries.add(tmplt(ALL_ENTRY_TEMPLATE).add("id", kr).render());
shapeDefinitions.append("\n").append(tmplt(ALL_TEMPLATE)
.add("all_entries", StringUtils.join(all_entries, " OR\n\t")).render());
}
if (required_value_sets.size() > 0) {
shapeDefinitions.append("\n#---------------------- Value Sets ------------------------\n");
List<String> sortedVS = new ArrayList<String>();
for (ValueSet vs : required_value_sets)
sortedVS.add(genValueSet(vs));
Collections.sort(sortedVS, new Comparator<String>() {
@Override
public int compare(String o1, String o2) {
try {
return StringUtils.substringBetween(o1, "fhirvs:", " ")
.compareTo(StringUtils.substringBetween(o2, "fhirvs:", " "));
}
catch(Exception e){
debug("SORT COMPARISON FAILED BETWEEN \n\t\t" + o1 + "\n\t\t and \n\t\t" + o2);
debug(e.getMessage());
return 0;
}
}
});
for (String svs : sortedVS)
shapeDefinitions.append("\n").append(svs);
}
if ((unMappedFunctions != null) && (!unMappedFunctions.isEmpty())) {
debug("------------------------- Unmapped Functions ---------------------");
for (String um : unMappedFunctions) {
debug(um);
}
}
allStructures.append(shapeDefinitions + "\n");
StringBuffer allImports = new StringBuffer("");
if (!imports.isEmpty()) {
uniq_structures.forEach((StructureDefinition sdstruct) -> {
imports.removeIf(s -> s.contains(sdstruct.getName()));
});
imports.sort(Comparator.comparingInt(String::length));
imports.forEach((String imp) -> {
ST import_def = tmplt(IMPORT_TEMPLATE);
import_def.add("import", imp);
import_def.add("fileExt", ".shex");
allImports.append(import_def.render());
});
}
if (references.size() > 0) {
shapeDefinitions.append("\n#---------------------- Reference Types -------------------\n");
for (String r : references) {
shapeDefinitions.append("\n").append(tmplt(TYPED_REFERENCE_TEMPLATE).add("refType", r).render()).append("\n");
if (!"Resource".equals(r) && !known_resources.contains(r))
shapeDefinitions.append("\n").append(tmplt(TARGET_REFERENCE_TEMPLATE).add("refType", r).render()).append("\n");
}
}
shex_def.add("shapeDefinitions", shapeDefinitions);
if(completeModel && known_resources.size() > 0) {
shapeDefinitions.append("\n").append(tmplt(COMPLETE_RESOURCE_TEMPLATE)
.add("resources", StringUtils.join(known_resources, "> OR\n\t@<")).render());
List<String> all_entries = new ArrayList<String>();
for(String kr: known_resources)
all_entries.add(tmplt(ALL_ENTRY_TEMPLATE).add("id", kr).render());
shapeDefinitions.append("\n").append(tmplt(ALL_TEMPLATE)
.add("all_entries", StringUtils.join(all_entries, " OR\n\t")).render());
}
if (required_value_sets.size() > 0) {
shapeDefinitions.append("\n#---------------------- Value Sets ------------------------\n");
for (ValueSet vs : required_value_sets)
shapeDefinitions.append("\n").append(genValueSet(vs));
}
if ((unMappedFunctions != null)&&(!unMappedFunctions.isEmpty())) {
debug("------------------------- Unmapped Functions ---------------------");
for (String um : unMappedFunctions) {
debug(um);
}
}
allImports.append(start_cmd);
shex_def.add("imports", allImports);
shex_def.add("shapeDefinitions", allStructures.toString());
return shex_def.render();
}
private String getExtendedType(StructureDefinition sd){
private String getBaseTypeName(StructureDefinition sd){
if (sd == null)
return null;
String sId = sd.getId();
String bd = "";
String bd = null;
if (sd.hasBaseDefinition()) {
bd = sd.getBaseDefinition();
String[] els = bd.split("/");
bd = els[els.length - 1];
}
return bd;
}
private String getBaseTypeName(ElementDefinition ed){
if (ed == null)
return null;
return (ed.getType().size() > 0)? (ed.getType().get(0).getCode()) : null;
}
private String getExtendedType(StructureDefinition sd){
String bd = getBaseTypeName(sd);
String sId = sd.getId();
if (bd!=null) {
addImport("<" + bd + ">");
sId += "> EXTENDS @<" + bd;
}
@ -510,10 +574,10 @@ public class ShExGenerator {
}
private String getExtendedType(ElementDefinition ed){
if (ed == null)
return "";
String bd = (ed.getType().size() > 0)? (ed.getType().get(0).getCode()) : "";
if (bd != null && !bd.isEmpty() && !baseDataTypes.contains(bd)) {
String bd = getBaseTypeName(ed);
//if (bd != null && !baseDataTypes.contains(bd)) {
if (bd!=null) {
addImport("<" + bd + ">");
bd = "> EXTENDS @<" + bd;
}
return bd;
@ -535,19 +599,34 @@ public class ShExGenerator {
// if (sd.getName().equals("ActivityDefinition")){
// debug("ActivityDefinition found");
// }
if("Resource".equals(sd.getName())) {
shape_defn = tmplt(RESOURCE_SHAPE_TEMPLATE);
known_resources.add(sd.getName());
} else {
shape_defn = tmplt(SHAPE_DEFINITION_TEMPLATE).add("id", getExtendedType(sd));
known_resources.add(sd.getName());
ST resource_decl = tmplt(RESOURCE_DECL_TEMPLATE).
add("id", sd.getId()).
add("root", tmplt(ROOT_TEMPLATE));
shape_defn.add("resourceDecl", resource_decl.render());
if("Resource".equals(sd.getName())) {
shape_defn = tmplt(RESOURCE_SHAPE_TEMPLATE);
known_resources.add(sd.getName());
} else {
shape_defn = tmplt(SHAPE_DEFINITION_TEMPLATE).add("id", getExtendedType(sd));
known_resources.add(sd.getName());
if (baseDataTypes.contains(sd.getType())) {
shape_defn.add("resourceDecl", "\n");
} else {
if ("Element".equals(sd.getName()))
shape_defn.add("resourceDecl", tmplt(ROOT_TEMPLATE).render());
else {
String rootTmpl = tmplt(ROOT_TEMPLATE).render();
String btn = getBaseTypeName(sd);
if ((baseDataTypes.contains(btn))||
(shortIdException.contains(btn)))
rootTmpl = "\n";
ST resource_decl = tmplt(RESOURCE_DECL_TEMPLATE).
add("id", sd.getId()).
add("root", rootTmpl);
shape_defn.add("resourceDecl", resource_decl.render());
}
}
}
shape_defn.add("fhirType", " ");
}
// Generate the defining elements
List<String> elements = new ArrayList<String>();
@ -585,27 +664,27 @@ 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];
}
// Implement here if SD type == constraint source OR SD type is Primitive or DataType then add constraint to SD otherwise skip it.
//if ((sdType.equals(cstype)) || baseDataTypes.contains(sdType) || baseDataTypes.contains(bd)) {
//if ((sdType.equals(cstype)) || baseDataTypes.contains(sdType)) {
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);
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);
}
}
}
}
@ -623,24 +702,27 @@ 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);
@ -657,18 +739,29 @@ 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++)
toStore = "( ^fhir:" + backRefs[i] + " {" + toStore + "} )";
toStore = "^fhir:" + backRefs[i] + " {" + toStore + "}";
if (!contextOfUse.contains(toStore)) {
contextOfUse.add(toStore);
}
}
}
contextOfUseStr = "^fhir:extension { " + StringUtils.join(contextOfUse, " OR \n\t\t\t\t") + "\n\t\t}";
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);
@ -685,6 +778,7 @@ public class ShExGenerator {
String translated = "";
if (constraint != null) {
//if (false) {
String ce = constraint.getExpression();
String constItem = "FHIR-SD-Path:" + ed.getPath() + " Expression: " + ce;
try {
@ -700,11 +794,9 @@ public class ShExGenerator {
debug(" TRANSLATED\t"+ed.getPath()+"\t"+constraint.getHuman()+"\t"+constraint.getExpression()+"\t"+shexConstraint);
} catch (Exception e) {
String message = " FAILED to parse the constraint: " + constItem + " [ " + e.getMessage() + " ]";
// Now make this a comment so that it does not fail when schema is resolved in validator
// TODO: This needs to be fixed
// TODO: it should be
// translated = message
//String message = " FAILED to parse the constraint from Structure Definition: " + constItem + " [ " + e.getMessage() + " ]";
String message = " FAILED to parse the constraint from Structure Definition: " + constItem;
e.printStackTrace();
translated = "";
debug(message);
@ -811,16 +903,16 @@ 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))
@ -1014,7 +1106,7 @@ 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) ;
}
}
@ -1061,7 +1153,8 @@ 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;
@ -1225,7 +1318,12 @@ public class ShExGenerator {
if ((ed.getType().size() > 0) &&
(ed.getType().get(0).getCode().startsWith(Constants.NS_SYSTEM_TYPE))) {
shortId = "v";
if (changeShortName(sd, ed)) {
debug("VALUE NAME CHANGED to v from " + shortId + " for " + sd.getName() + ":" + ed.getPath());
shortId = "v";
}
typ = ed.getType().get(0).getWorkingCode();
}
@ -1249,13 +1347,17 @@ public class ShExGenerator {
innerTypes.add(new ImmutablePair<StructureDefinition, ElementDefinition>(sd, ed));
}
if ("BackboneElement".equals(typ))
typ = id;
defn = simpleElement(sd, ed, typ);
String refChoices = "";
if (id.endsWith("[x]")) {
defn = " (" + genChoiceTypes(sd, ed, shortId) + ") ";
defn += " AND { rdf:type IRI } ";
//defn = " (" + genChoiceTypes(sd, ed, shortId) + ")";
defn = " " + genChoiceTypes(sd, ed, shortId) + " ";
//defn += " AND { rdf:type IRI } ";
} else {
if (ed.getType().size() == 1) {
// Single entry
@ -1315,17 +1417,46 @@ public class ShExGenerator {
} else {
if (!refChoices.isEmpty()) {
defn += " AND {fhir:link \n\t\t\t@<" +
refChoices.replaceAll("_OR_", "> OR \n\t\t\t@<") + "> }";
refChoices.replaceAll("_OR_", "> OR \n\t\t\t@<") + "> ? }";
}
}
element_def.add("defn", defn);
addImport(defn);
element_def.add("card", card);
addComment(element_def, ed);
return element_def.render();
}
private boolean changeShortName(StructureDefinition sd, ElementDefinition ed){
return shortIdException.contains(sd.getName());
}
private void addImport(String typeDefn) {
if ((typeDefn != null) && (!typeDefn.isEmpty())) {
// String importType = StringUtils.substringBetween(typeDefn, "<", ">");
// if ((importType.indexOf(ONE_OR_MORE_PREFIX) == -1) &&
// (!imports.contains(importType)))
// imports.add(importType);
// }
Pattern p = Pattern.compile("<([^\\s>/]+)");
Matcher m = p.matcher(typeDefn);
while (m.find()) {
String tag = m.group(1);
//System.out.println("FOUND IMPORT: " + tag);
if (tag.indexOf(ONE_OR_MORE_PREFIX) != -1) {
tag = tag.substring(ONE_OR_MORE_PREFIX.length());
}
if ((tag.indexOf("_") != -1)||(tag.indexOf("_OR_") != -1))
continue;
if (!imports.contains(tag))
imports.add(tag);
}
}
}
private List<ElementDefinition> getChildren(StructureDefinition derived, ElementDefinition element) {
List<ElementDefinition> elements = derived.getSnapshot().getElement();
int index = elements.indexOf(element) + 1;
@ -1539,7 +1670,7 @@ 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) -> {
@ -1558,14 +1689,13 @@ 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);
@ -1573,7 +1703,9 @@ public class ShExGenerator {
// shex_choice_entry.add("id", "fhir:" + base+Character.toUpperCase(ext.charAt(0)) + ext.substring(1) + " ");
shex_choice_entry.add("id", "");
shex_choice_entry.add("card", "");
shex_choice_entry.add("defn", genTypeRef(sd, ed, id, typ));
String typeDefn = genTypeRef(sd, ed, id, typ);
shex_choice_entry.add("defn", typeDefn);
addImport(typeDefn);
shex_choice_entry.add("comment", " ");
return shex_choice_entry.render();
}
@ -1604,6 +1736,8 @@ public class ShExGenerator {
one_or_more_type.add("oomType", oomType);
one_or_more_type.add("origType", origType);
one_or_more_type.add("restriction", restriction);
addImport(origType);
addImport(restriction);
one_or_more_type.add("comment", "");
return one_or_more_type.render();
}
@ -1633,26 +1767,29 @@ 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.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 (!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);
//}
}
}
}
}
@ -1720,7 +1857,7 @@ public class ShExGenerator {
for(ValueSet.ValueSetExpansionContainsComponent vsec : vse.getValueset().getExpansion().getContains())
valid_codes.add("\"" + vsec.getCode() + "\"");
}
return vsd.add("val_list", valid_codes.size() > 0? " [" + StringUtils.join(valid_codes, " ") + ']' : " EXTERNAL").render();
return vsd.add("val_list", valid_codes.size() > 0? " [" + StringUtils.join(valid_codes, " ") + ']' : " xsd:string #EXTERNAL").render();
}

57
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ShexGeneratorTestUtils.java
View File

@ -20,21 +20,23 @@ public class ShexGeneratorTestUtils {
public String name;
public String url;
public String info;
public RESOURCE_CATEGORY kind;
public resDef(String _name, String _url, String _info){
public resDef(String _name, String _url, String _info, RESOURCE_CATEGORY _kind){
this.name = _name;
this.url = _url;
this.info = _info;
this.kind = _kind;
}
@Override
public String toString() {
return " " + name + "[ " + url + " ] ";
return " " + name + " (Kind: " + kind + " ) [ " + url + " ]";
}
}
public enum RESOURCE_CATEGORY{
LOGICAL_NAMES, STRUCTURE_DEFINITIONS, EXTENSIONS, PROFILES, ALL
LOGICAL_NAME, STRUCTURE_DEFINITION, EXTENSION, PROFILE, ALL, META_OR_EXAMPLE_OR_OTHER_IGNORE
}
/**
@ -48,26 +50,25 @@ public class ShexGeneratorTestUtils {
List<resDef> selSDs = new ArrayList<resDef>();
sds.forEach((StructureDefinition sd) -> {
switch(cat) {
case STRUCTURE_DEFINITIONS:
if (sd.getType().trim().equals(sd.getName().trim()))
selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
case STRUCTURE_DEFINITION:
if (getCategory(sd).equals(RESOURCE_CATEGORY.STRUCTURE_DEFINITION))
selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), RESOURCE_CATEGORY.STRUCTURE_DEFINITION));
break;
case LOGICAL_NAMES:
if (sd.getBaseDefinition() == null)
selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
case LOGICAL_NAME:
if (getCategory(sd).equals(RESOURCE_CATEGORY.LOGICAL_NAME))
selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), RESOURCE_CATEGORY.LOGICAL_NAME));
break;
case EXTENSIONS:
if ("Extension".equals(sd.getType()))
selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
case EXTENSION:
if (getCategory(sd).equals(RESOURCE_CATEGORY.EXTENSION))
selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), RESOURCE_CATEGORY.EXTENSION));
break;
case PROFILES:
if (!((sd.getBaseDefinition() == null) ||
("Extension".equals(sd.getType())) ||
(sd.getType().trim().equals(sd.getName().trim()))))
selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
case PROFILE:
if (getCategory(sd).equals(RESOURCE_CATEGORY.PROFILE))
selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), RESOURCE_CATEGORY.PROFILE));
break;
default:
selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), getCategory(sd)));
}
});
@ -81,6 +82,24 @@ public class ShexGeneratorTestUtils {
return selSDs;
}
private RESOURCE_CATEGORY getCategory(StructureDefinition sd) {
if ("Extension".equals(sd.getType()))
return RESOURCE_CATEGORY.EXTENSION;
if (sd.getBaseDefinition() == null)
return RESOURCE_CATEGORY.LOGICAL_NAME;
if (sd.getType().trim().equals(sd.getName().trim()))
return RESOURCE_CATEGORY.STRUCTURE_DEFINITION;
if (!((sd.getBaseDefinition() == null) ||
("Extension".equals(sd.getType())) ||
(sd.getType().trim().equals(sd.getName().trim()))))
return RESOURCE_CATEGORY.PROFILE;
return RESOURCE_CATEGORY.META_OR_EXAMPLE_OR_OTHER_IGNORE;
}
/**
* This method is used in testing only - during Resource Constraint translation to ShEx constructs.
* It can be used by future developers to avoid unnecessary processing of constraints
@ -196,7 +215,7 @@ public class ShexGeneratorTestUtils {
System.out.println("Printing " + title);
System.out.println("************************************************************************");
items.forEach((resDef item) -> {
System.out.println(item.name + " [" + item.url + "]");
System.out.println(item.name + " \t[" + item.url + "]\t" + item.info);
});
}
}

429
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ShexGeneratorTests.java
View File

@ -10,7 +10,6 @@ import java.util.List;
import es.weso.shex.Schema;
import es.weso.shex.validator.ShExsValidator;
import es.weso.shex.validator.ShExsValidatorBuilder;
import org.apache.commons.lang3.StringUtils;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
@ -28,15 +27,14 @@ import org.junit.jupiter.api.Test;
import static org.hl7.fhir.r5.test.ShexGeneratorTestUtils.printList;
public class ShexGeneratorTests {
public static List<String> selectedExtesnsions = new ArrayList<String>();
public ShExGenerator shexGenerator;
@BeforeAll
public static void setup() {
}
private void doTest(String name) throws FileNotFoundException, IOException, FHIRException, UcumException {
private void doTest(String name, ShexGeneratorTestUtils.RESOURCE_CATEGORY cat) throws FileNotFoundException, IOException, FHIRException, UcumException {
// ------- 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");
@ -46,82 +44,283 @@ public class ShexGeneratorTests {
// 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.doTestThis(name.toLowerCase(), name, false, ShExGenerator.ConstraintTranslationPolicy.ALL, true, true);
// Test with processing constraints flag
// ----------------- Uncomment following to testing/Debugging -----
// boolean processConstraints = false;
// this.doTestSingleSD(name.toLowerCase(), cat, name,
// false, ShExGenerator.ConstraintTranslationPolicy.ALL,
// true, true, false, processConstraints);
}
@Test
public void testId() throws FHIRException, IOException, UcumException {
doTest("id");
doTest("id", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testUri() throws FHIRException, IOException, UcumException {
doTest("uri");
doTest("uri", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testPatient() throws FHIRException, IOException, UcumException {
doTest("Patient", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testObservation() throws FHIRException, IOException, UcumException {
doTest("Observation");
doTest("Observation", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testRef() throws FHIRException, IOException, UcumException {
doTest("Reference");
doTest("Reference", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testAccount() throws FHIRException, IOException, UcumException {
doTest("Account");
doTest("Account", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testAppointment() throws FHIRException, IOException, UcumException {
doTest("Appointment");
doTest("Appointment", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testBundle() throws FHIRException, IOException, UcumException {
doTest("Bundle");
doTest("Bundle", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testAge() throws FHIRException, IOException, UcumException {
doTest("Age");
doTest("Age", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testMedicationRequest() throws FHIRException, IOException, UcumException {
doTest("MedicationRequest");
doTest("MedicationRequest", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testAllergyIntolerance() throws FHIRException, IOException, UcumException {
doTest("AllergyIntolerance");
doTest("AllergyIntolerance", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testCoding() throws FHIRException, IOException, UcumException {
doTest("Coding");
doTest("Coding", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testTiming() throws FHIRException, IOException, UcumException {
doTest("Timing");
doTest("Timing", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testSignature() throws FHIRException, IOException, UcumException {
doTest("Signature");
doTest("Signature", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testCapabilityStatement() throws FHIRException, IOException, UcumException {
doTest("CapabilityStatement", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Test
public void testElement() throws FHIRException, IOException, UcumException {
doTest("Element", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
}
@Ignore
public void testCapabilityStatement() throws FHIRException, IOException, UcumException {
doTest("CapabilityStatement");
public void doTestAllSingleSDMode() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process all extensions
// Process all types of constraints, do not skip
ShExGenerator.ConstraintTranslationPolicy.ALL,
// BatchMode - All Shex Schemas in one single file
false,
// process constraints or not
false
);
}
private void doTestThis(String shortName, String name, boolean useSelectedExtensions, ShExGenerator.ConstraintTranslationPolicy policy, boolean debugMode, boolean validateShEx) {
@Ignore
public void doTestAllBatchMode() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process all extensions
// 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
);
}
@Ignore
public void doTestGenericExtensionsOnlyPolicy() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process all extensions
ShExGenerator.ConstraintTranslationPolicy.GENERIC_ONLY,
// Process generic constraints only, ignore constraints of type 'context of use'
false,
// process constraints or not
true
);
}
@Ignore
public void doTestContextOfUseExtensionsOnlyPolicy() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process all extensions
ShExGenerator.ConstraintTranslationPolicy.CONTEXT_OF_USE_ONLY,
// Process constraints only where context of use found, skip otherwise
false,
// process constraints or not
true
);
}
@Ignore
public void doTestSelectedExtensions() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
true, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
false,
// process constraints or not
true
);
}
@Ignore
public void testStructureDefinitionsOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
false,
// process constraints or not
true
);
}
@Ignore
public void testExtensionsOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.EXTENSION, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
false,
// process constraints or not
true
);
}
@Ignore
public void testLogicalNamesOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.LOGICAL_NAME, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
false,
// process constraints or not
true
);
}
@Ignore
public void testProfilesOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.PROFILE, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
false,
// process constraints or not
true
);
}
private void processSDList(ShexGeneratorTestUtils.RESOURCE_CATEGORY cat,
List<StructureDefinition> sds,
boolean useSelectedExtensions,
ShExGenerator.ConstraintTranslationPolicy policy,
boolean batchMode, boolean processConstraints) {
if ((sds == null) || (sds.isEmpty())) {
throw new FHIRException("No StructuredDefinition found!");
}
ShexGeneratorTestUtils shexTestUtils = new ShexGeneratorTestUtils();
List<ShexGeneratorTestUtils.resDef> sdDefs = shexTestUtils.getSDs(sds, cat);
printList(cat.toString(), sdDefs);
System.out.println("************************************************************************");
System.out.println("Processing " + cat);
System.out.println("************************************************************************");
if (!batchMode) {
sdDefs.forEach((ShexGeneratorTestUtils.resDef resDef) -> {
String name = resDef.url;
if (resDef.url.indexOf("/") != -1) {
String els[] = resDef.url.split("/");
name = els[els.length - 1];
}
System.out.println("******************** " + resDef + " *********************");
doTestSingleSD(name, resDef.kind, resDef.url, useSelectedExtensions, policy, true, true, false, processConstraints);
});
} else {
doTestBatchSD(sds, useSelectedExtensions, policy, true, true, false, processConstraints);
}
System.out.println("************************ END PROCESSING ******************************");
System.out.println("************************************************************************");
List<String> skipped = this.shexGenerator.getExcludedStructureDefinitionUrls();
System.out.println("Total Items processed: " + sds.size());
System.out.println("************************************************************************");
}
private void doTestSingleSD(String shortName, ShexGeneratorTestUtils.RESOURCE_CATEGORY cat,
String name, boolean useSelectedExtensions,
ShExGenerator.ConstraintTranslationPolicy policy,
boolean debugMode, boolean validateShEx,
boolean excludeMetaSDs, boolean processConstraints) {
IWorkerContext ctx = TestingUtilities.getSharedWorkerContext();
StructureDefinition sd = ctx.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
if (sd == null) {
throw new FHIRException("StructuredDefinition for " + name + " was null");
throw new FHIRException("StructuredDefinition for " + name + "(Kind:" + cat + ") was null");
}
//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", shortName + ".shex");
@ -129,11 +328,14 @@ public class ShexGeneratorTests {
this.shexGenerator = new ShExGenerator(ctx);
this.shexGenerator.debugMode = debugMode;
this.shexGenerator.processConstraints = processConstraints;
this.shexGenerator.constraintPolicy = policy;
// ShEx Generator skips resources which are at Meta level of FHIR Resource definitions
this.shexGenerator.setExcludedStructureDefinitionUrls(
ShexGeneratorTestUtils.getMetaStructureDefinitionsToSkip());
if (excludeMetaSDs) {
// ShEx Generator skips resources which are at Meta level of FHIR Resource definitions
this.shexGenerator.setExcludedStructureDefinitionUrls(
ShexGeneratorTestUtils.getMetaStructureDefinitionsToSkip());
}
// when ShEx translates only selected resource extensions
if (useSelectedExtensions) {
@ -155,10 +357,11 @@ public class ShexGeneratorTests {
Schema sch = validator.schema();
Assert.assertNotNull(sch);
System.out.println("VALIDATION PASSED for ShEx Schema " + sd.getName());
System.out.println("VALIDATION PASSED for ShEx Schema " + sd.getName() + " (Kind:" + cat + ")");
} catch (Exception e) {
System.out.println("VALIDATION FAILED for ShEx Schema " + sd.getName());
//System.out.println("\t\t\tMessage: " + e.getMessage());
System.out.println("VALIDATION FAILED for ShEx Schema " + sd.getName() + " (Kind:" + cat + ")");
e.printStackTrace();
}
}
TextFile.stringToFile(schema, outPath.toString());
@ -168,136 +371,54 @@ public class ShexGeneratorTests {
}
}
@Ignore
public void doTestAll() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
private void doTestBatchSD(List<StructureDefinition> sds, boolean useSelectedExtensions,
ShExGenerator.ConstraintTranslationPolicy policy, boolean debugMode,
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");
try {
this.shexGenerator = new ShExGenerator(ctx);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process all extensions
ShExGenerator.ConstraintTranslationPolicy.ALL
// Process all types of constraints, do not skip
);
}
this.shexGenerator.debugMode = debugMode;
this.shexGenerator.processConstraints = processConstraints;
this.shexGenerator.constraintPolicy = policy;
@Ignore
public void doTestGenericExtensionsOnlyPolicy() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process all extensions
ShExGenerator.ConstraintTranslationPolicy.GENERIC_ONLY
// Process generic constraints only, ignore constraints of type 'context of use'
);
}
@Ignore
public void doTestContextOfUseExtensionsOnlyPolicy() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process all extensions
ShExGenerator.ConstraintTranslationPolicy.CONTEXT_OF_USE_ONLY
// Process constraints only where context of use found, skip otherwise
);
}
@Ignore
public void doTestSelectedExtensions() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
true, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL // Process all type of constraints
);
}
@Ignore
public void testStructureDefinitionsOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITIONS, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL // Process all type of constraints
);
}
@Ignore
public void testExtensionsOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.EXTENSIONS, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL // Process all type of constraints
);
}
@Ignore
public void testLogicalNamesOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.LOGICAL_NAMES, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL // Process all type of constraints
);
}
@Ignore
public void testProfilesOnly() throws FileNotFoundException, IOException, FHIRException, UcumException {
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
processSDList(
ShexGeneratorTestUtils.RESOURCE_CATEGORY.PROFILES, // Processing All kinds of Structure Definitions
sds, // List of Structure Definitions
false, //Process only given/selected extensions, ignore other extensions
ShExGenerator.ConstraintTranslationPolicy.ALL // Process all type of constraints
);
}
private void processSDList(ShexGeneratorTestUtils.RESOURCE_CATEGORY cat,
List<StructureDefinition> sds,
boolean useSelectedExtensions,
ShExGenerator.ConstraintTranslationPolicy policy) {
if ((sds == null) || (sds.isEmpty())) {
throw new FHIRException("No StructuredDefinition found!");
}
ShexGeneratorTestUtils shexTestUtils = new ShexGeneratorTestUtils();
List<ShexGeneratorTestUtils.resDef> sdDefs = shexTestUtils.getSDs(sds, cat);
printList(cat.toString(), sdDefs);
System.out.println("************************************************************************");
System.out.println("Processing " + cat);
System.out.println("************************************************************************");
sdDefs.forEach((ShexGeneratorTestUtils.resDef resDef) -> {
String name = resDef.url;
if (resDef.url.indexOf("/") != -1) {
String els[] = resDef.url.split("/");
name = els[els.length - 1];
if (excludeMetaSDs) {
// ShEx Generator skips resources which are at Meta level of FHIR Resource definitions
this.shexGenerator.setExcludedStructureDefinitionUrls(
ShexGeneratorTestUtils.getMetaStructureDefinitionsToSkip());
}
System.out.println("******************** " + resDef + " *********************");
doTestThis(name, resDef.url, useSelectedExtensions, policy, true, true);
});
System.out.println("************************ END PROCESSING ******************************");
// when ShEx translates only selected resource extensions
if (useSelectedExtensions) {
List<StructureDefinition> selExtns = new ArrayList<StructureDefinition>();
for (String eUrl : ShexGeneratorTestUtils.getSelectedExtensions()) {
StructureDefinition esd = ctx.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(eUrl, null));
if (esd != null)
selExtns.add(esd);
}
this.shexGenerator.setSelectedExtension(selExtns);
}
System.out.println("************************************************************************");
List<String> skipped = this.shexGenerator.getExcludedStructureDefinitionUrls();
System.out.println("Total Items processed: " + sds.size());
System.out.println("************************************************************************");
String schema = this.shexGenerator.generate(HTMLLinkPolicy.NONE, sds);
if (!schema.isEmpty()) {
if (validateShEx) {
try {
ShExsValidator validator = ShExsValidatorBuilder.fromStringSync(schema, "ShexC");
Schema sch = validator.schema();
Assert.assertNotNull(sch);
System.out.println("VALIDATION PASSED for ShEx Schema ALL SHEX STRUCTURES");
} catch (Exception e) {
System.out.println("VALIDATION FAILED for ShEx Schema ALL SHEX STRUCTURES");
e.printStackTrace();
}
}
TextFile.stringToFile(schema, outPath.toString());
}
} catch (IOException e) {
throw new RuntimeException(e);
}
}
}