mirror of
https://github.com/hapifhir/org.hl7.fhir.core.git
synced 2025-03-09 14:31:17 +00:00
Added IMPORT for all SDs, enabled batch SD ShEx Generation. Disabled Context translation temporarily
This commit is contained in:
dksharma
parent
5728cf94c2
commit
9ca531ff0a
@ -32,6 +32,8 @@ package org.hl7.fhir.r5.conformance;
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import java.util.*;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.tuple.ImmutablePair;
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@ -63,9 +65,10 @@ public class ShExGenerator {
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public ConstraintTranslationPolicy constraintPolicy = ConstraintTranslationPolicy.ALL;
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private static String SHEX_TEMPLATE = "$header$\n\n" +
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"$shapeDefinitions$";
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private static String SHEX_TEMPLATE =
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"$header$\n" +
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"$imports$\n" +
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"$shapeDefinitions$";
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// A header is a list of prefixes, a base declaration and a start node
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private static String FHIR = "http://hl7.org/fhir/";
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@ -75,7 +78,9 @@ public class ShExGenerator {
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"PREFIX fhirvs: <$fhirvs$>\n" +
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"PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> \n" +
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"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" +
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"BASE <http://hl7.org/fhir/shape/>\n$start$";
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"BASE <http://hl7.org/fhir/shape/>\n";
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private static String IMPORT_TEMPLATE = "IMPORT <$import$$fileExt$>\n";
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// Start template for single (open) entry
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private static String START_TEMPLATE = "\n\nstart=@<$id$> AND {fhir:nodeRole [fhir:treeRoot]}\n";
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@ -257,6 +262,8 @@ public class ShExGenerator {
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// Extensions are Structure Definitions with type as "Extension".
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private List<StructureDefinition> selectedExtensions;
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private List<String> selectedExtensionUrls;
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private List<String> imports;
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private FHIRPathEngine fpe;
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public ShExGenerator(IWorkerContext context) {
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@ -276,6 +283,7 @@ public class ShExGenerator {
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excludedSDUrls = new ArrayList<String>();
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selectedExtensions = new ArrayList<StructureDefinition>();
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selectedExtensionUrls = new ArrayList<String>();
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imports = new ArrayList<String>();
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fpe = new FHIRPathEngine(context);
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}
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@ -293,6 +301,7 @@ public class ShExGenerator {
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references.clear();
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required_value_sets.clear();
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known_resources.clear();
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imports.clear();
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return generate(links, list);
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}
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@ -369,7 +378,6 @@ public class ShExGenerator {
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shex_def.add("header",
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tmplt(HEADER_TEMPLATE).
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add("start", start_cmd).
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add("fhir", FHIR).
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add("fhirvs", FHIR_VS).render());
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@ -380,6 +388,7 @@ public class ShExGenerator {
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// We remove them. Also, it is possible for the same sd to have multiple hashes...
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uniq_structures = new LinkedList<StructureDefinition>();
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uniq_structure_urls = new HashSet<String>();
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StringBuffer allStructures = new StringBuffer("");
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for (StructureDefinition sd : structures) {
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// Exclusion Criteria...
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if ((excludedSDUrls != null) &&
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@ -415,79 +424,89 @@ public class ShExGenerator {
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}
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}
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boolean isShapeDefinitionEmpty = true;
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for (StructureDefinition sd : uniq_structures) {
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printBuildMessage(" ---- Generating ShEx for : " + sd.getName() + " [ " + sd.getUrl() + " ] ...");
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String shapeDefinitionStr = genShapeDefinition(sd, true);
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if (!shapeDefinitionStr.isEmpty()) {
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isShapeDefinitionEmpty = false;
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shapeDefinitions.append(shapeDefinitionStr);
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} else {
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printBuildMessage(" ---- WARNING! EMPTY/No ShEx SCHEMA Body generated for : " + sd.getName() + " [ " + sd.getUrl() + " ].\n" +
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"This might not be an issue, if this resource is normative base or a meta resource");
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shapeDefinitions.append("<" + sd.getName() + "> CLOSED {\n}");
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}
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else {
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printBuildMessage(" ---- EMPTY/No ShEx SCHEMA generated for : " + sd.getName() + " [ " + sd.getUrl() + " ].");
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if (!imports.isEmpty())
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imports.removeIf(s -> s.contains(sd.getName()));
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}
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shapeDefinitions.append(emitInnerTypes());
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// If data types are to be put in the same file
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if (doDatatypes) {
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shapeDefinitions.append("\n#---------------------- Data Types -------------------\n");
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while (emittedDatatypes.size() < datatypes.size() ||
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emittedInnerTypes.size() < innerTypes.size()) {
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shapeDefinitions.append(emitDataTypes());
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// As process data types, it may introduce some more inner types, so we repeat the call here.
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shapeDefinitions.append(emitInnerTypes());
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}
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}
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}
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// There was not shape generated. return empty.
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// No need to generate data types, references and valuesets
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if (isShapeDefinitionEmpty) {
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return "";
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}
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shapeDefinitions.append(emitInnerTypes());
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// If data types are to be put in the same file
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if(doDatatypes) {
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shapeDefinitions.append("\n#---------------------- Data Types -------------------\n");
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while (emittedDatatypes.size() < datatypes.size() ||
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emittedInnerTypes.size() < innerTypes.size()) {
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shapeDefinitions.append(emitDataTypes());
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// As process data types, it may introduce some more inner types, so we repeat the call here.
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shapeDefinitions.append(emitInnerTypes());
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if (oneOrMoreTypes.size() > 0) {
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shapeDefinitions.append("\n#---------------------- Cardinality Types (OneOrMore) -------------------\n");
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oneOrMoreTypes.forEach((String oomType) -> {
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shapeDefinitions.append(getOneOrMoreType(oomType));
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});
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}
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}
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if (oneOrMoreTypes.size() > 0) {
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shapeDefinitions.append("\n#---------------------- Cardinality Types (OneOrMore) -------------------\n");
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oneOrMoreTypes.forEach((String oomType) -> {
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shapeDefinitions.append(getOneOrMoreType(oomType));
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if (references.size() > 0) {
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shapeDefinitions.append("\n#---------------------- Reference Types -------------------\n");
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for (String r : references) {
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shapeDefinitions.append("\n").append(tmplt(TYPED_REFERENCE_TEMPLATE).add("refType", r).render()).append("\n");
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if (!"Resource".equals(r) && !known_resources.contains(r))
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shapeDefinitions.append("\n").append(tmplt(TARGET_REFERENCE_TEMPLATE).add("refType", r).render()).append("\n");
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}
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}
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if (completeModel && known_resources.size() > 0) {
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shapeDefinitions.append("\n").append(tmplt(COMPLETE_RESOURCE_TEMPLATE)
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.add("resources", StringUtils.join(known_resources, "> OR\n\t@<")).render());
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List<String> all_entries = new ArrayList<String>();
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for (String kr : known_resources)
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all_entries.add(tmplt(ALL_ENTRY_TEMPLATE).add("id", kr).render());
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shapeDefinitions.append("\n").append(tmplt(ALL_TEMPLATE)
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.add("all_entries", StringUtils.join(all_entries, " OR\n\t")).render());
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}
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if (required_value_sets.size() > 0) {
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shapeDefinitions.append("\n#---------------------- Value Sets ------------------------\n");
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for (ValueSet vs : required_value_sets)
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shapeDefinitions.append("\n").append(genValueSet(vs));
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}
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if ((unMappedFunctions != null) && (!unMappedFunctions.isEmpty())) {
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debug("------------------------- Unmapped Functions ---------------------");
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for (String um : unMappedFunctions) {
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debug(um);
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}
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}
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allStructures.append(shapeDefinitions + "\n");
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StringBuffer allImports = new StringBuffer("");
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if (!imports.isEmpty()) {
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imports.sort(Comparator.comparingInt(String::length));
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imports.forEach((String imp) -> {
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ST import_def = tmplt(IMPORT_TEMPLATE);
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import_def.add("import", imp);
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import_def.add("fileExt", ".shex");
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allImports.append(import_def.render());
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});
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}
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if (references.size() > 0) {
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shapeDefinitions.append("\n#---------------------- Reference Types -------------------\n");
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for (String r : references) {
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shapeDefinitions.append("\n").append(tmplt(TYPED_REFERENCE_TEMPLATE).add("refType", r).render()).append("\n");
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if (!"Resource".equals(r) && !known_resources.contains(r))
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shapeDefinitions.append("\n").append(tmplt(TARGET_REFERENCE_TEMPLATE).add("refType", r).render()).append("\n");
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}
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}
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shex_def.add("shapeDefinitions", shapeDefinitions);
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if(completeModel && known_resources.size() > 0) {
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shapeDefinitions.append("\n").append(tmplt(COMPLETE_RESOURCE_TEMPLATE)
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.add("resources", StringUtils.join(known_resources, "> OR\n\t@<")).render());
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List<String> all_entries = new ArrayList<String>();
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for(String kr: known_resources)
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all_entries.add(tmplt(ALL_ENTRY_TEMPLATE).add("id", kr).render());
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shapeDefinitions.append("\n").append(tmplt(ALL_TEMPLATE)
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.add("all_entries", StringUtils.join(all_entries, " OR\n\t")).render());
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}
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if (required_value_sets.size() > 0) {
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shapeDefinitions.append("\n#---------------------- Value Sets ------------------------\n");
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for (ValueSet vs : required_value_sets)
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shapeDefinitions.append("\n").append(genValueSet(vs));
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}
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if ((unMappedFunctions != null)&&(!unMappedFunctions.isEmpty())) {
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debug("------------------------- Unmapped Functions ---------------------");
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for (String um : unMappedFunctions) {
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debug(um);
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}
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}
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allImports.append(start_cmd);
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shex_def.add("imports", allImports);
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shex_def.add("shapeDefinitions", allStructures.toString());
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return shex_def.render();
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}
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@ -502,7 +521,7 @@ public class ShExGenerator {
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bd = sd.getBaseDefinition();
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String[] els = bd.split("/");
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bd = els[els.length - 1];
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addImport("<" + bd + ">");
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sId += "> EXTENDS @<" + bd;
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}
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@ -514,6 +533,7 @@ public class ShExGenerator {
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return "";
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String bd = (ed.getType().size() > 0)? (ed.getType().get(0).getCode()) : "";
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if (bd != null && !bd.isEmpty() && !baseDataTypes.contains(bd)) {
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addImport("<" + bd + ">");
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bd = "> EXTENDS @<" + bd;
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}
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return bd;
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@ -661,14 +681,14 @@ public class ShExGenerator {
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String[] backRefs = toStore.split("\\.");
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toStore = "a [fhir:" + backRefs[0] + "]";
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for (int i = 1; i < backRefs.length; i++)
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toStore = "( ^fhir:" + backRefs[i] + " {" + toStore + "} )";
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toStore = "^fhir:" + backRefs[i] + " {" + toStore + "}";
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if (!contextOfUse.contains(toStore)) {
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contextOfUse.add(toStore);
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}
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}
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}
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contextOfUseStr = "^fhir:extension { " + StringUtils.join(contextOfUse, " OR \n\t\t\t\t") + "\n\t\t}";
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contextOfUseStr = "^fhir:extension { " + StringUtils.join(contextOfUse, " OR \n ") + "\n }";
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}
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shape_defn.add("contextOfUse", contextOfUseStr);
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@ -684,7 +704,7 @@ public class ShExGenerator {
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private String translateConstraint(StructureDefinition sd, ElementDefinition ed, ElementDefinition.ElementDefinitionConstraintComponent constraint){
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String translated = "";
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if (constraint != null) {
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if (false) {
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String ce = constraint.getExpression();
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String constItem = "FHIR-SD-Path:" + ed.getPath() + " Expression: " + ce;
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try {
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@ -700,11 +720,9 @@ public class ShExGenerator {
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debug(" TRANSLATED\t"+ed.getPath()+"\t"+constraint.getHuman()+"\t"+constraint.getExpression()+"\t"+shexConstraint);
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} catch (Exception e) {
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String message = " FAILED to parse the constraint: " + constItem + " [ " + e.getMessage() + " ]";
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// Now make this a comment so that it does not fail when schema is resolved in validator
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// TODO: This needs to be fixed
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// TODO: it should be
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// translated = message
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//String message = " FAILED to parse the constraint from Structure Definition: " + constItem + " [ " + e.getMessage() + " ]";
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String message = " FAILED to parse the constraint from Structure Definition: " + constItem;
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e.printStackTrace();
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translated = "";
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debug(message);
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@ -1320,12 +1338,31 @@ public class ShExGenerator {
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}
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element_def.add("defn", defn);
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addImport(defn);
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element_def.add("card", card);
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addComment(element_def, ed);
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return element_def.render();
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}
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private void addImport(String typeDefn) {
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if ((typeDefn != null) && (!typeDefn.isEmpty())) {
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// String importType = StringUtils.substringBetween(typeDefn, "<", ">");
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// if ((importType.indexOf(ONE_OR_MORE_PREFIX) == -1) &&
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// (!imports.contains(importType)))
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// imports.add(importType);
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// }
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Pattern p = Pattern.compile("<([^\\s>/]+)");
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Matcher m = p.matcher(typeDefn);
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while (m.find()) {
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String tag = m.group(1);
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//System.out.println("FOUND IMPORT: " + tag);
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if ((tag.indexOf(ONE_OR_MORE_PREFIX) == -1) &&
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(!imports.contains(tag)))
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imports.add(tag);
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}
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}
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}
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private List<ElementDefinition> getChildren(StructureDefinition derived, ElementDefinition element) {
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List<ElementDefinition> elements = derived.getSnapshot().getElement();
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int index = elements.indexOf(element) + 1;
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@ -1573,7 +1610,9 @@ public class ShExGenerator {
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// shex_choice_entry.add("id", "fhir:" + base+Character.toUpperCase(ext.charAt(0)) + ext.substring(1) + " ");
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shex_choice_entry.add("id", "");
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shex_choice_entry.add("card", "");
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shex_choice_entry.add("defn", genTypeRef(sd, ed, id, typ));
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String typeDefn = genTypeRef(sd, ed, id, typ);
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shex_choice_entry.add("defn", typeDefn);
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addImport(typeDefn);
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shex_choice_entry.add("comment", " ");
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return shex_choice_entry.render();
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}
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@ -1604,6 +1643,8 @@ public class ShExGenerator {
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one_or_more_type.add("oomType", oomType);
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one_or_more_type.add("origType", origType);
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one_or_more_type.add("restriction", restriction);
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addImport(origType);
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addImport(restriction);
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one_or_more_type.add("comment", "");
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return one_or_more_type.render();
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}
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@ -20,21 +20,23 @@ public class ShexGeneratorTestUtils {
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public String name;
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public String url;
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public String info;
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public RESOURCE_CATEGORY kind;
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public resDef(String _name, String _url, String _info){
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public resDef(String _name, String _url, String _info, RESOURCE_CATEGORY _kind){
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this.name = _name;
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this.url = _url;
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this.info = _info;
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this.kind = _kind;
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}
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@Override
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public String toString() {
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return " " + name + "[ " + url + " ] ";
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return " " + name + " (Kind: " + kind + " ) [ " + url + " ]";
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}
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}
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public enum RESOURCE_CATEGORY{
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LOGICAL_NAMES, STRUCTURE_DEFINITIONS, EXTENSIONS, PROFILES, ALL
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LOGICAL_NAME, STRUCTURE_DEFINITION, EXTENSION, PROFILE, ALL, META_OR_EXAMPLE_OR_OTHER_IGNORE
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}
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/**
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@ -48,26 +50,25 @@ public class ShexGeneratorTestUtils {
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List<resDef> selSDs = new ArrayList<resDef>();
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sds.forEach((StructureDefinition sd) -> {
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switch(cat) {
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case STRUCTURE_DEFINITIONS:
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if (sd.getType().trim().equals(sd.getName().trim()))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
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case STRUCTURE_DEFINITION:
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if (getCategory(sd).equals(RESOURCE_CATEGORY.STRUCTURE_DEFINITION))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), RESOURCE_CATEGORY.STRUCTURE_DEFINITION));
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break;
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case LOGICAL_NAMES:
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if (sd.getBaseDefinition() == null)
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
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case LOGICAL_NAME:
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if (getCategory(sd).equals(RESOURCE_CATEGORY.LOGICAL_NAME))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), RESOURCE_CATEGORY.LOGICAL_NAME));
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break;
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case EXTENSIONS:
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if ("Extension".equals(sd.getType()))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
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case EXTENSION:
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if (getCategory(sd).equals(RESOURCE_CATEGORY.EXTENSION))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), RESOURCE_CATEGORY.EXTENSION));
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break;
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case PROFILES:
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if (!((sd.getBaseDefinition() == null) ||
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("Extension".equals(sd.getType())) ||
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(sd.getType().trim().equals(sd.getName().trim()))))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
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case PROFILE:
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if (getCategory(sd).equals(RESOURCE_CATEGORY.PROFILE))
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), RESOURCE_CATEGORY.PROFILE));
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break;
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default:
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd)));
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selSDs.add(new resDef(sd.getName(), sd.getUrl(), getSDInfo(sd), getCategory(sd)));
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}
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});
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@ -81,6 +82,24 @@ public class ShexGeneratorTestUtils {
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return selSDs;
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}
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private RESOURCE_CATEGORY getCategory(StructureDefinition sd) {
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if ("Extension".equals(sd.getType()))
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return RESOURCE_CATEGORY.EXTENSION;
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||||
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);
|
||||
});
|
||||
}
|
||||
}
|
||||
|
||||
@ -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;
|
||||
@ -36,92 +35,92 @@ public class ShexGeneratorTests {
|
||||
public static void setup() {
|
||||
}
|
||||
|
||||
private void doTest(String name) 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());
|
||||
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());
|
||||
|
||||
// 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);
|
||||
this.doTestSingleSD(name.toLowerCase(), cat, name, false, ShExGenerator.ConstraintTranslationPolicy.ALL, true, true, false);
|
||||
}
|
||||
@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 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);
|
||||
}
|
||||
|
||||
@Ignore
|
||||
public void testCapabilityStatement() throws FHIRException, IOException, UcumException {
|
||||
doTest("CapabilityStatement");
|
||||
doTest("CapabilityStatement", ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITION);
|
||||
}
|
||||
|
||||
private void doTestThis(String shortName, String name, boolean useSelectedExtensions, ShExGenerator.ConstraintTranslationPolicy policy, boolean debugMode, boolean validateShEx) {
|
||||
private void doTestSingleSD(String shortName, ShexGeneratorTestUtils.RESOURCE_CATEGORY cat, String name, boolean useSelectedExtensions, ShExGenerator.ConstraintTranslationPolicy policy, boolean debugMode, boolean validateShEx, boolean excludeMetaSDs) {
|
||||
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");
|
||||
@ -131,9 +130,11 @@ public class ShexGeneratorTests {
|
||||
this.shexGenerator.debugMode = debugMode;
|
||||
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 +156,10 @@ 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());
|
||||
@ -168,7 +169,55 @@ public class ShexGeneratorTests {
|
||||
}
|
||||
}
|
||||
|
||||
@Ignore
|
||||
private void doTestBatchSD(List<StructureDefinition> sds, boolean useSelectedExtensions, ShExGenerator.ConstraintTranslationPolicy policy, boolean debugMode, boolean validateShEx, boolean excludeMetaSDs) {
|
||||
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);
|
||||
|
||||
this.shexGenerator.debugMode = debugMode;
|
||||
this.shexGenerator.constraintPolicy = policy;
|
||||
|
||||
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) {
|
||||
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);
|
||||
}
|
||||
|
||||
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);
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void doTestAll() throws FileNotFoundException, IOException, FHIRException, UcumException {
|
||||
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
|
||||
|
||||
@ -176,8 +225,9 @@ public class ShexGeneratorTests {
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
|
||||
sds, // List of Structure Definitions
|
||||
false, //Process all extensions
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL,
|
||||
// Process all types of constraints, do not skip
|
||||
true
|
||||
);
|
||||
}
|
||||
|
||||
@ -189,8 +239,9 @@ public class ShexGeneratorTests {
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.ALL, // Processing All kinds of Structure Definitions
|
||||
sds, // List of Structure Definitions
|
||||
false, //Process all extensions
|
||||
ShExGenerator.ConstraintTranslationPolicy.GENERIC_ONLY
|
||||
ShExGenerator.ConstraintTranslationPolicy.GENERIC_ONLY,
|
||||
// Process generic constraints only, ignore constraints of type 'context of use'
|
||||
false
|
||||
);
|
||||
|
||||
}
|
||||
@ -203,8 +254,9 @@ public class ShexGeneratorTests {
|
||||
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
|
||||
ShExGenerator.ConstraintTranslationPolicy.CONTEXT_OF_USE_ONLY,
|
||||
// Process constraints only where context of use found, skip otherwise
|
||||
false
|
||||
);
|
||||
}
|
||||
|
||||
@ -216,7 +268,8 @@ public class ShexGeneratorTests {
|
||||
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
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
|
||||
false
|
||||
);
|
||||
}
|
||||
|
||||
@ -225,10 +278,11 @@ public class ShexGeneratorTests {
|
||||
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
|
||||
|
||||
processSDList(
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.STRUCTURE_DEFINITIONS, // Processing All kinds of Structure Definitions
|
||||
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
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
|
||||
false
|
||||
);
|
||||
}
|
||||
|
||||
@ -237,10 +291,11 @@ public class ShexGeneratorTests {
|
||||
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
|
||||
|
||||
processSDList(
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.EXTENSIONS, // Processing All kinds of Structure Definitions
|
||||
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
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
|
||||
false
|
||||
);
|
||||
}
|
||||
|
||||
@ -249,10 +304,11 @@ public class ShexGeneratorTests {
|
||||
List<StructureDefinition> sds = TestingUtilities.getSharedWorkerContext().fetchResourcesByType(StructureDefinition.class);
|
||||
|
||||
processSDList(
|
||||
ShexGeneratorTestUtils.RESOURCE_CATEGORY.LOGICAL_NAMES, // Processing All kinds of Structure Definitions
|
||||
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
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
|
||||
false
|
||||
);
|
||||
}
|
||||
|
||||
@ -260,17 +316,19 @@ public class ShexGeneratorTests {
|
||||
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
|
||||
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
|
||||
ShExGenerator.ConstraintTranslationPolicy.ALL, // Process all type of constraints
|
||||
false
|
||||
);
|
||||
}
|
||||
|
||||
private void processSDList(ShexGeneratorTestUtils.RESOURCE_CATEGORY cat,
|
||||
List<StructureDefinition> sds,
|
||||
boolean useSelectedExtensions,
|
||||
ShExGenerator.ConstraintTranslationPolicy policy) {
|
||||
ShExGenerator.ConstraintTranslationPolicy policy,
|
||||
boolean batchMode) {
|
||||
if ((sds == null) || (sds.isEmpty())) {
|
||||
throw new FHIRException("No StructuredDefinition found!");
|
||||
}
|
||||
@ -283,15 +341,20 @@ public class ShexGeneratorTests {
|
||||
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];
|
||||
}
|
||||
System.out.println("******************** " + resDef + " *********************");
|
||||
doTestThis(name, resDef.url, useSelectedExtensions, policy, true, true);
|
||||
});
|
||||
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);
|
||||
});
|
||||
} else {
|
||||
doTestBatchSD(sds, useSelectedExtensions, policy, true, true, false);
|
||||
}
|
||||
|
||||
|
||||
System.out.println("************************ END PROCESSING ******************************");
|
||||
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user