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more work on profile comparison

This commit is contained in:
Grahame Grieve 2019-09-13 00:26:25 +10:00
parent 461a8c5092
commit 3f75f9c605
3 changed files with 203 additions and 15 deletions
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188
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/CapabilityStatementUtilities.java
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@ -10,6 +10,8 @@ import java.io.OutputStream;
import java.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.List;
import java.util.UUID;
@ -18,22 +20,39 @@ import java.util.zip.ZipInputStream;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.CapabilityStatementUtilities.CapabilityStatementRestSorter;
import org.hl7.fhir.r5.conformance.ProfileComparer.ProfileComparison;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.BackboneElement;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceOperationComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestResourceSearchParamComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.CapabilityStatementRestSecurityComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.ResourceInteractionComponent;
import org.hl7.fhir.r5.model.CapabilityStatement.RestfulCapabilityMode;
import org.hl7.fhir.r5.model.CapabilityStatement.SystemInteractionComponent;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.utils.KeyGenerator;
import org.hl7.fhir.r5.utils.OperationOutcomeUtilities;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Element;
import org.hl7.fhir.r5.model.Enumeration;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.Property;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.MarkDownProcessor;
import org.hl7.fhir.utilities.Utilities;
@ -54,16 +73,14 @@ public class CapabilityStatementUtilities {
public class CapabilityStatementComparisonOutput {
public CapabilityStatementComparisonOutput() {
subset = new CapabilityStatement();
keygen.genId(subset);
subset.setDate(new Date());
subset.setId(UUID.randomUUID().toString().toLowerCase());
subset.setUrl("urn:uuid:"+subset.getId());
subset.setName("intersection of "+selfName+" and "+otherName);
subset.setStatus(PublicationStatus.DRAFT);
superset = new CapabilityStatement();
keygen.genId(superset);
superset.setDate(subset.getDate());
superset.setId(UUID.randomUUID().toString().toLowerCase());
superset.setUrl("urn:uuid:"+superset.getId());
superset.setName("union of "+selfName+" and "+otherName);
superset.setStatus(PublicationStatus.DRAFT);
}
@ -92,12 +109,14 @@ public class CapabilityStatementUtilities {
private XhtmlDocument html;
private MarkDownProcessor markdown = new MarkDownProcessor(Dialect.COMMON_MARK);
private String folder;
private KeyGenerator keygen;
// private String css;
public CapabilityStatementUtilities(SimpleWorkerContext context, String folder) throws IOException {
public CapabilityStatementUtilities(SimpleWorkerContext context, String folder, KeyGenerator keygen) throws IOException {
super();
this.context = context;
this.folder = folder;
this.keygen = keygen;
String f = Utilities.path(folder, "comparison.zip");
download("http://fhir.org/archive/comparison.zip", f);
unzip(f, folder);
@ -199,6 +218,8 @@ public class CapabilityStatementUtilities {
if (folder != null)
saveToFile();
output.outcome = OperationOutcomeUtilities.createOutcome(output.messages);
sortCapabilityStatement(output.subset);
sortCapabilityStatement(output.superset);
return output;
}
@ -419,7 +440,7 @@ public class CapabilityStatementUtilities {
union.setProfile(sdL.getUrl());
} else if (folder != null) {
try {
ProfileComparer pc = new ProfileComparer(context);
ProfileComparer pc = new ProfileComparer(context, keygen);
pc.setId("api-ep."+type);
pc.setTitle("Comparison - "+selfName+" vs "+otherName);
pc.setLeftName(selfName+": "+sdL.present());
@ -429,6 +450,18 @@ public class CapabilityStatementUtilities {
pc.compareProfiles(sdL, sdR);
System.out.println("Generate Comparison between "+pc.getLeftName()+" and "+pc.getRightName());
pc.generate(folder);
for (ProfileComparison cmp : pc.getComparisons()) {
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, cmp.getSubset().fhirType()+"-"+cmp.getSubset().getId()+".xml")), cmp.getSubset());
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, cmp.getSubset().fhirType()+"-"+cmp.getSubset().getId()+".json")), cmp.getSubset());
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, cmp.getSuperset().fhirType()+"-"+cmp.getSuperset().getId()+".xml")), cmp.getSuperset());
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, cmp.getSuperset().fhirType()+"-"+cmp.getSuperset().getId()+".json")), cmp.getSuperset());
}
for (ValueSet vs : pc.getValuesets()) {
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, vs.fhirType()+"-"+vs.getId()+".xml")), vs);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, vs.fhirType()+"-"+vs.getId()+".json")), vs);
}
intersection.setProfile(pc.getComparisons().get(0).getSubset().getUrl());
union.setProfile(pc.getComparisons().get(0).getSuperset().getUrl());
td.ah(pc.getId()+".html").tx("Comparison...");
@ -745,5 +778,148 @@ public class CapabilityStatementUtilities {
span.tx(text);
return span;
}
private int compareStr(String l, String r) {
if (l == null) {
if (r == null)
return (r == null) ? 0 : -1;
}
if (r == null)
return 1;
return l.compareTo(r);
}
public class CapabilityStatementRestSorter implements Comparator<CapabilityStatementRestComponent> {
@Override
public int compare(CapabilityStatementRestComponent l, CapabilityStatementRestComponent r) {
return compareStr(l.hasMode() ? l.getMode().toCode() : null, r.hasMode() ? r.getMode().toCode() : null);
}
}
public class CapabilityStatementRestResourceSorter implements Comparator<CapabilityStatementRestResourceComponent> {
@Override
public int compare(CapabilityStatementRestResourceComponent l, CapabilityStatementRestResourceComponent r) {
return compareStr(l.getType(), r.getType());
}
}
public class CapabilityStatementRestResourceInteractionSorter implements Comparator<ResourceInteractionComponent> {
@Override
public int compare(ResourceInteractionComponent l, ResourceInteractionComponent r) {
return compareStr(l.hasCode() ? l.getCode().toCode() : null, r.hasCode() ? r.getCode().toCode() : null);
}
}
public class SystemInteractionComponentSorter implements Comparator<SystemInteractionComponent> {
@Override
public int compare(SystemInteractionComponent l, SystemInteractionComponent r) {
return compareStr(l.hasCode() ? l.getCode().toCode() : null, r.hasCode() ? r.getCode().toCode() : null);
}
}
public class SearchParamSorter implements Comparator<CapabilityStatementRestResourceSearchParamComponent> {
@Override
public int compare(CapabilityStatementRestResourceSearchParamComponent l, CapabilityStatementRestResourceSearchParamComponent r) {
return compareStr(l.getName(), r.getName());
}
}
public class OperationSorter implements Comparator<CapabilityStatementRestResourceOperationComponent> {
@Override
public int compare(CapabilityStatementRestResourceOperationComponent l, CapabilityStatementRestResourceOperationComponent r) {
return compareStr(l.getName(), r.getName());
}
}
public class CanonicalTypeSorter implements Comparator<CanonicalType> {
@Override
public int compare(CanonicalType l, CanonicalType r) {
return compareStr(l.getValue(), r.getValue());
}
}
public class StringTypeSorter implements Comparator<StringType> {
@Override
public int compare(StringType l, StringType r) {
return compareStr(l.getValue(), r.getValue());
}
}
public class EnumSorter implements Comparator<Enumeration> {
@Override
public int compare(Enumeration l, Enumeration r) {
return compareStr(l.getCode(), r.getCode());
}
}
public class ExtensionSorter implements Comparator<Extension> {
@Override
public int compare(Extension l, Extension r) {
return compareStr(l.getUrl(), r.getUrl());
}
}
public class CodingSorter implements Comparator<Coding> {
@Override
public int compare(Coding l, Coding r) {
return compareStr(""+l.getSystem()+"#"+l.getCode(), ""+r.getSystem()+"#"+r.getCode());
}
}
public class CodeableConceptSorter implements Comparator<CodeableConcept> {
@Override
public int compare(CodeableConcept l, CodeableConcept r) {
Collections.sort(l.getCoding(), new CodingSorter());
Collections.sort(r.getCoding(), new CodingSorter());
return compareStr(cgen(l), cgen(r));
}
private String cgen(CodeableConcept cc) {
if (cc.hasCoding())
return ""+cc.getCodingFirstRep().getSystem()+"#"+cc.getCodingFirstRep().getCode();
return "~"+cc.getText();
}
}
private void sortCapabilityStatement(CapabilityStatement cs) {
sortExtensions(cs);
Collections.sort(cs.getRest(), new CapabilityStatementRestSorter());
for (CapabilityStatementRestComponent csr : cs.getRest()) {
Collections.sort(csr.getSecurity().getService(), new CodeableConceptSorter());
Collections.sort(csr.getCompartment(), new CanonicalTypeSorter());
Collections.sort(csr.getResource(), new CapabilityStatementRestResourceSorter());
for (CapabilityStatementRestResourceComponent r : csr.getResource()) {
Collections.sort(r.getSupportedProfile(), new CanonicalTypeSorter());
Collections.sort(r.getInteraction(), new CapabilityStatementRestResourceInteractionSorter());
Collections.sort(r.getReferencePolicy(), new EnumSorter());
Collections.sort(r.getSearchInclude(), new StringTypeSorter());
Collections.sort(r.getSearchRevInclude(), new StringTypeSorter());
Collections.sort(r.getSearchParam(), new SearchParamSorter());
Collections.sort(r.getOperation(), new OperationSorter());
}
Collections.sort(csr.getInteraction(), new SystemInteractionComponentSorter());
Collections.sort(csr.getSearchParam(), new SearchParamSorter());
Collections.sort(csr.getOperation(), new OperationSorter());
}
}
private void sortExtensions(DomainResource dr) {
Collections.sort(dr.getExtension(), new ExtensionSorter());
for (Property p : dr.children()) {
for (Base b : p.getValues()) {
if (b instanceof Element)
sortExtensions((Element) b);
}
}
}
private void sortExtensions(Element e) {
Collections.sort(e.getExtension(), new ExtensionSorter());
for (Property p : e.children()) {
for (Base b : p.getValues()) {
if (b instanceof Element)
sortExtensions((Element) b);
}
}
}
}

12
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileComparer.java
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@ -31,6 +31,8 @@ import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
@ -64,6 +66,7 @@ import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r5.utils.DefinitionNavigator;
import org.hl7.fhir.r5.utils.KeyGenerator;
import org.hl7.fhir.r5.utils.NarrativeGenerator;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
@ -96,7 +99,14 @@ import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
public class ProfileComparer implements ProfileKnowledgeProvider {
private IWorkerContext context;
private KeyGenerator keygen;
public ProfileComparer(IWorkerContext context, KeyGenerator keygen) {
super();
this.context = context;
this.keygen = keygen;
}
public ProfileComparer(IWorkerContext context) {
super();
this.context = context;
@ -326,6 +336,8 @@ public class ProfileComparer implements ProfileKnowledgeProvider {
// from here on in, any issues go in messages
outcome.superset = new StructureDefinition();
outcome.subset = new StructureDefinition();
keygen.genId(outcome.subset);
keygen.genId(outcome.superset);
if (outcome.ruleEqual(ln.path(), null,ln.path(), rn.path(), "Base Type is not compatible", false)) {
if (compareElements(outcome, ln.path(), ln, rn, null)) {
outcome.subset.setName("intersection of "+outcome.leftName()+" and "+outcome.rightName());

18
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/Validator.java
View File

@ -62,6 +62,7 @@ import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.UUID;
import org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementKind;
import org.hl7.fhir.r5.conformance.CapabilityStatementUtilities;
@ -84,6 +85,7 @@ import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.utils.KeyGenerator;
import org.hl7.fhir.r5.utils.NarrativeGenerator;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.validation.ValidationEngine.ScanOutputItem;
@ -306,7 +308,7 @@ public class Validator {
String nameLeft = chooseName(args, "leftName", (MetadataResource) resLeft);
String nameRight = chooseName(args, "rightName", (MetadataResource) resRight);
System.out.println("Comparing CapabilityStatements "+left+" to "+right);
CapabilityStatementUtilities pc = new CapabilityStatementUtilities(validator.getContext(), dest);
CapabilityStatementUtilities pc = new CapabilityStatementUtilities(validator.getContext(), dest, new KeyGenerator("http://fhir.org/temp/"+UUID.randomUUID().toString().toLowerCase()));
CapabilityStatement capL = (CapabilityStatement) resLeft;
CapabilityStatement capR = (CapabilityStatement) resRight;
CapabilityStatementComparisonOutput output = pc.isCompatible(nameLeft, nameRight, capL, capR);
@ -319,14 +321,12 @@ public class Validator {
b.append("\r\n");
}
TextFile.stringToFile(b.toString(), destTxt);
File txtFile = new File(destTxt);
Desktop.getDesktop().browse(txtFile.toURI());
new XmlParser().compose(new FileOutputStream(Utilities.path(dest, "union.xml")), output.getSuperset());
new XmlParser().compose(new FileOutputStream(Utilities.path(dest, "intersection.xml")), output.getSubset());
new XmlParser().compose(new FileOutputStream(Utilities.path(dest, "issues.xml")), output.getOutcome());
new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "union.json")), output.getSuperset());
new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "intersection.json")), output.getSubset());
new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "issues.json")), output.getOutcome());
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "CapabilityStatement-union.xml")), output.getSuperset());
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "CapabilityStatement-intersection.xml")), output.getSubset());
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "OperationOutcome-issues.xml")), output.getOutcome());
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "CapabilityStatement-union.json")), output.getSuperset());
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "CapabilityStatement-intersection.json")), output.getSubset());
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "OperationOutcome-issues.json")), output.getOutcome());
String destHtml = Utilities.path(dest, "index.html");
File htmlFile = new File(destHtml);