refactor profile handling in validator

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/IResourceValidator.java

@@ -60,7 +60,12 @@ public interface IResourceValidator {
     }
   }
   
+  public interface IValidationProfileUsageTracker {
+    void recordProfileUsage(StructureDefinition profile, Object appContext, Element element);
+  }
+  
   public interface IValidatorResourceFetcher {
+
     Element fetch(Object appContext, String url) throws FHIRFormatError, DefinitionException, FHIRException, IOException;
     ReferenceValidationPolicy validationPolicy(Object appContext, String path, String url);
     boolean resolveURL(Object appContext, String path, String url) throws IOException, FHIRException; 
@@ -114,6 +119,9 @@ public interface IResourceValidator {
   IValidatorResourceFetcher getFetcher();
   IResourceValidator setFetcher(IValidatorResourceFetcher value);
 
+  IValidationProfileUsageTracker getTracker();
+  IResourceValidator setTracker(IValidationProfileUsageTracker value);
+
   boolean isNoBindingMsgSuppressed();
   IResourceValidator setNoBindingMsgSuppressed(boolean noBindingMsgSuppressed);
   
@@ -133,6 +141,9 @@ public interface IResourceValidator {
   public boolean isErrorForUnknownProfiles();
   public void setErrorForUnknownProfiles(boolean errorForUnknownProfiles);
 
+  public boolean isShowMessagesFromReferences();
+  public void setShowMessagesFromReferences(boolean value);
+  
   public String getValidationLanguage();
   public void setValidationLanguage(String value);
   
@@ -155,34 +166,28 @@ public interface IResourceValidator {
    * @throws IOException 
    */
   void validate(Object Context, List<ValidationMessage> errors, org.hl7.fhir.r5.elementmodel.Element element) throws FHIRException;
-  void validate(Object Context, List<ValidationMessage> errors, org.hl7.fhir.r5.elementmodel.Element element, ValidationProfileSet profiles) throws FHIRException;
   void validate(Object Context, List<ValidationMessage> errors, org.hl7.fhir.r5.elementmodel.Element element, String profile) throws FHIRException;
-  void validate(Object Context, List<ValidationMessage> errors, org.hl7.fhir.r5.elementmodel.Element element, StructureDefinition profile) throws FHIRException;
+  void validate(Object Context, List<ValidationMessage> errors, org.hl7.fhir.r5.elementmodel.Element element, List<StructureDefinition> profiles) throws FHIRException;
   
   org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, InputStream stream, FhirFormat format) throws FHIRException;
-  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, InputStream stream, FhirFormat format, ValidationProfileSet profiles) throws FHIRException;
   org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, InputStream stream, FhirFormat format, String profile) throws FHIRException;
-  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, InputStream stream, FhirFormat format, StructureDefinition profile) throws FHIRException;
+  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, InputStream stream, FhirFormat format, List<StructureDefinition> profiles) throws FHIRException;
 
   org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.hl7.fhir.r5.model.Resource resource) throws FHIRException;
-  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.hl7.fhir.r5.model.Resource resource, ValidationProfileSet profiles) throws FHIRException;
   org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.hl7.fhir.r5.model.Resource resource, String profile) throws FHIRException;
-  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.hl7.fhir.r5.model.Resource resource, StructureDefinition profile) throws FHIRException;
+  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.hl7.fhir.r5.model.Resource resource, List<StructureDefinition> profiles) throws FHIRException;
 
   org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.w3c.dom.Element element) throws FHIRException;
-  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.w3c.dom.Element element, ValidationProfileSet profiles) throws FHIRException;
   org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.w3c.dom.Element element, String profile) throws FHIRException;
-  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.w3c.dom.Element element, StructureDefinition profile) throws FHIRException;
+  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.w3c.dom.Element element, List<StructureDefinition> profile) throws FHIRException;
 
   org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.w3c.dom.Document document) throws FHIRException;
-  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.w3c.dom.Document document, ValidationProfileSet profiles) throws FHIRException;
   org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.w3c.dom.Document document, String profile) throws FHIRException;
-  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.w3c.dom.Document document, StructureDefinition profile) throws FHIRException;
+  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, org.w3c.dom.Document document, List<StructureDefinition> profile) throws FHIRException;
 
   org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, JsonObject object) throws FHIRException;
-  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, JsonObject object, ValidationProfileSet profiles) throws FHIRException;
   org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, JsonObject object, String profile) throws FHIRException;
-  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, JsonObject object, StructureDefinition profile) throws FHIRException; 
+  org.hl7.fhir.r5.elementmodel.Element validate(Object Context, List<ValidationMessage> errors, JsonObject object, List<StructureDefinition> profile) throws FHIRException; 
 
 
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/ValidationProfileSet.java

@@ -1,111 +0,0 @@
-package org.hl7.fhir.r5.utils;
-
-/*-
- * #%L
- * org.hl7.fhir.r5
- * %%
- * Copyright (C) 2014 - 2019 Health Level 7
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.hl7.fhir.r5.model.StructureDefinition;
-
-public class ValidationProfileSet {
-
-  public static class ProfileRegistration {
-    private String profile; 
-    private boolean errorOnMissing;
-    
-    public ProfileRegistration(String profile, boolean errorOnMissing) {
-      super();
-      this.profile = profile;
-      this.errorOnMissing = errorOnMissing;
-    }
-    public String getProfile() {
-      return profile;
-    }
-    public boolean isErrorOnMissing() {
-      return errorOnMissing;
-    }
-    
-    
-  }
-  private List<ProfileRegistration> canonical = new ArrayList<ProfileRegistration>();
-  private List<StructureDefinition> definitions = new ArrayList<StructureDefinition>();
-  
-  public ValidationProfileSet(String profile, boolean isError) {
-    super();
-    canonical.add(new ProfileRegistration(profile, isError));
-  }
-
-  public ValidationProfileSet() {
-    super();
-  }
-
-  public ValidationProfileSet(StructureDefinition profile) {
-    super();
-    definitions.add(profile);
-    canonical.add(new ProfileRegistration(profile.getUrl(), true));
-  }
-
-  public ValidationProfileSet(List<String> profiles, boolean isError) {
-    super();
-    if (profiles != null)
-      for (String p : profiles)
-        canonical.add(new ProfileRegistration(p, isError));
-  }
-
-  public List<String> getCanonicalUrls() {
-    List<String> res = new ArrayList<String>();
-    for (ProfileRegistration c : canonical) {
-      res.add(c.getProfile());
-    }
-    return res;
-  }
-
-  public List<StructureDefinition> getDefinitions() {
-    return definitions;
-  }
-
-  public boolean empty() {
-    return canonical.isEmpty() && definitions.isEmpty();
-  }
-
-  public List<String> getCanonicalAll() {
-    Set<String> res = new HashSet<String>();
-    res.addAll(getCanonicalUrls());
-    for (StructureDefinition sd : definitions)
-      res.add(sd.getUrl());
-    return new ArrayList<String>(res);
-  }
-
-  public List<ProfileRegistration> getCanonical() {
-    return canonical;
-  }
-
-  public StructureDefinition fetch(String effectiveProfile) {
-    for (StructureDefinition sd : definitions) 
-      if (effectiveProfile.equals(sd.getUrl()))
-        return sd;
-    return null;
-  }
-
-}

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java

@@ -146,7 +146,6 @@ import org.hl7.fhir.r5.utils.StructureMapUtilities;
 import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;
 import org.hl7.fhir.r5.validation.ValidationEngine.ScanOutputItem;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
-import org.hl7.fhir.r5.utils.ValidationProfileSet;
 import org.hl7.fhir.utilities.IniFile;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
@@ -307,6 +306,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
   private PrintWriter mapLog;
   private boolean debug;
   private Set<String> loadedIgs = new HashSet<>();
+  private IValidatorResourceFetcher fetcher;
 
   private class AsteriskFilter implements FilenameFilter {
     String dir;
@@ -946,10 +946,24 @@ public class ValidationEngine implements IValidatorResourceFetcher {
   public OperationOutcome validate(FhirFormat format, InputStream stream, List<String> profiles) throws Exception {
     List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
     InstanceValidator validator = getValidator();
-    validator.validate(null, messages, stream, format, new ValidationProfileSet(profiles, true));
+    validator.validate(null, messages, stream, format, asSdList(profiles));
     return messagesToOutcome(messages);
   }
 
+  public List<StructureDefinition> asSdList(List<String> profiles) throws Error {
+    List<StructureDefinition> list = new ArrayList<>();
+    if (profiles != null) {
+      for (String p : profiles) {
+        StructureDefinition sd = context.fetchResource(StructureDefinition.class, p);
+        if (sd == null) {
+          throw new Error("Unable to resolve profile "+p);
+        }
+        list.add(sd);
+      }
+    }
+    return list;
+  }
+    
   public OperationOutcome validate(String source, List<String> profiles) throws Exception {
     List<String> l = new ArrayList<String>();
     l.add(source);
@@ -986,7 +1000,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
             try {
               System.out.println("Validate "+ref+" against "+ig.getUrl());
               messages.clear();
-              validator.validate(null, messages, new ByteArrayInputStream(cnt.focus), cnt.cntType, new ValidationProfileSet(url, true));
+              validator.validate(null, messages, new ByteArrayInputStream(cnt.focus), cnt.cntType, url);
               res.add(new ScanOutputItem(ref, ig, null, messagesToOutcome(messages)));
             } catch (Exception ex) {
               res.add(new ScanOutputItem(ref, ig, null, exceptionToOutcome(ex)));
@@ -1000,7 +1014,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
                 try {
                   System.out.println("Validate "+ref+" against "+sd.getUrl());
                   messages.clear();
-                  validator.validate(null, messages, new ByteArrayInputStream(cnt.focus), cnt.cntType, new ValidationProfileSet(sd.getUrl(), true));
+                  validator.validate(null, messages, new ByteArrayInputStream(cnt.focus), cnt.cntType, asSdList(sd));
                   res.add(new ScanOutputItem(ref, ig, sd, messagesToOutcome(messages)));
                 } catch (Exception ex) {
                   res.add(new ScanOutputItem(ref, ig, sd, exceptionToOutcome(ex)));
@@ -1014,6 +1028,12 @@ public class ValidationEngine implements IValidatorResourceFetcher {
     return res;
   }
   
+  private List<StructureDefinition> asSdList(StructureDefinition sd) {
+    List<StructureDefinition> res = new ArrayList<StructureDefinition>();
+    res.add(sd);
+    return res;
+  }
+
   private Resource resolve(Reference reference) {
     return null;
   }
@@ -1122,7 +1142,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
         validateSHEX(location, messages);
     }
     InstanceValidator validator = getValidator();
-    validator.validate(null, messages, new ByteArrayInputStream(source), cntType, new ValidationProfileSet(profiles, true));
+    validator.validate(null, messages, new ByteArrayInputStream(source), cntType, asSdList(profiles));
     return messagesToOutcome(messages);
   }
 
@@ -1140,7 +1160,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
     validator.setResourceIdRule(resourceIdRule);
     validator.setBestPracticeWarningLevel(bpWarnings);
     validator.setCheckDisplay(displayOption);   
-    validator.validate(null, messages, new ByteArrayInputStream(source), cntType, new ValidationProfileSet(profiles, true));
+    validator.validate(null, messages, new ByteArrayInputStream(source), cntType, asSdList(profiles));
     return messagesToOutcome(messages);
   }
   
@@ -1597,13 +1617,15 @@ public class ValidationEngine implements IValidatorResourceFetcher {
 
   @Override
   public Element fetch(Object appContext, String url) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
-    return null;
+    return fetcher != null ? fetcher.fetch(appContext, url) : null;
   }
 
   @Override
   public ReferenceValidationPolicy validationPolicy(Object appContext, String path, String url) {
     if (!url.startsWith("http://hl7.org/fhir")) {
       return ReferenceValidationPolicy.IGNORE;
+    } else if (fetcher != null) {
+      return fetcher.validationPolicy(appContext, path, url);
     } else {
       return ReferenceValidationPolicy.CHECK_EXISTS_AND_TYPE;      
     }
@@ -1620,6 +1642,9 @@ public class ValidationEngine implements IValidatorResourceFetcher {
        "http://hl7.org/fhir/workflow", "http://hl7.org/fhir/ConsentPolicy/opt-out", "http://hl7.org/fhir/ConsentPolicy/opt-in")) {
       return true;
     }
+    if (fetcher != null) {
+      return fetcher.resolveURL(appContext, path, url);
+    };
     return false;
   }
 
@@ -1711,6 +1736,14 @@ public class ValidationEngine implements IValidatorResourceFetcher {
     context.getExpansionParameters().addParameter("system-version", "http://snomed.info/sct|"+sct);
   }
 
+  public IValidatorResourceFetcher getFetcher() {
+    return fetcher;
+  }
+
+  public void setFetcher(IValidatorResourceFetcher fetcher) {
+    this.fetcher = fetcher;
+  }
+
 
 }
 

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTestSuite.java

@@ -119,6 +119,7 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
         throw new Exception("unknown version "+v);
     }
     vCurr = ve.get(v);
+    vCurr.setFetcher(this);
     TestingUtilities.fcontext = vCurr.getContext();
 
     if (content.has("use-test") && !content.get("use-test").getAsBoolean())
@@ -185,11 +186,12 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
       System.out.println("Name: " + name+" - profile : "+profile.get("source").getAsString());
       v = content.has("version") ? content.get("version").getAsString() : Constants.VERSION;
       StructureDefinition sd = loadProfile(filename, contents, v, messages);
+      val.getContext().cacheResource(sd);      
       List<ValidationMessage> errorsProfile = new ArrayList<ValidationMessage>();
       if (name.endsWith(".json"))
-        val.validate(null, errorsProfile, IOUtils.toInputStream(testCaseContent, Charsets.UTF_8), FhirFormat.JSON, sd);
+        val.validate(null, errorsProfile, IOUtils.toInputStream(testCaseContent, Charsets.UTF_8), FhirFormat.JSON, asSdList(sd));
       else
-         val.validate(null, errorsProfile, IOUtils.toInputStream(testCaseContent, Charsets.UTF_8), FhirFormat.XML, sd);
+         val.validate(null, errorsProfile, IOUtils.toInputStream(testCaseContent, Charsets.UTF_8), FhirFormat.XML, asSdList(sd));
       checkOutcomes(errorsProfile, profile);
     }
     if (content.has("logical")) {
@@ -218,6 +220,11 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
     }
   }
 
+  private List<StructureDefinition> asSdList(StructureDefinition sd) {
+    List<StructureDefinition> res = new ArrayList<StructureDefinition>();
+    res.add(sd);
+    return res;
+  }
 
   public StructureDefinition loadProfile(String filename, String contents, String v, List<ValidationMessage> messages)  throws IOException, FHIRFormatError, FileNotFoundException, FHIRException, DefinitionException {
     StructureDefinition sd = (StructureDefinition) loadResource(filename, contents, v);
@@ -355,15 +362,23 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
 
   @Override
   public Element fetch(Object appContext, String url) throws FHIRFormatError, DefinitionException, IOException, FHIRException {
-    if (url.equals("Patient/test"))
+    Element res = null;
-      return new ObjectConverter(TestingUtilities.context()).convert(new Patient());
+    if (url.equals("Patient/test")) {
-    if (TestingUtilities.findTestResource("validator", url.replace("/", "-").toLowerCase()+".json")) {
+      res = new ObjectConverter(TestingUtilities.context()).convert(new Patient());
-      return Manager.makeParser(TestingUtilities.context(), FhirFormat.JSON).parse(TestingUtilities.loadTestResourceStream("validator", url.replace("/", "-").toLowerCase()+".json"));
+    } else if (TestingUtilities.findTestResource("validator", url.replace("/", "-").toLowerCase()+".json")) {
+      res = Manager.makeParser(TestingUtilities.context(), FhirFormat.JSON).parse(TestingUtilities.loadTestResourceStream("validator", url.replace("/", "-").toLowerCase()+".json"));
+    } else if (TestingUtilities.findTestResource("validator", url.replace("/", "-").toLowerCase()+".xml")) {
+      res = Manager.makeParser(TestingUtilities.context(), FhirFormat.XML).parse(TestingUtilities.loadTestResourceStream("validator", url.replace("/", "-").toLowerCase()+".xml"));
     }
-    if (TestingUtilities.findTestResource("validator", url.replace("/", "-").toLowerCase()+".xml")) {
+    if (res == null && url.contains("/")) {
-      return Manager.makeParser(TestingUtilities.context(), FhirFormat.JSON).parse(TestingUtilities.loadTestResourceStream("validator", url.replace("/", "-").toLowerCase()+".xml"));
+      String tail = url.substring(url.indexOf("/")+1);
+      if (TestingUtilities.findTestResource("validator", tail.replace("/", "-").toLowerCase()+".json")) {
+        res = Manager.makeParser(TestingUtilities.context(), FhirFormat.JSON).parse(TestingUtilities.loadTestResourceStream("validator", tail.replace("/", "-").toLowerCase()+".json"));
+      } else if (TestingUtilities.findTestResource("validator", tail.replace("/", "-").toLowerCase()+".xml")) {
+        res =  Manager.makeParser(TestingUtilities.context(), FhirFormat.XML).parse(TestingUtilities.loadTestResourceStream("validator", tail.replace("/", "-").toLowerCase()+".xml"));
       }
-    return null;
+    }
+    return res;
   }
 
   @Override