Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core + fix conflicts + fix error message for document date missing

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/R5ToR5Loader.java

@@ -0,0 +1,180 @@
+package org.hl7.fhir.convertors;
+
+/*-
+ * #%L
+ * org.hl7.fhir.convertors
+ * %%
+ * 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.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.UUID;
+
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r5.formats.JsonParser;
+import org.hl7.fhir.r5.formats.XmlParser;
+import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.context.SimpleWorkerContext.IContextResourceLoader;
+import org.hl7.fhir.r5.model.Bundle;
+import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r5.model.Bundle.BundleType;
+import org.hl7.fhir.r5.model.CanonicalResource;
+import org.hl7.fhir.r5.model.CanonicalType;
+import org.hl7.fhir.r5.model.CodeSystem;
+import org.hl7.fhir.r5.model.ElementDefinition;
+import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
+import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
+import org.hl7.fhir.r5.model.UriType;
+import org.hl7.fhir.r5.model.ValueSet;
+
+/**
+ * This loader doesn't really do anything, but it's defined for structural consistency 
+ * 
+ * @author graha
+ *
+ */
+public class R5ToR5Loader extends BaseLoader implements IContextResourceLoader, VersionConvertorAdvisor50 {
+
+  public R5ToR5Loader(String[] types) {
+    super(types);
+  }
+
+  private List<CodeSystem> cslist = new ArrayList<>();
+  private boolean patchUrls;
+  private boolean killPrimitives;;
+  
+  @Override
+  public Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException {
+    Resource r5 = null;
+    if (isJson)
+      r5 = new JsonParser().parse(stream);
+    else
+      r5 = new XmlParser().parse(stream);
+    
+    Bundle b;
+    if (r5 instanceof Bundle)
+      b = (Bundle) r5;
+    else {
+      b = new Bundle();
+      b.setId(UUID.randomUUID().toString().toLowerCase());
+      b.setType(BundleType.COLLECTION);
+      b.addEntry().setResource(r5).setFullUrl(r5 instanceof CanonicalResource ? ((CanonicalResource) r5).getUrl() : null);
+    }
+    for (CodeSystem cs : cslist) {
+      BundleEntryComponent be = b.addEntry();
+      be.setFullUrl(cs.getUrl());
+      be.setResource(cs);
+    }
+    if (killPrimitives) {
+      List<BundleEntryComponent> remove = new ArrayList<BundleEntryComponent>();
+      for (BundleEntryComponent be : b.getEntry()) {
+        if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
+          StructureDefinition sd = (StructureDefinition) be.getResource();
+          if (sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE)
+            remove.add(be);
+        }
+      }
+      b.getEntry().removeAll(remove);
+    }
+    if (patchUrls) {
+      for (BundleEntryComponent be : b.getEntry()) {
+        if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
+          StructureDefinition sd = (StructureDefinition) be.getResource();
+          sd.setUrl(sd.getUrl().replace("http://hl7.org/fhir/", "http://hl7.org/fhir/4.0/"));
+          sd.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace").setValue(new UriType("http://hl7.org/fhir"));
+          for (ElementDefinition ed : sd.getSnapshot().getElement()) 
+            patchUrl(ed);
+          for (ElementDefinition ed : sd.getDifferential().getElement()) 
+            patchUrl(ed);
+        }
+      }
+    }
+    return b;
+  }
+
+  private void patchUrl(ElementDefinition ed) {
+    for (TypeRefComponent tr : ed.getType()) {
+      for (CanonicalType s : tr.getTargetProfile()) {
+        s.setValue(s.getValue().replace("http://hl7.org/fhir/", "http://hl7.org/fhir/4.0/"));
+      }
+      for (CanonicalType s : tr.getProfile()) {
+        s.setValue(s.getValue().replace("http://hl7.org/fhir/", "http://hl7.org/fhir/4.0/"));
+      }
+    }    
+  }
+
+  @Override
+  public boolean ignoreEntry(BundleEntryComponent src) {
+    return false;
+  }
+
+  @Override
+  public org.hl7.fhir.dstu2.model.Resource convertR2(org.hl7.fhir.r5.model.Resource resource) throws FHIRException {
+    return null;
+  }
+
+  @Override
+  public org.hl7.fhir.dstu2016may.model.Resource convertR2016May(org.hl7.fhir.r5.model.Resource resource) throws FHIRException {
+    return null;
+  }
+
+  @Override
+  public org.hl7.fhir.r4.model.Resource convertR4(org.hl7.fhir.r5.model.Resource resource) throws FHIRException {
+    return null;
+  }
+
+  @Override
+  public void handleCodeSystem(CodeSystem cs, ValueSet vs) {
+    cs.setId(vs.getId());
+    cs.setValueSet(vs.getUrl());
+    cslist.add(cs);
+    
+  }
+
+  @Override
+  public CodeSystem getCodeSystem(ValueSet src) {
+    return null;
+  }
+
+  public boolean isPatchUrls() {
+    return patchUrls;
+  }
+
+  public R5ToR5Loader setPatchUrls(boolean patchUrls) {
+    this.patchUrls = patchUrls;
+    return this;
+  }
+
+  public boolean isKillPrimitives() {
+    return killPrimitives;
+  }
+
+  public R5ToR5Loader setKillPrimitives(boolean killPrimitives) {
+    this.killPrimitives = killPrimitives;
+    return this;
+  }
+
+  @Override
+  public org.hl7.fhir.dstu3.model.Resource convertR3(org.hl7.fhir.r5.model.Resource resource) throws FHIRException {
+    return null;
+  }
+
+}