Merge pull request #482 from hapifhir/gg-202104-bugfixes-2

Ensure that CVX uses tx.fhir.org, not UTG definitions which are wrong…

RELEASE_NOTES.md

@@ -0,0 +1,3 @@
+Terminology: Ensure that CVX uses tx.fhir.org, not UTG definitions which are wrong
+Validator: Fix problems with Bundle validation for ids in collections and add additional search related validation
+Validator: Remove check on ElementDefinition.id for R2B

org.hl7.fhir.core.generator/readme.md

@@ -1,6 +1,6 @@
 The Java Core Code Generator
 
-Note: This code only generates tje R5 java code. Older generated models are now maintained by hand.
+Note: This code only generates the R5 java code. Older generated models are now maintained by hand.
 
 To run this code, run the class JavaCoreGenerator with 3 parameters:      
 * 1: fhir version to generate from (e.g. 4.1.0 or 'current'

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java

@@ -63,7 +63,7 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.hl7.fhir.utilities.validation.ValidationOptions;
 import org.hl7.fhir.utilities.validation.ValidationOptions.ValueSetMode;
 
-public class ValueSetCheckerSimple implements ValueSetChecker {
+public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChecker {
 
   private ValueSet valueset;
   private IWorkerContext context;

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetExpanderSimple.java

@@ -108,7 +108,7 @@ import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionParameterComponent;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.utilities.Utilities;
 
-public class ValueSetExpanderSimple implements ValueSetExpander {
+public class ValueSetExpanderSimple extends ValueSetWorker implements ValueSetExpander {
 
   public class PropertyFilter implements IConceptFilter {
 
@@ -567,7 +567,7 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
       copyImportContains(base.getExpansion().getContains(), null, expParams, imports);
     } else {
       CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
-      if ((cs == null || (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT))) {
+      if (isServerSide(inc.getSystem()) || (cs == null || (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT))) {
         doServerIncludeCodes(inc, heirarchical, exp, imports, expParams, extensions);
       } else {
         doInternalIncludeCodes(inc, exp, expParams, imports, cs);

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetWorker.java

@@ -0,0 +1,10 @@
+package org.hl7.fhir.r5.terminologies;
+
+import org.hl7.fhir.utilities.Utilities;
+
+public class ValueSetWorker {
+
+  protected boolean isServerSide(String url) {
+    return Utilities.existsInList(url, "http://hl7.org/fhir/sid/cvx");
+  }
+}

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java

@@ -631,6 +631,15 @@ public class I18nConstants {
   public static final String BUNDLE_RULE_UNKNOWN = "BUNDLE_RULE_UNKNOWN";
   public static final String BUNDLE_RULE_INVALID_INDEX = "BUNDLE_RULE_INVALID_INDEX";
   public static final String BUNDLE_RULE_PROFILE_UNKNOWN = "BUNDLE_RULE_PROFILE_UNKNOWN";
+  public static final String BUNDLE_SEARCH_NOSELF = "BUNDLE_SEARCH_NOSELF";
+  public static final String BUNDLE_SEARCH_SELF_NOT_UNDERSTOOD = "BUNDLE_SEARCH_SELF_NOT_UNDERSTOOD";
+  public static final String BUNDLE_SEARCH_ENTRY_NO_RESOURCE = "BUNDLE_SEARCH_ENTRY_NO_RESOURCE";
+  public static final String BUNDLE_SEARCH_ENTRY_TYPE_NOT_SURE = "BUNDLE_SEARCH_ENTRY_TYPE_NOT_SURE";
+  public static final String BUNDLE_SEARCH_ENTRY_NO_RESOURCE_ID = "BUNDLE_SEARCH_ENTRY_NO_RESOURCE_ID";
+  public static final String BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_MODE = "BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_MODE";
+  public static final String BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_NO_MODE = "BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_NO_MODE";
+  public static final String BUNDLE_SEARCH_NO_MODE = "BUNDLE_SEARCH_NO_MODE";
+  public static final String BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_OUTCOME = "BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_OUTCOME";
 }
 
 

org.hl7.fhir.utilities/src/main/resources/Messages.properties

@@ -643,3 +643,12 @@ CODESYSTEM_CS_SUPP_INVALID_CODE = The code ''{1}'' is not declared in the base C
 SD_VALUE_TYPE_IILEGAL = The element {0} has a {1} of type {2}, which is not in the list of allowed types ({3})
 SD_NO_TYPES_OR_CONTENTREF = The element {0} has no assigned types, and no content reference
 CODESYSTEM_CS_UNK_EXPANSION = The code provided ({2}) is not in the value set {0}, and a code is required from this value set. The system {1} is unknown.
+BUNDLE_SEARCH_NOSELF = SearchSet Bundles should have a self link that specifies what the search was
+BUNDLE_SEARCH_SELF_NOT_UNDERSTOOD = No types could be determined from the search string, so the types can't be checked
+BUNDLE_SEARCH_ENTRY_NO_RESOURCE = SearchSet Bundle Entries must have resources
+BUNDLE_SEARCH_ENTRY_TYPE_NOT_SURE = Unable to determine if this resource is a valid resource type for this search 
+BUNDLE_SEARCH_ENTRY_NO_RESOURCE_ID = Search results must have ids
+BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_MODE = This is not a matching resource type for the specified search ({0} expecting {1})
+BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_OUTCOME = This is not an OperationOutcome ({0})
+BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_NO_MODE = This is not a matching resource type for the specified search (is a search mode needed?) ({0} expecting {1})
+BUNDLE_SEARCH_NO_MODE = SearchSet bundles should have search modes on the entries

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/BaseValidator.java

@@ -125,9 +125,11 @@ public class BaseValidator {
 
   protected final String META = "meta";
   protected final String ENTRY = "entry";
+  protected final String LINK = "link";
   protected final String DOCUMENT = "document";
   protected final String RESOURCE = "resource";
   protected final String MESSAGE = "message";
+  protected final String SEARCHSET = "searchset";
   protected final String ID = "id";
   protected final String FULL_URL = "fullUrl";
   protected final String PATH_ARG = ":0";

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java

@@ -2005,7 +2005,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     }
     if (type.equals(ID)) {
       // work around an old issue with ElementDefinition.id
-      if (!context.getPath().equals("ElementDefinition.id") || VersionUtilities.versionsCompatible("1.4", this.context.getVersion())) {
+      if (!context.getPath().equals("ElementDefinition.id")) {
         rule(errors, IssueType.INVALID, e.line(), e.col(), path, FormatUtilities.isValidId(e.primitiveValue()), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_ID_VALID, e.primitiveValue());
       }
     }
@@ -4166,6 +4166,24 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         hc = hostContext.forContained(element);
       }
       stack.resetIds();
+      if (element.getSpecial() != null) {
+        switch (element.getSpecial()) {
+        case BUNDLE_ENTRY:
+          idstatus = IdStatus.OPTIONAL;
+          break;
+        case BUNDLE_OUTCOME:
+          idstatus = IdStatus.OPTIONAL;
+          break;
+        case CONTAINED:
+          idstatus = IdStatus.REQUIRED;
+          break;
+        case PARAMETER:
+          idstatus = IdStatus.OPTIONAL;
+          break;
+        default:
+          break;        
+        }
+      }
       if (trr.getProfile().size() == 1) {
         long t = System.nanoTime();
         StructureDefinition profile = this.context.fetchResource(StructureDefinition.class, trr.getProfile().get(0).asStringValue());

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/BundleValidator.java

@@ -73,6 +73,9 @@ public class BundleValidator extends BaseValidator{
         }
         checkAllInterlinked(errors, entries, stack, bundle, VersionUtilities.isR5Ver(context.getVersion()));
       }
+      if (type.equals(SEARCHSET)) {
+        checkSearchSet(errors, bundle, entries, stack);
+      }
       // We do not yet have rules requiring that the id and fullUrl match when dealing with messaging Bundles
       //      validateResourceIds(errors, entries, stack);
     }
@@ -122,6 +125,159 @@ public class BundleValidator extends BaseValidator{
     }
   }
 
+  private void checkSearchSet(List<ValidationMessage> errors, Element bundle, List<Element> entries, NodeStack stack) {
+    // warning: should have self link
+    List<Element> links = new ArrayList<Element>();
+    bundle.getNamedChildren(LINK, links);
+    Element selfLink = getSelfLink(links);
+    List<String> types = new ArrayList<>();
+    if (selfLink == null) {
+      warning(errors, IssueType.INVALID, bundle.line(), bundle.col(), stack.getLiteralPath(), false, I18nConstants.BUNDLE_SEARCH_NOSELF);
+    } else {
+      readSearchResourceTypes(selfLink.getNamedChildValue("url"), types);
+      if (types.size() == 0) {
+        hint(errors, IssueType.INVALID, bundle.line(), bundle.col(), stack.getLiteralPath(), false, I18nConstants.BUNDLE_SEARCH_SELF_NOT_UNDERSTOOD);
+      }
+    }
+
+    Boolean searchMode = readHasSearchMode(entries);
+    if (searchMode == false) { // if no resources have search mode
+      boolean typeProblem = false;
+      String rtype = null;
+      int count = 0;
+      for (Element entry : entries) {
+        NodeStack estack = stack.push(entry, count, null, null);
+        count++;
+        Element res = entry.getNamedChild("resource");
+        if (rule(errors, IssueType.INVALID, bundle.line(), bundle.col(), estack.getLiteralPath(), res != null, I18nConstants.BUNDLE_SEARCH_ENTRY_NO_RESOURCE)) {
+          NodeStack rstack = estack.push(res, -1, null, null);
+          String rt = res.fhirType();
+          Boolean ok = checkSearchType(types, rt);
+          if (ok == null) {
+            typeProblem = true;
+            hint(errors, IssueType.INVALID, bundle.line(), bundle.col(), rstack.getLiteralPath(), selfLink == null, I18nConstants.BUNDLE_SEARCH_ENTRY_TYPE_NOT_SURE);                       
+            String id = res.getNamedChildValue("id");
+            warning(errors, IssueType.INVALID, bundle.line(), bundle.col(), rstack.getLiteralPath(), id != null || "OperationOutcome".equals(rt), I18nConstants.BUNDLE_SEARCH_ENTRY_NO_RESOURCE_ID);
+          } else if (ok) {
+            if (!"OperationOutcome".equals(rt)) {
+              String id = res.getNamedChildValue("id");
+              warning(errors, IssueType.INVALID, bundle.line(), bundle.col(), rstack.getLiteralPath(), id != null, I18nConstants.BUNDLE_SEARCH_ENTRY_NO_RESOURCE_ID);
+              if (rtype != null && !rt.equals(rtype)) {
+                typeProblem = true;
+              } else if (rtype == null) {
+                rtype = rt;
+              }
+            }
+          } else {
+            typeProblem = true;
+            warning(errors, IssueType.INVALID, bundle.line(), bundle.col(), estack.getLiteralPath(), false, I18nConstants.BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_NO_MODE, rt, types);            
+          }
+        }
+      }      
+      if (typeProblem) {
+        warning(errors, IssueType.INVALID, bundle.line(), bundle.col(), stack.getLiteralPath(), !typeProblem, I18nConstants.BUNDLE_SEARCH_NO_MODE);
+      } else {
+        hint(errors, IssueType.INVALID, bundle.line(), bundle.col(), stack.getLiteralPath(), !typeProblem, I18nConstants.BUNDLE_SEARCH_NO_MODE);        
+      }
+    } else {
+      int count = 0;
+      for (Element entry : entries) {
+        NodeStack estack = stack.push(entry, count, null, null);
+        count++;
+        Element res = entry.getNamedChild("resource");
+        String sm = null;
+        Element s = entry.getNamedChild("search");
+        if (s != null) {
+          sm = s.getNamedChildValue("mode");
+        }
+        warning(errors, IssueType.INVALID, bundle.line(), bundle.col(), estack.getLiteralPath(), sm != null, I18nConstants.BUNDLE_SEARCH_NO_MODE);
+        if (rule(errors, IssueType.INVALID, bundle.line(), bundle.col(), estack.getLiteralPath(), res != null, I18nConstants.BUNDLE_SEARCH_ENTRY_NO_RESOURCE)) {
+          NodeStack rstack = estack.push(res, -1, null, null);
+          String rt = res.fhirType();
+          String id = res.getNamedChildValue("id");
+          if (sm != null) {
+            if ("match".equals(sm)) {
+              rule(errors, IssueType.INVALID, bundle.line(), bundle.col(), rstack.getLiteralPath(), id != null, I18nConstants.BUNDLE_SEARCH_ENTRY_NO_RESOURCE_ID);
+              rule(errors, IssueType.INVALID, bundle.line(), bundle.col(), rstack.getLiteralPath(), types.size() == 0 || checkSearchType(types, rt), I18nConstants.BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_MODE, rt, types);
+            } else if ("include".equals(sm)) {
+              rule(errors, IssueType.INVALID, bundle.line(), bundle.col(), rstack.getLiteralPath(), id != null, I18nConstants.BUNDLE_SEARCH_ENTRY_NO_RESOURCE_ID);
+            } else { // outcome
+              rule(errors, IssueType.INVALID, bundle.line(), bundle.col(), rstack.getLiteralPath(), "OperationOutcome".equals(rt), I18nConstants.BUNDLE_SEARCH_ENTRY_WRONG_RESOURCE_TYPE_OUTCOME, rt);
+            }
+          }
+        }
+      }
+    }      
+  }
+
+  private Boolean checkSearchType(List<String> types, String rt) {
+    if (types.size() == 0) {
+      return null;
+    } else {      
+      return Utilities.existsInList(rt, types);
+    }
+  }
+
+  private Boolean readHasSearchMode(List<Element> entries) {
+    boolean all = true;
+    boolean any = false;
+    for (Element entry : entries) {
+      String sm = null;
+      Element s = entry.getNamedChild("search");
+      if (s != null) {
+        sm = s.getNamedChildValue("mode");
+      }
+      if (sm != null) {
+        any = true;
+      } else {
+        all = false;
+      }
+    }
+    if (all) {
+      return true;
+    } else if (any) {
+      return null;      
+    } else {
+      return false;
+    }
+  }
+
+  private void readSearchResourceTypes(String ref, List<String> types) {
+    if (ref == null) {
+      return;
+    }
+    String[] head = null;
+    String[] tail = null;
+    if (ref.contains("?")) {
+      head = ref.substring(0, ref.indexOf("?")).split("\\/");
+      tail = ref.substring(ref.indexOf("?")+1).split("\\&");
+    } else {
+      head = ref.split("\\/");
+    }
+    if (head == null || head.length == 0) {
+      return;
+    } else if (context.getResourceNames().contains(head[head.length-1])) {
+      types.add(head[head.length-1]);
+    } else if (tail != null) {
+      for (String s : tail) {
+        if (s.startsWith("_type=")) {
+          for (String t : s.substring(6).split("\\,")) {
+            types.add(t);
+          }
+        }
+      }      
+    }
+  }
+
+  private Element getSelfLink(List<Element> links) {
+    for (Element link : links) {
+      if ("self".equals(link.getNamedChildValue("relation"))) {
+        return link;
+      }
+    }
+    return null;
+  }
+
   private void validateDocument(List<ValidationMessage> errors, List<Element> entries, Element composition, NodeStack stack, String fullUrl, String id) {
     // first entry must be a composition
     if (rule(errors, IssueType.INVALID, composition.line(), composition.col(), stack.getLiteralPath(), composition.getType().equals("Composition"), I18nConstants.BUNDLE_BUNDLE_ENTRY_DOCUMENT)) {