Merge pull request #804 from hapifhir/gg-202205-pv

Gg 202205 pv

RELEASE_NOTES.md

@@ -1,7 +1,7 @@
 ## Validator Changes
 
-* no changes
+* Handle invalid HTTP responses better when accessing packages
 
 ## Other code changes
 
-* no changes
+* Fix various rendering NPEs

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/CodeSystemComparer.java

@@ -422,7 +422,7 @@ public class CodeSystemComparer extends CanonicalResourceComparer {
     ConceptPropertyComponent cp = null;
     if (cd != null) {
       for (ConceptPropertyComponent t : cd.getProperty()) {
-        if (t.getCode().equals(c)) {
+        if (t.hasCode() && t.getCode().equals(c)) {
           cp = t;
         }
       }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java

@@ -3800,6 +3800,9 @@ public class ProfileUtilities extends TranslatingUtilities {
     if (contentReference.contains("#")) {
       String url = contentReference.substring(0, contentReference.indexOf("#"));
       contentReference = contentReference.substring(contentReference.indexOf("#"));
+      if (Utilities.noString(url)) {
+        url = source.getUrl();
+      }
       if (!url.equals(source.getUrl())) {
         source = context.fetchResource(StructureDefinition.class, url);
         if (source == null) {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java

@@ -490,11 +490,13 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
         types = new String[] { "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem", "Measures" };
       }
       for (PackageResourceInformation pri : pi.listIndexedResources(types)) {
-        try {
+        if (!pri.getFilename().contains("ig-r4")) {
-          registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageVersion(pi.id(), pi.version(), pi.dateAsDate()));
+          try {
-          t++;
+            registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageVersion(pi.id(), pi.version(), pi.dateAsDate()));
-        } catch (FHIRException e) {
+            t++;
-          throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, pri.getFilename(), pi.name(), pi.version(), e.getMessage()), e);
+          } catch (FHIRException e) {
+            throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, pri.getFilename(), pi.name(), pi.version(), e.getMessage()), e);
+          }
         }
       }
     }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/SimpleHTTPClient.java

@@ -71,8 +71,12 @@ public class SimpleHTTPClient {
     public void checkThrowException() throws IOException {
       if (code >= 300) {
         String filename = Utilities.path("[tmp]", "fhir-http-"+(++counter)+".log");
-        TextFile.bytesToFile(content, filename);
+        if (content.length == 0) {
-        throw new IOException("Invalid HTTP response "+code+" from "+source+" ("+message+") (content in "+filename+")");
+          throw new IOException("Invalid HTTP response "+code+" from "+source+" ("+message+") (no content)");          
+        } else {
+          TextFile.bytesToFile(content, filename);
+          throw new IOException("Invalid HTTP response "+code+" from "+source+" ("+message+") (content in "+filename+")");
+        }
       }      
     }    
   }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/PackageHacker.java

@@ -27,7 +27,7 @@ public class PackageHacker {
   private static boolean useSecureReferences = false;
   
   public static void main(String[] args) throws FileNotFoundException, IOException {
-    new PackageHacker().edit("M:\\web\\hl7.org\\fhir\\5.0.0-snapshot1\\hl7.fhir.r5.examples.tgz");
+    new PackageHacker().edit("/Users/grahamegrieve/work/test-cases/validator/swiss.mednet.fhir#0.5.0.tgz");
   }
 
   private void edit(String name) throws FileNotFoundException, IOException {
@@ -59,7 +59,7 @@ public class PackageHacker {
 
   private void change(JsonObject npm, Map<String, byte[]> content) throws FileNotFoundException, IOException {
     fixVersions(npm);
-    npm.remove("notForPublication");
+//    npm.remove("notForPublication");
 //    npm.addProperty("url", "http://hl7.org/fhir/us/carin-rtpbc/STU1");
 //    npm.remove("name");
 //    npm.addProperty("name", "hl7.fhir.uv.smart-app-launch");
@@ -69,10 +69,14 @@ public class PackageHacker {
 ////    npm.addProperty("description", "Group Wrapper that includes all the R4 packages");
 //    npm.remove("url");
 //    npm.addProperty("url", "https://terminology.hl7.org/1.0.0/");
-//    npm.remove("dependencies");
+    npm.remove("dependencies");
-//    JsonObject dep = new JsonObject();
+    JsonObject dep = new JsonObject();
-//    npm.add("dependencies", dep);
+    npm.add("dependencies", dep);
-//    dep.addProperty("hl7.fhir.r3.core", "3.0.1");
+    dep.addProperty("hl7.fhir.r4.core", "4.0.1");
+    dep.addProperty("ch.fhir.ig.ch-core", "2.0.0");
+    dep.addProperty("ch.fhir.ig.ch-epr-term", "2.0.4");
+    dep.addProperty("ch.fhir.ig.ch-emed","2.0.0");
+
 //    dep.addProperty("hl7.fhir.r4.examples", "4.0.1");
 //    dep.addProperty("hl7.fhir.r4.expansions", "4.0.1");
 //    dep.addProperty("hl7.fhir.r4.elements", "4.0.1");

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ipa/IPAValidator.java

@@ -0,0 +1,84 @@
+package org.hl7.fhir.validation.ipa;
+
+import java.util.List;
+
+import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.validation.instance.InstanceValidator;
+
+/**
+ * You give this validator three parameters:
+ *   URL of server
+ *   access token for the server (most be already logged in)
+ *   patient ID - the patient ID that was authorised by the log in
+ *   
+ * @author grahamegrieve
+ *
+ */
+public class IPAValidator {
+
+  private String address;
+  private String token;
+  private String urn;
+  private InstanceValidator validator;
+  
+  public IPAValidator(String address, String token, String urn, InstanceValidator validator) {
+    super();
+    this.address = address;
+    this.token = token;
+    this.urn = urn;
+    this.validator = validator;
+  }
+  
+  public String getAddress() {
+    return address;
+  }
+  public void setAddress(String address) {
+    this.address = address;
+  }
+  public String getToken() {
+    return token;
+  }
+  public void setToken(String token) {
+    this.token = token;
+  }
+  public String getUrn() {
+    return urn;
+  }
+  public void setUrn(String urn) {
+    this.urn = urn;
+  }
+  public InstanceValidator getValidator() {
+    return validator;
+  }
+  public void setValidator(InstanceValidator validator) {
+    this.validator = validator;
+  }
+
+  public void validate() {
+    List<Patient> patients = searchPatients();
+    // check list of patients that have access to
+    // require that at least one of the patients matches the URL
+    // validate all resources and links
+    // validate search parameters
+    // check self links
+    
+//    AllergyIntolerance  patient patient+clinical-status
+//    Condition patient patient+category, patient+clinical-status, patient+code, patient+onset-date, patient+category+clinical_status
+//    DocumentReference _id, patient, patient+category, patient+type  patient+category+date, patient+status, patient+type+period
+//    Immunization  patient patient+date, patient+status
+//    MedicationRequest patient patient+intent, patient+intent+authoredon, patient+intent+status
+//    MedicationStatement subject subject+status
+//    Observation patient+category, patient+code, patient+category+date patient+category+status, patient+code+date
+//    Patient _id, identifier birthdate, family, gender, given, name, family+gender, birthdate+family, birthdate+name, gender+name
+    
+    
+    
+    
+    
+  }
+
+  private List<Patient> searchPatients() {
+    
+    return null;
+  }
+}