compile fixes and fixes for David

hapifhir · Jan 16, 2025 · 3d0a3c4 · 3d0a3c4
1 parent f5081ae
commit 3d0a3c4
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Showing 5 changed files with 19 additions and 22 deletions.
diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
@@ -1710,9 +1710,6 @@ public ValidationResult validateCode(ValidationOptions options, CodeableConcept
       }
     }
     Set<String> unknownSystems = new HashSet<>();
-    if ("8517006".equals(code.getCodingFirstRep().getCode())) {
-      DebugUtilities.breakpoint();
-    }
 
     List<OperationOutcomeIssueComponent> issues = new ArrayList<>();
 

diff --git a/...hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/filesystem/ManagedFileAccess.java b/...hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/filesystem/ManagedFileAccess.java
@@ -131,19 +131,7 @@ public static File file(String path, String filepath) throws IOException {
   }
 
   public static File file(File root, String filepath) throws IOException {
-    switch (accessPolicy) {
-    case DIRECT:
-      if (!inAllowedPaths(root.getAbsolutePath())) {
-        throw new IOException("The path '"+root.getAbsolutePath()+"' cannot be accessed by policy");
-      }
-      return new File(root.getAbsolutePath(), filepath);
-    case MANAGED:
-      return accessor.file(Utilities.path(root.getAbsolutePath(), filepath));
-    case PROHIBITED:
-      throw new IOException("Access to files is not allowed by local security policy");
-    default:
-      throw new IOException("Internal Error");
-    }
+    return file(root.getAbsolutePath(), filepath);
   }
   /** 
    * Open a FileInputStream, conforming to local security policy 

diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationTimeTracker.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationTimeTracker.java
@@ -7,6 +7,7 @@ public class ValidationTimeTracker {
   private long loadTime = 0;
   private long fpeTime = 0;
   private long specTime = 0;
+  private long aiTime = 0;
 
   public long getOverall() {
     return overall;
@@ -28,13 +29,19 @@ public long getSpecTime() {
     return specTime;
   }
 
+  public long getAiTime() {
+    return aiTime;
+  }
   public void load(long start) {
     loadTime = loadTime + (System.nanoTime() - start);
   }
 
   public void overall(long start) {  
     overall = overall + (System.nanoTime() - start);
   }
+  public void ai(long start) {  
+    aiTime = aiTime + (System.nanoTime() - start);
+  }
 
   public void tx(long start, String s) {
     long ms = (System.nanoTime() - start) / 1000000;
@@ -61,5 +68,6 @@ public void reset() {
     loadTime = 0;
     fpeTime = 0;
     specTime = 0;
+    aiTime = 0;
   }
 }
diff --git a/...hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java b/...hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
@@ -1024,6 +1024,7 @@ public void validate(Object appContext, List<ValidationMessage> errors, String p
     errors.removeAll(messagesToRemove);
     timeTracker.overall(t);
     if (aiService != null && !textsToCheck.isEmpty()) {
+      t = System.nanoTime();
       CodeAndTextValidator ctv = new CodeAndTextValidator(cacheFolder, aiService);
       List<CodeAndTextValidationResult> results = null;
       try {
@@ -1045,6 +1046,7 @@ public void validate(Object appContext, List<ValidationMessage> errors, String p
           }
         }
       }
+      timeTracker.ai(t);
     }
 
     if (DEBUG_ELEMENT) {
@@ -7815,7 +7817,9 @@ public long timeNoTX() {
     return (timeTracker.getOverall() - timeTracker.getTxTime()) / 1000000;
   }
   public String reportTimes() {
-    String s = String.format("Times (ms): overall = %d:4, tx = %d, sd = %d, load = %d, fpe = %d, spec = %d", timeTracker.getOverall() / 1000000, timeTracker.getTxTime() / 1000000, timeTracker.getSdTime() / 1000000, timeTracker.getLoadTime() / 1000000, timeTracker.getFpeTime() / 1000000, timeTracker.getSpecTime() / 1000000);
+    String s = String.format("Times (ms): overall = %d:4, tx = %d, sd = %d, load = %d, fpe = %d, spec = %d, ai = %d",
+        timeTracker.getOverall() / 1000000, timeTracker.getTxTime() / 1000000, timeTracker.getSdTime() / 1000000, 
+        timeTracker.getLoadTime() / 1000000, timeTracker.getFpeTime() / 1000000, timeTracker.getSpecTime() / 1000000, timeTracker.getAiTime() / 1000000);
     timeTracker.reset();
     return s;
   }

diff --git a/...l7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationEngineTests.java b/...l7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationEngineTests.java
@@ -333,7 +333,7 @@ public void testResolveRelativeFileInvalid() throws Exception {
       ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Observation.json")));
       ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Patient.json")));
       OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "resolution", "relative-url-invalid.json"), null);
-      Assertions.assertTrue(checkOutcomes("testResolveRelativeFileValid", op, 
+      Assertions.assertTrue(checkOutcomes("testResolveRelativeFileInvalid", op, 
           "Observation.subject null error/structure: Unable to find a profile match for Patient/example-newborn among choices: http://hl7.org/fhir/test/StructureDefinition/PatientRule\n"+
           "Observation.subject null information/structure: Details for Patient/example-newborn matching against profile http://hl7.org/fhir/test/StructureDefinition/PatientRule|0.1.0\n"+
           "Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer\n"+
@@ -359,7 +359,7 @@ public void testResolveRelativeFileError() throws Exception {
       ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Observation.json")));
       ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Patient.json")));
       OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "resolution", "relative-url-error.json"), null);
-      Assertions.assertTrue(checkOutcomes("testResolveRelativeFileValid", op, 
+      Assertions.assertTrue(checkOutcomes("testResolveRelativeFileError", op, 
           "Observation.subject null error/structure: Unable to resolve resource with reference 'patient/example-newborn-x'\n"+
           "Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer\n"+
           "Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have an effective[x] ()\n"+
@@ -383,7 +383,7 @@ public void testResolveAbsoluteValid() throws Exception {
     ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Observation.json")));
     ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Patient.json")));
     OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "resolution", "absolute-url-valid.json"), null);
-    Assertions.assertTrue(checkOutcomes("testResolveRelativeFileValid", op, 
+    Assertions.assertTrue(checkOutcomes("testResolveAbsoluteValid", op, 
         "Observation.subject.resolve().ofType(Patient).managingOrganization null error/structure: Unable to resolve resource with reference 'Organization/1'\n"+
         "Observation.subject.resolve().ofType(Patient).managingOrganization null information/informational: Fetching 'Organization/1' failed. System details: org.hl7.fhir.exceptions.FHIRException: The URL 'Organization/1' is not known to the FHIR validator, and a resolution context has not been provided as part of the setup / parameters\n"+
         "Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer\n"+
@@ -402,7 +402,7 @@ public void testResolveAbsoluteInvalid() throws Exception {
       ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Observation.json")));
       ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Patient.json")));
       OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "resolution", "absolute-url-invalid.json"), null);
-      Assertions.assertTrue(checkOutcomes("testResolveRelativeFileValid", op, 
+      Assertions.assertTrue(checkOutcomes("testResolveAbsoluteInvalid", op, 
           "Observation.subject null error/structure: Unable to find a profile match for https://hl7.org/fhir/R4/patient-example-newborn.json among choices: http://hl7.org/fhir/test/StructureDefinition/PatientRule\n"+
           "Observation.subject null information/structure: Details for https://hl7.org/fhir/R4/patient-example-newborn.json matching against profile http://hl7.org/fhir/test/StructureDefinition/PatientRule|0.1.0\n"+
           "Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer\n"+
@@ -421,7 +421,7 @@ public void testResolveAbsoluteError() throws Exception {
       ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Observation.json")));
       ve.seeResource(new JsonParser().parse(TestingUtilities.loadTestResourceStream("validator", "resolution", "StructureDefinition-Patient.json")));
       OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "resolution", "absolute-url-error.json"), null);
-      Assertions.assertTrue(checkOutcomes("testResolveRelativeFileValid", op, 
+      Assertions.assertTrue(checkOutcomes("testResolveAbsoluteError", op, 
           "Observation.subject null error/structure: Unable to resolve resource with reference 'http://hl7x.org/fhir/R4/Patient/Patient/example-newborn'\n"+
           "Observation.subject null information/informational: Fetching 'http://hl7x.org/fhir/R4/Patient/Patient/example-newborn' failed. System details: java.net.UnknownHostException: hl7x.org\n"+
           "Observation null warning/invalid: Best Practice Recommendation: In general, all observations should have a performer\n"+