Testing Part 1

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

@@ -665,7 +665,8 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     }
     return expandVS(vs, cacheOk, heirarchical);
   }
-  
+
+
   @Override
   public ValueSetExpansionOutcome expandVS(ConceptSetComponent inc, boolean hierarchical) throws TerminologyServiceException {
     ValueSet vs = new ValueSet();
@@ -713,6 +714,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     return res;
   }
 
+  //TESTME
   @Override
   public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean heirarchical) {
     if (expParameters == null)
@@ -721,6 +723,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     return expandVS(vs, cacheOk, heirarchical, false, p);
   }
 
+  //TESTME
   @Override
   public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean heirarchical, boolean incompleteOk) {
     if (expParameters == null)
@@ -729,6 +732,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     return expandVS(vs, cacheOk, heirarchical, incompleteOk, p);
   }
 
+  //TESTME
   public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean heirarchical, boolean incompleteOk, Parameters p)  {
     if (p == null) {
       throw new Error(formatMessage(I18nConstants.NO_PARAMETERS_PROVIDED_TO_EXPANDVS));
@@ -947,12 +951,12 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     return code.hasVersion() ? code.getSystem()+"|"+code.getVersion() : code.getSystem();
   }
 
+  //TESTME
   @Override
-  public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs, ValidationContextCarrier ctxt) {
+  public ValidationResult validateCode(final ValidationOptions optionsArg, final Coding code, final ValueSet vs, final ValidationContextCarrier ctxt) {
-    if (options == null) {
+
-      options = ValidationOptions.defaults();
+    ValidationOptions options = optionsArg != null ? optionsArg : ValidationOptions.defaults();
-    }
+
-    
     if (code.hasSystem()) {
       codeSystemsUsed.add(code.getSystem());
     }
@@ -1036,6 +1040,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     }
   }
 
+  //TESTME
   @Override
   public ValidationResult validateCode(ValidationOptions options, CodeableConcept code, ValueSet vs) {
     CacheToken cacheToken = txCache.generateValidationToken(options, code, vs);
@@ -1084,7 +1089,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     return res;
   }
 
-  private ValidationResult validateOnServer(ValueSet vs, Parameters pin, ValidationOptions options) throws FHIRException {
+  protected ValidationResult validateOnServer(ValueSet vs, Parameters pin, ValidationOptions options) throws FHIRException {
     boolean cache = false;
     if (vs != null) {
       for (ConceptSetComponent inc : vs.getCompose().getInclude()) {

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

@@ -94,6 +94,7 @@ public class TerminologyCache {
   public class CacheToken {
     private String name;
     private String key;
+    @Getter
     private String request;
     private boolean hasVersion;
 
@@ -124,7 +125,6 @@ public class TerminologyCache {
 
   private CapabilityStatement capabilityStatementCache = null;
 
-
   public boolean hasCapabilityStatement() {
     return capabilityStatementCache != null;
   }
@@ -183,6 +183,7 @@ public class TerminologyCache {
   public void clear() {
     caches.clear();
   }
+
   public CacheToken generateValidationToken(ValidationOptions options, Coding code, ValueSet vs) {
     CacheToken ct = new CacheToken();
     if (code.hasSystem())
@@ -198,7 +199,7 @@ public class TerminologyCache {
     } catch (IOException e) {
       throw new Error(e);
     }
-    ct.key = String.valueOf(hashNWS(ct.request));
+    ct.key = String.valueOf(hashJson(ct.request));
     return ct;
   }
 
@@ -227,7 +228,7 @@ public class TerminologyCache {
     } catch (IOException e) {
       throw new Error(e);
     }
-    ct.key = String.valueOf(hashNWS(ct.request));
+    ct.key = String.valueOf(hashJson(ct.request));
     return ct;
   }
   
@@ -268,7 +269,7 @@ public class TerminologyCache {
     } catch (IOException e) {
       throw new Error(e);
     }
-    ct.key = String.valueOf(hashNWS(ct.request));
+    ct.key = String.valueOf(hashJson(ct.request));
     return ct;
   }
 
@@ -500,6 +501,35 @@ public class TerminologyCache {
     }
   }
 
+
+
+  private CacheEntry getCacheEntry(String request, String resultString) throws IOException {
+    CacheEntry ce = new CacheEntry();
+    ce.persistent = true;
+    ce.request = request;
+    boolean e = resultString.charAt(0) == 'e';
+    resultString = resultString.substring(3);
+    JsonObject o = (JsonObject) new com.google.gson.JsonParser().parse(resultString);
+    String error = loadJS(o.get("error"));
+    if (e) {
+      if (o.has("valueSet"))
+        ce.e = new ValueSetExpansionOutcome((ValueSet) new JsonParser().parse(o.getAsJsonObject("valueSet")), error, TerminologyServiceErrorClass.UNKNOWN);
+      else
+        ce.e = new ValueSetExpansionOutcome(error, TerminologyServiceErrorClass.UNKNOWN);
+    } else {
+      String t = loadJS(o.get("severity"));
+      IssueSeverity severity = t == null ? null : IssueSeverity.fromCode(t);
+      String display = loadJS(o.get("display"));
+      String code = loadJS(o.get("code"));
+      String system = loadJS(o.get("system"));
+      String definition = loadJS(o.get("definition"));
+      t = loadJS(o.get("class"));
+      TerminologyServiceErrorClass errorClass = t == null ? null : TerminologyServiceErrorClass.valueOf(t);
+      ce.v = new ValidationResult(severity, error, system, new ConceptDefinitionComponent().setDisplay(display).setDefinition(definition).setCode(code)).setErrorClass(errorClass);
+    }
+    return ce;
+  }
+
   private void loadNamedCache(String fn) {
     int c = 0;
     try {
@@ -508,7 +538,7 @@ public class TerminologyCache {
 
       NamedCache nc = new NamedCache();
       nc.name = title;
-      caches.put(title, nc);
+
       if (src.startsWith("?"))
         src = src.substring(1);
       int i = src.indexOf(ENTRY_MARKER);
@@ -519,34 +549,15 @@ public class TerminologyCache {
         i = src.indexOf(ENTRY_MARKER);
         if (!Utilities.noString(s)) {
           int j = s.indexOf(BREAK);
-          String q = s.substring(0, j);
+          String request = s.substring(0, j);
           String p = s.substring(j + BREAK.length() + 1).trim();
-          CacheEntry ce = new CacheEntry();
+
-          ce.persistent = true;
+          CacheEntry cacheEntry = getCacheEntry(request, p);
-          ce.request = q;
+
-          boolean e = p.charAt(0) == 'e';
+          nc.map.put(String.valueOf(hashJson(cacheEntry.request)), cacheEntry);
-          p = p.substring(3);
+          nc.list.add(cacheEntry);
-          JsonObject o = (JsonObject) new com.google.gson.JsonParser().parse(p);
-          String error = loadJS(o.get("error"));
-          if (e) {
-            if (o.has("valueSet"))
-              ce.e = new ValueSetExpansionOutcome((ValueSet) new JsonParser().parse(o.getAsJsonObject("valueSet")), error, TerminologyServiceErrorClass.UNKNOWN);
-            else
-              ce.e = new ValueSetExpansionOutcome(error, TerminologyServiceErrorClass.UNKNOWN);
-          } else {
-            String t = loadJS(o.get("severity"));
-            IssueSeverity severity = t == null ? null : IssueSeverity.fromCode(t);
-            String display = loadJS(o.get("display"));
-            String code = loadJS(o.get("code"));
-            String system = loadJS(o.get("system"));
-            String definition = loadJS(o.get("definition"));
-            t = loadJS(o.get("class"));
-            TerminologyServiceErrorClass errorClass = t == null ? null : TerminologyServiceErrorClass.valueOf(t);
-            ce.v = new ValidationResult(severity, error, system, new ConceptDefinitionComponent().setDisplay(display).setDefinition(definition).setCode(code)).setErrorClass(errorClass);
-          }
-          nc.map.put(String.valueOf(hashNWS(ce.request)), ce);
-          nc.list.add(ce);
         }
+        caches.put(nc.name, nc);
       }
     } catch (Exception e) {
       throw new FHIRException("Error loading " + fn + ": " + e.getMessage() + " entry " + c, e);
@@ -580,7 +591,7 @@ public class TerminologyCache {
     return s;
   }
 
-  private String hashNWS(String s) {
+  private String hashJson(String s) {
     s = StringUtils.remove(s, ' ');
     s = StringUtils.remove(s, '\n');
     s = StringUtils.remove(s, '\r');

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/context/CacheTestUtils.java

@@ -0,0 +1,8 @@
+package org.hl7.fhir.r5.context;
+
+import org.hl7.fhir.utilities.validation.ValidationOptions;
+
+public class CacheTestUtils {
+    public static final ValidationOptions validationOptions =  new ValidationOptions().guessSystem().setVersionFlexible(false);
+
+}

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/context/SimpleWorkerContextTests.java

@@ -0,0 +1,52 @@
+package org.hl7.fhir.r5.context;
+
+import org.hl7.fhir.exceptions.DefinitionException;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r5.formats.IParser;
+import org.hl7.fhir.r5.formats.ParserType;
+import org.hl7.fhir.r5.model.CodeableConcept;
+import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.model.ValueSet;
+import org.hl7.fhir.r5.utils.validation.IResourceValidator;
+import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
+import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
+import org.hl7.fhir.utilities.npm.NpmPackage;
+import org.hl7.fhir.r5.model.Coding;
+import org.hl7.fhir.utilities.validation.ValidationOptions;
+import org.junit.jupiter.api.Test;
+import org.mockito.ArgumentMatchers;
+import org.mockito.Mockito;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.List;
+
+import static org.mockito.Mockito.mock;
+
+public class SimpleWorkerContextTests {
+  @Test
+  public void testValidateCodingOnServer() throws IOException {
+    SimpleWorkerContext context = Mockito.spy(new SimpleWorkerContext());
+    IWorkerContext.ValidationResult result = mock(IWorkerContext.ValidationResult.class);
+
+    Mockito.doReturn(result).when(context).validateOnServer(ArgumentMatchers.any(), ArgumentMatchers.any(), ArgumentMatchers.any());
+    ValidationOptions validationOptions = new ValidationOptions().guessSystem().setVersionFlexible(false);
+    ValueSet valueSet = new ValueSet();
+    ValidationContextCarrier ctxt = null;
+    context.validateCode(validationOptions, new Coding(), valueSet, ctxt);
+  }
+
+  @Test
+  public void testValidateCodableConceptOnServer() throws IOException {
+    SimpleWorkerContext context = Mockito.spy(new SimpleWorkerContext());
+    IWorkerContext.ValidationResult result = mock(IWorkerContext.ValidationResult.class);
+
+    Mockito.doReturn(result).when(context).validateOnServer(ArgumentMatchers.any(), ArgumentMatchers.any(), ArgumentMatchers.any());
+    ValidationOptions validationOptions = new ValidationOptions().guessSystem().setVersionFlexible(false);
+    ValueSet valueSet = new ValueSet();
+
+    CodeableConcept codeableConcept = new CodeableConcept();
+
+    context.validateCode(validationOptions, codeableConcept, valueSet);
+  }
+}

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/context/TerminologyCacheTests.java

@@ -0,0 +1,74 @@
+package org.hl7.fhir.r5.context;
+
+import com.google.gson.JsonElement;
+import com.google.gson.JsonParser;
+import org.checkerframework.checker.units.qual.C;
+import org.hl7.fhir.r5.model.CodeableConcept;
+import org.hl7.fhir.r5.model.Coding;
+import org.hl7.fhir.r5.model.ValueSet;
+import org.junit.jupiter.api.Test;
+
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+public class TerminologyCacheTests {
+
+  private JsonParser jsonParser = new JsonParser();
+
+  private JsonElement getJsonFromFile(String filename) throws URISyntaxException, IOException {
+    final Path path = Paths.get("src","test","resources", "context", filename);
+    final String stringValue = new String ( Files.readAllBytes(path));
+    return jsonParser.parse(stringValue);
+  };
+
+  @Test
+  public void testCodingCacheTokenGeneration() throws IOException, URISyntaxException {
+    Object lock = new Object();
+    TerminologyCache terminologyCache = new TerminologyCache(lock, null);
+    ValueSet valueSet = new ValueSet();
+
+    Coding coding = new Coding();
+    coding.setCode("dummyCode");
+    TerminologyCache.CacheToken cacheToken = terminologyCache.generateValidationToken(CacheTestUtils.validationOptions,
+      coding, valueSet );
+
+    JsonElement actual = jsonParser.parse(cacheToken.getRequest());
+    JsonElement expected = getJsonFromFile("codingEmptyValueSet.json");
+
+    assertEquals(expected, actual);
+  }
+
+  @Test
+  public void testCodableConceptCacheTokenGeneration() throws IOException, URISyntaxException {
+    Object lock = new Object();
+    TerminologyCache terminologyCache = new TerminologyCache(lock, null);
+    CodeableConcept concept = new CodeableConcept();
+    concept.addCoding(new Coding().setCode("dummyCode"));
+    ValueSet valueSet = new ValueSet();
+    TerminologyCache.CacheToken cacheToken = terminologyCache.generateValidationToken(CacheTestUtils.validationOptions,
+      concept, valueSet );
+
+    JsonElement actual = jsonParser.parse(cacheToken.getRequest());
+    JsonElement expected = getJsonFromFile("codableConceptEmptyValueSet.json");
+
+    assertEquals(expected, actual);
+  }
+
+  @Test
+  public void testDummyCache() throws IOException {
+    Object lock = new Object();
+    Path path =  Paths.get("src","test","resources", "context", "dummyCache");
+    TerminologyCache cache = new TerminologyCache(lock, path.toString());
+
+    assertTrue(cache.hasTerminologyCapabilities());
+    assertTrue(cache.hasCapabilityStatement());
+
+
+  }
+}

org.hl7.fhir.r5/src/test/resources/context/codableConceptEmptyValueSet.json

@@ -0,0 +1,18 @@
+{
+  "code": {
+    "coding": [
+      {
+        "code": "dummyCode"
+      }
+    ]
+  },
+  "valueSet": {
+    "resourceType": "ValueSet"
+  },
+  "lang": "null",
+  "useServer": "true",
+  "useClient": "true",
+  "guessSystem": "true",
+  "valueSetMode": "ALL_CHECKS",
+  "versionFlexible": "false"
+}

org.hl7.fhir.r5/src/test/resources/context/codingEmptyValueSet.json

@@ -0,0 +1,14 @@
+{
+  "code": {
+    "code": "dummyCode"
+  },
+  "valueSet": {
+    "resourceType": "ValueSet"
+  },
+  "lang": "null",
+  "useServer": "true",
+  "useClient": "true",
+  "guessSystem": "true",
+  "valueSetMode": "ALL_CHECKS",
+  "versionFlexible": "false"
+}

org.hl7.fhir.r5/src/test/resources/context/dummyCache/.capabilityStatement.cache

@@ -0,0 +1,62 @@
+{
+  "resourceType" : "CapabilityStatement",
+  "id" : "FhirServer",
+  "meta" : {
+    "tag" : [{
+      "system" : "http://hl7.org/fhir/v3/ObservationValue",
+      "code" : "SUBSETTED",
+      "display" : "Subsetted"
+    }]
+  },
+  "url" : "http://fhir.healthintersections.com.au/open/metadata",
+  "version" : "4.0.1-2.0.12-SNAPSHOT",
+  "name" : "FHIR Reference Server Conformance Statement",
+  "status" : "active",
+  "date" : "2022-01-10T11:07:19.254Z",
+  "contact" : [{
+    "telecom" : [{
+      "system" : "other",
+      "value" : "http://healthintersections.com.au/"
+    }]
+  }],
+  "kind" : "instance",
+  "instantiates" : ["http://hl7.org/fhir/CapabilityStatement/terminology-server"],
+  "software" : {
+    "name" : "Reference Server",
+    "version" : "2.0.12-SNAPSHOT",
+    "releaseDate" : "2021-12-20T02:28:03.769Z"
+  },
+  "fhirVersion" : "4.0.1",
+  "format" : ["application/fhir+xml",
+  "application/fhir+json"],
+  "rest" : [{
+    "mode" : "server",
+    "security" : {
+      "cors" : true
+    },
+    "operation" : [{
+      "name" : "expand",
+      "definition" : "http://hl7.org/fhir/OperationDefinition/ValueSet-expand"
+    },
+    {
+      "name" : "lookup",
+      "definition" : "http://hl7.org/fhir/OperationDefinition/ValueSet-lookup"
+    },
+    {
+      "name" : "validate-code",
+      "definition" : "http://hl7.org/fhir/OperationDefinition/Resource-validate"
+    },
+    {
+      "name" : "translate",
+      "definition" : "http://hl7.org/fhir/OperationDefinition/ConceptMap-translate"
+    },
+    {
+      "name" : "closure",
+      "definition" : "http://hl7.org/fhir/OperationDefinition/ConceptMap-closure"
+    },
+    {
+      "name" : "versions",
+      "definition" : "/OperationDefinition/fso-versions"
+    }]
+  }]
+}

org.hl7.fhir.r5/src/test/resources/context/dummyCache/http___dummysite.org_fhir_CodeSystem_dummy.cache

@@ -0,0 +1,11 @@
+-------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "http://dummysite.org/fhir/CodeSystem/dummy",
+  "code" : "Every 4 weeks"
+}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"true"}####
+v: {
+  "severity" : "error",
+  "error" : "The code system 'http://dummysite.org/fhir/CodeSystem/dummy' is not known (encountered paired with code = 'Every 4 weeks'); The code provided (http://dummysite.org/fhir/CodeSystem/dummy#Every 4 weeks) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r4)",
+  "class" : "CODESYSTEM_UNSUPPORTED"
+}
+-------------------------------------------------------------------------------------

org.hl7.fhir.r5/src/test/resources/context/dummyCache/ucum.cache

@@ -0,0 +1,49 @@
+-------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "http://unitsofmeasure.org",
+  "code" : "L/min"
+}, "valueSet" :null, "lang":"fi", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
+v: {
+  "display" : "L/min",
+  "code" : "L/min",
+  "system" : "http://unitsofmeasure.org"
+}
+-------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "http://unitsofmeasure.org",
+  "code" : "21612-7"
+}, "valueSet" :null, "lang":"fi", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
+v: {
+  "severity" : "error",
+  "error" : "Error processing Unit: '21612-7': Expected \"/\" or \".\" at character 6; The code \"21612-7\" is not valid in the system http://unitsofmeasure.org; The code provided (http://unitsofmeasure.org#21612-7) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r3)"
+}
+-------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "http://unitsofmeasure.org",
+  "code" : "tbl"
+}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
+v: {
+  "severity" : "error",
+  "error" : "Error processing Unit: 'tbl': The unit \"tbl\" is unknown at character 1; The code \"tbl\" is not valid in the system http://unitsofmeasure.org; The code provided (http://unitsofmeasure.org#tbl) is not valid in the value set 'All codes known to the system' (from http://tx.fhir.org/r3)"
+}
+-------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "http://unitsofmeasure.org",
+  "code" : "mmol/L"
+}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
+v: {
+  "display" : "mmol/L",
+  "code" : "mmol/L",
+  "system" : "http://unitsofmeasure.org"
+}
+-------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "http://unitsofmeasure.org",
+  "code" : "[lb_av]"
+}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"true"}####
+v: {
+  "display" : "[lb_av]",
+  "code" : "[lb_av]",
+  "system" : "http://unitsofmeasure.org"
+}
+-------------------------------------------------------------------------------------

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java

@@ -287,7 +287,7 @@ public class ValidationService {
         System.out.println("No such cached session exists for session id " + sessionId + ", re-instantiating validator.");
       }
       System.out.print("  Load FHIR v" + cliContext.getSv() + " from " + definitions);
-      ValidationEngine validator = new ValidationEngine(definitions, cliContext.getSv(), cliContext.getTxCache(), tt, "fhir/validator");
+      ValidationEngine validator = new ValidationEngine(definitions, cliContext.getSv(), tt, "fhir/validator");
       sessionId = sessionCache.cacheSession(validator);
 
       FhirPublication ver = FhirPublication.fromCode(cliContext.getSv());