rework txTester to support additional test files, and better R4/R5 lo…

…gging
hapifhir · Jan 12, 2025 · 6b52ee5 · 6b52ee5
1 parent 0cee7d4
commit 6b52ee5
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Showing 17 changed files with 458 additions and 115 deletions.
diff --git a/...7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR2.java b/...7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR2.java
@@ -265,4 +265,10 @@ public Parameters translate(Parameters params) throws FHIRException {
     return (Parameters) VersionConvertorFactory_10_50.convertResource(client.translate((org.hl7.fhir.dstu2.model.Parameters) VersionConvertorFactory_10_50.convertResource(params)));
   }
 
+  @Override
+  public void setConversionLogger(ITerminologyConversionLogger logger) {
+    // TODO Auto-generated method stub
+
+  }
+
 }
diff --git a/...7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR3.java b/...7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR3.java
@@ -268,4 +268,10 @@ public Parameters translate(Parameters params) throws FHIRException {
     return (Parameters) VersionConvertorFactory_30_50.convertResource(client.transform((org.hl7.fhir.dstu3.model.Parameters) VersionConvertorFactory_30_50.convertResource(params)));
   }
 
+  @Override
+  public void setConversionLogger(ITerminologyConversionLogger logger) {
+    // TODO Auto-generated method stub
+
+  }
+
 }
diff --git a/...7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR4.java b/...7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR4.java
@@ -11,6 +11,8 @@
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.utils.client.EFhirClientException;
 import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
+import org.hl7.fhir.r5.formats.IParser.OutputStyle;
+import org.hl7.fhir.r5.formats.JsonParser;
 import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.CanonicalResource;
 import org.hl7.fhir.r5.model.CapabilityStatement;
@@ -28,9 +30,10 @@
 
 public class TerminologyClientR4 implements ITerminologyClient {
 
-  private final FHIRToolingClient client; // todo: use the R2 client
+  private final FHIRToolingClient client; 
   private ClientHeaders clientHeaders;
   private String id;
+  private ITerminologyConversionLogger logger;
 
   public TerminologyClientR4(String id, String address, String userAgent) throws URISyntaxException {
     this.client = new FHIRToolingClient(address, userAgent);
@@ -71,7 +74,7 @@ public FhirPublication getActualVersion() {
 
   @Override
   public TerminologyCapabilities getTerminologyCapabilities() throws FHIRException {
-    return (TerminologyCapabilities) VersionConvertorFactory_40_50.convertResource(client.getTerminologyCapabilities());
+    return (TerminologyCapabilities) convertResource("getTerminologyCapabilities.response", client.getTerminologyCapabilities());
   }
 
   @Override
@@ -81,29 +84,30 @@ public String getAddress() {
 
   @Override
   public ValueSet expandValueset(ValueSet vs, Parameters p) throws FHIRException {
-    org.hl7.fhir.r4.model.ValueSet vs2 = vs == null ? null : (org.hl7.fhir.r4.model.ValueSet) VersionConvertorFactory_40_50.convertResource(vs);
-    org.hl7.fhir.r4.model.Parameters p2 = p == null ? null :  (org.hl7.fhir.r4.model.Parameters) VersionConvertorFactory_40_50.convertResource(p);
+    org.hl7.fhir.r4.model.ValueSet vs2 = vs == null ? null : (org.hl7.fhir.r4.model.ValueSet) convertResource("expandValueset.valueset", vs);
+    org.hl7.fhir.r4.model.Parameters p2 = p == null ? null :  (org.hl7.fhir.r4.model.Parameters) convertResource("expandValueset.parameters", p);
     try {
       vs2 = client.expandValueset(vs2, p2); // todo: second parameter
-      return (ValueSet) VersionConvertorFactory_40_50.convertResource(vs2);
+      return (ValueSet) convertResource("expandValueset.response", vs2);
     } catch (org.hl7.fhir.r4.utils.client.EFhirClientException e) {
       if (e.getServerErrors().size() > 0) {
-        throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), (org.hl7.fhir.r5.model.OperationOutcome) VersionConvertorFactory_40_50.convertResource(e.getServerErrors().get(0)));
+        throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), (org.hl7.fhir.r5.model.OperationOutcome) convertResource("expandValueset.error", e.getServerErrors().get(0)));
       } else {
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage());        
       }
     }
   }
 
+
   @Override
   public Parameters validateCS(Parameters pin) throws FHIRException {
     try {
-      org.hl7.fhir.r4.model.Parameters p2 = (org.hl7.fhir.r4.model.Parameters) VersionConvertorFactory_40_50.convertResource(pin);
+      org.hl7.fhir.r4.model.Parameters p2 = (org.hl7.fhir.r4.model.Parameters) convertResource("validateCS.request", pin);
       p2 = client.operateType(org.hl7.fhir.r4.model.CodeSystem.class, "validate-code", p2);
-      return (Parameters) VersionConvertorFactory_40_50.convertResource(p2);
+      return (Parameters) convertResource("validateCS.response", p2);
     } catch (EFhirClientException e) {
       if (e.getServerErrors().size() == 1) {
-        OperationOutcome op =  (OperationOutcome) VersionConvertorFactory_40_50.convertResource(e.getServerErrors().get(0));
+        OperationOutcome op =  (OperationOutcome) convertResource("validateCS.error", e.getServerErrors().get(0));
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), op, e);
       } else {
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), e);        
@@ -117,12 +121,12 @@ public Parameters validateCS(Parameters pin) throws FHIRException {
   @Override
   public Parameters subsumes(Parameters pin) throws FHIRException {
     try {
-      org.hl7.fhir.r4.model.Parameters p2 = (org.hl7.fhir.r4.model.Parameters) VersionConvertorFactory_40_50.convertResource(pin);
+      org.hl7.fhir.r4.model.Parameters p2 = (org.hl7.fhir.r4.model.Parameters) convertResource("subsumes.request", pin);
       p2 = client.operateType(org.hl7.fhir.r4.model.CodeSystem.class, "subsumes", p2);
-      return (Parameters) VersionConvertorFactory_40_50.convertResource(p2);
+      return (Parameters) convertResource("subsumes.response", p2);
     } catch (EFhirClientException e) {
       if (e.getServerErrors().size() == 1) {
-        OperationOutcome op =  (OperationOutcome) VersionConvertorFactory_40_50.convertResource(e.getServerErrors().get(0));
+        OperationOutcome op =  (OperationOutcome) convertResource("subsumes.error", e.getServerErrors().get(0));
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), op, e);
       } else {
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), e);        
@@ -135,12 +139,12 @@ public Parameters subsumes(Parameters pin) throws FHIRException {
   @Override
   public Parameters validateVS(Parameters pin) throws FHIRException {
     try {
-      org.hl7.fhir.r4.model.Parameters p2 = (org.hl7.fhir.r4.model.Parameters) VersionConvertorFactory_40_50.convertResource(pin);
+      org.hl7.fhir.r4.model.Parameters p2 = (org.hl7.fhir.r4.model.Parameters) convertResource("validateVS.request", pin);
       p2 = client.operateType(org.hl7.fhir.r4.model.ValueSet.class, "validate-code", p2);
-      return (Parameters) VersionConvertorFactory_40_50.convertResource(p2);
+      return (Parameters) convertResource("validateVS.response", p2);
     } catch (EFhirClientException e) {
       if (e.getServerErrors().size() == 1) {
-        OperationOutcome op =  (OperationOutcome) VersionConvertorFactory_40_50.convertResource(e.getServerErrors().get(0));
+        OperationOutcome op =  (OperationOutcome) convertResource("validateVS.error", e.getServerErrors().get(0));
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), op, e);
       } else {
         throw new org.hl7.fhir.r5.utils.client.EFhirClientException(e.getCode(), e.getMessage(), e);        
@@ -175,22 +179,22 @@ public ITerminologyClient setRetryCount(int retryCount) throws FHIRException {
 
   @Override
   public CapabilityStatement getCapabilitiesStatementQuick() throws FHIRException {
-    return (CapabilityStatement) VersionConvertorFactory_40_50.convertResource(client.getCapabilitiesStatementQuick());
+    return (CapabilityStatement) convertResource("getCapabilitiesStatementQuick.response", client.getCapabilitiesStatementQuick());
   }
 
   @Override
   public CapabilityStatement getCapabilitiesStatement() throws FHIRException {
-    return (CapabilityStatement) VersionConvertorFactory_40_50.convertResource(client.getCapabilitiesStatement());
+    return (CapabilityStatement) convertResource("getCapabilitiesStatement.response", client.getCapabilitiesStatement());
   }
 
   @Override
   public Parameters lookupCode(Map<String, String> params) throws FHIRException {
-    return (Parameters) VersionConvertorFactory_40_50.convertResource(client.lookupCode(params));
+    return (Parameters) convertResource("lookupCode.response", client.lookupCode(params));
   }
 
   @Override
   public Parameters lookupCode(Parameters params) throws FHIRException {
-    return (Parameters) VersionConvertorFactory_40_50.convertResource(client.lookupCode((org.hl7.fhir.r4.model.Parameters) VersionConvertorFactory_40_50.convertResource(params)));
+    return (Parameters) convertResource("lookupCode.response", client.lookupCode((org.hl7.fhir.r4.model.Parameters) convertResource("lookupCode.request", params)));
   }
 
   @Override
@@ -200,8 +204,8 @@ public int getRetryCount() throws FHIRException {
 
   @Override
   public Bundle validateBatch(Bundle batch) {
-    org.hl7.fhir.r4.model.Bundle result = client.transaction((org.hl7.fhir.r4.model.Bundle) VersionConvertorFactory_40_50.convertResource(batch));
-    return result == null ? null : (Bundle) VersionConvertorFactory_40_50.convertResource(result);
+    org.hl7.fhir.r4.model.Bundle result = client.transaction((org.hl7.fhir.r4.model.Bundle) convertResource("validateBatch.request", batch));
+    return result == null ? null : (Bundle) convertResource("validateBatch.response", result);
   }
 
   @Override
@@ -216,7 +220,7 @@ public CanonicalResource read(String type, String id) {
     if (r4 == null) {
       throw new FHIRException("Unable to fetch resource " + Utilities.pathURL(getAddress(), type, id));
     }
-    org.hl7.fhir.r5.model.Resource r5 = VersionConvertorFactory_40_50.convertResource(r4);
+    org.hl7.fhir.r5.model.Resource r5 = convertResource("read.result", r4);
     if (r5 == null) {
       throw new FHIRException("Unable to convert resource " + Utilities.pathURL(getAddress(), type, id) + " to R5 (internal representation)");
     }
@@ -278,12 +282,55 @@ public int getUseCount() {
   @Override
   public Bundle search(String type, String criteria) {    
     org.hl7.fhir.r4.model.Bundle result = client.search(type, criteria);
-    return result == null ? null : (Bundle) VersionConvertorFactory_40_50.convertResource(result);
+    return result == null ? null : (Bundle) convertResource("search.result", result);
   }
 
   @Override
   public Parameters translate(Parameters params) throws FHIRException {  
-    return (Parameters) VersionConvertorFactory_40_50.convertResource(client.translate((org.hl7.fhir.r4.model.Parameters) VersionConvertorFactory_40_50.convertResource(params)));
+    return (Parameters) convertResource("translate.response", client.translate((org.hl7.fhir.r4.model.Parameters) convertResource("translate.request", params)));
+  }
+
+  private org.hl7.fhir.r4.model.Resource convertResource(String name, org.hl7.fhir.r5.model.Resource resource) {
+    if (logger != null) {
+      try {
+        logger.log(name, resource.fhirType(), "r5", new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(resource));
+      } catch (IOException e) {
+        throw new FHIRException(e);
+      }
+    }
+    org.hl7.fhir.r4.model.Resource res = VersionConvertorFactory_40_50.convertResource(resource);
+    if (logger != null) {
+      try {
+        logger.log(name, resource.fhirType(), "r4", new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).composeBytes(res));
+      } catch (IOException e) {
+        throw new FHIRException(e);
+      }
+    }
+    return res;
+  }
+
+  private org.hl7.fhir.r5.model.Resource convertResource(String name, org.hl7.fhir.r4.model.Resource resource) {
+    if (logger != null && name != null) {
+      try {
+        logger.log(name, resource.fhirType(), "r4", new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).composeBytes(resource));
+      } catch (IOException e) {
+        throw new FHIRException(e);
+      }
+    }
+    org.hl7.fhir.r5.model.Resource res = VersionConvertorFactory_40_50.convertResource(resource);
+    if (logger != null && name != null) {
+      try {
+        logger.log(name, resource.fhirType(), "r5", new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).composeBytes(res));
+      } catch (IOException e) {
+        throw new FHIRException(e);
+      }
+    }
+    return res;
+  }
+
+  @Override
+  public void setConversionLogger(ITerminologyConversionLogger logger) {
+    this.logger = logger;    
   }
 
 }
diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/ITerminologyClient.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/ITerminologyClient.java
@@ -76,4 +76,10 @@ public interface ITerminologyClient {
   String getUserAgent();
   int getUseCount();
   Bundle search(String type, String criteria); 
+
+  // internal conversion logging
+  public interface ITerminologyConversionLogger {
+    void log(String name, String resourceType, String version, byte[] cnt);
+  }
+  void setConversionLogger(ITerminologyConversionLogger logger);
 }
diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/TerminologyClientR5.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/TerminologyClientR5.java
@@ -275,5 +275,11 @@ public Parameters translate(Parameters params) throws FHIRException {
     return client.translate(params);
   }
 
+  @Override
+  public void setConversionLogger(ITerminologyConversionLogger logger) {
+    // TODO Auto-generated method stub
+
+  }
+
 
 }
diff --git a/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java b/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
@@ -477,6 +477,11 @@ public static File createDirectory(String path) throws IOException {
     return ManagedFileAccess.file(path);
   }
 
+  public static File createDirectoryNC(String path) throws IOException {
+    ManagedFileAccess.file(path).mkdirs();
+    return ManagedFileAccess.file(path);
+  }
+
   public static String changeFileExt(String name, String ext) {
     if (name.lastIndexOf('.') > -1)
       return name.substring(0, name.lastIndexOf('.')) + ext;

diff --git a/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/json/model/JsonObject.java b/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/json/model/JsonObject.java
@@ -35,6 +35,18 @@ public JsonObject add(String name, JsonElement value) throws JsonException {
     propMap.put(name, p);
     return this;
   }
+
+  public JsonObject add(int index, String name, JsonElement value) throws JsonException {
+    check(name != null, "Json Property Name is null");
+    check(value != null, "Json Property Value is null");
+    if (get(name) != null) {
+      check(false, "Name '"+name+"' already exists (value = "+get(name).toString()+")");
+    }
+    JsonProperty p = new JsonProperty(name, value);
+    properties.add(index, p);
+    propMap.put(name, p);
+    return this;
+  }
 
   public JsonObject addIfNotNull(String name, JsonElement value) throws JsonException {
     if (value != null) {
@@ -347,6 +359,16 @@ public JsonArray forceArray(String name) throws JsonException {
     }
     return getJsonArray(name);
   }
+
+  public JsonArray forceArray(int index, String name) throws JsonException {
+    if (has(name) && !hasArray(name)) {
+      remove(name);
+    }
+    if (!has(name)) {
+      add(index, name, new JsonArray());
+    }
+    return getJsonArray(name);
+  }
 
   public List<JsonObject> getJsonObjects(String name) {
     List<JsonObject> res = new ArrayList<>();

diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/tasks/TxPackTask.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/tasks/TxPackTask.java
@@ -6,6 +6,7 @@
 import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
 import org.hl7.fhir.utilities.TimeTracker;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.validation.ValidationEngine;
 import org.hl7.fhir.validation.cli.model.CliContext;
 import org.hl7.fhir.validation.cli.services.ValidationService;
@@ -47,7 +48,7 @@ public void executeTask(ValidationService validationService, ValidationEngine va
     String pid = cliContext.getPackageName();
     boolean json = cliContext.getFormat() != FhirFormat.XML;
     String output = cliContext.getOutput();
-    File f = new File(output);
+    File f = ManagedFileAccess.file(output);
     ExpansionPackageGeneratorOutputType t = ExpansionPackageGeneratorOutputType.FOLDER;
     if (f.exists() && f.isDirectory()) {
       t = ExpansionPackageGeneratorOutputType.FOLDER;

diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/tasks/TxTestsTask.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/tasks/TxTestsTask.java
@@ -49,7 +49,11 @@ public void executeTask(CliContext cliContext, String[] args, TimeTracker tt, Ti
       if (output == null ) {
         output = Utilities.path("[tmp]");
       }
-      boolean ok = new TxTester(new TxTester.InternalTxLoader(version), tx, false, loadExternals(externals)).setOutput(output).execute(cliContext.getModeParams(), filter);
+      TxTester txTester = new TxTester(new TxTester.InternalTxLoader(version), tx, false, loadExternals(externals));
+      for (String input : cliContext.getInputs()) {
+        txTester.addLoader(new TxTester.InternalTxLoader(input, true));
+      }
+      boolean ok = txTester.setOutput(output).execute(cliContext.getModeParams(), filter);
       SystemExitManager.setError(ok ? 0 : 1);
       SystemExitManager.finish();
   }

diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java
@@ -405,7 +405,7 @@ else if (args[i].equals(HTML_OUTPUT)) {
         cliContext.setOutputStyle(args[++i]);
       } else if (args[i].equals(ADVSIOR_FILE)) {
         cliContext.setAdvisorFile(args[++i]);
-        File f = new File(cliContext.getAdvisorFile());
+        File f = ManagedFileAccess.file(cliContext.getAdvisorFile());
         if (!f.exists()) {
           throw new Error("Cannot find advisor file "+cliContext.getAdvisorFile());
         } else if (!Utilities.existsInList(Utilities.getFileExtension(f.getName()), "json", "txt")) {

diff --git a/...l7.fhir.validation/src/main/java/org/hl7/fhir/validation/special/TxServiceTestHelper.java b/...l7.fhir.validation/src/main/java/org/hl7/fhir/validation/special/TxServiceTestHelper.java
@@ -12,6 +12,7 @@
 import org.hl7.fhir.utilities.FhirPublication;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
 import org.hl7.fhir.utilities.i18n.I18nConstants;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.validation.ValidationOptions;
@@ -174,7 +175,7 @@ public static String getDiffForValidation(String id, IWorkerContext context, Str
             parameters.addParameter(validationResult.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED ? "x-caused-by-unknown-system" :  "x-unknown-system", new CanonicalType(s));
           }
         }
-        if (validationResult.getIssues().size() > 0) {
+        if (validationResult.getIssues().size() > 0) { 
           operationOutcome = new OperationOutcome();
           operationOutcome.getIssue().addAll(validationResult.getIssues());
           parameters.addParameter().setName("issues").setResource(operationOutcome);
@@ -205,12 +206,12 @@ public static void writeDiffToFileSystem(String testName, String expected, Strin
     }
     String fullExpected = rootDirectory + "/expected/";
     String fullActual = rootDirectory + "/actual/";
-    File expectedDirectory = new File(fullExpected);
+    File expectedDirectory = ManagedFileAccess.file(fullExpected);
     if (!expectedDirectory.exists()) {
       expectedDirectory.mkdirs();
     }
 
-    File actualDirectory = new File(fullActual);
+    File actualDirectory = ManagedFileAccess.file(fullActual);
     if (!actualDirectory.exists()) {
       actualDirectory.mkdirs();
     }