Merge pull request #1220 from hapifhir/gg-202304-rework-tx2

restore external terminology server tests

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

@@ -5,9 +5,10 @@ public class Servers {
   public static final String TX_SERVER_PROD = "http://tx.fhir.org";
   public static final String TX_SERVER_DEV = "http://tx-dev.fhir.org";
   public static final String TX_SERVER_LOCAL = "http://local.fhir.org";
+  public static final String TX_SERVER_LOCAL2 = "http://local.fhir.org:8090";
   
   public static boolean isTxFhirOrg(String s) {
-    return Utilities.existsInList(s.replace("https://", "http://"), TX_SERVER_PROD, TX_SERVER_DEV, TX_SERVER_LOCAL);
+    return Utilities.startsWithInList(s.replace("https://", "http://"), TX_SERVER_PROD, TX_SERVER_DEV, TX_SERVER_LOCAL);
   }
 
 }

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

@@ -4,6 +4,7 @@ import java.io.File;
 import java.io.IOException;
 import java.net.Authenticator;
 import java.net.PasswordAuthentication;
+import java.net.URISyntaxException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Locale;
@@ -84,6 +85,8 @@ import org.hl7.fhir.validation.cli.utils.Display;
 import org.hl7.fhir.validation.cli.utils.EngineMode;
 import org.hl7.fhir.validation.cli.utils.Params;
 import org.hl7.fhir.validation.special.R4R5MapTester;
+import org.hl7.fhir.validation.special.TxTester;
+import org.hl7.fhir.validation.special.TxTester.InternalTxLoader;
 import org.hl7.fhir.validation.testexecutor.TestExecutor;
 import org.hl7.fhir.validation.testexecutor.TestExecutorParams;
 
@@ -135,7 +138,7 @@ public class ValidatorCli {
       if (destinationDirectoryValid(Params.getParam(args, Params.DESTINATION))) {
         doLeftRightComparison(args, cliContext, tt);
       }
-    } else if (Params.hasParam(args, Params.TEST)) {
+    } else if (Params.hasParam(args, Params.TEST) || Params.hasParam(args, Params.TX_TESTS)) {
       parseTestParamsAndExecute(args);
     } else if (Params.hasParam(args, Params.SPECIAL)) {
       executeSpecial(args);
@@ -208,19 +211,29 @@ public class ValidatorCli {
     }
   }
 
-  protected static void parseTestParamsAndExecute(String[] args) {
+  protected static void parseTestParamsAndExecute(String[] args) throws IOException, URISyntaxException {
-    final String testModuleParam = Params.getParam(args, Params.TEST_MODULES);
+    if (Params.hasParam(args, Params.TX_TESTS)) {
-    final String testClassnameFilter = Params.getParam(args, Params.TEST_NAME_FILTER);
+      final String source = Params.getParam(args, Params.SOURCE);
-    final String testCasesDirectory = Params.getParam(args, Params.TEST);
+      final String output = Params.getParam(args, Params.OUTPUT);
-    final String txCacheDirectory = Params.getParam(args, Params.TERMINOLOGY_CACHE);
+      final String version = Params.getParam(args, Params.VERSION);
-    assert TestExecutorParams.isValidModuleParam(testModuleParam) : "Invalid test module param: " + testModuleParam;
+      final String tx = Params.getParam(args, Params.TERMINOLOGY);
-    final String[] moduleNamesArg = TestExecutorParams.parseModuleParam(testModuleParam);
+      final String filter = Params.getParam(args, Params.FILTER);
+      boolean ok = new TxTester(new InternalTxLoader(source, output)).setOutput(output).execute(tx, version, filter);
+      System.exit(ok ? 1 : 0);
+    } else {
+      final String testModuleParam = Params.getParam(args, Params.TEST_MODULES);
+      final String testClassnameFilter = Params.getParam(args, Params.TEST_NAME_FILTER);
+      final String testCasesDirectory = Params.getParam(args, Params.TEST);
+      final String txCacheDirectory = Params.getParam(args, Params.TERMINOLOGY_CACHE);
+      assert TestExecutorParams.isValidModuleParam(testModuleParam) : "Invalid test module param: " + testModuleParam;
+      final String[] moduleNamesArg = TestExecutorParams.parseModuleParam(testModuleParam);
 
-    assert TestExecutorParams.isValidClassnameFilterParam(testClassnameFilter) : "Invalid regex for test classname filter: " + testClassnameFilter;
+      assert TestExecutorParams.isValidClassnameFilterParam(testClassnameFilter) : "Invalid regex for test classname filter: " + testClassnameFilter;
 
-    new TestExecutor(moduleNamesArg).executeTests(testClassnameFilter, txCacheDirectory, testCasesDirectory);
+      new TestExecutor(moduleNamesArg).executeTests(testClassnameFilter, txCacheDirectory, testCasesDirectory);
 
-    System.exit(0);
+      System.exit(0);
+    }
   }
 
   private static String[] addAdditionalParamsForIpsParam(String[] args) {

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java

@@ -57,6 +57,7 @@ public class Params {
   public static final String CONVERT = "-convert";
   public static final String FHIRPATH = "-fhirpath";
   public static final String TEST = "-tests";
+  public static final String TX_TESTS = "-txTests";
   public static final String HELP = "help";
   public static final String COMPARE = "-compare";
   public static final String SPREADSHEET = "-spreadsheet";

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/special/TxTester.java

@@ -4,11 +4,23 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.InputStream;
+import java.net.HttpURLConnection;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.net.URL;
+import java.nio.file.Path;
+import java.sql.Date;
+import java.text.SimpleDateFormat;
 import java.util.ArrayList;
+import java.util.Calendar;
 import java.util.Collections;
+import java.util.GregorianCalendar;
 import java.util.List;
+import java.util.Locale;
+import java.util.TimeZone;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
 
 import org.hl7.fhir.convertors.txClient.TerminologyClientFactory;
 import org.hl7.fhir.exceptions.DefinitionException;
@@ -27,8 +39,10 @@ import org.hl7.fhir.utilities.FhirPublication;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.json.JsonException;
+import org.hl7.fhir.utilities.json.model.JsonArray;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
+import org.hl7.fhir.utilities.npm.NpmPackage;
 
 public class TxTester {
 
@@ -42,6 +56,7 @@ public class TxTester {
   private String server;
   private ITxTesterLoader loader;
   private String error;
+  private String output;
   
 
   public TxTester(ITxTesterLoader loader) {
@@ -50,30 +65,61 @@ public class TxTester {
   }
 
   public static void main(String[] args) throws Exception {
-    new TxTester(new InternalLoader(args[0])).execute(args[1], args[2]);
+    new TxTester(new InternalTxLoader(args[0])).execute(args[1], args[2], args[3]);
   }
   
-  public void execute(String server, String filter) {
+  public boolean execute(String server, String version, String filter) throws IOException, URISyntaxException {
     this.server = server;
-    System.out.println("Run terminology service Tests");
+    if (output == null) {
+      output = Utilities.path("[tmp]", serverId());
+    }
     
+    System.out.println("Run terminology service Tests");
+    System.out.println("  Source for tests: "+loader.describe());
+    System.out.println("  Output Directory: "+output);
+    System.out.println("  Term Service Url: "+server);
+    if (version != null) {
+      System.out.println("  Tx  FHIR Version: "+version);
+    }
+    if (filter != null) {
+      System.out.println("  Filter Parameter: "+filter);
+    }
+    
+    JsonObject json = new JsonObject();
+    json.add("date", new SimpleDateFormat("EEE, MMM d, yyyy HH:mmZ", new Locale("en", "US")).format(Calendar.getInstance().getTime()) + timezone());
     try {
       JsonObject tests = loadTests();
       TerminologyClient tx = connectToServer();
       boolean ok = checkClient(tx);
       for (JsonObject suite : tests.getJsonObjects("suites")) {
-        ok = runSuite(suite, tx, filter) && ok;
+        ok = runSuite(suite, tx, filter, json.forceArray("suites")) && ok;
       }
+      TextFile.stringToFile(JsonParser.compose(json, true), Utilities.path(output, "test-results.json"));
       if (ok) {
         System.out.println("Terminology Service Tests all passed");
+        return true;
       } else {
         System.out.println("Terminology Service Tests did not all pass");
+        return false;
       }        
     } catch (Exception e) {
       System.out.println("Exception running Terminology Service Tests: "+e.getMessage());
       e.printStackTrace();
+      return false;
     }
   }
+  
+
+  private String timezone() {
+    TimeZone tz = TimeZone.getDefault();
+    Calendar cal = GregorianCalendar.getInstance(tz);
+    int offsetInMillis = tz.getOffset(cal.getTimeInMillis());
+
+    String offset = String.format("%02d:%02d", Math.abs(offsetInMillis / 3600000), Math.abs((offsetInMillis / 60000) % 60));
+    offset = (offsetInMillis >= 0 ? "+" : "-") + offset;
+
+    return offset;
+  }
 
   private boolean checkClient(TerminologyClient tx) {
     tx.getCapabilitiesStatementQuick();
@@ -98,23 +144,33 @@ public class TxTester {
     TerminologyClient tx = connectToServer();
     checkClient(tx);
     List<Resource> setup = loadSetupResources(suite);
-    if (runTest(test, tx, setup, "*")) {
+    if (runTest(test, tx, setup, "*", null)) {
       return null;      
     } else {
       return error;
     }
   }
-  private boolean runSuite(JsonObject suite, TerminologyClient tx, String filter) throws FHIRFormatError, FileNotFoundException, IOException {
+  private boolean runSuite(JsonObject suite, TerminologyClient tx, String filter, JsonArray output) throws FHIRFormatError, FileNotFoundException, IOException {
     System.out.println("Group "+suite.asString("name"));
+    JsonObject outputS = new JsonObject();
+    if (output != null) {
+      output.add(outputS);
+    }
+    outputS.add("name", suite.asString("name"));
     List<Resource> setup = loadSetupResources(suite);
     boolean ok = true;
     for (JsonObject test : suite.getJsonObjects("tests")) {
-      ok = runTest(test, tx, setup, filter) && ok;      
+      ok = runTest(test, tx, setup, filter, outputS.forceArray("tests")) && ok;      
     }
     return ok;
   }
 
-  private boolean runTest(JsonObject test, TerminologyClient tx, List<Resource> setup, String filter) {    
+  private boolean runTest(JsonObject test, TerminologyClient tx, List<Resource> setup, String filter, JsonArray output) { 
+    JsonObject outputT = new JsonObject();
+    if (output != null) {
+      output.add(outputT);
+    }
+    outputT.add("name", test.asString("name"));
     if (Utilities.noString(filter) || filter.equals("*") || test.asString("name").contains(filter)) {
       System.out.print("  Test "+test.asString("name")+": ");
       try {
@@ -142,6 +198,10 @@ public class TxTester {
           System.out.println("    "+msg);
           error = msg;
         }  
+        outputT.add("status", msg == null ? "pass" : "fail");
+        if (msg != null) {
+          outputT.add("message", msg);
+        }
         return msg == null;
       } catch (Exception e) {
         System.out.println("  ... Exception: "+e.getMessage());
@@ -151,6 +211,7 @@ public class TxTester {
         return false;
       }
     } else {
+      outputT.add("status", "ignored");
       return true;
     }
   }
@@ -213,14 +274,73 @@ public class TxTester {
     return res;
   }
   
-  public static class InternalLoader implements ITxTesterLoader {
+  public String getOutput() {
+    return output;
+  }
+
+  public TxTester setOutput(String output) {
+    this.output = output;
+    return this;
+  }
+
+  public static class InternalTxLoader implements ITxTesterLoader {
 
     private String folder;
     
-    public InternalLoader(String folder) {
+    public InternalTxLoader(String folder) {
       this.folder = folder;
     }
+    
+    public InternalTxLoader(String source, String local) throws IOException {
+      if (source.startsWith("http://") || source.startsWith("https://")) {
+        this.folder = Utilities.path(local, "source");
 
+        URL url = new URL(zipUrl(source));
+        HttpURLConnection connection = (HttpURLConnection) url.openConnection();
+        connection.setRequestMethod("GET");
+        InputStream zip = connection.getInputStream();
+        unzip(zip); 
+      } else {
+        this.folder = source;
+      }
+    }
+
+    public void unzip(InputStream is) throws IOException {
+      try (ZipInputStream zipIn = new ZipInputStream(is)) {
+        for (ZipEntry ze; (ze = zipIn.getNextEntry()) != null; ) {
+          if (ze.getName().startsWith("fhir-test-cases-master/tx/")) {
+            Path path = Path.of(Utilities.path(this.folder, ze.getName().substring(26))).normalize();
+            String pathString = path.toFile().getAbsolutePath();
+            if (!path.startsWith(Path.of(this.folder).normalize())) {
+              // see: https://snyk.io/research/zip-slip-vulnerability
+              throw new RuntimeException("Entry with an illegal path: " + ze.getName());
+            }
+            if (ze.isDirectory()) {
+              Utilities.createDirectory(pathString);
+            } else {
+              Utilities.createDirectory(Utilities.getDirectoryForFile(pathString));
+              TextFile.streamToFileNoClose(zipIn, pathString);
+            }
+          }
+        }
+      }
+    }
+
+
+    private String zipUrl(String template) {
+      if (!template.startsWith("https://github.")) {
+        throw new FHIRException("Cannot refer to source by URL unless referring to a github repository: "+template);
+      } else if (Utilities.charCount(template, '/') == 4) {
+        return Utilities.pathURL(template, "archive", "master.zip");      
+      } else if (Utilities.charCount(template, '/') == 6) {
+        String[] p = template.split("\\/");
+        return Utilities.pathURL("https://"+p[2], p[3], p[4], "archive", p[6]+".zip");      
+      } else {
+        throw new FHIRException("Source syntax in URL referring to a github repository was not understood: "+template);
+      }
+    }
+
+    
     @Override
     public String describe() {
       return folder;

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/terminology/tests/ExternalTerminologyServiceTests.java

@@ -1,6 +1,5 @@
 package org.hl7.fhir.terminology.tests;
 
-import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
@@ -18,38 +17,15 @@ import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
-import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
-import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.formats.JsonParser;
 import org.hl7.fhir.r5.formats.XmlParser;
-import org.hl7.fhir.r5.model.Coding;
 import org.hl7.fhir.r5.model.Constants;
-import org.hl7.fhir.r5.model.OperationOutcome;
-import org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity;
-import org.hl7.fhir.r5.model.OperationOutcome.IssueType;
-import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
 import org.hl7.fhir.r5.model.Resource;
-import org.hl7.fhir.r5.model.ValueSet;
-import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
-import org.hl7.fhir.r5.model.CodeableConcept;
-import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionParameterComponent;
-import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
-import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
-import org.hl7.fhir.r5.test.utils.CompareUtilities;
 import org.hl7.fhir.r5.test.utils.TestingUtilities;
-import org.hl7.fhir.terminology.tests.ExternalTerminologyServiceTests.JsonObjectPair;
-import org.hl7.fhir.utilities.FhirPublication;
 import org.hl7.fhir.utilities.Servers;
-import org.hl7.fhir.utilities.TextFile;
-import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.json.model.JsonObject;
-import org.hl7.fhir.utilities.validation.ValidationOptions;
-import org.hl7.fhir.validation.ValidationEngine;
 import org.hl7.fhir.validation.special.TxTester;
 import org.hl7.fhir.validation.special.TxTester.ITxTesterLoader;
-import org.hl7.fhir.validation.tests.ValidationEngineTests;
-import org.hl7.fhir.validation.tests.utilities.TestUtilities;
-import org.junit.AfterClass;
 import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.jupiter.api.Assertions;
@@ -58,9 +34,7 @@ import org.junit.runners.Parameterized;
 import org.junit.runners.Parameterized.Parameters;
 
 import com.google.common.base.Charsets;
-import com.google.gson.JsonSyntaxException;
 
-@Ignore
 @RunWith(Parameterized.class)
 public class ExternalTerminologyServiceTests implements ITxTesterLoader {
 
@@ -74,6 +48,7 @@ public class ExternalTerminologyServiceTests implements ITxTesterLoader {
   }
 
   private static final String SERVER = Servers.TX_SERVER_DEV;
+//  private static final String SERVER = Servers.TX_SERVER_LOCAL2;
 
   @Parameters(name = "{index}: id {0}")
   public static Iterable<Object[]> data() throws IOException {