Versioning and NewRefreshIg Merge (#526)

* Versioning and NewRefreshIg Merge * Revert test * Updating refresh TerserUtil usage to clear field before update * Update * Added test cases for external reference and Versioning * Added test cases for external reference and Versioning 2 * Reduced test IG Size * Reduced test IG Size and update location * Removed use of Junit, replaced my TestNg Framework * Using afterSuite instead of method * Test update * Fix paths * Fix urls --------- Co-authored-by: c-schuler <[email protected]> Co-authored-by: JP <[email protected]>
cqframework · May 3, 2024 · 2ca0172 · 2ca0172
1 parent 1f3a5c8
commit 2ca0172
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diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/operation/ig/LibraryRefresh.java b/tooling/src/main/java/org/opencds/cqf/tooling/operation/ig/LibraryRefresh.java
@@ -14,6 +14,7 @@
 import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.opencds.cqf.tooling.npm.LibraryLoader;
 import org.opencds.cqf.tooling.npm.NpmPackageManager;
+import org.opencds.cqf.tooling.parameter.RefreshIGParameters;
 import org.opencds.cqf.tooling.processor.CqlProcessor;
 import org.opencds.cqf.tooling.utilities.CanonicalUtils;
 import org.opencds.cqf.tooling.utilities.IOUtils;
@@ -48,9 +49,12 @@ public LibraryRefresh(IGInfo igInfo) {
               Collections.singletonList(igInfo.getCqlBinaryPath()), libraryLoader, new IGLoggingService(logger), ucumService,
               igInfo.getPackageId(), igInfo.getCanonical(), true);
    }
-
    @Override
    public List<IBaseResource> refresh() {
+      return refresh(null);
+   }
+
+   public List<IBaseResource> refresh(RefreshIGParameters params) {
       List<IBaseResource> refreshedLibraries = new ArrayList<>();
       this.cqlProcessor.execute();
       if (getIgInfo().isRefreshLibraries()) {
@@ -72,6 +76,7 @@ public List<IBaseResource> refresh() {
                   refreshDataRequirements(library, info);
                   refreshRelatedArtifacts(library, info);
                   refreshParameters(library, info);
+                  refreshVersion(library, params);
                   refreshedLibraries.add(library);
                   this.libraryPackages.add(new LibraryPackage(library, getFhirContext(), info));
                }

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/operation/ig/NewRefreshIGOperation.java b/tooling/src/main/java/org/opencds/cqf/tooling/operation/ig/NewRefreshIGOperation.java
@@ -23,7 +23,7 @@ public void execute(String[] args) {
          this.params = new RefreshIGArgumentProcessor().parseAndConvert(args);
          IGInfo info = new IGInfo(null, params);
          LibraryRefresh libraryRefresh = new LibraryRefresh(info);
-         publishLibraries(info, libraryRefresh.refresh());
+         publishLibraries(info, libraryRefresh.refresh(this.params));
          PlanDefinitionRefresh planDefinitionRefresh = new PlanDefinitionRefresh(info, libraryRefresh.getCqlProcessor(), libraryRefresh.getLibraryPackages());
          publishPlanDefinitions(info, planDefinitionRefresh.refresh());
          if (!planDefinitionRefresh.getPlanDefinitionPackages().isEmpty()) {

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/operation/ig/Refresh.java b/tooling/src/main/java/org/opencds/cqf/tooling/operation/ig/Refresh.java
@@ -7,6 +7,7 @@
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r5.model.*;
+import org.opencds.cqf.tooling.parameter.RefreshIGParameters;
 import org.opencds.cqf.tooling.utilities.BundleUtils;
 import org.opencds.cqf.tooling.utilities.constants.CqfmConstants;
 import org.opencds.cqf.tooling.utilities.converters.ResourceAndTypeConverter;
@@ -29,10 +30,19 @@ public Refresh(IGInfo igInfo) {
    public abstract List<IBaseResource> refresh();
 
    public void refreshDate(IBaseResource resource) {
+      TerserUtil.clearField(getIgInfo().getFhirContext(), "date", resource);
       TerserUtil.setField(getIgInfo().getFhirContext(), "date", resource,
               ResourceAndTypeConverter.convertType(getFhirContext(), new DateTimeType(new Date())));
    }
 
+    public void refreshVersion(IBaseResource resource, RefreshIGParameters params) {
+        if (params != null && params.updatedVersion != null && !params.updatedVersion.isEmpty()) {
+            TerserUtil.clearField(getIgInfo().getFhirContext(), "version", resource);
+            TerserUtil.setField(getIgInfo().getFhirContext(), "version", resource,
+                    ResourceAndTypeConverter.convertType(getFhirContext(), new StringType(params.updatedVersion)));
+        }
+    }
+
    public void validatePrimaryLibraryReference(IBaseResource resource) {
       if ((resource instanceof PlanDefinition && !((PlanDefinition) resource).hasLibrary())
               || (resource instanceof Measure && !((Measure) resource).hasLibrary())) {

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/parameter/RefreshIGParameters.java b/tooling/src/main/java/org/opencds/cqf/tooling/parameter/RefreshIGParameters.java
@@ -25,4 +25,5 @@ public class RefreshIGParameters {
     public String libraryOutputPath;
     public String measureOutputPath;
     public Boolean verboseMessaging;
+    public String updatedVersion;
 }
diff --git a/.../src/main/java/org/opencds/cqf/tooling/processor/argument/RefreshIGArgumentProcessor.java b/.../src/main/java/org/opencds/cqf/tooling/processor/argument/RefreshIGArgumentProcessor.java
@@ -16,7 +16,7 @@
 
 
 public class RefreshIGArgumentProcessor {
-    public static final String[] OPERATION_OPTIONS = {"RefreshIG"};
+    public static final String[] OPERATION_OPTIONS = {"RefreshIG", "NewRefreshIG"};
     public static final String[] INI_OPTIONS = {"ini"};
     public static final String[] ROOT_DIR_OPTIONS = {"root-dir", "rd"};
     public static final String[] IG_PATH_OPTIONS = {"ip", "ig-path"};
@@ -28,6 +28,7 @@ public class RefreshIGArgumentProcessor {
     public static final String[] INCLUDE_TERMINOLOGY_OPTIONS = {"t", "include-terminology"};
     public static final String[] INCLUDE_PATIENT_SCENARIOS_OPTIONS = {"p", "include-patients"};
     public static final String[] VERSIONED_OPTIONS = {"v", "versioned"};
+    public static final String[] UPDATED_VERSION_OPTIONS = {"uv", "updated-version"};
     public static final String[] FHIR_URI_OPTIONS = {"fs", "fhir-uri"};
     public static final String[] MEASURE_TO_REFRESH_PATH = {"mtrp", "measure-to-refresh-path"};
     public static final String[] RESOURCE_PATH_OPTIONS = {"rp", "resourcepath"};
@@ -45,6 +46,7 @@ public OptionParser build() {
 
         OptionSpecBuilder iniBuilder = parser.acceptsAll(asList(INI_OPTIONS), "Path to ig ini file");
         OptionSpecBuilder rootDirBuilder = parser.acceptsAll(asList(ROOT_DIR_OPTIONS), "Root directory of the ig");
+        OptionSpecBuilder updatedVersionBuilder = parser.acceptsAll(asList(UPDATED_VERSION_OPTIONS), "Version for the new libraries");
         OptionSpecBuilder igPathBuilder = parser.acceptsAll(asList(IG_PATH_OPTIONS),"Path to the IG, relative to the root directory");
         OptionSpecBuilder resourcePathBuilder = parser.acceptsAll(asList(RESOURCE_PATH_OPTIONS),"Use multiple times to define multiple resource directories, relative to the root directory.");
         OptionSpecBuilder libraryPathBuilder = parser.acceptsAll(asList(LIBRARY_PATH_OPTIONS), "Provide a single path, relative to the root directory, for library resources. The path will be added to the resource directories available to the refresh processing.");
@@ -58,6 +60,7 @@ public OptionParser build() {
         OptionSpecBuilder shouldVerboseMessaging = parser.acceptsAll(asList(SHOULD_APPLY_SOFTWARE_SYSTEM_STAMP_OPTIONS),"Indicates that a complete list of errors during library, measure, and test case refresh are included upon failure.");
 
         OptionSpec<String> ini = iniBuilder.withRequiredArg().describedAs("Path to the IG ini file");
+        OptionSpec<String> updatedVersion = updatedVersionBuilder.withOptionalArg().describedAs("Updated version of the IG");
         OptionSpec<String> rootDir = rootDirBuilder.withOptionalArg().describedAs("Root directory of the IG");
         OptionSpec<String> igPath = igPathBuilder.withRequiredArg().describedAs("Path to the IG, relative to the root directory");
         OptionSpec<String> resourcePath = resourcePathBuilder.withOptionalArg().describedAs("directory of resources");
@@ -124,6 +127,11 @@ public RefreshIGParameters parseAndConvert(String[] args) {
         String fhirUri = (String)options.valueOf(FHIR_URI_OPTIONS[0]);
         String measureToRefreshPath = (String)options.valueOf(MEASURE_TO_REFRESH_PATH[0]);
 
+        String updatedVersion = (String)options.valueOf(UPDATED_VERSION_OPTIONS[0]);
+        if(updatedVersion == null) {
+            updatedVersion = "";
+        }
+
         String libraryOutputPath = (String)options.valueOf(LIBRARY_OUTPUT_PATH_OPTIONS[0]);
         if (libraryOutputPath == null) {
             libraryOutputPath = "";
@@ -178,6 +186,7 @@ public RefreshIGParameters parseAndConvert(String[] args) {
         ip.measureToRefreshPath = measureToRefreshPath;
         ip.libraryOutputPath = libraryOutputPath;
         ip.measureOutputPath = measureOutputPath;
+        ip.updatedVersion = updatedVersion;
         ip.verboseMessaging = verboseMessaging;
         return ip;
     }

diff --git a/tooling/src/test/java/org/opencds/cqf/tooling/RefreshTest.java b/tooling/src/test/java/org/opencds/cqf/tooling/RefreshTest.java
@@ -78,8 +78,7 @@ protected void copyResourcesToTargetDir(String targetDirectory, String resourceD
         File outputDirectory = new File(targetDirectory);
         outputDirectory.mkdirs();
         URL url = RefreshTest.class.getResource(resourceDirectoryPath);
-        String path = url.getPath();
-        File resourceDirectory = new File(path);
+        File resourceDirectory = FileUtils.toFile(url);
         FileUtils.copyDirectory(resourceDirectory, outputDirectory);
     }
 

diff --git a/tooling/src/test/java/org/opencds/cqf/tooling/operation/RefreshIGOperationTest.java b/tooling/src/test/java/org/opencds/cqf/tooling/operation/RefreshIGOperationTest.java
@@ -25,7 +25,6 @@
 import org.opencds.cqf.tooling.RefreshTest;
 import org.opencds.cqf.tooling.parameter.RefreshIGParameters;
 import org.opencds.cqf.tooling.processor.IGProcessor;
-import org.opencds.cqf.tooling.processor.TestCaseProcessor;
 import org.opencds.cqf.tooling.processor.argument.RefreshIGArgumentProcessor;
 import org.opencds.cqf.tooling.utilities.IOUtils;
 import org.opencds.cqf.tooling.utilities.ResourceUtils;
@@ -47,7 +46,6 @@
 
 import static org.testng.Assert.*;
 import org.hl7.fhir.r4.model.Group;
-import org.hl7.fhir.r4.model.Reference;
 public class RefreshIGOperationTest extends RefreshTest {
 	protected final Logger logger = LoggerFactory.getLogger(this.getClass());
 	public RefreshIGOperationTest() {
@@ -64,7 +62,7 @@ public RefreshIGOperationTest() {
 	private final String LIB_TYPE = "Library";
 	private final String MEASURE_TYPE = "Measure";
 
-	private final String INI_LOC = "target" + separator + "refreshIG" + separator + "ig.ini";
+	private final String INI_LOC = Path.of("target","refreshIG","ig.ini").toString();
 
 
 	// Store the original standard out before changing it.
@@ -147,7 +145,7 @@ public void testBundledFiles() throws IOException {
 			wireMockServer.stop();
 		}
 
-		// determine fhireContext for measure lookup
+		// determine fhirContext for measure lookup
 		FhirContext fhirContext = IGProcessor.getIgFhirContext(getFhirVersion(ini));
 
 		// get list of measures resulting from execution

diff --git a/tooling/src/test/resources/NewRefreshIG/ig.ini b/tooling/src/test/resources/NewRefreshIG/ig.ini
@@ -0,0 +1,4 @@
+[IG]
+ig = input/cqf-us.xml
+template = cqf.fhir.template
+usage-stats-opt-out = false
diff --git a/tooling/src/test/resources/NewRefreshIG/input/cqf-us.xml b/tooling/src/test/resources/NewRefreshIG/input/cqf-us.xml
@@ -0,0 +1,134 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ImplementationGuide xmlns="http://hl7.org/fhir" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://hl7.org/fhir ../input-cache/schemas/R5/fhir-single.xsd">
+  <id value="fhir.cqf.us.common"/>
+<!--  <extension url="http://hl7.org/fhir/tools/StructureDefinition/igpublisher-spreadsheet">
+    <valueString value="resources-spreadsheet.xml"/>
+  </extension>-->
+  <url value="http://fhir.org/guides/cqf/us/common/ImplementationGuide/fhir.cqf.us.common"/>
+  <version value="0.1.0"/>
+  <name value="CQFUSCommon"/>
+  <title value="Clinical Quality Framework Common FHIR Assets (US-Based)"/>
+  <status value="draft"/>
+  <experimental value="false"/>
+  <publisher value="Clinical Quality Framework"/>
+  <contact>
+    <telecom>
+      <system value="url"/>
+      <value value="http://github.com/cqframework"/>
+    </telecom>
+  </contact>
+  <description value="This implementation guide contains common FHIR assets for use in US-based CQFramework content IGs, including the USCore-ModelInfo and USCommon libraries."/>
+  <jurisdiction>
+    <coding>
+      <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
+      <code value="840"/>
+      <display value="USA"/>
+    </coding>
+  </jurisdiction>
+  <packageId value="fhir.cqf.us.common"/>
+  <license value="CC0-1.0"/>
+  <fhirVersion value="4.0.1"/>
+  <!-- Do not declare this dependency, since we would like to use this IG to fix
+  the reference problems in CPG as well...
+  <dependsOn id="cpg">
+    <uri value="http://hl7.org/fhir/uv/cpg/ImplementationGuide/hl7.fhir.uv.cpg"/>
+    <packageId value="hl7.fhir.uv.cpg"/>
+    <version value="1.0.0"/>
+  </dependsOn>-->
+  <dependsOn id="cqf">
+    <uri value="http://fhir.org/guides/cqf/common/ImplementationGuide/fhir.cqf.common"/>
+    <packageId value="fhir.cqf.common"/>
+    <version value="4.0.1"/>
+  </dependsOn>
+  <dependsOn id="uscore">
+    <uri value="http://hl7.org/fhir/us/core/ImplementationGuide/hl7.fhir.us.core"/>
+    <packageId value="hl7.fhir.us.core"/>
+    <version value="3.1.1"/>
+  </dependsOn>
+  <definition>
+    <page>
+      <!-- The root will always be toc.html - the template will force it if you don't do it -->
+      <nameUrl value="toc.html"/>
+      <title value="Table of Contents"/>
+      <generation value="html"/>
+      <page>
+        <nameUrl value="index.html"/>
+        <title value="Home"/>
+        <generation value="html"/>
+      </page>
+      <page>
+        <nameUrl value="downloads.html"/>
+        <title value="Downloads"/>
+        <generation value="html"/>
+      </page>
+      <page>
+        <nameUrl value="license.html"/>
+        <title value="License"/>
+        <generation value="markdown"/>
+      </page>
+    </page>
+    <!-- copyright year is a mandatory parameter -->
+    <parameter>
+      <code value="copyrightyear"/>
+      <value value="2019+"/>
+    </parameter>
+    <!-- releaselabel should be the ballot status for HL7-published IGs. -->
+    <parameter>
+      <code value="releaselabel"/>
+      <value value="CI Build"/>
+    </parameter>
+    <parameter>
+      <code value="find-other-resources"/>
+      <value value="true"/>
+    </parameter>
+    <!-- This parameter indicates to the publisher that it should translate and package CQL libraries. See the example library resources for more -->
+    <!-- Disabling because the publisher tooling does not know how to deal with FHIRHelpers and FHIR-ModelInfo in this IG -->
+    <parameter>
+      <code value="path-binary"/>
+      <value value="input/cql"/>
+    </parameter>
+<!--    <parameter>-->
+<!--      <code value="path-resource"/>-->
+<!--      <value value="input/resources/device"/>-->
+<!--    </parameter>-->
+    <parameter>
+      <code value="path-resource"/>
+      <value value="input/resources/library"/>
+    </parameter>
+<!--    <parameter>-->
+<!--      <code value="path-resource"/>-->
+<!--      <value value="input/resources/questionnaire"/>-->
+<!--    </parameter>-->
+<!--    <parameter>-->
+<!--      <code value="path-liquid"/>-->
+<!--      <value value="templates\liquid"/>-->
+<!--    </parameter>-->
+<!--    <parameter>-->
+<!--      <code value="path-suppressed-warnings"/>-->
+<!--      <value value="input/ignoreWarnings.txt"/>-->
+<!--    </parameter>-->
+<!--    &lt;!&ndash; Allow the domain CPG. This does prevent a few of the errors,-->
+<!--    but the canonical URLs for extensions and profiles from this domain still result in errors... &ndash;&gt;-->
+<!--    <parameter>-->
+<!--      <code value="extension-domain"/>-->
+<!--      <value value="http://hl7.org/fhir/uv/cpg"/>-->
+<!--    </parameter>-->
+<!-- Uncomment one or more of these if you want to limit which syntaxes are supported or want to disable the display of mappings
+    <parameter>
+      <code value="excludexml"/>
+      <value value="true"/>
+    </parameter>
+    <parameter>
+      <code value="excludejson"/>
+      <value value="true"/>
+    </parameter>
+    <parameter>
+      <code value="excludettl"/>
+      <value value="true"/>
+    </parameter>
+    <parameter>
+      <code value="excludemap"/>
+      <value value="true"/>
+    </parameter>-->
+  </definition>
+</ImplementationGuide>