Merge branch 'master' into br-fix-bundling

.vscode/settings.json

@@ -19,5 +19,5 @@
         "testng"
     ],
     "java.compile.nullAnalysis.mode": "automatic",
-    "java.jdt.ls.vmargs": "-XX:+UseParallelGC -XX:GCTimeRatio=4 -XX:AdaptiveSizePolicyWeight=90 -Dsun.zip.disableMemoryMapping=true -Xmx2G -Xms100m -Xlog:disable"
+    "java.jdt.ls.vmargs": "-XX:+UseParallelGC -XX:GCTimeRatio=4 -XX:AdaptiveSizePolicyWeight=90 -Dsun.zip.disableMemoryMapping=true -Xmx4G -Xms100m -Xlog:disable"
 }

tooling/src/main/java/org/opencds/cqf/tooling/library/LibraryProcessor.java

@@ -42,7 +42,7 @@
 
 public class LibraryProcessor extends BaseProcessor {
     private static final Logger logger = LoggerFactory.getLogger(LibraryProcessor.class);
-    public static final String ResourcePrefix = "library-";
+    public static final String ResourcePrefix = "Library-";
 
     public static String getId(String baseId) {
         return ResourcePrefix + baseId;
@@ -270,14 +270,14 @@ protected List<Library> refreshGeneratedContent(List<Library> sourceLibraries) {
     }
 
     public List<Library> refreshGeneratedContent(String cqlDirectoryPath, String fhirVersion) {
-        List<String> result = new ArrayList<String>();
+        var result = new ArrayList<String>();
         File input = new File(cqlDirectoryPath);
         if (input.exists() && input.isDirectory()) {
             result.add(input.getAbsolutePath());
         }
         setBinaryPaths(result);
 
-        List<Library> libraries = new ArrayList<Library>();
+        var libraries = new ArrayList<Library>();
         return internalRefreshGeneratedContent(libraries);
     }
 
@@ -320,6 +320,11 @@ private List<Library> internalRefreshGeneratedContent(List<Library> sourceLibrar
                     sourceLibraries.add(newLibrary);
                 }
             }
+            else
+            {
+                logger.warn("No identifier found for CQL file {}", fileInfo.getPath());
+            }
+
         }
 
         List<Library> resources = new ArrayList<Library>();

tooling/src/main/java/org/opencds/cqf/tooling/npm/NpmPackageManager.java

@@ -133,9 +133,10 @@ private void loadCorePackage() {
     }
 
     private void loadIg(ImplementationGuide.ImplementationGuideDependsOnComponent dep, int index) throws IOException {
+        logger.info("Loading IG Dependency {}#{}", dep.getUri(), dep.getVersion());
         String name = dep.getId();
         if (!dep.hasId()) {
-            logger.info("Dependency '{}' has no id, so can't be referred to in markdown in the IG", idForDep(dep));
+            logger.warn("Dependency '{}' has no id, so can't be referred to in markdown in the IG", idForDep(dep));
             name = "u" + Utilities.makeUuidLC().replace("-", "");
         }
         if (!isValidIGToken(name)) {
@@ -155,10 +156,9 @@ private void loadIg(ImplementationGuide.ImplementationGuideDependsOnComponent de
             throw new IllegalArgumentException(
                     "You must specify a version for the IG " + packageId + " (" + canonical + ")");
 
-        NpmPackage pi = packageId == null ? null : pcm.loadPackageFromCacheOnly(packageId, igver);
-        if (pi != null)
-            npmList.add(pi);
+        NpmPackage pi = pcm.loadPackage(packageId, igver);
         if (pi == null) {
+            logger.warn("Dependency " + name + " (" + canonical + ") not found by FilesystemPackageCacheManager");
             pi = resolveDependency(canonical, packageId, igver);
             if (pi == null) {
                 if (Utilities.noString(packageId))
@@ -169,6 +169,8 @@ private void loadIg(ImplementationGuide.ImplementationGuideDependsOnComponent de
             }
         }
 
+        npmList.add(pi);
+
         logger.debug(
                 "Load " + name + " (" + canonical + ") from " + packageId + "#" + igver);
 

tooling/src/main/java/org/opencds/cqf/tooling/operation/ig/CqlRefresh.java

@@ -0,0 +1,98 @@
+package org.opencds.cqf.tooling.operation.ig;
+
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.opencds.cqf.tooling.parameter.RefreshIGParameters;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+public class CqlRefresh extends Refresh {
+
+    private static final Logger logger = LoggerFactory.getLogger(CqlRefresh.class);
+    private final Pattern VERSION_PATTERN = Pattern.compile("^(library\\s+(\\S+)\\s+version\\s+)'[0-9]+\\.[0-9]+\\.[0-9]+'");
+    private final Pattern INCLUDE_PATTERN = Pattern.compile("^(include\\s+(\\S+)\\s+version\\s+)'([0-9]+\\.[0-9]+\\.[0-9]+)'(\\s+called\\s+(\\S+))?");
+
+    public CqlRefresh(IGInfo igInfo) {
+        super(igInfo);
+    }
+
+    @Override
+    public List<IBaseResource> refresh() {
+        return List.of();
+    }
+
+    public void refreshCql(IGInfo igInfo, RefreshIGParameters params) {
+        Map<String, String> updatedLibraries = refreshCqlFile(igInfo.getCqlBinaryPath(), params.updatedVersion);
+        updateCqlReferences(igInfo.getCqlBinaryPath(), updatedLibraries);
+    }
+
+    private Map<String, String> refreshCqlFile(String cqlBinaryPath, String updatedVersion) {
+        Map<String, String> updatedLibraries = new HashMap<>();
+        try (Stream<Path> paths = Files.walk(Paths.get(cqlBinaryPath))) {
+            List<Path> files = paths
+                    .filter(Files::isRegularFile)
+                    .filter(path -> path.toString().endsWith(".cql"))
+                    .collect(Collectors.toList());
+
+            for (Path file : files) {
+                List<String> lines = Files.readAllLines(file);
+                for (int i = 0; i < lines.size(); i++) {
+                    Matcher matcher = VERSION_PATTERN.matcher(lines.get(i));
+                    if (matcher.matches()) {
+                        String libraryName = matcher.group(2);
+                        String updatedLine = matcher.replaceFirst("$1'" + updatedVersion + "'");
+                        lines.set(i, updatedLine);
+                        Files.write(file, lines);
+                        updatedLibraries.put(libraryName, updatedVersion);
+                        break;
+                    }
+                }
+            }
+        } catch (IOException e) {
+            logger.error("Error updating cql files: {}", e.getMessage());
+        }
+        return updatedLibraries;
+    }
+
+    private void updateCqlReferences(String cqlBinaryPath, Map<String, String> updatedLibraries) {
+        try (Stream<Path> paths = Files.walk(Paths.get(cqlBinaryPath))) {
+            List<Path> files = paths
+                    .filter(Files::isRegularFile)
+                    .filter(path -> path.toString().endsWith(".cql"))
+                    .collect(Collectors.toList());
+
+            for (Path file : files) {
+                List<String> lines = Files.readAllLines(file);
+                boolean fileUpdated = false;
+                for (int i = 0; i < lines.size(); i++) {
+                    Matcher matcher = INCLUDE_PATTERN.matcher(lines.get(i));
+                    while (matcher.find()) {
+                        String libraryName = matcher.group(2);
+                        String newVersion = updatedLibraries.get(libraryName);
+                        if (newVersion != null && !matcher.group(3).equals(newVersion)) {
+                            String calledPart = matcher.group(4) != null ? matcher.group(4) : "";
+                            String newLine = matcher.replaceFirst("$1'" + newVersion + "'" + calledPart);
+                            lines.set(i, newLine);
+                            fileUpdated = true;
+                        }
+                    }
+                }
+                if (fileUpdated) {
+                    Files.write(file, lines);
+                }
+            }
+        } catch (IOException e) {
+            logger.error("Error updating CQL references: {}", e.getMessage());
+        }
+    }
+
+}

tooling/src/main/java/org/opencds/cqf/tooling/operation/ig/LibraryRefresh.java

@@ -66,6 +66,10 @@ public List<IBaseResource> refresh(RefreshIGParameters params) {
             logger.info("Refreshing {}", library.getIdElement());
 
             for (CqlProcessor.CqlSourceFileInformation info : cqlProcessor.getAllFileInformation()) {
+               if (info.getIdentifier() == null) {
+                  logger.warn("No identifier found for CQL file {}", info.getPath());
+               }
+
                if (info.getIdentifier().getId().endsWith(name)) {
                   // TODO: should likely verify or resolve/refresh the following elements:
                   //  cpg-knowledgeCapability, cpg-knowledgeRepresentationLevel, url, identifier, status,

tooling/src/main/java/org/opencds/cqf/tooling/operation/ig/NewRefreshIGOperation.java

@@ -22,6 +22,8 @@ public void execute(String[] args) {
       try {
          this.params = new RefreshIGArgumentProcessor().parseAndConvert(args);
          IGInfo info = new IGInfo(null, params);
+         CqlRefresh cqlRefresh = new CqlRefresh(info);
+         cqlRefresh.refreshCql(info, params);
          LibraryRefresh libraryRefresh = new LibraryRefresh(info);
          publishLibraries(info, libraryRefresh.refresh(this.params));
          PlanDefinitionRefresh planDefinitionRefresh = new PlanDefinitionRefresh(info, libraryRefresh.getCqlProcessor(), libraryRefresh.getLibraryPackages());

tooling/src/main/java/org/opencds/cqf/tooling/processor/CqlProcessor.java

@@ -2,6 +2,7 @@
 
 import java.io.File;
 import java.io.FilenameFilter;
+import java.nio.file.Files;
 import java.nio.file.Paths;
 import java.util.*;
 import java.util.stream.Collectors;
@@ -34,13 +35,17 @@
 import org.opencds.cqf.tooling.npm.NpmLibrarySourceProvider;
 import org.opencds.cqf.tooling.npm.NpmModelInfoProvider;
 import org.opencds.cqf.tooling.utilities.ResourceUtils;
+import org.slf4j.Logger;
 
 public class CqlProcessor {
 
+    private static final Logger log = org.slf4j.LoggerFactory.getLogger(CqlProcessor.class);
+
     /**
      * information about a cql file
      */
     public class CqlSourceFileInformation {
+        private final String path;
         private CqlTranslatorOptions options;
         private VersionedIdentifier identifier;
         private byte[] cql;
@@ -50,6 +55,15 @@ public class CqlSourceFileInformation {
         private List<RelatedArtifact> relatedArtifacts = new ArrayList<>();
         private List<DataRequirement> dataRequirements = new ArrayList<>();
         private List<ParameterDefinition> parameters = new ArrayList<>();
+
+        public CqlSourceFileInformation(String path) {
+            this.path = path;
+        }
+
+        public String getPath() {
+            return path;
+        }
+
         public CqlTranslatorOptions getOptions() {
             return options;
         }
@@ -361,7 +375,7 @@ public static ValidationMessage exceptionToValidationMessage(File file, CqlCompi
 
     private void translateFile(LibraryManager libraryManager, File file, CqlCompilerOptions options) {
 //        logger.logMessage(String.format("Translating CQL source in file %s", file.toString()));
-        CqlSourceFileInformation result = new CqlSourceFileInformation();
+        CqlSourceFileInformation result = new CqlSourceFileInformation(file.getAbsolutePath());
         fileMap.put(file.getAbsoluteFile().toString(), result);
 
         if (options.getValidateUnits()) {
@@ -382,6 +396,8 @@ private void translateFile(LibraryManager libraryManager, File file, CqlCompiler
 
 
             if (!severeErrorList.isEmpty()) {
+                var messages = severeErrorList.stream().map(x -> x.getMessage()).reduce("", (x, y) -> x + "\n" + y);
+                log.warn("CQL Processing failed with errors count: {}, messages: {}", severeErrorList.size(), messages);
                 result.getErrors().add(new ValidationMessage(ValidationMessage.Source.Publisher, IssueType.EXCEPTION, file.getName(),
                         String.format("CQL Processing failed with (%d) errors.", translator.getErrors().size()), IssueSeverity.ERROR));
             }
@@ -390,6 +406,7 @@ private void translateFile(LibraryManager libraryManager, File file, CqlCompiler
                     result.setOptions(new CqlTranslatorOptions().withCqlCompilerOptions(options));
                     // convert to base64 bytes
                     // NOTE: Publication tooling requires XML content
+                    result.setCql(Files.readAllBytes(file.toPath()));
                     result.setElm(translator.toXml().getBytes());
                     result.setIdentifier(translator.toELM().getIdentifier());
                     result.setJsonElm(translator.toJson().getBytes());