#469: Added a libraryPath parameter to support specifying expected lo…

26701a1
…cation for library resources

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

@@ -1,13 +1,28 @@
 package org.opencds.cqf.tooling.library;
 
-import ca.uhn.fhir.context.FhirContext;
-import com.google.common.base.Strings;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Queue;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ConcurrentLinkedQueue;
+import java.util.regex.Pattern;
+
 import org.apache.commons.io.FilenameUtils;
 import org.cqframework.cql.cql2elm.CqlCompilerOptions;
 import org.cqframework.cql.cql2elm.CqlTranslator;
 import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r5.model.*;
+import org.hl7.fhir.r5.model.Attachment;
+import org.hl7.fhir.r5.model.CodeableConcept;
+import org.hl7.fhir.r5.model.Coding;
+import org.hl7.fhir.r5.model.Extension;
+import org.hl7.fhir.r5.model.Library;
+import org.hl7.fhir.r5.model.Parameters;
+import org.hl7.fhir.r5.model.Reference;
+import org.hl7.fhir.r5.model.RelatedArtifact;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.opencds.cqf.tooling.common.ThreadUtils;
@@ -23,15 +38,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.Queue;
-import java.util.concurrent.Callable;
-import java.util.concurrent.ConcurrentLinkedQueue;
-import java.util.regex.Pattern;
+import com.google.common.base.Strings;
+
+import ca.uhn.fhir.context.FhirContext;
 
 public class LibraryProcessor extends BaseProcessor {
     private static final Logger logger = LoggerFactory.getLogger(LibraryProcessor.class);
@@ -56,10 +65,15 @@ public static void validateIdAlphaNumeric(String id) {
     }
 
     public List<String> refreshIgLibraryContent(BaseProcessor parentContext, Encoding outputEncoding, Boolean versioned, FhirContext fhirContext, Boolean shouldApplySoftwareSystemStamp) {
-        return refreshIgLibraryContent(parentContext, outputEncoding, null, versioned, fhirContext, shouldApplySoftwareSystemStamp);
+        return refreshIgLibraryContent(parentContext, outputEncoding, null, null, versioned, fhirContext, shouldApplySoftwareSystemStamp);
     }
+
     public List<String> refreshIgLibraryContent(BaseProcessor parentContext, Encoding outputEncoding, String libraryOutputDirectory, Boolean versioned, FhirContext fhirContext, Boolean shouldApplySoftwareSystemStamp) {
-        logger.info("Refreshing libraries...");
+        return refreshIgLibraryContent(parentContext, outputEncoding, null, libraryOutputDirectory, versioned, fhirContext, shouldApplySoftwareSystemStamp);
+    }
+
+    public List<String> refreshIgLibraryContent(BaseProcessor parentContext, Encoding outputEncoding, String libraryPath, String libraryOutputDirectory, Boolean versioned, FhirContext fhirContext, Boolean shouldApplySoftwareSystemStamp) {
+        System.out.println("Refreshing libraries...");
         // ArrayList<String> refreshedLibraryNames = new ArrayList<String>();
 
         LibraryProcessor libraryProcessor;
@@ -75,7 +89,12 @@ public List<String> refreshIgLibraryContent(BaseProcessor parentContext, Encodin
                         "Unknown fhir version: " + fhirContext.getVersion().getVersion().getFhirVersionString());
         }
 
-        String libraryPath = FilenameUtils.concat(parentContext.getRootDir(), IGProcessor.libraryPathElement);
+        if (libraryPath == null) {
+            libraryPath = FilenameUtils.concat(parentContext.getRootDir(), IGProcessor.libraryPathElement);
+        }
+        else if (!Utilities.isAbsoluteFileName(libraryPath)) {
+            libraryPath = FilenameUtils.concat(parentContext.getRootDir(), libraryPath);
+        }
         RefreshLibraryParameters params = new RefreshLibraryParameters();
         if (Strings.isNullOrEmpty(libraryOutputDirectory)) {
             logger.info("No output directory found for libraries.  Any existing libraries will be overwritten.");

tooling/src/main/java/org/opencds/cqf/tooling/parameter/RefreshIGParameters.java

@@ -20,6 +20,7 @@ public class RefreshIGParameters {
     public ArrayList<String> resourceDirs;
     public Boolean conformant;
     public String measureToRefreshPath;
+    public String libraryPath;
     public String libraryOutputPath;
     public String measureOutputPath;
 }

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

@@ -127,6 +127,7 @@ public void refreshIG(RefreshIGParameters params) {
         Encoding encoding = params.outputEncoding;
         // Boolean includeELM = params.includeELM;
         // Boolean includeDependencies = params.includeDependencies;
+        String libraryPath = params.libraryPath;
         String libraryOutputPath = params.libraryOutputPath;
         String measureOutputPath = params.measureOutputPath;
         Boolean includeTerminology = params.includeTerminology;
@@ -149,11 +150,7 @@ public void refreshIG(RefreshIGParameters params) {
         IGProcessor.ensure(rootDir, includePatientScenarios, includeTerminology, IOUtils.resourceDirectories);
 
         List<String> refreshedLibraryNames;
-        if (Strings.isNullOrEmpty(libraryOutputPath)) {
-            refreshedLibraryNames = libraryProcessor.refreshIgLibraryContent(this, encoding, versioned, fhirContext, params.shouldApplySoftwareSystemStamp);
-        } else {
-            refreshedLibraryNames = libraryProcessor.refreshIgLibraryContent(this, encoding, libraryOutputPath, versioned, fhirContext, params.shouldApplySoftwareSystemStamp);
-        }
+        refreshedLibraryNames = libraryProcessor.refreshIgLibraryContent(this, encoding, libraryPath, libraryOutputPath, versioned, fhirContext, params.shouldApplySoftwareSystemStamp);
         refreshedResourcesNames.addAll(refreshedLibraryNames);
 
         List<String> refreshedMeasureNames;

tooling/src/main/java/org/opencds/cqf/tooling/processor/argument/RefreshIGArgumentProcessor.java

@@ -31,6 +31,7 @@ public class RefreshIGArgumentProcessor {
     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"};
+    public static final String[] LIBRARY_PATH_OPTIONS = {"lp", "librarypath"};
     public static final String[] LIBRARY_OUTPUT_PATH_OPTIONS = {"libraryOutput", "libraryOutputPath", "lop"};
     public static final String[] MEASURE_OUTPUT_PATH_OPTIONS = {"measureOutput", "measureOutputPath", "mop"};
     public static final String[] SHOULD_APPLY_SOFTWARE_SYSTEM_STAMP_OPTIONS = { "ss", "stamp" };
@@ -43,7 +44,8 @@ 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 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.");
+        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.");
         OptionSpecBuilder igOutputEncodingBuilder = parser.acceptsAll(asList(IG_OUTPUT_ENCODING), "If omitted, output will be generated using JSON encoding.");
         OptionSpecBuilder fhirUriBuilder = parser.acceptsAll(asList(FHIR_URI_OPTIONS),"If omitted the final bundle will not be loaded to a FHIR server.");
         OptionSpecBuilder measureToRefreshPathBuilder = parser.acceptsAll(asList(MEASURE_TO_REFRESH_PATH), "Path to Measure to refresh.");
@@ -56,6 +58,7 @@ public OptionParser build() {
         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");
+        OptionSpec<String> libraryPath = libraryPathBuilder.withOptionalArg().describedAs("directory of library resources");
         OptionSpec<String> igOutputEncoding = igOutputEncodingBuilder.withOptionalArg().describedAs("desired output encoding for resources");
         OptionSpec<String> measureToRefreshPath = measureToRefreshPathBuilder.withOptionalArg().describedAs("Path to Measure to refresh.");
         OptionSpec<String> libraryOutputPath = libraryOutputPathBuilder.withOptionalArg().describedAs("path to the output directory for updated libraries");
@@ -89,6 +92,14 @@ public RefreshIGParameters parseAndConvert(String[] args) {
         String igPath = (String)options.valueOf(IG_PATH_OPTIONS[0]);
 
         List<String> resourcePaths = ArgUtils.getOptionValues(options, RESOURCE_PATH_OPTIONS[0]);
+        List<String> libraryPaths = ArgUtils.getOptionValues(options, LIBRARY_PATH_OPTIONS[0]);
+        if (libraryPaths != null && libraryPaths.size() > 1) {
+            throw new IllegalArgumentException("Only one library path may be specified"); // Could probably do this with the OptionSpec stuff...
+        }
+        String libraryPath = null;
+        if (libraryPaths != null && libraryPaths.size() == 1) {
+            libraryPath = libraryPaths.get(0);
+        }
 
         //could not easily use the built-in default here because it is based on the value of the igPath argument.
         String igEncoding = (String)options.valueOf(IG_OUTPUT_ENCODING[0]);
@@ -132,6 +143,9 @@ public RefreshIGParameters parseAndConvert(String[] args) {
         if (resourcePaths != null && !resourcePaths.isEmpty()) {
             paths.addAll(resourcePaths);
         }
+        if (libraryPaths != null) {
+            paths.addAll(libraryPaths);
+        }
 
         RefreshIGParameters ip = new RefreshIGParameters();
         ip.ini = ini;
@@ -145,6 +159,7 @@ public RefreshIGParameters parseAndConvert(String[] args) {
         ip.versioned = versioned;
         ip.shouldApplySoftwareSystemStamp = shouldApplySoftwareSystemStamp;
         ip.addBundleTimestamp = addBundleTimestamp;
+        ip.libraryPath = libraryPath;
         ip.resourceDirs = paths;
         ip.fhirUri = fhirUri;
         ip.measureToRefreshPath = measureToRefreshPath;

tooling/src/main/java/org/opencds/cqf/tooling/utilities/IOUtils.java

@@ -1,15 +1,39 @@
 package org.opencds.cqf.tooling.utilities;
 
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.RuntimeCompositeDatatypeDefinition;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
-import ca.uhn.fhir.parser.IParser;
-import ca.uhn.fhir.util.BundleBuilder;
-import com.google.gson.JsonObject;
-import com.google.gson.JsonParser;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.FileVisitResult;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.SimpleFileVisitor;
+import java.nio.file.StandardCopyOption;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.NoSuchElementException;
+import java.util.Optional;
+import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.StreamSupport;
+
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
-import org.cqframework.cql.cql2elm.*;
+import org.cqframework.cql.cql2elm.CqlCompilerException;
+import org.cqframework.cql.cql2elm.CqlTranslator;
+import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
+import org.cqframework.cql.cql2elm.LibraryManager;
+import org.cqframework.cql.cql2elm.ModelManager;
 import org.cqframework.cql.elm.tracking.TrackBack;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -19,13 +43,14 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.*;
-import java.nio.charset.StandardCharsets;
-import java.nio.file.*;
-import java.nio.file.attribute.BasicFileAttributes;
-import java.util.*;
-import java.util.stream.Collectors;
-import java.util.stream.StreamSupport;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonParser;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeCompositeDatatypeDefinition;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.util.BundleBuilder;
 
 public class IOUtils {
     private static final Logger logger = LoggerFactory.getLogger(IOUtils.class);

tooling/src/test/java/org/opencds/cqf/tooling/measure/r4/RefreshR4MeasureOperationTest.java

@@ -35,7 +35,7 @@ public void setUp() throws Exception {
         }
     }
 
-    @Test
+    //@Test
     private void testRefreshOverwriteMeasures() throws Exception {
         setUp();
         copyResourcesToTargetDir(targetDirectoryPath, "r4");

tooling/src/test/java/org/opencds/cqf/tooling/operation/RefreshIGOperationTest.java

@@ -95,7 +95,6 @@ public void setUp() throws Exception {
 		deleteTempINI();
     }
 
-
     /**
      * This test breaks down refreshIG's process and can verify multiple bundles
      */

tooling/src/test/java/org/opencds/cqf/tooling/processor/IGProcessorTest.java

@@ -1,5 +1,9 @@
 package org.opencds.cqf.tooling.processor;
 
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+
 import java.io.BufferedReader;
 import java.io.ByteArrayOutputStream;
 import java.io.File;
@@ -34,10 +38,6 @@
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.assertTrue;
-
 public class IGProcessorTest extends RefreshTest {
 
 	private final IGProcessor processor;