Merge pull request #313 from cqframework/RefreshOperationAndProcessor…

…TestInfrastructure

Refresh Testing Infrastructure

src/main/java/org/opencds/cqf/tooling/common/BaseCqfmSoftwareSystemHelper.java

@@ -8,6 +8,7 @@
 
 
 public abstract class BaseCqfmSoftwareSystemHelper {
+    public static final String separator = System.getProperty("file.separator");
     private String rootDir;
     protected String getRootDir() {
         return this.rootDir;
@@ -17,7 +18,7 @@ protected String getRootDir() {
     private static String cqfToolingDeviceName = "cqf-tooling";
 //    private static String cqfToolingDeviceReferenceID = "#" + cqfToolingDeviceName;
     private static String cqfmSoftwareSystemExtensionUrl = "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem";
-    protected static String devicePath = "/input/resources/device";
+    protected static String devicePath = separator + "input" + separator + "resources" + separator + "device";
 
     protected String getCqfToolingDeviceName() { return cqfToolingDeviceName; }
 //    protected String getCqfToolingDeviceReferenceID() { return cqfToolingDeviceReferenceID; }
@@ -52,6 +53,9 @@ protected Boolean getSystemIsValid(CqfmSoftwareSystem system) {
     protected void EnsureDevicePath() {
         try {
             IOUtils.ensurePath(rootDir + devicePath);
+            if (!IOUtils.resourceDirectories.contains(rootDir + devicePath)) {
+                IOUtils.resourceDirectories.add(rootDir + devicePath);
+            }
         }
         catch (IOException ex) {
             LogUtils.putException("EnsureDevicePath", ex.getMessage());

src/main/java/org/opencds/cqf/tooling/common/r4/CqfmSoftwareSystemHelper.java

@@ -96,6 +96,7 @@ public <T extends DomainResource> void ensureSoftwareSystemExtensionAndDevice(T
 
             /* Create the device if one doesn't already exist */
             if (device == null) {
+                System.out.println("Creating Device");
                 device = createSoftwareSystemDevice(system);
             }
 

src/main/java/org/opencds/cqf/tooling/measure/MeasureProcessor.java

@@ -10,7 +10,6 @@
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r5.model.Measure;
-import org.hl7.fhir.utilities.Utilities;
 import org.opencds.cqf.tooling.library.LibraryProcessor;
 import org.opencds.cqf.tooling.measure.r4.R4MeasureProcessor;
 import org.opencds.cqf.tooling.measure.stu3.STU3MeasureProcessor;
@@ -21,10 +20,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.File;
-import java.io.IOException;
 import java.util.*;
-import java.util.stream.Collectors;
 
 public class MeasureProcessor extends BaseProcessor {
     public static final String ResourcePrefix = "measure-";
@@ -34,8 +30,11 @@ public static String getId(String baseId) {
         return ResourcePrefix + baseId;
     }
     private Logger logger = LoggerFactory.getLogger(this.getClass());
-
     public List<String> refreshIgMeasureContent(BaseProcessor parentContext, Encoding outputEncoding, Boolean versioned, FhirContext fhirContext, String measureToRefreshPath) {
+        return refreshIgMeasureContent(parentContext, outputEncoding, null, versioned, fhirContext, measureToRefreshPath);
+    }
+
+    public List<String> refreshIgMeasureContent(BaseProcessor parentContext, Encoding outputEncoding, String measureOutputDirectory, Boolean versioned, FhirContext fhirContext, String measureToRefreshPath) {
 
         System.out.println("Refreshing measures...");
 
@@ -59,6 +58,7 @@ public List<String> refreshIgMeasureContent(BaseProcessor parentContext, Encodin
         params.fhirContext = fhirContext;
         params.encoding = outputEncoding;
         params.versioned = versioned;
+        params.measureOutputDirectory = measureOutputDirectory;
         return measureProcessor.refreshMeasureContent(params);
     }
 

src/main/java/org/opencds/cqf/tooling/measure/r4/R4MeasureProcessor.java

@@ -13,6 +13,7 @@
 public class R4MeasureProcessor extends MeasureProcessor {
 
     private String measurePath;
+    private String measureOutputDirectory;
     private IOUtils.Encoding encoding;
     private static CqfmSoftwareSystemHelper cqfmHelper;
 
@@ -23,13 +24,21 @@ private String getMeasurePath(String measurePath) {
         }
         return measurePath;
     }
+    /*
+        Refresh all measure resources in the given measurePath
+        If the path is not specified, or is not a known directory, process
+        all known measure resources overriding any currently existing files.
+    */
+    protected List<String> refreshMeasures(String measurePath, IOUtils.Encoding encoding) {
+        return refreshMeasures(measurePath, null, encoding);
+    }
 
     /*
         Refresh all measure resources in the given measurePath
         If the path is not specified, or is not a known directory, process
         all known measure resources
     */
-    protected List<String> refreshMeasures(String measurePath, IOUtils.Encoding encoding) {
+    protected List<String> refreshMeasures(String measurePath, String measureOutputDirectory, IOUtils.Encoding encoding) {
         File file = measurePath != null ? new File(measurePath) : null;
         Map<String, String> fileMap = new HashMap<String, String>();
         List<org.hl7.fhir.r5.model.Measure> measures = new ArrayList<>();
@@ -69,7 +78,16 @@ else if (file.isDirectory()) {
                 // TODO: This prevents mangled names from being output
                 // It would be nice for the tooling to generate library shells, we have enough information to,
                 // but the tooling gets confused about the ID and the filename and what gets written is garbage
-                IOUtils.writeResource(measure, filePath, fileEncoding, fhirContext, this.versioned);
+                String outputPath = filePath;
+                if (measureOutputDirectory != null) {
+                    File measureDirectory = new File(measureOutputDirectory);
+                    if (!measureDirectory.exists()) {
+                        //TODO: add logger and log non existant directory for writing
+                    } else {
+                        outputPath = measureDirectory.getAbsolutePath();
+                    }
+                }
+                IOUtils.writeResource(measure, outputPath, fileEncoding, fhirContext, this.versioned);
                 String refreshedMeasureName;
                 if (this.versioned && refreshedMeasure.getVersion() != null) {
                     refreshedMeasureName = refreshedMeasure.getName() + "-" + refreshedMeasure.getVersion();
@@ -104,12 +122,17 @@ public List<String> refreshMeasureContent(RefreshMeasureParameters params) {
         }
 
         measurePath = params.measurePath;
+        measureOutputDirectory = params.measureOutputDirectory;
         fhirContext = params.fhirContext;
         encoding = params.encoding;
         versioned = params.versioned;
 
         R4MeasureProcessor.cqfmHelper = new CqfmSoftwareSystemHelper(rootDir);
 
-        return refreshMeasures(measurePath, encoding);
+        if (measureOutputDirectory != null) {
+            return refreshMeasures(measurePath, measureOutputDirectory, encoding);
+        } else {
+            return refreshMeasures(measurePath, encoding);
+        }
     }
 }

src/main/java/org/opencds/cqf/tooling/measure/r4/RefreshR4MeasureOperation.java

@@ -1,6 +1,7 @@
 package org.opencds.cqf.tooling.measure.r4;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.parser.JsonParser;
 import ca.uhn.fhir.parser.XmlParser;
 
@@ -16,20 +17,28 @@
 import java.util.NoSuchElementException;
 import java.util.Optional;
 
+import com.google.common.base.Strings;
+
 public class RefreshR4MeasureOperation extends RefreshGeneratedContentOperation {
 
     private JsonParser jsonParser;
     private XmlParser xmlParser;
-    private CqfmSoftwareSystemHelper cqfmHelper = new CqfmSoftwareSystemHelper();
+    private CqfmSoftwareSystemHelper cqfmHelper;
 
     public RefreshR4MeasureOperation() {
-        super("src/main/resources/org/opencds/cqf/tooling/measure/output/r4", "-RefreshR4Measure", FhirContext.forR4());
+        super("src/main/resources/org/opencds/cqf/tooling/measure/output/r4", "-RefreshR4Measure", FhirContext.forCached(FhirVersionEnum.R4));
+        cqfmHelper = new CqfmSoftwareSystemHelper("src/main/resources/org/opencds/cqf/tooling/measure/output/r4");
         jsonParser = (JsonParser)this.getFhirContext().newJsonParser();
         xmlParser = (XmlParser)this.getFhirContext().newXmlParser();
     }
 
     public RefreshR4MeasureOperation(String pathToMeasures) {
-        super(FilenameUtils.getPath(pathToMeasures), "-RefreshR4Measure", FhirContext.forR4(), null, pathToMeasures);
+        super(pathToMeasures, "-RefreshR4Measure", FhirContext.forCached(FhirVersionEnum.R4), null, pathToMeasures);
+        if (!Strings.isNullOrEmpty(getOutputPath())) {
+            cqfmHelper = new CqfmSoftwareSystemHelper(getOutputPath());
+        } else {
+            cqfmHelper = new CqfmSoftwareSystemHelper();
+        }
         jsonParser = (JsonParser)this.getFhirContext().newJsonParser();
         xmlParser = (XmlParser)this.getFhirContext().newXmlParser();
         xmlParser = (XmlParser)this.getFhirContext().newXmlParser();

src/main/java/org/opencds/cqf/tooling/measure/stu3/RefreshStu3MeasureOperation.java

@@ -1,6 +1,7 @@
 package org.opencds.cqf.tooling.measure.stu3;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.parser.JsonParser;
 import ca.uhn.fhir.parser.XmlParser;
 
@@ -16,21 +17,29 @@
 import java.util.NoSuchElementException;
 import java.util.Optional;
 
+import com.google.common.base.Strings;
+
 public class RefreshStu3MeasureOperation extends RefreshGeneratedContentOperation {
 
     private JsonParser jsonParser;
     private XmlParser xmlParser;
-    private CqfmSoftwareSystemHelper cqfmHelper = new CqfmSoftwareSystemHelper();
+    private CqfmSoftwareSystemHelper cqfmHelper;
 
     //NOTE: Only consumed from OperationFactory - that call should come through a proper Operation that calls a processor.
     public RefreshStu3MeasureOperation() {
-        super("src/main/resources/org/opencds/cqf/tooling/measure/output/stu3", "-RefreshStu3Measure", FhirContext.forDstu3());
+        super("src/main/resources/org/opencds/cqf/tooling/measure/output/stu3", "-RefreshStu3Measure", FhirContext.forCached(FhirVersionEnum.DSTU3));
+        cqfmHelper = new CqfmSoftwareSystemHelper("src/main/resources/org/opencds/cqf/tooling/measure/output/r4");
         jsonParser = (JsonParser)this.getFhirContext().newJsonParser();
         xmlParser = (XmlParser)this.getFhirContext().newXmlParser();
     }
 
     public RefreshStu3MeasureOperation(String pathToMeasures) {
-        super(FilenameUtils.getPath(pathToMeasures), "-RefreshStu3Measure", FhirContext.forDstu3(), null, pathToMeasures);
+        super(pathToMeasures, "-RefreshStu3Measure", FhirContext.forCached(FhirVersionEnum.DSTU3), null, pathToMeasures);
+        if (!Strings.isNullOrEmpty(getOutputPath())) {
+            cqfmHelper = new CqfmSoftwareSystemHelper(getOutputPath());
+        } else {
+            cqfmHelper = new CqfmSoftwareSystemHelper();
+        }
         jsonParser = (JsonParser)this.getFhirContext().newJsonParser();
         xmlParser = (XmlParser)this.getFhirContext().newXmlParser();
     }

src/main/java/org/opencds/cqf/tooling/operation/RefreshGeneratedContentOperation.java

@@ -1,5 +1,7 @@
 package org.opencds.cqf.tooling.operation;
 
+import com.google.common.base.Strings;
+
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.opencds.cqf.tooling.Operation;
 import org.opencds.cqf.tooling.utilities.IOUtils;
@@ -61,7 +63,11 @@ public void execute(String[] args) {
     }
 
     public void output(IBaseResource resource, IOUtils.Encoding encoding) {
-        IOUtils.writeResource(resource, pathToMeasures, encoding, fhirContext);
+        if (Strings.isNullOrEmpty(getOutputPath())) {
+            IOUtils.writeResource(resource, pathToMeasures, encoding, fhirContext);
+        } else {
+            IOUtils.writeResource(resource, getOutputPath(), encoding, fhirContext);
+        }
     }
 
     public abstract void refreshGeneratedContent();

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

@@ -18,4 +18,6 @@ public class RefreshIGParameters {
     public ArrayList<String> resourceDirs;
     public Boolean conformant;
     public String measureToRefreshPath;
+    public String libraryOutputPath;
+    public String measureOutputPath;
 }

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

@@ -45,4 +45,9 @@ The path to the measure resource(s)
     An initialized processor context that can provide the IG context directly
      */
     public IProcessorContext parentContext;
+
+    /*
+    Directory target for writing output
+     */
+    public String measureOutputDirectory;
 }

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

@@ -1,10 +1,14 @@
 package org.opencds.cqf.tooling.processor;
 
+import static java.util.Objects.requireNonNull;
+
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
+import com.google.common.base.Strings;
+
 import org.apache.commons.io.FilenameUtils;
 import org.hl7.fhir.utilities.Utilities;
 import org.opencds.cqf.tooling.library.LibraryProcessor;
@@ -30,6 +34,14 @@ public IGProcessor(IGBundleProcessor igBundleProcessor, LibraryProcessor library
     }
     //mega ig method
     public void publishIG(RefreshIGParameters params) {
+        requireNonNull(params.includeDependencies, "includeDependencies can not be null");
+        requireNonNull(params.includeELM, "includeELM can not be null");
+        requireNonNull(params.includePatientScenarios, "includePatientScenarios can not be null");
+        requireNonNull(params.includeTerminology, "includeTerminology can not be null");
+        requireNonNull(params.versioned, "versioned can not be null");
+        requireNonNull(params.resourceDirs, "resourceDirs can not be null");
+        requireNonNull(params.outputEncoding, "outputEncoding can not be null");
+        requireNonNull(params.ini, "ini can not be null");
         if (params.ini != null) {
             initializeFromIni(params.ini);
         }
@@ -101,6 +113,8 @@ public void refreshIG(RefreshIGParameters params) {
         Encoding encoding = params.outputEncoding;
         // Boolean includeELM = params.includeELM;
         // Boolean includeDependencies = params.includeDependencies;
+        String libraryOutputPath = params.libraryOutputPath;
+        String measureOutputPath = params.measureOutputPath;
         Boolean includeTerminology = params.includeTerminology;
         Boolean includePatientScenarios = params.includePatientScenarios;
         Boolean versioned = params.versioned;
@@ -121,11 +135,19 @@ public void refreshIG(RefreshIGParameters params) {
         IGProcessor.ensure(rootDir, includePatientScenarios, includeTerminology, IOUtils.resourceDirectories);
 
         List<String> refreshedLibraryNames;
-        refreshedLibraryNames = libraryProcessor.refreshIgLibraryContent(this, encoding, versioned, fhirContext);
+        if (Strings.isNullOrEmpty(libraryOutputPath)) {
+            refreshedLibraryNames = libraryProcessor.refreshIgLibraryContent(this, encoding, versioned, fhirContext);
+        } else {
+            refreshedLibraryNames = libraryProcessor.refreshIgLibraryContent(this, encoding, libraryOutputPath, versioned, fhirContext);
+        }
         refreshedResourcesNames.addAll(refreshedLibraryNames);
 
         List<String> refreshedMeasureNames;
-        refreshedMeasureNames = measureProcessor.refreshIgMeasureContent(this, encoding, versioned, fhirContext, measureToRefreshPath);
+        if (Strings.isNullOrEmpty(measureOutputPath)) {
+            refreshedMeasureNames = measureProcessor.refreshIgMeasureContent(this, encoding, versioned, fhirContext, measureToRefreshPath);
+        } else {
+            refreshedMeasureNames = measureProcessor.refreshIgMeasureContent(this, encoding, measureOutputPath, versioned, fhirContext, measureToRefreshPath);
+        }
         refreshedResourcesNames.addAll(refreshedMeasureNames);
 
         if (refreshedResourcesNames.isEmpty()) {

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

@@ -31,6 +31,8 @@ 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_OUTPUT_PATH_OPTIONS = {"libraryOutput", "libraryOutputPath", "lop"};
+    public static final String[] MEASURE_OUTPUT_PATH_OPTIONS = {"measureOutput", "measureOutputPath", "mop"};
 
     @SuppressWarnings("unused")
     public OptionParser build() {
@@ -43,13 +45,17 @@ public OptionParser build() {
         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.");
+        OptionSpecBuilder libraryOutputPathBuilder = parser.acceptsAll(asList(LIBRARY_OUTPUT_PATH_OPTIONS),"If omitted, the libraries will overwrite any existing libraries");
+        OptionSpecBuilder measureOutputPathBuilder = parser.acceptsAll(asList(MEASURE_OUTPUT_PATH_OPTIONS),"If omitted, the measures will overwrite any existing measures");
 
         OptionSpec<String> ini = iniBuilder.withRequiredArg().describedAs("Path to the IG ini file");
         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> 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");
+        OptionSpec<String> measureOutputPath = measureOutputPathBuilder.withOptionalArg().describedAs("path to the output directory for updated measures");
 
         //TODO: FHIR user / password (and other auth options)
         OptionSpec<String> fhirUri = fhirUriBuilder.withOptionalArg().describedAs("uri of fhir server");  
@@ -92,6 +98,16 @@ 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 libraryOutputPath = (String)options.valueOf(LIBRARY_OUTPUT_PATH_OPTIONS[0]);
+        if (libraryOutputPath == null) {
+            libraryOutputPath = "";
+        }
+
+        String measureOutputPath = (String)options.valueOf(MEASURE_OUTPUT_PATH_OPTIONS[0]);
+        if (measureOutputPath == null) {
+            measureOutputPath = "";
+        }
+
         ArrayList<String> paths = new ArrayList<String>();
         if (resourcePaths != null && !resourcePaths.isEmpty()) {
             paths.addAll(resourcePaths);
@@ -110,6 +126,8 @@ public RefreshIGParameters parseAndConvert(String[] args) {
         ip.resourceDirs = paths;
         ip.fhirUri = fhirUri;
         ip.measureToRefreshPath = measureToRefreshPath;
+        ip.libraryOutputPath = libraryOutputPath;
+        ip.measureOutputPath = measureOutputPath;
 
         return ip;
     }

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

@@ -898,6 +898,12 @@ public static HashSet<String> getDevicePaths(FhirContext fhirContext) {
         }
         return devicePaths;
     }
+
+    // TODO: This should not be necessary this is awful... For now it is needed for passing tests in Travis
+    public static void clearDevicePaths() {
+        devicePaths = new HashSet<String>();
+    }
+
     private static void setupDevicePaths(FhirContext fhirContext) {
         HashMap<String, IBaseResource> resources = new LinkedHashMap<String, IBaseResource>();
         for(String dir : resourceDirectories) {

src/test/java/org/opencds/cqf/tooling/CqfmSoftwareSystemTest.java

@@ -0,0 +1,6 @@
+package org.opencds.cqf.tooling;
+
+public interface CqfmSoftwareSystemTest {
+    public static final String separator = System.getProperty("file.separator");
+    public static final String cqfmSoftwareSystemExtensionUrl = "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem";
+}