Add a CQL export option to the StripGeneratedContent operation (#511)

* Add CQL export to StripContent operation

* More cleanup / refactoring of the strip content processor

* Add suppression for errorneous warning

* Cleanup and a test

* Fix coment

* Fix parameter name

* Further clean-up

* Swap to utility functions

.vscode/settings.json

@@ -8,11 +8,14 @@
         "conceptmap",
         "Cqfm",
         "cqloptions",
+        "DEPENDSON",
+        "Dstu",
         "Fhir",
         "opencds",
         "pagecontent",
         "plandefinition",
         "qicore",
+        "stripcontent",
         "testng"
     ],
     "java.compile.nullAnalysis.mode": "automatic",

tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/BaseContentStripper.java

@@ -0,0 +1,201 @@
+package org.opencds.cqf.tooling.operations.stripcontent;
+
+import static com.google.common.base.Preconditions.checkNotNull;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.List;
+import java.util.Set;
+
+import static org.opencds.cqf.tooling.utilities.converters.ResourceAndTypeConverter.convertFromR5Resource;
+import static org.opencds.cqf.tooling.utilities.converters.ResourceAndTypeConverter.convertToR5Resource;
+
+import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r5.model.Attachment;
+import org.hl7.fhir.r5.model.DomainResource;
+import org.hl7.fhir.r5.model.Extension;
+import org.hl7.fhir.r5.model.Library;
+import org.hl7.fhir.r5.model.Measure;
+import org.hl7.fhir.r5.model.Parameters;
+import org.hl7.fhir.r5.model.PlanDefinition;
+import org.hl7.fhir.r5.model.Questionnaire;
+import org.hl7.fhir.r5.model.RelatedArtifact;
+import org.hl7.fhir.r5.model.Resource;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.parser.IParser;
+
+/**
+ * This class is used to strip autogenerated content from FHIR resources. This includes narrative,
+ * extensions added by the tooling, related artifacts that are auto detected from the CQL,
+ * contained resources added by the tooling, and ELM generated from the CQL.
+ * 
+ * This class converts the resource to its R5 equivalent, strips the content, and then converts
+ * back to the original FHIR version.
+ * 
+ * The T parameter is used to specify the version of the Resource base class to use for the operation
+ * and conversions.
+ */
+abstract class BaseContentStripper<T extends IAnyResource> implements ContentStripper {
+    protected abstract FhirContext context();
+
+    public void stripFile(File inputFile, File outputFile, ContentStripperOptions options) {
+        var resource = parseResource(inputFile);
+
+        var upgraded = convertToR5Resource(context(), resource);
+        stripResource(upgraded, outputFile, options);
+
+        @SuppressWarnings("unchecked")
+        var downgraded = (T) convertFromR5Resource(context(), upgraded);
+        writeResource(outputFile, downgraded);
+    }
+
+    protected void writeContent(File f, String content) {
+        if (!f.getParentFile().exists()) {
+            f.getParentFile().mkdirs();
+        }
+
+        try (var writer = new BufferedWriter(new FileWriter(f))) {
+            writer.write(content);
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    protected IParser parserForFile(File file) {
+        if (file.getName().endsWith(".json")) {
+            return context().newJsonParser();
+        } else if (file.getName().endsWith(".xml")) {
+            return context().newXmlParser();
+        } else {
+            throw new IllegalArgumentException(String.format("unsupported file type: %s", file.getName()));
+        }
+    }
+
+    protected IBaseResource parseResource(File file) {
+        var parser = parserForFile(file);
+        try (var reader = new FileReader(file)) {
+            return parser.parseResource(reader);
+        }
+        catch (IOException | DataFormatException e) {
+            throw new RuntimeException(String.format("Error parsing file %s", file.getName()), e);
+        }
+    }
+
+    protected void writeResource(File file, IBaseResource resource) {
+        var parser = parserForFile(file).setPrettyPrint(true);
+        var output = parser.encodeResourceToString(resource);
+        writeContent(file, output);
+    }
+
+    // Output file is required because the CQL export functionality requires knowledge of the library
+    // file location to correctly set the Library.content.url property.
+    private Resource stripResource(IBaseResource resource, File outputFile, ContentStripperOptions options) {
+        switch (resource.fhirType()) {
+            case "Library":
+                return stripLibrary((Library) resource, outputFile, options);
+            case "Measure":
+                return stripMeasure((Measure) resource, options);
+            case "PlanDefinition":
+                return stripPlanDefinition((PlanDefinition) resource, options);
+            case "Questionnaire":
+                return stripQuestionnaire((Questionnaire) resource, options);
+            default:
+                return stripResource((DomainResource) resource, options);
+        }
+    }
+
+    private boolean isCqlOptionsParameters(Resource resource) {
+        if (!(resource instanceof Parameters)) {
+            return false;
+        }
+
+        var parameters = (Parameters) resource;
+        return "options".equals(parameters.getId());
+    }
+
+    private void filterContained(List<Resource> contained) {
+        contained.removeIf(this::isCqlOptionsParameters);
+    }
+
+    private void filterExtensions(List<Extension> extensions, Set<String> strippedExtensions) {
+        extensions.removeIf(x -> strippedExtensions.contains(x.getUrl()));
+    }
+
+    private void filterContent(List<Attachment> attachments, Set<String> strippedContentTypes) {
+        attachments.removeIf(x -> strippedContentTypes.contains(x.getContentType()));
+    }
+
+    private void filterRelatedArtifacts(List<RelatedArtifact> artifacts) {
+        artifacts.removeIf(x -> RelatedArtifact.RelatedArtifactType.DEPENDSON.equals(x.getType()));
+    }
+
+    // Strip library includes functionality to export the cql file,
+    // so it requires knowledge of the target directory for the Library.
+    private Library stripLibrary(Library library, File libraryFile, ContentStripperOptions options) {
+        stripResource(library, options);
+        library.setParameter(null);
+        library.setDataRequirement(null);
+        filterRelatedArtifacts(library.getRelatedArtifact());
+        filterContent(library.getContent(), options.strippedContentTypes());
+        exportCql(library.getContent(), library.getName(), libraryFile, options.cqlExportDirectory());
+        return library;
+    }
+
+    private Measure stripMeasure(Measure measure, ContentStripperOptions options) {
+        stripResource(measure, options);
+        filterRelatedArtifacts(measure.getRelatedArtifact());
+        return measure;
+    }
+
+    private PlanDefinition stripPlanDefinition(PlanDefinition planDefinition, ContentStripperOptions options) {
+        stripResource(planDefinition, options);
+        filterRelatedArtifacts(planDefinition.getRelatedArtifact());
+        return planDefinition;
+    }
+
+    private Questionnaire stripQuestionnaire(Questionnaire questionnaire, ContentStripperOptions options) {
+        stripResource(questionnaire, options);
+        filterRelatedArtifacts(questionnaire.getRelatedArtifact());
+        return questionnaire;
+    }
+
+    private DomainResource stripResource(DomainResource resource, ContentStripperOptions options) {
+        resource.setText(null);
+        filterExtensions(resource.getExtension(), options.strippedExtensionUrls());
+        filterContained(resource.getContained());
+        return resource;
+    }
+
+    private void exportCql(Attachment content, String libraryName, File libraryFile, File cqlExportDirectory) {
+        checkNotNull(libraryName, "libraryName must be provided");
+        if (content.getData() == null || cqlExportDirectory == null) {
+            return;
+        }
+
+        // CQL content is encoded as base64, so we need to decode it
+        // to get back to the original CQL.
+        var base64 = content.getDataElement().getValueAsString();
+        var cql = new String(java.util.Base64.getDecoder().decode(base64));
+
+        var cqlFileName = libraryName + ".cql";
+        var cqlFile = cqlExportDirectory.toPath().resolve(cqlFileName).toFile();
+
+        content.setUrl(libraryFile.toPath().relativize(cqlFile.toPath()).toString());
+        content.setDataElement(null);
+        writeContent(cqlFile, cql);
+    }
+
+    private void exportCql(List<Attachment> content, String libraryName, File libraryOutputFile, File cqlExportDirectory) {
+        for (Attachment attachment : content) {
+            if (ContentStripperOptions.CQL_CONTENT_TYPE.equals(attachment.getContentType())) {
+               exportCql(attachment, libraryName, libraryOutputFile, cqlExportDirectory);
+            }
+        }
+    }
+}

tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripper.java

@@ -0,0 +1,8 @@
+package org.opencds.cqf.tooling.operations.stripcontent;
+
+import java.io.File;
+
+// Intentionally package-private. This is a package-internal API for ContentStripper
+interface ContentStripper {
+    void stripFile(File inputPath, File outputPath, ContentStripperOptions options);
+}

tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperDstu3.java

@@ -0,0 +1,11 @@
+package org.opencds.cqf.tooling.operations.stripcontent;
+
+import org.hl7.fhir.dstu3.model.Resource;
+import ca.uhn.fhir.context.FhirContext;
+
+class ContentStripperDstu3 extends BaseContentStripper<Resource> {
+    @Override
+    protected FhirContext context() {
+        return FhirContext.forDstu3Cached();
+    }
+}

tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperOptions.java

@@ -0,0 +1,62 @@
+package org.opencds.cqf.tooling.operations.stripcontent;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+// Intentionally package-private. This is a package-internal API for ContentStripper
+class ContentStripperOptions {
+    static final String CQL_CONTENT_TYPE = "text/cql";
+    static final String ELM_JSON_CONTENT_TYPE =  "application/elm+json";
+    static final String ELM_XML_CONTENT_TYPE = "application/elm+xml";
+
+    static final Set<String> DEFAULT_STRIPPED_CONTENT_TYPES = new HashSet<>(
+            Arrays.asList(ELM_JSON_CONTENT_TYPE, ELM_XML_CONTENT_TYPE));
+
+    static final Set<String> DEFAULT_STRIPPED_EXTENSION_URLS = new HashSet<>(
+            Arrays.asList("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-parameter",
+                    "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-dataRequirement",
+                    "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-logicDefinition",
+                    "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem",
+                    "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode",
+                    "http://hl7.org/fhir/StructureDefinition/cqf-cqlOptions"));
+
+    private ContentStripperOptions() {
+        // Intentionally empty, forces use of the static factory
+    }
+
+    public static ContentStripperOptions defaultOptions() {
+        return new ContentStripperOptions();
+    }
+
+    private File cqlExportDirectory;
+    public File cqlExportDirectory() {
+        return cqlExportDirectory;
+    }
+    public ContentStripperOptions cqlExportDirectory(File cqlExportDirectory) {
+        this.cqlExportDirectory = cqlExportDirectory;
+        return this;
+    }
+
+    private Set<String> strippedContentTypes = DEFAULT_STRIPPED_CONTENT_TYPES;
+    public Set<String> strippedContentTypes() {
+        return this.strippedContentTypes;
+    }
+
+    public ContentStripperOptions strippedContentTypes(Set<String> strippedContentTypes) {
+        this.strippedContentTypes = strippedContentTypes;
+        return this;
+    }
+
+    private Set<String> strippedExtensionUrls = DEFAULT_STRIPPED_EXTENSION_URLS;
+    public Set<String> strippedExtensionUrls() {
+        return this.strippedExtensionUrls;
+    }
+
+    public ContentStripperOptions strippedExtensionUrls(Set<String> strippedExtensionUrls) {
+        this.strippedExtensionUrls = strippedExtensionUrls;
+        return this;
+    }
+
+}

tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperR4.java

@@ -0,0 +1,11 @@
+package org.opencds.cqf.tooling.operations.stripcontent;
+
+import org.hl7.fhir.r4.model.Resource;
+import ca.uhn.fhir.context.FhirContext;
+
+class ContentStripperR4 extends BaseContentStripper<Resource> {
+    @Override
+    protected FhirContext context() {
+        return FhirContext.forR4Cached();
+    }
+}

tooling/src/main/java/org/opencds/cqf/tooling/operations/stripcontent/ContentStripperR5.java

@@ -0,0 +1,12 @@
+package org.opencds.cqf.tooling.operations.stripcontent;
+
+import org.hl7.fhir.r5.model.Resource;
+
+import ca.uhn.fhir.context.FhirContext;
+
+class ContentStripperR5 extends BaseContentStripper<Resource> {
+    @Override
+    protected FhirContext context() {
+        return FhirContext.forR5Cached();
+    }
+}