Merge pull request #198 from cqframework/br-bundle-to-resources-opera…

…tion

Adding BundleToResources operation

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

@@ -0,0 +1,173 @@
+package org.opencds.cqf.tooling.operation;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.opencds.cqf.tooling.Operation;
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.List;
+
+public class BundleToResources extends Operation {
+
+    private String encoding; // -encoding (-e)
+    private String path; // -path (-p)
+    private String version; // -version (-v) Can be dstu2, stu3, or r4
+
+    private IBaseResource theResource;
+    private List<IBaseResource> theResources = new ArrayList<>();
+    private FhirContext context;
+
+    @Override
+    public void execute(String[] args) {
+        setOutputPath("src/main/resources/org/opencds/cqf/tooling/bundle/output"); // default
+
+        for (String arg : args) {
+            if (arg.equals("-BundleToResources")) continue;
+            String[] flagAndValue = arg.split("=");
+            if (flagAndValue.length < 2) {
+                throw new IllegalArgumentException("Invalid argument: " + arg);
+            }
+            String flag = flagAndValue[0];
+            String value = flagAndValue[1];
+
+            switch (flag.replace("-", "").toLowerCase()) {
+                case "encoding":
+                case "e":
+                    encoding = value.toLowerCase();
+                    break;
+                case "outputpath":
+                case "op":
+                    setOutputPath(value);
+                    break; // -outputpath (-op)
+                case "path":
+                case "p":
+                    path = value;
+                    break;
+                case "version": case "v":
+                    version = value;
+                    break;
+                default: throw new IllegalArgumentException("Unknown flag: " + flag);
+            }
+        }
+
+        if (path == null) {
+            throw new IllegalArgumentException("The path to a Bundle or directory of resources is required");
+        }
+
+        File file = new File(path);
+        File[] bundles = null;
+        if (file.isDirectory()) {
+            bundles = file.listFiles();
+        }
+        else {
+            bundles = new File[] { file };
+        }
+
+        if (encoding == null) {
+            encoding = "json";
+        }
+
+        if (version == null) {
+            context = FhirContext.forR4();
+        }
+        else {
+            switch (version.toLowerCase()) {
+                case "dstu2":
+                    context = FhirContext.forDstu2();
+                    break;
+                case "stu3":
+                    context = FhirContext.forDstu3();
+                    break;
+                case "r4":
+                    context = FhirContext.forR4();
+                    break;
+                default:
+                    throw new IllegalArgumentException("Unknown fhir version: " + version);
+            }
+        }
+
+        getResources(bundles);
+
+        if (context.getVersion().getVersion() == FhirVersionEnum.DSTU3) {
+            // foreach resource, if it's a bundle, output all the resources it contains
+            for (IBaseResource resource : theResources) {
+                if (resource instanceof org.hl7.fhir.dstu3.model.Bundle) {
+                    org.hl7.fhir.dstu3.model.Bundle bundle = (org.hl7.fhir.dstu3.model.Bundle)resource;
+                    for (org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
+                        if (entry.getResource() != null) {
+                            output(entry.getResource(), context);
+                        }
+                    }
+                }
+            }
+        }
+        else if (context.getVersion().getVersion() == FhirVersionEnum.R4) {
+            for (IBaseResource resource : theResources) {
+                if (resource instanceof org.hl7.fhir.r4.model.Bundle) {
+                    org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle)resource;
+                    for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) {
+                        if (entry.getResource() != null) {
+                            output(entry.getResource(), context);
+                        }
+                    }
+                }
+            }
+        }
+
+        // TODO: add DSTU2
+    }
+
+    private void getResources(File[] resources) {
+        for (File resource : resources) {
+
+            if(resource.isDirectory()) {
+                getResources(resource.listFiles());
+                continue;
+            }
+
+            if (resource.getPath().endsWith(".xml")) {
+                try {
+                    theResource = context.newXmlParser().parseResource(new FileReader(resource));
+                } catch (FileNotFoundException e) {
+                    e.printStackTrace();
+                    throw new RuntimeException(e.getMessage());
+                }
+                catch (Exception e) {
+                    continue;
+                }
+            }
+            else if (resource.getPath().endsWith(".json")) {
+                try {
+                    theResource = context.newJsonParser().parseResource(new FileReader(resource));
+                } catch (FileNotFoundException e) {
+                    e.printStackTrace();
+                    throw new RuntimeException(e.getMessage());
+                }
+                catch (Exception e) {
+                    continue;
+                }
+            }
+            else {
+                continue;
+            }
+            theResources.add(theResource);
+        }
+    }
+
+    // Output
+    public void output(IBaseResource resource, FhirContext context) {
+        try (FileOutputStream writer = new FileOutputStream(getOutputPath() + "/" + resource.getIdElement().getResourceType() + "-" + resource.getIdElement().getIdPart() + "." + encoding)) {
+            writer.write(
+                encoding.equals("json")
+                    ? context.newJsonParser().setPrettyPrint(true).encodeResourceToString(resource).getBytes()
+                    : context.newXmlParser().setPrettyPrint(true).encodeResourceToString(resource).getBytes()
+            );
+            writer.flush();
+        } catch (IOException e) {
+            e.printStackTrace();
+            throw new RuntimeException(e.getMessage());
+        }
+    }
+}