Fix get bytes for -1 or chunked content

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ICD11Generator.java

@@ -1,6 +1,5 @@
 package org.hl7.fhir.convertors.misc;
 
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.Date;
 import java.util.HashSet;
@@ -395,7 +394,7 @@ public class ICD11Generator {
 
 
   private JsonObject fetchJson(String source) throws IOException {
-    HTTPResult res = ManagedWebAccess.builder().withHeader("API-Version", "v2").withHeader("Accept-Language", "en").get(source,"application/json");
+    HTTPResult res = ManagedWebAccess.accessor().withHeader("API-Version", "v2").withHeader("Accept-Language", "en").get(source,"application/json");
     res.checkThrowException();
     return JsonParser.parseObject(res.getContent());
   }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/VSACImporter.java

@@ -46,10 +46,10 @@ public class VSACImporter extends OIDBasedValueSetImporter {
 
   public static void main(String[] args) throws FHIRException, IOException, ParseException, URISyntaxException {
     VSACImporter self = new VSACImporter();
-    self.process(args[0], args[1], args[2], "true".equals(args[3]), "true".equals(args[4]));
+    self.process(args[0], args[1], "true".equals(args[2]), "true".equals(args[3]));
   }
 
-  private void process(String source, String dest, String apiKey, boolean onlyNew, boolean onlyActive) throws FHIRException, IOException, URISyntaxException {
+  private void process(String source, String dest, boolean onlyNew, boolean onlyActive) throws FHIRException, IOException, URISyntaxException {
     CSVReader csv = new CSVReader(ManagedFileAccess.inStream(source));
     csv.readHeaders();
     Map<String, String> errs = new HashMap<>();
@@ -121,6 +121,7 @@ public class VSACImporter extends OIDBasedValueSetImporter {
       oo.addIssue().setSeverity(IssueSeverity.ERROR).setCode(IssueType.EXCEPTION).setDiagnostics(errs.get(oid)).addLocation(oid);
     }
     new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "other", "OperationOutcome-vsac-errors.json")), oo);
+    System.out.println();
     System.out.println("Done. " + i + " ValueSets in "+Utilities.describeDuration(System.currentTimeMillis() - tt));
   }
 

org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/client/ClientUtils.java

@@ -81,17 +81,10 @@ public class ClientUtils {
 
   private static boolean debugging = false;
 
-/*
-  @Getter
-  @Setter
-  private HttpHost proxy;
-*/
   @Getter
   @Setter
   private int timeout = 5000;
 
-
-
   @Setter
   @Getter
   private ToolingClientLogger logger;
@@ -109,8 +102,8 @@ public class ClientUtils {
   private String contentLanguage;
   private final TimeUnit timeoutUnit = TimeUnit.MILLISECONDS;
 
-  protected ManagedFhirWebAccessor getManagedWebAccessBuilder() {
+  protected ManagedFhirWebAccessor getManagedWebAccessor() {
-    return ManagedWebAccess.fhirBuilder().withRetries(retryCount).withTimeout(timeout, timeoutUnit).withLogger(logger);
+    return ManagedWebAccess.fhirAccessor().withRetries(retryCount).withTimeout(timeout, timeoutUnit).withLogger(logger);
   }
 
   public <T extends Resource> ResourceRequest<T> issueOptionsRequest(URI optionsUri, String resourceFormat,
@@ -119,9 +112,6 @@ public class ClientUtils {
       throw new FHIRException("Network Access is prohibited in this context");
     }
 
-    /*FIXME delete this after refactor
-    HttpOptions options = new HttpOptions(optionsUri);
-     */
     HTTPRequest httpRequest = new HTTPRequest()
       .withMethod(HTTPRequest.HttpMethod.OPTIONS)
       .withUrl(optionsUri.toString());
@@ -133,9 +123,7 @@ public class ClientUtils {
     if (FhirSettings.isProhibitNetworkAccess()) {
       throw new FHIRException("Network Access is prohibited in this context");
     }
-    /*FIXME delete this after refactor
+
-    HttpGet httpget = new HttpGet(resourceUri);
-     */
     HTTPRequest httpRequest = new HTTPRequest()
       .withMethod(HTTPRequest.HttpMethod.GET)
       .withUrl(resourceUri.toString());
@@ -159,9 +147,7 @@ public class ClientUtils {
     if (FhirSettings.isProhibitNetworkAccess()) {
       throw new FHIRException("Network Access is prohibited in this context");
     }
-    /*FIXME delete this after refactor
+
-    HttpPut httpPut = new HttpPut(resourceUri);
-     */
     HTTPRequest httpRequest = new HTTPRequest()
       .withMethod(HTTPRequest.HttpMethod.PUT)
       .withUrl(resourceUri.toString())
@@ -174,9 +160,7 @@ public class ClientUtils {
     if (FhirSettings.isProhibitNetworkAccess()) {
       throw new FHIRException("Network Access is prohibited in this context");
     }
-    /*FIXME delete this after refactor
+
-    HttpPost httpPost = new HttpPost(resourceUri);
-     */
     HTTPRequest httpRequest = new HTTPRequest()
       .withMethod(HTTPRequest.HttpMethod.POST)
       .withUrl(resourceUri.toString())
@@ -193,9 +177,7 @@ public class ClientUtils {
     if (FhirSettings.isProhibitNetworkAccess()) {
       throw new FHIRException("Network Access is prohibited in this context");
     }
-    /*FIXME delete this after refactor
+
-    HttpGet httpget = new HttpGet(resourceUri);
-     */
     HTTPRequest httpRequest = new HTTPRequest()
       .withMethod(HTTPRequest.HttpMethod.GET)
       .withUrl(resourceUri.toString());
@@ -208,9 +190,7 @@ public class ClientUtils {
     if (FhirSettings.isProhibitNetworkAccess()) {
       throw new FHIRException("Network Access is prohibited in this context");
     }
-    /*FIXME delete this after refactor
+
-    HttpPost httpPost = new HttpPost(resourceUri);
-     */
     HTTPRequest httpRequest = new HTTPRequest()
       .withMethod(HTTPRequest.HttpMethod.POST)
       .withUrl(resourceUri.toString())
@@ -224,9 +204,7 @@ public class ClientUtils {
     if (FhirSettings.isProhibitNetworkAccess()) {
       throw new FHIRException("Network Access is prohibited in this context");
     }
-    /*FIXME delete this after refactor
+
-    HttpDelete deleteRequest = new HttpDelete(resourceUri);
-     */
     HTTPRequest request = new HTTPRequest()
       .withMethod(HTTPRequest.HttpMethod.DELETE)
       .withUrl(resourceUri.toString());
@@ -248,8 +226,12 @@ public class ClientUtils {
     return issueResourceRequest(resourceFormat, request, Collections.emptyList(), timeoutLoading);
   }
   /**
-   * @param resourceFormat
+   * Issue a resource request.
-   * @return
+   * @param resourceFormat the expected FHIR format
+   * @param request the request to be sent
+   * @param headers any additional headers to add
+   *
+   * @return A ResourceRequest object containing the requested resource
    */
   protected <T extends Resource> ResourceRequest<T> issueResourceRequest(String resourceFormat, HTTPRequest request,
                                                                          @Nonnull Iterable<HTTPHeader> headers, int timeoutLoading) {
@@ -259,7 +241,7 @@ public class ClientUtils {
     Iterable<HTTPHeader> configuredHeaders = getFhirHeaders(request, resourceFormat, headers);
     try {
 
-      HTTPResult response = getManagedWebAccessBuilder().httpCall(request.withHeaders(configuredHeaders));
+      HTTPResult response = getManagedWebAccessor().httpCall(request.withHeaders(configuredHeaders));
       T resource = unmarshalReference(response, resourceFormat);
       return new ResourceRequest<T>(resource, response.getCode(), getLocationHeader(response.getHeaders()));
     } catch (IOException ioe) {
@@ -269,18 +251,21 @@ public class ClientUtils {
   }
 
   /**
-   * Method adds required request headers. TODO handle JSON request as well.
+   * Get required headers for FHIR requests.
    * 
-   * @param format
+   * @param httpRequest the request
+   * @param format the expected format
    */
   protected Iterable<HTTPHeader> getFhirHeaders(HTTPRequest httpRequest, String format) {
     return getFhirHeaders(httpRequest, format, null);
   }
 
   /**
-   * Method adds required request headers. TODO handle JSON request as well.
+   * Get required headers for FHIR requests.
    * 
-   * @param format
+   * @param httpRequest the request
+   * @param format the expected format
+   * @param headers any additional headers to add
    */
   protected Iterable<HTTPHeader> getFhirHeaders(HTTPRequest httpRequest, String format, Iterable<HTTPHeader> headers) {
     List<HTTPHeader> configuredHeaders = new ArrayList<>();
@@ -303,7 +288,6 @@ public class ClientUtils {
     return configuredHeaders;
   }
 
-  //FIXME this shouldn't set Content-Type header for GET requests
   protected static List<HTTPHeader> getResourceFormatHeaders(HTTPRequest httpRequest, String format) {
     List<HTTPHeader> headers = new ArrayList<>();
     headers.add(new HTTPHeader("Accept", format));
@@ -328,7 +312,7 @@ public class ClientUtils {
     HTTPResult response = null;
     try {
 
-      response = getManagedWebAccessBuilder().httpCall(request);
+      response = getManagedWebAccessor().httpCall(request);
       return response;
     } catch (IOException ioe) {
       if (ClientUtils.debugging) {
@@ -341,8 +325,8 @@ public class ClientUtils {
   /**
    * Unmarshals a resource from the response stream.
    * 
-   * @param response
+   * @param response The response from the server
-   * @return
+   * @return The unmarshalled resource
    */
   @SuppressWarnings("unchecked")
   protected <T extends Resource> T unmarshalReference(HTTPResult response, String format) {
@@ -369,8 +353,8 @@ public class ClientUtils {
   /**
    * Unmarshals Bundle from response stream.
    * 
-   * @param response
+   * @param response The response from the server
-   * @return
+   * @return The unmarshalled Bundle
    */
   protected Bundle unmarshalFeed(HTTPResult response, String format) {
     Bundle feed = null;
@@ -531,9 +515,6 @@ public class ClientUtils {
 
   public Bundle issuePostFeedRequest(URI resourceUri, Map<String, String> parameters, String resourceName,
       Resource resource, String resourceFormat) throws IOException {
-    /*FIXME delete this after refactor
-    HttpPost httpRequest = new HttpPost(resourceUri);
-     */
 
     HTTPRequest httpRequest = new HTTPRequest()
       .withMethod(HTTPRequest.HttpMethod.POST)
@@ -542,8 +523,9 @@ public class ClientUtils {
   List<HTTPHeader> headers = new ArrayList<>();
     headers.add(new HTTPHeader("Content-Type", "multipart/form-data; boundary=" + boundary));
     headers.add(new HTTPHeader("Accept", resourceFormat));
-    this.getFhirHeaders(httpRequest, null);
+    this.getFhirHeaders(httpRequest, null).forEach(headers::add);
-    HTTPResult response = sendPayload(httpRequest.withBody(encodeFormSubmission(parameters, resourceName, resource, boundary)));
+
+    HTTPResult response = sendPayload(httpRequest.withBody(encodeFormSubmission(parameters, resourceName, resource, boundary)).withHeaders(headers));
     return unmarshalFeed(response, resourceFormat);
   }
 
@@ -574,16 +556,16 @@ public class ClientUtils {
   }
 
   /**
-   * Method posts request payload
+   * Send an HTTP Post/Put Payload
    * 
-   * @param request
+   * @param request The request to be sent
-   * @return
+   * @return The response from the server
    */
   protected HTTPResult sendPayload(HTTPRequest request) {
     HTTPResult response = null;
     try {
 
-      response = getManagedWebAccessBuilder().httpCall(request);
+      response = getManagedWebAccessor().httpCall(request);
     } catch (IOException ioe) {
       throw new EFhirClientException("Error sending HTTP Post/Put Payload: " + ioe.getMessage(), ioe);
     }

org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/client/FHIRToolingClient.java

@@ -402,10 +402,13 @@ public class FHIRToolingClient extends FHIRBaseToolingClient {
 
 
   /**
-   * Helper method to prevent nesting of previously thrown EFhirClientExceptions
+   * Helper method to prevent nesting of previously thrown EFhirClientExceptions. If the e param is an instance of
-   * 
+   * EFhirClientException, it will be rethrown. Otherwise, a new EFhirClientException will be thrown with e as the
-   * @param e
+   * cause.
-   * @throws EFhirClientException
+   *
+   * @param message The EFhirClientException message.
+   * @param e The exception.
+   * @throws EFhirClientException representing the exception.
    */
   protected void handleException(String message, Exception e) throws EFhirClientException {
     if (e instanceof EFhirClientException) {
@@ -419,8 +422,8 @@ public class FHIRToolingClient extends FHIRBaseToolingClient {
    * Helper method to determine whether desired resource representation is Json or
    * XML.
    * 
-   * @param format
+   * @param format the format to check
-   * @return
+   * @return true if JSON, false if XML
    */
   protected boolean isJson(String format) {
     boolean isJson = false;

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/client/FHIRToolingClient.java

@@ -375,10 +375,14 @@ public class FHIRToolingClient extends FHIRBaseToolingClient {
   }
 
   /**
-   * Helper method to prevent nesting of previously thrown EFhirClientExceptions
+   * Helper method to prevent nesting of previously thrown EFhirClientExceptions. If the e param is an instance of
+   * EFhirClientException, it will be rethrown. Otherwise, a new EFhirClientException will be thrown with e as the
+   * cause.
    *
-   * @param e
+
-   * @throws EFhirClientException
+   * @param message The EFhirClientException message.
+   * @param e The exception
+   * @throws EFhirClientException EFhirClientException representing the exception.
    */
   protected void handleException(String message, Exception e) throws EFhirClientException {
     if (e instanceof EFhirClientException) {
@@ -389,11 +393,11 @@ public class FHIRToolingClient extends FHIRBaseToolingClient {
   }
 
   /**
-   * Helper method to determine whether desired resource representation
+   * Helper method to determine whether desired resource representation is Json or
-   * is Json or XML.
+   * XML.
    *
-   * @param format
+   * @param format the format
-   * @return
+   * @return true if the format is JSON, false otherwise
    */
   protected boolean isJson(String format) {
     boolean isJson = false;

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/client/network/Client.java

@@ -60,11 +60,7 @@ public class Client {
                                                                      String resourceFormat,
                                                                      String message,
                                                                      long timeout) throws IOException {
-    /*FIXME delete after refactor
+
-    Request.Builder request = new Request.Builder()
-      .method("OPTIONS", null)
-      .url(optionsUri.toURL());
-     */
     HTTPRequest request = new HTTPRequest()
       .withUrl(optionsUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.OPTIONS);
@@ -77,10 +73,6 @@ public class Client {
                                                                          Iterable<HTTPHeader> headers,
                                                                          String message,
                                                                          long timeout) throws IOException {
-    /*FIXME delete after refactor
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL());
-    */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.GET);
@@ -105,12 +97,7 @@ public class Client {
                                                                  String message,
                                                                  long timeout) throws IOException {
     if (payload == null) throw new EFhirClientException("PUT requests require a non-null payload");
-    /*FIXME delete after refactor
+
-    RequestBody body = RequestBody.create(payload);
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL())
-      .put(body);
-    */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.PUT)
@@ -133,12 +120,7 @@ public class Client {
                                                                   String message,
                                                                   long timeout) throws IOException {
     if (payload == null) throw new EFhirClientException("POST requests require a non-null payload");
-    /*FIXME delete after refactor
+
-    RequestBody body = RequestBody.create(MediaType.parse(resourceFormat + ";charset=" + DEFAULT_CHARSET), payload);
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL())
-      .post(body);
-     */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.POST)
@@ -147,11 +129,6 @@ public class Client {
   }
 
   public boolean issueDeleteRequest(URI resourceUri) throws IOException {
-    /*FIXME delete after refactor
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL())
-      .delete();
-     */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.DELETE);
@@ -159,10 +136,6 @@ public class Client {
   }
 
   public Bundle issueGetFeedRequest(URI resourceUri, String resourceFormat) throws IOException {
-    /*FIXME delete after refactor
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL());
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.GET);
@@ -176,12 +149,7 @@ public class Client {
                                      String resourceFormat) throws IOException {
     String boundary = "----WebKitFormBoundarykbMUo6H8QaUnYtRy";
     byte[] payload = ByteUtils.encodeFormSubmission(parameters, resourceName, resource, boundary);
-    /*FIXME delete after refactor
+
-    RequestBody body = RequestBody.create(MediaType.parse(resourceFormat + ";charset=" + DEFAULT_CHARSET), payload);
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL())
-      .post(body);
-    */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.POST)
@@ -196,12 +164,7 @@ public class Client {
                                  String message,
                                  int timeout) throws IOException {
     if (payload == null) throw new EFhirClientException("POST requests require a non-null payload");
-    /*FIXME delete after refactor
+
-    RequestBody body = RequestBody.create(MediaType.parse(resourceFormat + ";charset=" + DEFAULT_CHARSET), payload);
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL())
-      .post(body);
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.POST)

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/client/network/FhirRequestBuilder.java

@@ -56,9 +56,9 @@ public class FhirRequestBuilder {
 
   /**
    * Adds necessary default headers, formatting headers, and any passed in {@link HTTPHeader}s to the passed in
-   * {@link okhttp3.Request.Builder}
+   * {@link HTTPRequest}
    *
-   * @param request {@link okhttp3.Request.Builder} to add headers to.
+   * @param request {@link HTTPRequest} to add headers to.
    * @param format  Expected {@link Resource} format.
    * @param headers Any additional {@link HTTPHeader}s to add to the request.
    */
@@ -114,8 +114,8 @@ public class FhirRequestBuilder {
     return HTTPHeaderUtil.getSingleHeader(headers, CONTENT_LOCATION_HEADER);
   }
 
-  protected ManagedFhirWebAccessor getManagedWebAccessBuilder() {
+  protected ManagedFhirWebAccessor getManagedWebAccessor() {
-    return ManagedWebAccess.fhirBuilder().withRetries(retryCount).withTimeout(timeout, timeoutUnit).withLogger(logger);
+    return ManagedWebAccess.fhirAccessor().withRetries(retryCount).withTimeout(timeout, timeoutUnit).withLogger(logger);
   }
 
   public FhirRequestBuilder withResourceFormat(String resourceFormat) {
@@ -151,14 +151,14 @@ public class FhirRequestBuilder {
 
   public <T extends Resource> ResourceRequest<T> execute() throws IOException {
     HTTPRequest requestWithHeaders = formatHeaders(httpRequest, resourceFormat, headers);
-    HTTPResult response = getManagedWebAccessBuilder().httpCall(requestWithHeaders);
+    HTTPResult response = getManagedWebAccessor().httpCall(requestWithHeaders);
     T resource = unmarshalReference(response, resourceFormat);
     return new ResourceRequest<T>(resource, response.getCode(), getLocationHeader(response.getHeaders()));
   }
 
   public Bundle executeAsBatch() throws IOException {
     HTTPRequest requestWithHeaders = formatHeaders(httpRequest, resourceFormat, null);
-    HTTPResult response = getManagedWebAccessBuilder().httpCall(requestWithHeaders);
+    HTTPResult response = getManagedWebAccessor().httpCall(requestWithHeaders);
     return unmarshalFeed(response, resourceFormat);
   }
 
@@ -228,7 +228,7 @@ public class FhirRequestBuilder {
   /**
    * Returns the appropriate parser based on the format type passed in. Defaults to XML parser if a blank format is
    * provided...because reasons.
-   * <p>
+   * <p/>
    * Currently supports only "json" and "xml" formats.
    *
    * @param format One of "json" or "xml".

org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/utils/client/network/FhirRequestBuilderTests.java

@@ -16,7 +16,6 @@ public class FhirRequestBuilderTests {
   @Test
   @DisplayName("Test resource format headers are added correctly (GET).")
   void addResourceFormatHeadersGET() {
-    //FIXME tested here. Should get list of HTTPHeader.
     String testFormat = "yaml";
     HTTPRequest request = new HTTPRequest().withUrl("http://www.google.com").withMethod(HTTPRequest.HttpMethod.GET);
 
@@ -33,7 +32,6 @@ public class FhirRequestBuilderTests {
   @Test
   @DisplayName("Test resource format headers are added correctly (POST).")
   void addResourceFormatHeadersPOST() {
-    //FIXME tested here. Should get list of HTTPHeader.
     String testFormat = "yaml";
     HTTPRequest request = new HTTPRequest().withUrl("http://www.google.com").withMethod(HTTPRequest.HttpMethod.POST);
 

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/client/FHIRToolingClient.java

@@ -356,10 +356,14 @@ public class FHIRToolingClient extends FHIRBaseToolingClient {
   }
 
   /**
-   * Helper method to prevent nesting of previously thrown EFhirClientExceptions
+   * Helper method to prevent nesting of previously thrown EFhirClientExceptions. If the e param is an instance of
+   * EFhirClientException, it will be rethrown. Otherwise, a new EFhirClientException will be thrown with e as the
+   * cause.
    *
-   * @param e
+   * @param code The EFhirClientException code.
-   * @throws EFhirClientException
+   * @param message The EFhirClientException message.
+   * @param e The exception.
+   * @throws EFhirClientException representing the exception.
    */
   protected void handleException(int code, String message, Exception e) throws EFhirClientException {
     if (e instanceof EFhirClientException) {
@@ -370,11 +374,11 @@ public class FHIRToolingClient extends FHIRBaseToolingClient {
   }
 
   /**
-   * Helper method to determine whether desired resource representation is Json or
+   * Helper method to determine whether desired resource representation
-   * XML.
+   * is Json or XML.
    *
-   * @param format
+   * @param format The format
-   * @return
+   * @return true if the format is JSON, false otherwise
    */
   protected boolean isJson(String format) {
     boolean isJson = false;
@@ -539,7 +543,6 @@ public class FHIRToolingClient extends FHIRBaseToolingClient {
     headers.forEach(this.headers::add);
   }
 
-  //FIXME should be in ManagedWebAccess?
   private Iterable<HTTPHeader> generateHeaders(boolean hasBody) {
     // Add any other headers
     List<HTTPHeader> headers = new ArrayList<>(this.headers);

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/client/network/Client.java

@@ -31,9 +31,7 @@ public class Client {
 
   public <T extends Resource> ResourceRequest<T> issueOptionsRequest(URI optionsUri, String resourceFormat,
       String message, long timeout) throws IOException {
-    /*FIXME delete once refactor is done
+
-    Request.Builder request = new Request.Builder().method("OPTIONS", null).url(optionsUri.toURL());
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(optionsUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.OPTIONS);
@@ -42,10 +40,6 @@ public class Client {
 
   public <T extends Resource> ResourceRequest<T> issueGetResourceRequest(URI resourceUri, String resourceFormat,
       Iterable<HTTPHeader> headers, String message, long timeout) throws IOException {
-
-    /*FIXME delete once refactor is done
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL());
-    */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.GET);
@@ -61,10 +55,7 @@ public class Client {
       Iterable<HTTPHeader> headers, String message, long timeout) throws IOException {
     if (payload == null)
       throw new EFhirClientException("PUT requests require a non-null payload");
-   /*FIXME delete once refactor is done
+
-    RequestBody body = RequestBody.create(payload);
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL()).put(body);
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.PUT)
@@ -83,10 +74,7 @@ public class Client {
       String resourceFormat, Iterable<HTTPHeader> headers, String message, long timeout) throws IOException {
     if (payload == null)
       throw new EFhirClientException("POST requests require a non-null payload");
-    /*FIXME delete once refactor is done
+
-    RequestBody body = RequestBody.create(MediaType.parse(resourceFormat + ";charset=" + DEFAULT_CHARSET), payload);
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL()).post(body);
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.POST)
@@ -97,9 +85,6 @@ public class Client {
   }
 
   public boolean issueDeleteRequest(URI resourceUri, int timeout) throws IOException {
-    /*FIXME delete once refactor is done
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL()).delete();
-     */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.DELETE);
@@ -108,9 +93,6 @@ public class Client {
   }
 
   public Bundle issueGetFeedRequest(URI resourceUri, String resourceFormat, int timeout) throws IOException {
-    /*FIXME delete once refactor is done
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL());
-     */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.GET);
@@ -123,11 +105,6 @@ public class Client {
     String boundary = "----WebKitFormBoundarykbMUo6H8QaUnYtRy";
     byte[] payload = ByteUtils.encodeFormSubmission(parameters, resourceName, resource, boundary);
 
-    /*FIXME delete once refactor is done
-    RequestBody body = RequestBody.create(MediaType.parse(resourceFormat + ";charset=" + DEFAULT_CHARSET), payload);
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL()).post(body);
-    */
-
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.POST)
@@ -141,10 +118,7 @@ public class Client {
       throws IOException {
     if (payload == null)
       throw new EFhirClientException("POST requests require a non-null payload");
-    /*FIXME delete once refactor is done
+
-    RequestBody body = RequestBody.create(MediaType.parse(resourceFormat + ";charset=" + DEFAULT_CHARSET), payload);
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL()).post(body);
-     */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.POST)

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/client/network/FhirRequestBuilder.java

@@ -28,9 +28,7 @@ public class FhirRequestBuilder {
   protected static final String LOCATION_HEADER = "location";
   protected static final String CONTENT_LOCATION_HEADER = "content-location";
   protected static final String DEFAULT_CHARSET = "UTF-8";
-  /**
+
-   * The singleton instance of the HttpClient, used for all requests.
-   */
   private final HTTPRequest httpRequest;
   private String resourceFormat = null;
   private Iterable<HTTPHeader> headers = null;
@@ -62,9 +60,9 @@ public class FhirRequestBuilder {
 
   /**
    * Adds necessary default headers, formatting headers, and any passed in
-   * {@link HTTPHeader}s to the passed in {@link okhttp3.Request.Builder}
+   * {@link HTTPHeader}s to the passed in {@link HTTPRequest}
    *
-   * @param request {@link okhttp3.Request.Builder} to add headers to.
+   * @param request {@link HTTPRequest} to add headers to.
    * @param format  Expected {@link Resource} format.
    * @param headers Any additional {@link HTTPHeader}s to add to the request.
    */
@@ -122,8 +120,8 @@ public class FhirRequestBuilder {
     return HTTPHeaderUtil.getSingleHeader(headers, CONTENT_LOCATION_HEADER);
   }
 
-  protected ManagedFhirWebAccessor getManagedWebAccessBuilder() {
+  protected ManagedFhirWebAccessor getManagedWebAccessor() {
-    return ManagedWebAccess.fhirBuilder().withRetries(retryCount).withTimeout(timeout, timeoutUnit).withLogger(logger);
+    return ManagedWebAccess.fhirAccessor().withRetries(retryCount).withTimeout(timeout, timeoutUnit).withLogger(logger);
   }
 
   public FhirRequestBuilder withResourceFormat(String resourceFormat) {
@@ -160,7 +158,7 @@ public class FhirRequestBuilder {
 
   public <T extends Resource> ResourceRequest<T> execute() throws IOException {
     HTTPRequest requestWithHeaders = formatHeaders(httpRequest, resourceFormat, headers);
-    HTTPResult response = getManagedWebAccessBuilder().httpCall(requestWithHeaders);
+    HTTPResult response = getManagedWebAccessor().httpCall(requestWithHeaders);
 
     T resource = unmarshalReference(response, resourceFormat, null);
     return new ResourceRequest<T>(resource, response.getCode(), getLocationHeader(response.getHeaders()));
@@ -168,7 +166,7 @@ public class FhirRequestBuilder {
 
   public Bundle executeAsBatch() throws IOException {
     HTTPRequest requestWithHeaders = formatHeaders(httpRequest, resourceFormat, null);
-    HTTPResult response = getManagedWebAccessBuilder().httpCall(requestWithHeaders);
+    HTTPResult response = getManagedWebAccessor().httpCall(requestWithHeaders);
     return unmarshalFeed(response, resourceFormat);
   }
 
@@ -269,7 +267,7 @@ public class FhirRequestBuilder {
   /**
    * Returns the appropriate parser based on the format type passed in. Defaults
    * to XML parser if a blank format is provided...because reasons.
-   * <p>
+   * <p/>
    * Currently supports only "json" and "xml" formats.
    *
    * @param format One of "json" or "xml".

org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/utils/client/network/FhirRequestBuilderTest.java

@@ -33,7 +33,6 @@ public class FhirRequestBuilderTest {
   @Test
   @DisplayName("Test resource format headers are added correctly (POST).")
   void addResourceFormatHeadersPOST() {
-    //FIXME tested here. Should get list of HTTPHeader.
     String testFormat = "yaml";
     HTTPRequest request = new HTTPRequest().withUrl("http://www.google.com").withMethod(HTTPRequest.HttpMethod.POST);
 

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/terminologies/TerminologyCacheManager.java

@@ -1,22 +1,14 @@
 package org.hl7.fhir.r4b.terminologies;
 
-import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
-import java.io.DataOutputStream;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.InputStreamReader;
 import java.io.OutputStream;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.Base64;
 import java.util.Date;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
@@ -156,7 +148,7 @@ public class TerminologyCacheManager {
     String url = "https://tx.fhir.org/post/tx-cache/" + ghOrg + "/" + ghRepo + "/" + ghBranch + ".zip";
     System.out.println("Sending tx-cache to " + url + " (" + Utilities.describeSize(bs.toByteArray().length) + ")");
 
-    HTTPResult res = ManagedWebAccess.builder()
+    HTTPResult res = ManagedWebAccess.accessor()
      .withBasicAuth(token.substring(0, token.indexOf(':')), token.substring(token.indexOf(':') + 1))
      .put(url, bs.toByteArray(), null, "application/zip");
     if (res.getCode() >= 300) {

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/utils/client/FHIRToolingClient.java

@@ -362,10 +362,14 @@ public class FHIRToolingClient extends FHIRBaseToolingClient{
   }
 
   /**
-   * Helper method to prevent nesting of previously thrown EFhirClientExceptions
+   * Helper method to prevent nesting of previously thrown EFhirClientExceptions. If the e param is an instance of
+   * EFhirClientException, it will be rethrown. Otherwise, a new EFhirClientException will be thrown with e as the
+   * cause.
    *
-   * @param e
+
-   * @throws EFhirClientException
+   * @param message The EFhirClientException message.
+   * @param e The exception
+   * @throws EFhirClientException EFhirClientException representing the exception.
    */
   protected void handleException(String message, Exception e) throws EFhirClientException {
     if (e instanceof EFhirClientException) {
@@ -379,8 +383,8 @@ public class FHIRToolingClient extends FHIRBaseToolingClient{
    * Helper method to determine whether desired resource representation is Json or
    * XML.
    *
-   * @param format
+   * @param format the format
-   * @return
+   * @return true if the format is JSON, false otherwise
    */
   protected boolean isJson(String format) {
     boolean isJson = false;

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/utils/client/network/Client.java

@@ -35,9 +35,6 @@ public class Client {
 
   public <T extends Resource> ResourceRequest<T> issueOptionsRequest(URI optionsUri, String resourceFormat,
       String message, long timeout) throws IOException {
-    /*FIXME delete once refactor is done
-    Request.Builder request = new Request.Builder().method("OPTIONS", null).url(optionsUri.toURL());
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(optionsUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.OPTIONS);
@@ -46,9 +43,6 @@ public class Client {
 
   public <T extends Resource> ResourceRequest<T> issueGetResourceRequest(URI resourceUri, String resourceFormat,
       Iterable<HTTPHeader> headers, String message, long timeout) throws IOException {
-/*FIXME delete once refactor is done
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL());
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.GET);
@@ -64,10 +58,7 @@ public class Client {
       Iterable<HTTPHeader> headers, String message, long timeout) throws IOException {
     if (payload == null)
       throw new EFhirClientException("PUT requests require a non-null payload");
-/*FIXME delete once refactor is done
+
-    RequestBody body = RequestBody.create(payload);
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL()).put(body);
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.PUT)
@@ -87,10 +78,6 @@ public class Client {
     if (payload == null)
       throw new EFhirClientException("POST requests require a non-null payload");
 
-    /*FIXME delete once refactor is done
-    RequestBody body = RequestBody.create(MediaType.parse(resourceFormat + ";charset=" + DEFAULT_CHARSET), payload);
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL()).post(body);
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.POST)
@@ -101,9 +88,6 @@ public class Client {
   }
 
   public boolean issueDeleteRequest(URI resourceUri) throws IOException {
-   /*FIXME delete once refactor is done
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL()).delete();
-    */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.DELETE);
@@ -112,9 +96,6 @@ public class Client {
   }
 
   public Bundle issueGetFeedRequest(URI resourceUri, String resourceFormat) throws IOException {
-    /*FIXME delete once refactor is done
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL());
-    */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.GET);
@@ -125,10 +106,7 @@ public class Client {
       Resource resource, String resourceFormat) throws IOException {
     String boundary = "----WebKitFormBoundarykbMUo6H8QaUnYtRy";
     byte[] payload = ByteUtils.encodeFormSubmission(parameters, resourceName, resource, boundary);
-    /*FIXME delete once refactor is done
+
-    RequestBody body = RequestBody.create(MediaType.parse(resourceFormat + ";charset=" + DEFAULT_CHARSET), payload);
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL()).post(body);
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.POST)
@@ -141,10 +119,7 @@ public class Client {
       String message, int timeout) throws IOException {
     if (payload == null)
       throw new EFhirClientException("POST requests require a non-null payload");
-    /*FIXME delete once refactor is done
+
-    RequestBody body = RequestBody.create(MediaType.parse(resourceFormat + ";charset=" + DEFAULT_CHARSET), payload);
-    Request.Builder request = new Request.Builder().url(resourceUri.toURL()).post(body);
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.POST)

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/utils/client/network/FhirRequestBuilder.java

@@ -51,7 +51,6 @@ public class FhirRequestBuilder {
   private ToolingClientLogger logger = null;
   private String source;
 
-  //TODO this should be the only constructor. There should be no okHttp exposure.
   public FhirRequestBuilder(HTTPRequest httpRequest, String source) {
     this.source = source;
     this.httpRequest = httpRequest;
@@ -103,17 +102,13 @@ public class FhirRequestBuilder {
   }
 
   /**
-   * Extracts the 'location' header from the passes in {@link Headers}. If no
+   * Extracts the 'location' header from the passed in {@link HTTPHeader}s. If no
    * value for 'location' exists, the value for 'content-location' is returned. If
    * neither header exists, we return null.
    *
-   * @param headers {@link Headers} to evaluate
+   * @param headers {@link HTTPHeader}s to evaluate
    * @return {@link String} header value, or null if no location headers are set.
    */
-  /**
-   * Extracts the 'location' header from. If no value for 'location' exists, the
-   * value for 'content-location' is returned. If neither header exists, we return null.
-   */
   protected static String getLocationHeader(Iterable<HTTPHeader> headers) {
     String locationHeader = HTTPHeaderUtil.getSingleHeader(headers, LOCATION_HEADER);
 
@@ -123,8 +118,8 @@ public class FhirRequestBuilder {
     return HTTPHeaderUtil.getSingleHeader(headers, CONTENT_LOCATION_HEADER);
   }
 
-  protected ManagedFhirWebAccessor getManagedWebAccessBuilder() {
+  protected ManagedFhirWebAccessor getManagedWebAccessor() {
-    return ManagedWebAccess.fhirBuilder().withRetries(retryCount).withTimeout(timeout, timeoutUnit).withLogger(logger);
+    return ManagedWebAccess.fhirAccessor().withRetries(retryCount).withTimeout(timeout, timeoutUnit).withLogger(logger);
   }
 
   public FhirRequestBuilder withResourceFormat(String resourceFormat) {
@@ -160,14 +155,14 @@ public class FhirRequestBuilder {
 
   public <T extends Resource> ResourceRequest<T> execute() throws IOException {
     HTTPRequest requestWithHeaders = formatHeaders(httpRequest, resourceFormat, headers);
-    HTTPResult response = getManagedWebAccessBuilder().httpCall(requestWithHeaders);
+    HTTPResult response = getManagedWebAccessor().httpCall(requestWithHeaders);
     T resource = unmarshalReference(response, resourceFormat, null);
     return new ResourceRequest<T>(resource, response.getCode(), getLocationHeader(response.getHeaders()));
   }
 
   public Bundle executeAsBatch() throws IOException {
     HTTPRequest requestWithHeaders = formatHeaders(httpRequest, resourceFormat, null);
-    HTTPResult response = getManagedWebAccessBuilder().httpCall(requestWithHeaders);return unmarshalFeed(response, resourceFormat);
+    HTTPResult response = getManagedWebAccessor().httpCall(requestWithHeaders);return unmarshalFeed(response, resourceFormat);
   }
 
   /**

org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/utils/client/network/FhirRequestBuilderTest.java

@@ -33,7 +33,6 @@ class FhirRequestBuilderTest {
   @Test
   @DisplayName("Test resource format headers are added correctly (POST).")
   void addResourceFormatHeadersPOST() {
-    //FIXME tested here. Should get list of HTTPHeader.
     String testFormat = "yaml";
     HTTPRequest request = new HTTPRequest().withUrl("http://www.google.com").withMethod(HTTPRequest.HttpMethod.POST);
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/TerminologyCacheManager.java

@@ -1,22 +1,14 @@
 package org.hl7.fhir.r5.terminologies;
 
-import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
-import java.io.DataOutputStream;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.InputStreamReader;
 import java.io.OutputStream;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.Base64;
 import java.util.Date;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
@@ -156,7 +148,7 @@ public class TerminologyCacheManager {
     // post it to
     String url = "https://tx.fhir.org/post/tx-cache/"+ghOrg+"/"+ghRepo+"/"+ghBranch+".zip";
     System.out.println("Sending tx-cache to "+url+" ("+Utilities.describeSize(bs.toByteArray().length)+")");
-    HTTPResult res = ManagedWebAccess.builder()
+    HTTPResult res = ManagedWebAccess.accessor()
         .withBasicAuth(token.substring(0, token.indexOf(':')), token.substring(token.indexOf(':') + 1))
         .put(url, bs.toByteArray(), null, "application/zip");
     

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/TerminologyClientR5.java

@@ -80,7 +80,6 @@ public class TerminologyClientR5 implements ITerminologyClient {
 
   public TerminologyClientR5(String id, String address, String userAgent) throws URISyntaxException {
     this.client = new FHIRToolingClient(address, userAgent);
-    //FIXME set up FHIR Tooling Client to use ManagedWebAccess
     setClientHeaders(new ClientHeaders());
     this.id = id;
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/client/FHIRToolingClient.java

@@ -403,10 +403,14 @@ public class FHIRToolingClient extends FHIRBaseToolingClient {
   }
 
   /**
-   * Helper method to prevent nesting of previously thrown EFhirClientExceptions
+   * Helper method to prevent nesting of previously thrown EFhirClientExceptions. If the e param is an instance of
+   * EFhirClientException, it will be rethrown. Otherwise, a new EFhirClientException will be thrown with e as the
+   * cause.
    *
-   * @param e
+   * @param code The EFhirClientException code.
-   * @throws EFhirClientException
+   * @param message The EFhirClientException message.
+   * @param e The exception.
+   * @throws EFhirClientException representing the exception.
    */
   protected void handleException(int code, String message, Exception e) throws EFhirClientException {
     if (e instanceof EFhirClientException) {
@@ -420,8 +424,8 @@ public class FHIRToolingClient extends FHIRBaseToolingClient {
    * Helper method to determine whether desired resource representation
    * is Json or XML.
    *
-   * @param format
+   * @param format The format
-   * @return
+   * @return true if the format is JSON, false otherwise
    */
   protected boolean isJson(String format) {
     boolean isJson = false;
@@ -595,7 +599,6 @@ public class FHIRToolingClient extends FHIRBaseToolingClient {
     headers.forEach(this.headers::add);
   }
 
-  //FIXME should be in ManagedWebAccess?
   private Iterable<HTTPHeader> generateHeaders(boolean hasBody) {
     // Add any other headers
     List<HTTPHeader> headers = new ArrayList<>(this.headers);

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/client/network/Client.java

@@ -35,11 +35,6 @@ public class Client {
                                                                      String resourceFormat,
                                                                      String message,
                                                                      long timeout) throws IOException {
-    /*FIXME delete once refactor is done
-    Request.Builder request = new Request.Builder()
-      .method("OPTIONS", null)
-      .url(optionsUri.toURL());
-      */
     HTTPRequest request = new HTTPRequest()
       .withUrl(optionsUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.OPTIONS);
@@ -51,11 +46,6 @@ public class Client {
                                                                          Iterable<HTTPHeader> headers,
                                                                          String message,
                                                                          long timeout) throws IOException {
-    /*FIXME delete once refactor is done
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL());
-
-     */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.GET);
@@ -78,12 +68,7 @@ public class Client {
                                                                  String message,
                                                                  long timeout) throws IOException {
     if (payload == null) throw new EFhirClientException(0, "PUT requests require a non-null payload");
-   /*FIXME delete once refactor is done
+
-    RequestBody body = RequestBody.create(payload);
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL())
-      .put(body);
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.PUT)
@@ -108,12 +93,7 @@ public class Client {
                                                                   String message,
                                                                   long timeout) throws IOException {
     if (payload == null) throw new EFhirClientException(0, "POST requests require a non-null payload");
-    /*FIXME delete once refactor is done
+
-    RequestBody body = RequestBody.create(MediaType.parse(getContentTypeWithDefaultCharset(resourceFormat)), payload);
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL())
-      .post(body);
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.POST)
@@ -124,11 +104,6 @@ public class Client {
   }
 
   public boolean issueDeleteRequest(URI resourceUri) throws IOException {
-    /*FIXME delete once refactor is done
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL())
-      .delete();
-     */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.DELETE);
@@ -136,10 +111,6 @@ public class Client {
   }
 
   public Bundle issueGetFeedRequest(URI resourceUri, String resourceFormat) throws IOException {
-    /*FIXME delete once refactor is done
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL());
-    */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.GET);
@@ -153,12 +124,7 @@ public class Client {
                                      String resourceFormat) throws IOException {
     String boundary = "----WebKitFormBoundarykbMUo6H8QaUnYtRy";
     byte[] payload = ByteUtils.encodeFormSubmission(parameters, resourceName, resource, boundary);
-    /*FIXME delete once refactor is done
+
-    RequestBody body = RequestBody.create(MediaType.parse(getContentTypeWithDefaultCharset(resourceFormat)), payload);
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL())
-      .post(body);
-*/
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.POST)
@@ -174,12 +140,7 @@ public class Client {
                                  String message,
                                  int timeout) throws IOException {
     if (payload == null) throw new EFhirClientException(0, "POST requests require a non-null payload");
-    /*FIXME delete once refactor is done
+
-    RequestBody body = RequestBody.create(MediaType.parse(resourceFormat + ";charset=" + DEFAULT_CHARSET), payload);
-    Request.Builder request = new Request.Builder()
-      .url(resourceUri.toURL())
-      .post(body);
-    */
     HTTPRequest request = new HTTPRequest()
       .withUrl(resourceUri.toURL())
       .withMethod(HTTPRequest.HttpMethod.POST)

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/client/network/FhirRequestBuilder.java

@@ -29,11 +29,6 @@ public class FhirRequestBuilder {
   protected static final String LOCATION_HEADER = "location";
   protected static final String CONTENT_LOCATION_HEADER = "content-location";
 
-  /**
-   * The singleton instance of the HttpClient, used for all requests.
-   */
- // private static OkHttpClient okHttpClient;
-  //private final Request.Builder httpRequest;
   private final HTTPRequest httpRequest;
   private String resourceFormat = null;
   private Iterable<HTTPHeader> headers = null;
@@ -55,7 +50,6 @@ public class FhirRequestBuilder {
 
   private String source;
 
-  //TODO this should be the only constructor. There should be no okHttp exposure.
   public FhirRequestBuilder(HTTPRequest httpRequest, String source) {
     this.source = source;
     this.httpRequest = httpRequest;
@@ -78,13 +72,11 @@ public class FhirRequestBuilder {
     return request.withHeaders(allHeaders);
   }
 
-  /**
-
-
   /**
    * Adds necessary headers for the given resource format provided.
    *
    * @param httpRequest {@link HTTPRequest} to add default headers to.
+   * @param format     Expected {@link Resource} format.
    */
   protected static Iterable<HTTPHeader> getResourceFormatHeaders(HTTPRequest httpRequest, String format) {
     List<HTTPHeader> headers = new ArrayList<>();
@@ -113,8 +105,8 @@ public class FhirRequestBuilder {
         || issue.getSeverity() == OperationOutcome.IssueSeverity.FATAL));
   }
 
-  protected ManagedFhirWebAccessor getManagedWebAccessBuilder() {
+  protected ManagedFhirWebAccessor getManagedWebAccessor() {
-    return ManagedWebAccess.fhirBuilder().withRetries(retryCount).withTimeout(timeout, timeoutUnit).withLogger(logger);
+    return ManagedWebAccess.fhirAccessor().withRetries(retryCount).withTimeout(timeout, timeoutUnit).withLogger(logger);
   }
 
   public FhirRequestBuilder withResourceFormat(String resourceFormat) {
@@ -150,14 +142,14 @@ public class FhirRequestBuilder {
 
   public <T extends Resource> ResourceRequest<T> execute() throws IOException {
     HTTPRequest requestWithHeaders = formatHeaders(httpRequest, resourceFormat, headers);
-    HTTPResult response = getManagedWebAccessBuilder().httpCall(requestWithHeaders);//getHttpClient().newCall(httpRequest.build()).execute();
+    HTTPResult response = getManagedWebAccessor().httpCall(requestWithHeaders);//getHttpClient().newCall(httpRequest.build()).execute();
     T resource = unmarshalReference(response, resourceFormat, null);
     return new ResourceRequest<T>(resource, response.getCode(), getLocationHeader(response.getHeaders()));
   }
 
   public Bundle executeAsBatch() throws IOException {
     HTTPRequest requestWithHeaders = formatHeaders(httpRequest, resourceFormat, null);
-    HTTPResult response = getManagedWebAccessBuilder().httpCall(requestWithHeaders);
+    HTTPResult response = getManagedWebAccessor().httpCall(requestWithHeaders);
     return unmarshalFeed(response, resourceFormat);
   }
 
@@ -258,7 +250,7 @@ public class FhirRequestBuilder {
   /**
    * Returns the appropriate parser based on the format type passed in. Defaults to XML parser if a blank format is
    * provided...because reasons.
-   * <p>
+   * <p/>
    * Currently supports only "json" and "xml" formats.
    *
    * @param format One of "json" or "xml".
@@ -279,8 +271,10 @@ public class FhirRequestBuilder {
   }
 
   /**
-   * Extracts the 'location' header from. If no value for 'location' exists, the
+   * Extracts the 'location' header from the passed headers. If no value for 'location' exists, the
    * value for 'content-location' is returned. If neither header exists, we return null.
+   *
+   * @param headers Headers to search for 'location' or 'content-location'.
    */
   protected static String getLocationHeader(Iterable<HTTPHeader> headers) {
     String locationHeader = HTTPHeaderUtil.getSingleHeader(headers, LOCATION_HEADER);

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/utils/client/network/FhirRequestBuilderTest.java

@@ -18,7 +18,6 @@ class FhirRequestBuilderTest {
   @Test
   @DisplayName("Test resource format headers are added correctly (GET).")
   void addResourceFormatHeadersGET() {
-    //FIXME tested here. Should get list of HTTPHeader.
     String testFormat = "yaml";
     HTTPRequest request = new HTTPRequest().withUrl("http://www.google.com").withMethod(HTTPRequest.HttpMethod.GET);
 
@@ -35,7 +34,6 @@ class FhirRequestBuilderTest {
   @Test
   @DisplayName("Test resource format headers are added correctly (POST).")
   void addResourceFormatHeadersPOST() {
-    //FIXME tested here. Should get list of HTTPHeader.
     String testFormat = "yaml";
     HTTPRequest request = new HTTPRequest().withUrl("http://www.google.com").withMethod(HTTPRequest.HttpMethod.POST);
 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/http/ManagedFhirWebAccessor.java

@@ -126,10 +126,9 @@ public class ManagedFhirWebAccessor extends ManagedWebAccessorBase<ManagedFhirWe
         }
         OkHttpClient okHttpClient = getOkHttpClient();
         //TODO check and throw based on httpRequest:
-        // if (!ManagedWebAccess.inAllowedPaths(url)) {
+
-        //      throw new IOException("The pathname '"+url+"' cannot be accessed by policy");
+        if (!ManagedWebAccess.inAllowedPaths(httpRequestWithDirectHeaders.getUrl().toString())) {
-        // }
+              throw new IOException("The pathname '"+httpRequestWithDirectHeaders.getUrl().toString()+"' cannot be accessed by policy");}
-        //TODO add auth headers to httpRequest
         Response response = okHttpClient.newCall(requestBuilder.build()).execute();
         return getHTTPResult(response);
       case MANAGED:
@@ -144,7 +143,7 @@ public class ManagedFhirWebAccessor extends ManagedWebAccessorBase<ManagedFhirWe
   }
 
   private HTTPResult getHTTPResult(Response execute) throws IOException {
-    return new HTTPResult(execute.request().url().toString(), execute.code(), execute.message(), execute.header("Content-Type"), execute.body() != null && execute.body().contentLength() > 0 ? execute.body().bytes() : null, getHeadersFromResponse(execute));
+    return new HTTPResult(execute.request().url().toString(), execute.code(), execute.message(), execute.header("Content-Type"), execute.body() != null && execute.body().contentLength() != 0 ? execute.body().bytes() : null, getHeadersFromResponse(execute));
   }
 
   private Iterable<HTTPHeader> getHeadersFromResponse(Response response) {

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/http/ManagedWebAccess.java

@@ -68,6 +68,7 @@ public class ManagedWebAccess {
   }
 
   private static WebAccessPolicy accessPolicy = WebAccessPolicy.DIRECT; // for legacy reasons
+  //TODO get this from fhir settings
   private static List<String> allowedDomains = new ArrayList<>();
   @Getter
   private static IWebAccessor accessor;
@@ -103,32 +104,32 @@ public class ManagedWebAccess {
     ManagedWebAccess.userAgent = userAgent;
   }
 
-  public static ManagedWebAccessor builder() {
+  public static ManagedWebAccessor accessor() {
     return new ManagedWebAccessor(userAgent, serverAuthDetails);
   }
 
-  public static ManagedFhirWebAccessor fhirBuilder() {
+  public static ManagedFhirWebAccessor fhirAccessor() {
     return new ManagedFhirWebAccessor(userAgent, serverAuthDetails);
   }
 
   public static HTTPResult get(String url) throws IOException {
-    return builder().get(url);
+    return accessor().get(url);
   }
 
   public static HTTPResult get(String url, String accept) throws IOException {
-    return builder().get(url, accept);
+    return accessor().get(url, accept);
   }
 
   public static HTTPResult post(String url, byte[] content, String contentType, String accept) throws IOException {
-    return builder().post(url, content, contentType, accept);
+    return accessor().post(url, content, contentType, accept);
   }
 
   public static HTTPResult put(String url, byte[] content, String contentType, String accept) throws IOException {
-    return builder().put(url, content, contentType, accept);
+    return accessor().put(url, content, contentType, accept);
   }
 
   public static HTTPResult httpCall(HTTPRequest httpRequest) throws IOException {
-    return fhirBuilder().httpCall(httpRequest);
+    return fhirAccessor().httpCall(httpRequest);
   }
 
   public static void loadFromFHIRSettings() {

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/PackageClient.java

@@ -175,13 +175,13 @@ public class PackageClient {
   }
  
   private InputStream fetchUrl(String source, String accept) throws IOException {
-    ManagedWebAccessor client = ManagedWebAccess.builder();
+    ManagedWebAccessor webAccessor = ManagedWebAccess.accessor();
     if (server.getAuthenticationMode() == HTTPAuthenticationMode.TOKEN) {
-      client.withToken(server.getToken());
+      webAccessor.withToken(server.getToken());
     } else if (server.getAuthenticationMode() == HTTPAuthenticationMode.BASIC) {
-      client.withBasicAuth(server.getUsername(), server.getPassword());
+      webAccessor.withBasicAuth(server.getUsername(), server.getPassword());
     }
-    HTTPResult res = client.get(source, accept);
+    HTTPResult res = webAccessor.get(source, accept);
     res.checkThrowException();
     return new ByteArrayInputStream(res.getContent());
   }

org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/http/ManagedFhirWebAccessorTests.java

@@ -10,7 +10,6 @@ public class ManagedFhirWebAccessorTests {
   @Test
   @DisplayName("Test default headers are added correctly.")
   void addDefaultAgentHeader() {
-    // FIXME move to ManagedFhirWebAccessBuilder
     HTTPRequest request = new HTTPRequest().withUrl("http://www.google.com");
 
     ManagedFhirWebAccessor builder = new ManagedFhirWebAccessor(expectedUserAgent, null);
@@ -22,7 +21,6 @@ public class ManagedFhirWebAccessorTests {
   @Test
   @DisplayName("Test default headers are added correctly.")
   void addDefaultBasicHeader() {
-    // FIXME move to ManagedFhirWebAccessBuilder
     HTTPRequest request = new HTTPRequest().withUrl("http://www.google.com");
 
     ManagedFhirWebAccessor builder = new ManagedFhirWebAccessor(expectedUserAgent, null)

org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/http/ManagedWebAccessAuthTests.java

@@ -207,4 +207,10 @@ public void testTokenAuthFromSettings() throws IOException, InterruptedException
       null,
      null, DUMMY_API_KEY);
   }
+
+  @Test
+  public void verifyAllowedPaths() {
+    //TODO the allowed paths cannot be set for now, meaning all will be allowed.
+    ManagedWebAccess.inAllowedPaths("http://www.anywhere.com");
+  }
 }