Add docs, better function names, and less logging

Author: kkoz

README.md

@@ -112,7 +112,7 @@ image region microservice server endpoint::
     ...
 
 
-    location ~ ^/(webclient|webgateway)/(render_(thumbnail_ngff|image|image_region|image_region_rdef|image_rdef|shape_mask)|get_thumbnails_ngff|histogram_json)/ {
+    location ~ ^/(webclient|webgateway)/(render_(thumbnail_ngff|image|image_region|image_region_rdef|image_rdef|shape_mask)|get_thumbnails_ngff|histogram_json|annotation)/ {
       proxy_pass http://image_region_backend;
     }
 

src/main/java/com/glencoesoftware/omero/ms/image/region/AnnotationRequestHandler.java

@@ -57,6 +57,13 @@ public AnnotationRequestHandler(
         this.annotationCtx = annotationCtx;
     }
 
+    /**
+     * Queries the database for the file metadata assiciated with the
+     * {@link OriginalFile} associated with the given {@link FileAnnotation}
+     * @param client OMERO client
+     * @return JsonObject with the {@link OriginalFile} ID and file name if
+     * present, otherwise null
+     */
     public JsonObject getFileIdAndNameForAnnotation(omero.client client) {
         Map<String, String> ctx = new HashMap<String, String>();
         ctx.put("omero.group", "-1");
@@ -74,7 +81,6 @@ public JsonObject getFileIdAndNameForAnnotation(omero.client client) {
             if (rows.isEmpty()) {
                 return null;
             }
-            log.info(rows.get(0).toString());
             JsonObject retObj = new JsonObject();
             retObj.put("originalFileId", ((RLong) rows.get(0).get(0)).getValue());
             retObj.put("originalFileName", ((RString) rows.get(0).get(1)).getValue());

src/main/java/com/glencoesoftware/omero/ms/image/region/ImageRegionMicroserviceVerticle.java

@@ -351,7 +351,7 @@ public void deploy(JsonObject config, Promise<Void> prom) {
         // Annotation Download
         router.get(
                 "/webclient/annotation/:annotationId")
-            .handler(this::getFileAnnotation);
+            .handler(this::downloadFileAnnotation);
 
         // ImageData request handlers
         router.get("/webgateway/imgData/:imageId/:keys*").handler(this::getImageData);
@@ -744,7 +744,7 @@ private void getImageData(RoutingContext event) {
         }
         imageDataCtx.injectCurrentTraceContext();
         vertx.eventBus().<JsonObject>request(
-                ImageRegionVerticle.GET_IMAGE_DATA,
+                ImageRegionVerticle.GET_IMAGE_DATA_EVENT,
                 Json.encode(imageDataCtx), result -> {
             String chunk = "";
             try {
@@ -827,7 +827,7 @@ private void getHistogramJson(RoutingContext event) {
         }
         histogramCtx.injectCurrentTraceContext();
         vertx.eventBus().<JsonObject>request(
-                ImageRegionVerticle.GET_HISTOGRAM_JSON,
+                ImageRegionVerticle.GET_HISTOGRAM_JSON_EVENT,
                 Json.encode(histogramCtx), result -> {
             final HttpServerResponse response = event.response();
             try {
@@ -944,8 +944,12 @@ private void getThumbnails(RoutingContext event) {
         });
     }
 
-    private void getFileAnnotation(RoutingContext event) {
-        log.info("Get File Annotation");
+    /**
+     * Downloads the {@link OriginalFile} associated with the given
+     * {@link FileAnnotation}
+     * @param event Current routing context
+     */
+    private void downloadFileAnnotation(RoutingContext event) {
         HttpServerRequest request = event.request();
         HttpServerResponse response = event.response();
         final AnnotationCtx annotationCtx;
@@ -960,7 +964,7 @@ private void getFileAnnotation(RoutingContext event) {
         }
         annotationCtx.injectCurrentTraceContext();
         vertx.eventBus().<JsonObject>request(
-                ImageRegionVerticle.GET_FILE_ANNOTATION_EVENT,
+                ImageRegionVerticle.GET_FILE_ANNOTATION_METADATA_EVENT,
                 Json.encode(annotationCtx), new Handler<AsyncResult<Message<JsonObject>>>() {
                     @Override
                     public void handle(AsyncResult<Message<JsonObject>> result) {

src/main/java/com/glencoesoftware/omero/ms/image/region/ImageRegionVerticle.java

@@ -67,13 +67,13 @@ public class ImageRegionVerticle extends OmeroMsAbstractVerticle {
     public static final String GET_THUMBNAILS_EVENT =
             "omero.get_thumbnails";
 
-    public static final String GET_IMAGE_DATA =
+    public static final String GET_IMAGE_DATA_EVENT =
             "omero.get_image_data";
 
-    public static final String GET_HISTOGRAM_JSON =
+    public static final String GET_HISTOGRAM_JSON_EVENT =
             "omero.get_histogram_json";
 
-    public static final String GET_FILE_ANNOTATION_EVENT =
+    public static final String GET_FILE_ANNOTATION_METADATA_EVENT =
             "omero.get_file_annotation";
 
     /** OMERO server host */
@@ -146,11 +146,11 @@ public void start(Promise<Void> startPromise) {
             vertx.eventBus().<String>consumer(
                     GET_THUMBNAILS_EVENT, this::getThumbnails);
             vertx.eventBus().<String>consumer(
-                    GET_IMAGE_DATA, this::getImageData);
+                    GET_IMAGE_DATA_EVENT, this::getImageData);
             vertx.eventBus().<String>consumer(
-                    GET_HISTOGRAM_JSON, this::getHistogramJson);
+                    GET_HISTOGRAM_JSON_EVENT, this::getHistogramJson);
             vertx.eventBus().<String>consumer(
-                    GET_FILE_ANNOTATION_EVENT, this::getFileAnnotation);
+                    GET_FILE_ANNOTATION_METADATA_EVENT, this::getFileAnnotationMetadata);
         } catch (Exception e) {
             startPromise.fail(e);
         }
@@ -494,7 +494,13 @@ private void getHistogramJson(Message<String> message) {
                 });
     }
 
-    private void getFileAnnotation(Message<String> message) {
+    /**
+     * Gets the file name and path of the {@link OriginalFile} associated with
+     * A given {@link FileAnnotation} and returns them as JSON
+     * @param message JSON-encoded event data. Required keys are
+     * <code>omeroSessionKey</code> (String) and <code>annotationId</code>
+     */
+    private void getFileAnnotationMetadata(Message<String> message) {
         ObjectMapper mapper = new ObjectMapper();
         AnnotationCtx annotationCtx;
         try {
@@ -524,7 +530,6 @@ private void getFileAnnotation(Message<String> message) {
         } catch (PermissionDeniedException
                  | CannotCreateSessionException e) {
             String v = "Permission denied";
-            log.debug(v);
             message.fail(403, v);
         } catch (Exception e) {
             String v = "Exception while getting annotation";