+
+ {cocoJobId && !loadingStates.cocoFormat && (
+
+ )}
diff --git a/src/main/java/org/ecocean/export/EncounterCOCOExportFile.java b/src/main/java/org/ecocean/export/EncounterCOCOExportFile.java
index d931e079ac..0e44fbe906 100644
--- a/src/main/java/org/ecocean/export/EncounterCOCOExportFile.java
+++ b/src/main/java/org/ecocean/export/EncounterCOCOExportFile.java
@@ -3,6 +3,7 @@
import org.ecocean.Annotation;
import org.ecocean.Encounter;
import org.ecocean.MarkedIndividual;
+import org.ecocean.MultiValue;
import org.ecocean.media.MediaAsset;
import org.ecocean.shepherd.core.Shepherd;
import org.json.JSONArray;
@@ -25,183 +26,318 @@
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
+/**
+ * Generates a COCO-format ZIP export from a list of encounters.
+ *
+ * Design: all JDO/database data is eagerly extracted into plain data structures
+ * during {@link #extractData()}, so the caller can close the DB transaction
+ * before calling {@link #writeTo(OutputStream)} which does long-running HTTP
+ * image downloads.
+ */
public class EncounterCOCOExportFile {
private static final Logger log = Logger.getLogger(EncounterCOCOExportFile.class.getName());
private static final int BUFFER_SIZE = 8192;
private static final int CONNECTION_TIMEOUT_MS = 30000;
private static final int READ_TIMEOUT_MS = 60000;
- private final List
encounters;
- private final Shepherd shepherd;
+ // Progress tracking for async exports
+ private volatile int totalImages;
+ private volatile int processedImages;
+ private volatile int failedImages;
+ private volatile String phase = "preparing";
+
+ // --- Plain data extracted from JDO objects ---
+ // Populated by extractData(), consumed by writeTo()
+ private Map mediaAssetUrls; // uuid -> webURL
+ private Map mediaAssetIsJpeg; // uuid -> true if JPEG
+ private Map mediaAssetMeta; // uuid -> metadata for JSON
+ private Map mediaAssetToImageId; // uuid -> sequential image ID
+ private Map categoryMap; // iaClass -> category ID
+ private Map individualIdMap; // individual ID -> sequential int
+ private List annotationDataList; // flattened annotation records
+
+ /** Immutable snapshot of image metadata needed for the COCO JSON. */
+ static class ImageMeta {
+ final String uuid;
+ final int width;
+ final int height;
+ final String dateTime; // nullable
+ final Double latitude; // nullable
+ final Double longitude; // nullable
+
+ ImageMeta(MediaAsset ma) {
+ this.uuid = ma.getUUID();
+ this.width = (int) ma.getWidth();
+ this.height = (int) ma.getHeight();
+ this.dateTime = ma.getDateTime() != null ? ma.getDateTime().toString() : null;
+ this.latitude = ma.getLatitude();
+ this.longitude = ma.getLongitude();
+ }
+ }
+ /** Immutable snapshot of one annotation's data needed for the COCO JSON. */
+ static class AnnotationData {
+ final String annotationId;
+ final String mediaAssetUuid;
+ final String iaClass;
+ final int[] bbox;
+ final String viewpoint; // nullable
+ final double theta;
+ final String individualId; // nullable
+ final String individualDisplayName; // nullable
+ final List allNames; // list of [key, value] pairs
+ final String locationId; // nullable
+ final String encounterId;
+
+ AnnotationData(Annotation ann, Encounter enc) {
+ this.annotationId = ann.getId();
+ this.mediaAssetUuid = ann.getMediaAsset().getUUID();
+ this.iaClass = ann.getIAClass().trim();
+ this.bbox = ann.getBbox();
+ this.viewpoint = ann.getViewpoint();
+ this.theta = ann.getTheta();
+ this.locationId = enc.getLocationID();
+ this.encounterId = enc.getCatalogNumber();
+
+ MarkedIndividual ind = enc.getIndividual();
+ if (ind != null && ind.getId() != null) {
+ this.individualId = ind.getId();
+ this.individualDisplayName = ind.getDisplayName();
+ this.allNames = extractNames(ind);
+ } else {
+ this.individualId = null;
+ this.individualDisplayName = null;
+ this.allNames = Collections.emptyList();
+ }
+ }
+
+ private static List extractNames(MarkedIndividual ind) {
+ List result = new ArrayList<>();
+ MultiValue names = ind.getNames();
+ if (names == null) return result;
+ Set keys = names.getKeys();
+ if (keys == null) return result;
+ for (String key : keys) {
+ List vals = names.getValuesByKey(key);
+ if (vals == null) continue;
+ for (String val : vals) {
+ result.add(new String[]{key, val});
+ }
+ }
+ return result;
+ }
+ }
+
+ /**
+ * Constructs the export file and eagerly extracts all data from JDO objects.
+ * After this constructor returns, the caller may close the DB transaction.
+ */
public EncounterCOCOExportFile(List encounters, Shepherd shepherd) {
- this.encounters = encounters;
- this.shepherd = shepherd;
+ extractData(encounters);
}
- public void writeTo(OutputStream outputStream) throws IOException {
- // Collect data
- Map mediaAssetMap = collectUniqueMediaAssets();
- Map categoryMap = buildCategoryMap();
- Map individualIdMap = buildIndividualIdMap();
+ public int getTotalImages() { return totalImages; }
+ public int getProcessedImages() { return processedImages; }
+ public int getFailedImages() { return failedImages; }
+ public String getPhase() { return phase; }
+
+ /**
+ * Eagerly extracts all needed data from JDO-managed objects into plain
+ * data structures. Must be called while the DB transaction is still active.
+ */
+ private void extractData(List encounters) {
+ // Collect unique media assets and their metadata/URLs/content types
+ mediaAssetUrls = new LinkedHashMap<>();
+ mediaAssetIsJpeg = new LinkedHashMap<>();
+ mediaAssetMeta = new LinkedHashMap<>();
+ for (Encounter enc : encounters) {
+ if (enc.getAnnotations() == null) continue;
+ for (Annotation ann : enc.getAnnotations()) {
+ if (!isValidAnnotation(ann)) continue;
+ MediaAsset ma = ann.getMediaAsset();
+ String uuid = ma.getUUID();
+ if (!mediaAssetUrls.containsKey(uuid)) {
+ URL url = ma.webURL();
+ mediaAssetUrls.put(uuid, url);
+ mediaAssetMeta.put(uuid, new ImageMeta(ma));
+ mediaAssetIsJpeg.put(uuid, detectIsJpeg(ma, url));
+ }
+ }
+ }
- // Assign image IDs
- Map mediaAssetToImageId = new LinkedHashMap<>();
+ // Assign sequential image IDs
+ mediaAssetToImageId = new LinkedHashMap<>();
int imageId = 1;
- for (String uuid : mediaAssetMap.keySet()) {
+ for (String uuid : mediaAssetUrls.keySet()) {
mediaAssetToImageId.put(uuid, imageId++);
}
- // Build JSON arrays
- JSONArray imagesArray = new JSONArray();
- for (Map.Entry entry : mediaAssetMap.entrySet()) {
- MediaAsset ma = entry.getValue();
- int imgId = mediaAssetToImageId.get(entry.getKey());
- imagesArray.put(buildImageObject(ma, imgId));
+ // Build category map
+ Set iaClasses = new LinkedHashSet<>();
+ for (Encounter enc : encounters) {
+ if (enc.getAnnotations() == null) continue;
+ for (Annotation ann : enc.getAnnotations()) {
+ String iaClass = ann.getIAClass();
+ if (iaClass != null && !iaClass.trim().isEmpty()) {
+ iaClasses.add(iaClass.trim());
+ }
+ }
+ }
+ categoryMap = new LinkedHashMap<>();
+ int catId = 1;
+ for (String iaClass : iaClasses) {
+ categoryMap.put(iaClass, catId++);
+ }
+
+ // Build individual ID map
+ Set individualIds = new TreeSet<>();
+ for (Encounter enc : encounters) {
+ MarkedIndividual ind = enc.getIndividual();
+ if (ind != null && ind.getId() != null) {
+ individualIds.add(ind.getId());
+ }
+ }
+ individualIdMap = new LinkedHashMap<>();
+ int idx = 0;
+ for (String indId : individualIds) {
+ individualIdMap.put(indId, idx++);
}
- JSONArray annotationsArray = new JSONArray();
- int annotationId = 1;
+ // Extract all annotation data
+ annotationDataList = new ArrayList<>();
for (Encounter enc : encounters) {
if (enc.getAnnotations() == null) continue;
for (Annotation ann : enc.getAnnotations()) {
if (!isValidAnnotation(ann)) continue;
- MediaAsset ma = ann.getMediaAsset();
- int imgId = mediaAssetToImageId.get(ma.getUUID());
- annotationsArray.put(buildAnnotationObject(ann, annotationId++, imgId,
- categoryMap, individualIdMap, enc));
+ annotationDataList.add(new AnnotationData(ann, enc));
}
}
+ }
- // Build complete COCO JSON
- JSONObject coco = new JSONObject();
- coco.put("info", buildInfo(individualIdMap));
- coco.put("licenses", buildLicenses());
- coco.put("categories", buildCategories(categoryMap));
- coco.put("images", imagesArray);
- coco.put("annotations", annotationsArray);
-
- // Write ZIP
+ /**
+ * Writes the COCO ZIP to the given output stream. This method performs
+ * long-running HTTP image downloads and does NOT require a DB transaction.
+ */
+ public void writeTo(OutputStream outputStream) throws IOException {
+ // Write ZIP: images first, then JSON manifest so it only references
+ // images that were actually written successfully.
try (ZipOutputStream zipOut = new ZipOutputStream(outputStream)) {
- // Write annotations.json
- log.info("COCO Export: Writing annotations JSON...");
- byte[] jsonBytes = coco.toString(2).getBytes(StandardCharsets.UTF_8);
- ZipEntry jsonEntry = new ZipEntry("coco/annotations/instances.json");
- zipOut.putNextEntry(jsonEntry);
- zipOut.write(jsonBytes);
- zipOut.closeEntry();
- zipOut.flush();
-
- // Write images with streaming to minimize memory usage
- int totalImages = mediaAssetMap.size();
- int processedImages = 0;
- int failedImages = 0;
+ totalImages = mediaAssetUrls.size();
+ processedImages = 0;
+ failedImages = 0;
+ phase = "images";
+ Set exportedUuids = new LinkedHashSet<>();
log.info("COCO Export: Starting export of " + totalImages + " images...");
- for (Map.Entry entry : mediaAssetMap.entrySet()) {
- MediaAsset ma = entry.getValue();
- processedImages++;
+ for (Map.Entry entry : mediaAssetUrls.entrySet()) {
+ String uuid = entry.getKey();
+ URL url = entry.getValue();
try {
- boolean success = writeImageToZip(ma, zipOut);
- if (!success) {
+ boolean success = writeImageToZip(uuid, url, zipOut);
+ if (success) {
+ exportedUuids.add(uuid);
+ } else {
failedImages++;
}
- // Progress logging every 100 images
- if (processedImages % 100 == 0) {
- log.info("COCO Export: Processed " + processedImages + "/" + totalImages +
- " images (" + failedImages + " failed)");
- }
} catch (Exception e) {
failedImages++;
- log.warning("COCO Export: Failed to export image " + ma.getUUID() + ": " + e.getMessage());
+ log.warning("COCO Export: Failed to export image " + uuid +
+ ": " + e.getMessage());
}
+ processedImages++;
+ if (processedImages % 100 == 0) {
+ log.info("COCO Export: Processed " + processedImages + "/" + totalImages +
+ " images (" + failedImages + " failed)");
+ }
+ }
+
+ // Build JSON arrays using only successfully exported images
+ phase = "manifest";
+ JSONArray imagesArray = new JSONArray();
+ for (String uuid : exportedUuids) {
+ ImageMeta meta = mediaAssetMeta.get(uuid);
+ int imgId = mediaAssetToImageId.get(uuid);
+ imagesArray.put(buildImageObject(meta, imgId));
}
+ JSONArray annotationsArray = new JSONArray();
+ int annotationId = 1;
+ for (AnnotationData ad : annotationDataList) {
+ if (!exportedUuids.contains(ad.mediaAssetUuid)) continue;
+ int imgId = mediaAssetToImageId.get(ad.mediaAssetUuid);
+ annotationsArray.put(buildAnnotationObject(ad, annotationId++, imgId));
+ }
+
+ JSONObject coco = new JSONObject();
+ coco.put("info", buildInfo());
+ coco.put("licenses", buildLicenses());
+ coco.put("categories", buildCategories());
+ coco.put("images", imagesArray);
+ coco.put("annotations", annotationsArray);
+
+ // Write annotations.json as the last entry
+ phase = "packaging";
+ log.info("COCO Export: Writing annotations JSON...");
+ byte[] jsonBytes = coco.toString(2).getBytes(StandardCharsets.UTF_8);
+ ZipEntry jsonEntry = new ZipEntry("coco/annotations/instances.json");
+ zipOut.putNextEntry(jsonEntry);
+ zipOut.write(jsonBytes);
+ zipOut.closeEntry();
+
zipOut.finish();
- log.info("COCO Export: Completed. " + (processedImages - failedImages) + "/" + totalImages +
+ log.info("COCO Export: Completed. " + exportedUuids.size() + "/" + totalImages +
" images exported successfully, " + failedImages + " failed.");
}
}
/**
* Writes an image directly to the ZipOutputStream using streaming.
- * This avoids loading entire images into memory, critical for large exports.
*
* @return true if image was written successfully, false if skipped
*/
- private boolean writeImageToZip(MediaAsset ma, ZipOutputStream zipOut) throws IOException {
- URL url = ma.webURL();
+ private boolean writeImageToZip(String uuid, URL url, ZipOutputStream zipOut) throws IOException {
if (url == null) {
- log.fine("COCO Export: Skipping image " + ma.getUUID() + " - no URL available");
+ log.fine("COCO Export: Skipping image " + uuid + " - no URL available");
return false;
}
- String contentType = detectContentType(url);
- boolean isJpeg = isJpegContentType(contentType);
+ boolean isJpeg = Boolean.TRUE.equals(mediaAssetIsJpeg.get(uuid));
- ZipEntry imgEntry = new ZipEntry("coco/images/" + ma.getUUID() + ".jpg");
+ ZipEntry imgEntry = new ZipEntry("coco/images/" + uuid + ".jpg");
zipOut.putNextEntry(imgEntry);
try {
if (isJpeg) {
- // Stream JPEG directly - most memory efficient
streamImageDirectly(url, zipOut);
} else {
- // Non-JPEG: must decode and re-encode (uses more memory but unavoidable)
convertAndWriteImage(url, zipOut);
}
} finally {
zipOut.closeEntry();
- zipOut.flush(); // Keep data flowing to client
+ zipOut.flush();
}
return true;
}
/**
- * Detects the content type of a URL, handling redirects.
+ * Determines if a MediaAsset is JPEG using DB metadata (no HTTP request).
+ * Falls back to URL path extension if metadata is unavailable.
*/
- private String detectContentType(URL url) {
- try {
- URLConnection conn = url.openConnection();
- conn.setConnectTimeout(CONNECTION_TIMEOUT_MS);
- conn.setReadTimeout(READ_TIMEOUT_MS);
-
- if (conn instanceof HttpURLConnection) {
- ((HttpURLConnection) conn).setRequestMethod("HEAD");
- ((HttpURLConnection) conn).setInstanceFollowRedirects(true);
- }
-
- String contentType = conn.getContentType();
-
- if (conn instanceof HttpURLConnection) {
- ((HttpURLConnection) conn).disconnect();
- }
-
- return contentType;
- } catch (Exception e) {
- // Fall back to checking file extension
+ private static boolean detectIsJpeg(MediaAsset ma, URL url) {
+ String[] mimeType = ma.getMimeType();
+ if (mimeType != null && mimeType.length >= 2) {
+ String minor = mimeType[1].split(";")[0].trim();
+ return "jpeg".equals(minor) || "jpg".equals(minor);
+ }
+ // Fall back to URL path extension
+ if (url != null) {
String path = url.getPath().toLowerCase();
- if (path.endsWith(".jpg") || path.endsWith(".jpeg")) {
- return "image/jpeg";
- }
- return null;
+ return path.endsWith(".jpg") || path.endsWith(".jpeg");
}
+ return false;
}
- /**
- * Checks if content type indicates JPEG.
- */
- private boolean isJpegContentType(String contentType) {
- if (contentType == null) return false;
- contentType = contentType.toLowerCase();
- return contentType.contains("image/jpeg") || contentType.contains("image/jpg");
- }
-
- /**
- * Streams image bytes directly from URL to ZipOutputStream without decoding.
- * This is the most memory-efficient method for JPEG images.
- */
private void streamImageDirectly(URL url, ZipOutputStream zipOut) throws IOException {
URLConnection conn = url.openConnection();
conn.setConnectTimeout(CONNECTION_TIMEOUT_MS);
@@ -224,10 +360,6 @@ private void streamImageDirectly(URL url, ZipOutputStream zipOut) throws IOExcep
}
}
- /**
- * Converts a non-JPEG image to JPEG and writes to ZipOutputStream.
- * This requires loading the image into memory but handles PNG, GIF, etc.
- */
private void convertAndWriteImage(URL url, ZipOutputStream zipOut) throws IOException {
URLConnection conn = url.openConnection();
conn.setConnectTimeout(CONNECTION_TIMEOUT_MS);
@@ -243,16 +375,21 @@ private void convertAndWriteImage(URL url, ZipOutputStream zipOut) throws IOExce
throw new IOException("Failed to decode image");
}
- // For images with alpha channel (PNG), convert to RGB for JPEG
if (image.getColorModel().hasAlpha()) {
BufferedImage rgbImage = new BufferedImage(
image.getWidth(), image.getHeight(), BufferedImage.TYPE_INT_RGB);
- rgbImage.createGraphics().drawImage(image, 0, 0, java.awt.Color.WHITE, null);
+ java.awt.Graphics2D g2d = rgbImage.createGraphics();
+ try {
+ g2d.drawImage(image, 0, 0, java.awt.Color.WHITE, null);
+ } finally {
+ g2d.dispose();
+ }
image = rgbImage;
}
- // Write directly to zip stream
- ImageIO.write(image, "jpg", zipOut);
+ java.io.ByteArrayOutputStream imgBuf = new java.io.ByteArrayOutputStream();
+ ImageIO.write(image, "jpg", imgBuf);
+ zipOut.write(imgBuf.toByteArray());
} finally {
if (conn instanceof HttpURLConnection) {
((HttpURLConnection) conn).disconnect();
@@ -260,174 +397,49 @@ private void convertAndWriteImage(URL url, ZipOutputStream zipOut) throws IOExce
}
}
- /**
- * Collects all unique MediaAssets from valid annotations.
- * An annotation is valid if it has a non-null/non-empty iaClass and a valid bbox.
- */
- private Map collectUniqueMediaAssets() {
- Map mediaAssetMap = new LinkedHashMap<>();
- for (Encounter enc : encounters) {
- if (enc.getAnnotations() == null) continue;
- for (Annotation ann : enc.getAnnotations()) {
- if (!isValidAnnotation(ann)) continue;
- MediaAsset ma = ann.getMediaAsset();
- if (ma != null && ma.getUUID() != null) {
- mediaAssetMap.putIfAbsent(ma.getUUID(), ma);
- }
- }
- }
- return mediaAssetMap;
- }
-
- /**
- * Builds a map from iaClass to sequential category ID.
- */
- private Map buildCategoryMap() {
- Set iaClasses = new LinkedHashSet<>();
- for (Encounter enc : encounters) {
- if (enc.getAnnotations() == null) continue;
- for (Annotation ann : enc.getAnnotations()) {
- String iaClass = ann.getIAClass();
- if (iaClass != null && !iaClass.trim().isEmpty()) {
- iaClasses.add(iaClass.trim());
- }
- }
- }
- Map categoryMap = new LinkedHashMap<>();
- int id = 1;
- for (String iaClass : iaClasses) {
- categoryMap.put(iaClass, id++);
- }
- return categoryMap;
- }
-
- /**
- * Builds a map from MarkedIndividual UUID to sequential integer ID.
- */
- private Map buildIndividualIdMap() {
- Set individualIds = new TreeSet<>(); // TreeSet for sorted, deterministic order
- for (Encounter enc : encounters) {
- MarkedIndividual ind = enc.getIndividual();
- if (ind != null && ind.getId() != null) {
- individualIds.add(ind.getId());
- }
- }
- Map idMap = new LinkedHashMap<>();
- int idx = 0;
- for (String indId : individualIds) {
- idMap.put(indId, idx++);
- }
- return idMap;
- }
-
- /**
- * Checks if an annotation is valid for COCO export.
- */
private boolean isValidAnnotation(Annotation ann) {
if (ann == null) return false;
String iaClass = ann.getIAClass();
if (iaClass == null || iaClass.trim().isEmpty()) return false;
int[] bbox = ann.getBbox();
if (bbox == null || bbox.length < 4) return false;
- if (bbox[2] <= 0 || bbox[3] <= 0) return false; // width/height must be positive
+ if (bbox[2] <= 0 || bbox[3] <= 0) return false;
MediaAsset ma = ann.getMediaAsset();
if (ma == null || ma.getUUID() == null) return false;
return true;
}
- /**
- * Builds the "info" section of COCO JSON.
- */
- private JSONObject buildInfo(Map individualIdMap) {
- JSONObject info = new JSONObject();
- info.put("description", "Wildbook COCO Export");
- info.put("version", "1.0");
- info.put("date_created", ZonedDateTime.now().format(DateTimeFormatter.ISO_INSTANT));
- info.put("contributor", "Wildbook");
+ // --- JSON builders using plain data (no JDO access) ---
- JSONObject idMapping = new JSONObject();
- for (Map.Entry entry : individualIdMap.entrySet()) {
- idMapping.put(entry.getKey(), entry.getValue());
- }
- info.put("individual_id_mapping", idMapping);
- return info;
- }
-
- /**
- * Builds the "licenses" section of COCO JSON.
- */
- private JSONArray buildLicenses() {
- JSONArray licenses = new JSONArray();
- JSONObject license = new JSONObject();
- license.put("id", 1);
- license.put("name", "See Wildbook Terms");
- license.put("url", "");
- licenses.put(license);
- return licenses;
- }
-
- /**
- * Builds the "categories" section of COCO JSON.
- */
- private JSONArray buildCategories(Map categoryMap) {
- JSONArray categories = new JSONArray();
- for (Map.Entry entry : categoryMap.entrySet()) {
- JSONObject cat = new JSONObject();
- cat.put("id", entry.getValue());
- cat.put("name", entry.getKey());
- cat.put("supercategory", "animal");
- categories.put(cat);
- }
- return categories;
- }
-
- /**
- * Builds an image object for COCO JSON.
- */
- private JSONObject buildImageObject(MediaAsset ma, int imageId) {
+ private JSONObject buildImageObject(ImageMeta meta, int imageId) {
JSONObject img = new JSONObject();
img.put("id", imageId);
- img.put("file_name", ma.getUUID() + ".jpg");
- img.put("width", (int) ma.getWidth());
- img.put("height", (int) ma.getHeight());
- img.put("uuid", ma.getUUID());
-
- // Always include all fields - use null for missing values so every record
- // has the same schema (enables NaN counting in EDA instead of probing for missing keys)
- img.put("date_captured", ma.getDateTime() != null ? ma.getDateTime().toString() : JSONObject.NULL);
- Double lat = ma.getLatitude();
- Double lon = ma.getLongitude();
- img.put("gps_lat_captured", lat != null ? lat : JSONObject.NULL);
- img.put("gps_lon_captured", lon != null ? lon : JSONObject.NULL);
+ img.put("file_name", meta.uuid + ".jpg");
+ img.put("width", meta.width);
+ img.put("height", meta.height);
+ img.put("uuid", meta.uuid);
+ img.put("date_captured", meta.dateTime != null ? meta.dateTime : JSONObject.NULL);
+ img.put("gps_lat_captured", meta.latitude != null ? meta.latitude : JSONObject.NULL);
+ img.put("gps_lon_captured", meta.longitude != null ? meta.longitude : JSONObject.NULL);
return img;
}
- /**
- * Builds an annotation object for COCO JSON.
- */
- private JSONObject buildAnnotationObject(Annotation ann, int annotationId, int imageId,
- Map categoryMap,
- Map individualIdMap,
- Encounter enc) {
+ private JSONObject buildAnnotationObject(AnnotationData ad, int annotationId, int imageId) {
JSONObject annJson = new JSONObject();
annJson.put("id", annotationId);
annJson.put("image_id", imageId);
+ annJson.put("category_id", categoryMap.get(ad.iaClass));
- String iaClass = ann.getIAClass().trim();
- annJson.put("category_id", categoryMap.get(iaClass));
-
- int[] bbox = ann.getBbox();
+ int[] bbox = ad.bbox;
JSONArray bboxArray = new JSONArray();
- bboxArray.put(bbox[0]); // x
- bboxArray.put(bbox[1]); // y
- bboxArray.put(bbox[2]); // width
- bboxArray.put(bbox[3]); // height
+ bboxArray.put(bbox[0]);
+ bboxArray.put(bbox[1]);
+ bboxArray.put(bbox[2]);
+ bboxArray.put(bbox[3]);
annJson.put("bbox", bboxArray);
- int area = bbox[2] * bbox[3];
- annJson.put("area", area);
+ annJson.put("area", bbox[2] * bbox[3]);
- // Segmentation: rectangle polygon from bbox
JSONArray segmentation = new JSONArray();
JSONArray polygon = new JSONArray();
int x = bbox[0], y = bbox[1], w = bbox[2], h = bbox[3];
@@ -439,38 +451,70 @@ private JSONObject buildAnnotationObject(Annotation ann, int annotationId, int i
annJson.put("segmentation", segmentation);
annJson.put("iscrowd", 0);
+ annJson.put("uuid", ad.annotationId);
+ annJson.put("viewpoint", ad.viewpoint != null ? ad.viewpoint : JSONObject.NULL);
+ annJson.put("theta", ad.theta);
- // Custom fields
- annJson.put("uuid", ann.getId());
-
- String viewpoint = ann.getViewpoint();
- annJson.put("viewpoint", viewpoint != null ? viewpoint : JSONObject.NULL);
-
- annJson.put("theta", ann.getTheta());
-
- // Individual info
- MarkedIndividual ind = enc.getIndividual();
JSONArray individualIds = new JSONArray();
- if (ind != null && ind.getId() != null && individualIdMap.containsKey(ind.getId())) {
- individualIds.put(individualIdMap.get(ind.getId()));
- annJson.put("individual_uuid", ind.getId());
- String displayName = ind.getDisplayName();
- if (displayName != null) {
- annJson.put("name", displayName);
- } else {
- annJson.put("name", JSONObject.NULL);
+ if (ad.individualId != null && individualIdMap.containsKey(ad.individualId)) {
+ individualIds.put(individualIdMap.get(ad.individualId));
+ annJson.put("individual_uuid", ad.individualId);
+ annJson.put("name", ad.individualDisplayName != null ? ad.individualDisplayName : JSONObject.NULL);
+ JSONArray allNames = new JSONArray();
+ for (String[] kv : ad.allNames) {
+ JSONObject entry = new JSONObject();
+ entry.put("key", kv[0]);
+ entry.put("value", kv[1]);
+ allNames.put(entry);
}
+ annJson.put("all_names", allNames);
} else {
annJson.put("individual_uuid", JSONObject.NULL);
annJson.put("name", JSONObject.NULL);
+ annJson.put("all_names", new JSONArray());
}
annJson.put("individual_ids", individualIds);
- // Encounter info
- String locationId = enc.getLocationID();
- annJson.put("location_id", locationId != null ? locationId : JSONObject.NULL);
- annJson.put("encounter_id", enc.getCatalogNumber());
+ annJson.put("location_id", ad.locationId != null ? ad.locationId : JSONObject.NULL);
+ annJson.put("encounter_id", ad.encounterId);
return annJson;
}
+
+ private JSONObject buildInfo() {
+ JSONObject info = new JSONObject();
+ info.put("description", "Wildbook COCO Export");
+ info.put("version", "1.0");
+ info.put("date_created", ZonedDateTime.now().format(DateTimeFormatter.ISO_INSTANT));
+ info.put("contributor", "Wildbook");
+
+ JSONObject idMapping = new JSONObject();
+ for (Map.Entry entry : individualIdMap.entrySet()) {
+ idMapping.put(entry.getKey(), entry.getValue());
+ }
+ info.put("individual_id_mapping", idMapping);
+ return info;
+ }
+
+ private JSONArray buildLicenses() {
+ JSONArray licenses = new JSONArray();
+ JSONObject license = new JSONObject();
+ license.put("id", 1);
+ license.put("name", "See Wildbook Terms");
+ license.put("url", "");
+ licenses.put(license);
+ return licenses;
+ }
+
+ private JSONArray buildCategories() {
+ JSONArray categories = new JSONArray();
+ for (Map.Entry entry : categoryMap.entrySet()) {
+ JSONObject cat = new JSONObject();
+ cat.put("id", entry.getValue());
+ cat.put("name", entry.getKey());
+ cat.put("supercategory", "animal");
+ categories.put(cat);
+ }
+ return categories;
+ }
}
diff --git a/src/main/java/org/ecocean/ia/Task.java b/src/main/java/org/ecocean/ia/Task.java
index d840c5a561..b38d4b7a78 100644
--- a/src/main/java/org/ecocean/ia/Task.java
+++ b/src/main/java/org/ecocean/ia/Task.java
@@ -502,6 +502,14 @@ public String getStatus(Shepherd myShepherd) {
status = "completed";
} else if (logs.toString().indexOf("score") > -1) {
status = "completed";
+ } else if (islObj.optJSONObject("status") != null &&
+ islObj.optJSONObject("status").optJSONObject("error") != null &&
+ islObj.optJSONObject("status").optJSONObject("error").optBoolean(
+ "emptyTargetAnnotations", false)) {
+ // No target annotations to match against is a terminal state, not a failure.
+ // Treating it as completed lets import progress reach 100%.
+ System.out.println("[Task.getStatus] emptyTargetAnnotations detected for task " + getId() + ", marking completed");
+ status = "completed";
} else if (islObj.toString().indexOf("HTTP error code") > -1) {
status = "error";
} else if (!islObj.optString("queueStatus").equals("")) {
@@ -511,7 +519,7 @@ public String getStatus(Shepherd myShepherd) {
status = "queuing";
}
// if(islObj.optString("queueStatus").equals("queued")){sendIdentify=false;}
- // if(status.equals("waiting to queue"))System.out.println("islObj: "+islObj.toString());
+ if(status.equals("waiting to queue"))System.out.println("[Task.getStatus DEBUG] waiting to queue, islObj: "+islObj.toString());
}
return status;
}
diff --git a/src/main/java/org/ecocean/servlet/export/EncounterSearchExportCOCO.java b/src/main/java/org/ecocean/servlet/export/EncounterSearchExportCOCO.java
index 913a3055c5..30debce003 100644
--- a/src/main/java/org/ecocean/servlet/export/EncounterSearchExportCOCO.java
+++ b/src/main/java/org/ecocean/servlet/export/EncounterSearchExportCOCO.java
@@ -14,15 +14,45 @@
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
+import java.io.File;
+import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
-import java.io.PrintWriter;
+import java.io.RandomAccessFile;
+import java.nio.file.Files;
import java.util.ArrayList;
+import java.util.Iterator;
import java.util.List;
+import java.util.Map;
+import java.util.UUID;
import java.util.Vector;
+import java.util.concurrent.ConcurrentHashMap;
+/**
+ * Async COCO export servlet. Three actions:
+ * ?action=start — kicks off background export, returns JSON {"jobId":"..."}
+ * ?action=status&jobId=... — returns JSON with progress/completion
+ * ?action=download&jobId=... — streams the completed ZIP file
+ *
+ * Legacy (no action param) falls back to synchronous export for backwards compatibility.
+ */
public class EncounterSearchExportCOCO extends HttpServlet {
+ private static final long MAX_JOB_AGE_MS = 60 * 60 * 1000; // 1 hour
+
+ private static final Map jobs = new ConcurrentHashMap<>();
+
+ static class ExportJob {
+ final String jobId;
+ final long createdAt = System.currentTimeMillis();
+ volatile String status = "running"; // running | complete | error
+ volatile String errorMessage;
+ volatile File tempFile;
+ volatile EncounterCOCOExportFile exportFile;
+
+ ExportJob(String jobId) { this.jobId = jobId; }
+ }
+
public void init(ServletConfig config) throws ServletException {
super.init(config);
}
@@ -35,22 +65,240 @@ public void doGet(HttpServletRequest request, HttpServletResponse response)
public void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
+ String action = request.getParameter("action");
+ if ("start".equals(action)) {
+ handleStart(request, response);
+ } else if ("status".equals(action)) {
+ handleStatus(request, response);
+ } else if ("download".equals(action)) {
+ handleDownload(request, response);
+ } else {
+ handleSynchronous(request, response);
+ }
+ }
+
+ private void handleStart(HttpServletRequest request, HttpServletResponse response)
+ throws IOException {
+ purgeStaleJobs();
+
String context = ServletUtilities.getContext(request);
Shepherd myShepherd = new Shepherd(context);
- myShepherd.setAction("EncounterSearchExportCOCO.class");
-
+ myShepherd.setAction("EncounterSearchExportCOCO.start");
myShepherd.beginDBTransaction();
+ // Collect encounter IDs on the request thread (JDO objects stay local)
+ List encounterIds;
try {
- // Process query
EncounterQueryResult queryResult = EncounterQueryProcessor.processQuery(
myShepherd, request, "year descending, month descending, day descending");
Vector rEncounters = queryResult.getResult();
-
- // Filter hidden encounters
HiddenEncReporter hiddenData = new HiddenEncReporter(rEncounters, request, myShepherd);
- // Convert to list, excluding hidden
+ encounterIds = new ArrayList<>();
+ for (Object obj : rEncounters) {
+ Encounter enc = (Encounter) obj;
+ if (!hiddenData.contains(enc)) {
+ encounterIds.add(enc.getCatalogNumber());
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ sendJson(response, 500, "{\"error\":\"Query failed: " +
+ escapeJson(e.getMessage()) + "\"}");
+ return;
+ } finally {
+ myShepherd.rollbackDBTransaction();
+ myShepherd.closeDBTransaction();
+ }
+
+ String jobId = UUID.randomUUID().toString();
+ ExportJob job = new ExportJob(jobId);
+ jobs.put(jobId, job);
+
+ // Background thread opens its own Shepherd, extracts data, closes the
+ // DB transaction, then does the long-running image I/O without a DB connection.
+ List encIds = encounterIds;
+ Thread exportThread = new Thread(() -> {
+ // Phase 1: extract all JDO data while transaction is alive
+ Shepherd bgShepherd = new Shepherd(context);
+ bgShepherd.setAction("EncounterSearchExportCOCO.export-" + jobId);
+ bgShepherd.beginDBTransaction();
+ try {
+ List encounters = new ArrayList<>();
+ for (String id : encIds) {
+ Encounter enc = bgShepherd.getEncounter(id);
+ if (enc != null) encounters.add(enc);
+ }
+ // Constructor eagerly extracts all JDO data into plain objects
+ job.exportFile = new EncounterCOCOExportFile(encounters, bgShepherd);
+ } catch (Throwable t) {
+ t.printStackTrace();
+ job.status = "error";
+ job.errorMessage = t.getMessage() != null ? t.getMessage() : t.getClass().getName();
+ return;
+ } finally {
+ bgShepherd.rollbackDBTransaction();
+ bgShepherd.closeDBTransaction();
+ }
+
+ // Phase 2: write ZIP (image downloads + JSON manifest) — no DB needed
+ try {
+ File tmpDir = new File(CommonConfiguration.getUploadTmpDir(context));
+ if (!tmpDir.exists()) tmpDir.mkdirs();
+ File tempFile = File.createTempFile("wildbook-coco-export-", ".zip", tmpDir);
+ tempFile.deleteOnExit();
+ try (FileOutputStream fos = new FileOutputStream(tempFile)) {
+ job.exportFile.writeTo(fos);
+ }
+ job.tempFile = tempFile;
+ job.status = "complete";
+ } catch (Throwable t) {
+ t.printStackTrace();
+ job.status = "error";
+ job.errorMessage = t.getMessage() != null ? t.getMessage() : t.getClass().getName();
+ }
+ }, "coco-export-" + jobId);
+ exportThread.setDaemon(true);
+ exportThread.start();
+
+ sendJson(response, 200, "{\"jobId\":\"" + jobId + "\"}");
+ }
+
+ private void handleStatus(HttpServletRequest request, HttpServletResponse response)
+ throws IOException {
+ String jobId = request.getParameter("jobId");
+ ExportJob job = (jobId != null) ? jobs.get(jobId) : null;
+ if (job == null) {
+ sendJson(response, 404, "{\"error\":\"Job not found\"}");
+ return;
+ }
+ StringBuilder json = new StringBuilder();
+ json.append("{\"jobId\":\"").append(job.jobId).append("\"");
+ json.append(",\"status\":\"").append(job.status).append("\"");
+ if (job.exportFile != null) {
+ json.append(",\"totalImages\":").append(job.exportFile.getTotalImages());
+ json.append(",\"processedImages\":").append(job.exportFile.getProcessedImages());
+ json.append(",\"failedImages\":").append(job.exportFile.getFailedImages());
+ json.append(",\"phase\":\"").append(job.exportFile.getPhase()).append("\"");
+ }
+ if (job.errorMessage != null) {
+ json.append(",\"error\":\"").append(escapeJson(job.errorMessage)).append("\"");
+ }
+ json.append("}");
+ sendJson(response, 200, json.toString());
+ }
+
+ private static final java.util.logging.Logger log =
+ java.util.logging.Logger.getLogger(EncounterSearchExportCOCO.class.getName());
+
+ private void handleDownload(HttpServletRequest request, HttpServletResponse response)
+ throws IOException {
+ String jobId = request.getParameter("jobId");
+ ExportJob job = (jobId != null) ? jobs.get(jobId) : null;
+ if (job == null) {
+ log.warning("COCO Download: job not found, jobId=" + jobId);
+ sendJson(response, 404, "{\"error\":\"Job not found\"}");
+ return;
+ }
+ if (!"complete".equals(job.status) || job.tempFile == null || !job.tempFile.exists()) {
+ log.warning("COCO Download: job not ready, jobId=" + jobId +
+ " status=" + job.status + " tempFile=" + job.tempFile +
+ " exists=" + (job.tempFile != null && job.tempFile.exists()));
+ sendJson(response, 400, "{\"error\":\"Export not ready\"}");
+ return;
+ }
+
+ long fileLength = job.tempFile.length();
+ long start = 0;
+ long end = fileLength - 1;
+
+ String rangeHeader = request.getHeader("Range");
+ log.info("COCO Download: jobId=" + jobId + " fileLength=" + fileLength +
+ " Range=" + rangeHeader + " method=" + request.getMethod());
+
+ if (rangeHeader != null && rangeHeader.startsWith("bytes=")) {
+ String rangeSpec = rangeHeader.substring(6).trim();
+ String[] parts = rangeSpec.split("-", 2);
+ try {
+ if (!parts[0].isEmpty()) {
+ start = Long.parseLong(parts[0]);
+ }
+ if (parts.length > 1 && !parts[1].isEmpty()) {
+ end = Long.parseLong(parts[1]);
+ }
+ } catch (NumberFormatException e) {
+ response.setStatus(HttpServletResponse.SC_REQUESTED_RANGE_NOT_SATISFIABLE);
+ response.setHeader("Content-Range", "bytes */" + fileLength);
+ return;
+ }
+ if (start < 0 || start > end || start >= fileLength) {
+ response.setStatus(HttpServletResponse.SC_REQUESTED_RANGE_NOT_SATISFIABLE);
+ response.setHeader("Content-Range", "bytes */" + fileLength);
+ return;
+ }
+ if (end >= fileLength) {
+ end = fileLength - 1;
+ }
+ long contentLength = end - start + 1;
+ response.setStatus(HttpServletResponse.SC_PARTIAL_CONTENT);
+ response.setHeader("Content-Range",
+ "bytes " + start + "-" + end + "/" + fileLength);
+ response.setContentLengthLong(contentLength);
+ log.info("COCO Download: sending 206, start=" + start + " end=" + end +
+ " contentLength=" + contentLength);
+ } else {
+ response.setContentLengthLong(fileLength);
+ log.info("COCO Download: sending 200, full file, length=" + fileLength);
+ }
+
+ response.setContentType("application/zip");
+ response.setHeader("Content-Disposition",
+ "attachment; filename=\"wildbook-coco-export.zip\"");
+ response.setHeader("Accept-Ranges", "bytes");
+ // Tell nginx to stream directly to the client instead of buffering.
+ // Without this, nginx buffers up to proxy_max_temp_file_size (default 1GB),
+ // then stalls Tomcat's writes, eventually timing out and cutting the connection
+ // — causing browsers to restart the download in an infinite loop.
+ response.setHeader("X-Accel-Buffering", "no");
+
+ long bytesSent = 0;
+ OutputStream out = response.getOutputStream();
+ try (RandomAccessFile raf = new RandomAccessFile(job.tempFile, "r")) {
+ raf.seek(start);
+ byte[] buffer = new byte[65536];
+ long remaining = end - start + 1;
+ int read;
+ while (remaining > 0 && (read = raf.read(buffer, 0,
+ (int) Math.min(buffer.length, remaining))) != -1) {
+ out.write(buffer, 0, read);
+ remaining -= read;
+ bytesSent += read;
+ }
+ } catch (IOException e) {
+ log.warning("COCO Download: connection broken after " + bytesSent +
+ " bytes (of " + (end - start + 1) + " expected). " + e.getMessage());
+ throw e;
+ }
+ out.flush();
+ log.info("COCO Download: completed, sent " + bytesSent + " bytes for jobId=" + jobId);
+ }
+
+ /** Synchronous fallback for legacy/non-JS callers. */
+ private void handleSynchronous(HttpServletRequest request, HttpServletResponse response)
+ throws IOException {
+
+ String context = ServletUtilities.getContext(request);
+ Shepherd myShepherd = new Shepherd(context);
+ myShepherd.setAction("EncounterSearchExportCOCO.class");
+ myShepherd.beginDBTransaction();
+
+ // Phase 1: extract data while transaction is alive
+ EncounterCOCOExportFile exportFile;
+ try {
+ EncounterQueryResult queryResult = EncounterQueryProcessor.processQuery(
+ myShepherd, request, "year descending, month descending, day descending");
+ Vector rEncounters = queryResult.getResult();
+ HiddenEncReporter hiddenData = new HiddenEncReporter(rEncounters, request, myShepherd);
List encounters = new ArrayList<>();
for (Object obj : rEncounters) {
Encounter enc = (Encounter) obj;
@@ -58,30 +306,74 @@ public void doPost(HttpServletRequest request, HttpServletResponse response)
encounters.add(enc);
}
}
+ exportFile = new EncounterCOCOExportFile(encounters, myShepherd);
+ } catch (Exception e) {
+ e.printStackTrace();
+ if (!response.isCommitted()) {
+ sendJson(response, 500, "{\"error\":\"" + escapeJson(e.getMessage()) + "\"}");
+ }
+ return;
+ } finally {
+ myShepherd.rollbackDBTransaction();
+ myShepherd.closeDBTransaction();
+ }
- // Set response headers
- response.setContentType("application/zip");
- response.setHeader("Content-Disposition", "attachment; filename=\"wildbook-coco-export.zip\"");
+ // Phase 2: write ZIP (no DB needed)
+ File tempFile = null;
+ try {
+ File tmpDir = new File(CommonConfiguration.getUploadTmpDir(context));
+ if (!tmpDir.exists()) tmpDir.mkdirs();
+ tempFile = File.createTempFile("wildbook-coco-export-", ".zip", tmpDir);
+ tempFile.deleteOnExit();
+ try (FileOutputStream fos = new FileOutputStream(tempFile)) {
+ exportFile.writeTo(fos);
+ }
- // Write export
+ response.setContentType("application/zip");
+ response.setHeader("Content-Disposition",
+ "attachment; filename=\"wildbook-coco-export.zip\"");
+ response.setContentLengthLong(tempFile.length());
OutputStream out = response.getOutputStream();
- EncounterCOCOExportFile exportFile = new EncounterCOCOExportFile(encounters, myShepherd);
- exportFile.writeTo(out);
+ Files.copy(tempFile.toPath(), out);
out.flush();
} catch (Exception e) {
e.printStackTrace();
- response.setContentType("text/html");
- PrintWriter out = response.getWriter();
- out.println(ServletUtilities.getHeader(request));
- out.println("Error encountered
");
- out.println("Error: " + e.getMessage() + "
");
- out.println("Please let the webmaster know you encountered an error at: EncounterSearchExportCOCO servlet
");
- out.println(ServletUtilities.getFooter(context));
- out.close();
+ if (!response.isCommitted()) {
+ sendJson(response, 500, "{\"error\":\"" + escapeJson(e.getMessage()) + "\"}");
+ }
} finally {
- myShepherd.rollbackDBTransaction();
- myShepherd.closeDBTransaction();
+ if (tempFile != null) {
+ tempFile.delete();
+ }
+ }
+ }
+
+ private void sendJson(HttpServletResponse response, int status, String json)
+ throws IOException {
+ response.setStatus(status);
+ response.setContentType("application/json");
+ response.setCharacterEncoding("UTF-8");
+ response.getWriter().write(json);
+ }
+
+ private static String escapeJson(String s) {
+ if (s == null) return "";
+ return s.replace("\\", "\\\\").replace("\"", "\\\"")
+ .replace("\n", "\\n").replace("\r", "\\r");
+ }
+
+ private void purgeStaleJobs() {
+ long now = System.currentTimeMillis();
+ Iterator> it = jobs.entrySet().iterator();
+ while (it.hasNext()) {
+ ExportJob job = it.next().getValue();
+ if ((now - job.createdAt) > MAX_JOB_AGE_MS) {
+ if (job.tempFile != null && job.tempFile.exists()) {
+ job.tempFile.delete();
+ }
+ it.remove();
+ }
}
}
}
diff --git a/src/test/java/org/ecocean/export/EncounterCOCOExportFileTest.java b/src/test/java/org/ecocean/export/EncounterCOCOExportFileTest.java
index 97ec570347..b8b119b7a2 100644
--- a/src/test/java/org/ecocean/export/EncounterCOCOExportFileTest.java
+++ b/src/test/java/org/ecocean/export/EncounterCOCOExportFileTest.java
@@ -24,28 +24,17 @@
class EncounterCOCOExportFileTest {
@Test
- void testBuildsCOCOStructure() throws Exception {
- // Create mock objects
+ void testManifestExcludesFailedImages() throws Exception {
+ // When an image URL is null (download fails), the manifest should NOT
+ // reference that image or its annotations — ensuring consistency.
Shepherd shepherd = mock(Shepherd.class);
- // Create a mock MediaAsset
MediaAsset ma = mock(MediaAsset.class);
when(ma.getUUID()).thenReturn("test-media-uuid");
when(ma.getWidth()).thenReturn(800.0);
when(ma.getHeight()).thenReturn(600.0);
- when(ma.webURL()).thenReturn(null); // Skip actual image download in test
-
- // Create a mock Feature with bbox
- Feature feature = mock(Feature.class);
- JSONObject params = new JSONObject();
- params.put("x", 100);
- params.put("y", 200);
- params.put("width", 300);
- params.put("height", 400);
- params.put("theta", 0.5);
- when(feature.getParameters()).thenReturn(params);
-
- // Create a mock Annotation
+ when(ma.webURL()).thenReturn(null); // image cannot be fetched
+
Annotation ann = mock(Annotation.class);
when(ann.getId()).thenReturn("test-ann-uuid");
when(ann.getIAClass()).thenReturn("whale_shark");
@@ -54,12 +43,10 @@ void testBuildsCOCOStructure() throws Exception {
when(ann.getViewpoint()).thenReturn("left");
when(ann.getTheta()).thenReturn(0.5);
- // Create a mock MarkedIndividual
MarkedIndividual ind = mock(MarkedIndividual.class);
when(ind.getId()).thenReturn("test-individual-uuid");
when(ind.getDisplayName()).thenReturn("Stumpy");
- // Create a mock Encounter
Encounter enc = mock(Encounter.class);
ArrayList annotations = new ArrayList<>();
annotations.add(ann);
@@ -69,19 +56,16 @@ void testBuildsCOCOStructure() throws Exception {
List encounters = new ArrayList<>();
encounters.add(enc);
- // Run export
ByteArrayOutputStream baos = new ByteArrayOutputStream();
EncounterCOCOExportFile exportFile = new EncounterCOCOExportFile(encounters, shepherd);
exportFile.writeTo(baos);
- // Parse ZIP and extract annotations.json
byte[] zipBytes = baos.toByteArray();
assertTrue(zipBytes.length > 0, "Export should produce output");
String jsonContent = extractJsonFromZip(zipBytes);
assertNotNull(jsonContent, "Should contain annotations.json");
- // Verify JSON structure
JSONObject coco = new JSONObject(jsonContent);
assertTrue(coco.has("info"));
assertTrue(coco.has("licenses"));
@@ -89,21 +73,18 @@ void testBuildsCOCOStructure() throws Exception {
assertTrue(coco.has("images"));
assertTrue(coco.has("annotations"));
- // Verify categories
+ // Image failed to export, so both images and annotations arrays should be empty
+ assertEquals(0, coco.getJSONArray("images").length(),
+ "Failed images should be excluded from manifest");
+ assertEquals(0, coco.getJSONArray("annotations").length(),
+ "Annotations for failed images should be excluded from manifest");
+
+ // Categories are built from encounter data, independent of image success
JSONArray categories = coco.getJSONArray("categories");
assertEquals(1, categories.length());
assertEquals("whale_shark", categories.getJSONObject(0).getString("name"));
- // Verify annotations
- JSONArray anns = coco.getJSONArray("annotations");
- assertEquals(1, anns.length());
- JSONObject annJson = anns.getJSONObject(0);
- assertEquals("left", annJson.getString("viewpoint"));
- assertEquals(0.5, annJson.getDouble("theta"), 0.001);
- assertEquals("test-individual-uuid", annJson.getString("individual_uuid"));
- assertEquals("Stumpy", annJson.getString("name"));
-
- // Verify individual_id_mapping in info
+ // Individual mapping is also independent of image success
JSONObject info = coco.getJSONObject("info");
assertTrue(info.has("individual_id_mapping"));
JSONObject mapping = info.getJSONObject("individual_id_mapping");