REST /api/v0/acn/{instCode}/update accepts array of accessions for

MLSSTAT update

src/main/java/org/genesys2/server/servlet/controller/rest/AccessionController.java

@@ -17,12 +17,15 @@
 package org.genesys2.server.servlet.controller.rest;
 
 import java.io.IOException;
-import java.util.Iterator;
-import java.util.Map.Entry;
+import java.text.MessageFormat;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.impl.AccessionIdentifier3;
 import org.genesys2.server.service.GenesysService;
-import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.security.access.prepost.PreAuthorize;
@@ -37,6 +40,7 @@ import org.springframework.web.bind.annotation.ResponseBody;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ObjectNode;
 
 @Controller("restAccessionController")
 @PreAuthorize("isAuthenticated()")
@@ -80,58 +84,99 @@ public class AccessionController extends RestController {
 	boolean updateInstituteAccession(@PathVariable("instCode") String instCode, @RequestBody String content) throws JsonProcessingException, IOException {
 		// TODO Check user's permissions to update this WIEWS institute.
 		JsonNode json = mapper.readTree(content);
+		Map<DataJson, ObjectNode> batch = new HashMap<DataJson, ObjectNode>();
 
-		String genus = null;
-		String acceNumb = null;
-
-		for (Iterator<Entry<String, JsonNode>> fields = json.fields(); fields.hasNext();) {
-			Entry<String, JsonNode> field = fields.next();
-
-			String key = field.getKey();
-			JsonNode value = field.getValue();
-
-			if ("genus".equals(key)) {
-				genus = value.textValue();
-			} else if ("acceNumb".equals(key)) {
-				acceNumb = value.textValue();
+		if (json.isArray()) {
+			for (JsonNode j : json) {
+				DataJson dataJson = readAid3(j);
+				if (!instCode.equals(dataJson.instCode)) {
+					throw new RuntimeException("Accession does not belong to instCode=" + instCode + " acn=" + dataJson);
+				}
+				batch.put(dataJson, (ObjectNode) j);
 			}
+		} else {
+			DataJson dataJson = readAid3(json);
+			if (!instCode.equals(dataJson.instCode)) {
+				throw new RuntimeException("Accession does not belong to instCode=" + instCode + " acn=" + dataJson);
+			}
+			batch.put(dataJson, (ObjectNode) json);
 		}
 
-		if (LOG.isDebugEnabled())
-			LOG.debug("Loading accession " + instCode + "." + acceNumb + " genus=" + genus);
+		LOG.info("Batch processing " + batch.size() + " entries");
+		List<Accession> toSave = new ArrayList<Accession>();
 
+		for (DataJson dataJson : batch.keySet()) {
+			if (LOG.isDebugEnabled())
+				LOG.debug("Loading accession " + dataJson);
 
-		Accession accession = genesysService.getAccession(instCode, genus, acceNumb);
+			Accession accession = genesysService.getAccession(dataJson.instCode, dataJson.genus, dataJson.acceNumb);
 
 			if (accession == null) {
-			LOG.warn("No accession " + instCode + "." + acceNumb + " genus=" + genus);
-			throw new ResourceNotFoundException();
+				// LOG.warn("No accession " + dataJson);
+				continue;
 			}
 
+			ObjectNode accnJson = batch.get(dataJson);
 			boolean updated = false;
 
-		for (Iterator<Entry<String, JsonNode>> fields = json.fields(); fields.hasNext();) {
-			Entry<String, JsonNode> field = fields.next();
-
-			String key = field.getKey();
-			JsonNode value = field.getValue();
-
-			if ("mlsStat".equals(key)) {
+			JsonNode value = accnJson.get("mlsStat");
+			if (value != null) {
 				Boolean inMls = value.isNull() ? null : value.asBoolean();
 
 				if (inMls != accession.getMlsStatus()) {
-					if (LOG.isInfoEnabled())
-						LOG.info("Setting MLSSTAT to " + inMls);
+					if (LOG.isDebugEnabled())
+						LOG.debug("Setting MLSSTAT to " + inMls);
 					accession.setMlsStatus(inMls);
 					updated = true;
 				}
 			}
-		}
 
 			if (updated) {
-			genesysService.saveAccession(accession);
+				toSave.add(accession);
+			}
+		}
+
+		if (toSave.size() > 0) {
+			LOG.info("Storing " + toSave.size() + " accessions.");
+			genesysService.saveAccessions(toSave);
+		}
+
+		return toSave.size() > 0;
+	}
+
+	private DataJson readAid3(JsonNode json) {
+		DataJson dataJson = new DataJson();
+
+		dataJson.instCode = json.has("instCode") ? json.get("instCode").textValue() : null;
+		dataJson.acceNumb = json.has("acceNumb") ? json.get("acceNumb").textValue() : null;
+		dataJson.genus = json.has("genus") ? json.get("genus").textValue() : null;
+
+		return dataJson;
 	}
 
-		return updated;
+	public static class DataJson implements AccessionIdentifier3 {
+		public String instCode;
+		public String acceNumb;
+		public String genus;
+
+		@Override
+		public String getHoldingInstitute() {
+			return instCode;
+		}
+
+		@Override
+		public String getAccessionName() {
+			return acceNumb;
+		}
+
+		@Override
+		public String getGenus() {
+			return genus;
+		}
+
+		@Override
+		public String toString() {
+			return MessageFormat.format("AID3 instCode={0} acceNumb={1} genus={2}", instCode, acceNumb, genus);
+		}
 	}
 }