Merge branch 'accession-updates-instcode' into 'master'

Accession updates instcode

See merge request genesys-pgr/genesys-server!511

src/main/java/org/genesys2/server/api/v0/AccessionController.java

@@ -259,7 +259,7 @@ public class AccessionController extends ApiBaseController {
 					LOG.debug("Caused by {}", lastException.getMessage(), lastException);
 				}
 				// record error
-				response.add(new AccessionOpResponse(update.get("instituteCode").asText(), update.get("accessionNumber").asText(), update.get("taxonomy").get("genus").asText())
+				response.add(new AccessionOpResponse(update)
 					.setResult(new UpsertResult(UpsertResult.Type.ERROR)).setError(lastException.getMessage()));
 			}
 		}
@@ -327,7 +327,7 @@ public class AccessionController extends ApiBaseController {
 					LOG.info("Error deleting {}: {}", update.get("instituteCode").asText(), e.getMessage());
 				}
 
-				AccessionOpResponse accessionResponse = new AccessionOpResponse(update.get("instituteCode").asText(), update.get("accessionNumber").asText(), update.get("taxonomy").get("genus").asText());
+				AccessionOpResponse accessionResponse = new AccessionOpResponse(update);
 				accessionResponse.setError(getDetailedErrorMessage(e));
 				response.add(accessionResponse);
 			}

src/main/java/org/genesys2/server/api/v1/AccessionUploadController.java

@@ -160,7 +160,7 @@ public class AccessionUploadController {
 			if (lastException != null) {
 				LOG.warn("Upsert failed due to: {} data={}", lastException.getMessage(), update, lastException);
 				// record error
-				response.add(new AccessionOpResponse(update.get("instituteCode").asText(), update.get("accessionNumber").asText(), update.get("taxonomy").get("genus").asText())
+				response.add(new AccessionOpResponse(update)
 					.setResult(new UpsertResult(UpsertResult.Type.ERROR)).setError(getDetailedErrorMessage(lastException)));
 			}
 		}
@@ -227,7 +227,7 @@ public class AccessionUploadController {
 					LOG.info("Error deleting {}: {}", accn.get("instituteCode"), e.getMessage());
 				}
 
-				AccessionOpResponse accessionResponse = new AccessionOpResponse(accn.get("instituteCode").asText(), accn.get("accessionNumber").asText(), accn.get("taxonomy").get("genus").asText());
+				AccessionOpResponse accessionResponse = new AccessionOpResponse(accn);
 				accessionResponse.setError(getDetailedErrorMessage(e));
 				response.add(accessionResponse);
 			}

src/main/java/org/genesys2/server/api/v2/AccessionUploadController.java

@@ -149,7 +149,7 @@ public class AccessionUploadController extends ApiBaseController {
 			if (lastException != null) {
 				LOG.warn("Upsert failed due to: {} data={}", lastException.getMessage(), update, lastException);
 				// record error
-				response.add(new AccessionOpResponse(update.get("instituteCode").asText(), update.get("accessionNumber").asText(), update.get("taxonomy").get("genus").asText())
+				response.add(new AccessionOpResponse(update)
 						.setResult(new AccessionOpResponse.UpsertResult(AccessionOpResponse.UpsertResult.Type.ERROR)).setError(getDetailedErrorMessage(lastException)));
 			}
 		}
@@ -217,7 +217,7 @@ public class AccessionUploadController extends ApiBaseController {
 					LOG.info("Error deleting {}: {}", accn.get("instituteCode"), e.getMessage());
 				}
 
-				AccessionOpResponse accessionResponse = new AccessionOpResponse(accn.get("instituteCode").asText(), accn.get("accessionNumber").asText(), accn.get("taxonomy").get("genus").asText());
+				AccessionOpResponse accessionResponse = new AccessionOpResponse(accn);
 				accessionResponse.setError(getDetailedErrorMessage(e));
 				response.add(accessionResponse);
 			}

src/main/java/org/genesys2/server/model/genesys/AccessionAlias.java

@@ -51,8 +51,7 @@ public class AccessionAlias extends BasicModel implements AccessionRelated, Self
 
 	private static final Pattern HAS_WORD_CHARACTER = Pattern.compile("\\w", Pattern.MULTILINE);
 
-	// INSTCODE:alias
-	private static Pattern USED_BY_PATTERN = Pattern.compile("^(([A-Z]{3}\\d{3,4}):(.+))?$");
+	private static Pattern USED_BY_PATTERN = Pattern.compile("^((\\p{Alnum}+):(.+))?$");
 
 	public static enum AliasType {
 		ACCENAME(0), DONORNUMB(1), BREDNUMB(2), DATABASEID(3), LOCALNAME(4), OTHERNUMB(5), COLLNUMB(6);
@@ -101,9 +100,9 @@ public class AccessionAlias extends BasicModel implements AccessionRelated, Self
 	@Column(length = 2)
 	private String lang;
 
-	@javax.validation.constraints.Pattern(regexp = "[A-Z]{3}\\d{3,4}")
-	@Size(max = 7)
-	@Column(length = 7)
+	@javax.validation.constraints.Pattern(regexp = "\\p{Alnum}+")
+	@Size(max = 64)
+	@Column(length = 64)
 	private String usedBy;
 
 	public AccessionAlias() {

src/main/java/org/genesys2/server/service/worker/AccessionCounter.java

@@ -48,7 +48,7 @@ public class AccessionCounter implements InitializingBean, DisposableBean {
 	// Interval time (in ms) for scanning the queue for expired updates
 	private static final int DELAY_BETWEEN_QUEUESCANS = 5000; // 5 sec
 	// If a request comes before this delay (in ms), reschedule
-	private static final long MINTIME_BETWEEN_UPDATES = 60 * 60 * 1000; // 1 min
+	private static final long MINTIME_BETWEEN_UPDATES = 60 * 1000; // 1 min
 
 	private DelayQueue<DelayedObject<String>> instituteQueue;
 
@@ -150,7 +150,7 @@ public class AccessionCounter implements InitializingBean, DisposableBean {
 		@Override
 		public long getDelay(TimeUnit unit) {
 			long delay = unit.convert(expiryTime - System.currentTimeMillis(), TimeUnit.MILLISECONDS);
-			LOG.trace("{} scheduled in {}ms", this.obj, delay);
+			LOG.trace("{} scheduled in {}{}", this.obj, delay, unit.name());
 			return delay;
 		}
 

src/main/java/org/genesys2/server/service/worker/AccessionOpResponse.java

@@ -3,6 +3,11 @@ package org.genesys2.server.service.worker;
 import java.io.Serializable;
 import java.util.UUID;
 
+import org.genesys2.server.model.genesys.Accession;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.NullNode;
+
 /**
  * Upsert response
  */
@@ -10,6 +15,7 @@ public class AccessionOpResponse implements Serializable {
 	private static final long serialVersionUID = 3266359129838078166L;
 
 	private String instCode;
+	private String doi;
 	private String acceNumb;
 	private String genus;
 	private String error;
@@ -25,8 +31,7 @@ public class AccessionOpResponse implements Serializable {
 		}
 
 		/**
-		 * @param action
-		 *            UPSERT or INSERT or DELETE
+		 * @param action UPSERT or INSERT or DELETE
 		 */
 		public UpsertResult(Type action) {
 			this.action = action;
@@ -50,16 +55,42 @@ public class AccessionOpResponse implements Serializable {
 		}
 	}
 
-	public AccessionOpResponse(String instCode, String acceNumb, String genus) {
-		this.instCode = instCode;
-		this.acceNumb = acceNumb;
-		this.genus = genus;
+	public AccessionOpResponse(Accession accession) {
+		this.instCode = accession.getHoldingInstitute();
+		this.doi = accession.getDoi();
+		this.acceNumb = accession.getAccessionNumber();
+		this.genus = accession.getTaxonomy() != null ? accession.getTaxonomy().getGenus() : null;
+	}
+
+	public AccessionOpResponse(JsonNode accn) {
+		this.instCode = jsonT(accn, 0, "instituteCode");
+		this.doi = jsonT(accn, 0, "doi");
+		this.acceNumb = jsonT(accn, 0, "accessionNumber");
+		this.genus = jsonT(accn, 0, "taxonomy", "genus");
+	}
+
+	private static String jsonT(JsonNode node, int pos, String... path) {
+		if (node == null || pos > path.length - 1) {
+			return null;
+		}
+		JsonNode ch = node.get(path[pos]);
+		if (ch == null || ch instanceof NullNode) {
+			return null;
+		} else if (pos == path.length - 1) {
+			return ch.asText();
+		} else {
+			return jsonT(ch, pos + 1, path);
+		}
 	}
 
 	public String getInstCode() {
 		return instCode;
 	}
 
+	public String getDoi() {
+		return doi;
+	}
+
 	public String getAcceNumb() {
 		return acceNumb;
 	}

src/main/java/org/genesys2/server/service/worker/AccessionUploader.java

@@ -36,6 +36,7 @@ import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.time.StopWatch;
 import org.apache.commons.text.WordUtils;
 import org.genesys.blocks.model.BasicModel;
+import org.genesys.blocks.security.SecurityContextUtil;
 import org.genesys2.server.api.PleaseRetryException;
 import org.genesys2.server.exception.InvalidApiUsageException;
 import org.genesys2.server.model.genesys.Accession;
@@ -162,11 +163,11 @@ public class AccessionUploader implements InitializingBean {
 					throw new InvalidApiUsageException("instituteCode, accessionNumber OR doi missing in " + accn);
 				}
 				accessions.add(accession);
-				responses.add(new AccessionOpResponse(accession.getInstituteCode(), accession.getAccessionNumber(), accession.getTaxonomy().getGenus()));
+				responses.add(new AccessionOpResponse(accession));
 			} catch (IOException e) {
 				LOG.error("Could not parse input: {}", e.getMessage(), e);
 				accessions.add(null); // need to match get(index) with responses and updates
-				responses.add(new AccessionOpResponse(accn.get("instituteCode").asText(), accn.get("accessionNumber").asText(), accn.get("taxonomy").get("genus").asText())
+				responses.add(new AccessionOpResponse(accn)
 					.setResult(new UpsertResult(UpsertResult.Type.ERROR)).setError(e.getMessage()));
 			}
 		}
@@ -275,6 +276,9 @@ public class AccessionUploader implements InitializingBean {
 			if ("doi".equals(fieldName)) {
 				updateDoi(updateA.getDoi(), accession);
 			
+			} else if ("newInstituteCode".equals(fieldName)) {
+				updateInstitute(update.get("newInstituteCode").textValue(), accession);
+			
 			} else if ("accessionNumber".equals(fieldName) || "newAcceNumb".equals(fieldName)) {
 				updateAccessionNumber(update.get("accessionNumber"), update.get("newAcceNumb"), accession);
 
@@ -338,6 +342,22 @@ public class AccessionUploader implements InitializingBean {
 		return accession;
 	}
 
+	/**
+	 * Allow owner to change accession's institute code.
+	 * 
+	 * @param newInstituteCode
+	 * @param accession
+	 */
+	private void updateInstitute(String newInstituteCode, Accession accession) {
+		if (! newInstituteCode.equalsIgnoreCase(accession.getInstituteCode())) {
+			FaoInstitute newInstitute = faoInstituteRepository.findByCode(newInstituteCode);
+			if (SecurityContextUtil.hasRole("ADMINISTRATOR") || SecurityContextUtil.hasPermission(newInstitute, "WRITE")) {
+				accession.setInstitute(newInstitute);
+				accessionCounter.recountInstitute(newInstitute);
+			}
+		}
+	}
+
 	private void updateDoi(String doi, Accession accession) {
 		if (StringUtils.isNotBlank(doi)) {
 			if (accession.getDoi() != null && ! StringUtils.equals(doi, accession.getDoi())) {
@@ -703,7 +723,7 @@ public class AccessionUploader implements InitializingBean {
 				LOG.error("Could not parse input: {}", e.getMessage(), e);
 				toBeDeleted.add(null); // need to match get(index) with responses and updates
 
-				AccessionOpResponse response = new AccessionOpResponse(accn.get("instituteCode").asText(), accn.get("accessionNumber").asText(), accn.get("taxonomy").get("genus").asText());
+				AccessionOpResponse response = new AccessionOpResponse(accn);
 				response.setResult(new UpsertResult(UpsertResult.Type.ERROR)).setError(e.getMessage());
 				responses.add(response);
 			}
@@ -715,7 +735,7 @@ public class AccessionUploader implements InitializingBean {
 
 		for (Accession deletion: toBeDeleted) {
 			AccessionOpResponse response;
-			responses.add(response = new AccessionOpResponse(deletion.getHoldingInstitute(), deletion.getAccessionNumber(), deletion.getTaxonomy().getGenus()));
+			responses.add(response = new AccessionOpResponse(deletion));
 
 			Accession accession = existingAccessions.stream()
 					.filter(existing -> (