Added AccessionFilter#alias support

- alias name must contain at least one word character (number or letter)

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

@@ -45,6 +45,8 @@ public class AccessionAlias extends BasicModel implements AccessionRelated, Self
 
 	private static final long serialVersionUID = 4990299133164025782L;
 
+	private static final Pattern HAS_WORD_CHARACTER = Pattern.compile("\\w", Pattern.MULTILINE);
+
 	private static Pattern USED_BY_PATTERN = Pattern.compile("^((\\p{Alnum}+):(.+))?$");
 
 	public static enum AliasType {
@@ -99,15 +101,19 @@ public class AccessionAlias extends BasicModel implements AccessionRelated, Self
 
 	public AccessionAlias(AliasType aliasType, String name) {
 		this.aliasType = aliasType;
-		Matcher m = USED_BY_PATTERN.matcher(name);
-		if (m.matches()) {
-			this.usedBy = StringUtils.trimToNull(m.group(2));
-			this.name = StringUtils.trimToNull(m.group(3));
-		} else {
-			if (name.startsWith(":")) {
-				name = StringUtils.trimToNull(name.substring(1));
+		if (name != null) {
+			Matcher m = USED_BY_PATTERN.matcher(name);
+			if (m.matches()) {
+				this.usedBy = StringUtils.trimToNull(m.group(2));
+				this.name = StringUtils.trimToNull(m.group(3));
+			} else {
+				if (name.startsWith(":")) {
+					name = StringUtils.trimToNull(name.substring(1));
+				}
+				this.name = name;
 			}
-			this.name = name;
+		} else {
+			this.name = null;
 		}
 	}
 
@@ -167,7 +173,7 @@ public class AccessionAlias extends BasicModel implements AccessionRelated, Self
 	}
 	
 	public boolean isEmpty() {
-		return StringUtils.isBlank(name);
+		return StringUtils.isBlank(name) || ! HAS_WORD_CHARACTER.matcher(name).find();
 	}
 
 	@Override

src/main/java/org/genesys2/server/service/filter/AccessionFilter.java

@@ -91,6 +91,9 @@ public class AccessionFilter extends UuidModelFilter<AccessionFilter, Accession>
 	/** acce.lists uuid */
 	public Set<UUID> list;
 
+	/** accession aliases */
+	public StringFilter alias;
+
 
 	/* (non-Javadoc)
 	 * @see org.genesys.blocks.model.filters.BasicModelFilter#buildQuery()
@@ -169,6 +172,9 @@ public class AccessionFilter extends UuidModelFilter<AccessionFilter, Accession>
 		if (CollectionUtil.isNotEmpty(uuid)) {
 			and.and(accession.accessionId.uuid.in(uuid));
 		}
+		if (alias != null) {
+			and.and(alias.buildQuery(accession.accessionId.aliases.any().name));
+		}
 		// TODO Do we have to change this?
 		if (sgsv != null) {
 			and.and(accession.accessionId.duplSite.any().eq("NOR051"));

src/main/java/org/genesys2/server/service/filter/AppliedFiltersConverter.java

@@ -235,6 +235,10 @@ public class AppliedFiltersConverter {
 			f.lastModifiedDate = convertDateFilter(af);
 			break;
 		}
+		case FilterConstants.ALIAS: {
+			f.alias = convertStringFilter(af);
+			break;
+		}
 		default:
 			throw new RuntimeException("Unhandled Accession filter property=" + filterName);
 		}

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

@@ -409,7 +409,7 @@ public class AccessionUploader implements InitializingBean {
 				List<AccessionRemark> toRemove = existing.stream().filter(ex -> ex == null || ex.isEmpty() || remarks.stream().filter(rem -> ex.equalTo(rem)).count() == 0).collect(
 					Collectors.toList());
 				if (!toRemove.isEmpty() || !toAdd.isEmpty()) {
-					LOG.info("Removing: {} Adding: {}", toRemove, toAdd);
+					LOG.trace("Removing: {} Adding: {}", toRemove, toAdd);
 				}
 				existing.removeAll(toRemove);
 				existing.addAll(toAdd);

src/main/resources/liquibase/liquibase-changeLog.yml

@@ -4340,12 +4340,22 @@ databaseChangeLog:
                    join taxonomy2 t2 on a.taxonomyId2 = t2.id;
 
 - changeSet:
-      id: 1538732843596-5
-      author: vpavlov
-      comment: drop subset_accession
+      id:              1538732843596-5
+      author:          vpavlov
+      comment:         drop subset_accession
       changes:
       - dropTable:
-            tableName:                     subset_accession
+            tableName: subset_accession
+
+- changeSet:
+    id:                1539510451000-1
+    author:            mobreza
+    comment:           Add index on accession_alias#name
+    changes:
+    - sql:
+        sql:           >-
+           CREATE INDEX UK_cus8xep8hi5fv42o3ivu0name ON accession_alias(name(250))
+
 
 # ENABLE AFTER SOME TIME
 # - changeSet:

src/test/java/org/genesys/test/simpletest/NamesTest.java

@@ -16,6 +16,9 @@
 
 package org.genesys.test.simpletest;
 
+import static org.hamcrest.CoreMatchers.*;
+import static org.junit.Assert.assertThat;
+
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -24,6 +27,8 @@ import java.util.Set;
 import org.apache.commons.lang.ArrayUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.genesys.test.base.NoContextTest;
+import org.genesys2.server.model.genesys.AccessionAlias;
+import org.genesys2.server.model.genesys.AccessionAlias.AliasType;
 import org.junit.Test;
 
 public class NamesTest extends NoContextTest {
@@ -92,4 +97,27 @@ public class NamesTest extends NoContextTest {
 		}
 		return score;
 	}
+	
+	@Test
+	public void testAliasIsBlank() {
+		assertThat(new AccessionAlias(AliasType.ACCENAME, "").isEmpty(), is(true));
+		assertThat(new AccessionAlias(AliasType.OTHERNUMB, "-").isEmpty(), is(true));
+		assertThat(new AccessionAlias(AliasType.ACCENAME, null).isEmpty(), is(true));
+
+		assertThat(new AccessionAlias(AliasType.ACCENAME, "a").isEmpty(), is(false));
+		assertThat(new AccessionAlias(AliasType.ACCENAME, "0").isEmpty(), is(false));
+		assertThat(new AccessionAlias(AliasType.ACCENAME, "Z").isEmpty(), is(false));
+
+		assertThat(new AccessionAlias(AliasType.ACCENAME, "a0").isEmpty(), is(false));
+		assertThat(new AccessionAlias(AliasType.ACCENAME, "0d").isEmpty(), is(false));
+		assertThat(new AccessionAlias(AliasType.ACCENAME, "Z1").isEmpty(), is(false));
+
+		assertThat(new AccessionAlias(AliasType.ACCENAME, "aa-").isEmpty(), is(false));
+		assertThat(new AccessionAlias(AliasType.ACCENAME, "00-").isEmpty(), is(false));
+		assertThat(new AccessionAlias(AliasType.ACCENAME, "ZZ-").isEmpty(), is(false));
+
+		assertThat(new AccessionAlias(AliasType.ACCENAME, "aa-1").isEmpty(), is(false));
+		assertThat(new AccessionAlias(AliasType.ACCENAME, "00-2").isEmpty(), is(false));
+		assertThat(new AccessionAlias(AliasType.ACCENAME, "ZZ-3").isEmpty(), is(false));
+}
 }