Merge branch 'release/2.1.1'

pom.xml

@@ -3,7 +3,7 @@
 
   <groupId>net.sumaris</groupId>
   <artifactId>sumaris-pod</artifactId>
-  <version>2.1.0</version>
+  <version>2.1.1</version>
   <packaging>pom</packaging>
   <name>SUMARiS</name>
   <description>SUMARiS :: Maven parent</description>
@@ -51,6 +51,7 @@
   <modules>
     <module>sumaris-core-shared</module>
     <module>sumaris-test-shared</module>
+    <module>sumaris-xml-query</module>
     <module>sumaris-core</module>
     <module>sumaris-importation</module>
     <module>sumaris-extraction</module>
@@ -120,7 +121,7 @@
     <cglib.version>3.3.0</cglib.version>
     <ehcache.version>3.8.1</ehcache.version>
     <lombok.version>1.18.24</lombok.version>
-    <xmlquery.version>1.8</xmlquery.version>
+    <xmlquery.version>3.2</xmlquery.version>
     <jdom2.version>2.0.6</jdom2.version>
     <jaxen.version>1.2.0</jaxen.version>
     <spring.version>5.3.24</spring.version>
@@ -1182,13 +1183,19 @@
             <encoding>${project.build.sourceEncoding}</encoding>
             <compilerArgs>
               <arg>--enable-preview</arg>
+              <!--<arg>-AgeneratedSourcesDirectory=${project.build.outputDirectory}</arg>-->
             </compilerArgs>
             <annotationProcessorPaths>
               <path>
                 <groupId>org.projectlombok</groupId>
                 <artifactId>lombok</artifactId>
                 <version>${lombok.version}</version>
               </path>
+              <!--<path>
+                <groupId>net.sumaris</groupId>
+                <artifactId>sumaris-xml-query</artifactId>
+                <version>2.1.1-SNAPSHOT</version>
+              </path>-->
             </annotationProcessorPaths>
           </configuration>
         </plugin>

src/scripts/release.sh

@@ -51,7 +51,7 @@ echo "---- Prepare release [OK]"
 echo ""
 
 echo "---- Performing release..."
-mvn clean deploy -DperformRelease -DskipTests -Dspring.datasource.platform=hsqldb
+mvn clean deploy -DperformRelease -DskipTests -Dspring.sql.init.platform=hsqldb
 [[ $? -ne 0 ]] && exit 1
 echo "---- Perform release [OK]"
 echo ""

sumaris-core-shared/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>net.sumaris</groupId>
     <artifactId>sumaris-pod</artifactId>
-    <version>2.1.0</version>
+    <version>2.1.1</version>
   </parent>
 
   <artifactId>sumaris-core-shared</artifactId>

sumaris-core-shared/src/main/java/net/sumaris/core/config/ApplicationConfigAliasProvider.java

@@ -0,0 +1,30 @@
+/*
+ * #%L
+ * SUMARiS
+ * %%
+ * Copyright (C) 2019 SUMARiS Consortium
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-3.0.html>.
+ * #L%
+ */
+
+package net.sumaris.core.config;
+
+import org.nuiton.config.ApplicationConfig;
+
+public interface ApplicationConfigAliasProvider {
+
+    void addAlias(ApplicationConfig applicationConfig);
+}

sumaris-core-shared/src/main/java/net/sumaris/core/config/SumarisConfiguration.java

@@ -184,6 +184,11 @@ protected SumarisConfiguration(ConfigurableEnvironment env,
 
         // Define Alias
         addAlias(applicationConfig);
+        for (ApplicationConfigProvider provider : providers) {
+            if (provider instanceof ApplicationConfigAliasProvider) {
+                ((ApplicationConfigAliasProvider)provider).addAlias(applicationConfig);
+            }
+        }
 
         // parse config file and inline arguments
         try {

sumaris-core-shared/src/main/java/net/sumaris/core/config/SumarisConfigurationOption.java

@@ -142,7 +142,7 @@ public enum SumarisConfigurationOption implements ConfigOptionDef {
     DB_CREATE_SCRIPT_PATH(
         "sumaris.persistence.db.script",
         n("sumaris.config.option.db.script.description"),
-        "classpath:net/sumaris/core/db/changelog/${spring.datasource.platform}/sumaris.script",
+        "classpath:net/sumaris/core/db/changelog/${spring.sql.init.platform}/sumaris.script",
         String.class,
         false),
 

sumaris-core-shared/src/main/java/net/sumaris/core/jms/JmsConfiguration.java

@@ -73,6 +73,7 @@ public JmsListenerContainerFactory<?> jmsListenerContainerFactory(
             DefaultJmsListenerContainerFactory factory = new DefaultJmsListenerContainerFactory();
             factory.setConnectionFactory(jmsConnectionFactory);
             factory.setMessageConverter(messageConverter);
+            factory.setPubSubDomain(true); // Use Topic instead of Queue
 
             jmsListenerContainerFactoryConfigurer
                     .ifPresent(c -> c.configure(factory, jmsConnectionFactory));

sumaris-core-shared/src/main/java/net/sumaris/core/util/Dates.java

@@ -50,6 +50,8 @@ public class Dates extends org.apache.commons.lang3.time.DateUtils{
 
     public static String ISO_TIMESTAMP_SPEC = "yyyy-MM-dd'T'HH:mm:ss.SSSXXX";
 
+    public static String CSV_DATE_TIME = "yyyy-MM-dd HH:mm:ss";
+
     /**
      * Remove a amount of month to a date
      *

sumaris-core-shared/src/main/java/net/sumaris/core/util/sound/SoundUtils.java

@@ -101,6 +101,20 @@ public static void playWaiting(int count) {
         }
     }
 
+    public static void playFinished() {
+        try {
+            SoundUtils.tone(800, 100);
+            Thread.sleep(200);
+            SoundUtils.tone(800, 700, 0.7);
+            Thread.sleep(350);
+            SoundUtils.tone(800, 1000);
+            Thread.sleep(3000);
+        }
+        catch (Exception e) {
+            log.debug("Cannot play error sound: " + e.getMessage());
+        }
+    }
+
     private void playSound(File f) {
         Preconditions.checkArgument(f.exists());
 

sumaris-core/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>net.sumaris</groupId>
     <artifactId>sumaris-pod</artifactId>
-    <version>2.1.0</version>
+    <version>2.1.1</version>
   </parent>
 
   <artifactId>sumaris-core</artifactId>
@@ -34,7 +34,7 @@
     <test>AllTests</test>
 
     <!-- Default datasource type -->
-    <spring.datasource.platform>hsqldb</spring.datasource.platform>
+    <spring.sql.init.platform>hsqldb</spring.sql.init.platform>
   </properties>
 
   <dependencies>
@@ -377,7 +377,7 @@
       <activation>
         <activeByDefault>true</activeByDefault>
         <property>
-          <name>spring.datasource.platform</name>
+          <name>spring.sql.init.platform</name>
           <value>hsqldb</value>
         </property>
       </activation>
@@ -391,7 +391,7 @@
         <jdbc.password />
         <jdbc.driver>org.hsqldb.jdbc.JDBCDriver</jdbc.driver>
         <jdbc.schema>PUBLIC</jdbc.schema>
-        <spring.datasource.platform>hsqldb</spring.datasource.platform>
+        <spring.sql.init.platform>hsqldb</spring.sql.init.platform>
         <hibernate.dialect>net.sumaris.core.dao.technical.hibernate.spatial.dialect.HSQLSpatialDialect</hibernate.dialect>
         <hibernate.jdbcBatchSize>15</hibernate.jdbcBatchSize>
       </properties>
@@ -408,7 +408,7 @@
       <id>oracle</id>
       <activation>
         <property>
-          <name>spring.datasource.platform</name>
+          <name>spring.sql.init.platform</name>
           <value>oracle</value>
         </property>
       </activation>
@@ -420,7 +420,7 @@
         <jdbc.password>SUMARIS_TU</jdbc.password>
         <jdbc.schema>SUMARIS_TU</jdbc.schema>
         <jdbc.driver>oracle.jdbc.driver.OracleDriver</jdbc.driver>
-        <spring.datasource.platform>oracle</spring.datasource.platform>
+        <spring.sql.init.platform>oracle</spring.sql.init.platform>
         <hibernate.dialect>net.sumaris.core.dao.technical.hibernate.spatial.dialect.OracleSpatial10gDialect</hibernate.dialect>
         <hibernate.jdbcBatchSize>15</hibernate.jdbcBatchSize>
       </properties>
@@ -437,7 +437,7 @@
       <id>pgsql</id>
       <activation>
         <property>
-          <name>spring.datasource.platform</name>
+          <name>spring.sql.init.platform</name>
           <value>pgsql</value>
         </property>
       </activation>
@@ -449,7 +449,7 @@
         <jdbc.password>sumaris</jdbc.password>
         <jdbc.schema>public</jdbc.schema>
         <jdbc.driver>org.postgresql.Driver</jdbc.driver>
-        <spring.datasource.platform>pgsql</spring.datasource.platform>
+        <spring.sql.init.platform>pgsql</spring.sql.init.platform>
         <hibernate.dialect>net.sumaris.core.dao.technical.hibernate.spatial.dialect.PostgreSQL10Dialect</hibernate.dialect>
         <hibernate.jdbcBatchSize>15</hibernate.jdbcBatchSize>
       </properties>

sumaris-core/src/main/filtered-resources/application-hsqldb.properties

@@ -3,7 +3,7 @@ spring.datasource.driver-class-name=org.hsqldb.jdbc.JDBCDriver
 spring.datasource.username=sa
 spring.datasource.password=
 spring.datasource.url=@jdbc.url@
-spring.datasource.platform=@env@
+spring.sql.init.platform=@env@
 spring.datasource.hikari.connectionTestQuery=SELECT 1 FROM STATUS WHERE ID=1
 spring.datasource.hikari.initializationFailTimeout=-1
 

sumaris-core/src/main/filtered-resources/application-oracle.properties

@@ -6,7 +6,7 @@ spring.jpa.database-platform=net.sumaris.core.dao.technical.hibernate.spatial.di
 spring.jpa.properties.hibernate.dialect=${spring.jpa.database-platform}
 
 # Database connection
-spring.datasource.platform=oracle
+spring.sql.init.platform=oracle
 spring.datasource.username=<USERNAME>
 spring.datasource.password=
 spring.jpa.properties.hibernate.default_catalog=

sumaris-core/src/main/filtered-resources/application-pgsql.properties

@@ -6,7 +6,7 @@ spring.jpa.database-platform=net.sumaris.core.dao.technical.hibernate.spatial.di
 spring.jpa.properties.hibernate.dialect=${spring.jpa.database-platform}
 
 # Database connection
-spring.datasource.platform=pgsql
+spring.sql.init.platform=pgsql
 spring.datasource.username=sumaris
 spring.datasource.password=sumaris
 spring.jpa.properties.hibernate.default_catalog=sumaristest

sumaris-core/src/main/filtered-resources/application.properties

@@ -19,7 +19,7 @@ [email protected]@
 spring.datasource.username=@jdbc.username@
 spring.datasource.password=@jdbc.password@
 spring.datasource.url=@jdbc.url@
-spring.datasource.platform=@env@
+spring.sql.init.platform=@env@
 spring.datasource.hikari.connectionTestQuery=SELECT 1 FROM STATUS WHERE ID=1
 spring.datasource.hikari.initializationFailTimeout=-1
 

sumaris-core/src/main/java/net/sumaris/cli/action/data/DenormalizeTripsAction.java

@@ -60,6 +60,6 @@ public void run() {
         tripService.denormalizeByFilter(filterBuilder.build(), progression);
 
         // Play a beep
-        SoundUtils.playWaiting(2);
+        SoundUtils.playFinished();
     }
 }

sumaris-core/src/main/java/net/sumaris/core/dao/technical/JobSpecifications.java

@@ -76,16 +76,17 @@ default Specification<ProcessingHistory> hasStatus(String... status) {
     }
 
     default Specification<ProcessingHistory> hasJobStatus(JobStatusEnum... jobStatus) {
-        Integer[] statusIds = Arrays.stream(jobStatus)
+        if (ArrayUtils.isEmpty(jobStatus)) return null;
+        List<Integer> statusIds = Arrays.stream(jobStatus)
             .map(JobStatusEnum::getProcessingStatus)
             .filter(Objects::nonNull)
             .map(ProcessingStatusEnum::getId)
             .filter(id -> id != null && id >= 0)
-            .toArray(Integer[]::new);
-        if (ArrayUtils.isEmpty(statusIds)) return null;
+            .toList();
+        if (CollectionUtils.isEmpty(statusIds)) return null;
         return hasInnerJoinIds(
             ProcessingHistory.Fields.PROCESSING_STATUS,
-            statusIds);
+            statusIds.toArray(new Integer[0]));
     }
 
     List<JobVO> findAll(JobFilterVO filter);

sumaris-core/src/main/java/net/sumaris/core/dao/technical/schema/SumarisDatabaseMetadata.java

@@ -198,9 +198,9 @@ public Set<String> findTableNamesByPrefix(String tablePrefix, String schema, Str
 				if (tableName.toUpperCase().startsWith(tablePrefix.toUpperCase())) {
 					result.add(rs.getString("TABLE_NAME"));
 				}
-				// JDBC meta return a bad tableName: should never occur !!
+				// JDBC meta return a bad tableName (e.g. because '_' special character) => ignore
 				else {
-					log.warn("Invalid getTables() result: Table name '{}' should not be returned, because its not match the pattern '{}'. Please check like pattern, or Daos.getEscapedForLike() function", tableName, tablePrefix);
+					log.trace("Ignoring getTables() result, because table name '{}' not start with '{}'", tableName, tablePrefix);
 				}
 			}
 			return result;

sumaris-core/src/main/java/net/sumaris/core/model/data/PhysicalGear.java

@@ -59,7 +59,6 @@ public class PhysicalGear implements IRootDataEntity<Integer>,
 
     @ManyToOne(fetch = FetchType.LAZY, targetEntity = Gear.class)
     @JoinColumn(name = "gear_fk", nullable = false)
-
     private Gear gear;
 
     @Column(length = LENGTH_COMMENTS)

sumaris-core/src/main/java/net/sumaris/core/model/referential/pmfm/PmfmEnum.java

@@ -77,6 +77,10 @@ public enum PmfmEnum implements IEntityEnum, Serializable {
     BATCH_CALCULATED_WEIGHT_LENGTH(122, "BATCH_CALCULATED_WEIGHT_LENGTH"),
     BATCH_CALCULATED_WEIGHT_LENGTH_SUM(123, "BATCH_CALCULATED_WEIGHT_LENGTH_SUM"),
     BATCH_SORTING(176, "BATCH_SORTING"), // Adagio = 'SORTED' (id=200)
+    CHILD_GEAR(400, "CHILD_GEAR"),
+    CATCH_WEIGHT(57, "CATCH_WEIGHT"),
+    DISCARD_WEIGHT(56, "DISCARD_WEIGHT"),
+    BATCH_GEAR_POSITION(411, "BATCH_GEAR_POSITION"),
 
     IS_DEAD(94, "IS_DEAD"),
     DISCARD_REASON(95, "DISCARD_REASON"),
@@ -92,10 +96,11 @@ public enum PmfmEnum implements IEntityEnum, Serializable {
 
     CONTROL_TYPE(130, "CONTROL_TYPE"),
 
+    SIZE_UNLI_CAT(141, "SIZE_UNLI_CAT"),
     PRESERVATION(150, "PRESERVATION"),
     DRESSING(151, "DRESSING"),
     SIZE_CATEGORY(174, "SIZE_CATEGORY"),
-
+    TRAWL_SIZE_CAT(418, "TRAWL_SIZE_CAT"),
     PACKAGING(177, "PACKAGING"),
 
     TOTAL_PRICE(270, "TOTAL_PRICE"),

sumaris-core/src/main/java/net/sumaris/core/model/technical/extraction/rdb/ProductRdbSpeciesList.java

@@ -61,7 +61,7 @@ public class ProductRdbSpeciesList implements Serializable, IEntity<Integer> {
     public static final String COLUMN_COMMERCIAL_SIZE_CATEGORY = "commercial_size_category";
     public static final String COLUMN_SUBSAMPLING_CATEGORY = "subsampling_category";
     public static final String COLUMN_WEIGHT= "weight";
-    public static final String COLUMN_SUBSAMPLING_WEIGHT = "subsampling_weight";
+    public static final String COLUMN_SUBSAMPLE_WEIGHT = "subsample_weight";
     public static final String COLUMN_LENGTH_CODE = "length_code";
 
     @Id
@@ -119,8 +119,8 @@ public class ProductRdbSpeciesList implements Serializable, IEntity<Integer> {
     @Column(nullable = false, scale = 12, precision = 2, name = COLUMN_WEIGHT)
     private Double weight;
 
-    @Column( scale = 12, precision = 2, name = COLUMN_SUBSAMPLING_WEIGHT)
-    private Double subsamplingWeight;
+    @Column( scale = 12, precision = 2, name = COLUMN_SUBSAMPLE_WEIGHT)
+    private Double subsampleWeight;
 
     @Column(length = 5, name = COLUMN_LENGTH_CODE)
     private String lengthCode;

sumaris-core/src/main/java/net/sumaris/core/service/data/denormalize/DenormalizeOperationServiceImpl.java

@@ -105,6 +105,9 @@ public DenormalizedTripResultVO denormalizeByFilter(@NonNull OperationFilterVO o
         // Select only operation that should be update (if not force)
         operationFilter.setNeedBatchDenormalization(!baseOptions.isForce());
 
+        // DEBUG - force denormalization
+        //if (!this.production && !baseOptions.isForce()) operationFilter.setNeedBatchDenormalization(false);
+
         long operationTotal = operationService.countByFilter(operationFilter);
 
         boolean hasMoreData;