Merge branch 'hotfix-1.28.5'

PavlidisLab · Nov 25, 2022 · 9781080 · 9781080
2 parents 149417d + 1a70ea8
commit 9781080
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Showing 8 changed files with 23 additions and 26 deletions.
diff --git a/gemma-core/pom.xml b/gemma-core/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>gemma</artifactId>
         <groupId>gemma</groupId>
-        <version>1.28.4</version>
+        <version>1.28.5</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>gemma-core</artifactId>
@@ -384,7 +384,7 @@
         <dependency>
             <groupId>org.aspectj</groupId>
             <artifactId>aspectjweaver</artifactId>
-            <version>1.7.4</version>
+            <version>1.9.9.1</version>
         </dependency>
         <!-- bit array -->
         <!-- it can't be updated though because the binary format has changed, and we store those in the database -->

diff --git a/gemma-core/src/main/java/ubic/gemma/model/common/description/AnnotationValueObject.java b/gemma-core/src/main/java/ubic/gemma/model/common/description/AnnotationValueObject.java
@@ -56,6 +56,7 @@ public AnnotationValueObject( Long id ) {
     }
 
     public AnnotationValueObject( Characteristic c ) {
+        super( c );
         classUri = c.getCategoryUri();
         className = c.getCategory();
         termUri = c.getValueUri();

diff --git a/.../java/ubic/gemma/persistence/service/common/quantitationtype/QuantitationTypeDaoImpl.java b/.../java/ubic/gemma/persistence/service/common/quantitationtype/QuantitationTypeDaoImpl.java
@@ -166,6 +166,9 @@ public List<QuantitationTypeValueObject> loadValueObjectsWithExpressionExperimen
     }
 
     private void populateVectorType( Collection<QuantitationTypeValueObject> quantitationTypeValueObjects, ExpressionExperiment ee ) {
+        if ( quantitationTypeValueObjects.isEmpty() )
+            return;
+
         Set<Long> ids = quantitationTypeValueObjects.stream()
                 .map( QuantitationTypeValueObject::getId )
                 .collect( Collectors.toSet() );

diff --git a/gemma-core/src/main/resources/default.properties b/gemma-core/src/main/resources/default.properties
@@ -43,6 +43,8 @@ gemma.db.maxpoolidle=5
 gemma.db.maxtotal=75
 # This ensure some basic behaviors of our database
 gemma.db.sqlMode=STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION
+# Default timezone for storage of DATETIME that are mapped to exact moments (i.e. java.util.Date)
+gemma.db.timezone=America/Vancouver
 ############################################################
 # SECURITY
 # Used to elevate authorities for some methods.
@@ -141,7 +143,7 @@ gemma.transaction.maxretries=10
 #### Hibernate settings.  #####
 # See http://docs.jboss.org/hibernate/orm/3.3/reference/en/html/session-configuration.html
 # this should be set to validate in production
-gemma.hibernate.hbm2ddl.auto=none
+gemma.hibernate.hbm2ddl.auto=
 gemma.hibernate.max_fetch_depth=3
 gemma.hibernate.jdbc_fetch_size=128
 gemma.hibernate.default_fetch_size=32
@@ -157,7 +159,6 @@ gemma.hibernate.use_second_level_cache=true
 gemma.hibernate.generate_statistics=false
 gemma.hibernate.cache_use_structured_entries=false
 gemma.hibernate.format_sql=false
-gemma.hibernate.use_sql_comments=false
 gemma.hibernate.show_sql=false
 #### GRID CONFIG ####
 # Set to true to allow compute grid configuration

diff --git a/gemma-core/src/main/resources/ubic/gemma/applicationContext-hibernate.xml b/gemma-core/src/main/resources/ubic/gemma/applicationContext-hibernate.xml
@@ -67,6 +67,7 @@
 				<prop key="hibernate.dialect">org.hibernate.dialect.MySQL5InnoDBDialect</prop>
 				<prop key="hibernate.cache.query_cache_factory">org.hibernate.cache.StandardQueryCacheFactory</prop>
 				<!-- <prop key="hibernate.cache.region.factory_class">net.sf.ehcache.hibernate.EhCacheRegionFactory</prop> -->
+				<!--suppress SpringXmlModelInspection -->
 				<prop key="hibernate.hbm2ddl.auto">${gemma.hibernate.hbm2ddl.auto}</prop>
 				<prop key="hibernate.max_fetch_depth">${gemma.hibernate.max_fetch_depth}</prop>
 				<prop key="hibernate.jdbc.fetch_size">${gemma.hibernate.jdbc_fetch_size}</prop>
@@ -80,7 +81,6 @@
 				<prop key="hibernate.order_updates">${gemma.hibernate.order_updates}</prop>
 				<prop key="hibernate.order_inserts">${gemma.hibernate.order_inserts}</prop>
 				<prop key="hibernate.format_sql">${gemma.hibernate.format_sql}</prop>
-				<prop key="hibernate.use_sql_comments">${gemma.hibernate.use_sql_comments}</prop>
 				<prop key="hibernate.show_sql">${gemma.hibernate.show_sql}</prop>
 			</props>
 		</property>

diff --git a/gemma-core/src/main/resources/ubic/gemma/dataSource.xml b/gemma-core/src/main/resources/ubic/gemma/dataSource.xml
@@ -15,7 +15,7 @@
         <property name="maxWaitMillis" value="100000"/>
         <property name="testOnBorrow" value="true"/>
         <property name="validationQuery" value="SELECT 1"/>
-        <property name="connectionProperties" value="sessionVariables=sql_mode='${gemma.db.sqlMode}'"/>
+        <property name="connectionProperties" value="connectionTimeZone=${gemma.db.timezone};sessionVariables=sql_mode='${gemma.db.sqlMode}'"/>
     </bean>
 
 

diff --git a/gemma-web/pom.xml b/gemma-web/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>gemma</artifactId>
 		<groupId>gemma</groupId>
-		<version>1.28.4</version>
+		<version>1.28.5</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>gemma-web</artifactId>

diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
 	<name>Gemma</name>
 	<groupId>gemma</groupId>
 	<artifactId>gemma</artifactId>
-	<version>1.28.4</version>
+	<version>1.28.5</version>
 	<inceptionYear>2005</inceptionYear>
 	<description>The Gemma Project for meta-analysis of genomics data</description>
 	<url>https://gemma.msl.ubc.ca</url>
@@ -16,7 +16,7 @@
 	<parent>
 		<groupId>ubc.pavlab</groupId>
 		<artifactId>pavlab-starter-parent</artifactId>
-		<version>1.1.9</version>
+		<version>1.1.10</version>
 	</parent>
 	<modules>
 		<module>gemma-core</module>
@@ -354,7 +354,7 @@
 		<dependency>
 			<groupId>com.fasterxml.jackson.core</groupId>
 			<artifactId>jackson-databind</artifactId>
-			<version>${jackson.version}.2</version>
+			<version>${jackson.version}</version>
 		</dependency>
 
 		<!-- XML, XSLT and XPath -->
@@ -529,13 +529,6 @@
 				<version>7.1.1</version>
 			</plugin>
 		</plugins>
-		<extensions>
-			<extension>
-				<groupId>org.apache.maven.wagon</groupId>
-				<artifactId>wagon-ssh-external</artifactId>
-				<version>3.4.2</version>
-			</extension>
-		</extensions>
 	</build>
 	<repositories>
 		<repository>
@@ -565,17 +558,16 @@
 			</activation>
 			<distributionManagement>
 				<site>
-					<id>localDeploy</id>
-					<name>localDeploy</name>
-					<url>file:///space/gemmaData/gemma-devsite</url>
+					<id>pavlab</id>
+					<url>file:///space/web/maven-sites/${project.groupId}/gemma-${project.version}</url>
 				</site>
 			</distributionManagement>
 		</profile>
 	</profiles>
 	<distributionManagement>
 		<site>
-			<id>website</id>
-			<url>/space/gemmaData/gemma-devsite</url>
+			<id>pavlab</id>
+			<url>scpexe://frink.msl.ubc.ca/space/web/maven-sites/${project.groupId}/gemma-${project.version}</url>
 		</site>
 	</distributionManagement>
 	<reporting>
@@ -588,7 +580,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-javadoc-plugin</artifactId>
-				<version>3.3.1</version>
+				<version>3.3.2</version>
 				<configuration>
 					<quiet>true</quiet>
 					<source>8</source>
@@ -614,10 +606,10 @@
 		<spring.version>3.2.18.RELEASE</spring.version>
 		<spring.security.version>3.2.10.RELEASE</spring.security.version>
 		<jersey.version>2.25.1</jersey.version>
-		<jackson.version>2.13.4</jackson.version>
-		<swagger.version>2.2.4</swagger.version>
+		<jackson.version>2.14.1</jackson.version>
+		<swagger.version>2.2.7</swagger.version>
 		<jawr.version>3.9</jawr.version>
 		<lucene.version>3.6.2</lucene.version>
-		<slack.version>1.26.1</slack.version>
+		<slack.version>1.27.1</slack.version>
 	</properties>
 </project>