Merge branch 'hotfix-1.1.20'

Author: arteymix

pom.xml

@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.1.19</version>
+	<version>1.1.20</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 		<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
@@ -49,7 +49,7 @@
 		<dependency>
 			<groupId>org.apache.poi</groupId>
 			<artifactId>poi</artifactId>
-			<version>5.2.3</version>
+			<version>5.2.5</version>
 		</dependency>
 		<dependency>
 			<groupId>colt</groupId>
@@ -61,7 +61,7 @@
 		<dependency>
 			<groupId>commons-net</groupId>
 			<artifactId>commons-net</artifactId>
-			<version>3.9.0</version>
+			<version>3.10.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
@@ -76,12 +76,12 @@
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
-			<version>3.13.0</version>
+			<version>3.14.0</version>
 		</dependency>
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
-			<version>2.13.0</version>
+			<version>2.15.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
@@ -228,7 +228,7 @@
 		<dependency>
 			<groupId>com.opencsv</groupId>
 			<artifactId>opencsv</artifactId>
-			<version>5.8</version>
+			<version>5.9</version>
 			<exclusions>
 				<exclusion>
 					<groupId>commons-beanutils</groupId>
@@ -267,13 +267,13 @@
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-core</artifactId>
-			<version>2.19.0</version>
+			<version>2.21.1</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-slf4j-impl</artifactId>
-			<version>2.19.0</version>
+			<version>2.21.1</version>
 			<scope>test</scope>
 		</dependency>
 	</dependencies>

src/ubic/basecode/math/linearmodels/DesignMatrix.java

@@ -569,9 +569,17 @@ private DoubleMatrix<String, String> buildDesign( int columnNum, List<?> factorV
                 String contrastingValue = "";
                 assert tmp != null;
                 for ( int j = 0; j < tmp.rows(); j++ ) {
-                    boolean isBaseline = !factorValues.get( j ).equals( level );
+                    Object fv = factorValues.get(j);
+
+                    if (fv == null) {
+                        // This happens if a factorvalue is not assigned somehwere, as in a DEExclude situation.
+                        // In Gemma we can reach this during batch correction.
+                        throw new IllegalArgumentException("Null value for factor " + factorName + " at row " + j);
+                    }
+
+                    boolean isBaseline = !fv.equals( level );
                     if ( !isBaseline ) {
-                        contrastingValue = ( String ) factorValues.get( j );
+                        contrastingValue = ( String ) fv;
                     }
                     tmp.set( j, currentColumn, isBaseline ? 0.0 : 1.0 );
                 }

src/ubic/basecode/ontology/jena/AbstractOntologyResource.java

@@ -65,12 +65,6 @@ public String getLabel() {
         if ( label == null ) {
             label = res.getLabel( null );
         }
-        if ( label == null ) {
-            label = res.getLocalName();
-        }
-        if ( label == null ) {
-            label = res.getURI();
-        }
         return label;
     }
 
@@ -113,6 +107,12 @@ public int hashCode() {
     @Override
     public String toString() {
         String s = getLabel();
+        if ( s == null ) {
+            s = res.getLocalName();
+        }
+        if ( s == null ) {
+            s = res.getURI();
+        }
         if ( s == null ) {
             s = res.toString();
         }

src/ubic/basecode/ontology/jena/JenaUtils.java

@@ -1,5 +1,6 @@
 package ubic.basecode.ontology.jena;
 
+import com.hp.hpl.jena.ontology.ConversionException;
 import com.hp.hpl.jena.ontology.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.Restriction;
@@ -42,7 +43,15 @@ private static Collection<OntClass> getParentsInternal( OntModel model, Collecti
         ontClasses = ontClasses.stream()
                 .map( t -> t.inModel( model ) )
                 .filter( t -> t.canAs( OntClass.class ) )
-                .map( t -> t.as( OntClass.class ) )
+                .map( t -> {
+                    try {
+                        return t.as( OntClass.class );
+                    } catch ( ConversionException e ) {
+                        log.error( "Conversion failed for " + t, e );
+                        return null;
+                    }
+                } )
+                .filter( Objects::nonNull )
                 .collect( Collectors.toList() );
         if ( ontClasses.isEmpty() ) {
             return Collections.emptySet();
@@ -104,7 +113,15 @@ public static Collection<OntClass> getChildrenInternal( OntModel model, Collecti
         terms = terms.stream()
                 .map( t -> t.inModel( model ) )
                 .filter( t -> t.canAs( OntClass.class ) )
-                .map( t -> t.as( OntClass.class ) )
+                .map( t -> {
+                    try {
+                        return t.as( OntClass.class );
+                    } catch ( ConversionException e ) {
+                        log.error( "Conversion failed for " + t, e );
+                        return null;
+                    }
+                } )
+                .filter( Objects::nonNull )
                 .collect( Collectors.toList() );
         if ( terms.isEmpty() ) {
             return Collections.emptySet();

src/ubic/basecode/ontology/model/OntologyResource.java

@@ -28,11 +28,13 @@ public interface OntologyResource extends Comparable<OntologyResource> {
     /**
      * A label, if known, otherwise null.
      */
+    @Nullable
     String getLabel();
 
     /**
      * A URI if known, otherwise null.
      */
+    @Nullable
     String getUri();
 
     /**

test/ubic/basecode/math/TestStats.java

@@ -146,6 +146,14 @@ public final void testNumberOfDistinctValues() {
         actualReturn = Stats.numberofDistinctValues( new DoubleArrayList( new double[] { 1.0, 1.0, 3.0, 4.0, 4.00001,
                 5.0, 6.0 } ), 0.00001 );
         assertEquals( 6, actualReturn );
+
+        double[] rowAsList = new double[]{8.6154, 8.0668, 8.3417, 6.4633, 9.2136, 8.5676, 7.2155, 7.1609, 8.4329, 8.7668, 8.2165, 7.237, 9.3366,
+                6.8416, 8.2402, 7.4053, 6.8839, 7.5707, 6.9576, -2.0648, -2.0648, 0.0407, -2.0648, -2.0648, -2.0648, -2.0648, -2.0648, -2.0648,
+                -2.0648, -2.0648, -2.0648, -2.0648, -2.0648, -2.0648, -2.0648, -2.0648, -2.0648, -2.0648};
+        Double r = Stats.fractionDistinctValuesNonNA(new DoubleArrayList(rowAsList), 0.001);
+
+        assertEquals(0.552, r, 0.01);
+
     }