Merge branch 'release-1.0.29'

Author: Paul Pavlidis

pom.xml

@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.0.28</version>
+	<version>1.0.29</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 	<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>

src/ubic/basecode/ontology/search/IndexerSelector.java

@@ -68,6 +68,13 @@ public IndexerSelector() {
         unwantedForIndexing.add( "http://www.ebi.ac.uk/efo/gwas_trait" );
         unwantedForIndexing.add( "http://www.ebi.ac.uk/efo/definition_editor" );
         unwantedForIndexing.add( "http://www.ebi.ac.uk/efo/example_of_usage" );
+        unwantedForIndexing.add( "http://www.ebi.ac.uk/efo/creator" );
+        unwantedForIndexing.add( "http://www.ebi.ac.uk/efo/definition_citation" );
+        unwantedForIndexing.add( "http://www.geneontology.org/formats/oboInOwl#created_by" );
+        unwantedForIndexing.add( "http://purl.org/dc/elements/1.1/rights" );
+        unwantedForIndexing.add( "http://purl.org/dc/terms/license" );
+        unwantedForIndexing.add( "http://www.w3.org/2000/01/rdf-schema#comment" );
+        unwantedForIndexing.add( "http://www.w3.org/2002/07/owl#versioninfo" );
         unwantedForIndexing.add( "http://www.geneontology.org/formats/oboInOwl#Definition" );
         unwantedForIndexing.add( "http://purl.obolibrary.org/obo/IAO_0000115" ); // 'definition' - too often has extra
                                                                                  // junk.
@@ -94,7 +101,7 @@ public IndexerSelector() {
         unwantedForIndexing.add( "http://purl.obolibrary.org/obo/UBPROP_0000005" ); // external comment
         unwantedForIndexing.add( "http://purl.obolibrary.org/obo/UBPROP_0000011" ); // development notes
         unwantedForIndexing.add( "http://xmlns.com/foaf/0.1/depicted_by" ); // not sure how often this comes up as a problem, but it does for one case
-        
+
         unwantedForIndexing.add( "http://purl.obolibrary.org/obo/CLO_0037275" ); // problematic cell line annotation as in "this is not a glioblastoma"
     }
 
@@ -155,7 +162,7 @@ public boolean test( Statement s ) {
         if ( !retain && log.isDebugEnabled() ) {
             log.debug( "Removed: " + s );
         }
-        
+
         return retain;
     }
 }

test/ubic/basecode/util/NetUtilsTest.java

@@ -80,9 +80,9 @@ final public void testFtpFileSize() throws Exception {
             log.warn( "Could not connect to ftp.ncbi.nlm.nih.gov, skipping test" );
             return;
         }
-        long actualValue = NetUtils.ftpFileSize( f, "genomes/Pan_troglodytes/WGS_12Dec2003/WIBR.seq007.fa" );
-        long expectedValue = 131446617;
-        assertEquals( expectedValue, actualValue, 100000 ); // don't really care if they change the file size....
+        long actualValue = NetUtils.ftpFileSize( f, "genomes/all/annotation_releases/1026970/102/Nannospalax_galili_AR102_annotation_report.xml" );
+        long expectedValue = 79819;
+        assertEquals( expectedValue, actualValue, 10000 ); // don't really care if they change the file size....
     }
 
     @Test