Merge branch 'release-1.0.25'

Author: tesar-stepan

pom.xml

@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.0.24</version>
+	<version>1.0.25</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 	<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>

src/ontology.properties

@@ -13,23 +13,30 @@ load.nifstdOntology=false
 load.experimentalFactorOntology=false
 load.uberonOntology=false
 
-url.chebiOntology=http://ontologies.berkeleybop.org/chebi.owl
-url.diseaseOntology=http://ontologies.berkeleybop.org/doid.owl
-url.cellTypeOntology=http://ontologies.berkeleybop.org/cl.owl
-url.mouseDevelOntology=http://ontologies.berkeleybop.org/emap.owl
-url.humanDevelOntology=http://ontologies.berkeleybop.org/ehdaa2.owl
-url.mammalPhenotypeOntology=http://ontologies.berkeleybop.org/mp.owl
-url.humanPhenotypeOntology=http://ontologies.berkeleybop.org/hp.owl
+# where possible, use URLs from http://www.obofoundry.org/
+url.chebiOntology=http://purl.obolibrary.org/obo/chebi.owl
+url.diseaseOntology=http://purl.obolibrary.org/obo/doid.owl
+url.cellTypeOntology=http://purl.obolibrary.org/obo/cl.owl
+url.mouseDevelOntology=http://purl.obolibrary.org/obo/emapa.owl
+url.humanDevelOntology=http://purl.obolibrary.org/obo/ehdaa2.owl
+url.mammalPhenotypeOntology=http://purl.obolibrary.org/obo/mp.owl
+url.humanPhenotypeOntology=http://purl.obolibrary.org/obo/hp.owl
+url.seqOntology=http://purl.obolibrary.org/obo/so.owl
+url.unitsOntology=http://purl.obolibrary.org/obo/uo.owl
+url.cellLineOntology=https://raw.githubusercontent.com/CLO-ontology/CLO/master/src/ontology/clo-merged.owl
+# Uberon version without extensions: I think this is the right fil from purl
+#url.uberonOntology=http://ontologies.berkeleybop.org/uberon.owl
+url.uberonOntology=http://purl.obolibrary.org/obo/uberon.owl
+
+# as recommended at https://www.ebi.ac.uk/efo/faq.html#efodownload
+url.efOntology=https://raw.githubusercontent.com/EBISPOT/efo/master/efo.owl
 url.obiOntology=http://svn.code.sf.net/p/obi/code/releases/2016-10-11/obi.owl
-url.seqOntology=http://ontologies.berkeleybop.org/so.owl
-url.unitsOntology=http://ontologies.berkeleybop.org/uo.owl
-url.cellLineOntology=https://raw.githubusercontent.com/CLO-ontology/CLO/master/src/ontology/clo.owl
-url.efOntology=https://www.ebi.ac.uk/efo/efo.owl
-# version without extensions:
-url.uberonOntology=http://ontologies.berkeleybop.org/uberon.owl
 
+
+# no longer actively used.
 url.nifstdOntology=http://ontology.neuinfo.org/NIF/nif-gemma.owl
-url.fmaOntology=http://ontologies.berkeleybop.org/fma.owl
+url.fmaOntology=http://purl.obolibrary.org/obo/fma.owl
 
 ontology.index.dir=ontology.index.dir
 ontology.cache.dir=
+ncbo.api.key=

src/ubic/basecode/ontology/OntologyLoader.java

@@ -25,6 +25,7 @@
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.Reader;
+import java.net.HttpURLConnection;
 import java.net.URL;
 import java.net.URLConnection;
 import java.nio.file.Files;
@@ -59,7 +60,7 @@
 /**
  * Reads ontologies from OWL resources
  * 
- * @author paul
+ * @author  paul
  * @version $Id$
  */
 public class OntologyLoader {
@@ -70,13 +71,13 @@ public class OntologyLoader {
     private static final String TMP_CACHE_SUFFIX = ".tmp";
 
     /**
-     * @param url
-     * @param model
+     * @param  url
+     * @param  model
      * @return
      */
     public static Collection<OntologyResource> initialize( String url, OntModel model ) {
 
-        Collection<OntologyResource> result = new HashSet<OntologyResource>();
+        Collection<OntologyResource> result = new HashSet<>();
 
         ExtendedIterator<OntClass> classIt = model.listClasses();
         int count = 0;
@@ -139,9 +140,9 @@ public static Collection<OntologyResource> initialize( String url, OntModel mode
     /**
      * Load an ontology into memory. Use this type of model when fast access is critical and memory is available.
      * 
-     * @param is
-     * @param url, used as a key
-     * @param spec
+     * @param  is
+     * @param       url, used as a key
+     * @param  spec
      * @return
      */
     public static OntModel loadMemoryModel( InputStream is, String url, OntModelSpec spec ) {
@@ -154,7 +155,7 @@ public static OntModel loadMemoryModel( InputStream is, String url, OntModelSpec
      * Load an ontology into memory. Use this type of model when fast access is critical and memory is available. Uses
      * OWL_MEM_TRANS_INF
      * 
-     * @param url
+     * @param  url
      * @return
      */
     public static OntModel loadMemoryModel( String url ) {
@@ -166,7 +167,7 @@ public static OntModel loadMemoryModel( String url ) {
      * OWL_MEM_TRANS_INF
      * If load from URL fails, attempt to load from disk cache under @cacheName.
      * 
-     * @param url
+     * @param  url
      * @return
      */
     public static OntModel loadMemoryModel( String url, String cacheName ) {
@@ -176,7 +177,7 @@ public static OntModel loadMemoryModel( String url, String cacheName ) {
     /**
      * Load an ontology into memory. Use this type of model when fast access is critical and memory is available.
      * 
-     * @param url
+     * @param  url
      * @return
      */
     public static OntModel loadMemoryModel( String url, OntModelSpec spec ) {
@@ -187,9 +188,9 @@ public static OntModel loadMemoryModel( String url, OntModelSpec spec ) {
      * Load an ontology into memory. Use this type of model when fast access is critical and memory is available.
      * If load from URL fails, attempt to load from disk cache under @cacheName.
      * 
-     * @param url
-     * @param spec e.g. OWL_MEM_TRANS_INF
-     * @param cacheName unique name of this ontology, will be used to load from disk in case of failed url connection
+     * @param  url
+     * @param  spec      e.g. OWL_MEM_TRANS_INF
+     * @param  cacheName unique name of this ontology, will be used to load from disk in case of failed url connection
      * @return
      */
     public static OntModel loadMemoryModel( String url, OntModelSpec spec, String cacheName ) {
@@ -205,15 +206,34 @@ public static OntModel loadMemoryModel( String url, OntModelSpec spec, String ca
                 // help ensure mis-configured web servers aren't causing trouble.
                 urlc.setRequestProperty( "Accept", "application/rdf+xml" );
 
+                try {
+                    HttpURLConnection c = ( HttpURLConnection ) urlc;
+                    c.setInstanceFollowRedirects( true );
+                } catch ( ClassCastException e ) {
+                    // not via http, using a FileURLConnection.
+                }
+
                 if ( tries > 0 ) {
                     log.info( "Retrying connecting to " + url + " [" + tries + "/" + MAX_CONNECTION_TRIES
                             + " of max tries" );
                 } else {
-                    log.info( "Connecting to ontology from " + url );
+                    log.info( "Connecting to " + url );
                 }
 
                 urlc.connect(); // Will error here on bad URL
 
+                if ( urlc instanceof HttpURLConnection ) {
+                    String newUrl = urlc.getHeaderField( "Location" );
+
+                    if ( StringUtils.isNotBlank( newUrl ) ) {
+                        log.info( "Redirect to " + newUrl );
+                        urlc = new URL( newUrl ).openConnection();
+                        // help ensure mis-configured web servers aren't causing trouble.
+                        urlc.setRequestProperty( "Accept", "application/rdf+xml" );
+                        urlc.connect();
+                    }
+                }
+
                 break;
             } catch ( IOException e ) {
                 // try to recover.
@@ -343,7 +363,7 @@ public static boolean deleteOldCache( String cacheName ) {
     /**
      * Get model that is entirely in memory with default OntModelSpec.OWL_MEM_RDFS_INF.
      * 
-     * @param url
+     * @param  url
      * @return
      */
     static OntModel getMemoryModel( String url ) {
@@ -353,8 +373,8 @@ static OntModel getMemoryModel( String url ) {
     /**
      * Get model that is entirely in memory.
      * 
-     * @param url
-     * @param specification
+     * @param  url
+     * @param  specification
      * @return
      */
     static OntModel getMemoryModel( String url, OntModelSpec specification ) {
@@ -370,7 +390,7 @@ static OntModel getMemoryModel( String url, OntModelSpec specification ) {
     }
 
     /**
-     * @param name
+     * @param  name
      * @return
      */
     public static File getDiskCachePath( String name ) {
@@ -379,18 +399,16 @@ public static File getDiskCachePath( String name ) {
             return null;
         }
 
-        if (!new File(ontologyDir).exists()) {
-            new File(ontologyDir).mkdirs();
+        if ( !new File( ontologyDir ).exists() ) {
+            new File( ontologyDir ).mkdirs();
         }
-        
+
         assert ontologyDir != null;
 
         String path = ontologyDir + File.separator + "ontology" + File.separator + name;
 
         File indexFile = new File( path );
-        
-       
-        
+
         return indexFile;
     }
 

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

@@ -1,13 +1,13 @@
 /*
  * The baseCode project
- * 
+ *
  * Copyright (c) 2013 University of British Columbia
- * 
+ *
  * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with
  * the License. You may obtain a copy of the License at
- * 
+ *
  * http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on
  * an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the
  * specific language governing permissions and limitations under the License.
@@ -38,18 +38,17 @@
 
 /**
  * Represents a class in an ontology
- * 
+ *
  * @author Paul
- * @version $Id$
  */
 public class OntologyTermImpl extends AbstractOntologyResource implements OntologyTerm {
 
     private static final String HAS_ALTERNATE_ID = "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId";
     private static final String NOTHING = "http://www.w3.org/2002/07/owl#Nothing";
-    private static Set<String> REJECT_PARENT_URI = new HashSet<String>();
+    private static Set<String> REJECT_PARENT_URI = new HashSet<>();
 
     /**
-     * 
+     *
      */
     private static final long serialVersionUID = 1L;
 
@@ -95,7 +94,7 @@ public boolean equals( Object obj ) {
 
     @Override
     public Collection<String> getAlternativeIds() {
-        Collection<String> results = new HashSet<String>();
+        Collection<String> results = new HashSet<>();
 
         Property alternate = ResourceFactory.createProperty( HAS_ALTERNATE_ID );
         for ( StmtIterator it = this.ontResource.listProperties( alternate ); it.hasNext(); ) {
@@ -109,7 +108,7 @@ public Collection<String> getAlternativeIds() {
 
     @Override
     public Collection<AnnotationProperty> getAnnotations() {
-        Collection<AnnotationProperty> annots = new HashSet<AnnotationProperty>();
+        Collection<AnnotationProperty> annots = new HashSet<>();
         StmtIterator iterator = ontResource.listProperties();
         // this is a little slow because we have to go through all statements for the term.
         while ( iterator.hasNext() ) {
@@ -126,14 +125,14 @@ public Collection<AnnotationProperty> getAnnotations() {
 
     @Override
     public Collection<OntologyTerm> getChildren( boolean direct ) {
-        Collection<OntologyTerm> result = new HashSet<OntologyTerm>();
+        Collection<OntologyTerm> result = new HashSet<>();
         getChildren( direct, result );
         return result;
     }
 
     /*
      * (non-Javadoc)
-     * 
+     *
      * @see ubic.gemma.ontology.OntologyTerm#getComment()
      */
     @Override
@@ -144,7 +143,7 @@ public String getComment() {
 
     /*
      * (non-Javadoc)
-     * 
+     *
      * @see ubic.gemma.ontology.OntologyTerm#getIndividuals()
      */
     @Override
@@ -153,12 +152,12 @@ public Collection<OntologyIndividual> getIndividuals() {
     }
 
     /**
-     * @param direct
+     * @param  direct
      * @return
      */
     @Override
     public Collection<OntologyIndividual> getIndividuals( boolean direct ) {
-        Collection<OntologyIndividual> inds = new HashSet<OntologyIndividual>();
+        Collection<OntologyIndividual> inds = new HashSet<>();
         ExtendedIterator<? extends OntResource> iterator = this.ontResource.listInstances( direct );
         while ( iterator.hasNext() ) {
             Individual i = ( Individual ) iterator.next();
@@ -184,20 +183,20 @@ public Object getModel() {
 
     @Override
     public Collection<OntologyTerm> getParents( boolean direct ) {
-        Collection<OntologyTerm> result = new HashSet<OntologyTerm>();
+        Collection<OntologyTerm> result = new HashSet<>();
         this.getParents( direct, result );
         return result;
     }
 
     /**
-     * 
+     *
      */
     @Override
     public Collection<OntologyRestriction> getRestrictions() {
         /*
          * Remember that restrictions are superclasses.
          */
-        Collection<OntologyRestriction> result = new HashSet<OntologyRestriction>();
+        Collection<OntologyRestriction> result = new HashSet<>();
         ExtendedIterator<OntClass> iterator = ontResource.listSuperClasses( false );
         while ( iterator.hasNext() ) {
             OntClass c = iterator.next();
@@ -248,7 +247,7 @@ public Collection<OntologyRestriction> getRestrictions() {
 
     /*
      * (non-Javadoc)
-     * 
+     *
      * @see ubic.gemma.analysis.ontology.OntologyTerm#getTerm()
      */
     @Override
@@ -286,7 +285,7 @@ public int hashCode() {
 
     /*
      * (non-Javadoc)
-     * 
+     *
      * @see ubic.gemma.analysis.ontology.OntologyTerm#isRoot()
      */
     @Override
@@ -296,7 +295,7 @@ public boolean isRoot() {
 
     /*
      * (non-Javadoc)
-     * 
+     *
      * @see ubic.basecode.ontology.model.OntologyTerm#isTermObsolete()
      */
     @Override