Merge branch 'release-1.0.26'

Author: Paul Pavlidis

pom.xml

@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.0.25</version>
+	<version>1.0.26</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 	<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
@@ -15,32 +15,15 @@
 		<url>http://www.msl.ubc.ca/</url>
 	</organization>
 	<packaging>jar</packaging>
-	<scm>
-		<connection>scm:cvs:ext:@otto.pavlab.chibi.ubc.ca:/cvs:baseCode</connection>
-		<developerConnection>scm:cvs:ext:@otto.pavlab.chibi.ubc.ca:/cvs:baseCode</developerConnection>
-		<tag>baseCode-1_0_16</tag>
-	</scm>
 	<issueManagement>
-		<system>Bugzilla</system>
+		<system>GitHub</system>
 		<url>
-			http://www.chibi.ubc.ca/faculty/pavlidis/bugs/buglist.cgi?product=baseCode&amp;bug_status=__open__
-		</url>
+            https://github.com/PavlidisLab/baseCode/issues
+        </url>
 	</issueManagement>
 	<ciManagement>
-		<system>continuum</system>
-		<url>http://chibi.ubc.ca/faculty/pavlidis/bamboo/</url>
-		<notifiers>
-			<notifier>
-				<type>mail</type>
-				<sendOnError>true</sendOnError>
-				<sendOnFailure>true</sendOnFailure>
-				<sendOnSuccess>true</sendOnSuccess>
-				<sendOnWarning>true</sendOnWarning>
-				<configuration>
-					<address>paul@chibi.ubc.ca</address>
-				</configuration>
-			</notifier>
-		</notifiers>
+		<system>Jenkins</system>
+		<url>https://jenkins.pavlab.msl.ubc.ca</url>
 	</ciManagement>
 	<licenses>
 		<license>
@@ -53,7 +36,7 @@
 		<developer>
 			<name>Paul Pavlidis</name>
 			<id>pavlidis</id>
-			<email>paul@chibi.ubc.ca</email>
+			<email>paul@msl.ubc.ca</email>
 			<organization>University of British Columbia</organization>
 		</developer>
 	</developers>
@@ -517,7 +500,7 @@
 			<id>pavlab</id>
 			<name>PavLab</name>
 			<url>
-				http://www.chibi.ubc.ca/maven2
+				https://maven2.pavlab.msl.ubc.ca/
 			</url>
 			<layout>default</layout>
 			<snapshots>
@@ -565,7 +548,7 @@
 			<id>pavlab</id>
 			<name>PavLab</name>
 			<url>
-				http://www.chibi.ubc.ca/maven2
+				https://maven2.pavlab.msl.ubc.ca/
 			</url>
 			<layout>default</layout>
 			<snapshots>

src/ontology.properties

@@ -23,7 +23,8 @@ 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
+# according to http://www.obofoundry.org/ontology/clo.html this "should" point to https://raw.githubusercontent.com/CLO-ontology/CLO/master/src/ontology/clo_merged.owl
+url.cellLineOntology=http://purl.obolibrary.org/obo/clo.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