From bd8f43d25dcaf471d7426900a7ffa364b6f2a395 Mon Sep 17 00:00:00 2001 From: Jim Balhoff Date: Wed, 2 Aug 2017 10:17:39 -0400 Subject: [PATCH 1/2] Updated URI for unit ontology. --- src/org/obo/annotation/base/UserOntologyConfiguration.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/org/obo/annotation/base/UserOntologyConfiguration.java b/src/org/obo/annotation/base/UserOntologyConfiguration.java index 5c577d2..4f00e74 100644 --- a/src/org/obo/annotation/base/UserOntologyConfiguration.java +++ b/src/org/obo/annotation/base/UserOntologyConfiguration.java @@ -28,7 +28,7 @@ public class UserOntologyConfiguration implements OntologyConfiguration { defaultSources.add(new OntologySource("Museum Collections", new URL("http://svn.code.sf.net/p/phenoscape/code/trunk/vocab/fish_collection_abbreviation.obo"))); defaultSources.add(new OntologySource("Phenotypic Qualities", new URL("http://purl.obolibrary.org/obo/pato.obo"))); defaultSources.add(new OntologySource("Spatial Ontology", new URL("http://purl.obolibrary.org/obo/bspo.obo"))); - defaultSources.add(new OntologySource("Unit Ontology", new URL("http://unit-ontology.googlecode.com/svn/trunk/unit.obo"))); + defaultSources.add(new OntologySource("Unit Ontology", new URL("http://purl.obolibrary.org/obo/uo.obo"))); defaultSources.add(new OntologySource("OBO Relations", new URL("http://purl.obolibrary.org/obo/ro.obo"))); // need this? //defaultSources.add(new OntologySource("Gene Ontology", new URL("http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo"))); From 4dfcbbce12b0471266d7a6062eeda70df9edfe79 Mon Sep 17 00:00:00 2001 From: Jim Balhoff Date: Wed, 2 Aug 2017 10:18:06 -0400 Subject: [PATCH 2/2] Fixed null pointer exception in provisional term parser. --- src/org/phenoscape/util/ProvisionalTermUtil.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/org/phenoscape/util/ProvisionalTermUtil.java b/src/org/phenoscape/util/ProvisionalTermUtil.java index 1ae36e0..f9007cc 100644 --- a/src/org/phenoscape/util/ProvisionalTermUtil.java +++ b/src/org/phenoscape/util/ProvisionalTermUtil.java @@ -76,13 +76,14 @@ public static List getProvisionalTerms(OBOSession session) throws IOEx for (int i = 0; i < termResults.length(); i++) { final JSONObject provisionalTerm = termResults.getJSONObject(i); // this check should be removed once Bioportal implements server-side filtering by creator - final String creator = provisionalTerm.getString("creator"); - if (creator.equals(getUserID())) { - terms.add(createClassForProvisionalTerm(provisionalTerm, session)); + if (!provisionalTerm.isNull("creator")) { + final String creator = provisionalTerm.getString("creator"); + if (creator.equals(getUserID())) { + terms.add(createClassForProvisionalTerm(provisionalTerm, session)); + } } } return terms; - } }