Added the licences to be attached to dataset linked to ontologies #2264

intermine · Jun 2, 2020 · c4ac57f · c4ac57f
1 parent b78a363
commit c4ac57f
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Showing 10 changed files with 31 additions and 6 deletions.
diff --git a/bio/core/src/main/java/org/intermine/bio/dataconversion/OboConverter.java b/bio/core/src/main/java/org/intermine/bio/dataconversion/OboConverter.java
@@ -199,7 +199,7 @@ private void storeDataset(Item ontology) throws ObjectStoreException {
         Item datasetItem = createItem("DataSet");
         datasetItem.setAttribute("name", dataset);
         if (licence != null) {
-            datasetItem.setAttribute("licence", licence);
+            datasetItem.setAttributeIfNotNull("licence", licence);
         }
         datasetItem.setReference("dataSource", datasourceItem);
         store(datasetItem);

diff --git a/bio/core/src/main/java/org/intermine/bio/task/OboConverterTask.java b/bio/core/src/main/java/org/intermine/bio/task/OboConverterTask.java
@@ -75,7 +75,14 @@ public void setTermClass(String termClass) {
         this.termClass = termClass;
     }
 
-
+    /**
+     * Set the licence retrieved from the {bio-source}.properties file
+     *
+     * @param licence the licence
+     */
+    public void setLicence(String licence) {
+        this.licence = licence;
+    }
 
     /**
      * Run the task
@@ -106,6 +113,9 @@ public void execute() {
             OboConverter converter;
             if (file.endsWith(".obo")) {
                 converter = new OboConverter(writer, model, file, ontologyName, url, termClass);
+                if (licence != null) {
+                    converter.setLicence(licence);
+                }
             } else {
                 throw new IllegalArgumentException("Don't know how to deal with file " + file);
             }

diff --git a/bio/sources/do/do.properties b/bio/sources/do/do.properties
@@ -14,3 +14,4 @@ obo.ontology.url = http://www.disease-ontology.org
 # this class in a do_additions.xml file for this source
 obo.term.class = DOTerm
 
+obo.ontology.licence = https://creativecommons.org/publicdomain/zero/1.0/
diff --git a/bio/sources/eco/eco.properties b/bio/sources/eco/eco.properties
@@ -14,3 +14,4 @@ obo.ontology.url = http://www.evidenceontology.org/
 # this class in a eco_additions.xml file for this source
 obo.term.class = ECOTerm
 
+obo.ontology.licence = https://creativecommons.org/publicdomain/zero/1.0/
diff --git a/bio/sources/go/go.properties b/bio/sources/go/go.properties
@@ -2,3 +2,5 @@ have.file.obo = true
 obo.ontology.name=GO
 obo.ontology.url=http://www.geneontology.org
 obo.term.class=GOTerm
+
+obo.ontology.licence = https://creativecommons.org/licenses/by/4.0/
diff --git a/bio/sources/mammalian-phenotype-ontology/mammalian-phenotype-ontology.properties b/bio/sources/mammalian-phenotype-ontology/mammalian-phenotype-ontology.properties
@@ -8,9 +8,11 @@ have.file.obo = true
 obo.ontology.name = Mammalian Phenotype Ontology
 
 # set a URL at which more information on the ontology can be found
-obo.ontology.url = http://www.obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype
+obo.ontology.url = http://www.informatics.jax.org/vocab/mp_ontology
 
 # set the class name for terms that will be created, you may need to define
 # this class in a mammalian-phenotype-ontology_additions.xml file for this source
 obo.term.class = MammalianPhenotypeTerm
 
+obo.ontology.licence = http://creativecommons.org/licenses/by/4.0/
+
diff --git a/bio/sources/psi-mi-ontology/psi-mi-ontology.properties b/bio/sources/psi-mi-ontology/psi-mi-ontology.properties
@@ -4,7 +4,9 @@ compile.dependencies = intermine/objectstore/main,\
 
 have.file.obo = true
 obo.ontology.name=PSI Molecular Interactions
-obo.ontology.url=http://psidev.sourceforge.net/
+obo.ontology.url=https://github.com/HUPO-PSI/psi-mi-CV
 obo.term.class=InteractionTerm
 
+obo.ontology.licence = https://creativecommons.org/licenses/by/4.0/
+
 
diff --git a/bio/sources/so/so.properties b/bio/sources/so/so.properties
@@ -7,4 +7,5 @@ obo.ontology.name=Sequence Ontology
 obo.ontology.url=http://www.sequenceontology.org
 obo.term.class=SOTerm
 
+obo.ontology.licence = https://creativecommons.org/licenses/by/4.0/
 
diff --git a/bio/sources/uberon/uberon.properties b/bio/sources/uberon/uberon.properties
@@ -8,9 +8,11 @@ have.file.obo = true
 obo.ontology.name = Uber Anatomy Ontology
 
 # set a URL at which more information on the ontology can be found
-obo.ontology.url = http://obofoundry.org/wiki/index.php/UBERON:Main_Page
+obo.ontology.url = http://uberon.org/
 
 # set the class name for terms that will be created, you may need to define
 # this class in a uberon_additions.xml file for this source
 obo.term.class = AnatomyTerm
 
+obo.ontology.licence = http://creativecommons.org/licenses/by/3.0/
+
diff --git a/plugin/src/main/groovy/org/intermine/plugin/integrate/IntegrateUtils.groovy b/plugin/src/main/groovy/org/intermine/plugin/integrate/IntegrateUtils.groovy
@@ -240,6 +240,9 @@ class IntegrateUtils {
             }
         }
 
+        String licence = (bioSourceProperties.getProperty("obo.ontology.licence") != null) ?
+                bioSourceProperties.getProperty("obo.ontology.licence") : ""
+
         ant.taskdef(name: "convertOBO", classname: "org.intermine.bio.task.OboConverterTask") {
             classpath {
                 dirset(dir: gradleProject.getBuildDir().getAbsolutePath())
@@ -251,7 +254,8 @@ class IntegrateUtils {
                 osName: "osw." + COMMON_OS_PREFIX + "-tgt-items", modelName: "genomic",
                 ontologyName: bioSourceProperties.getProperty("obo.ontology.name"),
                 url: bioSourceProperties.getProperty("obo.ontology.url"),
-                termClass: bioSourceProperties.getProperty("obo.term.class"))
+                termClass: bioSourceProperties.getProperty("obo.term.class"),
+                licence: licence)
     }
 
     def loadSingleSource = { source ->