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Added codes for generating regulation-only closures #242

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Added codes for generating regulation-only closures #242

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6 changes: 5 additions & 1 deletion OWLTools-Core/src/main/java/owltools/graph/RelationSets.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ public class RelationSets {

public static final String ISA_PARTOF = "is_a/part_of";
public static final String REGULATES = "regulates/is_a/part_of";

public static final String REGULATES_ONLY = "regulates/part_of";
/*
* Should be using this in most cases.
*/
Expand All @@ -27,6 +27,10 @@ public static List<String> getRelationSet(String relset) {
rel_ids.add("RO:0002211");
rel_ids.add("RO:0002212");
rel_ids.add("RO:0002213");
}else if( relset.equals(REGULATES_ONLY) ){
rel_ids.add("RO:0002211");
rel_ids.add("RO:0002212");
rel_ids.add("RO:0002213");
}else if( relset.equals(COMMON) ){
rel_ids.add("BFO:0000050");
rel_ids.add("BFO:0000066");
Expand Down
14 changes: 13 additions & 1 deletion OWLTools-Solr/src/main/java/owltools/solrj/GafSolrDocumentLoader.java
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Expand Up @@ -327,6 +327,8 @@ private void add(Bioentity e) {
// added at the end of this section.
Map<String, String> isap_map = new HashMap<String, String>();
Map<String, String> reg_map = new HashMap<String, String>();
Map<String, String> reg_only_map = new HashMap<String, String>();

for (GeneAnnotation a : gafDocument.getGeneAnnotations(e.getId())) {
SolrInputDocument annotation_doc = new SolrInputDocument();

Expand Down Expand Up @@ -438,6 +440,12 @@ private void add(Bioentity e) {
Map<String, String> curr_reg_map = addClosureToAnnAndBio(reg, "regulates_closure", "regulates_closure_label", "regulates_closure_map",
cls, graph, annotation_doc, bioentity_doc, a.isNegated());
reg_map.putAll(curr_reg_map); // add to aggregate map

// Regulates ONLY closures.
List<String> reg_only = RelationSets.getRelationSet(RelationSets.REGULATES_ONLY);
Map<String, String> curr_reg_only_map = addClosureToAnnAndBio(reg_only, "regulates_only_closure", "regulates_only_closure_label", "regulates_only_closure_map",
cls, graph, annotation_doc, bioentity_doc, a.isNegated());
reg_only_map.putAll(curr_reg_only_map); // add to aggregate map
}

// Let's piggyback on a little of the work above and cache the extra stuff that we'll be adding to the bioenity at the end
Expand Down Expand Up @@ -544,7 +552,11 @@ private void add(Bioentity e) {
String jsonized_cmap = gson.toJson(reg_map);
bioentity_doc.addField("regulates_closure_map", jsonized_cmap);
}

if( ! reg_only_map.isEmpty() ){
String jsonized_cmap = gson.toJson(reg_only_map);
bioentity_doc.addField("regulates_only_closure_map", jsonized_cmap);
}

// Add c5 to bioentity.
// Compile closure map to JSON and add to the document.
String jsonized_direct_map = null;
Expand Down
8 changes: 6 additions & 2 deletions OWLTools-Solr/src/test/java/owltools/solrj/GafSolrDocumentLoaderTest.java
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Expand Up @@ -25,6 +25,7 @@
public class GafSolrDocumentLoaderTest {

private static int solrCount = 0;
private static int solrCountWithRegulatesOnly = 0;
private static OWLGraphWrapper graph;
private static TaxonTools taxonTools = null;
private static GafSolrDocumentLoader loader;
Expand All @@ -36,9 +37,12 @@ public static void setUpBeforeClass() throws Exception {
@Override
protected void addToServer(Collection<SolrInputDocument> docs)
throws SolrServerException, IOException {
for (SolrInputDocument doc: docs) {
if (doc.toString().contains("regulates_only_closure"))
solrCountWithRegulatesOnly +=1 ;
}
solrCount += docs.size();
}

};
ParserWrapper pw = new ParserWrapper();
pw.addIRIMapper(new CatalogXmlIRIMapper("../OWLTools-Annotation/src/test/resources/rules/ontology/extensions/catalog-v001.xml"));
Expand Down Expand Up @@ -83,6 +87,6 @@ public void test() throws Exception {
loader.load();

assertTrue(solrCount > 0);
assertTrue(solrCountWithRegulatesOnly > 0);
}

}