Update DefaultDiseaseDao and ModelServiceImpl to select disease model…

…s with type 'D', 'C' or '?'

exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/dao/DefaultDiseaseDao.java

@@ -101,7 +101,7 @@ public List<Disease> getDiseaseDataAssociatedWithGeneId(int geneId) {
                 "FROM entrez2sym e, disease_hp dhp, disease d " +
                 "WHERE dhp.disease_id = d.DISEASE_ID " +
                 "AND e.entrezid = d.GENE_ID " +
-                "AND d.TYPE in ('D', 'C')" +
+                "AND d.TYPE in ('D', 'C', '?')" +
                 "AND d.GENE_ID = ?";
 
         try (Connection connection = dataSource.getConnection()) {

exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/prioritisers/service/ModelServiceImpl.java

@@ -1,7 +1,7 @@
 /*
  * The Exomiser - A tool to annotate and prioritize genomic variants
  *
- * Copyright (c) 2016-2017 Queen Mary University of London.
+ * Copyright (c) 2016-2019 Queen Mary University of London.
  * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
  *
  * This program is free software: you can redistribute it and/or modify
@@ -62,7 +62,7 @@ public ModelServiceImpl(DataSource phenotypeDataSource) {
     public List<GeneModel> getHumanGeneDiseaseModels() {
         // We only connect to human2mouse_orthologs to get the human_gene_symbol but if there is no orthology mapping we get 0 results and no disease hit at all - this is daft!
         // Tried to replace with the below - should be more successful
-        String modelQuery = "SELECT distinct 'HUMAN' as organism, gene_id as entrez_id, symbol as human_gene_symbol, d.disease_id as disease_id, d.diseasename as disease_term, hp_id as pheno_ids FROM entrez2sym e, disease_hp M, disease d WHERE e.entrezid=d.gene_id and M.disease_id=d.disease_id"; 
+        String modelQuery = "SELECT distinct 'HUMAN' as organism, gene_id as entrez_id, symbol as human_gene_symbol, d.disease_id as disease_id, d.diseasename as disease_term, hp_id as pheno_ids FROM entrez2sym e, disease_hp M, disease d WHERE e.entrezid=d.gene_id and M.disease_id=d.disease_id AND d.TYPE in ('D', 'C', '?')";
         //String modelQuery = "SELECT 'HUMAN' as organism, gene_id as entrez_id, human_gene_symbol, d.disease_id as disease_id, d.diseasename as disease_term, hp_id as pheno_ids FROM human2mouse_orthologs hm, disease_hp M, disease d WHERE hm.entrez_id=d.gene_id AND M.disease_id=d.disease_id;";
         return runGeneDiseaseModelQuery(modelQuery);
     }

exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/prioritisers/dao/DefaultDiseaseDaoTest.java

@@ -97,4 +97,19 @@ public void testGetCnvDiseaseDataAssociatedWithGeneId() {
         List<Disease> expected = Lists.newArrayList(cnv) ;
         assertThat(instance.getDiseaseDataAssociatedWithGeneId(2222), equalTo(expected));
     }
+
+    @Test
+    public void testGetUnconfirmedDiseaseDataAssociatedWithGeneId() {
+        Disease disease = Disease.builder()
+                .diseaseId("OMIM:123456")
+                .diseaseName("Test unconfirmed disease association")
+                .diseaseType(Disease.DiseaseType.UNCONFIRMED)
+                .inheritanceMode(InheritanceMode.UNKNOWN)
+                .associatedGeneId(3333)
+                .associatedGeneSymbol("GENE3")
+                .phenotypeIds(ImmutableList.of("HP:0000002"))
+                .build();
+        List<Disease> expected = Lists.newArrayList(disease) ;
+        assertThat(instance.getDiseaseDataAssociatedWithGeneId(3333), equalTo(expected));
+    }
 }

exomiser-core/src/test/resources/sql/diseaseDaoTestData.sql

@@ -1,14 +1,17 @@
 insert into disease values  
 ('OMIM:101600',	'OMIM:176943',	'Craniofacial-skeletal-dermatologic dysplasia',	2263,	'D',	'D'),
 ('OMIM:101600',	'OMIM:136350',	'Pfeiffer syndrome',	2260,	'D',	'D'),
-('ORPHA:11111',	null,	'Test CNV disease',	2222,	'C',	null);
+('ORPHA:11111',	null,	'Test CNV disease',	2222,	'C',	null),
+('OMIM:123456',	null,	'Test unconfirmed disease association',	3333,	'?',	null);
 
 
 insert into disease_hp values
 ('OMIM:101600',	'HP:0000174,HP:0000194,HP:0000218,HP:0000238,HP:0000244,HP:0000272,HP:0000303,HP:0000316,HP:0000322,HP:0000324,HP:0000327,HP:0000348,HP:0000431,HP:0000452,HP:0000453,HP:0000470,HP:0000486,HP:0000494,HP:0000508,HP:0000586,HP:0000678,HP:0001156,HP:0001249,HP:0002308,HP:0002676,HP:0002780,HP:0003041,HP:0003070,HP:0003196,HP:0003272,HP:0003307,HP:0003795,HP:0004209,HP:0004322,HP:0004440,HP:0005048,HP:0005280,HP:0005347,HP:0006101,HP:0006110,HP:0009602,HP:0009773,HP:0010055,HP:0010669,HP:0011304'),
-('ORPHA:11111',	'HP:0000001');
+('ORPHA:11111',	'HP:0000001'),
+('OMIM:123456',	'HP:0000002');
 
 insert into ENTREZ2SYM VALUES
 (2263, 'FGFR2'),
 (2260, 'FGFR1'),
-(2222, 'GENE2');
+(2222, 'GENE2'),
+(3333, 'GENE3');