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add basic support for tracking gene type (not exposed anywhere) #638

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add basic support for tracking gene type (not exposed anywhere) #638

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1 change: 1 addition & 0 deletions gemma-core/src/main/java/ubic/gemma/core/loader/genome/gene/ncbi/NcbiGeneConverter.java
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Expand Up @@ -109,6 +109,7 @@ public Gene convert( NCBIGeneInfo info ) {
gene.setOfficialSymbol( info.getDefaultSymbol() );
gene.setOfficialName( info.getDescription() );
gene.setEnsemblId( info.getEnsemblId() );
gene.setType(info.getGeneType().toString());

/*
* NOTE we allow multiple discontinued or previous ids, separated by commas. This is a hack to account for cases
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10 changes: 10 additions & 0 deletions gemma-core/src/main/java/ubic/gemma/model/genome/Gene.java
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Expand Up @@ -18,6 +18,7 @@
*/
package ubic.gemma.model.genome;

import ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo;
import ubic.gemma.model.association.phenotype.PhenotypeAssociation;
import ubic.gemma.model.common.description.DatabaseEntry;
import ubic.gemma.model.genome.gene.GeneAlias;
Expand Down Expand Up @@ -47,13 +48,22 @@ public class Gene extends ChromosomeFeature {
private Set<DatabaseEntry> accessions = new HashSet<>();
private Multifunctionality multifunctionality;
private Set<PhenotypeAssociation> phenotypeAssociations = new HashSet<>();
private NCBIGeneInfo.GeneType type;

/**
* No-arg constructor added to satisfy javabean contract
*/
public Gene() {
}

public String getType() {
return type.toString();
}

public void setType( String type ) {
this.type = NCBIGeneInfo.typeStringToGeneType( type );
}

@Override
public boolean equals( Object object ) {
if ( this == object ) {
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4 changes: 4 additions & 0 deletions gemma-core/src/main/resources/ubic/gemma/model/genome/ChromosomeFeature.hbm.xml
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Expand Up @@ -64,6 +64,10 @@
<column name="ENSEMBL_ID" not-null="false" unique="false"
sql-type="VARCHAR(255)"/>
</property>
<property name="type" type="java.lang.String">
<column name="TYPE" not-null="false" unique="false"
sql-type="VARCHAR(255)"/>
</property>
<set name="products" lazy="true" fetch="select" inverse="true" cascade="all">
<cache usage="read-write"/>
<key foreign-key="GENE_PRODUCT_GENE_FKC">
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3 changes: 3 additions & 0 deletions gemma-core/src/test/java/ubic/gemma/core/loader/genome/gene/ncbi/NCBIGeneParserTest.java
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Expand Up @@ -20,6 +20,7 @@

import junit.framework.TestCase;
import org.springframework.core.io.ClassPathResource;
import ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo;

import java.io.InputStream;
import java.util.HashMap;
Expand All @@ -45,6 +46,8 @@ public void testParseGeneInfo() throws Exception {
ncbiGeneInfoParser.setFilter( false );
ncbiGeneInfoParser.parse( is );
TestCase.assertEquals( 99, ncbiGeneInfoParser.getResults().size() );
NCBIGeneInfo n = ncbiGeneInfoParser.getResults().iterator().next();
assertNotNull( n.getGeneType() );
}

}