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add new mongodb collection names for variant import #16

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da6d398
add new mongodb collection names for variant import
Nov 28, 2017
1580bc1
use combination keys for clinvar data
Nov 28, 2017
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8 changes: 8 additions & 0 deletions dcc-common-core/src/main/java/org/icgc/dcc/common/core/model/FieldNames.java
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Original file line number Diff line number Diff line change
Expand Up @@ -436,4 +436,12 @@ public static String getTestedTypeCountFieldName(FeatureType featureType) {
return SYNTHETIC_PREFIX + featureType.getId() + TESTED_DONOR_COUNT_SUFFIX;
}


/**
* Variant field names.
*/
public static final String CIVIC_VARIANT_ID = "variantID";
public static final String CLINVAR_ALLELE_ID = "alleleID";
public static final String CLINVAR_ASSEMBLY = "assembly";

}
12 changes: 4 additions & 8 deletions dcc-common-core/src/main/java/org/icgc/dcc/common/core/model/ReleaseCollection.java
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Expand Up @@ -21,13 +21,7 @@
import static com.google.common.collect.Iterables.transform;
import static com.google.common.collect.Lists.newArrayList;
import static java.util.Arrays.asList;
import static org.icgc.dcc.common.core.model.FieldNames.DIAGRAM_ID;
import static org.icgc.dcc.common.core.model.FieldNames.DRUG_ID;
import static org.icgc.dcc.common.core.model.FieldNames.FILE_ID;
import static org.icgc.dcc.common.core.model.FieldNames.GENE_SET_ID;
import static org.icgc.dcc.common.core.model.FieldNames.MONGO_INTERNAL_ID;
import static org.icgc.dcc.common.core.model.FieldNames.PATHWAY_REACTOME_ID;
import static org.icgc.dcc.common.core.model.FieldNames.RELEASE_ID;
import static org.icgc.dcc.common.core.model.FieldNames.*;
import static org.icgc.dcc.common.core.model.FieldNames.IdentifierFieldNames.SURROGATE_DONOR_ID;
import static org.icgc.dcc.common.core.model.FieldNames.IdentifierFieldNames.SURROGATE_MUTATION_ID;
import static org.icgc.dcc.common.core.model.FieldNames.ImporterFieldNames.CGC_ID;
Expand Down Expand Up @@ -62,7 +56,9 @@ public enum ReleaseCollection implements Identifiable {
GENE_SET_COLLECTION(UNDETERMINED, "GeneSet", newArrayList(GENE_SET_ID)),
DIAGRAM_COLLECTION(UNDETERMINED, "Diagram", newArrayList(DIAGRAM_ID)),
FILE_COLLECTION(UNDETERMINED, "File", newArrayList(FILE_ID)),
DRUG_COLLECTION(UNDETERMINED, "Drug", newArrayList(DRUG_ID));
DRUG_COLLECTION(UNDETERMINED, "Drug", newArrayList(DRUG_ID)),
CIVIC_COLLECTION(UNDETERMINED, "Civic", newArrayList(CIVIC_VARIANT_ID)),
CLINVAR_COLLECTION(UNDETERMINED, "Clinvar", newArrayList(CLINVAR_ALLELE_ID, CLINVAR_ASSEMBLY));

private final ReleaseDatabase parentDatabase;

Expand Down