TASK-6515 - Port Patch 1.10.6(.1) -> 2.2.1

cellbase-core/src/main/resources/configuration.yml

@@ -125,13 +125,14 @@ download:
 #    host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2021-07.xml.gz
 #    host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2022-02.xml.gz
 #    host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2022-11.xml.gz
-    host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2023-12.xml.gz
-    version: "2023-12-01"
+    host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/RCV_xml_old_format/ClinVarFullRelease_2024-05.xml.gz
+    version: 2024-05
   clinvarVariation:
 #    host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_2021-07.xml.gz
 #    host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_2022-02.xml.gz
 #    host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_2022-11.xml.gz
-    host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_2023-12.xml.gz
+    host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/VCV_xml_old_format/ClinVarVariationRelease_2024-05.xml.gz
+    version: 2024-05
   clinvarSummary:
     host: http://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz
     version: "2023-12-01"
@@ -158,10 +159,10 @@ download:
   genomicSuperDups:
     host: http://hgdownload.cse.ucsc.edu/goldenPath
   gwasCatalog:
-#    host: http://resources.opencb.org/opencb/cellbase/data/gwas/gwas_catalog_v1.0.2-associations_e106_r2022-05-17.tsv
-#    version: "1.0.2 associations_e106_r2022-05-17"
-    host: ftp://ftp.ebi.ac.uk/pub/databases/gwas/releases/2023/12/21/gwas-catalog-associations.tsv
-    version: "23-12-21"
+    #host: http://resources.opencb.org/opencb/cellbase/data/gwas/gwas_catalog_v1.0.2-associations_e106_r2022-05-17.tsv
+    host: "https://ftp.ebi.ac.uk/pub/databases/gwas/releases/2024/05/20/gwas-catalog-associations_ontology-annotated.tsv"
+    #version: "1.0.2 associations_e106_r2022-05-17"
+    version: "2024-05-20"
   hpo:
     ## Downlaod manually from here now:  https://hpo.jax.org/app/data/annotations
     host: https://ci.monarchinitiative.org/view/hpo/job/hpo.annotations/lastSuccessfulBuild/artifact/rare-diseases/util/annotation/phenotype_to_genes.txt

cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java

@@ -56,9 +56,9 @@ public class EtlCommons {
     public static final String PHARMGKB_VERSION_FILENAME = "pharmgkbVersion.json";
 
     public static final String CLINICAL_VARIANTS_FOLDER = "clinicalVariant";
-    public static final String CLINVAR_VERSION = "2022.11";
-    public static final String CLINVAR_DATE = "2022-11";
-    public static final String CLINVAR_XML_FILE = "ClinVarFullRelease_2022-11.xml.gz";
+    public static final String CLINVAR_VERSION = "2024-05";
+    public static final String CLINVAR_DATE = "2024-05";
+    public static final String CLINVAR_XML_FILE = "ClinVarFullRelease_2024-05.xml.gz";
     public static final String CLINVAR_EFO_FILE = "ClinVar_Traits_EFO_Names.csv";
     public static final String CLINVAR_SUMMARY_FILE = "variant_summary.txt.gz";
     public static final String CLINVAR_VARIATION_ALLELE_FILE = "variation_allele.txt.gz";

cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinVarIndexer.java

@@ -210,7 +210,7 @@ private void printSummary() {
     }
 
     private boolean updateRocksDB(SequenceLocation sequenceLocation, String variationId, String[] lineFields,
-                               String mateVariantString, Map<String, EFO> traitsToEfoTermsMap)
+                                  String mateVariantString, Map<String, EFO> traitsToEfoTermsMap)
             throws RocksDBException, IOException {
         // More than one variant being returned from the normalisation process would mean it's and MNV which has been
         // decomposed
@@ -266,13 +266,34 @@ private boolean updateRocksDB(AlleleLocationData alleleLocationData, PublicSetTy
                 }
 
                 // parse RCVs
-                String accession = publicSet.getReferenceClinVarAssertion().getClinVarAccession().getAcc();
-                String clinicalSignficanceDescription = publicSet.getReferenceClinVarAssertion()
-                        .getClinicalSignificance()
-                        .getDescription();
-                String reviewStatusName = publicSet.getReferenceClinVarAssertion().getClinicalSignificance()
-                        .getReviewStatus().name();
-                List<ObservationSet> getObservedIn = publicSet.getReferenceClinVarAssertion().getObservedIn();
+                String accession = null;
+                try {
+                    accession = publicSet.getReferenceClinVarAssertion().getClinVarAccession().getAcc();
+                } catch (Exception e) {
+                    logger.warn("Error getting accession. Ignore error and leave it as null.", e);
+                }
+                String clinicalSignficanceDescription = null;
+                try {
+                    clinicalSignficanceDescription = publicSet.getReferenceClinVarAssertion()
+                            .getClinicalSignificance()
+                            .getDescription();
+                } catch (Exception e) {
+                    logger.warn("Error getting clinical significance description. Ignore error and leave it as null.", e);
+                }
+                String reviewStatusName = null;
+                try {
+                    reviewStatusName = publicSet.getReferenceClinVarAssertion().getClinicalSignificance()
+                            .getReviewStatus().name();
+                } catch (Exception e) {
+                    logger.warn("Error getting review status name. Ignore error and leave it as null.", e);
+                }
+                List<ObservationSet> getObservedIn = null;
+                try {
+                    getObservedIn = publicSet.getReferenceClinVarAssertion().getObservedIn();
+                } catch (Exception e) {
+                    logger.warn("Error getting observed in. Ignore error and leave it as null.", e);
+                }
+
                 addNewEntries(variantAnnotation, publicSet, alleleLocationData.getAlleleId(), mateVariantString,
                         clinicalHaplotypeString, traitsToEfoTermsMap, accession, clinicalSignficanceDescription,
                         reviewStatusName, getObservedIn);
@@ -388,7 +409,7 @@ private void addNewEntries(VariantAnnotation variantAnnotation, PublicSetType pu
                                Map<String, EFO> traitsToEfoTermsMap, String accession,
                                String clinicalSignficanceDescription, String reviewStatusName,
                                List<ObservationSet> getObservedIn)
-        throws JsonProcessingException {
+            throws JsonProcessingException {
 
         List<Property> additionalProperties = new ArrayList<>(3);
         EvidenceSource evidenceSource = new EvidenceSource(EtlCommons.CLINVAR_DATA, CLINVAR_VERSION, CLINVAR_DATE);
@@ -544,7 +565,7 @@ private ModeOfInheritance getModeOfInheritance(String modeOfInheritance) {
     private List<GenomicFeature> getGenomicFeature(PublicSetType publicSet, String alleleId) {
         if (publicSet.getReferenceClinVarAssertion().getMeasureSet() != null) {
             return getGenomicFeature(publicSet.getReferenceClinVarAssertion().getMeasureSet());
-        // No measureSet means there must be genotypeSet
+            // No measureSet means there must be genotypeSet
         } else if (publicSet.getReferenceClinVarAssertion().getGenotypeSet() != null) {
             for (MeasureSetType measureSet : publicSet.getReferenceClinVarAssertion().getGenotypeSet().getMeasureSet()) {
                 if (measureSet.getMeasure() != null) {
@@ -596,7 +617,7 @@ private List<HeritableTrait> getHeritableTrait(PublicSetType publicSet, Map<Stri
         // root of the ReferenceClinvarAssertion rather than for each trait
         ModeOfInheritance modeOfInheritance
                 = getInheritanceModel(publicSet.getReferenceClinVarAssertion().getAttributeSet(),
-                        sourceInheritableTraitMap);
+                sourceInheritableTraitMap);
 
         for (TraitType trait : publicSet.getReferenceClinVarAssertion().getTraitSet().getTrait()) {
             String traitName = getTraitName(trait, publicSet);
@@ -649,14 +670,14 @@ private String getTraitName(TraitType trait, PublicSetType publicSet) {
         // Found preferred name
         if (i < trait.getName().size()) {
             return trait.getName().get(i).getElementValue().getValue();
-        // No preferred name indicated (e.g. RCV000013735 version Jan 2020); arbitrarily return first one
+            // No preferred name indicated (e.g. RCV000013735 version Jan 2020); arbitrarily return first one
         } else if (trait.getName().size() > 0) {
             logger.warn("ClinVar record found "
                     + publicSet.getReferenceClinVarAssertion().getClinVarAccession().getAcc()
                     + " with no preferred trait provided. Arbitrarily selecting first one: {}", trait.getName()
                     .get(0).getElementValue().getValue());
             return trait.getName().get(0).getElementValue().getValue();
-        // No trait name provided at all
+            // No trait name provided at all
         } else {
             throw new IllegalArgumentException("ClinVar record found "
                     + publicSet.getReferenceClinVarAssertion().getClinVarAccession().getAcc()

cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinicalIndexer.java

@@ -74,13 +74,12 @@ public abstract class ClinicalIndexer {
     protected VariantNormalizer normalizer;
 
     public ClinicalIndexer(Path genomeSequenceFilePath) throws IOException {
-        // Forcing decomposition here in all cases - assuming the way CellBase stores clinical variants from here
-        // onwards will be decomposed and Adaptors will deal with phased/no-phased queries
+        // Use the same OpenCGA normalization parameters
         VariantNormalizer.VariantNormalizerConfig variantNormalizerConfig
                 = (new VariantNormalizer.VariantNormalizerConfig())
                 .setReuseVariants(true)
-                .setNormalizeAlleles(false)
-                .setDecomposeMNVs(true);
+                .setNormalizeAlleles(true)
+                .setDecomposeMNVs(false);
 
         if (genomeSequenceFilePath != null) {
             logger.info("Enabling left aligning by using sequence at {}", genomeSequenceFilePath.toString());

cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/CosmicIndexer.java

@@ -41,7 +41,7 @@ public class CosmicIndexer extends ClinicalIndexer {
     private Pattern mutationGRCh37GenomePositionPattern;
     private Pattern snvPattern;
 
-    private static final String COSMIC_VERSION = "v95";
+    private static final String COSMIC_VERSION = "v99";
 
     private static final int GENE_NAMES_COLUMN = 0;
     private static final int HGNC_COLUMN = 3;