Merge pull request #713 from opencb/TASK-7097

TASK-7097 - Port Patch 6.3.0 -> 7.0.0 Xetabase 2.3.0 -> 3.0.0

.github/workflows/pull-request-approved.yml

@@ -24,7 +24,7 @@ jobs:
           chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh
           echo "github.event.pull_request.base.ref: ${{ github.event.pull_request.base.ref }}"
           echo "github.event.pull_request.head.ref: ${{ github.event.pull_request.head.ref }}"
-          xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }})
+          xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.base.ref }})
           echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY}
           echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT
         env:

.github/workflows/scripts/get-xetabase-branch.sh

@@ -19,11 +19,11 @@ get_xetabase_branch() {
     return 0
   fi
 
-  # Check if the branch name starts with "release-" and follows the patterns "release-a.b.x" or "release-a.b.c.x"
-  if [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.x$ ]] || [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.([0-9]+)\.x$ ]]; then
+  # Check if the branch name starts with "release-" and follows the patterns "release-a.x.x" or "release-a.b.x"
+  if [[ "$input_branch" =~ ^release-([0-9]+)\.x\.x$ ]] || [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.x$ ]]; then
     # Extract the MAJOR part of the branch name
     MAJOR=${BASH_REMATCH[1]}
-    # Calculate the XETABASE_MAJOR by subtracting 3 from MAJOR
+    # Calculate the XETABASE_MAJOR by subtracting 4 from MAJOR of cellbase
     XETABASE_MAJOR=$((MAJOR - 4))
     # Check if the XETABASE_MAJOR is negative
     if (( XETABASE_MAJOR < 0 )); then

cellbase-core/src/main/java/org/opencb/cellbase/core/exception/CellBaseException.java

@@ -22,8 +22,12 @@ public CellBaseException(String msg) {
         super(msg);
     }
 
-    public CellBaseException(String msg, Exception e) {
-        super(msg, e);
+    public CellBaseException(String msg, Throwable cause) {
+        super(msg, cause);
+    }
+
+    public CellBaseException(Throwable cause) {
+        super(cause);
     }
 }
 

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

@@ -106,13 +106,6 @@ download:
   clinvar:
 #    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
-<<<<<<< HEAD
-    host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2022-11.xml.gz
-  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/ClinVarFullRelease_2022-11.xml.gz
     host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/RCV_xml_old_format/ClinVarFullRelease_2024-05.xml.gz
     version: 2024-05
@@ -122,7 +115,6 @@ download:
 #    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/VCV_xml_old_format/ClinVarVariationRelease_2024-05.xml.gz
     version: 2024-05
->>>>>>> release-6.2.x
   clinvarSummary:
     host: http://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz
   clinvarVariationAllele:
@@ -147,15 +139,10 @@ download:
   genomicSuperDups:
     host: http://hgdownload.cse.ucsc.edu/goldenPath
   gwasCatalog:
-<<<<<<< HEAD
-    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: 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"
->>>>>>> release-6.2.x
   hpo:
     host: https://ci.monarchinitiative.org/view/hpo/job/hpo.annotations/lastSuccessfulBuild/artifact/rare-diseases/util/annotation/phenotype_to_genes.txt
   disgenet:

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

@@ -20,6 +20,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.opencb.biodata.formats.variant.clinvar.rcv.ClinvarParser;
 import org.opencb.biodata.formats.variant.clinvar.rcv.v64jaxb.*;
+import org.opencb.biodata.models.sequence.SequenceLocation;
 import org.opencb.biodata.models.variant.avro.*;
 import org.opencb.cellbase.lib.EtlCommons;
 import org.opencb.cellbase.lib.variant.VariantAnnotationUtils;

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

@@ -230,92 +230,4 @@ protected void addHaplotypeProperty(List<EvidenceEntry> evidenceEntryList, List<
             }
         }
     }
-
-    class SequenceLocation {
-        private String chromosome;
-        private int start;
-        private int end;
-        private String reference;
-        private String alternate;
-        private String strand;
-
-        SequenceLocation() {
-        }
-
-        SequenceLocation(String chromosome, int start, int end, String reference, String alternate) {
-            this(chromosome, start, end, reference, alternate, "+");
-        }
-
-        SequenceLocation(String chromosome, int start, int end, String reference, String alternate, String strand) {
-            this.chromosome = chromosome;
-            this.start = start;
-            this.end = end;
-            this.reference = reference;
-            this.alternate = alternate;
-            this.strand = strand;
-        }
-
-        @Override
-        public String toString() {
-            final StringBuilder sb = new StringBuilder("SequenceLocation{");
-            sb.append("chromosome='").append(chromosome).append('\'');
-            sb.append(", start=").append(start);
-            sb.append(", end=").append(end);
-            sb.append(", reference='").append(reference).append('\'');
-            sb.append(", alternate='").append(alternate).append('\'');
-            sb.append(", strand='").append(strand).append('\'');
-            sb.append('}');
-            return sb.toString();
-        }
-
-        public String getChromosome() {
-            return chromosome;
-        }
-
-        public int getStart() {
-            return start;
-        }
-
-        public int getEnd() {
-            return end;
-        }
-
-        public String getReference() {
-            return reference;
-        }
-
-        public String getAlternate() {
-            return alternate;
-        }
-
-        public String getStrand() {
-            return strand;
-        }
-
-        public void setChromosome(String chromosome) {
-            this.chromosome = chromosome;
-        }
-
-        public void setStart(int start) {
-            this.start = start;
-        }
-
-        public void setEnd(int end) {
-            this.end = end;
-        }
-
-        public void setReference(String reference) {
-            this.reference = reference;
-        }
-
-        public void setAlternate(String alternate) {
-            this.alternate = alternate;
-        }
-
-        public void setStrand(String strand) {
-            this.strand = strand;
-        }
-    }
-
-
 }

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

@@ -19,6 +19,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.VariantAnnotation;
+import org.opencb.cellbase.core.exception.CellBaseException;
 import org.opencb.cellbase.core.serializer.CellBaseSerializer;
 import org.opencb.cellbase.lib.EtlCommons;
 import org.opencb.cellbase.lib.builders.CellBaseBuilder;
@@ -99,7 +100,7 @@ public ClinicalVariantBuilder(Path clinvarXMLFile, Path clinvarSummaryFile, Path
         this.assembly = assembly;
     }
 
-    public void parse() throws IOException, RocksDBException {
+    public void parse() throws IOException, RocksDBException, CellBaseException {
 
         RocksDB rdb = null;
         Options dbOption = null;