Merge branch 'release-4.9.x' into release-4.10.x

cellbase-app/pom.xml

@@ -47,6 +47,10 @@
             <artifactId>commons-io</artifactId>
             <version>2.4</version>
         </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-collections4</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/DownloadCommandExecutor.java

@@ -21,10 +21,10 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.ObjectReader;
 import com.fasterxml.jackson.databind.ObjectWriter;
-import org.apache.commons.collections.map.HashedMap;
+import org.apache.commons.collections4.map.HashedMap;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.opencb.cellbase.core.config.Species;
 import org.opencb.commons.utils.FileUtils;
 

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/EtlCommons.java

@@ -1,6 +1,6 @@
 package org.opencb.cellbase.app.cli;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.opencb.commons.utils.FileUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/QueryGrpcCommandExecutor.java

@@ -58,7 +58,7 @@ public QueryGrpcCommandExecutor(CliOptionsParser.QueryGrpcCommandOptions queryGr
     public void execute() {
 
         channel = ManagedChannelBuilder.forAddress(queryGrpcCommandOptions.host, queryGrpcCommandOptions.port)
-                .usePlaintext(true)
+                .usePlaintext()
                 .build();
 
         Map<String, String> query = createQueryMap();

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/ValidationCommandExecutor.java

@@ -18,7 +18,7 @@
 
 import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.VariantAnnotation;
 import org.opencb.cellbase.app.cli.validation.VEPVariant;

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/VariantAnnotationCommandExecutor.java

@@ -537,7 +537,7 @@ private void getIndexes() throws IOException, RocksDBException {
     private void checkParameters() throws IOException {
 
         // Get reference genome
-        if (org.apache.commons.lang.StringUtils.isNotBlank(variantAnnotationCommandOptions.referenceFasta)) {
+        if (org.apache.commons.lang3.StringUtils.isNotBlank(variantAnnotationCommandOptions.referenceFasta)) {
             referenceFasta = Paths.get(variantAnnotationCommandOptions.referenceFasta);
             FileUtils.checkFile(referenceFasta);
         }

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/variant/annotation/JsonStringAnnotatorTask.java

@@ -19,7 +19,7 @@
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.MapperFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import org.mortbay.util.ajax.JSON;
+import org.eclipse.jetty.util.ajax.JSON;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.tools.variant.VariantNormalizer;
 import org.opencb.biodata.models.variant.avro.VariantAvro;

cellbase-app/src/main/java/org/opencb/cellbase/app/transform/GeneParser.java

@@ -16,7 +16,7 @@
 
 package org.opencb.cellbase.app.transform;
 
-import org.apache.commons.collections.map.HashedMap;
+import org.apache.commons.collections4.map.HashedMap;
 import org.opencb.biodata.formats.feature.gff.Gff2;
 import org.opencb.biodata.formats.feature.gtf.Gtf;
 import org.opencb.biodata.formats.feature.gtf.io.GtfReader;

cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/DOCMIndexer.java

@@ -1,7 +1,7 @@
 package org.opencb.cellbase.app.transform.clinical.variant;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
-import org.apache.commons.collections.map.HashedMap;
+import org.apache.commons.collections4.map.HashedMap;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.avro.*;
 import org.opencb.cellbase.app.cli.EtlCommons;

cellbase-app/src/main/java/org/opencb/cellbase/app/transform/clinical/variant/GwasParser.java

@@ -17,7 +17,7 @@
 package org.opencb.cellbase.app.transform.clinical.variant;
 
 import htsjdk.tribble.readers.TabixReader;
-import org.apache.commons.lang.math.NumberUtils;
+import org.apache.commons.lang3.math.NumberUtils;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.cellbase.app.transform.CellBaseParser;
 import org.opencb.cellbase.core.common.clinical.gwas.Gwas;

cellbase-app/src/test/java/org/opencb/cellbase/app/transform/DgvParserTest.java

@@ -4,7 +4,7 @@
 import com.fasterxml.jackson.databind.MapperFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.Test;
-import org.mortbay.util.ajax.JSON;
+import org.eclipse.jetty.util.ajax.JSON;
 import org.opencb.biodata.models.variant.avro.VariantAvro;
 import org.opencb.cellbase.core.serializer.CellBaseFileSerializer;
 import org.opencb.cellbase.core.serializer.CellBaseJsonFileSerializer;

cellbase-app/src/test/java/org/opencb/cellbase/app/transform/RepeatsParserTest.java

@@ -4,7 +4,7 @@
 import com.fasterxml.jackson.databind.MapperFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.Test;
-import org.mortbay.util.ajax.JSON;
+import org.eclipse.jetty.util.ajax.JSON;
 import org.opencb.biodata.models.variant.avro.Repeat;
 import org.opencb.biodata.models.variant.avro.VariantAvro;
 import org.opencb.cellbase.app.cli.EtlCommons;

cellbase-client/pom.xml

@@ -19,10 +19,20 @@
             <groupId>org.opencb.cellbase</groupId>
             <artifactId>cellbase-core</artifactId>
         </dependency>
+        <dependency>
+            <groupId>io.grpc</groupId>
+            <artifactId>grpc-all</artifactId>
+        </dependency>
+
         <dependency>
             <groupId>com.fasterxml.jackson.dataformat</groupId>
             <artifactId>jackson-dataformat-yaml</artifactId>
         </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+            <version>${jackson.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.glassfish.jersey.core</groupId>
             <artifactId>jersey-client</artifactId>

cellbase-client/src/main/java/org/opencb/cellbase/client/grpc/CellbaseGrpcClient.java

@@ -17,7 +17,7 @@ public class CellbaseGrpcClient {
 
     public CellbaseGrpcClient(String host, int port) {
         this.channel = ManagedChannelBuilder.forAddress(host, port)
-                .usePlaintext(true)
+                .usePlaintext()
                 .build();
 
         clients = new HashMap<>();

cellbase-core/pom.xml

@@ -23,7 +23,10 @@
             <groupId>org.opencb.biodata</groupId>
             <artifactId>biodata-tools</artifactId>
         </dependency>
-
+        <dependency>
+            <groupId>org.eclipse.jetty</groupId>
+            <artifactId>jetty-util-ajax</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.glassfish.jersey.core</groupId>
             <artifactId>jersey-client</artifactId>

cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsCalculator.java

@@ -1,6 +1,6 @@
 package org.opencb.cellbase.core.variant.annotation.hgvs;
 
-import org.apache.commons.lang.NotImplementedException;
+import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.StringUtils;
 import org.opencb.biodata.models.core.Exon;
 import org.opencb.biodata.models.core.Gene;

cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsTranscriptCalculator.java

@@ -1,6 +1,6 @@
 package org.opencb.cellbase.core.variant.annotation.hgvs;
 
-import org.apache.commons.lang.NotImplementedException;
+import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.StringUtils;
 import org.opencb.biodata.models.core.Transcript;
 import org.opencb.biodata.models.variant.Variant;

cellbase-core/src/test/java/org/opencb/cellbase/core/variant/annotation/hgvs/HgvsProteinCalculatorTest.java

@@ -7,7 +7,7 @@
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
-import org.mortbay.util.ajax.JSON;
+import org.eclipse.jetty.util.ajax.JSON;
 import org.opencb.biodata.models.core.Gene;
 import org.opencb.biodata.models.core.Transcript;
 import org.opencb.biodata.models.variant.Variant;

cellbase-lib/pom.xml

@@ -30,6 +30,14 @@
                 </exclusion>
             </exclusions>
         </dependency>
+        <dependency>
+            <groupId>org.eclipse.jetty</groupId>
+            <artifactId>jetty-util-ajax</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-collections4</artifactId>
+        </dependency>
         <!--<dependency>-->
             <!--<groupId>org.opencb.bionetdb</groupId>-->
             <!--<artifactId>bionetdb-core</artifactId>-->

cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/GeneMongoDBAdaptor.java

@@ -24,7 +24,7 @@
 import com.mongodb.client.model.Aggregates;
 import com.mongodb.client.model.Filters;
 import com.mongodb.client.model.Projections;
-import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.bson.Document;
 import org.bson.conversions.Bson;

cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/ClinicalMongoDBAdaptorTest.java

@@ -7,7 +7,7 @@
 import org.hamcrest.CoreMatchers;
 import org.junit.Before;
 import org.junit.Test;
-import org.mortbay.util.ajax.JSON;
+import org.eclipse.jetty.util.ajax.JSON;
 import org.opencb.biodata.models.core.Gene;
 import org.opencb.biodata.models.core.Region;
 import org.opencb.biodata.models.variant.Variant;

cellbase-lib/src/test/java/org/opencb/cellbase/lib/variant/annotation/hgvs/HgvsTranscriptCalculatorTest.java

@@ -6,7 +6,7 @@
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
-import org.mortbay.util.ajax.JSON;
+import org.eclipse.jetty.util.ajax.JSON;
 import org.opencb.biodata.models.core.Gene;
 import org.opencb.biodata.models.core.Transcript;
 import org.opencb.biodata.models.variant.Variant;

pom.xml

@@ -25,9 +25,9 @@
         <cellbase.version>4.10.1</cellbase.version>
         <compileSource>1.8</compileSource>
         <java-common-libs.version>3.7.5</java-common-libs.version>
-        <biodata.version>1.5.5</biodata.version>
+        <biodata.version>1.5.6</biodata.version>
         <bionetdb.version>0.1.0</bionetdb.version>
-        <jackson.version>2.9.8</jackson.version>
+        <jackson.version>2.13.3</jackson.version>
         <protobuf.version>3.1.0</protobuf.version>
         <grpc.version>1.0.1</grpc.version>
         <jersey.version>2.25.1</jersey.version>
@@ -121,6 +121,10 @@
                         <artifactId>log4j</artifactId>
                         <groupId>log4j</groupId>
                     </exclusion>
+                    <exclusion>
+                        <groupId>org.apache.avro</groupId>
+                        <artifactId>avro-ipc</artifactId>
+                    </exclusion>
                 </exclusions>
             </dependency>
             <dependency>
@@ -130,6 +134,46 @@
             </dependency>
 
             <!-- General dependencies -->
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-compress</artifactId>
+                <version>1.21</version>
+            </dependency>
+            <dependency>
+                <groupId>com.google.protobuf</groupId>
+                <artifactId>protobuf-java</artifactId>
+                <version>3.21.1</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-collections4</artifactId>
+                <version>4.4</version>
+            </dependency>
+            <dependency>
+                <groupId>org.eclipse.jetty</groupId>
+                <artifactId>jetty-util-ajax</artifactId>
+                <version>9.3.24.v20180605</version>
+            </dependency>
+            <dependency>
+                <groupId>io.grpc</groupId>
+                <artifactId>grpc-all</artifactId>
+                <version>1.48.0</version>
+            </dependency>
+            <dependency>
+                <groupId>com.fasterxml.jackson.core</groupId>
+                <artifactId>jackson-core</artifactId>
+                <version>${jackson.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>com.fasterxml.jackson.core</groupId>
+                <artifactId>jackson-databind</artifactId>
+                <version>${jackson.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>com.fasterxml.jackson.core</groupId>
+                <artifactId>jackson-annotations</artifactId>
+                <version>${jackson.version}</version>
+            </dependency>
             <dependency>
                 <groupId>com.fasterxml.jackson.module</groupId>
                 <artifactId>jackson-module-jsonSchema</artifactId>
@@ -145,6 +189,11 @@
                 <artifactId>jackson-dataformat-yaml</artifactId>
                 <version>${jackson.version}</version>
             </dependency>
+            <dependency>
+                <groupId>com.fasterxml.jackson.dataformat</groupId>
+                <artifactId>jackson-dataformat-xml</artifactId>
+                <version>${jackson.version}</version>
+            </dependency>
             <dependency>
                 <groupId>org.glassfish.jersey.core</groupId>
                 <artifactId>jersey-client</artifactId>