Merge pull request #222 from opencb/TASK-2094

TASK-2094 - ClassNotFoundException: org.apache.commons.collections.CollectionUtils
opencb · Sep 27, 2022 · ed2ae57 · ed2ae57
2 parents 358c8ee + 4bde5db
commit ed2ae57
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Showing 8 changed files with 22 additions and 11 deletions.
diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml
@@ -42,6 +42,12 @@
             <groupId>org.opencb.ga4gh</groupId>
             <artifactId>ga4gh</artifactId>
             <version>0.6.0a5</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.apache.avro</groupId>
+                    <artifactId>avro-ipc</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
 
         <dependency>

diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/BamManager.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/BamManager.java
@@ -27,7 +27,7 @@
 import htsjdk.samtools.util.BlockCompressedFilePointerUtil;
 import htsjdk.samtools.util.BlockCompressedInputStream;
 import htsjdk.samtools.util.Log;
-import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.collections4.CollectionUtils;
 import org.ga4gh.models.ReadAlignment;
 import org.opencb.biodata.models.alignment.RegionCoverage;
 import org.opencb.biodata.models.core.Region;

diff --git a/...-tools/src/main/java/org/opencb/biodata/tools/clinical/DefaultClinicalVariantCreator.java b/...-tools/src/main/java/org/opencb/biodata/tools/clinical/DefaultClinicalVariantCreator.java
@@ -19,8 +19,8 @@
 
 package org.opencb.biodata.tools.clinical;
 
-import org.apache.commons.collections.CollectionUtils;
-import org.apache.commons.collections.MapUtils;
+import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.collections4.MapUtils;
 import org.opencb.biodata.models.clinical.ClinicalDiscussion;
 import org.opencb.biodata.models.clinical.ClinicalProperty;
 import org.opencb.biodata.models.clinical.ClinicalProperty.ModeOfInheritance;

diff --git a/...ata-tools/src/main/java/org/opencb/biodata/tools/clinical/TeamClinicalVariantCreator.java b/...ata-tools/src/main/java/org/opencb/biodata/tools/clinical/TeamClinicalVariantCreator.java
@@ -19,8 +19,8 @@
 
 package org.opencb.biodata.tools.clinical;
 
-import org.apache.commons.collections.CollectionUtils;
-import org.apache.commons.collections.MapUtils;
+import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.collections4.MapUtils;
 import org.opencb.biodata.models.clinical.ClinicalDiscussion;
 import org.opencb.biodata.models.clinical.ClinicalProperty.ModeOfInheritance;
 import org.opencb.biodata.models.clinical.ClinicalProperty.Penetrance;

diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/pedigree/ModeOfInheritance.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/pedigree/ModeOfInheritance.java
@@ -1,7 +1,7 @@
 package org.opencb.biodata.tools.pedigree;
 
-import org.apache.commons.collections.CollectionUtils;
-import org.apache.commons.collections.MapUtils;
+import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.collections4.MapUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.Pair;
 import org.opencb.biodata.models.clinical.ClinicalProperty.Penetrance;

diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantJsonReader.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantJsonReader.java
@@ -1,9 +1,9 @@
 package org.opencb.biodata.tools.variant;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.MapperFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import org.mortbay.util.ajax.JSON;
 import org.opencb.biodata.formats.variant.io.VariantReader;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.biodata.models.variant.VariantBuilder;
@@ -109,7 +109,12 @@ public List<Variant> read(int batchSize) {
         String line;
         int i = 0;
         while ((i < batchSize) && (line = readLine()) != null) {
-            Variant variant = new Variant(jsonObjectMapper.convertValue(JSON.parse(line), VariantAvro.class));
+            Variant variant;
+            try {
+                variant = new Variant(jsonObjectMapper.readValue(line, VariantAvro.class));
+            } catch (JsonProcessingException e) {
+                throw new UncheckedIOException(e);
+            }
 
             // Read variants may not have the variant type set and this might cause NPE
             if (variant.getType() == null) {

diff --git a/...ls/src/main/java/org/opencb/biodata/tools/variant/stats/SampleVariantStatsCalculator.java b/...ls/src/main/java/org/opencb/biodata/tools/variant/stats/SampleVariantStatsCalculator.java
@@ -1,7 +1,7 @@
 package org.opencb.biodata.tools.variant.stats;
 
 import htsjdk.variant.vcf.VCFConstants;
-import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.Pair;
 import org.opencb.biodata.models.clinical.pedigree.Member;

diff --git a/...s/src/test/java/org/opencb/biodata/tools/variant/metadata/VariantMetadataManagerTest.java b/...s/src/test/java/org/opencb/biodata/tools/variant/metadata/VariantMetadataManagerTest.java
@@ -1,6 +1,6 @@
 package org.opencb.biodata.tools.variant.metadata;
 
-import org.apache.commons.collections.map.HashedMap;
+import org.apache.commons.collections4.map.HashedMap;
 import org.junit.Before;
 import org.junit.Test;
 import org.opencb.biodata.models.metadata.Individual;