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TASK-2094 - ClassNotFoundException: org.apache.commons.collections.CollectionUtils #222

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Sep 27, 2022
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TASK-2094 - ClassNotFoundException: org.apache.commons.collections.CollectionUtils #222

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f4f1d49
tools: Remove apache-commons v3 usage. Exclude unused avro-ipc #TASK-…
j-coll Sep 23, 2022
4bde5db
tools: Remove usages of apache.commons.collections v3 #TASK-2094
j-coll Sep 26, 2022
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6 changes: 6 additions & 0 deletions biodata-tools/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion biodata-tools/src/main/java/org/opencb/biodata/tools/alignment/BamManager.java
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Expand Up @@ -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;
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4 changes: 2 additions & 2 deletions ...-tools/src/main/java/org/opencb/biodata/tools/clinical/DefaultClinicalVariantCreator.java
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Expand Up @@ -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;
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4 changes: 2 additions & 2 deletions ...ata-tools/src/main/java/org/opencb/biodata/tools/clinical/TeamClinicalVariantCreator.java
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Expand Up @@ -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;
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4 changes: 2 additions & 2 deletions biodata-tools/src/main/java/org/opencb/biodata/tools/pedigree/ModeOfInheritance.java
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@@ -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;
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9 changes: 7 additions & 2 deletions biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantJsonReader.java
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@@ -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;
Expand Down Expand Up @@ -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) {
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2 changes: 1 addition & 1 deletion ...ls/src/main/java/org/opencb/biodata/tools/variant/stats/SampleVariantStatsCalculator.java
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@@ -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;
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2 changes: 1 addition & 1 deletion ...s/src/test/java/org/opencb/biodata/tools/variant/metadata/VariantMetadataManagerTest.java
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@@ -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;
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