tools: Remove usages of apache.commons.collections v3 #TASK-2094

opencb · Sep 26, 2022 · 4bde5db · 4bde5db
1 parent f4f1d49
commit 4bde5db
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Showing 6 changed files with 15 additions and 10 deletions.
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/...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;