Merge pull request #244 from TheJacksonLaboratory/update-dependencies

Update dependencies
monarch-initiative · Feb 26, 2024 · 1ac346b · 1ac346b
2 parents 5c65e77 + 60b41f9
commit 1ac346b
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Showing 17 changed files with 77 additions and 71 deletions.
diff --git a/pom.xml b/pom.xml
@@ -37,11 +37,13 @@
         <phenopacket-schema.version>2.0.2</phenopacket-schema.version>
         <silent.genes.version>0.2.5</silent.genes.version>
         <htsjdk.version>3.0.5</htsjdk.version>
+        <guava.version>33.0.0-jre</guava.version>
         <commons-csv.version>1.7</commons-csv.version>
-        <commons-io.version>2.8.0</commons-io.version>
-        <commons-net.version>3.8.0</commons-net.version>
-        <commons-compress.version>1.24.0</commons-compress.version>
-        <h2.version>1.4.200</h2.version>
+        <commons-io.version>2.15.1</commons-io.version>
+        <commons-net.version>3.9.0</commons-net.version>
+        <commons-compress.version>1.26.0</commons-compress.version>
+        <h2.version>2.2.220</h2.version>
+        <flyway.version>10.8.1</flyway.version>
     </properties>
 
     <developers>
@@ -127,7 +129,7 @@
             <dependency>
                 <groupId>com.google.guava</groupId>
                 <artifactId>guava</artifactId>
-                <version>31.1-jre</version>
+                <version>${guava.version}</version>
             </dependency>
             <dependency>
                 <groupId>com.google.errorprone</groupId>

diff --git a/...a-db/src/main/java/org/monarchinitiative/svanna/db/landscape/ClingenDosageElementDao.java b/...a-db/src/main/java/org/monarchinitiative/svanna/db/landscape/ClingenDosageElementDao.java
@@ -51,7 +51,7 @@ public int insertItem(DosageRegion item) {
         try (Connection connection = dataSource.getConnection()) {
             connection.setAutoCommit(false);
             String sql = "insert into SVANNA.CLINGEN_DOSAGE_ELEMENT(" +
-                    " CONTIG, START, END, " +
+                    " CONTIG, START_POS, END_POS, " +
                     " ID, DOSAGE_SENSITIVITY, DOSAGE_EVIDENCE) " +
                     " VALUES ( ?, ?, ?, ?, ?, ? )";
             try (PreparedStatement preparedStatement = connection.prepareStatement(sql)) {
@@ -83,11 +83,11 @@ public int insertItem(DosageRegion item) {
 
     @Override
     public List<DosageRegion> getOverlapping(GenomicRegion query) {
-        String sql = "select CONTIG, START, END, ID, DOSAGE_SENSITIVITY, DOSAGE_EVIDENCE " +
+        String sql = "select CONTIG, START_POS, END_POS, ID, DOSAGE_SENSITIVITY, DOSAGE_EVIDENCE " +
                 " from SVANNA.CLINGEN_DOSAGE_ELEMENT " +
                 "  where CONTIG = ? " +
-                "    and ? < END " +
-                "    and START < ?";
+                "    and ? < END_POS " +
+                "    and START_POS < ?";
         try (Connection connection = dataSource.getConnection();
              PreparedStatement preparedStatement = connection.prepareStatement(sql)) {
             preparedStatement.setInt(1, query.contigId());
@@ -119,8 +119,8 @@ public List<Dosage> geneDosageDataForHgncIdAndRegion(String hgncId, GenomicRegio
         String sql = "select distinct ID, DOSAGE_SENSITIVITY, DOSAGE_EVIDENCE " +
                 " from SVANNA.CLINGEN_DOSAGE_ELEMENT " +
                 "  where (CONTIG = ? " +
-                "      and ? < END " +
-                "      and START < ?) " +
+                "      and ? < END_POS " +
+                "      and START_POS < ?) " +
                 "    or ID = ?";
         try (Connection connection = dataSource.getConnection();
              PreparedStatement preparedStatement = connection.prepareStatement(sql)) {
@@ -146,7 +146,7 @@ private List<DosageRegion> processDosageRegionStatement(PreparedStatement prepar
                     continue;
                 }
                 Coordinates coordinates = Coordinates.of(CoordinateSystem.zeroBased(), // database invariant
-                        rs.getInt("START"), rs.getInt("END"));
+                        rs.getInt("START_POS"), rs.getInt("END_POS"));
                 GenomicRegion location = GenomicRegion.of(contig, Strand.POSITIVE, coordinates);
                 Dosage dosage = Dosage.of(rs.getString("ID"),
                         DosageSensitivity.valueOf(rs.getString("DOSAGE_SENSITIVITY")),

diff --git a/...na-db/src/main/java/org/monarchinitiative/svanna/db/landscape/DbPopulationVariantDao.java b/...na-db/src/main/java/org/monarchinitiative/svanna/db/landscape/DbPopulationVariantDao.java
@@ -60,7 +60,7 @@ private List<PopulationVariant> processStatement(PreparedStatement preparedState
                 }
                 regions.add(
                         BasePopulationVariant.of(
-                                GenomicRegion.of(contig, Strand.POSITIVE, CoordinateSystem.zeroBased(), rs.getInt("START"), rs.getInt("END")),
+                                GenomicRegion.of(contig, Strand.POSITIVE, CoordinateSystem.zeroBased(), rs.getInt("START_POS"), rs.getInt("END_POS")),
                                 rs.getString("ID"), VariantType.valueOf(rs.getString("VARIANT_TYPE")),
                                 rs.getFloat("ALLELE_FREQUENCY"), origin));
             }
@@ -74,7 +74,7 @@ public int insertItem(PopulationVariant item) {
 
         try (Connection connection = dataSource.getConnection()) {
             connection.setAutoCommit(false);
-            String sql = "insert into SVANNA.POPULATION_VARIANTS(CONTIG, START, END, " +
+            String sql = "insert into SVANNA.POPULATION_VARIANTS(CONTIG, START_POS, END_POS, " +
                     "ID, VARIANT_TYPE, ORIGIN, ALLELE_FREQUENCY) " +
                     "VALUES ( ?, ?, ?, ?, ?, ?, ? )";
             try (PreparedStatement preparedStatement = connection.prepareStatement(sql)) {
@@ -111,11 +111,11 @@ public Set<PopulationVariantOrigin> availableOrigins() {
     @Override
     public List<PopulationVariant> getOverlapping(GenomicRegion query, Set<PopulationVariantOrigin> origins) {
 
-        String sql = "select CONTIG, START, END, ID, VARIANT_TYPE, ORIGIN, ALLELE_FREQUENCY " +
+        String sql = "select CONTIG, START_POS, END_POS, ID, VARIANT_TYPE, ORIGIN, ALLELE_FREQUENCY " +
                 " from SVANNA.POPULATION_VARIANTS " +
                 "  where CONTIG = ? " +
-                "    and ? < END " +
-                "    and START < ?";
+                "    and ? < END_POS " +
+                "    and START_POS < ?";
         try (Connection connection = dataSource.getConnection();
              PreparedStatement preparedStatement = connection.prepareStatement(sql)) {
             preparedStatement.setInt(1, query.contigId());

diff --git a/svanna-db/src/main/java/org/monarchinitiative/svanna/db/landscape/EnhancerAnnotationDao.java b/svanna-db/src/main/java/org/monarchinitiative/svanna/db/landscape/EnhancerAnnotationDao.java
@@ -61,7 +61,7 @@ public int insertItem(Enhancer enhancer) {
 
         try (Connection connection = dataSource.getConnection()) {
             connection.setAutoCommit(false);
-            String enhancerSql = "insert into SVANNA.ENHANCERS(CONTIG, START, END, " +
+            String enhancerSql = "insert into SVANNA.ENHANCERS(CONTIG, START_POS, END_POS, " +
                     " ENHANCER_SOURCE, NAME, IS_DEVELOPMENTAL, TAU) " +
                     " VALUES ( ?, ?, ?, ?, ?, ?, ? )";
             String tissueSpecSql = "insert into SVANNA.ENHANCER_TISSUE_SPECIFICITY(ENHANCER_ID, " +
@@ -111,7 +111,7 @@ public int insertItem(Enhancer enhancer) {
     }
 
     public List<Enhancer> getAllItems() {
-        String sql = "select E.ENHANCER_ID, CONTIG, START, END, ENHANCER_SOURCE, NAME, IS_DEVELOPMENTAL, TAU, " +
+        String sql = "select E.ENHANCER_ID, CONTIG, START_POS, END_POS, ENHANCER_SOURCE, NAME, IS_DEVELOPMENTAL, TAU, " +
                 " TERM_ID, TERM_LABEL, HPO_ID, HPO_LABEL, SPECIFICITY " +
                 " from SVANNA.ENHANCERS E join SVANNA.ENHANCER_TISSUE_SPECIFICITY ETS on E.ENHANCER_ID = ETS.ENHANCER_ID";
         try (Connection connection = dataSource.getConnection();
@@ -157,12 +157,12 @@ public List<Enhancer> getOverlapping(GenomicRegion query) {
         try (Connection connection = dataSource.getConnection()) {
             if (!enhancerParameters.useFantom5()) {
                 // just VISTA
-                String enhancerSql = "select E.ENHANCER_ID, CONTIG, START, END, ENHANCER_SOURCE, NAME, IS_DEVELOPMENTAL, TAU, " +
+                String enhancerSql = "select E.ENHANCER_ID, CONTIG, START_POS, END_POS, ENHANCER_SOURCE, NAME, IS_DEVELOPMENTAL, TAU, " +
                         " TERM_ID, TERM_LABEL, HPO_ID, HPO_LABEL, SPECIFICITY " +
                         "   from SVANNA.ENHANCERS E join SVANNA.ENHANCER_TISSUE_SPECIFICITY ETS on E.ENHANCER_ID = ETS.ENHANCER_ID " +
                         " where E.CONTIG = ? " +
-                        "   and ? < E.END " +
-                        "   and E.START < ? " +
+                        "   and ? < E.END_POS " +
+                        "   and E.START_POS < ? " +
                         "   and E.IS_DEVELOPMENTAL = true";
                 try (PreparedStatement ps = connection.prepareStatement(enhancerSql)) {
                     ps.setInt(1, query.contigId());
@@ -172,12 +172,12 @@ public List<Enhancer> getOverlapping(GenomicRegion query) {
                 }
             } else {
                 // FANTOM5 and maybe VISTA
-                String enhancerSql = "select E.ENHANCER_ID, CONTIG, START, END, ENHANCER_SOURCE, NAME, IS_DEVELOPMENTAL, TAU, " +
+                String enhancerSql = "select E.ENHANCER_ID, CONTIG, START_POS, END_POS, ENHANCER_SOURCE, NAME, IS_DEVELOPMENTAL, TAU, " +
                         " TERM_ID, TERM_LABEL, HPO_ID, HPO_LABEL, SPECIFICITY " +
                         "   from SVANNA.ENHANCERS E join SVANNA.ENHANCER_TISSUE_SPECIFICITY ETS on E.ENHANCER_ID = ETS.ENHANCER_ID" +
                         " where E.CONTIG = ? " +
-                        "   and ? < E.END " +
-                        "   and E.START < ? " +
+                        "   and ? < E.END_POS " +
+                        "   and E.START_POS < ? " +
                         "   and (E.IS_DEVELOPMENTAL = ? or (E.IS_DEVELOPMENTAL = false and ETS.SPECIFICITY > ?))";
                 try (PreparedStatement ps = connection.prepareStatement(enhancerSql)) {
                     ps.setInt(1, query.contigId());
@@ -210,7 +210,7 @@ private List<Enhancer> processEnhancers(PreparedStatement statement) throws SQLE
 
                 if (!builders.containsKey(enhancerId)) {
                     // database invariant
-                    Coordinates coordinates = Coordinates.of(CoordinateSystem.zeroBased(), rs.getInt("START"), rs.getInt("END"));
+                    Coordinates coordinates = Coordinates.of(CoordinateSystem.zeroBased(), rs.getInt("START_POS"), rs.getInt("END_POS"));
                     GenomicRegion location = GenomicRegion.of(contig, Strand.POSITIVE, coordinates);
                     BaseEnhancer.Builder builder = BaseEnhancer.builder()
                             .location(location)

diff --git a/svanna-db/src/main/java/org/monarchinitiative/svanna/db/landscape/RepetitiveRegionDao.java b/svanna-db/src/main/java/org/monarchinitiative/svanna/db/landscape/RepetitiveRegionDao.java
@@ -30,7 +30,7 @@ public RepetitiveRegionDao(DataSource dataSource, GenomicAssembly genomicAssembl
     }
 
     public List<RepetitiveRegion> getAllItems() {
-        String sql = "select CONTIG, START, END, REPEAT_FAMILY from SVANNA.REPETITIVE_REGIONS";
+        String sql = "select CONTIG, START_POS, END_POS, REPEAT_FAMILY from SVANNA.REPETITIVE_REGIONS";
         try (Connection connection = dataSource.getConnection();
              PreparedStatement preparedStatement = connection.prepareStatement(sql)) {
             return processStatement(preparedStatement);
@@ -42,11 +42,11 @@ public List<RepetitiveRegion> getAllItems() {
 
     @Override
     public List<RepetitiveRegion> getOverlapping(GenomicRegion query) {
-        String sql = "select CONTIG, START, END, REPEAT_FAMILY " +
+        String sql = "select CONTIG, START_POS, END_POS, REPEAT_FAMILY " +
                 " from SVANNA.REPETITIVE_REGIONS " +
                 "  where CONTIG = ? " +
-                "    and ? < END " +
-                "    and START < ?";
+                "    and ? < END_POS " +
+                "    and START_POS < ?";
         try (Connection connection = dataSource.getConnection();
              PreparedStatement preparedStatement = connection.prepareStatement(sql)) {
             preparedStatement.setInt(1, query.contigId());
@@ -70,7 +70,7 @@ private List<RepetitiveRegion> processStatement(PreparedStatement preparedStatem
                 }
                 regions.add(RepetitiveRegion.of(contig,
                         Strand.POSITIVE, CoordinateSystem.zeroBased(), // database invariant
-                        rs.getInt("START"), rs.getInt("END"),
+                        rs.getInt("START_POS"), rs.getInt("END_POS"),
                         RepeatFamily.valueOf(rs.getString("REPEAT_FAMILY"))));
             }
         }
@@ -83,7 +83,7 @@ public int insertItem(RepetitiveRegion item) {
 
         try (Connection connection = dataSource.getConnection()) {
             connection.setAutoCommit(false);
-            String sql = "insert into SVANNA.REPETITIVE_REGIONS(CONTIG, START, END, REPEAT_FAMILY) " +
+            String sql = "insert into SVANNA.REPETITIVE_REGIONS(CONTIG, START_POS, END_POS, REPEAT_FAMILY) " +
                     "VALUES ( ?, ?, ?, ? )";
             try (PreparedStatement preparedStatement = connection.prepareStatement(sql)) {
                 preparedStatement.setInt(1, item.contigId());

diff --git a/svanna-db/src/main/java/org/monarchinitiative/svanna/db/landscape/TadBoundaryDao.java b/svanna-db/src/main/java/org/monarchinitiative/svanna/db/landscape/TadBoundaryDao.java
@@ -53,7 +53,7 @@ public int insertItem(TadBoundary item) {
 
         try (Connection connection = dataSource.getConnection()) {
             connection.setAutoCommit(false);
-            String sql = "insert into SVANNA.TAD_BOUNDARY(CONTIG, START, END, MIDPOINT, ID, STABILITY) " +
+            String sql = "insert into SVANNA.TAD_BOUNDARY(CONTIG, START_POS, END_POS, MIDPOINT, ID, STABILITY) " +
                     "VALUES ( ?, ?, ?, ?, ?, ?)";
             try (PreparedStatement preparedStatement = connection.prepareStatement(sql)) {
                 preparedStatement.setInt(1, item.contigId());

diff --git a/...db/src/test/resources/org/monarchinitiative/svanna/db/landscape/enhancer_create_table.sql b/...db/src/test/resources/org/monarchinitiative/svanna/db/landscape/enhancer_create_table.sql
@@ -5,16 +5,16 @@ create table SVANNA.ENHANCERS
 (
     ENHANCER_ID      INT auto_increment,
     CONTIG           INT          not null,
-    START            INT          not null,
-    END              INT          not null,
+    START_POS        INT          not null,
+    END_POS          INT          not null,
     ENHANCER_SOURCE  VARCHAR(50)  not null,
     NAME             VARCHAR(255) not null,
     IS_DEVELOPMENTAL BOOL         not null,
     TAU              DOUBLE       not null
 );
 
 create index SVANNA.ENHANCERS__CONTIG_START_END_IDX
-    on SVANNA.ENHANCERS (CONTIG, START, END);
+    on SVANNA.ENHANCERS (CONTIG, START_POS, END_POS);
 
 
 drop table if exists SVANNA.ENHANCER_TISSUE_SPECIFICITY;

diff --git a/...-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/enhancer_insert_data.sql b/...-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/enhancer_insert_data.sql
@@ -1,6 +1,6 @@
 truncate table SVANNA.ENHANCERS;
 
-insert into SVANNA.ENHANCERS(ENHANCER_ID, CONTIG, START, END, ENHANCER_SOURCE, NAME, IS_DEVELOPMENTAL, TAU)
+insert into SVANNA.ENHANCERS(ENHANCER_ID, CONTIG, START_POS, END_POS, ENHANCER_SOURCE, NAME, IS_DEVELOPMENTAL, TAU)
 values (1, 1, 10, 20, 'UNKNOWN', 'first', TRUE, .123),
        (2, 1, 30, 40, 'UNKNOWN', 'second', TRUE, .456);
 

diff --git a/.../resources/org/monarchinitiative/svanna/db/landscape/population_variants_create_table.sql b/.../resources/org/monarchinitiative/svanna/db/landscape/population_variants_create_table.sql
@@ -4,13 +4,13 @@ drop table if exists SVANNA.POPULATION_VARIANTS;
 create table SVANNA.POPULATION_VARIANTS
 (
     CONTIG           INT          not null,
-    START            INT          not null,
-    END              INT          not null,
+    START_POS        INT          not null,
+    END_POS          INT          not null,
 
     ID               VARCHAR(200) not null,
     VARIANT_TYPE     VARCHAR(20)  not null,
     ORIGIN           VARCHAR(40)  not null,
     ALLELE_FREQUENCY FLOAT        not null
 );
 create index SVANNA.POPULATION_VARIANTS__CONTIG_START_ON_POS_END_ON_POS_IDX
-    on SVANNA.POPULATION_VARIANTS (CONTIG, START, END);
+    on SVANNA.POPULATION_VARIANTS (CONTIG, START_POS, END_POS);
diff --git a/...t/resources/org/monarchinitiative/svanna/db/landscape/population_variants_insert_data.sql b/...t/resources/org/monarchinitiative/svanna/db/landscape/population_variants_insert_data.sql
@@ -1,4 +1,4 @@
-insert into SVANNA.POPULATION_VARIANTS(CONTIG, START, END, ID, VARIANT_TYPE, ORIGIN, ALLELE_FREQUENCY)
+insert into SVANNA.POPULATION_VARIANTS(CONTIG, START_POS, END_POS, ID, VARIANT_TYPE, ORIGIN, ALLELE_FREQUENCY)
 VALUES
        ( 1, 10, 10, 'abc', 'INS_ME_LINE1', 'DGV', 22.1),
        ( 1, 30, 30, 'def', 'INS', 'GNOMAD_SV', 23.4),

diff --git a/...t/resources/org/monarchinitiative/svanna/db/landscape/repetitive_regions_create_table.sql b/...t/resources/org/monarchinitiative/svanna/db/landscape/repetitive_regions_create_table.sql
@@ -5,9 +5,9 @@ create table SVANNA.REPETITIVE_REGIONS
 (
     ENHANCER_ID   INT auto_increment,
     CONTIG        INT         not null,
-    START         INT         not null,
-    END           INT         not null,
+    START_POS     INT         not null,
+    END_POS       INT         not null,
     REPEAT_FAMILY VARCHAR(50) not null
 );
 create index SVANNA.REPETITIVE_REGIONS__CONTIG_START_ON_POS_END_ON_POS_IDX
-    on SVANNA.REPETITIVE_REGIONS (CONTIG, START, END);
+    on SVANNA.REPETITIVE_REGIONS (CONTIG, START_POS, END_POS);
diff --git a/...st/resources/org/monarchinitiative/svanna/db/landscape/repetitive_regions_insert_data.sql b/...st/resources/org/monarchinitiative/svanna/db/landscape/repetitive_regions_insert_data.sql
@@ -1,4 +1,4 @@
-insert into SVANNA.REPETITIVE_REGIONS(CONTIG, START, END, REPEAT_FAMILY)
+insert into SVANNA.REPETITIVE_REGIONS(CONTIG, START_POS, END_POS, REPEAT_FAMILY)
 VALUES (1, 20, 30, 'DNA_hAT_Blackjack'),
        (1, 30, 40, 'SINE_tRNA_Deu'),
        (2, 30, 40, 'RNA_srpRNA');
diff --git a/...rc/test/resources/org/monarchinitiative/svanna/db/landscape/tad_boundary_create_table.sql b/...rc/test/resources/org/monarchinitiative/svanna/db/landscape/tad_boundary_create_table.sql
@@ -3,13 +3,13 @@ drop table if exists SVANNA.TAD_BOUNDARY;
 create table SVANNA.TAD_BOUNDARY
 (
     CONTIG    INT          not null,
-    START     INT          not null, -- zero-based start on POSITIVE strand
-    END       INT          not null, -- zero-based end on POSITIVE strand
+    START_POS INT          not null, -- zero-based start on POSITIVE strand
+    END_POS   INT          not null, -- zero-based end on POSITIVE strand
     MIDPOINT  INT          not null,
     ID        VARCHAR(200) not null,
     STABILITY FLOAT        not null
 );
 create index SVANNA.TAD_BOUNDARY__CONTIG_START_END_IDX
-    on SVANNA.TAD_BOUNDARY (CONTIG, START, END);
+    on SVANNA.TAD_BOUNDARY (CONTIG, START_POS, END_POS);
 create index SVANNA.TAD_BOUNDARY__CONTIG_MIDPOINT_IDX
     on SVANNA.TAD_BOUNDARY (CONTIG, MIDPOINT);
diff --git a/...src/test/resources/org/monarchinitiative/svanna/db/landscape/tad_boundary_insert_data.sql b/...src/test/resources/org/monarchinitiative/svanna/db/landscape/tad_boundary_insert_data.sql
@@ -1,4 +1,4 @@
-insert into SVANNA.TAD_BOUNDARY(CONTIG, START, END, MIDPOINT, ID, STABILITY)
+insert into SVANNA.TAD_BOUNDARY(CONTIG, START_POS, END_POS, MIDPOINT, ID, STABILITY)
 values
        ( 1, 20, 40, 30, 'one',   .8),
        ( 1, 30, 50, 40, 'two',   .9),

diff --git a/svanna-ingest/src/main/java/org/monarchinitiative/svanna/ingest/cmd/BuildDb.java b/svanna-ingest/src/main/java/org/monarchinitiative/svanna/ingest/cmd/BuildDb.java
@@ -449,7 +449,9 @@ private static void ingestTads(TadProperties properties, GenomicAssembly assembl
         URL mcArthurSupplement = new URL(properties.mcArthur2021Supplement());
         Path localPath = downloadUrl(mcArthurSupplement, tmpDir);
 
-        try (ZipFile zipFile = new ZipFile(localPath.toFile())) {
+        try (ZipFile zipFile = ZipFile.builder()
+                .setFile(localPath.toFile())
+                .get()) {
             // this is the single file from the entire ZIP that we're interested in
             String entryName = "emcarthur-TAD-stability-heritability-184f51a/data/boundariesByStability/100kbBookendBoundaries_mainText/100kbBookendBoundaries_byStability.bed";
             ZipArchiveEntry entry = zipFile.getEntry(entryName);
@@ -683,7 +685,7 @@ public Integer call() throws Exception {
             DigestUtils digest = new DigestUtils(MessageDigestAlgorithms.SHA_256);
 
             for (File resource : resources) {
-                if (LOGGER.isDebugEnabled()) LOGGER.debug("Calculating SHA256 digest for `{}`", resource);
+                LOGGER.debug("Calculating SHA256 digest for `{}`", resource);
                 String hexDigest = digest.digestAsHex(resource);
                 fileToDigest.put(resource, hexDigest);
             }

diff --git a/...na-ingest/src/main/java/org/monarchinitiative/svanna/ingest/io/ZipCompressionWrapper.java b/...na-ingest/src/main/java/org/monarchinitiative/svanna/ingest/io/ZipCompressionWrapper.java
@@ -1,8 +1,8 @@
 package org.monarchinitiative.svanna.ingest.io;
 
-import org.apache.commons.compress.archivers.ArchiveEntry;
+import org.apache.commons.compress.archivers.zip.ZipArchiveEntry;
 import org.apache.commons.compress.archivers.zip.ZipArchiveOutputStream;
-import org.apache.commons.compress.utils.IOUtils;
+import org.apache.commons.io.IOUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -36,7 +36,7 @@ public void addResource(File file, String name) throws IOException {
             return;
         }
 
-        ArchiveEntry entry = archive.createArchiveEntry(file, name);
+        ZipArchiveEntry entry = archive.createArchiveEntry(file, name);
         archive.putArchiveEntry(entry);
         if (attributes.isRegularFile()) {
             try (InputStream is = Files.newInputStream(file.toPath())) {