diff --git a/pom.xml b/pom.xml
index a0761b08..5ac99d43 100644
--- a/pom.xml
+++ b/pom.xml
@@ -37,11 +37,13 @@
2.0.2
0.2.5
3.0.5
+ 33.0.0-jre
1.7
- 2.8.0
- 3.8.0
- 1.24.0
- 1.4.200
+ 2.15.1
+ 3.9.0
+ 1.26.0
+ 2.2.220
+ 10.8.1
@@ -127,7 +129,7 @@
com.google.guava
guava
- 31.1-jre
+ ${guava.version}
com.google.errorprone
diff --git a/svanna-db/src/main/java/org/monarchinitiative/svanna/db/landscape/ClingenDosageElementDao.java b/svanna-db/src/main/java/org/monarchinitiative/svanna/db/landscape/ClingenDosageElementDao.java
index 3c465d1e..603468b4 100644
--- a/svanna-db/src/main/java/org/monarchinitiative/svanna/db/landscape/ClingenDosageElementDao.java
+++ b/svanna-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 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 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 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/svanna-db/src/main/java/org/monarchinitiative/svanna/db/landscape/DbPopulationVariantDao.java b/svanna-db/src/main/java/org/monarchinitiative/svanna/db/landscape/DbPopulationVariantDao.java
index ad3efd7c..fcaf3ec7 100644
--- a/svanna-db/src/main/java/org/monarchinitiative/svanna/db/landscape/DbPopulationVariantDao.java
+++ b/svanna-db/src/main/java/org/monarchinitiative/svanna/db/landscape/DbPopulationVariantDao.java
@@ -60,7 +60,7 @@ private List 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 availableOrigins() {
@Override
public List getOverlapping(GenomicRegion query, Set 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
index 2cd86ed7..e6dc76bf 100644
--- 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 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 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 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 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
index 6deca1b0..4b566747 100644
--- 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 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 getAllItems() {
@Override
public List 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 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
index 8a3d11c5..cc4bce0b 100644
--- 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/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/enhancer_create_table.sql b/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/enhancer_create_table.sql
index b07b405a..0b82ccb1 100644
--- a/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/enhancer_create_table.sql
+++ b/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/enhancer_create_table.sql
@@ -5,8 +5,8 @@ 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,
@@ -14,7 +14,7 @@ create table SVANNA.ENHANCERS
);
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/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/enhancer_insert_data.sql b/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/enhancer_insert_data.sql
index d60e0803..90b0cccb 100644
--- a/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/enhancer_insert_data.sql
+++ b/svanna-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/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/population_variants_create_table.sql b/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/population_variants_create_table.sql
index 86c3940f..d4cc2237 100644
--- a/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/population_variants_create_table.sql
+++ b/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/population_variants_create_table.sql
@@ -4,8 +4,8 @@ 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,
@@ -13,4 +13,4 @@ create table SVANNA.POPULATION_VARIANTS
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/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/population_variants_insert_data.sql b/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/population_variants_insert_data.sql
index 941d0b47..9a46849c 100644
--- a/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/population_variants_insert_data.sql
+++ b/svanna-db/src/test/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/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/repetitive_regions_create_table.sql b/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/repetitive_regions_create_table.sql
index 8690103d..1bd74521 100644
--- a/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/repetitive_regions_create_table.sql
+++ b/svanna-db/src/test/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/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/repetitive_regions_insert_data.sql b/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/repetitive_regions_insert_data.sql
index 8fd740dd..87c5716d 100644
--- a/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/repetitive_regions_insert_data.sql
+++ b/svanna-db/src/test/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');
\ No newline at end of file
diff --git a/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/tad_boundary_create_table.sql b/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/tad_boundary_create_table.sql
index 5689d2f7..7376bb4c 100644
--- a/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/tad_boundary_create_table.sql
+++ b/svanna-db/src/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/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/tad_boundary_insert_data.sql b/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/tad_boundary_insert_data.sql
index 7492faba..cd632dce 100644
--- a/svanna-db/src/test/resources/org/monarchinitiative/svanna/db/landscape/tad_boundary_insert_data.sql
+++ b/svanna-db/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
index eeb86f7f..fa09576c 100644
--- 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/svanna-ingest/src/main/java/org/monarchinitiative/svanna/ingest/io/ZipCompressionWrapper.java b/svanna-ingest/src/main/java/org/monarchinitiative/svanna/ingest/io/ZipCompressionWrapper.java
index 1baf07c0..d2488e8f 100644
--- a/svanna-ingest/src/main/java/org/monarchinitiative/svanna/ingest/io/ZipCompressionWrapper.java
+++ b/svanna-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())) {
diff --git a/svanna-ingest/src/main/resources/db/migration/V1.0.0__create_schema.sql b/svanna-ingest/src/main/resources/db/migration/V1.0.0__create_schema.sql
index 48f3b994..2584f16e 100644
--- a/svanna-ingest/src/main/resources/db/migration/V1.0.0__create_schema.sql
+++ b/svanna-ingest/src/main/resources/db/migration/V1.0.0__create_schema.sql
@@ -3,10 +3,10 @@ create schema if not exists SVANNA;
drop table if exists SVANNA.ENHANCERS;
create table SVANNA.ENHANCERS
(
- ENHANCER_ID INT auto_increment,
+ ENHANCER_ID INT GENERATED ALWAYS AS IDENTITY,
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
ENHANCER_SOURCE VARCHAR(50) not null,
NAME VARCHAR(255) not null,
IS_DEVELOPMENTAL BOOL not null,
@@ -14,7 +14,7 @@ create table SVANNA.ENHANCERS
);
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;
@@ -36,21 +36,21 @@ drop table if exists SVANNA.REPETITIVE_REGIONS;
create table SVANNA.REPETITIVE_REGIONS
(
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
REPEAT_FAMILY VARCHAR(50) not null
);
create
index SVANNA.REPETITIVE_REGIONS__CONTIG_START_END_IDX
- on SVANNA.REPETITIVE_REGIONS (CONTIG, START, END);
+ on SVANNA.REPETITIVE_REGIONS (CONTIG, START_POS, END_POS);
---------------------------------- POPULATION VARIANTS -----------------------------------------------------------------
drop table if exists SVANNA.POPULATION_VARIANTS;
create table SVANNA.POPULATION_VARIANTS
(
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
ID VARCHAR(200) not null,
VARIANT_TYPE VARCHAR(20) not null,
@@ -59,22 +59,22 @@ create table SVANNA.POPULATION_VARIANTS
);
create
index SVANNA.POPULATION_VARIANTS__CONTIG_START_END_IDX
- on SVANNA.POPULATION_VARIANTS (CONTIG, START, END);
+ on SVANNA.POPULATION_VARIANTS (CONTIG, START_POS, END_POS);
---------------------------------- TAD BOUNDARY ------------------------------------------------------------------------
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);
@@ -88,22 +88,24 @@ create table SVANNA.HP_TERM_MICA
IC_MICA FLOAT not null -- information content of the most common informative ancestor
);
drop index if exists SVANNA.HP_TERM_MICA__LEFT_VALUE_RIGHT_VALUE_IDX;
-create unique index SVANNA.HP_TERM_MICA__LEFT_VALUE_RIGHT_VALUE_IDX on SVANNA.HP_TERM_MICA (LEFT_VALUE, RIGHT_VALUE);
+create unique index SVANNA.HP_TERM_MICA__LEFT_VALUE_RIGHT_VALUE_IDX
+ on SVANNA.HP_TERM_MICA (LEFT_VALUE, RIGHT_VALUE);
---------------------------------- CLINGEN DOSAGE ELEMENT --------------------------------------------------------------
drop table if exists SVANNA.CLINGEN_DOSAGE_ELEMENT;
create table SVANNA.CLINGEN_DOSAGE_ELEMENT
(
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
ID VARCHAR(200) not null, -- HGNC ID or other ID if available
DOSAGE_SENSITIVITY VARCHAR(20) not null,
DOSAGE_EVIDENCE VARCHAR(20) not null
);
drop index if exists SVANNA.CLINGEN_DOSAGE_ELEMENT__CONTIG_START_END_IDX;
-create index SVANNA.CLINGEN_DOSAGE_ELEMENT__CONTIG_START_END_IDX on SVANNA.CLINGEN_DOSAGE_ELEMENT (CONTIG, START, END);
+create index SVANNA.CLINGEN_DOSAGE_ELEMENT__CONTIG_START_END_IDX
+ on SVANNA.CLINGEN_DOSAGE_ELEMENT (CONTIG, START_POS, END_POS);
-- TODO - we should update DA layer to use numeric IDs, where available
drop index if exists SVANNA.CLINGEN_DOSAGE_ELEMENT__ID;