From 19640407969376b083cf220a30f5e1ce7e7d9e2f Mon Sep 17 00:00:00 2001 From: alawi Date: Wed, 24 Apr 2024 23:07:14 +0200 Subject: [PATCH 1/2] Use toURI instead of getFile which doesn't have file scheme --- biojava-aa-prop/pom.xml | 6 +++--- biojava-alignment/pom.xml | 4 ++-- biojava-core/pom.xml | 2 +- .../nbio/core/sequence/io/FastaStreamerTest.java | 14 ++++++++------ biojava-genome/pom.xml | 6 +++--- biojava-integrationtest/pom.xml | 4 ++-- biojava-modfinder/pom.xml | 4 ++-- biojava-ontology/pom.xml | 2 +- biojava-protein-comparison-tool/pom.xml | 10 +++++----- biojava-protein-disorder/pom.xml | 4 ++-- biojava-structure-gui/pom.xml | 6 +++--- biojava-structure/pom.xml | 6 +++--- biojava-survival/pom.xml | 2 +- biojava-ws/pom.xml | 4 ++-- pom.xml | 2 +- 15 files changed, 39 insertions(+), 37 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index 7c3d994d5c..6c6bcb2d62 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT org.biojava biojava-structure - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 31ddaaf246..64e9042d34 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 5c294cdc97..9bfe594a80 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaStreamerTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaStreamerTest.java index 614c6f06c8..6c93c912c1 100644 --- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaStreamerTest.java +++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaStreamerTest.java @@ -5,6 +5,8 @@ import org.junit.Test; import java.io.IOException; +import java.net.URI; +import java.net.URISyntaxException; import java.nio.file.Path; import java.nio.file.Paths; import java.util.List; @@ -16,9 +18,9 @@ public class FastaStreamerTest { @Test - public void stream() throws IOException { - String file = this.getClass().getResource("PF00104_small.fasta.gz").getFile(); - Path path = Paths.get(file); + public void stream() throws IOException, URISyntaxException { + URI fileUri = this.getClass().getResource("PF00104_small.fasta.gz").toURI(); + Path path = Paths.get(fileUri); List sequences; sequences = FastaStreamer.from(path).stream().collect(Collectors.toList()); @@ -38,9 +40,9 @@ public void stream() throws IOException { } @Test - public void iterate() { - String file = this.getClass().getResource("PF00104_small.fasta.gz").getFile(); - Path path = Paths.get(file); + public void iterate() throws URISyntaxException { + URI fileUri = this.getClass().getResource("PF00104_small.fasta.gz").toURI(); + Path path = Paths.get(fileUri); int count = 0; for (ProteinSequence sequence : FastaStreamer.from(path).each()) { count++; diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index dd395e40b6..898d42594d 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT compile org.biojava biojava-alignment - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 4f1f34abd8..03ba45181b 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index ec919839e0..f013d4e6f9 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 6803c8a4f4..9762b35076 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index c5a32a81b6..7b819dbf0a 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT org.biojava biojava-core - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT org.biojava biojava-structure - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT org.biojava biojava-structure-gui - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index 46ad1f4154..a69135171e 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 05ebf00c97..e5ce572362 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT compile org.biojava biojava-core - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 6b82206a97..ed22484e53 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT biojava-structure biojava-structure @@ -44,13 +44,13 @@ org.biojava biojava-alignment - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT compile org.biojava biojava-core - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 37e75445eb..dcc460234b 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index 66580cb6ea..fd19c88670 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index 4af310f250..d492d29bd2 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.1.2-SNAPSHOT + 7.1.3-SNAPSHOT biojava BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the From d96cae47d66ea5d0644a077aabc74876ad37d4ea Mon Sep 17 00:00:00 2001 From: alawi Date: Wed, 24 Apr 2024 23:51:17 +0200 Subject: [PATCH 2/2] Reverting changes to pom files --- biojava-aa-prop/pom.xml | 6 +++--- biojava-alignment/pom.xml | 4 ++-- biojava-core/pom.xml | 2 +- biojava-genome/pom.xml | 6 +++--- biojava-integrationtest/pom.xml | 4 ++-- biojava-modfinder/pom.xml | 4 ++-- biojava-ontology/pom.xml | 2 +- biojava-protein-comparison-tool/pom.xml | 10 +++++----- biojava-protein-disorder/pom.xml | 4 ++-- biojava-structure-gui/pom.xml | 6 +++--- biojava-structure/pom.xml | 6 +++--- biojava-survival/pom.xml | 2 +- biojava-ws/pom.xml | 4 ++-- pom.xml | 2 +- 14 files changed, 31 insertions(+), 31 deletions(-) diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index 6c6bcb2d62..7c3d994d5c 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT org.biojava biojava-structure - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 64e9042d34..31ddaaf246 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT biojava-alignment biojava-alignment @@ -47,7 +47,7 @@ org.biojava biojava-core - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT compile diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 9bfe594a80..5c294cdc97 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 898d42594d..dd395e40b6 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT 4.0.0 biojava-genome @@ -70,13 +70,13 @@ org.biojava biojava-core - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT compile org.biojava biojava-alignment - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index 03ba45181b..4f1f34abd8 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT biojava-integrationtest jar @@ -40,7 +40,7 @@ org.biojava biojava-structure - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index f013d4e6f9..ec919839e0 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 9762b35076..6803c8a4f4 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT biojava-ontology diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml index 7b819dbf0a..c5a32a81b6 100644 --- a/biojava-protein-comparison-tool/pom.xml +++ b/biojava-protein-comparison-tool/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT biojava-protein-comparison-tool @@ -36,23 +36,23 @@ org.biojava biojava-alignment - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT org.biojava biojava-core - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT org.biojava biojava-structure - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT org.biojava biojava-structure-gui - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT net.sourceforge.jmol diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index a69135171e..46ad1f4154 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index e5ce572362..05ebf00c97 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT 4.0.0 biojava-structure-gui @@ -27,13 +27,13 @@ org.biojava biojava-structure - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT compile org.biojava biojava-core - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index ed22484e53..6b82206a97 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT biojava-structure biojava-structure @@ -44,13 +44,13 @@ org.biojava biojava-alignment - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT compile org.biojava biojava-core - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index dcc460234b..37e75445eb 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index fd19c88670..66580cb6ea 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT compile diff --git a/pom.xml b/pom.xml index d492d29bd2..4af310f250 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 7.1.3-SNAPSHOT + 7.1.2-SNAPSHOT biojava BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the