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Use toURI instead of getFile which doesn't have file scheme
1 parent 64cb303 commit 1964040

15 files changed

Lines changed: 39 additions & 37 deletions

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‎biojava-aa-prop/pom.xml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->

‎biojava-alignment/pom.xml‎

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Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-alignment</artifactId>
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<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>

‎biojava-core/pom.xml‎

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Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-core</artifactId>

‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaStreamerTest.java‎

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,8 @@
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import org.junit.Test;
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import java.io.IOException;
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import java.net.URI;
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import java.net.URISyntaxException;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.util.List;
@@ -16,9 +18,9 @@
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public class FastaStreamerTest {
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@Test
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public void stream() throws IOException {
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String file = this.getClass().getResource("PF00104_small.fasta.gz").getFile();
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Path path = Paths.get(file);
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public void stream() throws IOException, URISyntaxException {
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URI fileUri = this.getClass().getResource("PF00104_small.fasta.gz").toURI();
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Path path = Paths.get(fileUri);
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List<ProteinSequence> sequences;
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sequences = FastaStreamer.from(path).stream().collect(Collectors.toList());
@@ -38,9 +40,9 @@ public void stream() throws IOException {
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}
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@Test
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public void iterate() {
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String file = this.getClass().getResource("PF00104_small.fasta.gz").getFile();
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Path path = Paths.get(file);
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public void iterate() throws URISyntaxException {
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URI fileUri = this.getClass().getResource("PF00104_small.fasta.gz").toURI();
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Path path = Paths.get(fileUri);
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int count = 0;
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for (ProteinSequence sequence : FastaStreamer.from(path).each()) {
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count++;

‎biojava-genome/pom.xml‎

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Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-alignment</artifactId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>

‎biojava-integrationtest/pom.xml‎

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@@ -4,7 +4,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-integrationtest</artifactId>
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<packaging>jar</packaging>
@@ -40,7 +40,7 @@
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
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<dependency>

‎biojava-modfinder/pom.xml‎

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@@ -4,7 +4,7 @@
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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-modfinder</artifactId>
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<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
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<dependency>
3232
<groupId>org.biojava</groupId>
3333
<artifactId>biojava-structure</artifactId>
34-
<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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<type>jar</type>
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<scope>compile</scope>
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</dependency>

‎biojava-ontology/pom.xml‎

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Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
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<parent>
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<groupId>org.biojava</groupId>
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<artifactId>biojava</artifactId>
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<version>7.1.2-SNAPSHOT</version>
7+
<version>7.1.3-SNAPSHOT</version>
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</parent>
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1010
<artifactId>biojava-ontology</artifactId>

‎biojava-protein-comparison-tool/pom.xml‎

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Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
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<parent>
55
<artifactId>biojava</artifactId>
66
<groupId>org.biojava</groupId>
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<version>7.1.2-SNAPSHOT</version>
7+
<version>7.1.3-SNAPSHOT</version>
88
</parent>
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1010
<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
3636
<dependency>
3737
<groupId>org.biojava</groupId>
3838
<artifactId>biojava-alignment</artifactId>
39-
<version>7.1.2-SNAPSHOT</version>
39+
<version>7.1.3-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
45-
<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure</artifactId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-structure-gui</artifactId>
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<version>7.1.2-SNAPSHOT</version>
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<version>7.1.3-SNAPSHOT</version>
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</dependency>
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<dependency>
5858
<groupId>net.sourceforge.jmol</groupId>

‎biojava-protein-disorder/pom.xml‎

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Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
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<parent>
44
<artifactId>biojava</artifactId>
55
<groupId>org.biojava</groupId>
6-
<version>7.1.2-SNAPSHOT</version>
6+
<version>7.1.3-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-protein-disorder</artifactId>
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<packaging>jar</packaging>
@@ -63,7 +63,7 @@
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava-core</artifactId>
66-
<version>7.1.2-SNAPSHOT</version>
66+
<version>7.1.3-SNAPSHOT</version>
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</dependency>
6868
<!-- logging dependencies (managed by parent pom, don't set versions or
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scopes here) -->

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