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Fix FastaStreamerTest tests failing on windows due to URL handling #1093

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merged 2 commits into from
Apr 26, 2024
Merged

Fix FastaStreamerTest tests failing on windows due to URL handling #1093

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1964040
Use toURI instead of getFile which doesn't have file scheme
cometbroom Apr 24, 2024
d96cae4
Reverting changes to pom files
cometbroom Apr 24, 2024
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14 changes: 8 additions & 6 deletions biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaStreamerTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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<ProteinSequence> sequences;

sequences = FastaStreamer.from(path).stream().collect(Collectors.toList());
Expand All @@ -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++;
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