[med-svn] [Git][med-team/biojava-live][upstream] New upstream version 1.9.6+dfsg
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Fri Jun 30 06:26:31 BST 2023
Pierre Gruet pushed to branch upstream at Debian Med / biojava-live
Commits:
058c1b64 by Pierre Gruet at 2023-06-29T22:23:13+02:00
New upstream version 1.9.6+dfsg
- - - - -
17 changed files:
- + .github/workflows/ci.yml
- + .github/workflows/deploy.yml
- − .travis.yml
- README.md
- alignment/pom.xml
- biosql/pom.xml
- blast/pom.xml
- bytecode/pom.xml
- core/pom.xml
- gui/pom.xml
- phylo/pom.xml
- pom.xml
- sequencing/pom.xml
- sequencing/src/main/java/org/biojava/bio/program/fastq/FastqParser.java
- sequencing/src/test/java/org/biojava/bio/program/fastq/IlluminaFastqReaderTest.java
- sequencing/src/test/java/org/biojava/bio/program/fastq/SangerFastqReaderTest.java
- sequencing/src/test/java/org/biojava/bio/program/fastq/SolexaFastqReaderTest.java
Changes:
=====================================
.github/workflows/ci.yml
=====================================
@@ -0,0 +1,20 @@
+name: CI
+
+on: pull_request
+
+jobs:
+ build:
+ runs-on: ubuntu-latest
+
+ steps:
+ - uses: actions/checkout at v2
+ - uses: actions/setup-java at v2
+ with:
+ java-version: '11'
+ distribution: 'temurin'
+ - uses: actions/cache at v2
+ with:
+ path: ~/.m2
+ key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
+ restore-keys: ${{ runner.os }}-m2
+ - run: mvn --batch-mode --update-snapshots clean package
=====================================
.github/workflows/deploy.yml
=====================================
@@ -0,0 +1,29 @@
+name: Deploy Snapshot
+
+on:
+ push:
+ branches:
+ - master
+
+jobs:
+ build:
+ runs-on: ubuntu-latest
+ if: ${{ github.repository == 'biojava/biojava-legacy' }}
+ steps:
+ - uses: actions/checkout at v2
+ - uses: actions/setup-java at v2
+ with:
+ java-version: '11'
+ distribution: 'temurin'
+ server-id: sonatype-nexus-snapshots
+ server-username: MAVEN_USERNAME
+ server-password: MAVEN_PASSWORD
+ - uses: actions/cache at v2
+ with:
+ path: ~/.m2
+ key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
+ restore-keys: ${{ runner.os }}-m2
+ - env:
+ MAVEN_USERNAME: ${{ secrets.OSS_SONATYPE_USERNAME }}
+ MAVEN_PASSWORD: ${{ secrets.OSS_SONATYPE_PASSWORD }}
+ run: mvn --batch-mode -DskipTests=true deploy
=====================================
.travis.yml deleted
=====================================
@@ -1 +0,0 @@
-language: java
=====================================
README.md
=====================================
@@ -4,6 +4,3 @@ biojava-legacy
This repository contains code from BioJava 1.
The goal is to port all features present in BioJava 1 to the BioJava 3 codebase, available at https://github.com/biojava/biojava. However, until that goal is achieved this repository will remain active for minor changes and bug fixes.
-
-### Build Status
-[](https://travis-ci.org/biojava/biojava-legacy)
=====================================
alignment/pom.xml
=====================================
@@ -4,11 +4,11 @@
<parent>
<artifactId>biojava-legacy</artifactId>
<groupId>org.biojava</groupId>
- <version>1.9.5</version>
+ <version>1.9.6</version>
</parent>
<artifactId>alignment</artifactId>
<packaging>jar</packaging>
- <version>1.9.5</version>
+ <version>1.9.6</version>
<name>alignment</name>
<description>BioJava alignment module</description>
<dependencies>
=====================================
biosql/pom.xml
=====================================
@@ -4,11 +4,11 @@
<parent>
<artifactId>biojava-legacy</artifactId>
<groupId>org.biojava</groupId>
- <version>1.9.5</version>
+ <version>1.9.6</version>
</parent>
<artifactId>biosql</artifactId>
<packaging>jar</packaging>
- <version>1.9.5</version>
+ <version>1.9.6</version>
<name>biosql</name>
<description>BioJava biosql module</description>
<dependencies>
=====================================
blast/pom.xml
=====================================
@@ -4,11 +4,11 @@
<parent>
<artifactId>biojava-legacy</artifactId>
<groupId>org.biojava</groupId>
- <version>1.9.5</version>
+ <version>1.9.6</version>
</parent>
<artifactId>blast</artifactId>
<packaging>jar</packaging>
- <version>1.9.5</version>
+ <version>1.9.6</version>
<name>blast</name>
<description>BioJava blast module</description>
<dependencies>
=====================================
bytecode/pom.xml
=====================================
@@ -4,12 +4,12 @@
<parent>
<artifactId>biojava-legacy</artifactId>
<groupId>org.biojava</groupId>
- <version>1.9.5</version>
+ <version>1.9.6</version>
</parent>
<groupId>org.biojava</groupId>
<packaging>jar</packaging>
<artifactId>bytecode</artifactId>
- <version>1.9.5</version>
+ <version>1.9.6</version>
<name>bytecode</name>
<description>BioJava bytecode module</description>
<dependencies>
=====================================
core/pom.xml
=====================================
@@ -4,11 +4,11 @@
<parent>
<artifactId>biojava-legacy</artifactId>
<groupId>org.biojava</groupId>
- <version>1.9.5</version>
+ <version>1.9.6</version>
</parent>
<artifactId>core</artifactId>
<packaging>jar</packaging>
- <version>1.9.5</version>
+ <version>1.9.6</version>
<name>core</name>
<description>BioJava core module</description>
<dependencies>
=====================================
gui/pom.xml
=====================================
@@ -4,11 +4,11 @@
<parent>
<artifactId>biojava-legacy</artifactId>
<groupId>org.biojava</groupId>
- <version>1.9.5</version>
+ <version>1.9.6</version>
</parent>
<artifactId>gui</artifactId>
<packaging>jar</packaging>
- <version>1.9.5</version>
+ <version>1.9.6</version>
<name>gui</name>
<description>BioJava gui module</description>
<dependencies>
=====================================
phylo/pom.xml
=====================================
@@ -4,11 +4,11 @@
<parent>
<artifactId>biojava-legacy</artifactId>
<groupId>org.biojava</groupId>
- <version>1.9.5</version>
+ <version>1.9.6</version>
</parent>
<artifactId>phylo</artifactId>
<packaging>jar</packaging>
- <version>1.9.5</version>
+ <version>1.9.6</version>
<name>phylo</name>
<description>BioJava phylo module</description>
<dependencies>
=====================================
pom.xml
=====================================
@@ -9,7 +9,7 @@
<groupId>org.biojava</groupId>
<artifactId>biojava-legacy</artifactId>
<packaging>pom</packaging>
- <version>1.9.5</version>
+ <version>1.9.6</version>
<name>biojava-legacy</name>
<description>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 manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.</description>
<url>http://www.biojava.org</url>
@@ -28,7 +28,7 @@
<connection>scm:git:https://github.com/biojava/biojava-legacy</connection>
<developerConnection>scm:git:https://github.com/biojava/biojava-legacy</developerConnection>
<url>https://github.com/biojava/biojava-legacy</url>
- <tag>biojava-legacy-1.9.5</tag>
+ <tag>biojava-legacy-1.9.6</tag>
</scm>
<developers>
<developer>
@@ -151,23 +151,23 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>4.13.1</version>
+ <version>4.13.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>commons-dbcp</groupId>
<artifactId>commons-dbcp</artifactId>
- <version>1.2.2</version>
+ <version>1.4</version>
</dependency>
<dependency>
<groupId>javax.persistence</groupId>
<artifactId>persistence-api</artifactId>
- <version>1.0</version>
+ <version>1.0.2</version>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
- <version>2.2</version>
+ <version>2.3.1</version>
</dependency>
<dependency>
<groupId>org.jgrapht</groupId>
@@ -177,7 +177,7 @@
<dependency>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
- <version>2.12.0</version>
+ <version>2.12.2</version>
</dependency>
</dependencies>
</dependencyManagement>
=====================================
sequencing/pom.xml
=====================================
@@ -4,11 +4,11 @@
<parent>
<artifactId>biojava-legacy</artifactId>
<groupId>org.biojava</groupId>
- <version>1.9.5</version>
+ <version>1.9.6</version>
</parent>
<artifactId>sequencing</artifactId>
<packaging>jar</packaging>
- <version>1.9.5</version>
+ <version>1.9.6</version>
<name>sequencing</name>
<description>BioJava sequencing module</description>
<dependencyManagement>
@@ -16,7 +16,7 @@
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
- <version>24.1.1-jre</version>
+ <version>32.0.1-jre</version>
</dependency>
</dependencies>
</dependencyManagement>
=====================================
sequencing/src/main/java/org/biojava/bio/program/fastq/FastqParser.java
=====================================
@@ -49,16 +49,24 @@ final class FastqParser
{
throw new IllegalArgumentException("readable must not be null");
}
- FastqParserLineProcessor lineProcessor = new FastqParserLineProcessor(listener);
- CharStreams.readLines(readable, lineProcessor);
- if (lineProcessor.getState() == State.COMPLETE)
+ final FastqParserLineProcessor lineProcessor = new FastqParserLineProcessor(listener);
+ try
{
- listener.complete();
- lineProcessor.setState(State.DESCRIPTION);
+ CharStreams.readLines(readable, lineProcessor);
+
+ if (lineProcessor.getState() == State.COMPLETE)
+ {
+ listener.complete();
+ lineProcessor.setState(State.DESCRIPTION);
+ }
+ }
+ catch (IOException e)
+ {
+ throw new IOException("parse error at line " + lineProcessor.getLineNumber() + ", state " + lineProcessor.getState(), e);
}
if (lineProcessor.getState() != State.DESCRIPTION)
{
- throw new IOException("truncated sequence"); // at line " + lineNumber);
+ throw new IOException("truncated sequence at line " + lineProcessor.getLineNumber());
}
}
@@ -70,6 +78,9 @@ final class FastqParser
/** Parser state. */
private State state = State.DESCRIPTION;
+ /** Line number. */
+ private long lineNumber = 0;
+
/** Sequence length. */
private int sequenceLength = 0;
@@ -115,6 +126,16 @@ final class FastqParser
this.state = state;
}
+ /**
+ * Return the line number.
+ *
+ * @return the line number
+ */
+ private long getLineNumber()
+ {
+ return lineNumber;
+ }
+
@Override
public Object getResult()
{
@@ -124,6 +145,8 @@ final class FastqParser
@Override
public boolean processLine(final String line) throws IOException
{
+ lineNumber++;
+
String sequence = null;
String quality = null;
switch (state)
=====================================
sequencing/src/test/java/org/biojava/bio/program/fastq/IlluminaFastqReaderTest.java
=====================================
@@ -67,7 +67,7 @@ public final class IlluminaFastqReaderTest
}
catch (IOException e)
{
- assertTrue(e.getMessage().contains("description must begin with a '@' character"));
+ assertTrue(e.getCause().getMessage().contains("description must begin with a '@' character"));
}
}
@@ -82,7 +82,7 @@ public final class IlluminaFastqReaderTest
}
catch (IOException e)
{
- assertTrue(e.getMessage().contains("repeat description must match description"));
+ assertTrue(e.getCause().getMessage().contains("repeat description must match description"));
}
}
=====================================
sequencing/src/test/java/org/biojava/bio/program/fastq/SangerFastqReaderTest.java
=====================================
@@ -67,7 +67,7 @@ public final class SangerFastqReaderTest
}
catch (IOException e)
{
- assertTrue(e.getMessage().contains("description must begin with a '@' character"));
+ assertTrue(e.getCause().getMessage().contains("description must begin with a '@' character"));
}
}
@@ -82,7 +82,7 @@ public final class SangerFastqReaderTest
}
catch (IOException e)
{
- assertTrue(e.getMessage().contains("repeat description must match description"));
+ assertTrue(e.getCause().getMessage().contains("repeat description must match description"));
}
}
=====================================
sequencing/src/test/java/org/biojava/bio/program/fastq/SolexaFastqReaderTest.java
=====================================
@@ -67,7 +67,7 @@ public final class SolexaFastqReaderTest
}
catch (IOException e)
{
- assertTrue(e.getMessage().contains("description must begin with a '@' character"));
+ assertTrue(e.getCause().getMessage().contains("description must begin with a '@' character"));
}
}
@@ -82,7 +82,7 @@ public final class SolexaFastqReaderTest
}
catch (IOException e)
{
- assertTrue(e.getMessage().contains("repeat description must match description"));
+ assertTrue(e.getCause().getMessage().contains("repeat description must match description"));
}
}
View it on GitLab: https://salsa.debian.org/med-team/biojava-live/-/commit/058c1b641e4ec946630eac6388b96a88c668f1b8
--
View it on GitLab: https://salsa.debian.org/med-team/biojava-live/-/commit/058c1b641e4ec946630eac6388b96a88c668f1b8
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