From 38a0466698d37be02a948ec0f1ad139b9616fdd6 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Fri, 12 Mar 2021 12:57:56 -0600 Subject: [PATCH 1/9] [maven-release-plugin] prepare for next development iteration --- alignment/pom.xml | 4 ++-- biosql/pom.xml | 4 ++-- blast/pom.xml | 4 ++-- bytecode/pom.xml | 4 ++-- core/pom.xml | 4 ++-- gui/pom.xml | 4 ++-- phylo/pom.xml | 4 ++-- pom.xml | 4 ++-- sequencing/pom.xml | 4 ++-- 9 files changed, 18 insertions(+), 18 deletions(-) diff --git a/alignment/pom.xml b/alignment/pom.xml index 35e9915..1ecd504 100644 --- a/alignment/pom.xml +++ b/alignment/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.5 + 1.9.6-SNAPSHOT alignment jar - 1.9.5 + 1.9.6-SNAPSHOT alignment BioJava alignment module diff --git a/biosql/pom.xml b/biosql/pom.xml index b83c306..23c80ae 100644 --- a/biosql/pom.xml +++ b/biosql/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.5 + 1.9.6-SNAPSHOT biosql jar - 1.9.5 + 1.9.6-SNAPSHOT biosql BioJava biosql module diff --git a/blast/pom.xml b/blast/pom.xml index 839eb2e..9994bce 100644 --- a/blast/pom.xml +++ b/blast/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.5 + 1.9.6-SNAPSHOT blast jar - 1.9.5 + 1.9.6-SNAPSHOT blast BioJava blast module diff --git a/bytecode/pom.xml b/bytecode/pom.xml index a029184..9b6e18c 100644 --- a/bytecode/pom.xml +++ b/bytecode/pom.xml @@ -4,12 +4,12 @@ biojava-legacy org.biojava - 1.9.5 + 1.9.6-SNAPSHOT org.biojava jar bytecode - 1.9.5 + 1.9.6-SNAPSHOT bytecode BioJava bytecode module diff --git a/core/pom.xml b/core/pom.xml index a6a42df..79a1efd 100644 --- a/core/pom.xml +++ b/core/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.5 + 1.9.6-SNAPSHOT core jar - 1.9.5 + 1.9.6-SNAPSHOT core BioJava core module diff --git a/gui/pom.xml b/gui/pom.xml index 7507a1a..04ce14c 100644 --- a/gui/pom.xml +++ b/gui/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.5 + 1.9.6-SNAPSHOT gui jar - 1.9.5 + 1.9.6-SNAPSHOT gui BioJava gui module diff --git a/phylo/pom.xml b/phylo/pom.xml index 56e2358..b3cc949 100644 --- a/phylo/pom.xml +++ b/phylo/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.5 + 1.9.6-SNAPSHOT phylo jar - 1.9.5 + 1.9.6-SNAPSHOT phylo BioJava phylo module diff --git a/pom.xml b/pom.xml index e0e34df..9ee9537 100644 --- a/pom.xml +++ b/pom.xml @@ -9,7 +9,7 @@ org.biojava biojava-legacy pom - 1.9.5 + 1.9.6-SNAPSHOT biojava-legacy 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. http://www.biojava.org @@ -28,7 +28,7 @@ scm:git:https://github.com/biojava/biojava-legacy scm:git:https://github.com/biojava/biojava-legacy https://github.com/biojava/biojava-legacy - biojava-legacy-1.9.5 + HEAD diff --git a/sequencing/pom.xml b/sequencing/pom.xml index 8014896..ba33e89 100644 --- a/sequencing/pom.xml +++ b/sequencing/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.5 + 1.9.6-SNAPSHOT sequencing jar - 1.9.5 + 1.9.6-SNAPSHOT sequencing BioJava sequencing module From 8cd7e73c9748f4434a323ee6a715a768095b80e0 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Mon, 19 Apr 2021 10:40:14 -0500 Subject: [PATCH 2/9] Update dependency versions. --- pom.xml | 10 +++++----- sequencing/pom.xml | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pom.xml b/pom.xml index 9ee9537..b558617 100644 --- a/pom.xml +++ b/pom.xml @@ -151,23 +151,23 @@ junit junit - 4.13.1 + 4.13.2 test commons-dbcp commons-dbcp - 1.2.2 + 1.4 javax.persistence persistence-api - 1.0 + 1.0.2 javax.xml.bind jaxb-api - 2.2 + 2.3.1 org.jgrapht @@ -177,7 +177,7 @@ xerces xercesImpl - 2.12.0 + 2.12.1 diff --git a/sequencing/pom.xml b/sequencing/pom.xml index ba33e89..6f132a0 100644 --- a/sequencing/pom.xml +++ b/sequencing/pom.xml @@ -16,7 +16,7 @@ com.google.guava guava - 24.1.1-jre + 30.1.1-jre From 5b67960d2690e6320ece14b12643e3eb3fbbde69 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Fri, 10 Sep 2021 20:23:52 -0500 Subject: [PATCH 3/9] Add line number to error reporting. --- .../bio/program/fastq/FastqParser.java | 35 +++++++++++++++---- 1 file changed, 29 insertions(+), 6 deletions(-) diff --git a/sequencing/src/main/java/org/biojava/bio/program/fastq/FastqParser.java b/sequencing/src/main/java/org/biojava/bio/program/fastq/FastqParser.java index 7a01ab8..af997c8 100644 --- a/sequencing/src/main/java/org/biojava/bio/program/fastq/FastqParser.java +++ b/sequencing/src/main/java/org/biojava/bio/program/fastq/FastqParser.java @@ -49,16 +49,24 @@ static void parse(final Readable readable, final ParseListener listener) { 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 @@ private static class FastqParserLineProcessor implements LineProcessor /** Parser state. */ private State state = State.DESCRIPTION; + /** Line number. */ + private long lineNumber = 0; + /** Sequence length. */ private int sequenceLength = 0; @@ -115,6 +126,16 @@ private void setState(final State state) this.state = state; } + /** + * Return the line number. + * + * @return the line number + */ + private long getLineNumber() + { + return lineNumber; + } + @Override public Object getResult() { @@ -124,6 +145,8 @@ public Object getResult() @Override public boolean processLine(final String line) throws IOException { + lineNumber++; + String sequence = null; String quality = null; switch (state) From fba10c43025f06a0998b618fc50abcc3ffd66a50 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Wed, 17 Nov 2021 15:46:47 -0600 Subject: [PATCH 4/9] Migrate CI from Travis to Github Actions. --- .github/workflows/ci.yml | 20 ++++++++++++++++++++ .github/workflows/deploy.yml | 29 +++++++++++++++++++++++++++++ .travis.yml | 1 - README.md | 3 --- 4 files changed, 49 insertions(+), 4 deletions(-) create mode 100644 .github/workflows/ci.yml create mode 100644 .github/workflows/deploy.yml delete mode 100644 .travis.yml diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..9d8fc46 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,20 @@ +name: CI + +on: pull_request + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + - uses: actions/setup-java@v2 + with: + java-version: '11' + distribution: 'temurin' + - uses: actions/cache@v2 + with: + path: ~/.m2 + key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }} + restore-keys: ${{ runner.os }}-m2 + - run: mvn --batch-mode --update-snapshots clean package diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml new file mode 100644 index 0000000..723eb45 --- /dev/null +++ b/.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@v2 + - uses: actions/setup-java@v2 + with: + java-version: '11' + distribution: 'temurin' + server-id: sonatype-nexus-snapshots + server-username: MAVEN_USERNAME + server-password: MAVEN_PASSWORD + - uses: actions/cache@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 diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index dff5f3a..0000000 --- a/.travis.yml +++ /dev/null @@ -1 +0,0 @@ -language: java diff --git a/README.md b/README.md index 8e82e5c..565d856 100644 --- a/README.md +++ b/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 -[![Build Status](https://travis-ci.org/biojava/biojava-legacy.png)](https://travis-ci.org/biojava/biojava-legacy) From 106f1c69e6efe0f8c5cf1ef7bd10f7dfcd3e3a61 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Sun, 12 Dec 2021 18:56:57 -0600 Subject: [PATCH 5/9] Update guava dependency version to 31.0.1-jre. --- sequencing/pom.xml | 2 +- .../biojava/bio/program/fastq/IlluminaFastqReaderTest.java | 4 ++-- .../org/biojava/bio/program/fastq/SangerFastqReaderTest.java | 4 ++-- .../org/biojava/bio/program/fastq/SolexaFastqReaderTest.java | 4 ++-- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/sequencing/pom.xml b/sequencing/pom.xml index 6f132a0..5db3c50 100644 --- a/sequencing/pom.xml +++ b/sequencing/pom.xml @@ -16,7 +16,7 @@ com.google.guava guava - 30.1.1-jre + 31.0.1-jre diff --git a/sequencing/src/test/java/org/biojava/bio/program/fastq/IlluminaFastqReaderTest.java b/sequencing/src/test/java/org/biojava/bio/program/fastq/IlluminaFastqReaderTest.java index b2c5830..61f159c 100755 --- a/sequencing/src/test/java/org/biojava/bio/program/fastq/IlluminaFastqReaderTest.java +++ b/sequencing/src/test/java/org/biojava/bio/program/fastq/IlluminaFastqReaderTest.java @@ -67,7 +67,7 @@ public void testValidateDescription() throws Exception } 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 void testValidateRepeatDescription() throws Exception } catch (IOException e) { - assertTrue(e.getMessage().contains("repeat description must match description")); + assertTrue(e.getCause().getMessage().contains("repeat description must match description")); } } diff --git a/sequencing/src/test/java/org/biojava/bio/program/fastq/SangerFastqReaderTest.java b/sequencing/src/test/java/org/biojava/bio/program/fastq/SangerFastqReaderTest.java index 5a0d690..4bc68be 100755 --- a/sequencing/src/test/java/org/biojava/bio/program/fastq/SangerFastqReaderTest.java +++ b/sequencing/src/test/java/org/biojava/bio/program/fastq/SangerFastqReaderTest.java @@ -67,7 +67,7 @@ public void testValidateDescription() throws Exception } 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 void testValidateRepeatDescription() throws Exception } catch (IOException e) { - assertTrue(e.getMessage().contains("repeat description must match description")); + assertTrue(e.getCause().getMessage().contains("repeat description must match description")); } } diff --git a/sequencing/src/test/java/org/biojava/bio/program/fastq/SolexaFastqReaderTest.java b/sequencing/src/test/java/org/biojava/bio/program/fastq/SolexaFastqReaderTest.java index 208e7ba..bc3360b 100755 --- a/sequencing/src/test/java/org/biojava/bio/program/fastq/SolexaFastqReaderTest.java +++ b/sequencing/src/test/java/org/biojava/bio/program/fastq/SolexaFastqReaderTest.java @@ -67,7 +67,7 @@ public void testValidateDescription() throws Exception } 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 void testValidateRepeatDescription() throws Exception } catch (IOException e) { - assertTrue(e.getMessage().contains("repeat description must match description")); + assertTrue(e.getCause().getMessage().contains("repeat description must match description")); } } From b487df14a06cadb1fa9319f8a1870dc05ff11d09 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 27 Jan 2022 16:16:19 +0000 Subject: [PATCH 6/9] Bump xercesImpl from 2.12.1 to 2.12.2 Bumps xercesImpl from 2.12.1 to 2.12.2. --- updated-dependencies: - dependency-name: xerces:xercesImpl dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index b558617..7bb1fdf 100644 --- a/pom.xml +++ b/pom.xml @@ -177,7 +177,7 @@ xerces xercesImpl - 2.12.1 + 2.12.2 From d5ca53119f7bfbf726c5b9b6516bae2c693e0942 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Sun, 3 Apr 2022 14:39:47 -0500 Subject: [PATCH 7/9] Update guava dependency version to 31.1-jre. --- sequencing/pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sequencing/pom.xml b/sequencing/pom.xml index 5db3c50..309f45d 100644 --- a/sequencing/pom.xml +++ b/sequencing/pom.xml @@ -16,7 +16,7 @@ com.google.guava guava - 31.0.1-jre + 31.1-jre From 46102d69021a7a83507f51cb602dd6bcc679e365 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Tue, 27 Jun 2023 14:44:10 -0500 Subject: [PATCH 8/9] Update guava dependency version to 32.0.1-jre. --- sequencing/pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sequencing/pom.xml b/sequencing/pom.xml index 309f45d..721efac 100644 --- a/sequencing/pom.xml +++ b/sequencing/pom.xml @@ -16,7 +16,7 @@ com.google.guava guava - 31.1-jre + 32.0.1-jre From 724ab5937c22a8f96329626f9599a1ce838ef2bd Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Tue, 27 Jun 2023 14:58:21 -0500 Subject: [PATCH 9/9] [maven-release-plugin] prepare release biojava-legacy-1.9.6 --- alignment/pom.xml | 4 ++-- biosql/pom.xml | 4 ++-- blast/pom.xml | 4 ++-- bytecode/pom.xml | 4 ++-- core/pom.xml | 4 ++-- gui/pom.xml | 4 ++-- phylo/pom.xml | 4 ++-- pom.xml | 4 ++-- sequencing/pom.xml | 4 ++-- 9 files changed, 18 insertions(+), 18 deletions(-) diff --git a/alignment/pom.xml b/alignment/pom.xml index 1ecd504..ef5f4ed 100644 --- a/alignment/pom.xml +++ b/alignment/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.6-SNAPSHOT + 1.9.6 alignment jar - 1.9.6-SNAPSHOT + 1.9.6 alignment BioJava alignment module diff --git a/biosql/pom.xml b/biosql/pom.xml index 23c80ae..0c4792f 100644 --- a/biosql/pom.xml +++ b/biosql/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.6-SNAPSHOT + 1.9.6 biosql jar - 1.9.6-SNAPSHOT + 1.9.6 biosql BioJava biosql module diff --git a/blast/pom.xml b/blast/pom.xml index 9994bce..3d9f87e 100644 --- a/blast/pom.xml +++ b/blast/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.6-SNAPSHOT + 1.9.6 blast jar - 1.9.6-SNAPSHOT + 1.9.6 blast BioJava blast module diff --git a/bytecode/pom.xml b/bytecode/pom.xml index 9b6e18c..d555324 100644 --- a/bytecode/pom.xml +++ b/bytecode/pom.xml @@ -4,12 +4,12 @@ biojava-legacy org.biojava - 1.9.6-SNAPSHOT + 1.9.6 org.biojava jar bytecode - 1.9.6-SNAPSHOT + 1.9.6 bytecode BioJava bytecode module diff --git a/core/pom.xml b/core/pom.xml index 79a1efd..498b7f9 100644 --- a/core/pom.xml +++ b/core/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.6-SNAPSHOT + 1.9.6 core jar - 1.9.6-SNAPSHOT + 1.9.6 core BioJava core module diff --git a/gui/pom.xml b/gui/pom.xml index 04ce14c..af14200 100644 --- a/gui/pom.xml +++ b/gui/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.6-SNAPSHOT + 1.9.6 gui jar - 1.9.6-SNAPSHOT + 1.9.6 gui BioJava gui module diff --git a/phylo/pom.xml b/phylo/pom.xml index b3cc949..144e024 100644 --- a/phylo/pom.xml +++ b/phylo/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.6-SNAPSHOT + 1.9.6 phylo jar - 1.9.6-SNAPSHOT + 1.9.6 phylo BioJava phylo module diff --git a/pom.xml b/pom.xml index 7bb1fdf..c73ce6d 100644 --- a/pom.xml +++ b/pom.xml @@ -9,7 +9,7 @@ org.biojava biojava-legacy pom - 1.9.6-SNAPSHOT + 1.9.6 biojava-legacy 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. http://www.biojava.org @@ -28,7 +28,7 @@ scm:git:https://github.com/biojava/biojava-legacy scm:git:https://github.com/biojava/biojava-legacy https://github.com/biojava/biojava-legacy - HEAD + biojava-legacy-1.9.6 diff --git a/sequencing/pom.xml b/sequencing/pom.xml index 721efac..b755e6c 100644 --- a/sequencing/pom.xml +++ b/sequencing/pom.xml @@ -4,11 +4,11 @@ biojava-legacy org.biojava - 1.9.6-SNAPSHOT + 1.9.6 sequencing jar - 1.9.6-SNAPSHOT + 1.9.6 sequencing BioJava sequencing module