From ba744579d7c1833c71c24bd30199079c19b691bd Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Thu, 14 Jan 2021 12:22:53 +0100 Subject: [PATCH 01/19] Depend on KNIME 4.3 and knime-python-wrapper v2.0.4 --- plugin/META-INF/MANIFEST.MF | 10 +++++----- targetplatform/KNIME-AP-4.0.target | 9 +++++---- tests/pom.xml | 31 +++++++++++++++++++++--------- 3 files changed, 32 insertions(+), 18 deletions(-) diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF index de6189a..2e574cf 100644 --- a/plugin/META-INF/MANIFEST.MF +++ b/plugin/META-INF/MANIFEST.MF @@ -7,12 +7,12 @@ Bundle-RequiredExecutionEnvironment: JavaSE-1.8 Bundle-Activator: nl.esciencecenter.e3dchem.sygma.Activator Bundle-Vendor: Netherlands eScience Center Require-Bundle: org.eclipse.core.runtime, - org.knime.workbench.core;bundle-version="[4.0.0,5.0.0)", - org.knime.workbench.repository;bundle-version="[4.0.0,5.0.0)", - org.knime.base;bundle-version="[4.0.0,5.0.0)", + org.knime.workbench.core;bundle-version="[4.3.0,5.0.0)", + org.knime.workbench.repository;bundle-version="[4.3.0,5.0.0)", + org.knime.base;bundle-version="[4.3.0,5.0.0)", org.rdkit.knime.types, - org.knime.chem.types;bundle-version="[4.0.0,5.0.0)", - nl.esciencecenter.e3dchem.python.plugin;bundle-version="[2.0.1,3.0.0)", + org.knime.chem.types;bundle-version="[4.3.0,5.0.0)", + nl.esciencecenter.e3dchem.python.plugin;bundle-version="[2.0.4,3.0.0)", nl.esciencecenter.e3dchem.plugin;bundle-version="[1.0.0,2.0.0)" Bundle-ActivationPolicy: lazy Bundle-ClassPath: . diff --git a/targetplatform/KNIME-AP-4.0.target b/targetplatform/KNIME-AP-4.0.target index 07debd7..d3704a5 100644 --- a/targetplatform/KNIME-AP-4.0.target +++ b/targetplatform/KNIME-AP-4.0.target @@ -2,6 +2,7 @@ + @@ -11,12 +12,12 @@ - + - + @@ -26,7 +27,7 @@ - + @@ -35,7 +36,7 @@ -Dsun.java2d.d3d=false -Dosgi.classloader.lock=classname -XX:+UnlockDiagnosticVMOptions --XX:+UnsyncloadClass +-XX:+UnsyncloadClass -XX:+UseG1GC -ea -Dorg.eclipse.swt.internal.gtk.cairoGraphics=false diff --git a/tests/pom.xml b/tests/pom.xml index 1cb034b..0f53d74 100644 --- a/tests/pom.xml +++ b/tests/pom.xml @@ -1,6 +1,6 @@ - + 4.0.0 @@ -29,7 +29,7 @@ - org.apache.maven.plugins @@ -57,12 +57,9 @@ - - - + + + @@ -110,6 +107,22 @@ ${tycho.testArgLine} ${tycho.test.jvmArgs} + + org.eclipse.tycho + target-platform-configuration + ${tycho.version} + + + + + eclipse-feature + org.knime.features.core + 0.0.0 + + + + + From 68045af815d9bb4be4600c5eaec9d7bd84958e23 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Thu, 14 Jan 2021 13:46:12 +0100 Subject: [PATCH 02/19] Swallow config.loadFromInDialog exception --- .../e3dchem/sygma/PredictMetabolitesDialog.java | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesDialog.java b/plugin/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesDialog.java index 6a7872b..9af691a 100644 --- a/plugin/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesDialog.java +++ b/plugin/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesDialog.java @@ -49,7 +49,11 @@ protected PredictMetabolitesDialog() { public void loadAdditionalSettingsFrom(NodeSettingsRO settings, PortObjectSpec[] specs) throws NotConfigurableException { super.loadAdditionalSettingsFrom(settings, specs); - config.loadFromInDialog(settings); + try { + config.loadFromInDialog(settings); + } catch (InvalidSettingsException e) { + e.printStackTrace(); + } pythonOptions.loadSettingsFrom(config); } @@ -57,7 +61,11 @@ public void loadAdditionalSettingsFrom(NodeSettingsRO settings, PortObjectSpec[] public void loadAdditionalSettingsFrom(NodeSettingsRO settings, DataTableSpec[] specs) throws NotConfigurableException { super.loadAdditionalSettingsFrom(settings, specs); - config.loadFromInDialog(settings); + try { + config.loadFromInDialog(settings); + } catch (InvalidSettingsException e) { + e.printStackTrace(); + } pythonOptions.loadSettingsFrom(config); } From 65ee744eb0514fb9e34dcb90e48e976b3acdab1d Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Thu, 14 Jan 2021 14:04:03 +0100 Subject: [PATCH 03/19] Also require KNIME 4.3 for tests --- targetplatform/KNIME-AP-4.0.target | 2 +- tests/META-INF/MANIFEST.MF | 12 ++++++------ tests/pom.xml | 5 +++++ 3 files changed, 12 insertions(+), 7 deletions(-) diff --git a/targetplatform/KNIME-AP-4.0.target b/targetplatform/KNIME-AP-4.0.target index d3704a5..47f8e7d 100644 --- a/targetplatform/KNIME-AP-4.0.target +++ b/targetplatform/KNIME-AP-4.0.target @@ -12,7 +12,7 @@ - + diff --git a/tests/META-INF/MANIFEST.MF b/tests/META-INF/MANIFEST.MF index fd59ec7..dc784ed 100644 --- a/tests/META-INF/MANIFEST.MF +++ b/tests/META-INF/MANIFEST.MF @@ -5,14 +5,14 @@ Bundle-SymbolicName: nl.esciencecenter.e3dchem.sygma.tests Bundle-Version: 1.2.1.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-1.8 Require-Bundle: org.junit, - org.knime.core;bundle-version="[4.0.0,5.0.0)", - org.knime.base;bundle-version="[4.0.0,5.0.0)", - org.knime.testing;bundle-version="[4.0.0,5.0.0)", + org.knime.core;bundle-version="[4.3.0,5.0.0)", + org.knime.base;bundle-version="[4.3.0,5.0.0)", + org.knime.testing;bundle-version="[4.3.0,5.0.0)", org.rdkit.knime.nodes, - org.knime.chem.base;bundle-version="[4.0.0,5.0.0)", - org.knime.python2.serde.flatbuffers;bundle-version="[4.0.0,5.0.0)", + org.knime.chem.base;bundle-version="[4.3.0,5.0.0)", + org.knime.python2.serde.flatbuffers;bundle-version="[4.3.0,5.0.0)", nl.esciencecenter.e3dchem.knime.testing.plugin;bundle-version="[1.0.0,2.0.0)", - nl.esciencecenter.e3dchem.python.plugin;bundle-version="[2.0.3,3.0.0)", + nl.esciencecenter.e3dchem.python.plugin;bundle-version="[2.0.4,3.0.0)", nl.esciencecenter.e3dchem.sygma.plugin Bundle-Vendor: Netherlands eScience Center Bundle-ClassPath: . diff --git a/tests/pom.xml b/tests/pom.xml index 0f53d74..5eaa7c3 100644 --- a/tests/pom.xml +++ b/tests/pom.xml @@ -119,6 +119,11 @@ org.knime.features.core 0.0.0 + + eclipse-feature + org.knime.features.testing.application + 0.0.0 + From 44eaa0a9a089a6658e43fe96688b66052748d649 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Thu, 14 Jan 2021 14:19:24 +0100 Subject: [PATCH 04/19] Use absolute paths to test workflow --- .../e3dchem/sygma/PredictMetabolitesWorkflowTest.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesWorkflowTest.java b/tests/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesWorkflowTest.java index 6836c1b..09eed50 100644 --- a/tests/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesWorkflowTest.java +++ b/tests/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesWorkflowTest.java @@ -45,13 +45,13 @@ public static void setUpPythonUtils() throws MalformedURLException, IOException, public void test_simple() throws IOException, InvalidSettingsException, CanceledExecutionException, UnsupportedWorkflowVersionException, LockFailedException, InterruptedException { File workflowDir = new File("src/knime/SyGMa-test"); - runner.runTestWorkflow(workflowDir); + runner.runTestWorkflow(workflowDir.getAbsoluteFile()); } @Test public void test_duplicate() throws IOException, InvalidSettingsException, CanceledExecutionException, UnsupportedWorkflowVersionException, LockFailedException, InterruptedException { File workflowDir = new File("src/knime/SyGMa-duplicate-test"); - runner.runTestWorkflow(workflowDir); + runner.runTestWorkflow(workflowDir.getAbsoluteFile()); } } From a100dd2c10225825d6482c352be4634b0f68164f Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Thu, 14 Jan 2021 14:51:50 +0100 Subject: [PATCH 05/19] Use conda forge for CI --- .travis.yml | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/.travis.yml b/.travis.yml index b78a80a..6036f97 100644 --- a/.travis.yml +++ b/.travis.yml @@ -2,21 +2,20 @@ language: java jdk: openjdk8 cache: directories: - - $HOME/.m2 - - $HOME/.cache/pip - - $HOME/conda - - $HOME/.sonar/cache + - $HOME/.m2 + - $HOME/.cache/pip + - $HOME/conda + - $HOME/.sonar/cache before_install: - if [ ! -e $HOME/conda/bin/activate ]; then wget -nc https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh; bash Miniconda3-latest-Linux-x86_64.sh -f -b -p $HOME/conda; fi - source $HOME/conda/bin/activate root - - conda install -y -q -c rdkit rdkit pandas protobuf + - conda install -y -q -c conda-forge rdkit pandas protobuf - pip install sygma install: -- mvn package -B + - mvn package -B script: xvfb-run mvn verify -B after_success: - - mvn sonar:sonar -Dsonar.login=$SONAR_TOKEN - + - mvn sonar:sonar -Dsonar.login=$SONAR_TOKEN From c017ad6cf09bbcf2baf9d951cc84acfbe927f04c Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 12 Feb 2021 10:12:30 +0100 Subject: [PATCH 06/19] Replace Travis with GH Actions --- .github/workflows/build.yml | 44 +++++++++++++++++++++++++++++++++++++ .travis.yml | 21 ------------------ README.md | 22 +++++++++---------- 3 files changed, 54 insertions(+), 33 deletions(-) create mode 100644 .github/workflows/build.yml delete mode 100644 .travis.yml diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml new file mode 100644 index 0000000..ee5b5ba --- /dev/null +++ b/.github/workflows/build.yml @@ -0,0 +1,44 @@ +# This workflow will build a Java project with Maven +# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven + +name: Java CI with Maven + +on: + push: + pull_request: + types: + - "opened" + - "reopened" + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - name: Set up JDK 1.8 + uses: actions/setup-java@v1 + with: + java-version: 1.8 + - name: Setup miniconda + uses: conda-incubator/setup-miniconda@v2 + # - name: Cache deps + # uses: actions/cache@v2 + # with: + # path: | + # ~/.m2 + # ~/.cache/pip + # ~/conda_pkgs_dir + # ~/.sonar/cache + # key: ${{ runner.os }}-${{ hashFiles('.github/workflows/build.yml') }} + - name: OS dependencies + run: sudo apt-get install xvfb + - name: Conda dependencies + run: conda install -y -q -c conda-forge rdkit pandas protobuf + - name: Python dependencies + run: pip install sygma + - name: Build with Maven + run: mvn -B package + - name: Run tests + run: xvfb-run mvn verify -B + - name: SonarCloud analysis + run: mvn sonar:sonar -Dsonar.login=$SONAR_TOKEN diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 6036f97..0000000 --- a/.travis.yml +++ /dev/null @@ -1,21 +0,0 @@ -language: java -jdk: openjdk8 -cache: - directories: - - $HOME/.m2 - - $HOME/.cache/pip - - $HOME/conda - - $HOME/.sonar/cache -before_install: - - if [ ! -e $HOME/conda/bin/activate ]; then - wget -nc https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh; - bash Miniconda3-latest-Linux-x86_64.sh -f -b -p $HOME/conda; - fi - - source $HOME/conda/bin/activate root - - conda install -y -q -c conda-forge rdkit pandas protobuf - - pip install sygma -install: - - mvn package -B -script: xvfb-run mvn verify -B -after_success: - - mvn sonar:sonar -Dsonar.login=$SONAR_TOKEN diff --git a/README.md b/README.md index 026d9dc..37cfb01 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,6 @@ The [SyGMa](https://github.com/3D-e-Chem/sygma) [KNIME](https://www.knime.org) nodes for the **Sy**stematic **G**eneration of potential **M**et**a**bolites. -[![Build Status](https://travis-ci.org/3D-e-Chem/knime-sygma.svg?branch=master)](https://travis-ci.org/3D-e-Chem/knime-sygma) [![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma&metric=alert_status)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma) [![Coverage](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma&metric=coverage)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1168387.svg)](https://doi.org/10.5281/zenodo.1168387) @@ -11,8 +10,8 @@ The [SyGMa](https://github.com/3D-e-Chem/sygma) [KNIME](https://www.knime.org) n Requirements: -* KNIME, https://www.knime.org, version 4.0 or higher -* SyGMa Python library, https://github.com/3D-e-Chem/sygma +- KNIME, https://www.knime.org, version 4.0 or higher +- SyGMa Python library, https://github.com/3D-e-Chem/sygma Steps to get the SyGMa KNIME nodes inside KNIME: @@ -81,12 +80,11 @@ This can be skipped by running maven offline using `mvn -o`. 3. Run tests with `mvn verify` 4. Optionally, test node by installing it in KNIME from a local update site 5. Append new release to an update site - 1. Make clone of an update site repo - 2. Append release to the update site with `mvn install -Dtarget.update.site=` -6. Commit and push changes in this repo and update site repo. -7. Create a GitHub release -8. Update Zenodo entry - 1. Correct authors -9. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release -10. Update CITIATION.cff with new DOI - +6. Make clone of an update site repo +7. Append release to the update site with `mvn install -Dtarget.update.site=` +8. Commit and push changes in this repo and update site repo. +9. Create a GitHub release +10. Update Zenodo entry +11. Correct authors +12. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release +13. Update CITIATION.cff with new DOI From ac41329ef0b8da78c5998a2c48c6acb567e46339 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 12 Feb 2021 10:21:52 +0100 Subject: [PATCH 07/19] Re-order expected columns --- ...workflow-configuration-representation.json | 3 + .../.artifacts/workflow-configuration.json | 3 + .../knime/SyGMa-duplicate-test/.savedWithData | 2 +- .../Molecule Type Cast (#18)/port_1/data.xml | 8 +- .../Molecule Type Cast (#18)/port_1/data.zip | Bin 747 -> 881 bytes .../Molecule Type Cast (#18)/port_1/spec.xml | 28 +- .../Molecule Type Cast (#18)/settings.xml | 14 +- .../Predict metabolites (#15)/settings.xml | 23 +- .../Predict metabolites (#17)/port_1/data.xml | 31 +- .../Predict metabolites (#17)/port_1/data.zip | Bin 2221 -> 720 bytes .../port_1/r0/data.xml | 13 + .../port_1/r0/r0/data.xml | 7 + .../port_1/r0/r0/data.zip | Bin 0 -> 3459 bytes .../port_1/r0/r0/spec.xml | 192 +++++ .../port_1/r0/spec.xml | 192 +++++ .../Predict metabolites (#17)/port_1/spec.xml | 42 +- .../Predict metabolites (#17)/settings.xml | 25 +- .../RDKit From Molecule (#2)/port_1/data.xml | 3 +- .../RDKit From Molecule (#2)/port_1/data.zip | Bin 969 -> 1088 bytes .../RDKit From Molecule (#2)/port_1/spec.xml | 3 + .../RDKit From Molecule (#2)/port_2/data.xml | 3 +- .../RDKit From Molecule (#2)/port_2/data.zip | Bin 599 -> 642 bytes .../RDKit From Molecule (#2)/port_2/spec.xml | 2 + .../RDKit From Molecule (#2)/settings.xml | 8 +- .../Table Creator (#1)/port_1/data.xml | 3 +- .../Table Creator (#1)/port_1/data.zip | Bin 775 -> 834 bytes .../Table Creator (#1)/port_1/spec.xml | 2 + .../Table Creator (#1)/settings.xml | 8 +- .../settings.xml | 70 +- .../knime/SyGMa-duplicate-test/workflow.knime | 35 +- .../knime/SyGMa-duplicate-test/workflow.svg | 370 ++++---- ...workflow-configuration-representation.json | 3 + .../.artifacts/workflow-configuration.json | 3 + tests/src/knime/SyGMa-test/.savedWithData | 2 +- .../Column Resorter (#13)/port_1/data.xml | 30 + .../Column Resorter (#13)/port_1/spec.xml | 246 ++++++ .../Column Resorter (#13)/settings.xml | 49 ++ .../Molecule Type Cast (#12)/port_1/data.xml | 8 +- .../Molecule Type Cast (#12)/port_1/data.zip | Bin 795 -> 874 bytes .../Molecule Type Cast (#12)/port_1/spec.xml | 28 +- .../Molecule Type Cast (#12)/settings.xml | 14 +- .../internal/execErrout | 1 + .../internal/execOutput | 1 + .../Predict metabolites (#1)/port_1/data.xml | 33 + .../Predict metabolites (#1)/port_1/data.zip | Bin 0 -> 896 bytes .../port_1/r0/data.xml | 13 + .../port_1/r0/r0/data.xml | 7 + .../port_1/r0/r0/data.zip | Bin 0 -> 17989 bytes .../port_1/r0/r0/spec.xml | 246 ++++++ .../port_1/r0/spec.xml | 246 ++++++ .../Predict metabolites (#1)/port_1/spec.xml | 230 +++++ .../Predict metabolites (#1)/settings.xml | 40 +- .../RDKit From Molecule (#3)/port_1/data.xml | 3 +- .../RDKit From Molecule (#3)/port_1/data.zip | Bin 1258 -> 1480 bytes .../RDKit From Molecule (#3)/port_1/spec.xml | 3 + .../RDKit From Molecule (#3)/port_2/data.xml | 3 +- .../RDKit From Molecule (#3)/port_2/data.zip | Bin 597 -> 640 bytes .../RDKit From Molecule (#3)/port_2/spec.xml | 2 + .../RDKit From Molecule (#3)/settings.xml | 8 +- .../SyGMa-test/Row Filter (#5)/settings.xml | 20 +- .../Table Creator (#2)/port_1/data.xml | 3 +- .../Table Creator (#2)/port_1/data.zip | Bin 831 -> 914 bytes .../Table Creator (#2)/port_1/spec.xml | 2 + .../Table Creator (#2)/settings.xml | 8 +- .../settings.xml | 72 +- .../Table Reader (#11)/port_1/data.xml | 3 +- .../Table Reader (#11)/port_1/data.zip | Bin 2119 -> 2587 bytes .../Table Reader (#11)/port_1/spec.xml | 6 + .../Table Reader (#11)/settings.xml | 13 +- .../Testflow Configuration (#7)/settings.xml | 7 +- tests/src/knime/SyGMa-test/workflow.knime | 71 +- tests/src/knime/SyGMa-test/workflow.svg | 805 ++++++++++-------- 72 files changed, 2574 insertions(+), 745 deletions(-) create mode 100644 tests/src/knime/SyGMa-duplicate-test/.artifacts/workflow-configuration-representation.json create mode 100644 tests/src/knime/SyGMa-duplicate-test/.artifacts/workflow-configuration.json create mode 100644 tests/src/knime/SyGMa-duplicate-test/Predict metabolites (#17)/port_1/r0/data.xml create mode 100644 tests/src/knime/SyGMa-duplicate-test/Predict metabolites (#17)/port_1/r0/r0/data.xml create mode 100644 tests/src/knime/SyGMa-duplicate-test/Predict metabolites (#17)/port_1/r0/r0/data.zip create mode 100644 tests/src/knime/SyGMa-duplicate-test/Predict metabolites (#17)/port_1/r0/r0/spec.xml create mode 100644 tests/src/knime/SyGMa-duplicate-test/Predict metabolites (#17)/port_1/r0/spec.xml create mode 100644 tests/src/knime/SyGMa-test/.artifacts/workflow-configuration-representation.json create mode 100644 tests/src/knime/SyGMa-test/.artifacts/workflow-configuration.json create mode 100644 tests/src/knime/SyGMa-test/Column Resorter (#13)/port_1/data.xml create mode 100644 tests/src/knime/SyGMa-test/Column Resorter (#13)/port_1/spec.xml create mode 100644 tests/src/knime/SyGMa-test/Column Resorter (#13)/settings.xml create mode 100644 tests/src/knime/SyGMa-test/Predict metabolites (#1)/internal/execErrout create mode 100644 tests/src/knime/SyGMa-test/Predict metabolites (#1)/internal/execOutput create mode 100644 tests/src/knime/SyGMa-test/Predict metabolites (#1)/port_1/data.xml create mode 100644 tests/src/knime/SyGMa-test/Predict metabolites (#1)/port_1/data.zip create mode 100644 tests/src/knime/SyGMa-test/Predict metabolites (#1)/port_1/r0/data.xml create mode 100644 tests/src/knime/SyGMa-test/Predict metabolites (#1)/port_1/r0/r0/data.xml create mode 100644 tests/src/knime/SyGMa-test/Predict metabolites (#1)/port_1/r0/r0/data.zip create mode 100644 tests/src/knime/SyGMa-test/Predict metabolites (#1)/port_1/r0/r0/spec.xml create mode 100644 tests/src/knime/SyGMa-test/Predict metabolites (#1)/port_1/r0/spec.xml create mode 100644 tests/src/knime/SyGMa-test/Predict metabolites (#1)/port_1/spec.xml diff --git a/tests/src/knime/SyGMa-duplicate-test/.artifacts/workflow-configuration-representation.json b/tests/src/knime/SyGMa-duplicate-test/.artifacts/workflow-configuration-representation.json new file mode 100644 index 0000000..9d0b266 --- /dev/null +++ b/tests/src/knime/SyGMa-duplicate-test/.artifacts/workflow-configuration-representation.json @@ -0,0 +1,3 @@ + +{ +} \ No newline at end of file diff --git a/tests/src/knime/SyGMa-duplicate-test/.artifacts/workflow-configuration.json b/tests/src/knime/SyGMa-duplicate-test/.artifacts/workflow-configuration.json new file mode 100644 index 0000000..9d0b266 --- /dev/null +++ b/tests/src/knime/SyGMa-duplicate-test/.artifacts/workflow-configuration.json @@ -0,0 +1,3 @@ + +{ +} \ No newline at end of file diff --git a/tests/src/knime/SyGMa-duplicate-test/.savedWithData b/tests/src/knime/SyGMa-duplicate-test/.savedWithData index 6cc26af..73514fb 100644 --- a/tests/src/knime/SyGMa-duplicate-test/.savedWithData +++ b/tests/src/knime/SyGMa-duplicate-test/.savedWithData @@ -1,4 +1,4 @@ Do not delete this file! This file serves to indicate that the workflow was written as part of the usual save routine (not exported). -Workflow was last saved by user vagrant on Fri Feb 10 12:08:55 UTC 2017 \ No newline at end of file +Workflow was last saved by user verhoes on Fri Feb 12 10:21:23 CET 2021 \ No newline at end of file diff --git a/tests/src/knime/SyGMa-duplicate-test/Molecule Type Cast (#18)/port_1/data.xml b/tests/src/knime/SyGMa-duplicate-test/Molecule Type Cast (#18)/port_1/data.xml index 224e5fd..99f723f 100644 --- a/tests/src/knime/SyGMa-duplicate-test/Molecule Type Cast (#18)/port_1/data.xml +++ b/tests/src/knime/SyGMa-duplicate-test/Molecule Type Cast (#18)/port_1/data.xml @@ -1,12 +1,13 @@ - - + + + - + @@ -25,6 +26,7 @@ + diff --git a/tests/src/knime/SyGMa-duplicate-test/Molecule Type Cast (#18)/port_1/data.zip b/tests/src/knime/SyGMa-duplicate-test/Molecule Type Cast (#18)/port_1/data.zip index 0f6a862dbbff751f0bd7eef3e4f51744da916a1c..8233eacd37617931d51273d023776cf65f5dcc13 100644 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a/tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/port_1/spec.xml b/tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/port_1/spec.xml index 64c1f10..418ba13 100644 --- a/tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/port_1/spec.xml +++ b/tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/port_1/spec.xml @@ -28,6 +28,7 @@ + @@ -39,6 +40,7 @@ + @@ -60,5 +62,6 @@ + diff --git a/tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/port_2/data.xml b/tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/port_2/data.xml index 9708e20..7fc4d77 100644 --- a/tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/port_2/data.xml +++ b/tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/port_2/data.xml @@ -1,6 +1,7 @@ - + + diff --git a/tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/port_2/data.zip b/tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/port_2/data.zip index 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b/tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/settings.xml index 6fc3707..b04e9ca 100644 --- a/tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/settings.xml +++ b/tests/src/knime/SyGMa-duplicate-test/RDKit From Molecule (#2)/settings.xml @@ -75,10 +75,10 @@ - + - - + + @@ -120,6 +120,6 @@ - + diff --git a/tests/src/knime/SyGMa-duplicate-test/Table Creator (#1)/port_1/data.xml b/tests/src/knime/SyGMa-duplicate-test/Table Creator (#1)/port_1/data.xml index 6dd0a47..be938af 100644 --- a/tests/src/knime/SyGMa-duplicate-test/Table Creator (#1)/port_1/data.xml +++ b/tests/src/knime/SyGMa-duplicate-test/Table Creator (#1)/port_1/data.xml @@ -1,6 +1,7 @@ - + + diff --git a/tests/src/knime/SyGMa-duplicate-test/Table Creator (#1)/port_1/data.zip b/tests/src/knime/SyGMa-duplicate-test/Table Creator (#1)/port_1/data.zip index 97831e4ad7ade563126cd013287b5c7003548fdb..b12578a2dc37721a1ca5999347696c46cb7dc995 100644 GIT binary patch literal 834 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Difference Checker (#16)/settings.xml b/tests/src/knime/SyGMa-duplicate-test/Table Difference Checker (#16)/settings.xml index 9534a57..04afc29 100644 --- a/tests/src/knime/SyGMa-duplicate-test/Table Difference Checker (#16)/settings.xml +++ b/tests/src/knime/SyGMa-duplicate-test/Table Difference Checker (#16)/settings.xml @@ -14,11 +14,21 @@ + + + + + + + + + + @@ -29,11 +39,21 @@ + + + + + + + + + + @@ -44,11 +64,21 @@ + + + + + + + + + + @@ -59,11 +89,21 @@ + + + + + + + + + + @@ -74,11 +114,21 @@ + + + + + + + + + + @@ -89,11 +139,21 @@ + + + + + + + + + + @@ -104,12 +164,12 @@ - - + + - - - + + + diff --git a/tests/src/knime/SyGMa-duplicate-test/workflow.knime b/tests/src/knime/SyGMa-duplicate-test/workflow.knime index 674531d..1d8779c 100644 --- a/tests/src/knime/SyGMa-duplicate-test/workflow.knime +++ b/tests/src/knime/SyGMa-duplicate-test/workflow.knime @@ -1,13 +1,14 @@ - - + + + - - - + + + @@ -24,8 +25,8 @@ - - + + @@ -40,8 +41,8 @@ - - + + @@ -56,8 +57,8 @@ - - + + @@ -72,8 +73,8 @@ - - + + @@ -88,8 +89,8 @@ - - + + @@ -104,8 +105,8 @@ - - + + diff --git a/tests/src/knime/SyGMa-duplicate-test/workflow.svg b/tests/src/knime/SyGMa-duplicate-test/workflow.svg index bd6b581..1ee06d6 100644 --- a/tests/src/knime/SyGMa-duplicate-test/workflow.svg +++ b/tests/src/knime/SyGMa-duplicate-test/workflow.svg @@ -1,13 +1,13 @@ @@ -15,106 +15,106 @@ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + Drug moleculesConvert toRDKit molPhase 1Node 16Phase 1Node 18Convert toRDKit molPhase 1Node 16Phase 1Node 18Table Creator z0AcYMQmyAQi/v//D8b42LgAEwOFgHHUC8PBC+SA/8iWkuUFKXFpspz1nyaBSFYY AL3wn2ouAAACsD91D5+uFwAAAABJRU5ErkJggg==" xlink:actuate="onLoad"/> - RDKit From Molecule - SyGMa Metabolites + xlink:href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQCAYAAAAf8/9hAAAAPklEQVR42mNgGAWM +eOT+k6geReN/EgwlTxEMMNEqDP4T629GEr3DSIlr/5MaPkQFMBOtYuE/sQYzUjsV +kgwAZzAOAUyLhbIAAAAASUVORK5CYII=" xlink:actuate="onLoad"/> - Table DifferenceTable DifferenceChecker + points=" 626 120 635 124 626 129" stroke="none"/> - + SyGMa Metabolites + xlink:href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQCAYAAAAf8/9hAAAAPklEQVR42mNgGAWM +eOT+k6geReN/EgwlTxEMMNEqDP4T629GEr3DSIlr/5MaPkQFMBOtYuE/sQYzUjsV +kgwAZzAOAUyLhbIAAAAASUVORK5CYII=" xlink:actuate="onLoad"/> + points=" 346 210 355 214 346 219" stroke="none"/> - + Molecule Type Cast + points=" 486 210 495 214 486 219" stroke="none"/> - + Drug moleculesDrug moleculesConvert toConvert toRDKit molRDKit molPhase 1Phase 1Node 16Node 16Phase 1Phase 1Node 18Node 18Table Creator - RDKit From Molecule - SyGMa Metabolites + xlink:href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQCAYAAAAf8/9hAAAAPklEQVR42mNgGAWM +eOT+k6geReN/EgwlTxEMMNEqDP4T629GEr3DSIlr/5MaPkQFMBOtYuE/sQYzUjsV +kgwAZzAOAUyLhbIAAAAASUVORK5CYII=" xlink:actuate="onLoad"/> - Table DifferenceTable DifferenceChecker + points=" 626 120 635 124 626 129" stroke="none"/> - + SyGMa Metabolites + xlink:href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQCAYAAAAf8/9hAAAAPklEQVR42mNgGAWM +eOT+k6geReN/EgwlTxEMMNEqDP4T629GEr3DSIlr/5MaPkQFMBOtYuE/sQYzUjsV +kgwAZzAOAUyLhbIAAAAASUVORK5CYII=" xlink:actuate="onLoad"/> + points=" 346 210 355 214 346 219" stroke="none"/> - + Molecule Type Cast + points=" 486 210 495 214 486 219" stroke="none"/> + points=" 527 210 536 214 527 219" stroke="none"/> - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/tests/src/knime/SyGMa-test/.artifacts/workflow-configuration-representation.json b/tests/src/knime/SyGMa-test/.artifacts/workflow-configuration-representation.json new file mode 100644 index 0000000..9d0b266 --- /dev/null +++ b/tests/src/knime/SyGMa-test/.artifacts/workflow-configuration-representation.json @@ -0,0 +1,3 @@ + +{ +} \ No newline at end of file diff --git a/tests/src/knime/SyGMa-test/.artifacts/workflow-configuration.json b/tests/src/knime/SyGMa-test/.artifacts/workflow-configuration.json new file mode 100644 index 0000000..9d0b266 --- /dev/null +++ b/tests/src/knime/SyGMa-test/.artifacts/workflow-configuration.json @@ -0,0 +1,3 @@ + +{ +} \ No newline at end of file diff --git a/tests/src/knime/SyGMa-test/.savedWithData b/tests/src/knime/SyGMa-test/.savedWithData index b623993..e93d07a 100644 --- a/tests/src/knime/SyGMa-test/.savedWithData +++ b/tests/src/knime/SyGMa-test/.savedWithData @@ -1,4 +1,4 @@ Do not delete this file! This file serves to indicate that the workflow was written as part of the usual save routine (not exported). -Workflow was last saved by user vagrant on Fri Feb 10 10:18:31 UTC 2017 \ No newline at end of file +Workflow was last saved by user verhoes on Fri Feb 12 10:20:27 CET 2021 \ No newline at end of file diff --git a/tests/src/knime/SyGMa-test/Column Resorter (#13)/port_1/data.xml b/tests/src/knime/SyGMa-test/Column Resorter (#13)/port_1/data.xml new file mode 100644 index 0000000..28c4043 --- /dev/null +++ b/tests/src/knime/SyGMa-test/Column Resorter (#13)/port_1/data.xml @@ -0,0 +1,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/src/knime/SyGMa-test/Column Resorter (#13)/port_1/spec.xml b/tests/src/knime/SyGMa-test/Column Resorter (#13)/port_1/spec.xml new file mode 100644 index 0000000..58259f4 --- /dev/null +++ b/tests/src/knime/SyGMa-test/Column Resorter (#13)/port_1/spec.xml @@ -0,0 +1,246 @@ + + + + + + + + + + + + + + + + + + + + + + + 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b/tests/src/knime/SyGMa-test/Table Reader (#11)/settings.xml index 9928fad..ee2b0c8 100644 --- a/tests/src/knime/SyGMa-test/Table Reader (#11)/settings.xml +++ b/tests/src/knime/SyGMa-test/Table Reader (#11)/settings.xml @@ -21,14 +21,19 @@ + + + + + - + - - + + @@ -63,6 +68,6 @@ - + diff --git a/tests/src/knime/SyGMa-test/Testflow Configuration (#7)/settings.xml b/tests/src/knime/SyGMa-test/Testflow Configuration (#7)/settings.xml index a41a2ab..215caf0 100644 --- a/tests/src/knime/SyGMa-test/Testflow Configuration (#7)/settings.xml +++ b/tests/src/knime/SyGMa-test/Testflow Configuration (#7)/settings.xml @@ -16,6 +16,9 @@ + + + @@ -31,6 +34,8 @@ + + @@ -51,6 +56,6 @@ - + diff --git a/tests/src/knime/SyGMa-test/workflow.knime b/tests/src/knime/SyGMa-test/workflow.knime index 82eb2a9..36f621d 100644 --- a/tests/src/knime/SyGMa-test/workflow.knime +++ b/tests/src/knime/SyGMa-test/workflow.knime @@ -1,16 +1,17 @@ - - + + + - - - + + + - + @@ -24,8 +25,8 @@ - - + + @@ -40,8 +41,8 @@ - - + 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+0100 Subject: [PATCH 08/19] Debug sygma install failure --- .github/workflows/build.yml | 4 +++- README.md | 1 + 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index ee5b5ba..7b4f24c 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -33,7 +33,9 @@ jobs: - name: OS dependencies run: sudo apt-get install xvfb - name: Conda dependencies - run: conda install -y -q -c conda-forge rdkit pandas protobuf + run: conda install -y -q -c conda-forge pip wheel rdkit pandas protobuf + - run: pip list + - run: echo 'from rdkit.Chem.inchi import INCHI_AVAILABLE;print(INCHI_AVAILABLE)' | python - - name: Python dependencies run: pip install sygma - name: Build with Maven diff --git a/README.md b/README.md index 37cfb01..63e1ee3 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,7 @@ The [SyGMa](https://github.com/3D-e-Chem/sygma) [KNIME](https://www.knime.org) nodes for the **Sy**stematic **G**eneration of potential **M**et**a**bolites. +![Java CI with Maven](https://github.com/3D-e-Chem/knime-sygma/workflows/Java%20CI%20with%20Maven/badge.svg) [![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma&metric=alert_status)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma) [![Coverage](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma&metric=coverage)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1168387.svg)](https://doi.org/10.5281/zenodo.1168387) From 85525e4efb787e14b3e89a633016db575be222fa Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 12 Feb 2021 10:39:29 +0100 Subject: [PATCH 09/19] Activate conda env --- .github/workflows/build.yml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 7b4f24c..5023910 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -21,21 +21,21 @@ jobs: java-version: 1.8 - name: Setup miniconda uses: conda-incubator/setup-miniconda@v2 - # - name: Cache deps - # uses: actions/cache@v2 - # with: - # path: | - # ~/.m2 - # ~/.cache/pip - # ~/conda_pkgs_dir - # ~/.sonar/cache - # key: ${{ runner.os }}-${{ hashFiles('.github/workflows/build.yml') }} + with: + auto-update-conda: true + auto-activate-base: true + activate-environment: "" + - name: Cache deps + uses: actions/cache@v2 + with: + path: | + ~/.m2 + ~/conda_pkgs_dir + key: ${{ runner.os }}-${{ hashFiles('.github/workflows/build.yml') }} - name: OS dependencies run: sudo apt-get install xvfb - name: Conda dependencies run: conda install -y -q -c conda-forge pip wheel rdkit pandas protobuf - - run: pip list - - run: echo 'from rdkit.Chem.inchi import INCHI_AVAILABLE;print(INCHI_AVAILABLE)' | python - - name: Python dependencies run: pip install sygma - name: Build with Maven From e5865448761e8b35c5d12fcd806cd15111ae1e7e Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 12 Feb 2021 10:49:18 +0100 Subject: [PATCH 10/19] Use default test conda env --- .github/workflows/build.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 5023910..9cd81ab 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -23,8 +23,7 @@ jobs: uses: conda-incubator/setup-miniconda@v2 with: auto-update-conda: true - auto-activate-base: true - activate-environment: "" + python-version: 3.8 - name: Cache deps uses: actions/cache@v2 with: @@ -36,6 +35,9 @@ jobs: run: sudo apt-get install xvfb - name: Conda dependencies run: conda install -y -q -c conda-forge pip wheel rdkit pandas protobuf + - run: which conda + - run: which python + - run: which pip - name: Python dependencies run: pip install sygma - name: Build with Maven From 503960d068e0169b74949a033dd2f361f2eeee7d Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 12 Feb 2021 10:54:05 +0100 Subject: [PATCH 11/19] Conda env troubles --- .github/workflows/build.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 9cd81ab..4429af4 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -23,6 +23,7 @@ jobs: uses: conda-incubator/setup-miniconda@v2 with: auto-update-conda: true + activate-environment: test python-version: 3.8 - name: Cache deps uses: actions/cache@v2 @@ -36,6 +37,7 @@ jobs: - name: Conda dependencies run: conda install -y -q -c conda-forge pip wheel rdkit pandas protobuf - run: which conda + - run: conda list - run: which python - run: which pip - name: Python dependencies From c2221d1fc1b6b2d3243837522f6c17ca78e4d6a9 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 12 Feb 2021 11:00:56 +0100 Subject: [PATCH 12/19] Force bash login shell --- .github/workflows/build.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 4429af4..f86f32f 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -13,6 +13,9 @@ on: jobs: build: runs-on: ubuntu-latest + defaults: + run: + shell: bash -l {0} steps: - uses: actions/checkout@v2 - name: Set up JDK 1.8 @@ -37,7 +40,7 @@ jobs: - name: Conda dependencies run: conda install -y -q -c conda-forge pip wheel rdkit pandas protobuf - run: which conda - - run: conda list + - run: conda env list - run: which python - run: which pip - name: Python dependencies From ca0910139132dd2f4d007a744f8ccf9c69f8b986 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 12 Feb 2021 11:14:20 +0100 Subject: [PATCH 13/19] More CI fixes --- .github/workflows/build.yml | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index f86f32f..1592006 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -28,21 +28,24 @@ jobs: auto-update-conda: true activate-environment: test python-version: 3.8 - - name: Cache deps + - name: Cache Maven packages + uses: actions/cache@v2 + with: + path: ~/.m2 + key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml', '**/MANIFEST.MF', 'targetplatform/*.target') }} + restore-keys: ${{ runner.os }}-m2 + - name: Cache conda deps uses: actions/cache@v2 with: path: | - ~/.m2 ~/conda_pkgs_dir + ~/.cache/pip key: ${{ runner.os }}-${{ hashFiles('.github/workflows/build.yml') }} + restore-keys: ${{ runner.os }}-pip - name: OS dependencies run: sudo apt-get install xvfb - name: Conda dependencies run: conda install -y -q -c conda-forge pip wheel rdkit pandas protobuf - - run: which conda - - run: conda env list - - run: which python - - run: which pip - name: Python dependencies run: pip install sygma - name: Build with Maven @@ -50,4 +53,7 @@ jobs: - name: Run tests run: xvfb-run mvn verify -B - name: SonarCloud analysis - run: mvn sonar:sonar -Dsonar.login=$SONAR_TOKEN + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} + run: mvn sonar:sonar From de576574b7bb5d09580a64f5535774a46eb225f7 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 12 Feb 2021 11:51:52 +0100 Subject: [PATCH 14/19] Addd link to build badge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 63e1ee3..31ffe44 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ The [SyGMa](https://github.com/3D-e-Chem/sygma) [KNIME](https://www.knime.org) nodes for the **Sy**stematic **G**eneration of potential **M**et**a**bolites. -![Java CI with Maven](https://github.com/3D-e-Chem/knime-sygma/workflows/Java%20CI%20with%20Maven/badge.svg) +[![Java CI with Maven](https://github.com/3D-e-Chem/knime-sygma/workflows/Java%20CI%20with%20Maven/badge.svg)](https://github.com/3D-e-Chem/knime-sygma/actions?query=workflow%3A%22Java+CI+with+Maven%22) [![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma&metric=alert_status)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma) [![Coverage](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma&metric=coverage)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.sygma%3Anl.esciencecenter.e3dchem.sygma) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1168387.svg)](https://doi.org/10.5281/zenodo.1168387) From 11ea91a39d0ba07875a3a2a2d80b5d14280f7f62 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 12 Feb 2021 12:01:59 +0100 Subject: [PATCH 15/19] Use jdk11 for SC --- .github/workflows/build.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 1592006..2c10e00 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -52,6 +52,10 @@ jobs: run: mvn -B package - name: Run tests run: xvfb-run mvn verify -B + - name: Set up JDK 11 for SonarCloud analysis + uses: actions/setup-java@v1 + with: + java-version: 11 - name: SonarCloud analysis env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} From ad695699791e387f7aab433290322fadfe1720c2 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 12 Feb 2021 12:12:54 +0100 Subject: [PATCH 16/19] make SC happy --- .../e3dchem/sygma/PredictMetabolitesDialog.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesDialog.java b/plugin/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesDialog.java index 9af691a..8ce1c04 100644 --- a/plugin/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesDialog.java +++ b/plugin/src/java/nl/esciencecenter/e3dchem/sygma/PredictMetabolitesDialog.java @@ -52,7 +52,7 @@ public void loadAdditionalSettingsFrom(NodeSettingsRO settings, PortObjectSpec[] try { config.loadFromInDialog(settings); } catch (InvalidSettingsException e) { - e.printStackTrace(); + // swallow error } pythonOptions.loadSettingsFrom(config); } @@ -64,7 +64,7 @@ public void loadAdditionalSettingsFrom(NodeSettingsRO settings, DataTableSpec[] try { config.loadFromInDialog(settings); } catch (InvalidSettingsException e) { - e.printStackTrace(); + // swallow error } pythonOptions.loadSettingsFrom(config); } From 1fc9a1c3c318b8b96e7aad7ec12a3e67cc924bf3 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 12 Feb 2021 12:47:05 +0100 Subject: [PATCH 17/19] Updated CHANGELOG --- CHANGELOG.md | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 619f667..25bcdaa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,10 +1,21 @@ # Change Log + All notable changes to this project will be documented in this file. This project adheres to [Semantic Versioning](http://semver.org/). The file is formatted as described on http://keepachangelog.com/. ## [Unreleased] +## [2.0.0] - 2021-02-12 + +### Fixed + +- Support KNIME 4.3 ([#16](https://github.com/3D-e-Chem/knime-sygma/issues/16) [5](https://github.com/3D-e-Chem/knime-python-wrapper/issues/5)) + +### Removed + +- Support for KNIME versions older than 4.3 + ## [1.2.1] - 2019-06-27 ### Changes @@ -91,3 +102,17 @@ Switched to GPLv3 license due to license of [Python wrapper](https://github.com/ Initial release. Skeleton generated by https://github.com/3D-e-Chem/knime-python-node-archetype + +[unreleased]: https://github.com/3D-e-Chem/knime-sygma/compare/v2.0.0...HEAD +[2.0.0]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.2.1...v2.2.0 +[1.2.1]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.2.0...v1.2.1 +[1.2.0]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.1.5...v1.2.0 +[1.1.5]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.1.4...v1.1.5 +[1.1.4]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.1.3...v1.1.4 +[1.1.3]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.1.2...v1.1.3 +[1.1.2]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.1.1...v1.1.2 +[1.1.1]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.1.0...v1.1.1 +[1.1.0]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.0.2...v1.1.0 +[1.0.2]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.0.1...v1.0.2 +[1.0.1]: https://github.com/3D-e-Chem/knime-sygma/compare/v1.0.0...v1.0.1 +[1.0.0]: https://github.com/3D-e-Chem/knime-sygma/releases/tag/v1.0.0 From 7cd43fd6d6cc9b83d24c2bc2a8b04c295f7251bd Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 12 Feb 2021 12:48:21 +0100 Subject: [PATCH 18/19] Bump to v2.0.0 --- feature/feature.xml | 2 +- feature/pom.xml | 2 +- p2/category.xml | 2 +- p2/pom.xml | 2 +- plugin/META-INF/MANIFEST.MF | 2 +- plugin/pom.xml | 2 +- pom.xml | 2 +- targetplatform/pom.xml | 2 +- tests/META-INF/MANIFEST.MF | 2 +- tests/pom.xml | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/feature/feature.xml b/feature/feature.xml index ca92ef6..df127bb 100644 --- a/feature/feature.xml +++ b/feature/feature.xml @@ -2,7 +2,7 @@ diff --git a/feature/pom.xml b/feature/pom.xml index eb6a13e..7aa566d 100644 --- a/feature/pom.xml +++ b/feature/pom.xml @@ -5,7 +5,7 @@ nl.esciencecenter.e3dchem.sygma nl.esciencecenter.e3dchem.sygma - 1.2.1-SNAPSHOT + 2.0.0-SNAPSHOT nl.esciencecenter.e3dchem.sygma.feature diff --git a/p2/category.xml b/p2/category.xml index 003b3c8..d116264 100644 --- a/p2/category.xml +++ b/p2/category.xml @@ -1,6 +1,6 @@ - + diff --git a/p2/pom.xml b/p2/pom.xml index a4fdc2f..51e2707 100644 --- a/p2/pom.xml +++ b/p2/pom.xml @@ -4,7 +4,7 @@ nl.esciencecenter.e3dchem.sygma nl.esciencecenter.e3dchem.sygma - 1.2.1-SNAPSHOT + 2.0.0-SNAPSHOT nl.esciencecenter.e3dchem.sygma.p2 eclipse-repository diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF index 2e574cf..f928c9e 100644 --- a/plugin/META-INF/MANIFEST.MF +++ b/plugin/META-INF/MANIFEST.MF @@ -2,7 +2,7 @@ Manifest-Version: 1.0 Bundle-ManifestVersion: 2 Bundle-Name: Sygma KNIME nodes Bundle-SymbolicName: nl.esciencecenter.e3dchem.sygma.plugin;singleton:=true -Bundle-Version: 1.2.1.qualifier +Bundle-Version: 2.0.0.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-1.8 Bundle-Activator: nl.esciencecenter.e3dchem.sygma.Activator Bundle-Vendor: Netherlands eScience Center diff --git a/plugin/pom.xml b/plugin/pom.xml index 7282aa3..d87bf72 100644 --- a/plugin/pom.xml +++ b/plugin/pom.xml @@ -5,7 +5,7 @@ nl.esciencecenter.e3dchem.sygma nl.esciencecenter.e3dchem.sygma - 1.2.1-SNAPSHOT + 2.0.0-SNAPSHOT nl.esciencecenter.e3dchem.sygma.plugin eclipse-plugin diff --git a/pom.xml b/pom.xml index aad22a4..52e0625 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ 4.0.0 nl.esciencecenter.e3dchem.sygma nl.esciencecenter.e3dchem.sygma - 1.2.1-SNAPSHOT + 2.0.0-SNAPSHOT pom diff --git a/targetplatform/pom.xml b/targetplatform/pom.xml index eed83dd..7dc2c4e 100644 --- a/targetplatform/pom.xml +++ b/targetplatform/pom.xml @@ -20,7 +20,7 @@ Contributors: nl.esciencecenter.e3dchem.sygma nl.esciencecenter.e3dchem.sygma - 1.2.1-SNAPSHOT + 2.0.0-SNAPSHOT diff --git a/tests/META-INF/MANIFEST.MF b/tests/META-INF/MANIFEST.MF index dc784ed..59de031 100644 --- a/tests/META-INF/MANIFEST.MF +++ b/tests/META-INF/MANIFEST.MF @@ -2,7 +2,7 @@ Manifest-Version: 1.0 Bundle-ManifestVersion: 2 Bundle-Name: Tests Bundle-SymbolicName: nl.esciencecenter.e3dchem.sygma.tests -Bundle-Version: 1.2.1.qualifier +Bundle-Version: 2.0.0.qualifier Bundle-RequiredExecutionEnvironment: JavaSE-1.8 Require-Bundle: org.junit, org.knime.core;bundle-version="[4.3.0,5.0.0)", diff --git a/tests/pom.xml b/tests/pom.xml index 5eaa7c3..6fe4210 100644 --- a/tests/pom.xml +++ b/tests/pom.xml @@ -6,7 +6,7 @@ nl.esciencecenter.e3dchem.sygma nl.esciencecenter.e3dchem.sygma - 1.2.1-SNAPSHOT + 2.0.0-SNAPSHOT nl.esciencecenter.e3dchem.sygma.tests From ca5ff307b3519a8d4898fd42de0c55bd96e03cc6 Mon Sep 17 00:00:00 2001 From: Stefan Verhoeven Date: Fri, 12 Feb 2021 12:52:38 +0100 Subject: [PATCH 19/19] Make conda cache unique --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 2c10e00..cab5891 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -40,7 +40,7 @@ jobs: path: | ~/conda_pkgs_dir ~/.cache/pip - key: ${{ runner.os }}-${{ hashFiles('.github/workflows/build.yml') }} + key: ${{ runner.os }}-pip-${{ hashFiles('.github/workflows/build.yml') }} restore-keys: ${{ runner.os }}-pip - name: OS dependencies run: sudo apt-get install xvfb