Merge pull request #9 from 3D-e-Chem/knime4

Knime4

.travis.yml

@@ -1,12 +1,11 @@
 # To trigger a Travis-CI build for every GitHub push or Pull Request:
 # 1. Goto https://travis-ci.org/profile/3D-e-Chem
 # 2. Flip the switch for the `knime-silicos-it` repo
-sudo: false
 language: java
 matrix:
  include:
  - os: linux
-   jdk: oraclejdk8
+   jdk: openjdk8
    addons:
     apt:
       packages:

.zenodo.json

@@ -0,0 +1,4 @@
+{
+  "title": "KNIME Silicos-it nodes",
+  "license": "Apache-2.0"
+}

CHANGELOG.md

@@ -5,6 +5,12 @@ The file is formatted as described on http://keepachangelog.com/.
 
 ## [Unreleased]
 
+## [1.1.3] - 2019-06-27
+
+### Changes
+
+- Requires KNIME 4.0 [#8](https://github.com/3D-e-Chem/knime-silicos-it/issues/8)
+
 ## [1.1.2] - 2017-11-08
 
 ### Fixed

CITATION.cff

@@ -0,0 +1,15 @@
+# YAML 1.2
+# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
+cff-version: 1.0.3
+message: If you use this software, please cite it as below.
+title: KNIME nodes and example workflows for software made by Silicos-it, ie. align-it, shape-it
+doi: 10.5281/zenodo.1043818
+authors:
+- given-names: Stefan
+  family-names: Verhoeven
+  affiliation: Netherlands eScience Center
+  orcid: https://orcid.org/0000-0002-5821-2060
+version: 1.1.2
+date-released: 2017-11-08
+repository-code: https://github.com/3D-e-Chem/knime-silicos-it
+license: Apache-2.0

README.md

@@ -3,8 +3,8 @@
 KNIME nodes and example workflows for software made by [Silicos-it](http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/index.html) like shape-it to align molecules based on shape and align-it to align molecules based on their pharmacophore.
 
 [![Build Status Linux & OSX](https://travis-ci.org/3D-e-Chem/knime-silicos-it.svg?branch=master)](https://travis-ci.org/3D-e-Chem/knime-silicos-it)
-[![SonarQube Gate](https://sonarqube.com/api/badges/gate?key=nl.esciencecenter.e3dchem.knime.silicosit:nl.esciencecenter.e3dchem.knime.silicosit)](https://sonarqube.com/dashboard?id=nl.esciencecenter.e3dchem.knime.silicosit:nl.esciencecenter.e3dchem.knime.silicosit)
-[![SonarQube Coverage](https://sonarqube.com/api/badges/measure?key=nl.esciencecenter.e3dchem.knime.silicosit:nl.esciencecenter.e3dchem.knime.silicosit&metric=coverage)](https://sonarqube.com/component_measures/domain/Coverage?id=nl.esciencecenter.e3dchem.knime.silicosit:nl.esciencecenter.e3dchem.knime.silicosit)
+[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.knime.silicosit%3Anl.esciencecenter.e3dchem.knime.silicosit&metric=alert_status)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.knime.silicosit%3Anl.esciencecenter.e3dchem.knime.silicosit)
+[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.knime.silicosit%3Anl.esciencecenter.e3dchem.knime.silicosit&metric=coverage)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.knime.silicosit%3Anl.esciencecenter.e3dchem.knime.silicosit)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.597793.svg)](https://doi.org/10.5281/zenodo.597793)
 
 This project uses [Eclipse Tycho](https://www.eclipse.org/tycho/) to perform build steps.
@@ -13,7 +13,7 @@ This project uses [Eclipse Tycho](https://www.eclipse.org/tycho/) to perform bui
 
 Requirements:
 
-* KNIME, https://www.knime.org, version 3.3 or higher
+* KNIME, https://www.knime.org, version 4.0 or higher
 
 Steps to get the Silicos-it KNIME node inside KNIME:
 
@@ -52,30 +52,19 @@ See `./.travis.yml` file how to trigger a Travis-CI build for every push or pull
 
 # Development
 
-Steps to get development environment setup:
+Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup:
 
-1. Download KNIME SDK from https://www.knime.org/downloads/overview
-2. Install/Extract/start KNIME SDK
-3. Start SDK
-4. Install m2e (Maven integration for Eclipse) + Test workflows in JUnit + Chem base + Python
-
-    1. Goto Help > Install new software ...
-    2. Make sure Update site http://update.knime.org/analytics-platform/3.3 and https://3d-e-chem.github.io/updates are in the pull down list otherwise add them
-    3. Select --all sites-- in work with pulldown
-    4. Select m2e (Maven integration for Eclipse)
-    5. Select `Test Knime workflows from a Junit test`
-    6. Select `Splash & node category for 3D-e-Chem KNIME nodes`
-    7. Select `KNIME Base Chemistry Types & Nodes`
-    8. Select `KNIME Python Integration`
-    9. Install software & restart
-
-5. Import this repo as an Existing Maven project
+1. Install Java 8
+2. Install Eclipse for [RCP and RAP developers](https://www.eclipse.org/downloads/packages/release/2018-12/r/eclipse-ide-rcp-and-rap-developers)
+3. Configure Java 8 inside Eclipse Window > Preferences > Java > Installed JREs
+4. Import this repo as an Existing Maven project
+5. Activate target platform by going to Window > Preferences > Plug-in Development > Target Platform and check the `KNIME Analytics Platform (4.0) - nl.esciencecenter.e3dchem.knime.silicosit.targetplatform/KNIME-AP-4.0.target` target definition.
 
 During import the Tycho Eclipse providers must be installed.
 
 ## Meta nodes
 
-This plugin uses metanodes as it's public nodes. The are created in the following way:
+This plugin uses metanodes as it's public nodes. They are created in the following way:
 
 1. The meta nodes are first created and tested inside the example workflows in the `examples/` directory.
 2. The `name` and `customDescription` field inside `examples/**/workflow.knime` is filled.
@@ -120,6 +109,5 @@ This can be skipped by running maven offline using `mvn -o`.
 7. Create a GitHub release
 8. Update Zenodo entry
   1. Correct authors
-  2. Correct license
 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

bin.linux/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: KNIME nodes for Silicos-it software, Linux binaries
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.silicosit.bin.linux;singleton:=true
-Bundle-Version: 1.1.2.qualifier
+Bundle-Version: 1.1.3.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Vendor: Netherlands eScience Center
 Bundle-ActivationPolicy: lazy

bin.linux/pom.xml

@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>nl.esciencecenter.e3dchem.knime.silicosit</groupId>
-    <version>1.1.2-SNAPSHOT</version>
+    <version>1.1.3-SNAPSHOT</version>
     <artifactId>nl.esciencecenter.e3dchem.knime.silicosit</artifactId>
   </parent>
   <artifactId>nl.esciencecenter.e3dchem.knime.silicosit.bin.linux</artifactId>

bin.macosx/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: KNIME nodes for Silicos-it software, Mac OSX binaries
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.silicosit.bin.macosx;singleton:=true
-Bundle-Version: 1.1.2.qualifier
+Bundle-Version: 1.1.3.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Vendor: Netherlands eScience Center
 Bundle-ActivationPolicy: lazy

bin.macosx/pom.xml

@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>nl.esciencecenter.e3dchem.knime.silicosit</groupId>
-    <version>1.1.2-SNAPSHOT</version>
+    <version>1.1.3-SNAPSHOT</version>
     <artifactId>nl.esciencecenter.e3dchem.knime.silicosit</artifactId>
   </parent>
   <artifactId>nl.esciencecenter.e3dchem.knime.silicosit.bin.macosx</artifactId>

feature/feature.xml

@@ -2,7 +2,7 @@
 <feature
       id="nl.esciencecenter.e3dchem.knime.silicosit.feature"
       label="Silicos-it KNIME nodes"
-      version="1.1.2.qualifier"
+      version="1.1.3.qualifier"
       provider-name="Netherlands eScience Center"
       os="linux,macosx"
       arch="x86_64">

feature/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.knime.silicosit</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.knime.silicosit</artifactId>
-		<version>1.1.2-SNAPSHOT</version>
+		<version>1.1.3-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>nl.esciencecenter.e3dchem.knime.silicosit.feature</artifactId>

p2/category.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <site>
-   <feature url="features/nl.esciencecenter.e3dchem.knime.silicosit.feature-1.1.2.qualifier.jar" id="nl.esciencecenter.e3dchem.knime.silicosit.feature" version="1.1.2.qualifier">
+   <feature url="features/nl.esciencecenter.e3dchem.knime.silicosit.feature-1.1.3.qualifier.jar" id="nl.esciencecenter.e3dchem.knime.silicosit.feature" version="1.1.3.qualifier">
       <category name="nl.esciencecenter.3D-e-Chem"/>
    </feature>
    <category-def name="nl.esciencecenter.3D-e-Chem" label="KNIME 3D-e-Chem Contributions">

p2/pom.xml

@@ -4,7 +4,7 @@
     <parent>
         <artifactId>nl.esciencecenter.e3dchem.knime.silicosit</artifactId>
         <groupId>nl.esciencecenter.e3dchem.knime.silicosit</groupId>
-        <version>1.1.2-SNAPSHOT</version>
+        <version>1.1.3-SNAPSHOT</version>
     </parent>
     <artifactId>nl.esciencecenter.e3dchem.knime.silicosit.p2</artifactId>
     <packaging>eclipse-repository</packaging>

plugin/META-INF/MANIFEST.MF

@@ -2,15 +2,15 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: KNIME nodes for Silicos-it software
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.silicosit.plugin;singleton:=true
-Bundle-Version: 1.1.2.qualifier
+Bundle-Version: 1.1.3.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Vendor: Netherlands eScience Center
 Require-Bundle: org.eclipse.core.runtime,
- org.knime.workbench.core;bundle-version="[3.3.0,4.0.0)",
- org.knime.workbench.repository;bundle-version="[3.3.0,4.0.0)",
- org.knime.base;bundle-version="[3.3.0,4.0.0)",
- org.knime.chem.base;bundle-version="[3.3.0,4.0.0)",
- org.knime.python.nodes;bundle-version="[3.3.0,4.0.0)",
+ 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.chem.base;bundle-version="[4.0.0,5.0.0)",
+ org.knime.python.nodes;bundle-version="[4.0.0,5.0.0)",
  nl.esciencecenter.e3dchem.plugin,
  nl.esciencecenter.e3dchem.knime.pharmacophore.plugin;bundle-version="[1.0.0,2.0.0)"
 Bundle-ActivationPolicy: lazy

plugin/pom.xml

@@ -4,11 +4,12 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.knime.silicosit</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.knime.silicosit</artifactId>
-		<version>1.1.2-SNAPSHOT</version>
+		<version>1.1.3-SNAPSHOT</version>
 	</parent>
 	<artifactId>nl.esciencecenter.e3dchem.knime.silicosit.plugin</artifactId>
 	<packaging>eclipse-plugin</packaging>
 	<properties>
 		<sonar.jacoco.reportPaths>../tests/target/jacoco.exec</sonar.jacoco.reportPaths>
+		<sonar.junit.reportsPath>../tests/target/surefire-reports</sonar.junit.reportsPath>
 	</properties>
 </project>

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>nl.esciencecenter.e3dchem.knime.silicosit</groupId>
 	<artifactId>nl.esciencecenter.e3dchem.knime.silicosit</artifactId>
-	<version>1.1.2-SNAPSHOT</version>
+	<version>1.1.3-SNAPSHOT</version>
 	<packaging>pom</packaging>
 
 	<scm>
@@ -26,34 +26,16 @@
 	</prerequisites>
 
 	<properties>
-		<knime.version>3.3</knime.version>
-		<knime.update.site>http://update.knime.org/analytics-platform/${knime.version}/</knime.update.site>
-		<tycho.version>1.0.0</tycho.version>
-		<tycho.extras.version>1.0.0</tycho.extras.version>
+		<tycho.version>1.4.0</tycho.version>
+		<tycho.extras.version>1.4.0</tycho.extras.version>
 		<tycho.test.jvmArgs>-Xmx512m</tycho.test.jvmArgs>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+                <target.file>KNIME-AP-4.0</target.file>
 		<tycho.scmUrl>scm:git:https://github.com/3D-e-Chem/knime-silicos-it.git</tycho.scmUrl>
-		<sonar.host.url>https://sonarqube.com</sonar.host.url>
+		<sonar.host.url>https://sonarcloud.io</sonar.host.url>
 		<sonar.organization>3d-e-chem</sonar.organization>
 	</properties>
-	<repositories>
-		<repository>
-			<id>knime</id>
-			<layout>p2</layout>
-			<url>${knime.update.site}</url>
-		</repository>
-		<repository>
-			<id>3d-e-chem</id>
-			<layout>p2</layout>
-			<url>https://3d-e-chem.github.io/updates</url>
-		</repository>
-		<repository>
-			<id>swtbot</id>
-			<layout>p2</layout>
-			<url>http://download.eclipse.org/technology/swtbot/releases/latest/</url>
-		</repository>
-	</repositories>
 	<build>
 		<plugins>
 			<plugin>
@@ -82,6 +64,14 @@
 							<arch>x86_64</arch>
 						</environment>
 					</environments>
+                    <target>
+						<artifact>
+							<groupId>nl.esciencecenter.e3dchem.knime.silicosit</groupId>
+							<artifactId>nl.esciencecenter.e3dchem.knime.silicosit.targetplatform</artifactId>
+							<version>${project.version}</version>
+							<classifier>${target.file}</classifier>
+						</artifact>
+					</target>
 				</configuration>
 			</plugin>
 			<plugin>
@@ -132,6 +122,8 @@
 							<generate>true</generate>
 						</sourceReferences>
 						<format>'v'yyyyMMddHHmm</format>
+						<!-- Uncomment to package with uncommited code-->
+						<!-- <jgit.dirtyWorkingTree>warning</jgit.dirtyWorkingTree> -->
 					</configuration>
 				</plugin>
 			</plugins>
@@ -144,5 +136,6 @@
 		<module>tests</module>
 		<module>bin.linux</module>
 		<module>bin.macosx</module>
+                <module>targetplatform</module>
     </modules>
 </project>

targetplatform/KNIME-AP-4.0.target

@@ -0,0 +1,49 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><?pde version="3.8"?><target name="KNIME Analytics Platform (4.0)" sequenceNumber="1512743962">
+<locations>
+<location includeAllPlatforms="false" includeConfigurePhase="false" includeMode="planner" includeSource="true" type="InstallableUnit">
+<unit id="com.knime.features.explorer.serverspace.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.base.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.dbdrivers.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.ensembles.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.ext.itemset.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.ext.jep.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.ext.poi.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.js.quickforms.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.json.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.personalproductivity.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.testingapplication.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.xml.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.python.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.chem.types.feature.group" version="0.0.0"/>
+<unit id="org.knime.targetPlatform.feature.group" version="0.0.0"/>
+<repository location="https://update.knime.org/analytics-platform/4.0/"/>
+</location>
+	<location includeAllPlatforms="false" includeConfigurePhase="false" includeMode="planner" includeSource="true" type="InstallableUnit">
+		<unit id="nl.esciencecenter.e3dchem.knime.testing.plugin" version="0.0.0"/>
+		<unit id="nl.esciencecenter.e3dchem.plugin" version="0.0.0"/>
+		<unit id="nl.esciencecenter.e3dchem.knime.pharmacophore.plugin" version="0.0.0"/>
+		<repository location="https://3d-e-chem.github.io/updates"/>
+	</location>
+		<location includeAllPlatforms="false" includeConfigurePhase="false" includeMode="planner" includeSource="true" type="InstallableUnit">
+		<unit id="org.eclipse.swtbot.eclipse.feature.group" version="0.0.0"/>
+		<unit id="org.eclipse.swtbot.eclipse.test.junit.feature.group" version="0.0.0"/>
+		<repository location="http://download.eclipse.org/technology/swtbot/releases/latest/"/>
+	</location>
+</locations>
+<targetJRE path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
+<launcherArgs>
+<vmArgs>-server
+-Dsun.java2d.d3d=false
+-Dosgi.classloader.lock=classname
+-XX:+UnlockDiagnosticVMOptions
+-XX:+UnsyncloadClass 
+-XX:+UseG1GC
+-ea
+-Dorg.eclipse.swt.internal.gtk.cairoGraphics=false
+-Dorg.eclipse.swt.internal.gtk.useCairo=false
+-Dorg.eclipse.swt.browser.IEVersion=10001
+-Dsun.awt.noerasebackground=true
+-Dsun.net.client.defaultReadTimeout=0
+-Dorg.eclipse.swt.internal.gtk.disablePrinting</vmArgs>
+</launcherArgs>
+</target>

targetplatform/pom.xml

@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- 
+Copyright (c) 2010, 2015 SAP AG and others.
+All rights reserved. This program and the accompanying materials
+are made available under the terms of the Eclipse Public License v1.0
+which accompanies this distribution, and is available at
+http://www.eclipse.org/legal/epl-v10.html
+
+Contributors:
+    SAP AG - initial API and implementation
+-->
+<project
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
+	xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+	<modelVersion>4.0.0</modelVersion>
+
+	<artifactId>nl.esciencecenter.e3dchem.knime.silicosit.targetplatform</artifactId>
+	<packaging>pom</packaging>
+
+	<parent>
+		<artifactId>nl.esciencecenter.e3dchem.knime.silicosit</artifactId>
+		<groupId>nl.esciencecenter.e3dchem.knime.silicosit</groupId>
+		<version>1.1.3-SNAPSHOT</version>
+	</parent>
+
+</project>

tests/META-INF/MANIFEST.MF

@@ -2,12 +2,12 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Tests
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.silicosit.tests
-Bundle-Version: 1.1.2.qualifier
+Bundle-Version: 1.1.3.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: org.junit;bundle-version="4.12.0",
- org.knime.core;bundle-version="[3.3.0,4.0.0)",
- org.knime.base;bundle-version="[3.3.0,4.0.0)",
- org.knime.testing;bundle-version="[3.3.0,4.0.0)",
+ 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.eclipse.ui;bundle-version="3.108.0",
  org.eclipse.swtbot.eclipse.finder;bundle-version="2.6.0",
  org.eclipse.swtbot.junit4_x;bundle-version="2.6.0",