Merge pull request #15 from 3D-e-Chem/knime4

Knime4

.travis.yml

@@ -1,9 +1,8 @@
-sudo: false
 language: java
 matrix:
  include:
  - os: linux
-   jdk: oraclejdk8
+   jdk: openjdk8
    addons:
     apt:
       packages:

.zenodo.json

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

CHANGELOG.md

@@ -5,6 +5,12 @@ The file is formatted as described on http://keepachangelog.com/.
 
 ## [Unreleased]
 
+## [0.3.5] 2019-06-27
+
+### Changes
+
+- Requires KNIME 4.0 [#14](https://github.com/3D-e-Chem/knime-plants/issues/14)
+
 ## [0.3.4] 2018-02-07
 
 ### Fixed

README.md

@@ -6,8 +6,8 @@ PLANTS homepage at http://www.mnf.uni-tuebingen.de/fachbereiche/pharmazie-und-bi
 
 [![Build Status Linux & OS X ](https://travis-ci.org/3D-e-Chem/knime-plants.svg?branch=master)](https://travis-ci.org/3D-e-Chem/knime-plants)
 [![Build status Windows ](https://ci.appveyor.com/api/projects/status/wnwuac96jd7v76ri?svg=true)](https://ci.appveyor.com/project/3D-e-Chem/knime-plants)
-[![SonarQube Gate](https://sonarqube.com/api/badges/gate?key=nl.esciencecenter.e3dchem.knime.plants:nl.esciencecenter.e3dchem.knime.plants)](https://sonarqube.com/dashboard?id=nl.esciencecenter.e3dchem.knime.plants:nl.esciencecenter.e3dchem.knime.plants)
-[![SonarQube Coverage](https://sonarqube.com/api/badges/measure?key=nl.esciencecenter.e3dchem.knime.plants:nl.esciencecenter.e3dchem.knime.plants&metric=coverage)](https://sonarqube.com/component_measures/domain/Coverage?id=nl.esciencecenter.e3dchem.knime.plants:nl.esciencecenter.e3dchem.knime.plants)
+[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.knime.plants%3Anl.esciencecenter.e3dchem.knime.plants&metric=alert_status)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.knime.plants%3Anl.esciencecenter.e3dchem.knime.plants)
+[![Coverage](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.knime.plants%3Anl.esciencecenter.e3dchem.knime.plants&metric=coverage)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.knime.plants%3Anl.esciencecenter.e3dchem.knime.plants)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.997272.svg)](https://doi.org/10.5281/zenodo.997272)
 
 This project uses [Eclipse Tycho](https://www.eclipse.org/tycho/) to perform build steps.
@@ -24,7 +24,7 @@ The PLANTS KNIME nodes themselves have the Apache 2.0 license.
 
 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 PLANTS KNIME node inside KNIME:
 
@@ -57,46 +57,19 @@ The update site can be used to perform a local installation.
 
 # Development
 
-Steps to get development environment 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) + KNIME Testing framework + Vernalis + SWTBot
-
-    1. Goto Window -> Preferences -> Install/Update -> Available Software Sites
-    2. Make sure the following Software Sites (or a version of them) are present otherwise add them:
-
-      * http://update.knime.org/analytics-platform/3.3
-      * http://update.knime.org/community-contributions/trusted/3.3
-      * https://3d-e-chem.github.io/updates
-      * http://download.eclipse.org/eclipse/updates/4.6
-      * http://download.eclipse.org/releases/neon
-      * http://download.eclipse.org/technology/swtbot/releases/latest/
-
-    3. Goto Help -> Check for updates
-    4. Install any updates found & restart
-    5. Goto Help > Install new software ...
-    6. Select --All Available sites-- in work with pulldown
-    7. Wait for list to be filled, `Pending...` should disappear
-    8. Select the following items:
-
-	* m2e (Maven integration for Eclipse)
-	* Test Knime workflows from a Junit test
-	* Splash & node category for 3D-e-Chem KNIME nodes
-	* Vernalis
-	* SWTBot for Eclipse Testing
-	* SWtBot JUnit Headless launchers for Eclipse
-		
-    5. Install software & restart
-
-5. Import this repo as an Existing Maven project
-
-After the import the Maven plugin connections must be setup, a Discover m2e connections dialog will popup to install all requested connectors, after the installation restart eclipse.
+Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup:
+
+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.plants.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.
@@ -141,7 +114,7 @@ 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
-  3. Add https://doi.org/10.1007/11839088_22 as `is referenced by this upload` related identifier
+  2. Add https://doi.org/10.1007/11839088_22 as `is referenced by this upload` related identifier
 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 PLANTS, Linux binaries
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.bin.linux;singleton:=true
-Bundle-Version: 0.3.4.qualifier
+Bundle-Version: 0.3.5.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.plants</groupId>
-    <version>0.3.4-SNAPSHOT</version>
+    <version>0.3.5-SNAPSHOT</version>
     <artifactId>nl.esciencecenter.e3dchem.knime.plants</artifactId>
   </parent>
   <artifactId>nl.esciencecenter.e3dchem.knime.plants.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 PLANTS, MacOSX binaries
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.bin.macosx;singleton:=true
-Bundle-Version: 0.3.4.qualifier
+Bundle-Version: 0.3.5.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.plants</groupId>
-    <version>0.3.4-SNAPSHOT</version>
+    <version>0.3.5-SNAPSHOT</version>
     <artifactId>nl.esciencecenter.e3dchem.knime.plants</artifactId>
   </parent>
   <artifactId>nl.esciencecenter.e3dchem.knime.plants.bin.macosx</artifactId>

bin.windows/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: KNIME nodes for PLANTS, Windows binaries
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.bin.windows;singleton:=true
-Bundle-Version: 0.3.4.qualifier
+Bundle-Version: 0.3.5.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Vendor: Netherlands eScience Center
 Bundle-ActivationPolicy: lazy

bin.windows/pom.xml

@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>nl.esciencecenter.e3dchem.knime.plants</groupId>
-    <version>0.3.4-SNAPSHOT</version>
+    <version>0.3.5-SNAPSHOT</version>
     <artifactId>nl.esciencecenter.e3dchem.knime.plants</artifactId>
   </parent>
   <artifactId>nl.esciencecenter.e3dchem.knime.plants.bin.windows</artifactId>

bin.windows32/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: KNIME nodes for PLANTS, Windows binaries 32bit
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.bin.windows32;singleton:=true
-Bundle-Version: 0.3.4.qualifier
+Bundle-Version: 0.3.5.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Vendor: Netherlands eScience Center
 Bundle-ActivationPolicy: lazy

bin.windows32/pom.xml

@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>nl.esciencecenter.e3dchem.knime.plants</groupId>
-    <version>0.3.4-SNAPSHOT</version>
+    <version>0.3.5-SNAPSHOT</version>
     <artifactId>nl.esciencecenter.e3dchem.knime.plants</artifactId>
   </parent>
   <artifactId>nl.esciencecenter.e3dchem.knime.plants.bin.windows32</artifactId>

feature/feature.xml

@@ -2,7 +2,7 @@
 <feature
       id="nl.esciencecenter.e3dchem.knime.plants.feature"
       label="KNIME PLANTS extension"
-      version="0.3.4.qualifier"
+      version="0.3.5.qualifier"
       provider-name="Netherlands eScience Center"
       os="linux,macosx,win32"
       arch="x86,x86_64">

feature/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.knime.plants</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.knime.plants</artifactId>
-		<version>0.3.4-SNAPSHOT</version>
+		<version>0.3.5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>nl.esciencecenter.e3dchem.knime.plants.feature</artifactId>

p2/category.xml

@@ -1,19 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <site>
-   <feature id="nl.esciencecenter.e3dchem.knime.plants.feature" version="0.3.4.qualifier">
+   <feature id="nl.esciencecenter.e3dchem.knime.plants.feature" version="0.3.5.qualifier">
       <category name="nl.esciencecenter.3D-e-Chem"/>
    </feature>
-   <feature id="nl.esciencecenter.e3dchem.knime.plants.feature.source" version="0.3.4.qualifier">
-      <category name="nl.esciencecenter.3D-e-Chem.sources"/>
-   </feature>
-<category-def name="nl.esciencecenter.3D-e-Chem" label="KNIME 3D-e-Chem Contributions">
+   <category-def name="nl.esciencecenter.3D-e-Chem" label="KNIME 3D-e-Chem Contributions">
      <description>
         3D-e-Chem: Collection KNIME nodes &amp; Extensions for the NLeSC 3d-e-Chem project
       </description>
    </category-def>
-   <category-def name="nl.esciencecenter.3D-e-Chem.sources" label="KNIME 3D-e-Chem Contributions Sources">
-      <description>
-         3D-e-Chem Sources: Sources of KNIME nodes &amp; Extensions for the NLeSC 3d-e-Chem project
-     </description>
-  </category-def>
 </site>

p2/pom.xml

@@ -4,7 +4,7 @@
     <parent>
         <artifactId>nl.esciencecenter.e3dchem.knime.plants</artifactId>
         <groupId>nl.esciencecenter.e3dchem.knime.plants</groupId>
-        <version>0.3.4-SNAPSHOT</version>
+        <version>0.3.5-SNAPSHOT</version>
     </parent>
     <artifactId>nl.esciencecenter.e3dchem.knime.plants.p2</artifactId>
     <packaging>eclipse-repository</packaging>

plugin/META-INF/MANIFEST.MF

@@ -2,17 +2,17 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: KNIME nodes for PLANTS
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.knime.plants.plugin;singleton:=true
-Bundle-Version: 0.3.4.qualifier
+Bundle-Version: 0.3.5.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Activator: nl.esciencecenter.e3dchem.knime.plants.Activator
 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.core;bundle-version="[3.3.0,4.0.0)",
- org.knime.chem.types;bundle-version="[3.3.0,4.0.0)",
- com.vernalis.knime;bundle-version="[1.8.0,2.0.0)",
+ 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.core;bundle-version="[4.0.0,5.0.0)",
+ org.knime.chem.types;bundle-version="[4.0.0,5.0.0)",
+ com.vernalis.knime;bundle-version="[1.20.3,2.0.0)",
  nl.esciencecenter.e3dchem.plugin,
  org.eclipse.jface
 Bundle-ActivationPolicy: lazy

plugin/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.knime.plants</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.knime.plants</artifactId>
-		<version>0.3.4-SNAPSHOT</version>
+		<version>0.3.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>nl.esciencecenter.e3dchem.knime.plants.plugin</artifactId>
 	<packaging>eclipse-plugin</packaging>