Merge pull request #32 from 3D-e-Chem/knime43

Drop Python nodes
3D-e-Chem · Feb 12, 2021 · 02cb22c · 02cb22c
2 parents 19d101b + 68dc3f9
commit 02cb22c
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -0,0 +1,45 @@
+# 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
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up JDK 1.8
+      uses: actions/setup-java@v1
+      with:
+        java-version: 1.8
+    - name: Cache Maven packages
+      uses: actions/cache@v2
+      with:
+        path: ~/.m2
+        key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml', '**/MANIFEST.MF', 'targetplatform/*.target') }}
+        restore-keys: ${{ runner.os }}-m2
+    - name: OS dependencies
+      run: sudo apt-get install xvfb
+    - name: Build with Maven
+      run: mvn -B package
+    - name: Run tests
+      run: xvfb-run mvn verify -B
+    - name: Set up JDK 11 for SonarCloud analysis
+      uses: actions/setup-java@v1
+      with:
+        java-version: 11
+    - name: SonarCloud analysis
+      run: mvn sonar:sonar -Dsonar.login=$SONAR_TOKEN
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
diff --git a/.travis.yml b/.travis.yml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,10 +1,17 @@
 # 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
 
+## [3.0.0] - 2021-02-12
+
+## Removed
+
+- Python based nodes in favour of web service nodes ([#25](https://github.com/3D-e-Chem/knime-kripodb/issues/25))
+
 ## [2.5.0] - 2019-09-25
 
 ### Deprecated
@@ -51,7 +58,7 @@ The file is formatted as described on http://keepachangelog.com/.
 
 ### Added
 
-- Pure Java nodes to fetch fragment information and similarites from web service (#17) 
+- Pure Java nodes to fetch fragment information and similarites from web service (#17)
 
 ## Changed
 
@@ -94,7 +101,7 @@ Retracted due to unresolved compilation problems.
 
 - Nest Kripo nodes under /community/3D-e-Chem (#7)
 
-## [2.1.0] - 2016-07-14 
+## [2.1.0] - 2016-07-14
 
 ### Added
 
@@ -163,3 +170,23 @@ Version >= 2.0.0 uses KripoDB Knime node which have there own dialog with combo
 
 - Python templates to use KripoDB package
 - Example workflow on Github repo.
+
+[unreleased]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.5.0...HEAD
+[2.5.0]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.4.2...v2.5.0
+[2.4.2]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.3.1...v2.4.2
+[2.4.1]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.3.0...v2.3.1
+[2.3.0]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.2.1...v2.3.0
+[2.2.1]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.2.0...v2.2.1
+[2.2.0]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.1.5...v2.2.0
+[2.1.5]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.1.4...v2.1.5
+[2.1.4]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.1.3...v2.1.4
+[2.1.3]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.1.2...v2.1.3
+[2.1.2]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.1.1...v2.1.2
+[2.1.1]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.1.0...v2.1.1
+[2.1.0]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.0.1...v2.1.0
+[2.0.1]: https://github.com/3D-e-Chem/knime-kripodb/compare/v2.0.0...v2.0.1
+[2.0.0]: https://github.com/3D-e-Chem/knime-kripodb/compare/v1.0.3...v2.0.0
+[1.0.3]: https://github.com/3D-e-Chem/knime-kripodb/compare/v1.0.2...v1.0.3
+[1.0.2]: https://github.com/3D-e-Chem/knime-kripodb/compare/v1.0.1...v1.0.2
+[1.0.1]: https://github.com/3D-e-Chem/knime-kripodb/compare/v1.0.0...v1.0.1
+[1.0.0]: https://github.com/3D-e-Chem/knime-kripodb/releases/tag/v1.0.0
diff --git a/README.md b/README.md
@@ -4,8 +4,7 @@ KRIPO stands for [Key Representation of Interaction in POckets](http://dx.doi.or
 
 [KNIME](http://www.knime.org) nodes for KripoDB (https://github.com/3D-e-Chem/kripodb).
 
-[![Build Status](https://travis-ci.org/3D-e-Chem/knime-kripodb.svg?branch=master)](https://travis-ci.org/3D-e-Chem/knime-kripodb)
-[![Build status](https://ci.appveyor.com/api/projects/status/3way61l0ojtbhcrv?svg=true)](https://ci.appveyor.com/project/3D-e-Chem/knime-kripodb)
+[![Java CI with Maven](https://github.com/3D-e-Chem/knime-kripodb/workflows/Java%20CI%20with%20Maven/badge.svg)](https://github.com/3D-e-Chem/knime-kripodb/actions?query=workflow%3A%22Java+CI+with+Maven%22)
 [![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.kripodb%3Anl.esciencecenter.e3dchem.kripodb&metric=alert_status)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.kripodb%3Anl.esciencecenter.e3dchem.kripodb)
 [![Coverage](https://sonarcloud.io/api/project_badges/measure?project=nl.esciencecenter.e3dchem.kripodb%3Anl.esciencecenter.e3dchem.kripodb&metric=coverage)](https://sonarcloud.io/dashboard?id=nl.esciencecenter.e3dchem.kripodb%3Anl.esciencecenter.e3dchem.kripodb)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.597262.svg)](https://doi.org/10.5281/zenodo.597262)
@@ -14,11 +13,11 @@ KRIPO stands for [Key Representation of Interaction in POckets](http://dx.doi.or
 
 Requirements:
 
-* KNIME, https://www.knime.org, version 4.0 or higher
+- KNIME, https://www.knime.org, version 4.0 or higher
 
 Optionally:
 
-* KripoDB Python package & data files, https://github.com/3D-e-Chem/kripodb,
+- KripoDB Python package & data files, https://github.com/3D-e-Chem/kripodb,
   required to start local running kripo web service instead of the public [one](http://3d-e-chem.vu-compmedchem.nl/kripodb/ui).
 
 Steps to get KripoDB nodes inside KNIME:
@@ -42,7 +41,7 @@ Other workflows using the KripoDB nodes can be found at https://github.com/3D-e-
 
 Development requirements:
 
-* Maven, https://maven.apache.org
+- Maven, https://maven.apache.org
 
 Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup:
 
@@ -57,7 +56,7 @@ During import the Tycho Eclipse providers must be installed.
 
 ## Build
 
-```
+```shell
 mvn package
 ```
 
@@ -66,7 +65,7 @@ An Eclipse update site will be made in `p2/target/repository` repository.
 
 ## Tests
 
-```
+```shell
 mvn verify
 ```
 
@@ -78,18 +77,21 @@ See https://github.com/3D-e-Chem/knime-testflow for more information about workf
 
 The web service client is generated using [Swagger Code Generator](https://github.com/swagger-api/swagger-codegen) and stored inside `plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/client/` directory.
 
-1. Start KripoDB webservice
-```
+1. Start [KripoDB webservice](https://github.com/3D-e-Chem/kripodb#web-service)
+
+```shell
 kripodb serve data/similarities.frozen.h5 data/fragments.sqlite data/pharmacophores.h5
 ```
 
 2. Download swagger code generator
-```
+
+```shell
 wget http://repo1.maven.org/maven2/io/swagger/swagger-codegen-cli/2.2.3/swagger-codegen-cli-2.2.3.jar
 ```
 
 3. Generate a client for KripoDB web service
-```
+
+```shell
 java -jar swagger-codegen-cli-2.2.3.jar generate \
 --input-spec http://localhost:8084/kripo/swagger.json \
 --output client \
@@ -98,13 +100,15 @@ java -jar swagger-codegen-cli-2.2.3.jar generate \
 ```
 
 4. Compile client
-```
+
+```shell
 cd client
 mvn package
 ```
 
 5. Populate plugin with client source code and dependencies
-```
+
+```shell
 mkdir ../plugin/lib
 cp target/lib/gson-* target/lib/logging-interceptor-* target/lib/ok* target/lib/swagger-annotations-* ../plugin/lib/
 rm -r ../plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/client
@@ -120,22 +124,23 @@ cp -r src/main/java/nl/esciencecenter/e3dchem/kripodb/ws/client ../plugin/src/ja
 3. Create package with `mvn package`, will create update site in `p2/target/repository`
 4. Test node by installing it from local update site
 5. Append new release to 3D-e-Chem update site
-  1. Make clone of https://github.com/3D-e-Chem/3D-e-Chem.github.io repo
-  2. Append release to 3D-e-Chem update site with `mvn install -Dtarget.update.site=<3D-e-Chem repo/updates>`
-6. Commit and push changes in this repo and 3D-e-Chem.github.io repo
-7. Create a Github release
-8. Update Zenodo entry
-  1. Correct authors
-  2. To Related/alternate identifiers section add http://dx.doi.org/10.1186/1758-2946-6-S1-O26 as `is cited by this upload` entry.
-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 https://github.com/3D-e-Chem/3D-e-Chem.github.io repo
+7. Append release to 3D-e-Chem update site with `mvn install -Dtarget.update.site=<3D-e-Chem repo/updates>`
+8. Commit and push changes in this repo and 3D-e-Chem.github.io repo
+9. Create a Github release
+10. Update Zenodo entry
+11. Correct authors
+12. To Related/alternate identifiers section add http://dx.doi.org/10.1186/1758-2946-6-S1-O26 as `is cited by this upload` entry.
+13. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release
+14. Update CITIATION.cff with new DOI
 
 # Create stub recordings for integration tests
 
 The test workflow are tested against a mocked web server and not the actual http://3d-e-chem.vu-compmedchem.nl/kripodb site.
 The mock server is called [WireMock](http://WireMock.org/) and normally gives empty responses.
 To have WireMock server return filled responses, stubs stored in `tests/src/test/resources/` directory must be provided.
 The stubs can be recorded by starting a WireMock server in recording mode by:
+
 ```
 java -jar tests/lib/wiremock-standalone-2.5.0.jar --proxy-all="http://3d-e-chem.vu-compmedchem.nl/" \
 --port=8089 --record-mappings --verbose --root-dir=tests/src/test/resources/
@@ -144,11 +149,12 @@ java -jar tests/lib/wiremock-standalone-2.5.0.jar --proxy-all="http://localhost:
 ```
 
 Then in a KNIME workflow in the KripoDB nodes set the base path to http://localhost:8089.
-Executing the workflow will fetch data from http://3d-e-chem.vu-compmedchem.nl/kripodb  via the WireMock server and cause new stubs to be recorded in the `tests/src/test/resources/` directory.
+Executing the workflow will fetch data from http://3d-e-chem.vu-compmedchem.nl/kripodb via the WireMock server and cause new stubs to be recorded in the `tests/src/test/resources/` directory.
 
 To run the test workflows from inside KNIME desktop enviroment start the WireMock server in mock mode by:
 
-```
+```shell
 java -jar tests/lib/wiremock-standalone-2.5.0.jar --port=8089 --verbose --root-dir=tests/src/test/resources/
 ```
+
 Then import the test workflows in `tests/src/knime/` directory, select the workflow in the KNIME explorer and in the context menu (right-click) select `Run as workflow test`.
diff --git a/appveyor.yml b/appveyor.yml
diff --git a/feature/feature.xml b/feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="nl.esciencecenter.e3dchem.kripodb.feature"
       label="KripoDB nodes for KNIME"
-      version="2.5.0.qualifier"
+      version="3.0.0.qualifier"
       provider-name="Netherlands eScience Center">
 
    <description url="https://github.com/3D-e-Chem/knime-kripodb">

diff --git a/feature/pom.xml b/feature/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.kripodb</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.kripodb</artifactId>
-		<version>2.5.0-SNAPSHOT</version>
+		<version>3.0.0-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>nl.esciencecenter.e3dchem.kripodb.feature</artifactId>

diff --git a/p2/category.xml b/p2/category.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <site>
-   <feature id="nl.esciencecenter.e3dchem.kripodb.feature" version="2.5.0.qualifier">
+   <feature id="nl.esciencecenter.e3dchem.kripodb.feature" version="3.0.0.qualifier">
       <category name="nl.esciencecenter.3D-e-Chem"/>
    </feature>
    <category-def name="nl.esciencecenter.3D-e-Chem" label="KNIME 3D-e-Chem Contributions">

diff --git a/p2/pom.xml b/p2/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>nl.esciencecenter.e3dchem.kripodb</artifactId>
         <groupId>nl.esciencecenter.e3dchem.kripodb</groupId>
-        <version>2.5.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
     </parent>
     <artifactId>nl.esciencecenter.e3dchem.kripodb.p2</artifactId>
     <packaging>eclipse-repository</packaging>

diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF
@@ -2,14 +2,13 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: 3D-e-Chem KNIME KripoDB nodes
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.kripodb.plugin;singleton:=true
-Bundle-Version: 2.5.0.qualifier
+Bundle-Version: 3.0.0.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Activator: nl.esciencecenter.e3dchem.kripodb.Activator
 Require-Bundle: org.knime.core;bundle-version="[4.0.0,5.0.0)",
  org.knime.base;bundle-version="[4.0.0,5.0.0)",
  org.knime.chem.types;bundle-version="[4.0.0,5.0.0)",
  org.rdkit.knime.types,
- nl.esciencecenter.e3dchem.python.plugin;bundle-version="[2.0.1,3.0.0)",
  nl.esciencecenter.e3dchem.plugin;bundle-version="[1.0.0,2.0.0)",
  nl.esciencecenter.e3dchem.knime.pharmacophore.plugin;bundle-version="[1.0.0,2.0.0)"
 Bundle-Vendor: Netherlands eScience Center
@@ -23,4 +22,3 @@ Bundle-ClassPath: lib/gson-2.8.1.jar,
 Export-Package: nl.esciencecenter.e3dchem.kripodb,
  nl.esciencecenter.e3dchem.kripodb.fragments,
  nl.esciencecenter.e3dchem.kripodb.fragmentsbysimilarity
-Import-Package: org.knime.python2.config
diff --git a/plugin/plugin.xml b/plugin/plugin.xml
@@ -9,13 +9,6 @@
           locked="false"
           name="KripoDB"
           path="/community/3d-e-chem"/>
-    <category
-          description="Category containing Kripo nodes for using local files"
-          icon="nl/esciencecenter/e3dchem/kripodb/kripo.png"
-          level-id="local"
-          locked="false"
-          name="For local files"
-          path="/community/3d-e-chem/kripodb"/>
     </extension>
 
     <extension point="org.knime.workbench.repository.nodes">
@@ -34,20 +27,5 @@
                deprecated="false"
                factory-class="nl.esciencecenter.e3dchem.kripodb.ws.pharmacophores.PharmacophoresFactory">
         </node>
-        <node
-               category-path="/community/3d-e-chem/kripodb/local"
-               deprecated="true"
-               factory-class="nl.esciencecenter.e3dchem.kripodb.fragmentsbysimilarity.FragmentBySimilarityFactory">
-        </node>
-        <node
-               category-path="/community/3d-e-chem/kripodb/local"
-               deprecated="true"
-               factory-class="nl.esciencecenter.e3dchem.kripodb.fragments.FragmentByIdFactory">
-        </node>
-        <node
-               category-path="/community/3d-e-chem/kripodb/local"
-               deprecated="true"
-               factory-class="nl.esciencecenter.e3dchem.kripodb.local.pharmacophores.PharmacophoresFactory">
-        </node>
     </extension>
 </plugin>