Merge branch 'master' of github.com:3D-e-Chem/knime-kripodb

CHANGELOG.md

@@ -5,6 +5,12 @@ The file is formatted as described on http://keepachangelog.com/.
 
 ## Unreleased
 
+## [2.5.0] - 2019-09-25
+
+### Deprecated
+
+- Python based nodes in favour of web service nodes ([#25](https://github.com/3D-e-Chem/knime-kripodb/issues/25))
+
 ## [2.4.2] - 2019-07-02
 
 ### Changed

README.md

@@ -19,8 +19,7 @@ Requirements:
 Optionally:
 
 * KripoDB Python package & data files, https://github.com/3D-e-Chem/kripodb,
-  required when nodes which use local Kripo files are used.
-  Nodes which talk to web service work without the KripoDB Python package.
+  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:
 
@@ -39,8 +38,6 @@ The workflow can be run by importing it into KNIME as an archive.
 
 Other workflows using the KripoDB nodes can be found at https://github.com/3D-e-Chem/workflows
 
-Make sure the Python used by KNIME is the same the Python with kripodb package installed.
-
 # Development
 
 Development requirements:

feature/feature.xml

@@ -2,7 +2,7 @@
 <feature
       id="nl.esciencecenter.e3dchem.kripodb.feature"
       label="KripoDB nodes for KNIME"
-      version="2.4.2.qualifier"
+      version="2.5.0.qualifier"
       provider-name="Netherlands eScience Center">
 
    <description url="https://github.com/3D-e-Chem/knime-kripodb">

feature/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.kripodb</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.kripodb</artifactId>
-		<version>2.4.2-SNAPSHOT</version>
+		<version>2.5.0-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>nl.esciencecenter.e3dchem.kripodb.feature</artifactId>

p2/category.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <site>
-   <feature id="nl.esciencecenter.e3dchem.kripodb.feature" version="2.4.2.qualifier">
+   <feature id="nl.esciencecenter.e3dchem.kripodb.feature" version="2.5.0.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

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>nl.esciencecenter.e3dchem.kripodb</artifactId>
         <groupId>nl.esciencecenter.e3dchem.kripodb</groupId>
-        <version>2.4.2-SNAPSHOT</version>
+        <version>2.5.0-SNAPSHOT</version>
     </parent>
     <artifactId>nl.esciencecenter.e3dchem.kripodb.p2</artifactId>
     <packaging>eclipse-repository</packaging>

plugin/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ 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: 2.4.2.qualifier
+Bundle-Version: 2.5.0.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)",

plugin/plugin.xml

@@ -36,17 +36,17 @@
         </node>
         <node
                category-path="/community/3d-e-chem/kripodb/local"
-               deprecated="false"
+               deprecated="true"
                factory-class="nl.esciencecenter.e3dchem.kripodb.fragmentsbysimilarity.FragmentBySimilarityFactory">
         </node>
         <node
                category-path="/community/3d-e-chem/kripodb/local"
-               deprecated="false"
+               deprecated="true"
                factory-class="nl.esciencecenter.e3dchem.kripodb.fragments.FragmentByIdFactory">
         </node>
         <node
                category-path="/community/3d-e-chem/kripodb/local"
-               deprecated="false"
+               deprecated="true"
                factory-class="nl.esciencecenter.e3dchem.kripodb.local.pharmacophores.PharmacophoresFactory">
         </node>
     </extension>

plugin/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.kripodb</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.kripodb</artifactId>
-		<version>2.4.2-SNAPSHOT</version>
+		<version>2.5.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>nl.esciencecenter.e3dchem.kripodb.plugin</artifactId>
 	<packaging>eclipse-plugin</packaging>

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdDialog.java

@@ -24,7 +24,9 @@
  * creation of a simple dialog with standard components. If you need a more
  * complex dialog please derive directly from
  * {@link org.knime.core.node.NodeDialogPane}.
+ * @deprecated
  */
+@Deprecated
 public class FragmentByIdDialog extends DefaultNodeSettingsPane {
 	private PythonOptionsPanel<FragmentsByIdConfig> pythonOptions;
 

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdFactory.java

@@ -7,7 +7,9 @@
 /**
  * <code>NodeFactory</code> for the "FragmentBySimilarity" Node.
  *
+ * @deprecated
  */
+@Deprecated
 public class FragmentByIdFactory extends NodeFactory<FragmentByIdModel> {
 
 	/**

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdFactory.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<knimeNode icon="./default.png" type="Manipulator"
+<knimeNode icon="./default.png" type="Manipulator" deprecated="true"
 	xmlns="http://knime.org/node/v2.8" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://knime.org/node/v2.10 http://knime.org/node/v2.10.xsd">
 	<name>Fragment information (local files)</name>
@@ -22,7 +22,7 @@
 				Information includes the fragment molecule and it's associated protein
 				identifiers.
 			</p>
-			<h2>Resolving "Library kripodb.canned is missing" error</h2>
+			<h3>Resolving "Library kripodb.canned is missing" error</h3>
 			<p>
 				This node requires the
 				<a href="https://github.com/3D-e-Chem/kripodb">kripodb</a>
@@ -156,6 +156,4 @@
 		<outPort index="0" name="Fragment information">Table with Kripo fragment information.
 		</outPort>
 	</ports>
-	<views>
-	</views>
 </knimeNode>

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdModel.java

@@ -14,7 +14,9 @@
 /**
  * This is the model implementation of FragmentBySimilarity.
  *
+ * @deprecated
  */
+@Deprecated
 public class FragmentByIdModel extends KripoNodeModel<FragmentsByIdConfig> {
 	public FragmentByIdModel() {
 		super(new PortType[] { BufferedDataTable.TYPE }, new PortType[] { BufferedDataTable.TYPE });

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentsByIdConfig.java

@@ -13,6 +13,7 @@
 
 import nl.esciencecenter.e3dchem.kripodb.KripoPythonConfig;
 
+@Deprecated
 public class FragmentsByIdConfig extends KripoPythonConfig {
 	private static final String DEFAULT_IDTYPE = "fragment";
 	private static final String CFG_IDCOLNAME = "id_column";

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityDialog.java

@@ -24,7 +24,10 @@
  * creation of a simple dialog with standard components. If you need a more
  * complex dialog please derive directly from
  * {@link org.knime.core.node.NodeDialogPane}.
+ * 
+ * @deprecated
  */
+@Deprecated
 public class FragmentBySimilarityDialog extends DefaultNodeSettingsPane {
 	private PythonOptionsPanel<FragmentsBySimilarityConfig> pythonOptions;
 

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityFactory.java

@@ -7,7 +7,9 @@
 /**
  * <code>NodeFactory</code> for the "FragmentBySimilarity" Node.
  *
+ * @deprecated
  */
+@Deprecated
 public class FragmentBySimilarityFactory extends NodeFactory<FragmentBySimilarityModel> {
 
 	/**

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityFactory.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<knimeNode icon="./default.png" type="Manipulator"
+<knimeNode icon="./default.png" type="Manipulator" deprecated="true"
 	xmlns="http://knime.org/node/v2.8" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://knime.org/node/v2.10 http://knime.org/node/v2.10.xsd">
 	<name>Similar fragments (local files)</name>
@@ -22,7 +22,7 @@
 				subpocket associated with the query fragment based on the fingerprint
 				similarity matrix.
 			</p>
-			<h2>Resolving "Library kripodb.canned is missing" error</h2>
+			<h3>Resolving "Library kripodb.canned is missing" error</h3>
 			<p>
 				This node requires the
 				<a href="https://github.com/3D-e-Chem/kripodb">kripodb</a>
@@ -128,6 +128,4 @@
 			and scores vs the input table.
 		</outPort>
 	</ports>
-	<views>
-	</views>
 </knimeNode>

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresConfig.java

@@ -11,6 +11,7 @@
 
 import nl.esciencecenter.e3dchem.kripodb.KripoPythonConfig;
 
+@Deprecated
 public class PharmacophoresConfig extends KripoPythonConfig {
 	private static final String CFG_IDCOLNAME = "id_column";
 	private static final String CFG_PHARMACOPHORESDB = "pharmacophoresdb";

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresDialog.java

@@ -14,6 +14,7 @@
 import nl.esciencecenter.e3dchem.kripodb.ws.WsNodeDialog;
 import nl.esciencecenter.e3dchem.python.PythonOptionsPanel;
 
+@Deprecated
 public class PharmacophoresDialog extends WsNodeDialog {
 	private PythonOptionsPanel<PharmacophoresConfig> pythonOptions;
 

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresFactory.java

@@ -4,6 +4,7 @@
 import org.knime.core.node.NodeFactory;
 import org.knime.core.node.NodeView;
 
+@Deprecated
 public class PharmacophoresFactory extends NodeFactory<PharmacophoresModel> {
 
 	@Override

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresFactory.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<knimeNode icon="./default.png" type="Manipulator"
+<knimeNode icon="./default.png" type="Manipulator" deprecated="true"
 	xmlns="http://knime.org/node/v2.8" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://knime.org/node/v2.10 http://knime.org/node/v2.10.xsd">
 	<name>Pharmacophore (local files)</name>
@@ -18,7 +18,7 @@
 			<p>
 				Retrieve Kripo pharmacophores from local Kripo pharmacophores database file.
 			</p>
-			<h2>Resolving "Library kripodb.canned is missing" error</h2>
+			<h3>Resolving "Library kripodb.canned is missing" error</h3>
 			<p>
 				This node requires the
 				<a href="https://github.com/3D-e-Chem/kripodb">kripodb</a>
@@ -116,6 +116,4 @@
 		<outPort index="0" name="Fragment pharmacophore">Table with Kripo fragment pharmacophore.
 		</outPort>
 	</ports>
-	<views>
-	</views>
 </knimeNode>

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresModel.java

@@ -11,6 +11,7 @@
 
 import nl.esciencecenter.e3dchem.kripodb.KripoNodeModel;
 
+@Deprecated
 public class PharmacophoresModel extends KripoNodeModel<PharmacophoresConfig> {
 
 	public PharmacophoresModel() {

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/fragments/FragmentByIdFactory.xml

@@ -26,11 +26,14 @@
 				files are from the same dataset.
 			</p>
 			<p>The public <a href="http://3d-e-chem.vu-compmedchem.nl/kripodb">web service</a> most recent data update was <a href="http://3d-e-chem.vu-compmedchem.nl/kripodb/version.txt">on</a>.</p>
+			<p>Instead of using the public kripo webservice it is also possible to <a href="https://github.com/3D-e-Chem/kripodb#web-service">run a local web service</a>.</p>
 		</intro>
-
-		<option name="Identifiers">The column containing the Kripo identifiers
-		</option>
-		<option name="Type of identifier">Can be fragment or PDB code.</option>
+
+		<tab name="Options">
+			<option name="Identifiers">The column containing the Kripo identifiers
+			</option>
+			<option name="Type of identifier">Can be fragment or PDB code.</option>
+		</tab>
 		<tab name="Advanced Options">
 			<option name="Base path">Url to use as base path for Kripo webservice
 			</option>
@@ -48,6 +51,4 @@
 		<outPort index="0" name="Fragment information">Table with Kripo fragment information.
 		</outPort>
 	</ports>
-	<views>
-	</views>
 </knimeNode>

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/fragmentsbysimilarity/FragmentBySimilarityFactory.xml

@@ -26,13 +26,16 @@
 				files are from the same dataset.
 			</p>
 			<p>The public <a href="http://3d-e-chem.vu-compmedchem.nl/kripodb">web service</a> most recent data update was <a href="http://3d-e-chem.vu-compmedchem.nl/kripodb/version.txt">on</a>.</p>
+			<p>Instead of using the public kripo webservice it is also possible to <a href="https://github.com/3D-e-Chem/kripodb#web-service">run a local web service</a>.</p>
 		</intro>
-		<option name="Fragment identifiers">The column containing the Kripo fragment
-			identifiers
-		</option>
-		<option name="Cutoff">Cutoff, scores below cutoff are discarded.
-		</option>
-		<option name="Limit">Maximum number of hits for each query.</option>
+		<tab name="Options">
+			<option name="Fragment identifiers">The column containing the Kripo fragment
+				identifiers
+			</option>
+			<option name="Cutoff">Cutoff, scores below cutoff are discarded.
+			</option>
+			<option name="Limit">Maximum number of hits for each query.</option>
+		</tab>
 		<tab name="Advanced Options">
 			<option name="Base path">Url to use as base path for Kripo webservice
 			</option>
@@ -48,6 +51,4 @@
 			and scores vs the input table.
 		</outPort>
 	</ports>
-	<views>
-	</views>
 </knimeNode>

plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/pharmacophores/PharmacophoresFactory.xml

@@ -19,10 +19,13 @@
 				Retrieve Kripo pharmacophores.
 			</p>
 			<p>The public <a href="http://3d-e-chem.vu-compmedchem.nl/kripodb">web service</a> most recent data update was <a href="http://3d-e-chem.vu-compmedchem.nl/kripodb/version.txt">on</a>.</p>
+			<p>Instead of using the public kripo webservice it is also possible to <a href="https://github.com/3D-e-Chem/kripodb#web-service">run a local web service</a>.</p>
 		</intro>
 
-		<option name="Kripo Fragment Identifiers">The column containing the Kripo identifiers
-		</option>
+		<tab name="Options">
+			<option name="Kripo Fragment Identifiers">The column containing the Kripo identifiers
+			</option>
+		</tab>
 		<tab name="Advanced Options">
 			<option name="Base path">Url to use as base path for Kripo webservice
 			</option>
@@ -37,6 +40,4 @@
 		<outPort index="0" name="Fragment pharmacophore">Table with Kripo fragment pharmacophore.
 		</outPort>
 	</ports>
-	<views>
-	</views>
 </knimeNode>

pom.xml

@@ -5,7 +5,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>nl.esciencecenter.e3dchem.kripodb</groupId>
 	<artifactId>nl.esciencecenter.e3dchem.kripodb</artifactId>
-	<version>2.4.2-SNAPSHOT</version>
+	<version>2.5.0-SNAPSHOT</version>
 	<packaging>pom</packaging>
 
 	<organization>

targetplatform/KNIME-AP-4.0.target

@@ -15,6 +15,7 @@
 <unit id="org.knime.features.xml.feature.group" version="0.0.0"/>
 <unit id="org.knime.features.chem.types.feature.group" version="0.0.0"/>
 <unit id="org.knime.features.python2.feature.group" version="0.0.0"/>
+<unit id="org.knime.features.ext.chromium.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>
@@ -23,6 +24,7 @@
 		<unit id="nl.esciencecenter.e3dchem.plugin" version="0.0.0"/>
 		<unit id="nl.esciencecenter.e3dchem.python.plugin" version="0.0.0"/>
 		<unit id="nl.esciencecenter.e3dchem.knime.pharmacophore.plugin" version="0.0.0"/>
+		<unit id="nl.esciencecenter.e3dchem.knime.molviewer.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">
@@ -46,4 +48,4 @@
 -Dsun.net.client.defaultReadTimeout=0
 -Dorg.eclipse.swt.internal.gtk.disablePrinting</vmArgs>
 </launcherArgs>
-</target>
+</target>

targetplatform/pom.xml

@@ -20,7 +20,7 @@ Contributors:
 	<parent>
 		<artifactId>nl.esciencecenter.e3dchem.kripodb</artifactId>
 		<groupId>nl.esciencecenter.e3dchem.kripodb</groupId>
-		<version>2.4.2-SNAPSHOT</version>
+		<version>2.5.0-SNAPSHOT</version>
 	</parent>
 
 </project>

tests/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Tests
 Bundle-SymbolicName: nl.esciencecenter.e3dchem.kripodb.tests
-Bundle-Version: 2.4.2.qualifier
+Bundle-Version: 2.5.0.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: org.junit,
  org.knime.core;bundle-version="[4.0.0,5.0.0)",