diff --git a/CHANGELOG.md b/CHANGELOG.md
index e869497..edf782e 100644
--- a/CHANGELOG.md
+++ b/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
diff --git a/README.md b/README.md
index c328518..e864eaa 100644
--- a/README.md
+++ b/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:
diff --git a/examples/Knime-KripoDB-example.knwf b/examples/Knime-KripoDB-example.knwf
new file mode 100644
index 0000000..b79dbcf
Binary files /dev/null and b/examples/Knime-KripoDB-example.knwf differ
diff --git a/examples/Knime-KripoDB-example.zip b/examples/Knime-KripoDB-example.zip
deleted file mode 100644
index b768d6b..0000000
Binary files a/examples/Knime-KripoDB-example.zip and /dev/null differ
diff --git a/feature/feature.xml b/feature/feature.xml
index 6c671f3..5a142e6 100644
--- a/feature/feature.xml
+++ b/feature/feature.xml
@@ -2,7 +2,7 @@
diff --git a/feature/pom.xml b/feature/pom.xml
index b26b35c..0507d84 100644
--- a/feature/pom.xml
+++ b/feature/pom.xml
@@ -6,7 +6,7 @@
nl.esciencecenter.e3dchem.kripodbnl.esciencecenter.e3dchem.kripodb
- 2.4.2-SNAPSHOT
+ 2.5.0-SNAPSHOTnl.esciencecenter.e3dchem.kripodb.feature
diff --git a/p2/category.xml b/p2/category.xml
index e572222..ed4c98c 100644
--- a/p2/category.xml
+++ b/p2/category.xml
@@ -1,6 +1,6 @@
-
+
diff --git a/p2/pom.xml b/p2/pom.xml
index c6e5b0d..e32323c 100644
--- a/p2/pom.xml
+++ b/p2/pom.xml
@@ -3,7 +3,7 @@
nl.esciencecenter.e3dchem.kripodbnl.esciencecenter.e3dchem.kripodb
- 2.4.2-SNAPSHOT
+ 2.5.0-SNAPSHOTnl.esciencecenter.e3dchem.kripodb.p2eclipse-repository
diff --git a/plugin/META-INF/MANIFEST.MF b/plugin/META-INF/MANIFEST.MF
index 3a62e2f..c42f35c 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: 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)",
diff --git a/plugin/plugin.xml b/plugin/plugin.xml
index 6066945..aa74508 100644
--- a/plugin/plugin.xml
+++ b/plugin/plugin.xml
@@ -36,17 +36,17 @@
diff --git a/plugin/pom.xml b/plugin/pom.xml
index bc1bc20..1c732ae 100644
--- a/plugin/pom.xml
+++ b/plugin/pom.xml
@@ -6,7 +6,7 @@
nl.esciencecenter.e3dchem.kripodbnl.esciencecenter.e3dchem.kripodb
- 2.4.2-SNAPSHOT
+ 2.5.0-SNAPSHOTnl.esciencecenter.e3dchem.kripodb.plugineclipse-plugin
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdDialog.java b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdDialog.java
index d1d0dd3..2946d89 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdDialog.java
+++ b/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 pythonOptions;
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdFactory.java b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdFactory.java
index 96cb59a..99fcc4a 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdFactory.java
+++ b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdFactory.java
@@ -7,7 +7,9 @@
/**
* NodeFactory for the "FragmentBySimilarity" Node.
*
+ * @deprecated
*/
+@Deprecated
public class FragmentByIdFactory extends NodeFactory {
/**
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdFactory.xml b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdFactory.xml
index a80cdfa..dc29cfe 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdFactory.xml
+++ b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdFactory.xml
@@ -1,5 +1,5 @@
-Fragment information (local files)
@@ -22,7 +22,7 @@
Information includes the fragment molecule and it's associated protein
identifiers.
-
Resolving "Library kripodb.canned is missing" error
+
Resolving "Library kripodb.canned is missing" error
This node requires the
kripodb
@@ -156,6 +156,4 @@
Table with Kripo fragment information.
-
-
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdModel.java b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdModel.java
index f213535..f5c4f88 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentByIdModel.java
+++ b/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 {
public FragmentByIdModel() {
super(new PortType[] { BufferedDataTable.TYPE }, new PortType[] { BufferedDataTable.TYPE });
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentsByIdConfig.java b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentsByIdConfig.java
index 5f5d264..1ff550b 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragments/FragmentsByIdConfig.java
+++ b/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";
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityDialog.java b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityDialog.java
index 8a34022..5cb2a61 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityDialog.java
+++ b/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 pythonOptions;
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityFactory.java b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityFactory.java
index 550479b..0ac06b6 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityFactory.java
+++ b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityFactory.java
@@ -7,7 +7,9 @@
/**
* NodeFactory for the "FragmentBySimilarity" Node.
*
+ * @deprecated
*/
+@Deprecated
public class FragmentBySimilarityFactory extends NodeFactory {
/**
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityFactory.xml b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityFactory.xml
index cc22ec8..8e3668f 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityFactory.xml
+++ b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/fragmentsbysimilarity/FragmentBySimilarityFactory.xml
@@ -1,5 +1,5 @@
-Similar fragments (local files)
@@ -22,7 +22,7 @@
subpocket associated with the query fragment based on the fingerprint
similarity matrix.
-
Resolving "Library kripodb.canned is missing" error
+
Resolving "Library kripodb.canned is missing" error
This node requires the
kripodb
@@ -128,6 +128,4 @@
and scores vs the input table.
-
-
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresConfig.java b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresConfig.java
index 2614097..aaa02ad 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresConfig.java
+++ b/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";
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresDialog.java b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresDialog.java
index 8994e96..ec105ca 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresDialog.java
+++ b/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 pythonOptions;
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresFactory.java b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresFactory.java
index 1cca06f..2a02383 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresFactory.java
+++ b/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 {
@Override
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresFactory.xml b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresFactory.xml
index 6e2cef3..adb5273 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresFactory.xml
+++ b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresFactory.xml
@@ -1,5 +1,5 @@
-Pharmacophore (local files)
@@ -18,7 +18,7 @@
Retrieve Kripo pharmacophores from local Kripo pharmacophores database file.
-
Resolving "Library kripodb.canned is missing" error
+
Resolving "Library kripodb.canned is missing" error
This node requires the
kripodb
@@ -116,6 +116,4 @@
Table with Kripo fragment pharmacophore.
-
-
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresModel.java b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresModel.java
index 9348e1b..d925e4f 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/local/pharmacophores/PharmacophoresModel.java
+++ b/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 {
public PharmacophoresModel() {
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/fragments/FragmentByIdFactory.xml b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/fragments/FragmentByIdFactory.xml
index feff351..171c14d 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/fragments/FragmentByIdFactory.xml
+++ b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/fragments/FragmentByIdFactory.xml
@@ -26,11 +26,14 @@
files are from the same dataset.
The public web service most recent data update was on.
+
Instead of using the public kripo webservice it is also possible to run a local web service.
-
-
-
+
+
+
+
+
@@ -48,6 +51,4 @@
Table with Kripo fragment information.
-
-
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/fragmentsbysimilarity/FragmentBySimilarityFactory.xml b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/fragmentsbysimilarity/FragmentBySimilarityFactory.xml
index 2586869..f7e8ada 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/fragmentsbysimilarity/FragmentBySimilarityFactory.xml
+++ b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/fragmentsbysimilarity/FragmentBySimilarityFactory.xml
@@ -26,13 +26,16 @@
files are from the same dataset.
The public web service most recent data update was on.
+
Instead of using the public kripo webservice it is also possible to run a local web service.
-
-
-
+
+
+
+
+
@@ -48,6 +51,4 @@
and scores vs the input table.
-
-
diff --git a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/pharmacophores/PharmacophoresFactory.xml b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/pharmacophores/PharmacophoresFactory.xml
index ab71fbc..c3c94aa 100644
--- a/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/pharmacophores/PharmacophoresFactory.xml
+++ b/plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/pharmacophores/PharmacophoresFactory.xml
@@ -19,10 +19,13 @@
Retrieve Kripo pharmacophores.
The public web service most recent data update was on.
+
Instead of using the public kripo webservice it is also possible to run a local web service.