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.kripodb nl.esciencecenter.e3dchem.kripodb - 2.4.2-SNAPSHOT + 2.5.0-SNAPSHOT nl.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.kripodb nl.esciencecenter.e3dchem.kripodb - 2.4.2-SNAPSHOT + 2.5.0-SNAPSHOT nl.esciencecenter.e3dchem.kripodb.p2 eclipse-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.kripodb nl.esciencecenter.e3dchem.kripodb - 2.4.2-SNAPSHOT + 2.5.0-SNAPSHOT nl.esciencecenter.e3dchem.kripodb.plugin eclipse-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.

- + + + @@ -37,6 +40,4 @@ Table with Kripo fragment pharmacophore. - - diff --git a/pom.xml b/pom.xml index c4d836a..3754d68 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ 4.0.0 nl.esciencecenter.e3dchem.kripodb nl.esciencecenter.e3dchem.kripodb - 2.4.2-SNAPSHOT + 2.5.0-SNAPSHOT pom diff --git a/targetplatform/KNIME-AP-4.0.target b/targetplatform/KNIME-AP-4.0.target index 8abeb8f..ae3db94 100644 --- a/targetplatform/KNIME-AP-4.0.target +++ b/targetplatform/KNIME-AP-4.0.target @@ -15,6 +15,7 @@ + @@ -23,6 +24,7 @@ + @@ -46,4 +48,4 @@ -Dsun.net.client.defaultReadTimeout=0 -Dorg.eclipse.swt.internal.gtk.disablePrinting - + \ No newline at end of file diff --git a/targetplatform/pom.xml b/targetplatform/pom.xml index 7b9962b..dee4a8e 100644 --- a/targetplatform/pom.xml +++ b/targetplatform/pom.xml @@ -20,7 +20,7 @@ Contributors: nl.esciencecenter.e3dchem.kripodb nl.esciencecenter.e3dchem.kripodb - 2.4.2-SNAPSHOT + 2.5.0-SNAPSHOT diff --git a/tests/META-INF/MANIFEST.MF b/tests/META-INF/MANIFEST.MF index b6f2bd9..f793585 100644 --- a/tests/META-INF/MANIFEST.MF +++ b/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)", diff --git a/tests/pom.xml b/tests/pom.xml index ba88711..5764a11 100644 --- a/tests/pom.xml +++ b/tests/pom.xml @@ -5,7 +5,7 @@ nl.esciencecenter.e3dchem.kripodb nl.esciencecenter.e3dchem.kripodb - 2.4.2-SNAPSHOT + 2.5.0-SNAPSHOT nl.esciencecenter.e3dchem.kripodb.tests