Merge pull request #22 from 3D-e-Chem/ws-only-nodes

Create Python and Swagger based implementation of nodes

.gitignore

@@ -15,3 +15,4 @@ target
 .classpath
 
 swagger-codegen-cli-*.jar
+/client

CHANGELOG.md

@@ -5,6 +5,16 @@ Formatted as described on http://keepachangelog.com/
 
 ## Unreleased
 
+## [2.2.0] - 2017-03-05
+
+### Added
+
+- Pure Java nodes to fetch fragment information and similarites from web service (#17) 
+
+## Changed
+
+- Python nodes only work for local files, no longer for web service urls
+
 ## [2.1.5] - 2017-03-01
 
 Requires KripoDB v2.2.0 or higher.

README.md

@@ -1,5 +1,7 @@
 # KripoDB KNIME nodes
 
+KRIPO stands for [Key Representation of Interaction in POckets](http://dx.doi.org/10.1186/1758-2946-6-S1-O26).
+
 [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)
@@ -13,7 +15,12 @@
 Requirements:
 
 * KNIME, https://www.knime.org
-* KripoDB Python package & optional data files, https://github.com/3D-e-Chem/kripodb
+
+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.
 
 Steps to get KripoDB nodes inside KNIME:
 
@@ -80,23 +87,60 @@ Tests in `tests` module will have been run with results in `test/target/surefire
 There are unit tests and workflow tests both are executed in the KNIME eclipse application.
 See https://github.com/3D-e-Chem/knime-testflow for more information about workflow tests.
 
+# Create web service client
+
+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
+```
+kripodb serve data/similarities.frozen.h5 data/fragments.sqlite
+```
+
+2. Download swagger code generator
+```
+wget http://repo1.maven.org/maven2/io/swagger/swagger-codegen-cli/2.2.2/swagger-codegen-cli-2.2.2.jar
+```
+
+3. Generate a client for KripoDB web service
+```
+java -jar swagger-codegen-cli-2.2.2.jar generate \
+--input-spec http://localhost:8084/kripo/swagger.json \
+--output client \
+--lang java \
+--config swagger-codegen.config.json
+```
+
+4. Compile client
+```
+cd client
+mvn package
+```
+
+5. Populate plugin with client source code and dependencies
+```
+mkdir ../plugin/lib
+cp target/lib/gson-* target/lib/logging-interceptor-* target/lib/ok* target/lib/swagger-annotations-* ../plugin/lib/
+cp -r src/main/java/nl/esciencecenter/e3dchem/kripodb/ws/client ../plugin/src/java/nl/esciencecenter/e3dchem/kripodb/ws/
+```
+
+6. Update plugin/META-INF/MANIFEST.MF, plugin/build.properties files to reflect contents of lib/
+
 ## New release
 
-1. Update versions in pom files with `mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version>` command.
-2. Manually update version of "source" feature in `p2/category.xml` file.
-3. Commit and push changes
-4. Create package with `mvn package`, will create update site in `p2/target/repository`
-5. Test node by installing it from local update site
-4. Append new release to 3D-e-Chem update site
+1. Update versions in pom files with `mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version>-SNAPSHOT` command.
+2. Commit and push changes
+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>`
-5. Commit and push changes in this repo and 3D-e-Chem.github.io repo
-6. Create a Github release
-7. Update Zenodo entry
+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. Fix authors
   2. Fix license
   3. To Related/alternate identifiers section add http://dx.doi.org/10.1186/1758-2946-6-S1-O26 as `is cited by this upload` entry.
-8. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release
+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
 
 # Create stub recordings for integration tests
 

feature/feature.xml

@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <feature
       id="nl.esciencecenter.e3dchem.kripodb.feature"
-      label="KripoDB nodes for Knime"
-      version="2.1.5"
+      label="KripoDB nodes for KNIME"
+      version="2.2.0.qualifier"
       provider-name="Netherlands eScience Center">
 
    <description url="https://github.com/3D-e-Chem/knime-kripodb">
-      Knimes nodes for interacting with Kripo data files.
+      KNIME nodes for interacting with Kripo data files.
    </description>
 
    <copyright url="https://www.esciencecenter.nl">

feature/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.kripodb</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.kripodb</artifactId>
-		<version>2.1.5</version>
+		<version>2.2.0-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>nl.esciencecenter.e3dchem.kripodb.feature</artifactId>

p2/category.xml

@@ -1,19 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <site>
-   <feature url="features/nl.esciencecenter.e3dchem.kripodb.feature-2.1.5.jar" id="nl.esciencecenter.e3dchem.kripodb.feature" version="2.1.5">
+   <feature url="features/nl.esciencecenter.e3dchem.kripodb.feature-2.2.0.qualifier.jar" id="nl.esciencecenter.e3dchem.kripodb.feature" version="2.2.0.qualifier">
       <category name="nl.esciencecenter.3D-e-Chem"/>
    </feature>
-   <feature url="features/nl.esciencecenter.e3dchem.kripodb.feature.source_2.1.5.jar" id="nl.esciencecenter.e3dchem.kripodb.feature.source" version="2.1.5">
-      <category name="nl.esciencecenter.3D-e-Chem.sources"/>
-   </feature>
    <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

@@ -3,7 +3,7 @@
     <parent>
         <artifactId>nl.esciencecenter.e3dchem.kripodb</artifactId>
         <groupId>nl.esciencecenter.e3dchem.kripodb</groupId>
-        <version>2.1.5</version>
+        <version>2.2.0-SNAPSHOT</version>
     </parent>
     <artifactId>nl.esciencecenter.e3dchem.kripodb.p2</artifactId>
     <packaging>eclipse-repository</packaging>

plugin/META-INF/MANIFEST.MF

@@ -2,18 +2,24 @@ 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: 2.1.5
+Bundle-Version: 2.2.0.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Bundle-Activator: nl.esciencecenter.e3dchem.kripodb.Activator
 Require-Bundle: org.knime.core;bundle-version="[3.1.0,4.0.0)",
  org.knime.base;bundle-version="[3.1.0,4.0.0)",
  org.knime.python;bundle-version="[3.1.0,4.0.0)",
+ org.knime.chem.types;bundle-version="[3.1.0,4.0.0)",
  org.rdkit.knime.types;bundle-version="[3.0.0,4.0.0)",
  nl.esciencecenter.e3dchem.python.plugin;bundle-version="[1.1.0,2.0.0)",
  nl.esciencecenter.e3dchem.plugin;bundle-version="[1.0.0,2.0.0)"
 Bundle-Vendor: Netherlands eScience Center
 Bundle-ActivationPolicy: lazy
-Bundle-ClassPath: .
+Bundle-ClassPath: lib/gson-2.6.2.jar,
+ lib/logging-interceptor-2.7.5.jar,
+ lib/okhttp-2.7.5.jar,
+ lib/okio-1.6.0.jar,
+ lib/swagger-annotations-1.5.12.jar,
+ .
 Export-Package: nl.esciencecenter.e3dchem.kripodb,
  nl.esciencecenter.e3dchem.kripodb.fragments,
  nl.esciencecenter.e3dchem.kripodb.fragmentsbysimilarity

plugin/build.properties

@@ -2,4 +2,9 @@ source.. = src/java/
 output.. = target/classes/
 bin.includes = META-INF/,\
                .,\
-               plugin.xml
+               plugin.xml,\
+               lib/gson-2.6.2.jar,\
+               lib/logging-interceptor-2.7.5.jar,\
+               lib/okhttp-2.7.5.jar,\
+               lib/okio-1.6.0.jar,\
+               lib/swagger-annotations-1.5.12.jar

plugin/plugin.xml

@@ -9,20 +9,35 @@
           locked="false"
           name="KripoDB"
           path="/community/3d-e-chem"/>
-  </extension>
+    <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">
         <node
                category-path="/community/3d-e-chem/kripodb"
                deprecated="false"
-               factory-class="nl.esciencecenter.e3dchem.kripodb.fragmentsbysimilarity.FragmentBySimilarityFactory"
-               id="nl.esciencecenter.e3dchem.kripodb.fragmentsbysimilarity.FragmentBySimilarityFactory">
+               factory-class="nl.esciencecenter.e3dchem.kripodb.ws.fragmentsbysimilarity.FragmentBySimilarityFactory">
         </node>
         <node
                category-path="/community/3d-e-chem/kripodb"
                deprecated="false"
-               factory-class="nl.esciencecenter.e3dchem.kripodb.fragments.FragmentByIdFactory"
-               id="nl.esciencecenter.e3dchem.kripodb.fragments.FragmentByIdFactory">
+               factory-class="nl.esciencecenter.e3dchem.kripodb.ws.fragments.FragmentByIdFactory">
+        </node>
+        <node
+               category-path="/community/3d-e-chem/kripodb/local"
+               deprecated="false"
+               factory-class="nl.esciencecenter.e3dchem.kripodb.fragmentsbysimilarity.FragmentBySimilarityFactory">
+        </node>
+        <node
+               category-path="/community/3d-e-chem/kripodb/local"
+               deprecated="false"
+               factory-class="nl.esciencecenter.e3dchem.kripodb.fragments.FragmentByIdFactory">
         </node>
     </extension>
 </plugin>

plugin/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>nl.esciencecenter.e3dchem.kripodb</groupId>
 		<artifactId>nl.esciencecenter.e3dchem.kripodb</artifactId>
-		<version>2.1.5</version>
+		<version>2.2.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>nl.esciencecenter.e3dchem.kripodb.plugin</artifactId>
 	<packaging>eclipse-plugin</packaging>

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

@@ -2,38 +2,60 @@
 <knimeNode icon="./default.png" type="Manipulator"
 	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</name>
+	<name>Fragment information (local files)</name>
 
 	<shortDescription>
 		Find Kripo fragment information by their identifier.
 	</shortDescription>
 
 	<fullDescription>
-		<intro>Find Kripo fragment information by their identifier.
-		<p>
-		Information includes the fragment molecule and it's associated protein identifiers.
-		</p>
-		<h2>Resolving "'kripodb' Python package not found" error</h2>
-		<p>This node requires the <a href="https://github.com/3D-e-Chem/kripodb">kripodb</a> Python package.</p>
-		<p>
-		If the kripodb Python package was not installed then go to <a href="https://github.com/3D-e-Chem/kripodb#install">https://github.com/3D-e-Chem/kripodb#install</a> and follow the installation instructions.
-		To test if the package is installed run <i>kripodb --version</i> on the command line, it should print a version number if installed.
-		</p>
-		<p>
-		If the kripodb Python package was already installed then make sure that KNIME is using the same Python executable.
-		In the File menu > Preferences > KNIME > Python make sure the path to the Python executable is the same Python which has the kripodb package installed.
-		</p>
+		<intro>
+			<p>
+				KRIPO stands for
+				<a href="http://dx.doi.org/10.1186/1758-2946-6-S1-O26">Key Representation of Interaction in POckets</a>
+				.
+			</p>
+			<p>
+				Find Kripo fragment information by their identifier.
+			</p>
+			<p>
+				Information includes the fragment molecule and it's associated protein
+				identifiers.
+			</p>
+			<h2>Resolving "'kripodb' Python package not found" error</h2>
+			<p>
+				This node requires the
+				<a href="https://github.com/3D-e-Chem/kripodb">kripodb</a>
+				Python package.
+			</p>
+			<p>
+				If the kripodb Python package was not installed then go to
+				<a href="https://github.com/3D-e-Chem/kripodb#install">https://github.com/3D-e-Chem/kripodb#install</a>
+				and follow the installation instructions.
+				To test if the package is installed run
+				<i>kripodb --version</i>
+				on the command line, it should print a version number if installed.
+			</p>
+			<p>
+				If the kripodb Python package was already installed then make sure
+				that KNIME is using the same Python executable.
+				In the File menu > Preferences > KNIME > Python make sure the path to
+				the Python executable is the same Python which has the kripodb
+				package installed.
+			</p>
 		</intro>
 
 		<option name="Identifiers">The column containing the Kripo identifiers
 		</option>
 		<option name="Fragments database (Selected File)">
-			Location of Kripo fragments database, can be the base url of kripodb webservice or a local SQLite file.
+			Location of Kripo fragments database, can be the base url of kripodb
+			webservice or a local SQLite file.
 			<p>
 				Available datasets:
 				<ul>
 					<li>
-						Protein Data Bank, use web service at <a href="http://3d-e-chem.vu-compmedchem.nl/kripodb">http://3d-e-chem.vu-compmedchem.nl/kripodb</a>
+						Protein Data Bank, use web service at
+						<a href="http://3d-e-chem.vu-compmedchem.nl/kripodb">http://3d-e-chem.vu-compmedchem.nl/kripodb</a>
 						or download from
 						<a href="http://3d-e-chem.vu-compmedchem.nl/kripodb/fragments.sqlite">here</a>
 						, in 3D-e-Chem VM available at '/data/kripo/pdb/fragments.sqlite'
@@ -55,7 +77,13 @@
 			<p>When combining this node with other Kripo nodes make sure the
 				files are from the same dataset.
 			</p>
-			<p>For example getting a <b>KeyError: '&lt;fragment id&gt;' not found</b> error most likely means the '/data/kripo/pdb/fragments.sqlite' file is out of sync and must be re-downloaded from <a href="http://3d-e-chem.vu-compmedchem.nl/kripodb/fragments.sqlite">here</a></p>
+			<p>
+				For example getting a
+				<b>KeyError: '&lt;fragment id&gt;' not found</b>
+				error most likely means the '/data/kripo/pdb/fragments.sqlite' file
+				is out of sync and must be re-downloaded from
+				<a href="http://3d-e-chem.vu-compmedchem.nl/kripodb/fragments.sqlite">here</a>
+			</p>
 		</option>
 		<option name="Type of identifier">Can be fragment or PDB code.</option>
 	</fullDescription>