Added a method to create a data set from a list of materials

bioclipse · Sep 11, 2013 · e0eda80 · e0eda80
1 parent b40f764
commit e0eda80
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Showing 4 changed files with 84 additions and 2 deletions.
diff --git a/plugins/net.bioclipse.opentox.nm/META-INF/MANIFEST.MF b/plugins/net.bioclipse.opentox.nm/META-INF/MANIFEST.MF
@@ -14,7 +14,9 @@ Require-Bundle: org.eclipse.ui,
  org.springframework.osgi.aopalliance.osgi,
  net.bioclipse.rdf,
  net.bioclipse.business,
- net.bioclipse.usermanager
+ net.bioclipse.usermanager,
+ net.bioclipse.nm,
+ net.bioclipse.opentox
 Bundle-RequiredExecutionEnvironment: JavaSE-1.7
 Import-Package: org.apache.log4j
 Bundle-ActivationPolicy: lazy
diff --git a/plugins/net.bioclipse.opentox.nm/src/net/bioclipse/opentox/nm/api/Dataset.java b/plugins/net.bioclipse.opentox.nm/src/net/bioclipse/opentox/nm/api/Dataset.java
@@ -0,0 +1,48 @@
+/* Copyright (C) 2013  Egon Willighagen <egonw@users.sf.net>
+ * 
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2.1 of the License, or (at your option)
+ * any later version. All we ask is that proper credit is given for our work,
+ * which includes - but is not limited to - adding the above copyright notice to
+ * the beginning of your source code files, and to any copyright notice that you
+ * may distribute with programs based on this work.
+ * 
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+ * details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation, Inc.,
+ * 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package net.bioclipse.opentox.nm.api;
+
+import java.util.List;
+
+import net.bioclipse.core.domain.IMaterial;
+import net.bioclipse.nm.business.NmManager;
+
+import org.eclipse.core.runtime.IProgressMonitor;
+
+public class Dataset {
+
+	private static NmManager nm = new NmManager();
+
+	public static String createNewDataset(String service,
+		List<IMaterial> materials, IProgressMonitor monitor)
+	throws Exception {
+		String nmxContent = nm.asNMX(materials);
+		return net.bioclipse.opentox.api.Dataset.createNewDataset(
+			normalizeURI(service), nmxContent, monitor
+		);
+	}
+
+	public static String normalizeURI(String datasetURI) {
+		datasetURI = datasetURI.replaceAll("\\n", "");
+		datasetURI = datasetURI.replaceAll("\\r", "");
+		if (!datasetURI.endsWith("/")) datasetURI += "/";
+		return datasetURI;
+	}
+}
diff --git a/...ins/net.bioclipse.opentox.nm/src/net/bioclipse/opentox/nm/business/IOpenToxNmManager.java b/...ins/net.bioclipse.opentox.nm/src/net/bioclipse/opentox/nm/business/IOpenToxNmManager.java
@@ -10,10 +10,14 @@
  ******************************************************************************/
 package net.bioclipse.opentox.nm.business;
 
+import java.util.List;
+
 import net.bioclipse.core.PublishedClass;
 import net.bioclipse.core.PublishedMethod;
 import net.bioclipse.core.Recorded;
 import net.bioclipse.core.business.BioclipseException;
+import net.bioclipse.core.domain.IMaterial;
+import net.bioclipse.jobs.BioclipseUIJob;
 import net.bioclipse.managers.business.IBioclipseManager;
 
 @PublishedClass(
@@ -29,4 +33,11 @@ public interface IOpenToxNmManager extends IBioclipseManager {
     )
     public String downloadMaterialAsNMXFile(String materialURI) throws BioclipseException;
 
+    @Recorded
+    @PublishedMethod(
+        methodSummary="Creates a new dataset.",
+        params="String service, List<? extends IMaterial>  materials"
+    )
+    public String createDataset(String service, List<? extends IMaterial>  materials) throws BioclipseException;
+    public void createDataset(String service, List<? extends IMaterial> materials, BioclipseUIJob<String> uiJob) throws BioclipseException;
 }
diff --git a/plugins/net.bioclipse.opentox.nm/src/net/bioclipse/opentox/nm/business/OpenToxNmManager.java b/plugins/net.bioclipse.opentox.nm/src/net/bioclipse/opentox/nm/business/OpenToxNmManager.java
@@ -10,9 +10,14 @@
  ******************************************************************************/
 package net.bioclipse.opentox.nm.business;
 
+import java.util.List;
+
 import net.bioclipse.business.BioclipsePlatformManager;
 import net.bioclipse.core.business.BioclipseException;
+import net.bioclipse.core.domain.IMaterial;
+import net.bioclipse.jobs.IReturner;
 import net.bioclipse.managers.business.IBioclipseManager;
+import net.bioclipse.opentox.nm.api.Dataset;
 
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.NullProgressMonitor;
@@ -33,7 +38,23 @@ public String downloadMaterialAsNMXFile(String materialURI, IProgressMonitor mon
 
     	return result;
     }
-
+
+    public void createDataset(String service, List<IMaterial> materials, IReturner<String> returner, IProgressMonitor monitor)
+    throws BioclipseException {
+    	if (monitor == null) monitor = new NullProgressMonitor();
+
+    	monitor.beginTask("Creating an OpenTox API data set ...", 1);
+    	try {
+			String dataset = Dataset.createNewDataset(service, materials, monitor);
+			monitor.done();
+			returner.completeReturn( dataset ); 
+		} catch (Exception exc) {
+			throw new BioclipseException(
+				"Exception while creating dataset: " + exc.getMessage()
+			);
+		}
+    }
+
     /**
      * Gives a short one word name of the manager used as variable name when
      * scripting.