Author: kono
Date: 2011-05-03 11:15:01 -0700 (Tue, 03 May 2011)
New Revision: 24900
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/BioGridPreprocessor.java
Removed:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/BioGridPreprocessor.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessor.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/InteractionFilePreprocessor.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/PsiMiToSif.java
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/InteractionFilePreprocessor.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/PsiMiToSif.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessorTest.java
Log:
Package name had been changed.
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
2011-05-03 17:48:38 UTC (rev 24899)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
2011-05-03 18:15:01 UTC (rev 24900)
@@ -14,7 +14,7 @@
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.task.internal.loadnetwork.AbstractLoadNetworkTask;
-import
org.cytoscape.task.internal.quickstart.remote.InteractionFilePreprocessor;
+import
org.cytoscape.task.internal.quickstart.datasource.InteractionFilePreprocessor;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
2011-05-03 17:48:38 UTC (rev 24899)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
2011-05-03 18:15:01 UTC (rev 24900)
@@ -15,7 +15,7 @@
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.task.internal.loadnetwork.LoadNetworkFileTask;
import org.cytoscape.task.internal.loadnetwork.LoadNetworkURLTask;
-import
org.cytoscape.task.internal.quickstart.remote.InteractionFilePreprocessor;
+import
org.cytoscape.task.internal.quickstart.datasource.InteractionFilePreprocessor;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.Task;
Deleted:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/BioGridPreprocessor.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessor.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/BioGridPreprocessor.java
2011-05-03 18:15:01 UTC (rev 24900)
@@ -1,165 +0,0 @@
-package org.cytoscape.task.internal.quickstart.remote;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Properties;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
-
-import org.cytoscape.property.CyProperty;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class BioGridPreprocessor implements InteractionFilePreprocessor {
-
- private static final Logger logger = LoggerFactory
- .getLogger(BioGridPreprocessor.class);
-
- private static final String DB_NAME = "BioGRID";
- private static final String SOURCE_URL =
"http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.1.74/BIOGRID-ORGANISM-3.1.74.mitab.zip";;
-
- private static final String INTERACTION_DIR_NAME = "interactions";
- private static final String DEF_USER_DIR =
System.getProperty("user.home");
-
- private final PsiMiToSif p2s;
- private final File dataFileDirectory;
-
- private final Map<String, URL> sourceMap;
-
- private URL sourceFileLocation;
-
- private boolean isLatest;
-
- public BioGridPreprocessor(final CyProperty<Properties> properties) {
- this.isLatest = false;
-
- this.p2s = new PsiMiToSif();
- this.sourceMap = new HashMap<String, URL>();
- try {
- sourceFileLocation = new URL(SOURCE_URL);
- } catch (MalformedURLException e) {
- e.printStackTrace();
- }
-
- if (properties == null)
- throw new NullPointerException("Property service is
null.");
-
- final Properties props = properties.getProperties();
-
- if (props == null)
- throw new NullPointerException("Property is missing.");
-
- String configDirectory = props
- .getProperty(CyProperty.DEFAULT_CONFIG_DIR);
- if (configDirectory == null || configDirectory.trim().length()
== 0)
- configDirectory = DEF_USER_DIR;
-
- final File configFileLocation = new File(configDirectory,
- CyProperty.DEFAULT_CONFIG_DIR);
- this.dataFileDirectory = new File(configFileLocation,
- INTERACTION_DIR_NAME);
- if (!dataFileDirectory.exists())
- dataFileDirectory.mkdir();
-
- logger.debug("BioGrid interaction data directory: "
- + dataFileDirectory.toString());
- }
-
- @Override
- public void processFile(URL source) throws IOException {
- if (source != null)
- this.sourceFileLocation = source;
-
- boolean test = isUpToDate();
- System.out.println("UP2DATE = " + test);
- if (!test) {
- final InputStream is = sourceFileLocation.openStream();
- extractEntrey(is);
- }
- }
-
- private boolean isUpToDate() throws IOException {
- final File[] files = this.dataFileDirectory.listFiles();
- boolean up2date = false;
-
- for (File file : files) {
- final String name = file.getName();
- final Pattern pattern = Pattern.compile("BIOGRID");
- final Matcher matcher = pattern.matcher(name);
- boolean test = matcher.find();
- if (test) {
- up2date = true;
- this.sourceMap.put(createFileName(name),
file.toURI().toURL());
- }
- }
- return up2date;
- }
-
- private void extractEntrey(final InputStream sourceInputStream)
- throws IOException {
- ZipInputStream zis = new ZipInputStream(sourceInputStream);
- try {
-
- // Extract list of entries
- ZipEntry zen = null;
- String entryName = null;
-
- while ((zen = zis.getNextEntry()) != null) {
- entryName = zen.getName();
- System.out.println("SESSION entry name: " +
entryName);
- File outFile = new File(dataFileDirectory,
entryName + ".sif");
- outFile.createNewFile();
- FileWriter outWriter = new FileWriter(outFile);
- String line;
- final BufferedReader br = new BufferedReader(
- new InputStreamReader(zis));
-
- int count = 0;
- while ((line = br.readLine()) != null) {
- if (line.startsWith("#"))
- continue;
- outWriter.write(p2s.toSif(line) + "\n");
- count++;
- }
- zis.closeEntry();
- outWriter.close();
- this.sourceMap.put(createFileName(entryName),
outFile.toURI()
- .toURL());
- logger.debug("Entries: " + count);
- }
-
- } finally {
- if (zis != null)
- zis.close();
- zis = null;
- }
- }
-
- private String createFileName(final String originalFileName) {
- final String sourceName = DB_NAME + ": "
- + originalFileName.split("-")[2] + "
Interactome";
- return sourceName;
- }
-
- @Override
- public boolean isLatest() {
- // TODO Auto-generated method stub
- return true;
- }
-
- @Override
- public Map<String, URL> getDataSourceMap() {
- return sourceMap;
- }
-
-}
Copied:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/BioGridPreprocessor.java
(from rev 24878,
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessor.java)
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/BioGridPreprocessor.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/BioGridPreprocessor.java
2011-05-03 18:15:01 UTC (rev 24900)
@@ -0,0 +1,163 @@
+package org.cytoscape.task.internal.quickstart.datasource;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import org.cytoscape.property.CyProperty;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class BioGridPreprocessor implements InteractionFilePreprocessor {
+
+ private static final Logger logger = LoggerFactory
+ .getLogger(BioGridPreprocessor.class);
+
+ private static final String DB_NAME = "BioGRID";
+ private static final String SOURCE_URL =
"http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.1.74/BIOGRID-ORGANISM-3.1.74.mitab.zip";;
+
+ private static final String INTERACTION_DIR_NAME = "interactions";
+ private static final String DEF_USER_DIR =
System.getProperty("user.home");
+
+ private final PsiMiToSif p2s;
+ private final File dataFileDirectory;
+
+ private final Map<String, URL> sourceMap;
+
+ private URL sourceFileLocation;
+
+ private boolean isLatest;
+
+ public BioGridPreprocessor(final CyProperty<Properties> properties) {
+ this.isLatest = false;
+
+ this.p2s = new PsiMiToSif();
+ this.sourceMap = new HashMap<String, URL>();
+ try {
+ sourceFileLocation = new URL(SOURCE_URL);
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ }
+
+ if (properties == null)
+ throw new NullPointerException("Property service is
null.");
+
+ final Properties props = properties.getProperties();
+
+ if (props == null)
+ throw new NullPointerException("Property is missing.");
+
+ String configDirectory = props
+ .getProperty(CyProperty.DEFAULT_CONFIG_DIR);
+ if (configDirectory == null || configDirectory.trim().length()
== 0)
+ configDirectory = DEF_USER_DIR;
+
+ final File configFileLocation = new File(configDirectory,
+ CyProperty.DEFAULT_CONFIG_DIR);
+ this.dataFileDirectory = new File(configFileLocation,
+ INTERACTION_DIR_NAME);
+ if (!dataFileDirectory.exists())
+ dataFileDirectory.mkdir();
+
+ logger.debug("BioGrid interaction data directory: "
+ + dataFileDirectory.toString());
+ }
+
+ @Override
+ public void processFile(URL source) throws IOException {
+ if (source != null)
+ this.sourceFileLocation = source;
+
+ boolean test = isUpToDate();
+ if (!test) {
+ final InputStream is = sourceFileLocation.openStream();
+ extractEntrey(is);
+ }
+ }
+
+ private boolean isUpToDate() throws IOException {
+ final File[] files = this.dataFileDirectory.listFiles();
+ boolean up2date = false;
+
+ for (File file : files) {
+ final String name = file.getName();
+ final Pattern pattern = Pattern.compile("BIOGRID");
+ final Matcher matcher = pattern.matcher(name);
+ boolean test = matcher.find();
+ if (test) {
+ up2date = true;
+ this.sourceMap.put(createFileName(name),
file.toURI().toURL());
+ }
+ }
+ return up2date;
+ }
+
+ private void extractEntrey(final InputStream sourceInputStream)
+ throws IOException {
+ ZipInputStream zis = new ZipInputStream(sourceInputStream);
+ try {
+
+ // Extract list of entries
+ ZipEntry zen = null;
+ String entryName = null;
+
+ while ((zen = zis.getNextEntry()) != null) {
+ entryName = zen.getName();
+ File outFile = new File(dataFileDirectory,
entryName + ".sif");
+ outFile.createNewFile();
+ FileWriter outWriter = new FileWriter(outFile);
+ String line;
+ final BufferedReader br = new BufferedReader(
+ new InputStreamReader(zis));
+
+ int count = 0;
+ while ((line = br.readLine()) != null) {
+ if (line.startsWith("#"))
+ continue;
+ outWriter.write(p2s.toSif(line) + "\n");
+ count++;
+ }
+ zis.closeEntry();
+ outWriter.close();
+ this.sourceMap.put(createFileName(entryName),
outFile.toURI()
+ .toURL());
+ logger.debug("Entries: " + count);
+ }
+
+ } finally {
+ if (zis != null)
+ zis.close();
+ zis = null;
+ }
+ }
+
+ private String createFileName(final String originalFileName) {
+ final String sourceName = DB_NAME + ": "
+ + originalFileName.split("-")[2] + "
Interactome";
+ return sourceName;
+ }
+
+ @Override
+ public boolean isLatest() {
+ // TODO Auto-generated method stub
+ return true;
+ }
+
+ @Override
+ public Map<String, URL> getDataSourceMap() {
+ return sourceMap;
+ }
+
+}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/InteractionFilePreprocessor.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/InteractionFilePreprocessor.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/InteractionFilePreprocessor.java
2011-05-03 18:15:01 UTC (rev 24900)
@@ -1,4 +1,4 @@
-package org.cytoscape.task.internal.quickstart.remote;
+package org.cytoscape.task.internal.quickstart.datasource;
import java.io.IOException;
import java.net.URL;
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/PsiMiToSif.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/PsiMiToSif.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/datasource/PsiMiToSif.java
2011-05-03 18:15:01 UTC (rev 24900)
@@ -1,4 +1,4 @@
-package org.cytoscape.task.internal.quickstart.remote;
+package org.cytoscape.task.internal.quickstart.datasource;
public class PsiMiToSif {
Deleted:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessor.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessor.java
2011-05-03 17:48:38 UTC (rev 24899)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessor.java
2011-05-03 18:15:01 UTC (rev 24900)
@@ -1,163 +0,0 @@
-package org.cytoscape.task.internal.quickstart.remote;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Properties;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
-
-import org.cytoscape.property.CyProperty;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class BioGridPreprocessor implements InteractionFilePreprocessor {
-
- private static final Logger logger = LoggerFactory
- .getLogger(BioGridPreprocessor.class);
-
- private static final String DB_NAME = "BioGRID";
- private static final String SOURCE_URL =
"http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.1.74/BIOGRID-ORGANISM-3.1.74.mitab.zip";;
-
- private static final String INTERACTION_DIR_NAME = "interactions";
- private static final String DEF_USER_DIR =
System.getProperty("user.home");
-
- private final PsiMiToSif p2s;
- private final File dataFileDirectory;
-
- private final Map<String, URL> sourceMap;
-
- private URL sourceFileLocation;
-
- private boolean isLatest;
-
- public BioGridPreprocessor(final CyProperty<Properties> properties) {
- this.isLatest = false;
-
- this.p2s = new PsiMiToSif();
- this.sourceMap = new HashMap<String, URL>();
- try {
- sourceFileLocation = new URL(SOURCE_URL);
- } catch (MalformedURLException e) {
- e.printStackTrace();
- }
-
- if (properties == null)
- throw new NullPointerException("Property service is
null.");
-
- final Properties props = properties.getProperties();
-
- if (props == null)
- throw new NullPointerException("Property is missing.");
-
- String configDirectory = props
- .getProperty(CyProperty.DEFAULT_CONFIG_DIR);
- if (configDirectory == null || configDirectory.trim().length()
== 0)
- configDirectory = DEF_USER_DIR;
-
- final File configFileLocation = new File(configDirectory,
- CyProperty.DEFAULT_CONFIG_DIR);
- this.dataFileDirectory = new File(configFileLocation,
- INTERACTION_DIR_NAME);
- if (!dataFileDirectory.exists())
- dataFileDirectory.mkdir();
-
- logger.debug("BioGrid interaction data directory: "
- + dataFileDirectory.toString());
- }
-
- @Override
- public void processFile(URL source) throws IOException {
- if (source != null)
- this.sourceFileLocation = source;
-
- boolean test = isUpToDate();
- if (!test) {
- final InputStream is = sourceFileLocation.openStream();
- extractEntrey(is);
- }
- }
-
- private boolean isUpToDate() throws IOException {
- final File[] files = this.dataFileDirectory.listFiles();
- boolean up2date = false;
-
- for (File file : files) {
- final String name = file.getName();
- final Pattern pattern = Pattern.compile("BIOGRID");
- final Matcher matcher = pattern.matcher(name);
- boolean test = matcher.find();
- if (test) {
- up2date = true;
- this.sourceMap.put(createFileName(name),
file.toURI().toURL());
- }
- }
- return up2date;
- }
-
- private void extractEntrey(final InputStream sourceInputStream)
- throws IOException {
- ZipInputStream zis = new ZipInputStream(sourceInputStream);
- try {
-
- // Extract list of entries
- ZipEntry zen = null;
- String entryName = null;
-
- while ((zen = zis.getNextEntry()) != null) {
- entryName = zen.getName();
- File outFile = new File(dataFileDirectory,
entryName + ".sif");
- outFile.createNewFile();
- FileWriter outWriter = new FileWriter(outFile);
- String line;
- final BufferedReader br = new BufferedReader(
- new InputStreamReader(zis));
-
- int count = 0;
- while ((line = br.readLine()) != null) {
- if (line.startsWith("#"))
- continue;
- outWriter.write(p2s.toSif(line) + "\n");
- count++;
- }
- zis.closeEntry();
- outWriter.close();
- this.sourceMap.put(createFileName(entryName),
outFile.toURI()
- .toURL());
- logger.debug("Entries: " + count);
- }
-
- } finally {
- if (zis != null)
- zis.close();
- zis = null;
- }
- }
-
- private String createFileName(final String originalFileName) {
- final String sourceName = DB_NAME + ": "
- + originalFileName.split("-")[2] + "
Interactome";
- return sourceName;
- }
-
- @Override
- public boolean isLatest() {
- // TODO Auto-generated method stub
- return true;
- }
-
- @Override
- public Map<String, URL> getDataSourceMap() {
- return sourceMap;
- }
-
-}
Deleted:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/InteractionFilePreprocessor.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/InteractionFilePreprocessor.java
2011-05-03 17:48:38 UTC (rev 24899)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/InteractionFilePreprocessor.java
2011-05-03 18:15:01 UTC (rev 24900)
@@ -1,24 +0,0 @@
-package org.cytoscape.task.internal.quickstart.remote;
-
-import java.io.IOException;
-import java.net.URL;
-import java.util.Map;
-
-public interface InteractionFilePreprocessor {
-
- /**
- *
- * @param sourceFileLocation
- * @throws IOException
- */
- void processFile(URL source) throws IOException;
-
- /**
- * Check local data is up-to-date or not.
- *
- * @return true if latest.
- */
- boolean isLatest();
-
- Map<String, URL> getDataSourceMap();
-}
Deleted:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/PsiMiToSif.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/PsiMiToSif.java
2011-05-03 17:48:38 UTC (rev 24899)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/PsiMiToSif.java
2011-05-03 18:15:01 UTC (rev 24900)
@@ -1,28 +0,0 @@
-package org.cytoscape.task.internal.quickstart.remote;
-
-public class PsiMiToSif {
-
- private static final String TAB = "\t";
- private static final String SEPARATOR = "\\|";
- private static final int COLUMN_COUNT = 15;
-
- public String toSif(final String line) {
- final String[] entry = line.split(TAB);
-
- // Validate entry list.
- if (entry == null || entry.length < COLUMN_COUNT)
- return null;
-
- String[] sourceID = entry[0].split(SEPARATOR);
- String[] targetID = entry[1].split(SEPARATOR);
- final String sourceRawID = sourceID[0].split(":")[1];
- final String targetRawID = targetID[0].split(":")[1];
-
- final String[] interactionID = entry[13].split(SEPARATOR);
- final String interaction = interactionID[0];
- if(interaction == null || interaction.length() == 0)
- return null;
-
- return sourceRawID + " " + interaction + " " + targetRawID;
- }
-}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
2011-05-03 17:48:38 UTC (rev 24899)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
2011-05-03 18:15:01 UTC (rev 24900)
@@ -16,7 +16,7 @@
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.task.internal.creation.NewNetworkSelectedNodesOnlyTask;
import
org.cytoscape.task.internal.quickstart.ImportNetworkFromPublicDataSetTask;
-import
org.cytoscape.task.internal.quickstart.remote.InteractionFilePreprocessor;
+import
org.cytoscape.task.internal.quickstart.datasource.InteractionFilePreprocessor;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
Modified:
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-05-03 17:48:38 UTC (rev 24899)
+++
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-05-03 18:15:01 UTC (rev 24900)
@@ -636,7 +636,7 @@
auto-export="interfaces" />
<osgi:set id="processorSetRef"
-
interface="org.cytoscape.task.internal.quickstart.remote.InteractionFilePreprocessor"
+
interface="org.cytoscape.task.internal.quickstart.datasource.InteractionFilePreprocessor"
cardinality="0..N">
<osgi:listener bind-method="addProcessor"
unbind-method="removeProcessor"
ref="importTaskUtil" />
Modified:
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-05-03 17:48:38 UTC (rev 24899)
+++
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-05-03 18:15:01 UTC (rev 24900)
@@ -350,7 +350,7 @@
</bean>
<bean id="bioGridPreprocessor"
-
class="org.cytoscape.task.internal.quickstart.remote.BioGridPreprocessor">
+
class="org.cytoscape.task.internal.quickstart.datasource.BioGridPreprocessor">
<constructor-arg ref="cyPropertyServiceRef" />
</bean>
Modified:
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessorTest.java
===================================================================
---
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessorTest.java
2011-05-03 17:48:38 UTC (rev 24899)
+++
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessorTest.java
2011-05-03 18:15:01 UTC (rev 24900)
@@ -7,6 +7,7 @@
import java.util.Properties;
import org.cytoscape.property.CyProperty;
+import org.cytoscape.task.internal.quickstart.datasource.BioGridPreprocessor;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
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