Hi,
I am getting a peculiar stack trace upon trying to define the plugin.
do you think it could be caused by using Base2.2 classes in a Base2.1.1
codebase? i tried to include the revised classes in the plugin JAR.. but
i suppose this probably doesn't work..
i had to include Base2.2 versions of
net.sf.basedb.core.Path
net.sf.basedb.util.FileExportOutputStream
net.sf.basedb.core.plugin.AbstractExporterPlugin
net.sf.basedb.core.plugin.ExportOutputStream
net.sf.basedb.core.plugin.ImmediateDownloadExporter
do you think it would be safe to just replace these files in 2.1.1
and rebuild it?
-keith
Version
BASE 2.1.1 (build #2996; schema #20)
Web server
Apache Tomcat/5.5.20
Database Dialect
org.hibernate.dialect.MySQLInnoDBDialect
JDBC Driver
com.mysql.jdbc.Driver (version 3.1)
Java runtime
Java(TM) 2 Runtime Environment, Standard Edition
(1.5.0_06-112),
Apple Computer, Inc. <http://apple.com/>
Operating system
Mac OS X
ppc
10.4.8
Memory
Total: 89.1 MB
Free: 55.7 MB
Max: 494.5 MB
Browser
Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.0.8) Gecko/20061025
Firefox/1.5.0.8
Error message
Could not instantiate plugin class: edu.ucsd.basedb.plugins.DownloadPlugin
Stack trace
...at PluginDefinition.newInstance(PluginDefinition.java:930)
...at PluginDefinition.loadPluginInformation(PluginDefinition.java:1026)
...at PluginDefinition.getNew(PluginDefinition.java:140)
...at
org.apache.jsp.admin.plugindefinitions.index_jsp._jspService(index_jsp.java:160)
...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:334)
...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
...at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at
net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71)
...at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
...at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
...at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
...at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
...at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
...at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
...at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
...at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
...at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
...at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
...at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
...at java.lang.Thread.run(Thread.java:613)
Caused by: java.util.zip.ZipException
...at java.util.zip.ZipFile.open(Native Method)
...at java.util.zip.ZipFile.(ZipFile.java:203)
...at java.util.jar.JarFile.(JarFile.java:132)
...at java.util.jar.JarFile.(JarFile.java:97)
...at net.sf.basedb.util.JarClassLoader.loadJarFile(JarClassLoader.java:206)
...at net.sf.basedb.util.JarClassLoader.(JarClassLoader.java:144)
...at net.sf.basedb.util.JarClassLoader.getInstance(JarClassLoader.java:85)
...at PluginDefinition.newInstance(PluginDefinition.java:919)
...at PluginDefinition.loadPluginInformation(PluginDefinition.java:1026)
...at PluginDefinition.getNew(PluginDefinition.java:140)
...at
org.apache.jsp.admin.plugindefinitions.index_jsp._jspService(index_jsp.java:160)
...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:334)
...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
...at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at
net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71)
...at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
...at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
...at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
...at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
...at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
...at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
...at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
...at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
...at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
...at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
...at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
...at java.lang.Thread.run(Thread.java:613)
> Is there a way to get the Httpresponse object from inside a plugin?
Not really, since plugins are executed in the background or maybe even
on a different server.
In the the upcoming 2.2 release we have added the interface
net.sf.basedb.core.plugin.ImmediateDownloadExporter
that more or less makes it possible for a plugin to send the output to
the HTTP response. Look at the source code some of the existing export
plugins (for example HelpExporter) to see how to use it.
/*
Copyright (C) 2006 Nicklas Nordborg
This file is part of BASE - BioArray Software Environment.
Available at http://base.thep.lu.se/
BASE is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
BASE 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330,
Boston, MA 02111-1307, USA.
*/
package edu.ucsd.basedb.plugins;
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.EnumSet;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import net.sf.basedb.core.Annotation;
import net.sf.basedb.core.AnnotationType;
import net.sf.basedb.core.BaseException;
import net.sf.basedb.core.BioAssaySet;
import net.sf.basedb.core.DbControl;
import net.sf.basedb.core.File;
import net.sf.basedb.core.Include;
import net.sf.basedb.core.InvalidUseOfNullException;
import net.sf.basedb.core.Item;
import net.sf.basedb.core.ItemParameterType;
import net.sf.basedb.core.ItemQuery;
import net.sf.basedb.core.ItemResultList;
import net.sf.basedb.core.Job;
import net.sf.basedb.core.Permission;
import net.sf.basedb.core.PluginParameter;
import net.sf.basedb.core.ProgressReporter;
import net.sf.basedb.core.RawBioAssay;
import net.sf.basedb.core.RequestInformation;
import net.sf.basedb.core.plugin.About;
import net.sf.basedb.core.plugin.AboutImpl;
import net.sf.basedb.core.plugin.AbstractExporterPlugin;
import net.sf.basedb.core.plugin.ExportOutputStream;
import net.sf.basedb.core.plugin.GuiContext;
import net.sf.basedb.core.plugin.InteractivePlugin;
import net.sf.basedb.core.plugin.Permissions;
import net.sf.basedb.core.plugin.Plugin;
import net.sf.basedb.core.plugin.Request;
import net.sf.basedb.core.plugin.Response;
/**
An example analysis plugin that creates a new bioassay set
by multiplying each intensitity value with the same factor, filtering
out intensities below a cutoff value.
@base.modified $Date: 2006/12/19 02:54:21 $
@author Nicklas
@version 2.0
*/
public class DownloadPlugin
extends AbstractExporterPlugin
implements InteractivePlugin
{
private static final About about =
new AboutImpl
(
"Download RawBioAssay source files",
"A plugin that downloads bioassays",
"2.0",
"2006, Keith Ching",
null,
null,
"http://bioinformatics-renlab.ucsd.edu";
);
/*
From the AbstractExporterPlugin class
--------------------------------------------
*/
private static final Set<GuiContext> guiContexts =
Collections.singleton(
new GuiContext(Item.RAWBIOASSAY, GuiContext.Type.LIST)
);
// Job configuration is created by getConfigureJob()
private RequestInformation configureJob;
// The selected source bioassay set
private ItemParameterType<RawBioAssay> rawBioAssaysType;
private PluginParameter<RawBioAssay> rawBioAssaysParameter;
private static final Set<Permissions> permissions = new
HashSet<Permissions>();
/**
Create a new plugin instance.
*/
public DownloadPlugin()
{}
/*
From the Plugin interface
-------------------------------------------
*/
public About getAbout()
{
return about;
}
public Plugin.MainType getMainType()
{
return Plugin.MainType.EXPORT;
}
public boolean supportsConfigurations()
{
return false;
}
public boolean requiresConfiguration()
{
return false;
}
/**
Request use access to Experiment:s and read access to RawBioAssay:s,
ArrayDesign:s,
Formulas:s, Job:s and and Reporter:s.
*/
public Collection<Permissions> getPermissions()
{
if (permissions.size() == 0)
{
// Grant write access to RawBioAssays and read access to
ArrayDesign, File and Reporter
// permissions.add(new Permissions(Item.EXPERIMENT, null,
EnumSet.of(Permission.USE)));
permissions.add(new Permissions(Item.RAWBIOASSAY, null,
EnumSet.of(Permission.READ)));
permissions.add(new Permissions(Item.FILE, null,
EnumSet.of(Permission.CREATE, Permission.WRITE)));
// permissions.add(new Permissions(Item.FORMULA, null,
EnumSet.of(Permission.READ)));
permissions.add(new Permissions(Item.JOB, null,
EnumSet.of(Permission.READ)));
// permissions.add(new Permissions(Item.REPORTER, null,
EnumSet.of(Permission.READ)));
permissions.add(new Permissions(Item.FILE, null,
EnumSet.of(Permission.CREATE, Permission.WRITE)));
permissions.add(new Permissions(Item.DIRECTORY, null,
EnumSet.of(Permission.CREATE, Permission.WRITE)));
permissions.add(new Permissions(Item.USER, null,
EnumSet.of(Permission.READ)));
permissions.add(new Permissions(Item.CLIENT, null,
EnumSet.of(Permission.READ)));
}
return permissions;
}
private net.sf.basedb.core.File getRawBioAssayFile(DbControl dc,
RawBioAssay rawBioAssay){
net.sf.basedb.core.File file = null;
if(!rawBioAssay.isAnnotated()){
throw new BaseException("RawBioAssay
"+rawBioAssay.getName()+" has no annotations");
}
// get all annotation types for rawbioassay
ItemQuery<AnnotationType> typeQuery =
AnnotationType.getQuery(Item.RAWBIOASSAY);
typeQuery.include(Include.MINE, Include.SHARED,
Include.IN_PROJECT, Include.OTHERS);
ItemResultList<AnnotationType> typeList = typeQuery.list(dc);
for(AnnotationType type : typeList){
if(type.getName().equals("FileID")){
Annotation ann =
rawBioAssay.getAnnotationSet().getAnnotation(type);
int fileID = (Integer)ann.getValues().get(0);
file = net.sf.basedb.core.File.getById(dc,
fileID);
}
}
if(typeList.isEmpty()){
throw new BaseException("No annotations");
}
if(file == null){
throw new BaseException("FileID not found.");
}
return file;
}
@SuppressWarnings("unchecked")
protected void performExport(ExportOutputStream out, ProgressReporter
progress)
throws IOException
{
// Open a connection to the database
// sc is set by init() method
DbControl dc = sc.newDbControl();
try
{
ZipOutputStream zipOut = new ZipOutputStream(new
BufferedOutputStream(out));
zipOut.setMethod(ZipOutputStream.DEFLATED);
zipOut.setLevel(6);
List<RawBioAssay> sources =
(List<RawBioAssay>)job.getValues("rawBioAssays");
// rawBioAssays parameter
if (sources == null || sources.size() == 0)
{
throw new InvalidUseOfNullException("sources");
}
final int BUFFER = 2048;
byte data[] = new byte[BUFFER];
int filecount = 0;
for (RawBioAssay rba : sources)
{
dc.reattachItem(rba);
File file = getRawBioAssayFile(dc, rba);
if (progress != null){
progress.display( (int) (filecount *
100 / sources.size()) , "Adding "+file.getName());
}
InputStream in = file.getDownloadStream(0);
BufferedInputStream buf = new
BufferedInputStream(in, BUFFER);
ZipEntry entry = new ZipEntry(file.getName());
zipOut.putNextEntry(entry);
int count;
while((count = buf.read(data, 0, BUFFER)) !=
-1){
zipOut.write(data, 0, count);
}
buf.close();
filecount++;
if (progress != null){
progress.display( (int) (filecount *
100 / sources.size()) , "Added "+file.getName());
}
}
zipOut.close();
out.close();
}catch (BaseException be)
{
// All exceptions must be catched and sent back
// using the response object
progress.display(0, be.getMessage());
}
finally
{
// IMPORTANT!!! Make sure opened connections are closed
if (dc != null) dc.close();
}
}
// -------------------------------------------
/*
From the InteractivePlugin interface
-------------------------------------------
*/
/**
Return a set containing the context [BIOASSAYSET, ITEM].
*/
public Set<GuiContext> getGuiContexts()
{
return guiContexts;
}
/**
Check if the item is a [EMAIL PROTECTED] BioAssaySet}.
*/
public String isInContext(GuiContext context, Object item)
{
String message = null;
// if (item == null)
// {
// message = "The object is null";
// }
// else if (!(item instanceof RawBioAssay))
// {
// message = "The object is not a RawBioAssay: " + item;
// }
return message;
}
/**
The [EMAIL PROTECTED] Request#COMMAND_CONFIGURE_PLUGIN} command
will not ask
for any parameters.
<p>
The [EMAIL PROTECTED] Request#COMMAND_CONFIGURE_JOB} command
will ask for
a bioassay set, a multiplcation factor and a cutoff value.
*/
public RequestInformation getRequestInformation(GuiContext context,
String command)
throws BaseException
{
RequestInformation requestInformation = null;
if (command.equals(Request.COMMAND_CONFIGURE_JOB))
{
requestInformation = getConfigureJob(context);
}
return requestInformation;
}
/**
Store configuration settings for [EMAIL PROTECTED]
Request#COMMAND_CONFIGURE_PLUGIN} and
[EMAIL PROTECTED] Request#COMMAND_CONFIGURE_JOB}.
*/
public void configure(GuiContext context, Request request, Response
response)
{
String command = request.getCommand();
try
{
if (command.equals(Request.COMMAND_CONFIGURE_JOB))
{
List<Throwable> errors =
validateRequestParameters(getConfigureJob(context).getParameters(), request);
if (errors != null)
{
response.setError(errors.size()+"
invalid parameter(s) were found in the request", errors);
return;
}
storeValues(job, request,
rawBioAssaysParameter);
response.setDone("Job configuration complete",
Job.ExecutionTime.SHORT);
// TODO - maybe check file size to make a
better estimate
}
}
catch (Throwable ex)
{
response.setError(ex.getMessage(), Arrays.asList(ex));
}
}
// -------------------------------------------
private RequestInformation getConfigureJob(GuiContext context)
{
if (configureJob == null)
{
DbControl dc = sc.newDbControl();
Set<Integer> rawset =
sc.getCurrentContext(Item.RAWBIOASSAY).getSelected();
List<RawBioAssay> rawBioAssays = new
ArrayList<RawBioAssay>();
for (Integer rawid : rawset) {
rawBioAssays.add(RawBioAssay.getById(dc,
rawid.intValue()));
}
rawBioAssaysType = new
ItemParameterType<RawBioAssay>(RawBioAssay.class, null, true, 0, rawBioAssays);
rawBioAssaysParameter = new
PluginParameter<RawBioAssay>(
"rawBioAssays", "Raw bioassays", "Select the
raw bioassays to download",
rawBioAssaysType);
// Create parameter list and request informaion
List<PluginParameter<?>> parameters = new
ArrayList<PluginParameter<?>>();
parameters.add(rawBioAssaysParameter);
configureJob = new RequestInformation
(
Request.COMMAND_CONFIGURE_JOB,
"Specify rawbioassays to download",
about.getDescription(),
parameters
);
// close the connection
if (dc != null) dc.close();
}
return configureJob;
}
}
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