Re: [base] downloading files

2006-12-20 Thread Keith Ching

yeah, there are too many changes to integrate into 2.1.1
the 2.1.2pre branch does not have the new classes

i tried to upgrade to the trunk, but it blows in too many places..  so i 
guess i'll just wait for

the classes to be released..

thanks again for all the help,

-keith

Nicklas Nordborg wrote:

Keith Ching wrote:
  

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?



It is nothing that we recommend and we are not going to help you with 
any problems resulting from mixing two BASE versions. The immediate 
download functionality also depends on changes in JSP pages and other 
java classes.


If you check ticket #189 (http://base.thep.lu.se/ticket/189) you can see 
all changes related to this issue. To get to the changes you have to 
look in the Change history list and find the links with numbers inside 
square brackets, for example: [2854].


/Nicklas

  

-keith




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--
Keith Ching, Ph.D.
Bioinformatics, Laboratory of Gene Regulation
Ludwig Institute for Cancer Research
9500 Gilman Drive, #0653
CMM East, Room 3020
La Jolla, CA 92093-0653

[EMAIL PROTECTED]
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[base] downloading files

2006-12-19 Thread Keith Ching
I have a List of File objects.  what is the best way to zip them all 
together and download it?
Is there a way to get the Httpresponse object from inside a plugin?  If 
the files are really large,
would it better to write the outputstream to the local filesystem and 
have the user find and download
the archive from inside their home dir?

is there a nice File.Action.addZip ?

thanks,

-keith

-- 
Keith Ching, Ph.D.
Bioinformatics, Laboratory of Gene Regulation
Ludwig Institute for Cancer Research
9500 Gilman Drive, #0653
CMM East, Room 3020
La Jolla, CA 92093-0653

[EMAIL PROTECTED]
858-822-5767


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Re: [base] downloading files

2006-12-19 Thread Nicklas Nordborg
Keith Ching wrote:
 I have a List of File objects.  what is the best way to zip them all 
 together and download it?

I assume that you want to this with a plugin. I think the best way is to 
create a new File (net.sf.basedb.core.File) object and then use 
java.util.zip.ZipOutputStream for writing to the new file.

 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.

 If 
 the files are really large,
 would it better to write the outputstream to the local filesystem and 
 have the user find and download
 the archive from inside their home dir?

Maybe. I don't think a zip stream needs much memory or uses very much 
CPU. The main problem is probably slow network connections. If you use 
the net.sf.basedb.core.plugin.AbstractExportPlugin as a base class it 
can help you with supporting both immediate download and saving to the 
file system.

 
 is there a nice File.Action.addZip ?

No.

/Nicklas

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Re: [base] downloading files

2006-12-19 Thread Keith Ching
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 

Re: [base] downloading files

2006-12-19 Thread Keith Ching
sorry.. i'm careless..  i called my jar file DownloadFilePlugins.jar 
instead of DownloadFilePlugin.jar
and it couldn't find / load it but it threw a pretty impressive 
stack trace..

-keith

Keith Ching wrote:
 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

   


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