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FIJI update site setup issues on windows

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FIJI update site setup issues on windows

Unruh, Jay-2
50 posts
Hi everyone,

I am finally in the process of setting up my own update site and am running into some problems.  I followed the instructions on the wiki (http://fiji.sc/wiki/index.php/How_to_set_up_and_populate_an_update_site) using the sftp modality.  FIJI is able to recognize the web address and placed the blank db.xml.gz there correctly.  When I go to upload my jar file, the program recognizes the jar and dependencies as it should, but after clicking upload to server and entering my password, nothing happens.  I don't get any error messages.  My upload is only 1.5 MB, so I wouldn't expect a long lag time.  I clicked Apply changes and it replies that the update was successful, but nothing uploads and upon restart, my jar is still listed as a local-only file.

Are there ways to debug this process?  Debug mode didn't give me any added info.  I am on a windows 7 64-bit machine.  My desired update site is here:

http://research.stowers.org/imagejplugins/updates

Any suggestions would be appreciated.

Thanks,
Jay

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Re: FIJI update site setup issues on windows

dscho
1631 posts
Hi Jay,

On Fri, 25 Jan 2013, Jay Unruh wrote:

> I am finally in the process of setting up my own update site and am
> running into some problems.  I followed the instructions on the wiki
> (http://fiji.sc/wiki/index.php/How_to_set_up_and_populate_an_update_site)
> using the sftp modality.  FIJI is able to recognize the web address and
> placed the blank db.xml.gz there correctly.  When I go to upload my jar
> file, the program recognizes the jar and dependencies as it should, but
> after clicking upload to server and entering my password, nothing
> happens.  I don't get any error messages.  My upload is only 1.5 MB, so
> I wouldn't expect a long lag time.  I clicked Apply changes and it
> replies that the update was successful, but nothing uploads and upon
> restart, my jar is still listed as a local-only file.
>
> Are there ways to debug this process?  Debug mode didn't give me any
> added info.  I am on a windows 7 64-bit machine.  My desired update site
> is here:
>
> http://research.stowers.org/imagejplugins/updates
>
> Any suggestions would be appreciated.

I suspect that there are some exceptions on the console. Could you try the
steps described in http://fiji.sc/Console_Debugging to make them visible,
please?

Ciao,
Johannes

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Re: FIJI update site setup issues on windows

Unruh, Jay-2
50 posts
Very nice, I was wondering how to enter the console mode from FIJI.

Here is the error message I get:

Found 297 plugins.
Created service: imagej.thread.DefaultThreadService
Created service: imagej.event.DefaultEventService
Created service: imagej.plugin.DefaultPluginService
Found 3 upload mechanisms.
com.jcraft.jsch.JSchException: failed to send channel request
        at com.jcraft.jsch.Request.write(Request.java:65)
        at com.jcraft.jsch.RequestSftp.request(RequestSftp.java:47)
        at com.jcraft.jsch.ChannelSftp.start(ChannelSftp.java:190)
        at com.jcraft.jsch.Channel.connect(Channel.java:200)
        at com.jcraft.jsch.Channel.connect(Channel.java:144)
        at imagej.updater.ssh.SFTPOperations.<init>(SFTPOperations.java:74)
        at imagej.updater.ssh.SFTPFileUploader.login(SFTPFileUploader.java:76)
        at imagej.updater.core.FilesUploader.login(FilesUploader.java:339)
        at imagej.updater.gui.UpdaterFrame.upload(UpdaterFrame.java:828)
        at imagej.updater.gui.UpdaterFrame$7$1.run(UpdaterFrame.java:343)

Can I force it to use one of the alternative upload mechanisms?  I also don't understand why it is finding 297 plugins.  I should have less than 100.  Perhaps it is not reading the plugins.config?

Thanks,
Jay

-----Original Message-----
From: Johannes Schindelin [mailto:[hidden email]]
Sent: Friday, January 25, 2013 11:30 AM
To: Unruh, Jay
Cc: [hidden email]
Subject: Re: FIJI update site setup issues on windows

Hi Jay,

On Fri, 25 Jan 2013, Jay Unruh wrote:

> I am finally in the process of setting up my own update site and am
> running into some problems.  I followed the instructions on the wiki
> (http://fiji.sc/wiki/index.php/How_to_set_up_and_populate_an_update_si
> te) using the sftp modality.  FIJI is able to recognize the web
> address and placed the blank db.xml.gz there correctly.  When I go to
> upload my jar file, the program recognizes the jar and dependencies as
> it should, but after clicking upload to server and entering my
> password, nothing happens.  I don't get any error messages.  My upload
> is only 1.5 MB, so I wouldn't expect a long lag time.  I clicked Apply
> changes and it replies that the update was successful, but nothing
> uploads and upon restart, my jar is still listed as a local-only file.
>
> Are there ways to debug this process?  Debug mode didn't give me any
> added info.  I am on a windows 7 64-bit machine.  My desired update
> site is here:
>
> http://research.stowers.org/imagejplugins/updates
>
> Any suggestions would be appreciated.

I suspect that there are some exceptions on the console. Could you try the steps described in http://fiji.sc/Console_Debugging to make them visible, please?

Ciao,
Johannes

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Re: FIJI update site setup issues on windows

dscho
1631 posts
Hi Jay,

On Fri, 25 Jan 2013, Unruh, Jay wrote:

> Very nice, I was wondering how to enter the console mode from FIJI.

Note: I just uploaded changes to the Fiji update site which print the
console messages to the Log window when you activate the Debug mode in
Edit>Options>Misc...

> Found 297 plugins.
> Created service: imagej.thread.DefaultThreadService
> Created service: imagej.event.DefaultEventService
> Created service: imagej.plugin.DefaultPluginService
> Found 3 upload mechanisms.
> com.jcraft.jsch.JSchException: failed to send channel request
>         at com.jcraft.jsch.Request.write(Request.java:65)
>         at com.jcraft.jsch.RequestSftp.request(RequestSftp.java:47)
>         at com.jcraft.jsch.ChannelSftp.start(ChannelSftp.java:190)
>         at com.jcraft.jsch.Channel.connect(Channel.java:200)
>         at com.jcraft.jsch.Channel.connect(Channel.java:144)
>         at imagej.updater.ssh.SFTPOperations.<init>(SFTPOperations.java:74)

From http://fiji.sc/SFTPOperations.java#l74 it looks as if the connection
via sftp fails, which is funny because you managed to put a db.xml.gz
there.

If you send me a mail with credentials to test the connection myself, I
will debug this tomorrow.

> Can I force it to use one of the alternative upload mechanisms?

Yes, if you skip the "sftp:" prefix, it will use ssh.

> I also don't understand why it is finding 297 plugins.

This is ImageJ2 speaking... And it refers to commands. You probably have
installed all the components from the ImageJ update site, correct?

Ciao,
Johannes

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