Fiji Updater for deploying ImageJ [was: Re: JarUpdater: An easy way to distribute plugin updates]

[ctrueden]

Hi Jarek,

This is the multi-site updater feature of the upcoming Fiji release. There
> could even be minimal distributions which set up update sites already.
>

As Johannes says, your suggestion is exactly the direction we are taking
things. Fiji is the mechanism by which the ImageJDev team plans to deploy
ImageJ2 and accompanying plugins later this year.

While Fiji started out as a distribution mechanism for TrakEM2, Simple
Neurite Tracer and other otherwise-difficult-to-deploy plugins, it has
become clear that it can serve as a powerful and general deployment platform
for ImageJ across many different fields of endeavor. For example, we have
been working with the Micro-Manager team to better integrate Micro-Manager
and Fiji, using an update site maintained by the Micro-Manager team. The
core multi-updater functionality is largely functional now and as Johannes
indicated will be available with the forthcoming release of Fiji.

We recently had a Fiji/ImageJDev hackathon in Madison, where we made great
progress on these goals. (I will be sending an update email to the list next
week with a summary of our efforts.) We will keep the community posted as
these features develop.

Regards,
Curtis

On Fri, Mar 4, 2011 at 10:48 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Jarek,
>
> On Fri, 4 Mar 2011, Jarek Sacha wrote:
>
> > Fiji is much more than the updater; it is also a distribution of large
> > amount of plugins. What would be nice, is to separate the updater
> > mechanism from the other Fiji plugins. Something similar to the Update
> > Centers provided, for instance, by Eclipse and NetBeans. User could
> > select which update centers to use. Even better which plugin clusters to
> > use. User could control which types of plugins he/she is interested in.
> > Having a standard way to provide plugins, other projects that provide
> > plugins (including the main ImageJ website) could setup their update
> > centers that would be registered with ImageJ website.
>
> This is the multi-site updater feature of the upcoming Fiji release. There
> could even be minimal distributions which set up update sites already.
>
> > I do appreciate the complexity of resolving dependencies and conflicts
> > between library versions, and creating update descriptions for the
> > updater. That is the reason why solution to this so appealing to many
> > users of ImageJ. Unless you are using Fiji with all of its plugins and
> > only its plugins, it has to be done manually.
>
> Unfortunately, I made myself misunderstood. For the updater to work, it is
> absolutely crucial that there is a custom launcher. We put a lot of work
> and thought into this (as well as some unfortunate trial and error), but
> if you think you can do better without Fiji (but still handling updating
> in-use files and dependencies properly), do go ahead.
>
> Hth,
> Johannes
>

[Jarek Sacha-2]

Curtis, Johannes:

On 3/4/2011 2:57 PM, Curtis Rueden wrote:
> The core multi-updater functionality is largely functional now and as
> Johannes indicated will be available with the forthcoming release of Fiji.
I am looking forward to be able to setup an update site for ij-plugins
project. Is there documentation available how to do that?

Jarek
http://ij-plugins.sf.net

[dscho]

Hi,

On Sun, 6 Mar 2011, Jarek Sacha wrote:

> On 3/4/2011 2:57 PM, Curtis Rueden wrote:
>
> > The core multi-updater functionality is largely functional now and as
> > Johannes indicated will be available with the forthcoming release of
> > Fiji.
>
> I am looking forward to be able to setup an update site for ij-plugins
> project. Is there documentation available how to do that?

No, there is none so far yet. If you're interested in writing it, I would
gladly tell you via IRC or Skype (probably assisting you in setting up the
update site while doing so). Otherwise, please be patient.

Ciao,
Johannes

[dscho]

Hi,

On Mon, 7 Mar 2011, Johannes Schindelin wrote:

> On Sun, 6 Mar 2011, Jarek Sacha wrote:
>
> > On 3/4/2011 2:57 PM, Curtis Rueden wrote:
> >
> > > The core multi-updater functionality is largely functional now and
> > > as Johannes indicated will be available with the forthcoming release
> > > of Fiji.
> >
> > I am looking forward to be able to setup an update site for ij-plugins
> > project. Is there documentation available how to do that?
>
> No, there is none so far yet. If you're interested in writing it, I
> would gladly tell you via IRC or Skype (probably assisting you in
> setting up the update site while doing so). Otherwise, please be
> patient.

Gavin A Price contacted me and worked with me through the process. He also
fulfilled more than the promise to provide documentation on the Wiki. He
made tutorials that are very easy to follow for both people who want to
set up an update site, and for people who want to follow update sites set
up by others:

        http://pacific.mpi-cbg.de/How_to_add_a_plugin_distribution_site

for users, and

        http://pacific.mpi-cbg.de/How_to_setup_a_plugin_distribution_site

for people who want to set up their own update sites.

Thanks, Gavin, very much!

[Jarek Sacha-2]

Great thanks to Gavin for providing the instructions.

I was trying to setup an update site for the IJ-Plugins Project hosted
at SourceForge. I create a directory as described. I started the "Add
update site" dialog and filled up fields:

Name:  IJ-Plugins Project
URL:  http://sourceforge.net/projects/ij-plugins/files/fiji_update
SSH Host:  frs.sourceforge.net
Upload directory: home/frs/project/i/ij/ij-plugin/fiji_update

When I click on OK am getting error: "Not a valid URL:
http://sourceforge.net/projects/ij-plugins/files/fiji_update". Any ideas?

Note that I tested the site, I can upload files using sftp with no problems.

Thanks,

Jarek

On 4/6/2011 6:21 PM, Johannes Schindelin wrote:

> Gavin A Price contacted me and worked with me through the process. He
> also
> fulfilled more than the promise to provide documentation on the Wiki. He
> made tutorials that are very easy to follow for both people who want to
> set up an update site, and for people who want to follow update sites set
> up by others:
>
> http://pacific.mpi-cbg.de/How_to_add_a_plugin_distribution_site
>
> for users, and
>
> http://pacific.mpi-cbg.de/How_to_setup_a_plugin_distribution_site
>
> for people who want to set up their own update sites.
>
> Thanks, Gavin, very much!
>

[dscho]

Hi,

On Sat, 9 Apr 2011, Jarek Sacha wrote:

> Great thanks to Gavin for providing the instructions.

Indeed!

The fascinating part for me was that I expected questions about this and
that, and instead saw the tutorials on the Fiji Wiki!

Thanks, Gavin!

> I was trying to setup an update site for the IJ-Plugins Project hosted
> at SourceForge. I create a directory as described. I started the "Add
> update site" dialog and filled up fields:
>
> Name:  IJ-Plugins Project
> URL:  http://sourceforge.net/projects/ij-plugins/files/fiji_update
> SSH Host:  frs.sourceforge.net
> Upload directory: home/frs/project/i/ij/ij-plugin/fiji_update

As can be seen in Gavin's description, you need a webserver that can serve
static files:

http://pacific.mpi-cbg.de/How_to_set_up_and_populate_an_update_site

SourceForge's File Release System instead serves redirections to mirrors.
No static files. Until somebody who needs this setup to be handled
implements support for it, the Fiji Updater will lack this support.

> When I click on OK am getting error: "Not a valid URL:
> http://sourceforge.net/projects/ij-plugins/files/fiji_update". Any ideas?

The reason for this is that it is indeed not a valid URL. However, instead
of reporting that the plugin database was not found -- as would have been
the case if the webserver would serve static files -- it serves a
redirection page which Fiji's Updater cannot parse.

But SourceForge _can_ serve static files. In your case, the URL would look
something like

        http://ij-plugins.sourceforge.net/fiji/

The only problem there is that you cannot access that webspace with a
password-protected SSH account. It is only possible using a private/public
key pair.

So just for you, I now implemented a feature in the Fiji Updater that
let's you read the information stored in your ~/.ssh/config (which is
the typical setup for SSH) to reuse a private key.

Hopefully this feature works for you, and if it does not, hopefully you
will find my gift a useful start to make it work. I do not need that
feature myself at all.

Ciao,
Johannes

P.S.: as the only remark about SSH access was "I can upload files using
sftp" I assumed that you use OpenSSH in spite of your screenshots
suggesting that you are on a Windows machine. So maybe you use Putty, but
I can only guess! If it is Putty, then the private keys are stored
somewhere else, I am certain, and it might not be as straight-forward to
reuse them in the Fiji Updater. As I rarely develop on Windows, and as I
should really take care of problems that are my own, I do hope that you
manage to get this to work with little assistance from my side.