micro-manager-general

[micro-manager-general] Origin of 5 files in 3rdpartypublic/classext/

[Pariksheet N. <par...@gm...>]

Hi fellow developers,

I'm trying to package the classext dependencies[1] from the
3rdpartypublic repository.
Can someone confirm the upstream source of 5 of those files?

I need to know where the source code is located- the URL of either the
version control repository or (better) as the source code tarball.
So far I've guessed what 3 of them might be-

    data.json.jar         <- https://github.com/clojure/data.json
    lwm.jar         <- https://github.com/arthuredelstein/lwm
    clooj.jar         <- https://github.com/arthuredelstein/clooj
    TSFProto.jar
    gproto.jar

I can't find their reference from the wiki, google-fu, etc.

Thank you,
Pariksheet

[1] https://valelab.ucsf.edu/svn/3rdpartypublic/classext/

Re: [micro-manager-general] Origin of 5 files in 3rdpartypublic/classext/

[Nico S. <ni...@cm...>]

Hi Pariksheet,

> I'm trying to package the classext dependencies[1] from the
> 3rdpartypublic repository.
> Can someone confirm the upstream source of 5 of those files?
> 
> I need to know where the source code is located- the URL of either the
> version control repository or (better) as the source code tarball.
> So far I've guessed what 3 of them might be-
> 
>    data.json.jar         <- https://github.com/clojure/data.json
>    lwm.jar         <- https://github.com/arthuredelstein/lwm
>    clooj.jar         <- https://github.com/arthuredelstein/clooj

I think you are correct about all three (but Arthur can confirm).

>    gproto.jar

This is a compiled version of Google Protocol Buffers.  I don't extactly remember how I build it but it was straight from the sources provided by Google (most likely version 2.3).

>    TSFProto.jar

This jar contains code to read and write Tagged Spot Format (TSF) files.  This is to store single molecule data such as in STORM/PALM imaging (it is used by the Localization plugin in Micro-Manager.  You can find the sources here:

https://valelab.ucsf.edu/svn/valelabtools/TSFProto


Hope this helps!


Best,

Nico

Re: [micro-manager-general] Origin of 5 files in 3rdpartypublic/classext/

[Pariksheet N. <par...@gm...>]

Thanks, Nico!

Re: [micro-manager-general] Origin of 5 files in 3rdpartypublic/classext/

[Arthur D. E. <art...@gm...>]

Hi Pariksheet,


> > I need to know where the source code is located- the URL of either the
> > version control repository or (better) as the source code tarball.
> > So far I've guessed what 3 of them might be-
> >
> >    data.json.jar         <- https://github.com/clojure/data.json
> >    lwm.jar         <- https://github.com/arthuredelstein/lwm
> >    clooj.jar         <- https://github.com/arthuredelstein/clooj
>
> I think you are correct about all three (but Arthur can confirm).
>
> Yes, this is correct. However, the versions aren't always in sync, so you
might get errors if you use the latest commits to github. However, the
contemporaneous source code files (with the .clj suffix) for each of these
jars, as found in 3rdpartypublic/classext, are included inside the jars.

Best regards,
Arthur

Re: [micro-manager-general] Origin of 5 files in 3rdpartypublic/classext/

[Pariksheet N. <par...@gm...>]

Hi Arthur,

On Mon, Apr 2, 2012 at 11:41 PM, Arthur D. Edelstein
<art...@gm...> wrote:
> ... the versions aren't always in sync, so you
> might get errors if you use the latest commits to github. However, the
> contemporaneous source code files (with the .clj suffix) for each of these
> jars, as found in 3rdpartypublic/classext, are included inside the jars.
>

I'm hosting an ebuild overlay to build micro-manager on Gentoo
GNU/Linux [1], and Gentoo builds packages from source.
The Gentoo Java general guidelines discourage downloading .jars when
the source is available [2]

For your projects lwm and clooj-
1) What do you think about uploading release tarballs of your source
(e.g. under the Downloads tab in Github)?
2) Alternatively you could add version numbers tag to your git source
(e.g. to the match the jars in the classext folder) for your projects
and then I can download a tagged version of your git repo using
EGIT_COMMIT [3].

I understand what Nico said earlier about the convenience of using the
3rdpartypublic repo.
The reason I'm not using the jars directly is they will likely prevent
acceptance of the packages into Portage.
Benefits of getting Micro-manager formally accepted in Gentoo's
package manager would be:
- The Java or the Sci-Biology herd would have responsibility for
maintenance instead of the odd individual.
- Help from Gentoo developers for Micro-manager such as patch
submission, other QA, etc.

Of course, I don't want to encroach on your development bandwidth, so
hopefully there is an optimal solution for hosting the release source
of your projects.


> Best regards,
> Arthur
>

Thank you,
Pariksheet

[1] https://github.com/omsai/micromanager-overlay
[2] http://www.gentoo.org/proj/en/java/java-devel.xml
[3] http://devmanual.gentoo.org/eclass-reference/git-2.eclass/index.html

Re: [micro-manager-general] Origin of 5 files in 3rdpartypublic/classext/

[Pariksheet N. <par...@gm...>]

Hi Arthur,

Where can I get the source for ags.utils you're using in lwm?
https://github.com/arthuredelstein/lwm/blob/master/src/lwm/core.clj#L6

Is it from Gaussian.jar in the classpath of the build file?
https://github.com/arthuredelstein/lwm/blob/master/build

Then I can include it for my build:

>>> Compiling source in /var/tmp/portage/dev-java/lwm-9999/work/lwm-9999 ...
Compiling lwm.core to classes
Exception in thread "main" java.lang.ClassNotFoundException:
ags.utils.KdTree$SqrEuclid, compiling:(core.clj:1)
	at clojure.lang.Compiler$InvokeExpr.eval(Compiler.java:3342)
	at clojure.lang.Compiler.compile1(Compiler.java:6985)
	at clojure.lang.Compiler.compile1(Compiler.java:6975)
	at clojure.lang.Compiler.compile(Compiler.java:7046)
	at clojure.lang.RT.compile(RT.java:385)
	at clojure.lang.RT.load(RT.java:425)
	at clojure.lang.RT.load(RT.java:398)
	at clojure.core$load$fn__4610.invoke(core.clj:5386)
	at clojure.core$load.doInvoke(core.clj:5385)
	at clojure.lang.RestFn.invoke(RestFn.java:408)
	at clojure.core$load_one.invoke(core.clj:5200)
	at clojure.core$compile$fn__4615.invoke(core.clj:5397)
	at clojure.core$compile.invoke(core.clj:5396)
	at clojure.lang.Var.invoke(Var.java:401)
	at clojure.lang.Compile.main(Compile.java:59)
Caused by: java.lang.ClassNotFoundException: ags.utils.KdTree$SqrEuclid
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at clojure.lang.DynamicClassLoader.findClass(DynamicClassLoader.java:61)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:169)
	at lwm.core$loading__4505__auto__.invoke(core.clj:1)
	at clojure.lang.AFn.applyToHelper(AFn.java:159)
	at clojure.lang.AFn.applyTo(AFn.java:151)
	at clojure.lang.Compiler$InvokeExpr.eval(Compiler.java:3337)
	... 14 more

Thank you,
Pariksheet

Re: [micro-manager-general] Origin of 5 files in 3rdpartypublic/classext/

[Arthur D. E. <art...@gm...>]

Hi Pariksheet,

It is indeed inside Gaussian.jar. Nico is planning to switch to a java
version of lwm that I wrote, and I think the confusing structure will
then be simpler.

Arthur



On Sun, Apr 15, 2012 at 5:14 PM, Pariksheet Nanda
<par...@gm...> wrote:
> Hi Arthur,
>
> Where can I get the source for ags.utils you're using in lwm?
> https://github.com/arthuredelstein/lwm/blob/master/src/lwm/core.clj#L6
>
> Is it from Gaussian.jar in the classpath of the build file?
> https://github.com/arthuredelstein/lwm/blob/master/build
>
> Then I can include it for my build:
>
>>>> Compiling source in /var/tmp/portage/dev-java/lwm-9999/work/lwm-9999 ...
> Compiling lwm.core to classes
> Exception in thread "main" java.lang.ClassNotFoundException:
> ags.utils.KdTree$SqrEuclid, compiling:(core.clj:1)
>        at clojure.lang.Compiler$InvokeExpr.eval(Compiler.java:3342)
>        at clojure.lang.Compiler.compile1(Compiler.java:6985)
>        at clojure.lang.Compiler.compile1(Compiler.java:6975)
>        at clojure.lang.Compiler.compile(Compiler.java:7046)
>        at clojure.lang.RT.compile(RT.java:385)
>        at clojure.lang.RT.load(RT.java:425)
>        at clojure.lang.RT.load(RT.java:398)
>        at clojure.core$load$fn__4610.invoke(core.clj:5386)
>        at clojure.core$load.doInvoke(core.clj:5385)
>        at clojure.lang.RestFn.invoke(RestFn.java:408)
>        at clojure.core$load_one.invoke(core.clj:5200)
>        at clojure.core$compile$fn__4615.invoke(core.clj:5397)
>        at clojure.core$compile.invoke(core.clj:5396)
>        at clojure.lang.Var.invoke(Var.java:401)
>        at clojure.lang.Compile.main(Compile.java:59)
> Caused by: java.lang.ClassNotFoundException: ags.utils.KdTree$SqrEuclid
>        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
>        at java.security.AccessController.doPrivileged(Native Method)
>        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>        at clojure.lang.DynamicClassLoader.findClass(DynamicClassLoader.java:61)
>        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>        at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
>        at java.lang.Class.forName0(Native Method)
>        at java.lang.Class.forName(Class.java:169)
>        at lwm.core$loading__4505__auto__.invoke(core.clj:1)
>        at clojure.lang.AFn.applyToHelper(AFn.java:159)
>        at clojure.lang.AFn.applyTo(AFn.java:151)
>        at clojure.lang.Compiler$InvokeExpr.eval(Compiler.java:3337)
>        ... 14 more
>
> Thank you,
> Pariksheet
>
> ------------------------------------------------------------------------------
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> _______________________________________________
> micro-manager-general mailing list
> mic...@li...
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general

Re: [micro-manager-general] Origin of 5 files in 3rdpartypublic/classext/

[Pariksheet N. <par...@gm...>]

On Sun, Apr 15, 2012 at 9:18 PM, Arthur D. Edelstein
<art...@gm...> wrote:
> Nico is planning to switch to a java
> version of lwm that I wrote, and I think the confusing structure will
> then be simpler.
>

Cool, then in the meantime I'll move on on wrapping the other
dependencies in ebuilds like data.jason, clooj, etc...


> Arthur
>

Pariksheet

Re: [micro-manager-general] Origin of 5 files in 3rdpartypublic/classext/

[Pariksheet N. <par...@gm...>]

On Sun, Apr 15, 2012 at 9:18 PM, Arthur D. Edelstein
<art...@gm...> wrote:
> It is indeed inside Gaussian.jar. Nico is planning to switch to a java
> version of lwm that I wrote, and I think the confusing structure will
> then be simpler.
>
> Arthur
>

Hi Nico,

There seems to be a circular dependency between lwm and Gaussian plugins.
How would I go about compiling each of these from source?

Thanks,
Pariksheet