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What's wrong with this Java call?

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  What's wrong with this Java call? vjp2.at@at.BioStrategist.dot.dot.com - 2020-05-30 18:15 +0000
    Re: What's wrong with this Java call? Eric Sosman <esosman@comcast-dot-net.invalid> - 2020-05-30 15:40 -0400
      Re: What's wrong with this Java call? vjp2.at@at.BioStrategist.dot.dot.com - 2020-05-31 07:07 +0000
      Re: What's wrong with this Java Jython call? vjp2.at@at.BioStrategist.dot.dot.com - 2020-06-05 15:09 +0000
        Re: What's wrong with this Java Jython call? Daniele Futtorovic <da.futt.news@laposte-dot-net.invalid> - 2020-06-05 23:03 +0200
          Re: What's wrong with this Java Jython call? Daniele Futtorovic <da.futt.news@laposte-dot-net.invalid> - 2020-06-05 23:07 +0200
            Re: What's wrong with this Java Jython call? vjp2.at@at.BioStrategist.dot.dot.com - 2020-06-06 13:44 +0000
              Re: What's wrong with this Java Jython call? vjp2.at@at.BioStrategist.dot.dot.com - 2020-06-06 18:47 +0000
                Re: What's wrong with this Java Jython call? Daniele Futtorovic <da.futt.news@laposte-dot-net.invalid> - 2020-06-06 21:35 +0200
                  Re: What's wrong with this Java Jython call? vjp2.at@at.BioStrategist.dot.dot.com - 2020-06-13 11:15 +0000
                    Re: What's wrong with this Java Jython call? Daniele Futtorovic <da.futt.news@laposte-dot-net.invalid> - 2020-06-14 16:23 +0200
                      Re: What's wrong with this Java Jython call? vjp2.at@at.BioStrategist.dot.dot.com - 2020-06-15 10:10 +0000

#39475 — What's wrong with this Java call?

Java just spits out a list of options
Doesn't say much about what's wrong.
But it doesn't proceed.
I need to turn this bat into an exe to run from Portable Apps

@echo off
SET RD_HOME=.
SET JAVA_HOME=..\CommonFiles\JAVA
SET JAVA_COMMAND=%JAVA_HOME%\bin\java.exe
SET LOCAL_CLASSPATH=%RD_HOME%\org.RDKit.jar
"%JAVA_COMMAND%" -Xmx256m -classpath "%LOCAL_CLASSPATH%" >> err
"%JAVA_HOME%"\jython-standalone-2.5.jar >> err
jython -Djava.library.path="%RD_HOME%"\rdkit-masterCode\JavaWrappers\gmwrapper < "%RD_HOME%"\rdkit.py >> err
:END



				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39476

On 5/30/2020 2:15 PM, vjp2.at@at.BioStrategist.dot.dot.com wrote:
> Java just spits out a list of options
> Doesn't say much about what's wrong.
> But it doesn't proceed.
> I need to turn this bat into an exe to run from Portable Apps
> 
> @echo off
> SET RD_HOME=.
> SET JAVA_HOME=..\CommonFiles\JAVA
> SET JAVA_COMMAND=%JAVA_HOME%\bin\java.exe
> SET LOCAL_CLASSPATH=%RD_HOME%\org.RDKit.jar
> "%JAVA_COMMAND%" -Xmx256m -classpath "%LOCAL_CLASSPATH%" >> err

     Try "-jar" instead of "-classpath" here.  If that doesn't help,
leave "-classpath" as it is and add the name of the class you
want to execute:

     ...  -classpath "%LOCAL_CLASSPATH%" classname >> err

> "%JAVA_HOME%"\jython-standalone-2.5.jar >> err
> jython -Djava.library.path="%RD_HOME%"\rdkit-masterCode\JavaWrappers\gmwrapper < "%RD_HOME%"\rdkit.py >> err
> :END

-- 
esosman@comcast-dot-net.invalid
The Tooth Fairy has gone crypto and now pays in BiteCoin.
Two hundred thirty-five days to go.

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#39477

Thanks

now I have to figur eout what the classname is



				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39483 — Re: What's wrong with this Java Jython call?

Is it possible these thre lines are actually all one line?

*+-> "%JAVA_COMMAND%" -Xmx256m -classpath "%LOCAL_CLASSPATH%" >> err
*+-> "%JAVA_HOME%"\jython-standalone-2.5.jar >> err
*+-> jython -Djava.library.path="%RD_HOME%"\rdkit-masterCode\JavaWrappers\gmwrapper < "%RD_HOME%"\rdkit.py >> err




				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39485 — Re: What's wrong with this Java Jython call?

On 2020-06-05 17:09, vjp2.at@at.BioStrategist.dot.dot.com wrote:
> Is it possible these thre lines are actually all one line?
> 
> *+-> "%JAVA_COMMAND%" -Xmx256m -classpath "%LOCAL_CLASSPATH%" >> err
> *+-> "%JAVA_HOME%"\jython-standalone-2.5.jar >> err
> *+-> jython -Djava.library.path="%RD_HOME%"\rdkit-masterCode\JavaWrappers\gmwrapper < "%RD_HOME%"\rdkit.py >> err

The first two, yes, most likely. The third one, no.

-- 
DF.

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#39486 — Re: What's wrong with this Java Jython call?

On 2020-06-05 23:03, Daniele Futtorovic wrote:
> On 2020-06-05 17:09, vjp2.at@at.BioStrategist.dot.dot.com wrote:
>> Is it possible these thre lines are actually all one line?
>>
>> *+-> "%JAVA_COMMAND%" -Xmx256m -classpath "%LOCAL_CLASSPATH%" >> err
>> *+-> "%JAVA_HOME%"\jython-standalone-2.5.jar >> err
>> *+-> jython -Djava.library.path="%RD_HOME%"\rdkit-masterCode\JavaWrappers\gmwrapper < "%RD_HOME%"\rdkit.py >> err
> 
> The first two, yes, most likely. The third one, no.
> 

Actually, scratch that. They might be. I'm not that familiar with Jython
(a Python interpreter written in Java published by Google, if I'm not
mistaken), but maybe that's how it's invoked.

But the first two most definitely belong together, since neither on its
own would work.

-- 
DF.

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#39488 — Re: What's wrong with this Java Jython call?

Thanks, that may explain my problem


				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39490 — Re: What's wrong with this Java Jython call?

Well, it stopped bombing, but it doesn't give me the "prompt" either

THanks, though


				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39491 — Re: What's wrong with this Java Jython call?

On 2020-06-06 20:47, vjp2.at@at.BioStrategist.dot.dot.com wrote:
> Well, it stopped bombing, but it doesn't give me the "prompt" either
> 
> THanks, though
> 

You are feeding it a script:
> < "%RD_HOME%"\rdkit.py

Why should it give you a prompt?

-- 
DF.

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#39499 — Re: What's wrong with this Java Jython call?

First, many thanks.

Here's where I am.
1. Is the ";jython" correct?
2. I added -jar to run jython alone
3. the "wrappers" are files with extension .i
4. I posted a question on the RDKIT sourceforce list, no reply
5. Yes, I removed the script, but how do I use it to init then return to
      prompt? TEE? |?

Thanks again

@echo off
SET RD_HOME=.
SET JAVA_HOME=..\CommonFiles\JAVA
SET JAVA_COMMAND=%JAVA_HOME%\bin\java.exe
SET LOCAL_CLASSPATH=%RD_HOME%\org.RDKit.jar
"%JAVA_COMMAND%" -classpath "%LOCAL_CLASSPATH%"  -jar "%JAVA_HOME%"\jython-standalone-2.5.jar; jython -Djava.library.path="%RD_HOME%"\rdkit-master\Code\JavaWrappers\gmwrapper  
rem if remove semicolon complains jython not found in rdkit - of course it's in common
rem able to run jython as jar run print "hello" or print 3+4
rem some docs have rdkit.jar in gmwrapper; what are dlls but no exe doing here?
pause
rem < "%RD_HOME%"\start.rdk 
rem how can I run this and return to prompt?
:END

rem these are in start.rdk
rem from org.RDKit import *
rem from java import lang
rem lang.System.loadLibrary('GraphMolWrap')
rem m = RWMol.MolFromSmiles('c1ccccc1')
rem m.getNumAtoms()
6L


				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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#39501 — Re: What's wrong with this Java Jython call?

On 2020-06-13 13:15, vjp2.at@at.BioStrategist.dot.dot.com wrote:
> First, many thanks.
> 
> Here's where I am.
> 1. Is the ";jython" correct?
> 2. I added -jar to run jython alone
> 3. the "wrappers" are files with extension .i
> 4. I posted a question on the RDKIT sourceforce list, no reply
> 5. Yes, I removed the script, but how do I use it to init then return to
>       prompt? TEE? |?
> 
> Thanks again
> 
> @echo off
> SET RD_HOME=.
> SET JAVA_HOME=..\CommonFiles\JAVA
> SET JAVA_COMMAND=%JAVA_HOME%\bin\java.exe
> SET LOCAL_CLASSPATH=%RD_HOME%\org.RDKit.jar
> "%JAVA_COMMAND%" -classpath "%LOCAL_CLASSPATH%"  -jar "%JAVA_HOME%"\jython-standalone-2.5.jar; jython -Djava.library.path="%RD_HOME%"\rdkit-master\Code\JavaWrappers\gmwrapper  
> rem if remove semicolon complains jython not found in rdkit - of course it's in common
> rem able to run jython as jar run print "hello" or print 3+4
> rem some docs have rdkit.jar in gmwrapper; what are dlls but no exe doing here?
> pause
> rem < "%RD_HOME%"\start.rdk 
> rem how can I run this and return to prompt?
> :END
> 
> rem these are in start.rdk
> rem from org.RDKit import *
> rem from java import lang
> rem lang.System.loadLibrary('GraphMolWrap')
> rem m = RWMol.MolFromSmiles('c1ccccc1')
> rem m.getNumAtoms()
> 6L

> if remove semicolon complains jython not found in rdkit - of course
it's in common

This is weird.
What happens if you just run `jython` on the command line? From what I
could see the default jython install puts it on the $PATH. IOW what
happens if you remove everything from your line up to and including the
semicolon?

> how can I run this and return to prompt?

What is the problem exactly?

Is the script launching a background process that you wish to keep
alive, equivalent to running in background on Unix?

Or is the script supposed to return a value, but for some reason it's
not exiting properly and you would like it to exit properly?

If the latter, try adding a `sys.exit` at the end of your python code.
Maybe the loadLibrary call or something else that library does is
keeping the JVM alive.

-- 
DF.

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#39502 — Re: What's wrong with this Java Jython call?

I am finding multiple versions of instructions with different code
and the files in different locations

I am putting this off until I can get a fresh download (no broadband)
My download is on CD from 2015. (My project derailed by death in family)

As to the script, it is like an init or logon file.

I was hoping to run it then get back the prompt.

Thanks for your help

FYI, RDKit is a chemical synthesis program, like Macsyma but for Chemistry

				    - = -
	 Vasos Panagiotopoulos, Columbia'81+, Reagan, Mozart, Pindus
  blog: panix.com/~vjp2/ruminatn.htm - = - web:  panix.com/~vjp2/vasos.htm
   facebook.com/vasjpan2 - linkedin.com/in/vasjpan02 -  biostrategist.com
  ---{Nothing herein constitutes advice.  Everything fully disclaimed.}---

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