Jython Shutil (different behaviour between Windows, Linux, J/Python)!

Question

I'm using Jython, through Topspin (NMR Software running on Java) to run the following code:

home = "C:/Bruker/TopSpin3.2"
ep_zges_outdir = os.path.abspath(home + "/data/Testshutil/nmr/zges/")
data = ["EP_Saliva_140131_raw", "1", "1", "C:/Bruker/TopSpin3.2/data/Testshutil/nmr"]
ep_zges_list = [["EP_Saliva_140131_raw",25,334],...]

for sample in ep_zges_list:
    if data[0] == sample[0] and data[1] == str(sample[1]):
        src = os.path.abspath(data[3] + "/" + data[0] + "/" + data[1])
        dst = os.path.abspath(ep_zges_outdir + "/" + str(sample[2]))
        shutil.copytree(src, dst)

Proper imports were done and, when it works, no os.path.abspath is necessary.

This works perfectly in Windows/Linux python and through the same Software that runs Jython in CentOS. It does not run in the Software/Jython in Windows 7 and the following error is produced:

Traceback (most recent call last):
  File "C:/Bruker/TopSpin3.2/exp/stan/nmr/py/user/JF_test_code_8.py", line 41, in <module>
    shutil.copytree(os.path.abspath(data[3] + "/" + data[0] + "/" + data[1]), os.path.abspath(ep_zges_outdir + "/" + str(sample[2])))
  File "C:\Bruker\TopSpin3.2\jython\Lib\shutil.py", line 145, in copytree
    raise Error, errors
shutil.Error: [u'C:\\Bruker\\TopSpin3.2\\data\\Testshutil\\nmr\\EP_Saliva_140310_raw\\1\\pdata\\1', 
u'C:\\Bruker\\TopSpin3.2\\data\\Testshutil\\nmr\\zges\\334\\pdata\\1', 
"[Errno 5] Input/output error: u'C:\\\\Bruker\\\\TopSpin3.2\\\\data\\\\Testshutil\\\\nmr\\\\zges\\\\334\\\\pdata\\\\1'", 
u'C:\\Bruker\\TopSpin3.2\\data\\Testshutil\\nmr\\EP_Saliva_140310_raw\\1\\pdata', 
u'C:\\Bruker\\TopSpin3.2\\data\\Testshutil\\nmr\\zges\\334\\pdata', 
"[Errno 5] Input/output error: u'C:\\\\Bruker\\\\TopSpin3.2\\\\data\\\\Testshutil\\\\nmr\\\\zges\\\\334\\\\pdata'", 
u'C:\\Bruker\\TopSpin3.2\\data\\Testshutil\\nmr\\EP_Saliva_140310_raw\\1', 
u'C:\\Bruker\\TopSpin3.2\\data\\Testshutil\\nmr\\zges\\334', 
"[Errno 5] Input/output error: u'C:\\\\Bruker\\\\TopSpin3.2\\\\data\\\\Testshutil\\\\nmr\\\\zges\\\\334'"]

Software versions: Windows 7 SP1 64bit. Python 2.7 32bit. Jython 2.5.3 running on Topspin 3.2 and Java 1.7.0_51.

CentOS 6.5 32Bit Jython 2.5.3 running on Topspin 3.2 and Java 1.7.0_45

Geoff Bache · Accepted Answer · 2014-03-20 15:03:14Z

1

I think this is a Jython bug (a very annoying one). See

http://bugs.jython.org/issue1872

answered Mar 20, 2014 at 15:03

Geoff Bache

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1 Comment

Animismus Over a year ago

Thanks! I did what was described here for the copystat function: bugs.jython.org/msg7033

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