Re: [Pytom-mail] "Missing lxml in pytom" has been solved, but another problem happened!

[Dustin M. <dus...@gm...>]

Hi Haixin,

Sorry for a bit of delay, but the XML label "File" in your Reference tag
in your job should actually be "Filename". There are a few quirks like
this where the labels in the documentation slightly differ from the ones
the code expects.

If you run into an error like this again, (I think there's two more if I
remember correctly) just trace the error and make sure it's not looking for
a different label.

I also have a few other minor changes for common errors here if you run into
something similar it may be of help. Mainly if you see an "isInstance" error
it should be fixed here:

https://sourceforge.net/p/pytom/gitrepo/ci/461b64420e74643c92d2bba409469a4cc2b10375/

Hope that helps,
Dustin Morado
John Briggs Group
MRC LMB

___

Cheers,
Dustin M.


On Sun, Oct 1, 2017 at 5:42 AM, Haixin Sui <su...@ho...> wrote:

> Hi Tom and all
>
>
> The missing lxml problem has been solved. It looks like the eman2 and
> pytom environment interfere with each other. After I disabled
> eman2, changed PATH setting and reinstalled pytom, the lxml is now
> available under pytom. However, the UI still does not work.  In fact, I
> have exactly the same UI issue for the newly installed pytom on my home
> ubuntu laptop today. The work station in my lab is also an ubuntu 16.04.
> Has anyone complied a successful Pytem on an Ubuntu system?
>
>
> UI is not important if command lines work. However, I am not yet able
> to get the command lines work. I stuck with an IOError when trying the
> localization.py ("IOError: Reference XML should either have Particles or
> Filename for ParticleList"). I have attached the job.xml document, and
> included the screen-output in this email. The job.xml was modified from the
> example in the directory "pytom-tutorial/RibosFromLysate/localization",
> and I could find any problem with it.
>
>
> Please advise what I can do to figure out the cause of the problem.
>
>
> Thank you!
>
>
> Haixin
>
>
>
> ---------
> hsui@Thinkpad-HR16395:~/subtomo$ /home/hsui/suilab_apps/pytom/bin/pytom
> /home/hsui/suilab_apps/pytom/bin/localization.py job.xml 2 2 2
> PyTom v0.971
>
> This license affects the software package PyTom and all the herein
> distributed source / data files.
> Authors:
> Thomas Hrabe
> Yuxiang Chen
> Friedrich Foerster
>
> Copyright (c) 2008-2016
> Max-Planck-Institute for Biochemistry
> Dept. Molecular Structural Biology
> 82152 Martinsried, Germany
> http://www.pytom.org
>
> This program is free software: you can redistribute it and/or modify
> it under the terms of the GNU General Public License as published by
> the Free Software Foundation, either version 3 of the License, or
> (at your option) any later version.
>
> This program is distributed in the hope that it will be useful,
> but WITHOUT ANY WARRANTY; without even the implied warranty of
> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
> GNU General Public License for more details.
>
> The complete license can be obtained from
> http://www.gnu.org/licenses/gpl-3.0.html.
>
> Traceback (most recent call last):
>   File "/home/hsui/suilab_apps/pytom/bin/localization.py", line 82, in
> <module>
>     startLocalizationJob(jobName, splitX, splitY, splitZ,
> doSplitAngles=False)
>   File "/home/hsui/suilab_apps/pytom/bin/localization.py", line 10, in
> startLocalizationJob
>     job.fromXMLFile(filename)
>   File "/home/hsui/suilab_apps/pytom/basic/structures.py", line 74, in
> fromXMLFile
>     self.fromStr(lines)
>   File "/home/hsui/suilab_apps/pytom/basic/structures.py", line 47, in
> fromStr
>     self.fromXML(root)
>   File "/home/hsui/suilab_apps/pytom/localization/peak_job.py", line 111,
> in fromXML
>     self.reference.fromXML(ref)
>   File "/home/hsui/suilab_apps/pytom/basic/structures.py", line 587, in
> fromXML
>     raise IOError('Reference XML should either have Particles or Filename
> for ParticleList')
> IOError: Reference XML should either have Particles or Filename for
> ParticleList
>
>
>
> ------------------------------
> *From:* Haixin Sui <su...@ho...>
> *Sent:* Friday, September 29, 2017 5:56 PM
> *To:* pyt...@li...
> *Subject:* [Pytom-mail] Missing lxml in pytom?
>
> Hi ,
>
> I have lxml installed and it works fine in pyton environment. However,
> lxml can not be found in pytom environment.
> My pytom environment seems to be incorrect. Any idea what to do to fix it?
> I wonder if this is related to why the UI of the pytom did not work here.
>
> The test results are listed in this email.
>
> Thanks!
>
> Haixin
>
> Python 2.7
> ---------------------------------
> hsui@dalian:~/subtomo$ python
> Python 2.7.12 (default, Nov 19 2016, 06:48:10)
> [GCC 5.4.0 20160609] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from lxml import etree
> >>>
> -----------------------------------
>
>
> pytom:
> -----------------------------------
> hsui@dalian:~/subtomo$ pytom
> PyTom v0.971
>
> This license affects the software package PyTom and all the herein
> distributed source / data files.
> ......(removed for easy reading)
> Python 2.7.13 | packaged by conda-forge | (default, May  2 2017, 12:48:11)
> [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from lxml import etree
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> ImportError: No module named lxml
> -------------------------
>
>
> ------------------------------------------------------------
> ------------------
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