python + wx & uno to fill libreoffice using ubuntu 14.04 - python-2.7

I collected user data using a wx python gui and than I used uno to fill this data into an openoffice document under ubuntu 10.xx
user + my-script ( +empty document ) --> prefilled document
After upgrading to ubuntu 14.04 uno doesn't work with python 2.7 anymore and now we have libreoffice instead of openoffice in ubuntu. when I try to run my python2.7 code, it says:
ImportError: No module named uno
How could I bring it back to work?
what I tried:
installed https://pypi.python.org/pypi/unotools v0.3.3
sudo apt-get install libreoffice-script-provider-python
converted the code to python3 and got uno importable, but wx is not importable in python3 :-/
ImportError: No module named 'wx'
googled and read python3 only works with wx phoenix
so tried to install: http://wxpython.org/Phoenix/snapshot-builds/
but wasn't able to get it to run with python3
is there a way to get the uno bridge to work with py2.7 under ubuntu 14.04?
Or how to get wx to run with py3?
what else could I try?

Create a python macro in LibreOffice that will do the work of inserting the data into LibreOffice and then in your python 2.7 code envoke the macro.
As the macro is running from with LibreOffice it will use python3.
Here is an example of how to envoke a LibreOffice macro from the command line:
#!/usr/bin/python3
# -*- coding: utf-8 -*-
##
# a python script to run a libreoffice python macro externally
# NOTE: for this to run start libreoffice in the following manner
# soffice "--accept=socket,host=127.0.0.1,port=2002,tcpNoDelay=1;urp;" --writer --norestore
# OR
# nohup soffice "--accept=socket,host=127.0.0.1,port=2002,tcpNoDelay=1;urp;" --writer --norestore &
#
import uno
from com.sun.star.connection import NoConnectException
from com.sun.star.uno import RuntimeException
from com.sun.star.uno import Exception
from com.sun.star.lang import IllegalArgumentException
def uno_directmacro(*args):
localContext = uno.getComponentContext()
localsmgr = localContext.ServiceManager
resolver = localsmgr.createInstanceWithContext("com.sun.star.bridge.UnoUrlResolver", localContext )
try:
ctx = resolver.resolve("uno:socket,host=localhost,port=2002;urp;StarOffice.ComponentContext")
except NoConnectException as e:
print ("LibreOffice is not running or not listening on the port given - ("+e.Message+")")
return
msp = ctx.getValueByName("/singletons/com.sun.star.script.provider.theMasterScriptProviderFactory")
sp = msp.createScriptProvider("")
scriptx = sp.getScript('vnd.sun.star.script:directmacro.py$directmacro?language=Python&location=user')
try:
scriptx.invoke((), (), ())
except IllegalArgumentException as e:
print ("The command given is invalid ( "+ e.Message+ ")")
return
except RuntimeException as e:
print("An unknown error occurred: " + e.Message)
return
except Exception as e:
print ("Script error ( "+ e.Message+ ")")
print(e)
return
return(None)
uno_directmacro()
And this is the corresponding macro code within LibreOffice called "directmacro.py" and stored in the User area for libreOffice macros (which would normally be $HOME/.config/libreoffice/4/user/Scripts/python :
#!/usr/bin/python
from com.sun.star.awt.MessageBoxButtons import BUTTONS_OK, BUTTONS_OK_CANCEL, BUTTONS_YES_NO, BUTTONS_YES_NO_CANCEL, BUTTONS_RETRY_CANCEL, BUTTONS_ABORT_IGNORE_RETRY
from com.sun.star.awt.MessageBoxButtons import DEFAULT_BUTTON_OK, DEFAULT_BUTTON_CANCEL, DEFAULT_BUTTON_RETRY, DEFAULT_BUTTON_YES, DEFAULT_BUTTON_NO, DEFAULT_BUTTON_IGNORE
from com.sun.star.awt.MessageBoxType import MESSAGEBOX, INFOBOX, WARNINGBOX, ERRORBOX, QUERYBOX
def directmacro(*args):
import socket, time
class FontSlant():
from com.sun.star.awt.FontSlant import (NONE, ITALIC,)
#get the doc from the scripting context which is made available to all scripts
desktop = XSCRIPTCONTEXT.getDesktop()
model = desktop.getCurrentComponent()
text = model.Text
tRange = text.End
cursor = desktop.getCurrentComponent().getCurrentController().getViewCursor()
doc = XSCRIPTCONTEXT.getDocument()
parentwindow = doc.CurrentController.Frame.ContainerWindow
# your cannot insert simple text and text into a table with the same method
# so we have to know if we are in a table or not.
# oTable and oCurCell will be null if we are not in a table
oTable = cursor.TextTable
oCurCell = cursor.Cell
insert_text = "This is text inserted into a LibreOffice Document\ndirectly from a macro called externally"
Text_Italic = FontSlant.ITALIC
Text_None = FontSlant.NONE
cursor.CharPosture=Text_Italic
if oCurCell == None: # Are we inserting into a table or not?
text.insertString(cursor, insert_text, 0)
else:
cell = oTable.getCellByName(oCurCell.CellName)
cell.insertString(cursor, insert_text, False)
cursor.CharPosture=Text_None
return None
You will of course need to adapt the code to either accept data as arguments, read it from a file or whatever.

Ideally I would say use python 3, because python 2 is becoming outdated. The switch requires quite a bit of new coding changes, but better sooner than later. So I tried:
sudo pip3 install -U --pre \
-f http://wxpython.org/Phoenix/snapshot-builds/ \
wxPython_Phoenix
However this gave me errors, and I didn't want to spend the next couple of days working through them. Probably the pre-release versions are not ready for prime time yet.
So instead, what I recommend is to switch to AOO for now. See https://stackoverflow.com/a/27980255/5100564 for instructions. AOO does not have all the latest features that LO has, but it is a good solid Office product.
Apparently it is also possible to rebuild LibreOffice with python 2 using this script: https://gist.github.com/hbrunn/6f4a007a6ff7f75c0f8b

Related

Pyqt4 to Pyqt5 and python code error

i switch from Pyqt4 to Pyqt5 and from python2.7 to 3.4 and i found a bug in Pyqt5 so i upgrade it to the last version which is not suppoted by python3.4 . than i used python3.5 and it work fine except one module called pymaxwell.
always the app crash and closed and to confirm i go back to python2.7 and i use pyqt5 for python2.7 and the same error ; the app closed immediately and show me an error in a part in the code which is work well with pyqt4.
in the gif a comparaison between Pyqt4/Pyqt5 with python2.7
comparison
the part of the code which have problem:
self.btnMXSmxm()
self.mxs_filt.setChecked(True)
self.show_folder.setChecked(False)
inPath = self.input_mxs_scene_2.text();
self.input_mxs_scene.setText(inPath);
self.mxm_list.clear()
if len(inPath) == 0:
self.chosen_material.clear()
# loop over all mxs
else:
mxsList = self.input_mxs_scene.text()
print mxsList
if not len(mxsList) == 0:
scene = Cmaxwell(mwcallback);
ok = scene.readMXS(mxsList);
sceneMaterials = scene.getMaterialNames();
materialcount = int(scene.getMaterialsCount()[0])
if os.path.isfile(self.input_mxs_scene.text()):
for name in sceneMaterials:
scenematerial = scene.getMaterial(name)
problem solved;
i use python 3.5.4 and pyqt 5.9
now even i use read(file) or read(str(file)) don't give any error.
and i find that with pyqt5 it need new arrangement of some lines in the code.
i modify the code and it work :
mxsList = self.input_mxs_scene.text()
scene = Cmaxwell(mwcallback)
materialcount = int(scene.getMaterialsCount()[0])
if not len(inPath) == 0:
if os.path.isfile(self.input_mxs_scene.text()):
ok = scene.readMXS(mxsList)
sceneMaterials = scene.getMaterialNames()
if not len(mxsList) == 0:
for name in sceneMaterials:
scenematerial = scene.getMaterial(name)
# #print scenematerial
self.mxm_list.addItem(name)
i also add : from PyQt5.QtCore import *
that solve other problem with reading media files
after many tries with different versions of python and pyqt5 ; the best versions works well together , python 2.7.9 and pyqt5 from github :
PyQt 5.7.1 for Python 2.7

Running locally blastn against nt db thru python script

I have a fasta file with sequence that I want to blast locally to 'nt' database dowloaded on my computer from ncbi website
I dowloaded blast 2.6.0.
In order to access blast from anywhere, I did:
gedit ~/.bashrc
export PATH=/usr/local/ncbi-blast-2.6.0+/bin:$PATH
then I did:
source ~/.bashrc
Then I downloaded 'nt' database (155.6GB) and stored it in /usr/local/blastdb
I want to run in python script this command:
from Bio.Blast.Applications import NcbiblastnCommandline
cline = NcbiblastnCommandline(query="/home/proprietaire/Desktop/JADE/stage_scripts/seq_error_fasta.fasta", db="/usr/local/blastdb/nt", evalue=0.001, out="blast_result_local.xml", outfmt=5)
But it is not working for a reason. Please help me figure out what I'm doing wrong. Thank you for your help.
EDIT:
'seq_error_fasta.fasta' : is my fasta file with 64 sequences that I want to blast to 'nt' database.
My 'seq_error_fasta.fasta' contains sequence loaded with error like S, J, X so I want to blast them to 'nt' db in order to get the closest better sequence
I found out that I need to format the nt database dowloaded from ncbi so I did this:
makeblastdb -dbtype nucl -in nt
Then I added this after my cline variable in my python script:
stdout, stderr = cline()
The script is running but unfortunately I'm getting this error now:
Bus error (core dumped)
I think it's a ram memory problem so I thought that I need to shorten 'nt' db by taking only the bacteria sequence. I looked on NCBI for a whole bacteria only database but there is multiple database of different species like more then a thousand.
I also tried blast online using this script:
f = open('output_blast.xml','w')
for rec in SeqIO.parse(open("seq_error_fasta.fasta"), 'fasta):
result_handle = NCBIWWW.qblast("blastn", "nt", rec.format("fasta"), format_type="XML", alignments=1, perc_ident=95, expect= 0.001)
f.write(result_handle.read())
f.close()
but this only doing one query sequence and returning all hits, althought I specified 1 hit and 95% of identity.
This is driving me crazy lollll Please help
Download NCBI nr database:
$ mkdir db
$ cd db
$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr*
Run blast:
import io
import shlex
import subprocess
BLAST_OUTFMT6 = """\
'6 qacc sacc pident length mismatch gapopen qstart qend sstart send evalue bitscore qseq sseq'\
"""
BLAST_OUTFMT6_COLUMN_NAMES = [
'query_id', 'subject_id', 'pc_identity', 'alignment_length', 'mismatches', 'gap_opens',
'q_start', 'q_end', 's_start', 's_end', 'evalue', 'bitscore', 'qseq', 'sseq',
]
def blastp(sequence, db, evalue=0.001, max_target_seqs=100000):
system_command = (
'blastp -db {db} -outfmt {outfmt} -evalue {evalue} -max_target_seqs {max_target_seqs}'
.format(db=db, outfmt=BLAST_OUTFMT6, evalue=evalue, max_target_seqs=max_target_seqs)
)
cp = subprocess.Popen(
shlex.split(system_command),
stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
universal_newlines=True)
result, error_message = cp.communicate(sequence)
if error_message.strip():
print("Error: {}".format(error_message))
return result
if __name__ == '__main__':
result = blastp('AAAAAAAAAAAAAA', db='/path/to/db/nr')
print(result)

ImportError with nltk_train

I am trying to get my ways around with nltk-trainer (https://github.com/japerk/nltk-trainer). I managed to train Dutch taggers and chunkers with the commands (directly in Anaconda console):
python train_tagger.py conll2002 --fileids ned.train --classifier IIS --filename ~/nltk_data/taggers/conll2002_ned_IIS.pickle
python train_chunker.py conll2002 --fileids ned.train --classifier NaiveBayes --filename ~/nltk_data/chunkers/conll2002_ned_NaiveBayes.pickle
Then I run a little script to test the tagger and the chunker:
import nltk
from nltk.corpus import conll2002
# Loading training pickles
tokenizer = nltk.data.load('tokenizers/punkt/dutch.pickle')
tagger = nltk.data.load('taggers/conll2002_ned_IIS.pickle')
chunker = nltk.data.load('chunkers/conll2002_ned_NaiveBayes.pickle')
# Testing
test_sents = conll2002.tagged_sents(fileids="ned.testb")[0:1000]
print "tagger accuracy on test-set: " + str(tagger.evaluate(test_sents))
test_sents = conll2002.chunked_sents(fileids="ned.testb")[0:1000]
print "tagger accuracy on test-set: " + str(chunker.evaluate(test_sents))
This works fine from the nltk-trainer-master folder, but when I move the script elsewhere, I get an import error:
ImportError: No module named nltk_trainer.chunking.chunkers
How can I make this work outside the nltk-trainer-master folder, without copying the nltk_trainer folder?
(Python 2.7, nltk 3.2.1)

Sniff error in Scapy

I am trying to use scapy for one of my project. But, it gives the following error, When I test it.
NameError: name 'sniff' is not defined
import sys
from scapy import *
devices = set()
def PacketHandler(pkt):
if pkt.haslayer(Dot11) :
dot11_layer = pkt.getlayer(Dot11)
if dot11_layer.addr2 and ( dot11_layer.addr2 not in devices ):
devices.add(dot11_layer.addr2)
print dot11_layer.addr2
sniff(iface = sys.argv[1], count = int(sys.argv[2]), prn = PacketHandler)
if I change module name to scapy.all, it says there is no module.
Python version: 2.7
Scapy version: 2.3.3
I have just installed with pip install scapy.Any helps would be appreciated.
You must import Scapy as from scapy.all import *, and you must not name your script scapy.py (or any other script in the current directory or your PYTHONPATH)!

How to launch a Python Spyder session through script / shortcut?

I have this code to launch a Spyder IDE, in Anaconda 2, Python 2.7 :
from spyderlib import start_app
main1= start_app.main()
main1.load_session('/project27/_test01_.session.tar')
'''
from spyderlib.utils.iofuncs import load_session
load_session(filename+'.session.tar')
'''
Code method to load session is here: https://github.com/jromang/spyderlib/blob/master/spyderlib/spyder.py
#---- Sessions
def load_session(self, filename=None):
"""Load session"""
if filename is None:
self.redirect_internalshell_stdio(False)
filename, _selfilter = getopenfilename(self, _("Open session"),
getcwd(), _("Spyder sessions")+" (*.session.tar)")
self.redirect_internalshell_stdio(True)
if not filename:
return
if self.close():
self.next_session_name = filename
the 1st part comes from Anaconda Scripts where Spyder script.
It seems not working to load session.
Spyder sessions were removed in Spyder 3.0. Now the same functionality is provided by Projects (which also save the list of open files in the Editor), so please update to that version.
Besides, Spyder 3.1 will come with a new option called --project to load a project at startup (Spyder 3.1 will be released on January 17/2017).
For people still using only Spyder 2.0 (....), there is a small hack possible to create shortcut of session (SPyder session launched directly with shortcut).
Here, the code :
# -*- coding: utf-8 -*-
import sys, time, os
file_session= ''
if len(sys.argv) > 1 :
file_session= sys.argv[1]
print file_session
sys.argv= sys.argv[:1]
from spyderlib import start_app
if file_session != '' :
main1= start_app.main( file_session)
else :
main1= start_app.main()