Develop Reference

Owlrady2 Load imported onotologies from file not from url

I'm trying to load an ontology that imports some other ontologies. These other ontologies are located on my machine and not on the web. If I try my_ontology.load() it tries to load these other ontologies from their URI. But that fails.
How can I tell owlready2 where these ontologies are located?
The traceback looks like this:
Traceback (most recent call last):
File "~Software/PyOntologyChecker/app.py", line 12, in <module>
covid_onto = get_ontology_from_file(COVID_ONTOLOGY)
File "~Software/PyOntologyChecker/app.py", line 8, in get_ontology_from_file
return get_ontology("file://" + file_path).load()
File "~.local/lib/python3.8/site-packages/owlready2/namespace.py", line 813, in load
imported_ontologies = [self.world.get_ontology(self._unabbreviate(abbrev_iri)).load() for abbrev_iri in self.world._get_obj_triples_sp_o(self.storid, owl_imports)]
File "~.local/lib/python3.8/site-packages/owlready2/namespace.py", line 813, in <listcomp>
imported_ontologies = [self.world.get_ontology(self._unabbreviate(abbrev_iri)).load() for abbrev_iri in self.world._get_obj_triples_sp_o(self.storid, owl_imports)]
File "~.local/lib/python3.8/site-packages/owlready2/namespace.py", line 773, in load
except: raise OwlReadyOntologyParsingError("Cannot download '%s'!" % f)
owlready2.base.OwlReadyOntologyParsingError: Cannot download 'http://ontofox.hegroup.org/CHEBI_module11.owl'!

Assuming you have a local copy of CHEBI_module11.owl dependence (ex. SOME_DIR/HEBI_module11.owl), add its location into onto_path (as stated in the docs):
onto_path.append("SOME_DIR")
before doing my_ontology.load(). That tells Owlready2 to look for files in SOME_DIR. The path can be relative or absolute (like c:/data/ontologies).
The current Python's working directory is not scanned by default but can be set so with onto_path.append(".").
If a required ontology is described by URI not ending with a usual filename, like "http://rdf.webofcode.org/woc/", the local filename (woc in this case) should not have an extension.

cx_freeze and docx - problems when freezing

I have a simple program that takes input from the user and then does scraping with selenium. Since the user doesn't have Python environment installed I would like to convert it to *.exe. I usually use cx_freeze for that and I have successfully converted .py programs to .exe. At first it was missing some modules (like lxml) but I was able to solve it. Now I think I only have problem with docx package.
This is how I initiate the new document in my program (I guess this is what causes me problems):
doc = Document()
#then I do some stuff to it and add paragraph and in the end...
doc.save('results.docx')
When I run it from python everything works fine but when I convert to exe I get this error:
Traceback (most recent call last):
File "C:\Users\tyszkap\AppData\Local\Continuum\Anaconda3\lib\site-packages\cx_Freeze\initscripts\Console.py", line 27, in <module>
exec(code, m.__dict__)
File "tribunalRio.py", line 30, in <module>
File "C:\Users\tyszkap\AppData\Local\Continuum\Anaconda3\lib\site-packages\docx\api.py", line 25, in Document
document_part = Package.open(docx).main_document_part
File "C:\Users\tyszkap\AppData\Local\Continuum\Anaconda3\lib\site-packages\docx\opc\package.py", line 116, in open
pkg_reader = PackageReader.from_file(pkg_file)
File "C:\Users\tyszkap\AppData\Local\Continuum\Anaconda3\lib\site-packages\docx\opc\pkgreader.py", line 32, in from_file
phys_reader = PhysPkgReader(pkg_file)
File "C:\Users\tyszkap\AppData\Local\Continuum\Anaconda3\lib\site-packages\docx\opc\phys_pkg.py", line 31, in __new__
"Package not found at '%s'" % pkg_file
docx.opc.exceptions.PackageNotFoundError: Package not found at 'C:\Users\tyszkap\Dropbox (Dow Jones)\Python Projects\build\exe.win-a
md64-3.4\library.zip\docx\templates\default.docx'
This is my setup.py program:
from cx_Freeze import setup, Executable
executable = Executable( script = "tribunalRio.py" )
# Add certificate to the build
options = {
"build_exe": {'include_files' : ['default.docx'],
'packages' : ["lxml._elementpath", "inspect", "docx", "selenium"]
}
}
setup(
version = "0",
requires = [],
options = options,
executables = [executable])
I thought that explicitly adding default.docx to the package would solve the problem (I have even tried adding it to the library.zip but it gives me even more errors) but it didn't. I have seen this post but I don't know what they mean by:
copying the docx document.py module inside my function (instead of
using Document()
Any ideas? I know that freezing is not the best solution but I really don't want to build a web interface for such a simple program...
EDIT:
I have just tried this solution :
def find_data_file(filename):
if getattr(sys, 'frozen', False):
# The application is frozen
datadir = os.path.dirname(sys.executable)
else:
# The application is not frozen
# Change this bit to match where you store your data files:
datadir = os.path.dirname(__file__)
return os.path.join(datadir, filename)
doc = Document(find_data_file('default.docx'))
but again receive Traceback error (but the file is in this location...):
Traceback (most recent call last):
File "C:\Users\tyszkap\AppData\Local\Continuum\Anaconda3\lib\site-packages\cx_Freeze\initscripts\Console.py", line 27, in <module>
exec(code, m.__dict__)
File "tribunalRio.py", line 43, in <module>
File "C:\Users\tyszkap\AppData\Local\Continuum\Anaconda3\lib\site-packages\docx\api.py", line 25, in Document
document_part = Package.open(docx).main_document_part
File "C:\Users\tyszkap\AppData\Local\Continuum\Anaconda3\lib\site-packages\docx\opc\package.py", line 116, in open
pkg_reader = PackageReader.from_file(pkg_file)
File "C:\Users\tyszkap\AppData\Local\Continuum\Anaconda3\lib\site-packages\docx\opc\pkgreader.py", line 32, in from_file
phys_reader = PhysPkgReader(pkg_file)
File "C:\Users\tyszkap\AppData\Local\Continuum\Anaconda3\lib\site-packages\docx\opc\phys_pkg.py", line 31, in __new__
"Package not found at '%s'" % pkg_file
docx.opc.exceptions.PackageNotFoundError: Package not found at 'C:\Users\tyszkap\Dropbox (Dow Jones)\Python Projects\build\exe.win-a
md64-3.4\default.docx'
What am I doing wrong?

I expect you'll find the problem has to do with your freezing operation not placing the default Document() template in the expected location. It's stored as package data in the python-docx package as docx/templates/default.docx (see setup.py here: https://github.com/python-openxml/python-docx/blob/master/setup.py#L37)
I don't know how to fix that in your case, but that's where the problem is it looks like.

I had the same problem and managed to get around it by doing the following. First, I located the default.docx file in the site-packages. Then, I copied it in the same directory as my .py file. I also start the .docx file with Document() which has a docx=... flag, to which I assigned the value: os.path.join(os.getcwd(), 'default.docx') and now it looks like doc = Document(docx=os.path.join(os.getcwd(), 'default.docx')). The final step was to include the file in the freezing process. Et voilà! So far I have no problem.

Error generating Swagger server (Python Flask) from Swagger editor

I've used the Swagger Editor to manually generate my Swagger spec file and generated the files for a Python Flask server. Following the README I installed connexion, but when I run python app.py I get the error:
ValueError: need more than 1 value to unpack. Any ideas?
Full stack trace below:
No handlers could be found for logger "connexion.api"
Traceback (most recent call last):
File "app.py", line 5, in <module>
app.add_api('swagger.yaml')
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/connexion/app.py", line 144, in add_api
debug=self.debug)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/connexion/api.py", line 127, in __init__
self.add_paths()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/connexion/api.py", line 198, in add_paths
six.reraise(*sys.exc_info())
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/connexion/api.py", line 187, in add_paths
self.add_operation(method, path, endpoint, path_parameters)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/connexion/api.py", line 160, in add_operation
resolver=self.resolver)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/connexion/operation.py", line 168, in __init__
resolution = resolver.resolve(self)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/connexion/resolver.py", line 50, in resolve
return Resolution(self.resolve_function_from_operation_id(operation_id), operation_id)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/connexion/resolver.py", line 71, in resolve_function_from_operation_id
return self.function_resolver(operation_id)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/connexion/utils.py", line 106, in get_function_from_name
module_name, attr_path1 = module_name.rsplit('.', 1)
ValueError: need more than 1 value to unpack

I ran into this as well. From what I see, the generated code from Swagger seems to assume you're using Python 3. While connexion supports both Python 2.7 & 3.4+, it does need a __init__.py file in the generated python-flask-server/ base directory as well as inside the controllers/ subdirectory to work for Python 2.7 (Implicit Namespace Packages were introduced in Python 3.3). If you create those 2 empty files after generating the code, things should work. If the Swagger generator wants to support Python 2.7 (since connexion allows for it), it would just need to provide those files as well.

stack dump in twisted app.py 'application' error when using twistd but works with python?

I am trying to use twisted but when i try to run some of the example code provided with the twisted package, it seems to always crash when i use "twistd" instead of "python"
for example, using the example code given with twisted,
if i run to command : twisted -ny echoserv.py
Unhandled Error
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/twisted/application/app.py", line 652, in run
runApp(config)
File "/usr/lib/python2.7/site-packages/twisted/scripts/twistd.py", line 23, in runApp
_SomeApplicationRunner(config).run()
File "/usr/lib/python2.7/site-packages/twisted/application/app.py", line 386, in run
self.application = self.createOrGetApplication()
File "/usr/lib/python2.7/site-packages/twisted/application/app.py", line 451, in createOrGetApplication
application = getApplication(self.config, passphrase)
--- ---
File "/usr/lib/python2.7/site-packages/twisted/application/app.py", line 462, in getApplication
application = service.loadApplication(filename, style, passphrase)
File "/usr/lib/python2.7/site-packages/twisted/application/service.py", line 405, in loadApplication
application = sob.loadValueFromFile(filename, 'application', passphrase)
File "/usr/lib/python2.7/site-packages/twisted/persisted/sob.py", line 211, in loadValueFromFile
value = d[variable]
exceptions.KeyError: 'application'
Failed to load application: 'application'
Could not find 'application' in the file. To use 'twistd -y', your .tac
file must create a suitable object (e.g., by calling service.Application())
and store it in a variable named 'application'. twistd loads your .tac file
and scans the global variables for one of this name.
Please read the 'Using Application' HOWTO for details.
I was using Twisted version 11.0.0 but then i tried 12.0.0 but i have the same problem.
The version of python i am using is 2.7.2
Any ideas on what to do would be helpful. I have been trying to deal with this problem for a few days now. thanks!

twistd -y is meant to be used with a python file that contains a variable called application, there is none in this file, so it's not going to work.
You might want to spend some time reading twistd's documentation so you get a clearer idea of its role in the twisted ecosystem.

To use 'twistd -y', your .tac file must create a suitable object (e.g., by calling service.Application()) and store it in a variable named 'application'. twistd loads your .tac file and scans the global variables for one of this name.
Please read the 'Using Application' HOWTO for details.

py2exe/pyinstaller and DispatchWithEvents

I have a program that uses the win32com library to control iTunes, but have been having some issues getting it to compile into an executable. The problem seems to revolve around using DispatchWithEvents instead of Dispatch. I've created a very simple program to illustrate my problem:
import win32com.client
win32com.client.gencache.is_readonly = False #From py2exe wiki
class ITunesEvents(object):
def __init__(self): self.comEnabled = True
def OnCOMCallsDisabledEvent(self, reason): self.comEnabled = False
def OnCOMCallsEnabledEvent(self): self.comEnabled = True
# The first line works in the exe, the second doesn't.
itunes = win32com.client.Dispatch("iTunes.Application")
#itunes = win32com.client.DispatchWithEvents("iTunes.Application", ITunesEvents)
lib = getattr(itunes, "LibraryPlaylist")
src = getattr(lib, "Source")
playlists = getattr(src, "Playlists")
print "Found %i playlists." % getattr(playlists, "Count")
Using Dispatch, the program compiles and runs correctly. Using DispatchWithEvents, the program runs fine when called from the command line, but produces the following error when running the exe:
Traceback (most recent call last):
File "sandbox.py", line 16, in <module>
itunes = win32com.client.DispatchWithEvents("iTunes.Application", ITunesEvents)
File "win32com\client\__init__.pyc", line 252, in DispatchWithEvents
File "win32com\client\gencache.pyc", line 520, in EnsureModule
File "win32com\client\gencache.pyc", line 287, in MakeModuleForTypelib
File "win32com\client\makepy.pyc", line 259, in GenerateFromTypeLibSpec
File "win32com\client\gencache.pyc", line 141, in GetGeneratePath
IOError: [Errno 2] No such file or directory: '[distDir]\\library.zip\\win32com\\gen_py\\__init__.py'
I've also tried using PyInstaller, which gives a similar error:
File "<string>", line 16, in <module>
File "[outDir]/win32com.client", line 252, in DispatchWithEvents
File "[outDir]/win32com.client.gencache", line 520, in EnsureModule
File "[outDir]/win32com.client.gencache", line 287, in MakeModuleForTypelib
File "[outDir]/win32com.client.makepy", line 286, in GenerateFromTypeLibSpec
File "[outDir]/win32com.client.gencache", line 550, in AddModuleToCache
File "[outDir]/win32com.client.gencache", line 629, in _GetModule
File "[pyinstallerDir]\iu.py", line 455, in importHook
raise ImportError, "No module named %s" % fqname
ImportError: No module named win32com.gen_py.9E93C96F-CF0D-43F6-8BA8-B807A3370712x0x1x13
I know I can manually add the typelib in my setup.py file, but I'd like to run the code on computers with different versions of iTunes without recompiling so I'd prefer to dynamically create it. If there's no way to do this with the setup/spec, maybe there is another way to load the events? Thanks.
Addition:
Thanks to Ryan, I found I could take the generated py file and after a little digging, was able to come up with the following.
Take the generated py file (from makepy.py) and rename it somewhere like cominterface.py. Then you'll need to do the following to actually create the COM object with event handler.
import cominterface
from types import ClassType
from win32com.client import EventsProxy, _event_setattr_
class ItunesEvents:
'''iTunes events class. See cominterface for details.'''
def OnPlayerPlayEvent(self, t):print "Playing..."
def OnPlayerStopEvent(self, t): print "Stopping..."
itunes = cominterface.iTunesApp()
rClass = ClassType("COMEventClass", (itunes.__class__, itunes.default_source, ItunesEvents), {'__setattr__': _event_setattr_})
instance = rClass(itunes._oleobj_)
itunes.default_source.__init__(instance, instance)
#ItunesEvents.__init__(instance) #Uncomment this line if your events class has __init__.
itunes = EventsProxy(instance)
Then you can go about your business.

I was experiencing the exact same error.
This link put me in the right direction -->
http://www.py2exe.org/index.cgi/UsingEnsureDispatch
however it mentions that :
NB You must ensure that the python...\win32com.client.gen_py dir does not exist
to allow creation of the cache in %temp%
Which was a bit confusing.
What solved it for me was renaming "C:\Python26\Lib\site-packages\win32com\gen_py" to "C:\Python26\Lib\site-packages\win32com\gen_pybak" (when running py2exe)

This is the official way to do it.
(Edit: copied verbatim example from that link above)
import win32com.client
if win32com.client.gencache.is_readonly == True:
#allow gencache to create the cached wrapper objects
win32com.client.gencache.is_readonly = False
# under p2exe the call in gencache to __init__() does not happen
# so we use Rebuild() to force the creation of the gen_py folder
win32com.client.gencache.Rebuild()
# NB You must ensure that the python...\win32com.client.gen_py dir does not exist
# to allow creation of the cache in %temp%
# Use SAPI speech through IDispatch
from win32com.client.gencache import EnsureDispatch
from win32com.client import constants
voice = EnsureDispatch("Sapi.SpVoice", bForDemand=0)
voice.Speak( "Hello World.", constants.SVSFlagsAsync )

Instead of depending on the cache, I'd recommend going into the local cache directory, copying the generated file into your local project file, and naming it something like ITunesInterface.py, and calling to that explicitly. This will make py2exe pull it into your compiled app.