I'm trying to parse text from pdf file. while I was doing tutorial of how to PyPDF2 I got the following error. I did the search for an answer but ended up finding none. Any Help will be greatly appreciated.
Traceback (most recent call last):
File "D:/text_recognizer/main.py", line 4, in <module>
inputStream = PyPDF2.PdfFileReader(input)
File "D:\KimKanna's Class\python27\lib\site-packages\PyPDF2\pdf.py", line 1084, in __init__
self.read(stream)
File "D:\KimKanna's Class\python27\lib\site-packages\PyPDF2\pdf.py", line 1689, in read
stream.seek(-1, 2)
IOError: [Errno 22] Invalid argument
here is fullcode
import PyPDF2
with open(".\\pdf\\test_sample.pdf","rb") as input:
inputStream = PyPDF2.PdfFileReader(input)
In my case the .pdf I wanted to open is empty and not closed from previous python code in powershell(cmd prompt). So, when I tried to delete those files it says 'Close the file and try again'. (that was my "AHaa" moment)
So I stopped the py.exe from my Windows task manager and deleted those empty, not closed files. Then I run the same code with another files, It worked fine.. :)
Related
Starting a few days ago, after months without issue, I began having a giant error box keep popping up when editing my code in Atom. I believe it is from the Hydrogen plugin, the weird thing is even with this error the code still runs and does what I want it too.
I created a new conda environment, installing only what I needed (pandas, geopandas, descartes, jupyter) and even when using the new environment in Atom I am getting this issue. I've tried upgrading ipykernel but it is already the most recent version.
Error Message
[IPKernelApp] ERROR | Exception in message handler: Traceback (most recent call last): File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/ipykernel/kernelbase.py", line 268, in dispatch_shell yield gen.maybe_future(handler(stream, idents, msg)) File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/tornado/gen.py", line 762, in run value = future.result() File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/tornado/gen.py", line 234, in wrapper yielded = ctx_run(next, result) File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/ipykernel/kernelbase.py", line 583, in complete_request matches = yield gen.maybe_future(self.do_complete(code, cursor_pos)) File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/ipykernel/ipkernel.py", line 360, in do_complete return self._experimental_do_complete(code, cursor_pos) File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/ipykernel/ipkernel.py", line 385, in _experimental_do_complete completions = list(_rectify_completions(code, raw_completions)) File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/IPython/core/completer.py", line 484, in rectify_completions completions = list(completions) File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/IPython/core/completer.py", line 1818, in completions for c in self._completions(text, offset, _timeout=self.jedi_compute_type_timeout/1000): File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/IPython/core/completer.py", line 1861, in _completions matched_text, matches, matches_origin, jedi_matches = self._complete( File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/IPython/core/completer.py", line 2029, in _complete completions = self._jedi_matches( File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/IPython/core/completer.py", line 1373, in _jedi_matches interpreter = jedi.Interpreter( File "/home/username/anaconda3/envs/fresh/lib/python3.8/site-packages/jedi/api/init.py", line 725, in init super().init(code, environment=environment, TypeError: init() got an unexpected keyword argument 'column'
The latest jedi (0.18) release is incompatible with IPython 7.19 see this discussion. IPython: 7.20 (released Feb 1st 2020) and 8.0 (not yet released) have a compatibility fix.
The correct workaround at this time is to upgrade IPython:
pip install -U ipython==7.20
In future you can search for the final two lines of the trackback after removing all path fragments specific to your installation, this is searching for:
line 2029, in _complete completions = self._jedi_matches IPython/core/completer.py, line 1373, in _jedi_matches interpreter = jedi.Interpreter( jedi/api/init.py, line 725, in init super().init(code, environment=environment, TypeError: init() got an unexpected keyword argument 'column'
This will give you the relevant issues on GitHub in the first two Google result as for today.
I am a beginner to PyMOL and I am using it for my docking project. I have encountered errors using the Autodock/Vina plugin in PyMOL.
I was trying to carry out the set up for the grid and Error 1 occurred when I was clicking on the arrow that allows me to change the grid parameter x,y and z.
As for Error 2, it occurs when I tried to generate the receptor on the next page.
Under the log section, I also got a notice saying "Batch: prepare_receptor4.py -r C:\Users\User\Desktop\plugin-test\receptor.3ig7.pdb -o C:\Users\User\Desktop\plugin-test\receptor.3ig7.pdbqt -A checkhydrogen"
It would be appreciated if you would tell me what is missing or should be done to solve these errors.
I look forward to reading any of your replies and I thank you in advance,
Elayne
Error: 1
TypeError Exception in Tk callback
Function: <bound method Autodock.n_points_Y_changed of <pmg_tk.startup.autodock_plugin.Autodock object at 0x0000020649CD9388>> (type: <class 'method'>)
Args: ('scroll', '1', 'units')
Traceback (innermost last):
File "C:\Users\User\AppData\Local\Schrodinger\PyMOL2\lib\site-packages\Pmw.py", line 1823, in __call__
return self.func(*args)
TypeError: n_points_Y_changed() takes 2 positional arguments but 4 were given
Error: 2
FileNotFoundError Exception in Tk callback
Function: <bound method Autodock.generate_receptor of <pmg_tk.startup.autodock_plugin.Autodock object at 0x0000020649CD9388>> (type: <class 'method'>)
Args: ()
Traceback (innermost last):
File "C:\Users\User\AppData\Local\Schrodinger\PyMOL2\lib\site-packages\Pmw.py", line 1823, in __call__
return self.func(*args)
File "C:\Users\User\AppData\Local\Schrodinger\PyMOL2\lib\site-packages\pmg_tk\startup\autodock_plugin.py", line 1940, in generate_receptor
result, output = getstatusoutput(command)
File "C:\Users\User\AppData\Local\Schrodinger\PyMOL2\lib\site-packages\pmg_tk\startup\autodock_plugin.py", line 85, in getstatusoutput
p = Popen(args, stdout=PIPE, stderr=STDOUT, stdin=PIPE, env=env)
File "C:\Users\User\AppData\Local\Schrodinger\PyMOL2\lib\subprocess.py", line 800, in __init__
restore_signals, start_new_session)
File "C:\Users\User\AppData\Local\Schrodinger\PyMOL2\lib\subprocess.py", line 1207, in _execute_child
startupinfo)
FileNotFoundError: [WinError 2] The system cannot find the file specified
I'm also encountering the same issue on Windows, try running a linux distro on vmware and make sure to install Pymol with support for Python 2.7 because the script is not compatible with Python3.
When I launch the pydev debugger with LiClipse (latest versions of both) I get a "KeyError:" exception.
I have ensured that the workspace folder has the proper permissions. I get this problem even if I run LiClipse in Administrator mode.
I expect to be able to debug my python code. My actual results are the following errors:
pydev debugger: starting (pid: 15388)
Traceback (most recent call last):
File "C:\Program Files\Brainwy\LiClipse 5.2.4\plugins\org.python.pydev.core_7.2.1.201904261609\pysrc\pydevd_file_utils.py", line 487, in _original_file_to_client
return cache[filename]
KeyError: 'c:\\users\\xyz\\my documents\\liclipse workspace\\xyzjirabot\\xyzjirabot.py'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\Brainwy\LiClipse 5.2.4\plugins\org.python.pydev.core_7.2.1.201904261609\pysrc\_pydevd_bundle\pydevd_net_command_factory_xml.py", line 197, in make_thread_stack_str
py_db, curr_frame, frame_id_to_lineno
File "C:\Program Files\Brainwy\LiClipse 5.2.4\plugins\org.python.pydev.core_7.2.1.201904261609\pysrc\_pydevd_bundle\pydevd_net_command_factory_xml.py", line 170, in _iter_visible_frames_info
filename_in_utf8 = pydevd_file_utils.norm_file_to_client(abs_path_real_path_and_base[0])
File "C:\Program Files\Brainwy\LiClipse 5.2.4\plugins\org.python.pydev.core_7.2.1.201904261609\pysrc\pydevd_file_utils.py", line 489, in _original_file_to_client
translated = _path_to_expected_str(get_path_with_real_case(_AbsFile(filename)))
File "C:\Program Files\Brainwy\LiClipse 5.2.4\plugins\org.python.pydev.core_7.2.1.201904261609\pysrc\pydevd_file_utils.py", line 196, in _get_path_with_real_case
return _resolve_listing(drive, iter(parts))
File "C:\Program Files\Brainwy\LiClipse 5.2.4\plugins\org.python.pydev.core_7.2.1.201904261609\pysrc\pydevd_file_utils.py", line 159, in _resolve_listing
dir_contents = cache[resolved_lower] = os.listdir(resolved)
PermissionError: [WinError 5] Access is denied: 'C:\\Users\\xyz\\My Documents'
While I was posting this question I noticed that there is a capitalization difference with the file name being used as the key and the actual file path. I moved the workspace to the root of my C Drive and that seems to have fixed the problem.
I think it's the spaces in the filename. I moved it to \Users\kieveli\Source\LiClipseWorkspace\ and everything worked correctly.
Had the same issue - Path was set to "..\My Documents" instead of just "..\Documents". Changing the workspace to another directory fixed the problem
I am using Sublime Text 2 with some plugins. I can't seem to work with the Phpcs plugin, because after saving the file, it gives me an ugly error:
Writing file /Applications/XAMPP/xamppfiles/htdocs/myProject/application/libraries/Authentication.php with encoding UTF-8
Exception in thread Thread-15:
Traceback (most recent call last):
File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/threading.py", line 532, in __bootstrap_inner
self.run()
File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/threading.py", line 484, in run
self.__target(*self.__args, **self.__kwargs)
File "./phpcs.py", line 398, in run
File "./phpcs.py", line 128, in get_errors
File "./phpcs.py", line 194, in execute
File "./phpcs.py", line 197, in parse_report
File "./phpcs.py", line 149, in shell_out
File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/subprocess.py", line 623, in __init__
errread, errwrite)
File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/subprocess.py", line 1141, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
I have also tried to look into the respective files, but I don't know python at all so I don;t know what to do :-/
Could You please help ?
I ended up using SublimeLinter plugin that provides the showing-potential-errors feature that I wanted from the phpcs plugin.
The plugin is located in THIS GITHUB REPO.
Hope this helps anybody who is having a problem using the phpcs library.
#daniel: Thanks for help
I'm trying to run doxyclean but can't get it to work, any help would be appreciated...
I'm running from terminal :
./doxyclean.py --input=./xml/ --output=./clean/ --name="MyProject" --phone -v
I have my doxygen xml in the folder xml, in the same directory as doxyclean.py
The result is :
Checking arguments
Cleaning XML files:
Traceback (most recent call last):
File "./doxyclean.py", line 1220, in <module>
sys.exit(main())
File "./doxyclean.py", line 1171, in main
cleanXML(filePath, xmlOutputDirectory)
File "./doxyclean.py", line 93, in cleanXML
if not fileIsDocumented(filePath):
File "./doxyclean.py", line 62, in fileIsDocumented
originaldoc = minidom.parse(filePath)
File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/xml/dom/minidom.py", line 1918, in parse
return expatbuilder.parse(file)
File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/xml/dom/expatbuilder.py", line 924, in parse
result = builder.parseFile(fp)
File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/xml/dom/expatbuilder.py", line 207, in parseFile
parser.Parse(buffer, 0)
xml.parsers.expat.ExpatError: not well-formed (invalid token): line 17, column 155
thanks
did you try other ways, my suggestions
use different version of doxyclean
change the arguments to different style, maybe give full paths to the folders.
./doxyclean.py -i Users/xxx/doxyclean/xml/ -o ./clean/ -p
regenerate xml from doxygen
doxyclean works fine. I got this error too and I tried my suggestion 2 and it worked.