I am getting an error while trying to extract a .tar.gz archive using the tarfile library.
Here is the relevant code snippet:
# `gzip_archive_bytes_content` is the content of the gzip archive, in "bytes" format
repo_sources_file_object = io.BytesIO(gzip_archive_bytes_content)
repo_sources_tar_object = tarfile.TarFile(fileobj=repo_sources_file_object)
repo_sources_tar_object.extractall(path="/tmp/")
This the error I get:
Traceback (most recent call last):
File "/usr/local/lib/python3.7/tarfile.py", line 186, in nti
s = nts(s, "ascii", "strict")
File "/usr/local/lib/python3.7/tarfile.py", line 170, in nts
return s.decode(encoding, errors)
UnicodeDecodeError: 'ascii' codec can't decode byte 0x9a in position 1: ordinal not in range(128)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.7/tarfile.py", line 2289, in next
tarinfo = self.tarinfo.fromtarfile(self)
File "/usr/local/lib/python3.7/tarfile.py", line 1095, in fromtarfile
obj = cls.frombuf(buf, tarfile.encoding, tarfile.errors)
File "/usr/local/lib/python3.7/tarfile.py", line 1037, in frombuf
chksum = nti(buf[148:156])
File "/usr/local/lib/python3.7/tarfile.py", line 189, in nti
raise InvalidHeaderError("invalid header")
tarfile.InvalidHeaderError: invalid header
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.7/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/usr/local/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/usr/local/lib/python3.7/site-packages/my-package/__main__.py", line 87, in <module>
function(**function_args)
File "/usr/local/lib/python3.7/site-packages/my-package/chart.py", line 107, in reinstall
install()
File "/usr/local/lib/python3.7/site-packages/my-package/chart.py", line 89, in install
repo_sources_tar_object = tarfile.TarFile(fileobj=repo_sources_file_object)
File "/usr/local/lib/python3.7/tarfile.py", line 1484, in __init__
self.firstmember = self.next()
File "/usr/local/lib/python3.7/tarfile.py", line 2301, in next
raise ReadError(str(e))
tarfile.ReadError: invalid header
Python version: 3.7
I switched from instanciating directly a tarfile.TarFile object to using the tarfile.open() constructor, and it fixed it:
repo_sources_tar_object = tarfile.open(fileobj=repo_sources_file_object)
There is actually a warning on this in the documentation, here:
Do not use this class directly: use tarfile.open() instead.
The best practice is to use a context manager in order to automatically close the file when the job is done.
One could write:
import contextlib
import io
import tarfile
gzip_archive_bytes_content = b"..."
repo_sources_file_object = io.BytesIO(gzip_archive_bytes_content)
with contextlib.closing(tarfile.open(fileobj=repo_sources_file_object)) as arch:
arch.extractall(path="/tmp/")
This is available with tarfile.TarFile, but not with tarfile.open().
So you could write:
with tarfile.TarFile(...) as arch:
...
Related
I am trying to parse a gif file with Biopython, and am using the sample code from their website. This is the code:
from BCBio import GFF
in_file = "infile.gff"
in_handle = open(in_file)
for rec in GFF.parse(in_handle):
print(rec)
in_handle.close()
When I run the code I get the following error:
Traceback (most recent call last):
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/Bio/SeqIO/Interfaces.py", line 47, in __init__
self.stream = open(source, "r" + mode)
TypeError: expected str, bytes or os.PathLike object, not FakeHandle
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "get_genes_dpt.py", line 37, in <module>
for rec in GFF.parse(in_handle):
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 746, in parse
target_lines):
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 322, in parse_in_parts
for results in self.parse_simple(gff_files, limit_info, target_lines):
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 343, in parse_simple
for results in self._gff_process(gff_files, limit_info, target_lines):
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 637, in _gff_process
for out in self._lines_to_out_info(line_gen, limit_info, target_lines):
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 699, in _lines_to_out_info
fasta_recs = self._parse_fasta(FakeHandle(line_iter))
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 560, in _parse_fasta
return list(SeqIO.parse(in_handle, "fasta"))
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/Bio/SeqIO/__init__.py", line 607, in parse
return iterator_generator(handle)
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/Bio/SeqIO/FastaIO.py", line 183, in __init__
super().__init__(source, mode="t", fmt="Fasta")
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/Bio/SeqIO/Interfaces.py", line 51, in __init__
if source.read(0) != "":
TypeError: read() takes 1 positional argument but 2 were given
I am not sure how to fix the error as it seems I am passing a str and not a FakeHandle. I am running biopython 1.78 with conda.
I have installed librosa correctly with pip3 on ubuntu subsystem on windows, but when I try to execute a simple program like this one:
import librosa
data, sr = librosa.load('sound.mp3')
print(data.shape)
It is what happens:
/home/henistein/librosa/librosa/core/audio.py:144: UserWarning: PySoundFile failed. Trying audioread instead.
warnings.warn('PySoundFile failed. Trying audioread instead.')
Traceback (most recent call last):
File "/home/henistein/librosa/librosa/core/audio.py", line 128, in load
with sf.SoundFile(path) as sf_desc:
File "/home/henistein/.local/lib/python3.8/site-packages/soundfile.py", line 740, in __init__
self._file = self._open(file, mode_int, closefd)
File "/home/henistein/.local/lib/python3.8/site-packages/soundfile.py", line 1264, in _open
_error_check(_snd.sf_error(file_ptr),
File "/home/henistein/.local/lib/python3.8/site-packages/soundfile.py", line 1455, in _error_check
raise RuntimeError(prefix + _ffi.string(err_str).decode('utf-8', 'replace'))
RuntimeError: Error opening 'sound.mp3': File contains data in an unknown format.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "PerfectPitch.py", line 2, in <module>
data, sr = librosa.load('sound.mp3')
File "/home/henistein/librosa/librosa/core/audio.py", line 145, in load
y, sr_native = __audioread_load(path, offset, duration, dtype)
File "/home/henistein/librosa/librosa/core/audio.py", line 169, in __audioread_load
with audioread.audio_open(path) as input_file:
File "/home/henistein/.local/lib/python3.8/site-packages/audioread/__init__.py", line 116, in audio_open
raise NoBackendError()
audioread.exceptions.NoBackendError
What am I doing wrong?
According to the manual you'll probably also need to install ffmpeg, to allow for librosa to decode various formats.
Since you're working in the Ubuntu subsystem, simply
apt install ffmpeg
should do the trick.
Whenever I try to run my Rasa app using the run button in PyCharm, or try to use the debugger, I get the following error:
Traceback (most recent call last):
File "/Users/matthewspeck/anaconda3/envs/proj_env/lib/python3.6/site-packages/pykwalify/core.py", line 76, in __init__
self.source = yaml.load(stream)
File "/Users/matthewspeck/anaconda3/envs/proj_env/lib/python3.6/site-packages/ruamel/yaml/main.py", line 933, in load
loader = Loader(stream, version, preserve_quotes=preserve_quotes)
File "/Users/matthewspeck/anaconda3/envs/proj_env/lib/python3.6/site-packages/ruamel/yaml/loader.py", line 50, in __init__
Reader.__init__(self, stream, loader=self)
File "/Users/matthewspeck/anaconda3/envs/proj_env/lib/python3.6/site-packages/ruamel/yaml/reader.py", line 85, in __init__
self.stream = stream # type: Any # as .read is called
File "/Users/matthewspeck/anaconda3/envs/proj_env/lib/python3.6/site-packages/ruamel/yaml/reader.py", line 130, in stream
self.determine_encoding()
File "/Users/matthewspeck/anaconda3/envs/proj_env/lib/python3.6/site-packages/ruamel/yaml/reader.py", line 190, in determine_encoding
self.update_raw()
File "/Users/matthewspeck/anaconda3/envs/proj_env/lib/python3.6/site-packages/ruamel/yaml/reader.py", line 297, in update_raw
data = self.stream.read(size)
File "/Users/matthewspeck/anaconda3/envs/proj_env/lib/python3.6/encodings/ascii.py", line 26, in decode
return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 473: ordinal not in range(128)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/matthewspeck/project/trainer_app/app.py", line 25, in <module>
parser=False, core=True)
File "/Users/matthewspeck/project/trainer_app/rasa_model.py", line 165, in make_rasa_model
rasa_config=rasa_config
File "/Users/matthewspeck/project/trainer_app/rasa_model.py", line 66, in __init__
self._parser = create_agent(use_rasa_nlu=True, load_models=True)
File "/Users/matthewspeck/project/trainer_app/rasa.py", line 32, in create_agent
domain = create_domain()
File "/Users/matthewspeck/project/trainer_app/rasa.py", line 83, in create_domain
domain = ClarifyDomain.load(domain_path)
File "/Users/project/clarification/domain.py", line 39, in load
domain = TemplateDomain.load(filename)
File "/Users/matthewspeck/anaconda3/envs/proj_env/lib/python3.6/site-packages/rasa_core/domain.py", line 404, in load
cls.validate_domain_yaml(filename)
File "/Users/matthewspeck/anaconda3/envs/proj_env/lib/python3.6/site-packages/rasa_core/domain.py", line 438, in validate_domain_yaml
schema_files=[schema_file])
File "/Users/matthewspeck/anaconda3/envs/proj_env/lib/python3.6/site-packages/pykwalify/core.py", line 78, in __init__
raise CoreError(u"Unable to load any data from source yaml file")
pykwalify.errors.CoreError: <CoreError: error code 3: Unable to load any data from source yaml file: Path: '/'>
Process finished with exit code 1
However, when I run the app from my terminal, or from my text editor (I use VSCode), It runs with no problems whatsoever. I've looked online and every answer I see has something to do with Rasa, but nothing mentions problems with PyCharm.
I've also checked that the yaml for the domain is properly formatted, and it is. Anyone have any idea why I would be getting this error in PyCharm, but not in any other environment, and how I could fix it?
I believe your problem was fixed with Rasa version 0.12 ([changelog][1]): https://github.com/RasaHQ/rasa_core/blob/master/CHANGELOG.rst#0120---2018-11-11 .
I recommend upgrading to a newer version of Rasa Core which parses the training data correctly.
I try write a game with GoranM/bdx plugin. When i create plate with texture and try export to code I get fatal error.
Traceback (most recent call last):
File "C:\Users\Myuser\AppData\Roaming\Blender Foundation\Blender\2.79\scripts\addons\bdx\ops\exprun.py", line 225, in execute
export(self, context, bpy.context.scene.bdx.multi_blend_export, bpy.context.scene.bdx.diff_export)
File "C:\Users\Myuser\AppData\Roaming\Blender Foundation\Blender\2.79\scripts\addons\bdx\ops\exprun.py", line 123, in export
bpy.ops.export_scene.bdx(filepath=file_path, scene_name=scene.name, exprun=True)
File "C:\Program Files\Blender Foundation\Blender\2.79\scripts\modules\bpy\ops.py", line 189, in call
ret = op_call(self.idname_py(), None, kw)
RuntimeError: Error: Traceback (most recent call last):
File "C:\Users\Myuser\AppData\Roaming\Blender Foundation\Blender\2.79\scripts\addons\bdx\exporter.py", line 903, in execute
return export(context, self.filepath, self.scene_name, self.exprun, self.apply_modifier)
File "C:\Users\Myuser\AppData\Roaming\Blender Foundation\Blender\2.79\scripts\addons\bdx\exporter.py", line 829, in export
"models": srl_models(objects, apply_modifier),
File "C:\Users\Myuser\AppData\Roaming\Blender Foundation\Blender\2.79\scripts\addons\bdx\exporter.py", line 117, in srl_models
verts = vertices(mesh)
File "C:\Users\Myuser\AppData\Roaming\Blender Foundation\Blender\2.79\scripts\addons\bdx\exporter.py", line 53, in vertices
vert_uv = list(uv_layer[li].uv)
IndexError: bpy_prop_collection[index]: index 0 out of range, size 0
location: C:\Program Files\Blender Foundation\Blender\2.79\scripts\modules\bpy\ops.py:189
location: :-1
Maybe someone had same problem and you know how to fix it?
Go into Object Mode before calling that function.
bpy.ops.object.mode_set(mode='OBJECT', toggle=False)
I am using bencode library and I am trying to encode and decode binary data:
>>> import bencode
>>> bencode.Bencoder.decode(bencode.Bencoder.encode({'x': b'xyz'}))
Traceback (most recent call last):
File "<input>", line 1, in <module>
bencode.Bencoder.decode(bencode.Bencoder.encode({'x': b'xyz'}))
File "/home/pt12lol/virtualenv-python3/lib/python3.5/site-packages/bencode/__init__.py", line 228, in decode
return _decode(becode_string)
File "/home/pt12lol/virtualenv-python3/lib/python3.5/site-packages/bencode/__init__.py", line 197, in _decode
data = _decode_item(pf, six.next(src))
File "/home/pt12lol/virtualenv-python3/lib/python3.5/site-packages/bencode/__init__.py", line 178, in _decode_item
tok = next()
File "/home/pt12lol/virtualenv-python3/lib/python3.5/site-packages/bencode/__init__.py", line 147, in _tokenizer
s = m.group(m.lastindex) #
http://stackoverflow.com/questions/22489243/re-in-python-lastindex-attribute
AttributeError: 'NoneType' object has no attribute 'group'
How can I manage it?