Troubleshooting cbs_parse_data

[mike-battista]

Hey @conorwild, hope I'm putting this in the right place.

I think I've gotten as far as installing Docker and accessing the CBS Python image. Now I'm trying to use cbs_parse_data. Running the help command works fine, but with a real data file, I'm trying:

docker run cbs_parse_data CBS_Research_Example_Data_V2.csv parse_example

And I get:

Unable to find image 'cbs_parse_data:latest' locally
docker: Error response from daemon: pull access denied for cbs_parse_data, repository does not exist or may require 'docker login': denied: requested access to the resource is denied.

Any idea what could be going on? I'm in the directory with the file, which I've tried with and without spaces. With the access token thing, everything seemed to go okay and it said I was logged in.

Thanks so much. Excited to play with this once I get it working!

[conorwild]

Hey @mike-battista, it looks like you missing some of the Docker "magic" from your command. Try this:

docker run --rm -it -v $PWD:/tmp -w /tmp ghcr.io/theowenlab/cbspython:latest cbs_parse_data CBS_Research_Example_Data_V2.csv parse_example 

The error message you posted says that it is trying to find the cbs_parse_data:latest image - but the image is called cbspython:latest, and cbs_parse_data is the name of the script to execute within that container. Give that a shot!

[mike-battista]

I finally got around to trying this, and it worked for me too! Thanks so much @conorwild .

[SajeevanS]

Hey Conor,
So I'm trying out the cbs_parse_data line and running into errors. I run the above code changing my input and output file names, and I run into the following error below.

Any thoughts?

WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested Traceback (most recent call last): File "/opt/venv/bin/cbs_parse_data", line 33, in <module> sys.exit(load_entry_point('cbspython==0.1.0', 'console_scripts', 'cbs_parse_data')()) File "/opt/venv/lib/python3.9/site-packages/cbspython/scripts/parse_raw_data.py", line 95, in main report = cbs.Report( File "/opt/venv/lib/python3.9/site-packages/cbspython/cbsreport.py", line 263, in __init__ raise TypeError(f"Not sure how to handle {src}") TypeError: Not sure how to handle CBS_Data

[SajeevanS]

my file name is CBS_Data and I want it to name it as CBS_Data_clean

[conorwild]

Is it a CSV? Then you should use CBS_Data.csv. If it doesn't have that extension, then you should rename it to have that.

[SajeevanS]

I see! I think i'm making progress, but having some issues with setting up my directory.

MacBook-Pro-102:~ Sajeevan$ docker run --rm -it -v $PWD:/tmp -w /tmp ghcr.io/theowenlab/cbspython:latest cbs_parse_data CBS_Data.csv CBS_Data_clean
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Traceback (most recent call last):
File "/opt/venv/bin/cbs_parse_data", line 33, in
sys.exit(load_entry_point('cbspython==0.1.0', 'console_scripts', 'cbs_parse_data')())
File "/opt/venv/lib/python3.9/site-packages/cbspython/scripts/parse_raw_data.py", line 95, in main
report = cbs.Report(
File "/opt/venv/lib/python3.9/site-packages/cbspython/cbsreport.py", line 259, in init
self.data = pd.read_csv(src, delimiter=delimiter)
File "/opt/venv/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper
return func(*args, **kwargs)
File "/opt/venv/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv
return _read(filepath_or_buffer, kwds)
File "/opt/venv/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 575, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/opt/venv/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 934, in init
self._engine = self._make_engine(f, self.engine)
File "/opt/venv/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1218, in _make_engine
self.handles = get_handle( # type: ignore[call-overload]
File "/opt/venv/lib/python3.9/site-packages/pandas/io/common.py", line 786, in get_handle
handle = open(
FileNotFoundError: [Errno 2] No such file or directory: 'CBS_Data.csv'

[conorwild]

OK, first I notice that you are in your "home" directory (MacBook-Pro-102:~) and that might not be where your data is located. You need to change directory in your terminal to the directory where your CBS data export file is located. For example, if you put it on your desktop then you would cd ~/Desktop. Or, if it's in a subdirectory of your Documents folder called "CBS" then you would cd ~/Documents/CBS/. You have to run this in the directory where your data is located.

[SajeevanS]

IT WORKED!!! Thank you so much Conor!!! It definitely is a trial and error and a learning experience!! I got my output!