Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

GPL-984 BUG - Exceptions while processing UK Biocentre #315

Open
pjvv opened this issue Apr 19, 2021 · 0 comments
Open

GPL-984 BUG - Exceptions while processing UK Biocentre #315

pjvv opened this issue Apr 19, 2021 · 0 comments
Labels
Bug Something isn't working

Comments

@pjvv
Copy link
Contributor

pjvv commented Apr 19, 2021

Describe the bug
Seen in slack message:

2021-04-17 20:06:08,521 crawler.main                                 :113 ERROR   expected string or bytes-like object
Traceback (most recent call last):
 File "/code/crawler/main.py", line 109, in run
   centre_instance.process_files(add_to_dart)
 File "/code/crawler/file_processing.py", line 170, in process_files
   centre_file.process_samples(add_to_dart)
 File "/code/crawler/file_processing.py", line 404, in process_samples
   docs_to_insert = self.process_csv()
 File "/code/crawler/file_processing.py", line 773, in process_csv
   documents = self.parse_and_format_file_rows(csvreader)
 File "/code/crawler/file_processing.py", line 1044, in parse_and_format_file_rows
   if parsed_row := self.parse_and_format_row(row, line_number, seen_rows):
 File "/code/crawler/file_processing.py", line 1080, in parse_and_format_row
   modified_row = self.filtered_row(row, line_number)
 File "/code/crawler/file_processing.py", line 936, in filtered_row
   seen_headers, modified_row = self.extract_channel_fields(seen_headers, row, modified_row)
 File "/code/crawler/file_processing.py", line 1001, in extract_channel_fields
   if pattern.match(csv_field):
TypeError: expected string or bytes-like object
@pjvv pjvv added the Bug Something isn't working label Apr 19, 2021
@rl15 rl15 changed the title BUG - Exceptions while processing UK Biocentre GPL-984 BUG - Exceptions while processing UK Biocentre Apr 19, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Bug Something isn't working
Projects
None yet
Development

No branches or pull requests

1 participant