Skip to content

Allow notes to have pipes without breaking pipeline loading #136

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.

Sign up for GitHub

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

Merged
gnodar01 merged 4 commits into from
Dec 20, 2022
Merged

Allow notes to have pipes without breaking pipeline loading #136

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
126c096
split out note by regex rather than pipes
bethac07 Dec 13, 2022
d313299
Remove prints
bethac07 Dec 13, 2022
a2dca0b
Make sure we're grabbing the "]" at the end of the note, not just any…
bethac07 Dec 13, 2022
00f154c
Add back support for older pipelines
bethac07 Dec 13, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 9 additions & 1 deletion cellprofiler_core/pipeline/_pipeline.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -580,7 +580,15 @@ def setup_module(
raise ValueError("Invalid format for attributes: %s" % attribute_string)
# Fix for array dtypes which contain split separator
attribute_string = attribute_string.replace("dtype='|S", "dtype='S")
attribute_strings = attribute_string[1:-1].split("|")
if len(re.split("(?P<note>\|notes:\[.*?\]\|)",attribute_string)) ==3:
# 4674- sometimes notes have pipes
prenote,note,postnote = re.split("(?P<note>\|notes:\[.*?\]\|)",attribute_string)
attribute_strings = prenote[1:].split("|")
attribute_strings += [note[1:-1]]
attribute_strings += postnote[:-1].split("|")
else:
#old or weird pipeline without notes
attribute_strings = attribute_string[1:-1].split("|")
variable_revision_number = None
# make batch_state decodable from text pipelines
# NOTE, MAGIC HERE: These variables are **necessary**, even though they
Expand Down