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.

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

Jump to bottom

Solution for delimiter reading issue (#210) utilizing dynamic checkpoints #211

Merged
merged 2 commits into from
Sep 29, 2023
Merged

Solution for delimiter reading issue (#210) utilizing dynamic checkpoints #211

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
dd2ffab
Solution for delimiter reading issue utilizing dynamic checkpoints
JensWendt Sep 6, 2023
8738ad1
resolving Flake8 issues and implements better method to get file_length
JensWendt Sep 7, 2023
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
18 changes: 12 additions & 6 deletions omero/annotation_scripts/KeyVal_from_csv.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
import sys
import csv
import copy
from math import floor

from omero.util.populate_roi import DownloadingOriginalFileProvider

Expand Down Expand Up @@ -157,29 +158,34 @@ def keyval_from_csv(conn, script_params):
temp_file = provider.get_original_file_data(original_file)
# Needs omero-py 5.9.1 or later
temp_name = temp_file.name
file_length = original_file.size.val
with open(temp_name, 'rt', encoding='utf-8-sig') as file_handle:
try:
delimiter = csv.Sniffer().sniff(
file_handle.read(500), ",;\t").delimiter
file_handle.read(floor(file_length/4)), ",;\t").delimiter
print("Using delimiter: ", delimiter,
" after reading 500 characters")
f" after reading {floor(file_length/4)} characters")
except Exception:
file_handle.seek(0)
try:
delimiter = csv.Sniffer().sniff(
file_handle.read(1000), ",;\t").delimiter
file_handle.read(floor(file_length/2)),
",;\t").delimiter
print("Using delimiter: ", delimiter,
" after reading 1000 characters")
f"after reading {floor(file_length/2)} characters")
except Exception:
file_handle.seek(0)
try:
delimiter = csv.Sniffer().sniff(
file_handle.read(2000), ";,\t").delimiter
file_handle.read(floor(file_length*0.75)),
",;\t").delimiter
print("Using delimiter: ", delimiter,
" after reading 2000 characters")
f" after reading {floor(file_length*0.75)}"
" characters")
except Exception:
print("Failed to sniff delimiter, using ','")
delimiter = ","

# reset to start and read whole file...
file_handle.seek(0)
data = list(csv.reader(file_handle, delimiter=delimiter))
Expand Down