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

Enforce exact_match=True when listing JSON file for get_estimated_time for MPH #467

Open
wants to merge 64 commits into
base: main
Choose a base branch
from
Open

Enforce exact_match=True when listing JSON file for get_estimated_time for MPH #467

Changes from 5 commits
Commits
Show all changes
64 commits
Select commit Hold shift + click to select a range
ecfc03c
Enforce exact_match=True for get_estimated_time
alex-l-kong Aug 22, 2024
81abb38
Merge branch 'main' into mph_fov_name_fix
alex-l-kong Aug 22, 2024
221bcdd
Ensure we're not searching for the actual extension
alex-l-kong Sep 11, 2024
1762d50
Merge remote-tracking branch 'origin/mph_fov_name_fix' into mph_fov_n…
alex-l-kong Sep 11, 2024
fb2f4c0
Modify list_files to use "correct" syntax for exact_match=True and fi…
alex-l-kong Sep 12, 2024
0f4e63f
Make workflow of getting bin file easier
alex-l-kong Sep 12, 2024
553d4cc
Remove the == 0
alex-l-kong Sep 12, 2024
326e9c2
Add processing.json files to test
alex-l-kong Sep 13, 2024
2bd3ab4
Merge remote-tracking branch 'origin/mph_fov_name_fix' into mph_fov_n…
alex-l-kong Sep 13, 2024
a529f53
Fix bin file generation by simulating update only after .json file wr…
Oct 7, 2024
875da78
Formatting to avoid going over 100 characters per line
Oct 7, 2024
673cd53
Add trailing comma to please black linter
Oct 7, 2024
77c7cb6
Print statement debugging
Oct 8, 2024
4392878
See if an OSError is being thrown
Oct 8, 2024
660ec0a
More debugging statements: need to see the MPH process
Oct 8, 2024
6dea20b
Test the presence and contents of log_out
Oct 8, 2024
517687a
See what the actual log path is being set to
Oct 8, 2024
9737c5c
Try adding a simple logging statement at the beginning to force
Oct 8, 2024
db326a6
Try to set logging propagation to be False
Oct 8, 2024
57421cf
Fix pyproject.toml logging
Oct 8, 2024
53f18fa
Additional changes to pytest pyproject.toml
Oct 8, 2024
7e6ef2c
Lowercase true for pyproject.toml
Oct 8, 2024
fd021c6
Attempt to force pytest fixture to write to log file
Oct 17, 2024
58f915a
Add logging import
Oct 17, 2024
63f7388
Remove whitespace
Oct 17, 2024
170ab4d
Try to fix logging issue
Oct 17, 2024
93735fc
Overwrite pytest.txt with blank stuff
Oct 17, 2024
3d2832c
More testing fixes
Oct 17, 2024
c9b9439
Use the absolute path to the directory for accessing hte log
Oct 17, 2024
4db71a3
Adjust error message
Oct 17, 2024
a046bc3
Don't print add_blank
Oct 18, 2024
98013de
Check if the error is happening during the renaming phases
Oct 18, 2024
378a82a
Add some more tests in
Nov 12, 2024
1fef177
Actually get image_stitching to print out debug
Nov 12, 2024
7b08a84
Pin watchdog to version 6
Nov 12, 2024
1493401
Merge branch 'main' into mph_fov_name_fix
alex-l-kong Nov 12, 2024
e76de60
Update lock file
Nov 12, 2024
406172e
Merge remote-tracking branch 'origin/mph_fov_name_fix' into mph_fov_n…
Nov 12, 2024
8f80979
Add debug workflow to GitHub PR
Nov 12, 2024
5cb65a9
Remove the lock entirely
Nov 12, 2024
d50c4b4
Nuke file timer functionality
Nov 12, 2024
efc3fee
Test deleting the lock AND the timer
Nov 12, 2024
af9369f
Try pushing old slow copy tissue data
Nov 13, 2024
7aef668
removed debug
srivarra Nov 14, 2024
a7370e7
See if sleeping for 2 seconds will prevent the toffy segmentation err…
alex-l-kong Nov 20, 2024
0eed380
black formatting
alex-l-kong Nov 21, 2024
510c398
Massive test overhaul: see how many tests pass now
alex-l-kong Nov 21, 2024
d7e2eee
Remove old _slow_copy_tissue... function
alex-l-kong Nov 21, 2024
8590206
Linting checks
alex-l-kong Nov 21, 2024
6012a8f
PYCODESTYLE
alex-l-kong Nov 21, 2024
d1940eb
Add fixes to temporary work around list_folders and list_files in ros…
alex-l-kong Nov 21, 2024
5b3131b
Strict matching required between underscores: "pulse_height" will not…
alex-l-kong Nov 21, 2024
f66a6ff
Fix list_folders in normalize_image.py to correctly list all FOVs, ad…
alex-l-kong Nov 21, 2024
5c87125
Fix list_folders in merge_partial_runs
alex-l-kong Nov 21, 2024
542b5cc
Formatting
alex-l-kong Nov 21, 2024
51cb85b
Remove print statements
alex-l-kong Nov 21, 2024
87c2b1b
Remove debug comment
alex-l-kong Nov 21, 2024
9222a0f
Reset fov_watcher.py back to original
alex-l-kong Nov 21, 2024
085e900
More resetting
alex-l-kong Nov 21, 2024
f2f97ea
Remove unnecessary try-except block in fov_watcher_test.py
alex-l-kong Nov 21, 2024
d15c69f
Never mind, add old try-except back in (but don't print watcher lag)
alex-l-kong Nov 21, 2024
4ef4bb7
Fix copy_image_files with bad list_folders calls removed
alex-l-kong Nov 21, 2024
948baa5
ruff linting
alex-l-kong Nov 21, 2024
25e0126
Merge branch 'main' into mph_fov_name_fix
alex-l-kong Nov 21, 2024
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
3 changes: 2 additions & 1 deletion src/toffy/mph_comp.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,8 @@ def get_estimated_time(bin_file_dir, fov):
io_utils.validate_paths(bin_file_dir)

# get fov json file in bin_file_path
json_file = io_utils.list_files(bin_file_dir, fov + ".json")
json_file = sorted(io_utils.list_files(bin_file_dir, fov, exact_match=True))
json_file = list(filter(lambda f: ".json" in f, json_file))
alex-l-kong marked this conversation as resolved.
Show resolved Hide resolved
if len(json_file) == 0:
raise FileNotFoundError(f"The FOV name supplied doesn't have a JSON file: {fov}")

Expand Down
Loading