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tieneupintieneupin
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Added logs to empty 'except:' blocks
1 parent 28ceb5e commit 33b3478

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4 files changed

+64
-27
lines changed

4 files changed

+64
-27
lines changed

‎src/murfey/server/api/clem.py‎

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -200,9 +200,13 @@ def get_db_entry(
200200
db.refresh(db_entry)
201201
break
202202
except Exception:
203-
pass
204-
attempts += 1
205-
time.sleep(0.1)
203+
logger.warning(
204+
f"Attempt {attempts + 1} at refreshing database entry for "
205+
f"{str(file_path if file_path else series_name)!r} failed: \n"
206+
f"{traceback.format_exc()}"
207+
)
208+
attempts += 1
209+
time.sleep(0.1)
206210
else:
207211
raise RuntimeError(
208212
"Maximum number of attempts reached while trying to refresh database "

‎src/murfey/workflows/clem/__init__.py‎

Lines changed: 8 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,7 @@
33
import logging
44
import re
55
import time
6+
import traceback
67
from pathlib import Path
78
from typing import Optional, Type, Union
89

@@ -196,9 +197,13 @@ def get_db_entry(
196197
db.refresh(db_entry)
197198
break
198199
except Exception:
199-
pass
200-
attempts += 1
201-
time.sleep(0.1)
200+
logger.warning(
201+
f"Attempt {attempts + 1} at refreshing database entry for "
202+
f"{str(file_path if file_path else series_name)!r} failed: \n"
203+
f"{traceback.format_exc()}"
204+
)
205+
attempts += 1
206+
time.sleep(0.1)
202207
else:
203208
raise RuntimeError(
204209
"Maximum number of attempts reached while trying to refresh database "

‎src/murfey/workflows/clem/register_align_and_merge_results.py‎

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -102,9 +102,13 @@ def register_align_and_merge_result(
102102
murfey_db.refresh(clem_img_series)
103103
break
104104
except Exception:
105-
pass
106-
attempts += 1
107-
time.sleep(0.1)
105+
logger.warning(
106+
f"Attempt {attempts + 1} at refreshing database entry for "
107+
f"{str(result.series_name)!r} failed: \n"
108+
f"{traceback.format_exc()}"
109+
)
110+
attempts += 1
111+
time.sleep(0.1)
108112
else:
109113
raise RuntimeError(
110114
"Maximum number of attempts reached while trying to refresh database "

‎src/murfey/workflows/clem/register_preprocessing_results.py‎

Lines changed: 42 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -128,9 +128,13 @@ def register_lif_preprocessing_result(
128128
murfey_db.refresh(clem_img_stk)
129129
break
130130
except Exception:
131-
pass
132-
attempts += 1
133-
time.sleep(0.1)
131+
logger.warning(
132+
f"Attempt {attempts + 1} at refreshing database entry for "
133+
f"{str(result.image_stack)!r} failed: \n"
134+
f"{traceback.format_exc()}"
135+
)
136+
attempts += 1
137+
time.sleep(0.1)
134138
else:
135139
raise RuntimeError(
136140
"Maximum number of attempts reached while trying to refresh database "
@@ -150,9 +154,13 @@ def register_lif_preprocessing_result(
150154
murfey_db.refresh(clem_img_series)
151155
break
152156
except Exception:
153-
pass
154-
attempts += 1
155-
time.sleep(0.1)
157+
logger.warning(
158+
f"Attempt {attempts + 1} at refreshing database entry for "
159+
f"{str(result.series_name)!r} failed: \n"
160+
f"{traceback.format_exc()}"
161+
)
162+
attempts += 1
163+
time.sleep(0.1)
156164
else:
157165
raise RuntimeError(
158166
"Maximum number of attempts reached while trying to refresh database "
@@ -169,9 +177,13 @@ def register_lif_preprocessing_result(
169177
murfey_db.refresh(clem_metadata)
170178
break
171179
except Exception:
172-
pass
173-
attempts += 1
174-
time.sleep(0.1)
180+
logger.warning(
181+
f"Attempt {attempts + 1} at refreshing database entry for "
182+
f"{str(result.metadata)!r} failed: \n"
183+
f"{traceback.format_exc()}"
184+
)
185+
attempts += 1
186+
time.sleep(0.1)
175187
else:
176188
raise RuntimeError(
177189
"Maximum number of attempts reached while trying to refresh database "
@@ -352,9 +364,13 @@ def register_tiff_preprocessing_result(
352364
murfey_db.refresh(clem_tiff_file)
353365
break
354366
except Exception:
355-
pass
356-
attempts += 1
357-
time.sleep(0.1)
367+
logger.warning(
368+
f"Attempt {attempts + 1} at refreshing database entry for "
369+
f"{str(file)!r} failed: \n"
370+
f"{traceback.format_exc()}"
371+
)
372+
attempts += 1
373+
time.sleep(0.1)
358374
else:
359375
raise RuntimeError(
360376
"Maximum number of attempts reached while trying to refresh database "
@@ -374,9 +390,13 @@ def register_tiff_preprocessing_result(
374390
murfey_db.refresh(clem_img_stk)
375391
break
376392
except Exception:
377-
pass
378-
attempts += 1
379-
time.sleep(0.1)
393+
logger.warning(
394+
f"Attempt {attempts + 1} at refreshing database entry for "
395+
f"{str(result.image_stack)!r} failed: \n"
396+
f"{traceback.format_exc()}"
397+
)
398+
attempts += 1
399+
time.sleep(0.1)
380400
else:
381401
raise RuntimeError(
382402
"Maximum number of attempts reached while trying to refresh database "
@@ -395,9 +415,13 @@ def register_tiff_preprocessing_result(
395415
murfey_db.refresh(clem_img_series)
396416
break
397417
except Exception:
398-
pass
399-
attempts += 1
400-
time.sleep(0.1)
418+
logger.warning(
419+
f"Attempt {attempts + 1} at refreshing database entry for "
420+
f"{str(result.series_name)!r} failed: \n"
421+
f"{traceback.format_exc()}"
422+
)
423+
attempts += 1
424+
time.sleep(0.1)
401425
else:
402426
raise RuntimeError(
403427
"Maximum number of attempts reached while trying to refresh database "

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