sdf to SMILES

Description:
Substance_000000001_000025000.sdf.zip
I downloaded a sdf file from PubChem and I want to convert sdf to SMILES, but I have some problems. I am very anxious, I hope to get help.

RDKit Version:2018.09.1
Platform:macOS High Sierra 10.13.4
python:Python 3.6.5 |Anaconda, Inc.

result：[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 6187
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 6637
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 9297
[11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 9454
[11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 17 H, 2, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 15469
[11:23:40] ERROR: Explicit valence for atom # 17 H, 2, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 21963
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 11 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 25430
[11:23:40] ERROR: Explicit valence for atom # 11 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 17 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 25618
[11:23:40] ERROR: Explicit valence for atom # 17 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 26802
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 26919
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 27044
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 27169
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 27288
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 27407
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 27526
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 27649
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 27779
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 9 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 27911
[11:23:40] ERROR: Explicit valence for atom # 9 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 28040
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 29495
[11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 29606
[11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 29717
[11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 29830
[11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 30121
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 30759
[11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 30871
[11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 31948
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 32135
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 32292
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 32461
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 32628
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 32789
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 32950
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 33262
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 4 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 33429
[11:23:40] ERROR: Explicit valence for atom # 4 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 33632
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 33791
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 33926
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 34057
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 34228
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 34403
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 34568
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 34759
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 34878
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 35079
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 35262
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 35385
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 35496
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 35609
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 35808
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 36019
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 36128
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 36249
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 36390
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 36535
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 36688
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 36817
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 36960
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 37097
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 37222
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 37351
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 37464
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 24 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 37779
[11:23:40] ERROR: Explicit valence for atom # 24 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 24 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 38096
[11:23:40] ERROR: Explicit valence for atom # 24 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 24 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 38415
[11:23:40] ERROR: Explicit valence for atom # 24 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 24 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 38734
[11:23:40] ERROR: Explicit valence for atom # 24 N, 4, is greater than permitted
[11:23:40] WARNING: not removing hydrogen atom without neighbors
[11:23:40] WARNING: not removing hydrogen atom without neighbors
[11:23:40] Explicit valence for atom # 14 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 41791
[11:23:40] ERROR: Explicit valence for atom # 14 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 15 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 42743
[11:23:40] ERROR: Explicit valence for atom # 15 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 14 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 42869
[11:23:40] ERROR: Explicit valence for atom # 14 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 17 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 42995
[11:23:40] ERROR: Explicit valence for atom # 17 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 17 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 43121
[11:23:40] ERROR: Explicit valence for atom # 17 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 15 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 43245
[11:23:40] ERROR: Explicit valence for atom # 15 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 21 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 44189
[11:23:40] ERROR: Explicit valence for atom # 21 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 21 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 44343
[11:23:40] ERROR: Explicit valence for atom # 21 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 14 In, 7, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 44500
[11:23:40] ERROR: Explicit valence for atom # 14 In, 7, is greater than permitted
[11:23:40] Explicit valence for atom # 40 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 44746
[11:23:40] ERROR: Explicit valence for atom # 40 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 21 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 45185
[11:23:40] ERROR: Explicit valence for atom # 21 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 26 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 45442
[11:23:40] ERROR: Explicit valence for atom # 26 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 50 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 45829
[11:23:40] ERROR: Explicit valence for atom # 50 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 40 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 46787
[11:23:40] ERROR: Explicit valence for atom # 40 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 2 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 49982
[11:23:40] ERROR: Explicit valence for atom # 2 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 2 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 50060
[11:23:40] ERROR: Explicit valence for atom # 2 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 1 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 50141
[11:23:40] ERROR: Explicit valence for atom # 1 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 50241
[11:23:40] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 17 C, 5, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 50507
[11:23:40] ERROR: Explicit valence for atom # 17 C, 5, is greater than permitted
[11:23:40] Explicit valence for atom # 17 C, 5, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 50792
[11:23:40] ERROR: Explicit valence for atom # 17 C, 5, is greater than permitted
[11:23:40] Explicit valence for atom # 11 C, 5, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 51029
[11:23:40] ERROR: Explicit valence for atom # 11 C, 5, is greater than permitted
[11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 53031
[11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 56027
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 1 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 56670
[11:23:40] ERROR: Explicit valence for atom # 1 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 56757
[11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 56837
[11:23:40] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 56928
[11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 57087
[11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 57313
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 57392
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 57471
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 57550
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 6 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 57671
[11:23:40] ERROR: Explicit valence for atom # 6 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 6 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 57805
[11:23:40] ERROR: Explicit valence for atom # 6 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 6 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 57947
[11:23:40] ERROR: Explicit valence for atom # 6 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 6 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 58095
[11:23:40] ERROR: Explicit valence for atom # 6 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 1 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 58175
[11:23:40] ERROR: Explicit valence for atom # 1 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 3 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 58253
[11:23:40] ERROR: Explicit valence for atom # 3 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 1 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 61791
[11:23:40] ERROR: Explicit valence for atom # 1 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 64840
[11:23:40] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 67314
[11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 68206
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 68294
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 68384
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 68470
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 68559
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 68650
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 68741
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 68831
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 68921
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 69006
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 69091
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 69176
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 69261
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 69365
[11:23:40] ERROR: Explicit valence for atom # 7 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 69658
[11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 69758
[11:23:40] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 4 C, 5, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 70180
[11:23:40] ERROR: Explicit valence for atom # 4 C, 5, is greater than permitted
[11:23:40] Explicit valence for atom # 9 C, 5, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 70290
[11:23:40] ERROR: Explicit valence for atom # 9 C, 5, is greater than permitted
[11:23:40] Explicit valence for atom # 10 C, 5, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 70479
[11:23:40] ERROR: Explicit valence for atom # 10 C, 5, is greater than permitted
[11:23:40] Explicit valence for atom # 11 C, 5, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 70674
[11:23:40] ERROR: Explicit valence for atom # 11 C, 5, is greater than permitted
[11:23:40] Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 75495
[11:23:40] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 75587
[11:23:40] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 75670
[11:23:40] ERROR: Explicit valence for atom # 8 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 75766
[11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 75857
[11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 75948
[11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 76041
[11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 76134
[11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 76231
[11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 76330
[11:23:40] ERROR: Explicit valence for atom # 2 O, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 76412
[11:23:40] ERROR: Explicit valence for atom # 3 O, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 76494
[11:23:40] ERROR: Explicit valence for atom # 3 O, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 1 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 76609
[11:23:40] ERROR: Explicit valence for atom # 1 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 76721
[11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 77219
[11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 77298
[11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 77377
[11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 77456
[11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 79215
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] Explicit valence for atom # 13 C, 5, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 83871
[11:23:40] ERROR: Explicit valence for atom # 13 C, 5, is greater than permitted
[11:23:40] Explicit valence for atom # 21 C, 5, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 84056
[11:23:40] ERROR: Explicit valence for atom # 21 C, 5, is greater than permitted
[11:23:40] Explicit valence for atom # 17 C, 5, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 84213
[11:23:40] ERROR: Explicit valence for atom # 17 C, 5, is greater than permitted
[11:23:40] Explicit valence for atom # 16 C, 5, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 84366
[11:23:40] ERROR: Explicit valence for atom # 16 C, 5, is greater than permitted
[11:23:40] Explicit valence for atom # 16 C, 5, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 84519
[11:23:40] ERROR: Explicit valence for atom # 16 C, 5, is greater than permitted
[11:23:40] Explicit valence for atom # 13 C, 5, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 84657
[11:23:40] ERROR: Explicit valence for atom # 13 C, 5, is greater than permitted
[11:23:40] WARNING: not removing hydrogen atom without neighbors
[11:23:40] Explicit valence for atom # 3 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 90624
[11:23:40] ERROR: Explicit valence for atom # 3 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 95534
[11:23:40] ERROR: Explicit valence for atom # 6 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 5 K, 2, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 95790
[11:23:40] ERROR: Explicit valence for atom # 5 K, 2, is greater than permitted
[11:23:40] Explicit valence for atom # 15 H, 2, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 98395
[11:23:40] ERROR: Explicit valence for atom # 15 H, 2, is greater than permitted
[11:23:40] Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 100309
[11:23:40] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:40] Explicit valence for atom # 0 In, 6, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 102244
[11:23:40] ERROR: Explicit valence for atom # 0 In, 6, is greater than permitted
[11:23:40] Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:40] ERROR: Could not sanitize molecule ending on line 103429
[11:23:40] ERROR: Explicit valence for atom # 3 O, 3, is greater than permitted
[11:23:41] WARNING: not removing hydrogen atom without neighbors
[11:23:41] Explicit valence for atom # 2 O, 3, is greater than permitted
[11:23:41] ERROR: Could not sanitize molecule ending on line 104584
[11:23:41] ERROR: Explicit valence for atom # 2 O, 3, is greater than permitted
[11:23:41] Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:41] ERROR: Could not sanitize molecule ending on line 127594
[11:23:41] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:41] Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:41] ERROR: Could not sanitize molecule ending on line 127768
[11:23:41] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:41] Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:41] ERROR: Could not sanitize molecule ending on line 127856
[11:23:41] ERROR: Explicit valence for atom # 5 N, 4, is greater than permitted
[11:23:41] Explicit valence for atom # 2 N, 4, is greater than permitted
[11:23:41] ERROR: Could not sanitize molecule ending on line 157013
[11:23:41] ERROR: Explicit valence for atom # 2 N, 4, is greater than permitted
[11:23:41] Warning: conflicting stereochemistry at atom 20 ignored.
[11:23:41] Warning: conflicting stereochemistry at atom 20 ignored.
[11:23:41] Explicit valence for atom # 0 Cl, 7, is greater than permitted
[11:23:41] ERROR: Could not sanitize molecule ending on line 175069
[11:23:41] ERROR: Explicit valence for atom # 0 Cl, 7, is greater than permitted
[11:23:41] WARNING: not removing hydrogen atom without neighbors
[11:23:41] WARNING: not removing hydrogen atom without neighbors
[11:23:42] Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:42] ERROR: Could not sanitize molecule ending on line 490585
[11:23:42] ERROR: Explicit valence for atom # 4 N, 4, is greater than permitted
[11:23:43] Warning: conflicting stereochemistry at atom 2 ignored.
[11:23:44] Warning: conflicting stereochemistry at atom 11 ignored.
[11:23:44] Warning: conflicting stereochemistry at atom 11 ignored.
[11:23:44] Warning: conflicting stereochemistry at atom 3 ignored.
[11:23:44] Warning: conflicting stereochemistry at atom 3 ignored.
[11:23:44] Warning: conflicting stereochemistry at atom 10 ignored.
[11:23:44] Warning: conflicting stereochemistry at atom 10 ignored.
[11:23:44] Warning: conflicting stereochemistry at atom 8 ignored.
[11:23:44] Warning: conflicting stereochemistry at atom 8 ignored.
[11:23:44] Warning: conflicting stereochemistry at atom 14 ignored.
[11:23:44] Warning: conflicting stereochemistry at atom 14 ignored.
[11:23:44] Warning: conflicting stereochemistry at atom 13 ignored.
[11:23:44] Warning: conflicting stereochemistry at atom 13 ignored.
Traceback (most recent call last):
File "22.py", line 20, in
converter(sys.argv[1])
File "22.py", line 13, in converter
smi = Chem.MolToSmiles(mol)
Boost.Python.ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
did not match C++ signature:
MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=True, bool kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)

import sys
from rdkit import Chem

def converter(file_name):
    mols = [mol for mol in Chem.SDMolSupplier(file_name)]
    outname = file_name.split(".sdf")[0] + ".txt"
    out_file = open(outname, "w")
    for mol in mols:
        smi = Chem.MolToSmiles(mol)
        name = mol.GetProp("_Name")
        out_file.write("{}\t{}\n".format(smi, name))
    out_file.close()

if __name__ == "__main__":
    converter(sys.argv[1])

from rdkit.Chem.PandasTools import LoadSDF
df = LoadSDF(sdf_filename, smilesName='SMILES')

This will create a pandas DataFrame with 'SMILES' column

So how can we know which molecules are indeed invalid and remove them from the dataset?


_apply_label_matcher creates an unwarranted file on filesytsem

The test test_consumer_returns_alerts_rules_file calls
rules_file = self.harness.charm.prometheus_consumer.alerts()

which eventually calls _apply_label_matcher results in a file named 0.12 created in the charms folder, with the following contents:
process_cpu_seconds_total{juju_application="consumer-tester",juju_model="None",juju_model_uuid="f2c1b2a6-e006-11eb-ba80-0242ac130004"}

"0.12" happens to be the string after ">" in the alert rule. Seems like this is executed as a shell script.
./tests/unit/test_endpoint_consumer.py
69:                    "expr": "process_cpu_seconds_total > 0.12",

result = subprocess.run(" ".join(cmd), check=False, stdout=subprocess.PIPE, shell=True)

shell=True
🚨🚨 wait until it's passed a rule with expr: pass; rm -rf / 🚨🚨


Address comments for Segment Relocator Rebalance Config

Address remaining comments for #13863

Codecov Report
Attention: Patch coverage is 0% with 28 lines in your changes missing coverage. Please review.

Project coverage is 0.00%. Comparing base (59551e4) to head (7b9ba11).
Report is 1008 commits behind head on master.

Files with missing lines
Patch %
Lines

...va/org/apache/pinot/controller/ControllerConf.java
0.00%
17 Missing :warning:

...roller/helix/core/relocation/SegmentRelocator.java
0.00%
11 Missing :warning:

:exclamation:  There is a different number of reports uploaded between BASE (59551e4) and HEAD (7b9ba11). Click for more details.
HEAD has 53 uploads less than BASE

Flag
BASE (59551e4)
HEAD (7b9ba11)

integration
7
1

integration2
3
1

temurin
12
1

java-21
7
1

skip-bytebuffers-true
3
1

skip-bytebuffers-false
7
0

unittests
5
0

unittests1
2
0

java-11
5
0

unittests2
3
0

integration1
2
0

custom-integration1
2
0

Additional details and impacted files
@@              Coverage Diff              @@
##             master   #13963       +/-   ##
=============================================
- Coverage     61.75%    0.00%   -61.76%
=============================================
  Files          2436     2514       +78
  Lines        133233   139019     +5786
  Branches      20636    21368      +732
=============================================
- Hits          82274        0    -82274
- Misses        44911   139019    +94108
+ Partials       6048        0     -6048

Flag
Coverage Δ

custom-integration1
?

integration
0.00% <0.00%> (-0.01%)
:arrow_down:

integration1
?

integration2
0.00% <0.00%> (ø)

java-11
?

java-21
0.00% <0.00%> (-61.63%)
:arrow_down:

skip-bytebuffers-false
?

skip-bytebuffers-true
0.00% <0.00%> (-27.73%)
:arrow_down:

temurin
0.00% <0.00%> (-61.76%)
:arrow_down:

unittests
?

unittests1
?

unittests2
?

Flags with carried forward coverage won't be shown. Click here to find out more.

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.


[BUG] Keyword analysis does not work correctly with 'Run Keyword If'

Hello,
First, thx a lot for you plugin Robotframework, it is really great.
It's possible to disable the analysis code because it displays a lot of errors but the synthax is correct for Robot.
Run Keyword If  "${file_Name}" == "OLIS"    RG_OLIS
...         ELSE IF  "${file_Name}" == "DZ"     RG_DZ
...         ELSE IF  "${file_Name}" == "PLIS"    RG_PLIS
...         ELSE IF  "${file_Name}" == "OOS1"     RG_OOS1
...         ELSE IF  "${file_Name}" == "OOS2"     RG_OOS2
...         ELSE IF  "${file_Name}" == "VENT"     RG_VENTIL
...         ELSE IF  "${file_Name}" == "NUM"            RG_NUM
...         ELSE     Fatal Error  msg=Le nom ${file_Name} n'est pas reconnu
In this case my screen is not clear and is not easy to work with you plugin. (see attach file)
Regards
(sorry for my english)

You found a bug!!!!
I need to take a closer look at why the keyword analysis passes too many parameters on "Run Keyword If".
As a workaround you can disable the code analysis for single statements. Like this:
 Run Keyword If    "${file_Name}" == "OLIS"  RG_OLIS
    ...  ELSE IF  "${file_Name}" == "DZ"  RG_DZ
    ...  ELSE IF  "${file_Name}" == "PLIS"  RG_PLIS
    ...  ELSE IF  "${file_Name}" == "OOS1"  RG_OOS1
    ...  ELSE IF  "${file_Name}" == "OOS2"  RG_OOS2
    ...  ELSE IF  "${file_Name}" == "VENT"  RG_VENTIL
    ...  ELSE IF  "${file_Name}" == "NUM"  RG_NUM
    ...  ELSE  Fatal Error  msg=Le nom ${file_Name} n'est pas reconnu    # robotcode: ignore

The # robotcode: ignore at the end of the statement disables the code analysis.
Depending on the RobotFramework version >=4 you can also use the IF statement. This doesn't look that complicated to me.
IF    "${file_Name}" == "OLIS"
    RG_OLIS
ELSE IF    "${file_Name}" == "DZ"
    RG_DZ
ELSE IF    "${file_Name}" == "PLIS"
    RG_PLIS
ELSE IF    "${file_Name}" == "OOS1"
    RG_OOS1
ELSE IF    "${file_Name}" == "OOS2"
    RG_OOS2
ELSE IF    "${file_Name}" == "VENT"
    RG_VENTIL
ELSE IF    "${file_Name}" == "NUM"
    RG_NUM
ELSE
    Fatal Error    msg=Le nom ${file_Name} n'est pas reconnu
END

This is an often asked question, but the variable thing works as designed.
The short answer: The Set ... Varible keywords are evil!
a longer one here


Liquid Monitor does not see Ender IO Fluid Tank (Pressurized or regular)

See https://forum.feed-the-beast.com/threads/rftools-liquid-monitor-does-not-see-enderio-fluid-tank.209913/
I also see this on my custom modpack with:

Minecraft 1.10.2
Forge Mod Loader (FML) 1.10.2-<IP_ADDRESS>5
RFTools 1.1x-5.82
EnderCore 1.10.2-<IP_ADDRESS>-beta
Ender IO 1.10.2-3.1.156

Can see an EnderStorage Ender Tank next to it.

Did you report this to the EnderIO people? This is probably caused by them not implementing 'null' facing properly for their tank

Will be fixed in the next release of EnderIO

Thank you. :) I started here as there was also a thread mentioning it when I searched and Liquid Monitor is the device I want to use. I didn't see a similar thread nor bug for Ender IO, should I open one to track it? I found one where you talked with them about null facing, but that was for crashing the client, not Liquid Monitor (or similar) working and it was fixed/closed back in August 2016.

It is already fixed at their side and ready for next release so no need to open an issue with them

Awesome, thank you very much. :)


Define unit of measure for percent. Fixes #785.

Fixes #785.

Accidentally created PR to master. Will recreate onto develop.


Getting JAXB to work

Getting JAXB to work in a native image is not an easy task. See e.g. here: https://github.com/oracle/graal/issues/379 The conclusion there is that this will be only supported via the tracing agent. With a separate test program I succeeded to get that working according to the description given in the above reference. When I tried to manually apply the result to the client-maven-plugin I realized that for this I would need to add a proxyList but, at least according to the documentation, the client-maven-plugin does not support such a list. This is a missing feature and should be added. (Even better would be to integrate the output of the tracing agent directly.)

You might be able to work around that issue by providing
/src/main/resources/META-INF/native-image/proxy-config.json
/src/main/resources/META-INF/native-image/reflect-config.json
Or if you prefer command line approach you could use nativeImageArgs like
<nativeImageArgs>
    <list>-agentlib:native-image-agent=config-output-dir=$CONFIG_DIR,caller-filter-file=$FILTER_FILE_PATH</list>
    <list>--verbose</list>
</nativeImageArgs>

@lazar-mitrovic Thanks for the input. What you describe in the comment to #119 is basically what I already did with my above mentioned test program. So I know how to get that running with native-image. The problem is the client-maven-plugin which creates its on lists, overwriting others, merging these with other user input and then forward that to native-image. 1. What I do not know is what the right way would be to add the missing information so that I can be sure it is really picked up and not ignored or overwritten. 2. I was asking for a real future proof solution for this problem because it must be possible to provide these proxies in some official way.

mvn gluonfx:runagent should be enough now.


Guidance around using www in links

See discussion in Content Community thread early Jan 2017

@libbyv this might be a duplicate of #162?

Duplicate of https://github.com/govau/content-guide/issues/22


Added proxy support

Hi,
I have added proxy support to this gem, which is now usable behind a corporate firewall.
It now picks up the proxy settings from the standard environment variables http_proxy or HTTP_PROXY.
Net::HTTP::Proxy returns Net::HTTP when the proxy host is nil so the new code will fallback gracefully when neither of the two variables is set.
The corresponding commit is on the topic branch proxy_support.
Thanks,
Luca Bernardo Ciddio

Thanks you for your contribution!


E2E and Integration tests

E2E and Integration test to make sure that, the system still works after a pull request to main

Instead of mocking services, we can start the backend services as docker containers and perform the tests. This approach would allow us to check the coverage for the frontends. For the backends we can start them as nodejs process to calculate the coverage
We can import a realm in keycloak with a pre configured client for the issuer and verifier authorization.

I already added the setup with Testcontainers and a test for the settings and login functions. But we should add test for the issuance and presentation flow.
To make it less complicated we can use the API of the issuer and verifier so we do not need to jump between taps in playwright


Windows BSOD (GeForce 3080)

I enabled vgpu_unlock on a geforce 3080, setup one Windows 10 VM, installed GRID driver 460.32.04. It seems Windows does see one NVIDIA A6000-4Q instance, but after reboot Windows, it always BSOD. Any idea? Thx.

Why was this issue closed? Was the issue fixed, or??? The wiki says Ampere isn't supported, so I'm curious to know whether you actually got it working.

I’m guessing this is closed because ampere is currently unsupported: https://github.com/DualCoder/vgpu_unlock/issues/8#issuecomment-817062916


StorageHealthCheck - problem with overwriting file_name by some backends

There is an issue when some storage backend overwrites requested file_name to something else (for ex. avoiding duplicates) - and when it happens there is a problem with this backend implementation. Please look at this method on StorageHealthCheck
        storage = self.get_storage()
        # save the file
        file_name = storage.save(
            file_name, ContentFile(content=file_content)
        )
        # read the file and compare
        if not storage.exists(file_name):
            raise ServiceUnavailable('File does not exist')
        with storage.open(file_name) as f:
            if not f.read() == file_content:
                raise ServiceUnavailable('File content does not match')

Look at this line:
file_name = storage.save(
    file_name, ContentFile(content=file_content)
)

storage is allowed to overwrite the requested file_name - which is OK, and later the rest of code for this method is also OK - but since then this "file_name" may change.
Thats why this method:
def check_status(self):
        try:
            # write the file to the storage backend
            file_name = self.get_file_name()
            file_content = self.get_file_content()
            self.check_save(file_name, file_content)
            self.check_delete(file_name)
            return True
        except Exception:
            raise ServiceUnavailable('Unknown exception')

may not work OK because 'check_save' and 'check_delete' uses the "original" requested file_name - but as we've seen this "file_name" could be overwritten by check_save method - making method check_delete looking for invalid file_name.
It could be fixed by adding "return file_name" to "check_save" method, like this:
def check_save(self, file_name, file_content):
        storage = self.get_storage()
        # save the file
        file_name = storage.save(
            file_name, ContentFile(content=file_content)
        )
        # read the file and compare
        if not storage.exists(file_name):
            raise ServiceUnavailable('File does not exist')
        with storage.open(file_name) as f:
            if not f.read() == file_content:
                raise ServiceUnavailable('File content does not match')
        return file_name

And use that file name in check_status method:
def check_status(self):
        try:
            # write the file to the storage backend
            file_name = self.get_file_name()
            file_content = self.get_file_content()
            file_name = self.check_save(file_name, file_content)
            self.check_delete(file_name)
            return True
        except Exception:
            raise ServiceUnavailable('Unknown exception')

What do you think?

Codecov Report

Merging #200 into master will increase coverage by 0.07%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #200      +/-   ##
==========================================
+ Coverage   74.27%   74.35%   +0.07%
==========================================
  Files          32       32
  Lines         346      347       +1
==========================================
+ Hits          257      258       +1
  Misses         89       89

Impacted Files
Coverage Δ

health_check/storage/backends.py
90.69% <100%> (+0.22%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 4b532f5...e0112be. Read the comment docs.

Released in 3.7.1


fix alpha propagated object params docs

Changes
Propagated object params should be in beta feature since object params (TEP75) is in beta and propagating params is in stable (TEP107).
/kind cleanup
Signed-off-by: Yongxuan Zhang<EMAIL_ADDRESS>
Submitter Checklist
As the author of this PR, please check off the items in this checklist:

[ ] Has Docs if any changes are user facing, including updates to minimum requirements e.g. Kubernetes version bumps
[ ] Has Tests included if any functionality added or changed
[ ] Follows the commit message standard
[ ] Meets the Tekton contributor standards (including functionality, content, code)
[ ] Has a kind label. You can add one by adding a comment on this PR that contains /kind <type>. Valid types are bug, cleanup, design, documentation, feature, flake, misc, question, tep
[ ] Release notes block below has been updated with any user facing changes (API changes, bug fixes, changes requiring upgrade notices or deprecation warnings). See some examples of good release notes.
[ ] Release notes contains the string "action required" if the change requires additional action from users switching to the new release

Release Notes
NONE

/assign @chitrangpatel

/lgtm

/retest
pull-tekton-pipeline-build-tests — Pod scheduling timeout.

/lgtm

Thanks! lgtm!


Update button with own custom form

I would like to add 'UPDATE' button with my own custom edit form. It should work for  all table (for example batch update).
And it could be very nice if it possible to locate next to exportToCsv or New or Delete buttons.
Is that possible?

I think it can be done by customizing the search panel.
like this example:
https://gist.github.com/AllenFang/258cdfa92d6ce36a4d22ffd8b2aea17e#file-custom-search-panel-1-jsx


fix(frontends/lean/pp): insert line breaks in notations

The pretty-printer now allows line breaks in notations.  For example for infix operators we insert a line break after the operator, it looks like this:
def foo : ℕ → ℕ :=
λ (xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx : ℕ),
  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx +
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

(Right now the addition would be printed on a single line.)
It does not always produce the prettiest output, but it's good enough to make long equations (somewhat) readable.

Oh, I just noticed that this triggers an assertion violation in the format code.  I'll look at it.


Bug with nested ifs and lets

Prerequisites
Please put an X between the brackets as you perform the following steps:

[x] Check that your issue is not already filed:
https://github.com/leanprover/lean4/issues
[x] Reduce the issue to a minimal, self-contained, reproducible test case.
Avoid dependencies to Mathlib or Batteries.
[x] Test your test case against the latest nightly release, for example on
https://live.lean-lang.org/#project=lean-nightly
(You can also use the settings there to switch to “Lean nightly”)

Description
The following code gives (kernel) declaration has free variables 'getHexDigit?' on Lean 4.9.0-rc1.
def getHexDigit? (char : Char) : Option (Fin 16) :=
  if char.toNat < 0x0030 then
    none
  else
    let n := if char.toNat < 0xFF10 then char.toNat - 0x0030 else char.toNat - 0xFF10
    if h : n < 10 then
      some ⟨n, Nat.lt_trans h (by decide)⟩
    else if n >= 17 then
      let n := n - 7
      if h : n < 16 then
        some ⟨n, h⟩
      else if n >= 32 then
        let n := n - 32
        if h : n < 16 then
          some ⟨n, h⟩
        else
          none
      else
        none
    else
      none

Removing the second let or the third let eliminates the problem.
Context
Discovered while updating lean4-unicode-basic to v4.9.0-rc1. Posted on Zulip.
Versions
Lean (version 4.9.0-rc1, arm64-apple-darwin23.5.0, commit be6c4894e0a6, Release)
Impact
Add :+1: to issues you consider important. If others are impacted by this issue, please ask them to add :+1: to it.

Interestingly, when I minimized it to
example : Nat :=
  let n := 0
  if _ : True then
    let m := n
    if _ : m = 0 then
      let x := 0
      0
    else
      0
  else
    0

this is broken all the way back to Lean 4.0.0. It builds when changing the first line to example (_ : Nat) : Nat :=
The example provided by OP works on nightly-2024-05-22 and is broken on nightly-2024-05-23.

Great insight! I thought let reassignments might be the issue but that was a red herring.

I also found a (kernel) declaration has free variables issue involving let which I minimized to the following:
example: Nat :=
  let a: Nat := 1
  have: a = 1 := by rfl
  let b: Nat := 2
  have: b = 2 := by rfl
  have: a = a := by rfl
  let c := 1
  0

It also fails at version 4.0.0. I thought it might be related to this issue so I am adding it here.

I also found a (kernel) declaration has free variables issue involving let which I minimized to the following:
example: Nat :=
  let a: Nat := 1
  have: a = 1 := by rfl
  let b: Nat := 2
  have: b = 2 := by rfl
  have: a = a := by rfl
  let c := 1
  0

It also fails at version 4.0.0. I thought it might be related to this issue so I am adding it here.

Yup, same bug indeed; can remove all but the last OfNat
example: Nat :=
  let a: Nat := Nat.zero
  have: a = Nat.zero := rfl
  let b: Nat := Nat.zero
  have: a = b := rfl
  let c := 0
  Nat.zero

and then it gets assigned let c : Nat := OfNat.ofNat.{0} Nat 0 ((let b : Nat := Nat.zero; fun (this : Eq.{1} Nat _uniq.4 b) => instOfNatNat 0) this) as before, where _uniq.4 should be a.

I do not think that this was fixed by #4110. The change in #4110 seems fine, but it does not fix the underlying issue in (I think!) isDefEq.
Here's another test case that's simpler still:
example :=
  let a : Nat := Nat.zero
  fun (_ : True) =>
  let b : Nat := Nat.zero
  (fun (_ : a = b) => 0)

While #4110 makes some ill-formed metavariable assignments end up not mattering, they are still present. The issue seems to be that the OfNat instance metavariable for 0 forgets to include a as one of the let bindings it depends on.
If you add well-formedness checks to checkTypesAndAssign like so, then you can see this reflected as an elaboration error, as "typeclass instance problem is stuck".
private def checkTypesAndAssign (mvar : Expr) (v : Expr) : MetaM Bool :=
  withTraceNodeBefore `Meta.isDefEq.assign.checkTypes (return m!"({mvar} : {← inferType mvar}) := ({v} : {← inferType v})") do
    if !mvar.isMVar then
      trace[Meta.isDefEq.assign.checkTypes] "metavariable expected"
      return false
    else
      -- must check whether types are definitionally equal or not, before assigning and returning true
      let mvarType ← inferType mvar
      let vType ← inferType v
      if (← withTransparency TransparencyMode.default <| Meta.isExprDefEqAux mvarType vType) then
        unless (← MetavarContext.isWellFormed (← mvar.mvarId!.getDecl).lctx v) do
          throwError "in checkTypesAndAssign: metavariable has incompatible local context for value\n{indentD v}\nMetavariable:{indentD mvar.mvarId!}"
        unless (← MetavarContext.isWellFormed (← mvar.mvarId!.getDecl).lctx vType) do
          throwError "in checkTypesAndAssign: metavariable has incompatible local context for type\n{indentD v}\nMetavariable:{indentD mvar.mvarId!}"
        mvar.mvarId!.assign v
        pure true
      else
        pure false

Is there any justification in the PR for not zeta reducing being a bug in this comment? If not, I think a followup fix should change that comment.

I had a similar theory prior to changing the fix:
https://github.com/leanprover/lean4/commit/625b45ce47fe033e6d5131cfdb8be0c25ba8ba62 (this implementation is not good but the idea was essentially that this code doesn't loop through all let decls:
https://github.com/leanprover/lean4/blob/93fa9c8837e071a866b62e2ca73c22a362ccb988/src/Lean/Meta/ExprDefEq.lean#L390-L419
I backtracked on that idea because it wasn't clear to me that leaving in those fvars was indeed unintentional.

@kmill Your test case is failing for me on "Mathlib stable" but not latest or nightly

Closing until reconfirmation


Add nlopt package to jsk_3rdparty

The package is already released as name of ros-noetic-nlopt.
It looks the file is updated automatically. CC: @k-okada

@tfoote Thank you for the comment. It is really helpful information!
I ended up to change my package to require both nlopt (for melodic and older) and libnlopt-cxx-dev (for noetic) and find either of them in CMakeLists.txt:
# CMakeLists.txt
find_package(PkgConfig)
find_package(nlopt QUIET)
if (NOT nlopt_FOUND)
  pkg_check_modules(nlopt nlopt_cxx REQUIRED)
endif()

<!-- package.xml -->
<package format="3">
  <!-- omitted -->
  <depend condition="$ROS_DISTRO != noetic">nlopt</depend>
  <depend condition="$ROS_DISTRO == noetic">libnlopt-cxx-dev</depend>
  <!-- omitted -->
</package>


pythonPackages.molecule-plugins: 23.5.0 -> 23.5.3

Description of changes
https://github.com/ansible-community/molecule-plugins/releases/tag/v23.5.3

Things done

Built on platform(s)

[x] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)

[ ] sandbox = relaxed
[ ] sandbox = true

[ ] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[x] Tested basic functionality of all binary files (usually in ./result/bin/)
24.05 Release Notes (or backporting 23.05 and 23.11 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.

Add a :+1: reaction to pull requests you find important.

@ofborg build python312Packages.molecule-plugins


feat: expose text format errors

Give users a way to get humanized errors as string.
Leverage ajv's errorsText() method

expose errorsText function
use errorsText in the cli output

Thank you for the review. I applied some of the proposed fixes and will complete this PR in few days.

I'm not convinced of this api but I'm not sure how to do it another way since ajv has a particular output that does not match yours.. Let me know if you have suggestions.

Just released in 1.7.0
Thanks for contributing, the CLI output is much more readable now 👌


In rag how to make sure it doesnt answer out of context

Question Validation

[X] I have searched both the documentation and discord for an answer.

Question
I have a RAG for specific debugging problems, but if asked question about random things, it still answers, how to restrict this? Im using zephyr 7b

It's basically just prompt engineering. Or introducing a second llm call to tryvand get the llm to filter itself

You can use the an evaluator such as the FaithfulnessEvaluator (unfortunately, this is a binary evaluator).
For my current project, however, I am just measure how relevant is the the most relevant node (as assesed by the reranker):
	if response.source_nodes[0].score < 0.25:
		response_text = 'I cannot find an answer to that question in en.swissquote.lu. Please, rephrase the question.'
		source = 'No sources'
	else:
		response_text = str(response)

i tried add a post context prompt and it worked fairly well, thanks

Hi @JINO-ROHIT,
Can you help me with how you added post context prompt?

@Aekansh-Ak hey sure, what i did was -
post_prompt = """ if the information isnt available in the given context to formulate the answer, just reply with NO ANSWER""""
response = query_engine.query(SYS_PROMPT + user_query + post_prompt)
this is what worked for me


Composer could not find a composer.json file in /app

I'm getting this error just after cloning repo and running docker-compose up. Any suggestions?

Hi @gustavoper,
which OS are you using? Seems like the volumes do not work correctly. Please verify running:
docker-compose run php ls /opt/php

and for composer:
docker-compose run composer ls /app

if neither of them shows up the repository contents, your volumes could not be mounted, which is then a general problem in your Docker installation. You could also run docker-compose config to verify that the lokal paths are correctly set.

Same problem for me on Windows 10.  Here is an related issue: https://github.com/RobLoach/docker-composer/issues/124

I am closing this one here, as it seems to be an issue with docker-composer.


update packages

:white_check_mark: Build TheIdServer 8.0.0-fix-dependencies1-0256 completed (commit https://github.com/Aguafrommars/TheIdServer/commit/c7287255c3 by @invalid-email-address)

:x: Build TheIdServer 8.0.0-fix-dependencies1-0257 failed (commit https://github.com/Aguafrommars/TheIdServer/commit/bf943a790e by @invalid-email-address)

:white_check_mark: Build TheIdServer 8.0.0-fix-dependencies.1+257.build.3657 completed (commit https://github.com/Aguafrommars/TheIdServer/commit/bf943a790e by @invalid-email-address)


SAK-39953: resources > add ability to define custom copyright options

https://jira.sakaiproject.org/browse/SAK-39953
This PR introduces the following new features:

ability for an institution to define and use an arbitrary number of custom copyright options
** enabled/disabled via sakai.property "copyright.useCustom", which defaults to false
** custom copyright options are defined via /content/content-copyright/impl/src/bundle/org/sakaiproject/content/copyright/copyright.properties
ability to force users to explicitly select copyright status for files
** enabled/disabled via sakai.property "copyright.requireChoice", which defaults to false
** works with both default and custom copyright options
** if set to true, inputs a "Please select a copyright status" entry in the copyright drop down (always first element in the list)
** client and server side validation to reject saving the resource if the drop down was not set to a value other than the "Please select..."
adds the copyright drop down form field to the upload resources form (accessed from both the Resources tool and the Drop Box tool)
** one drop down, setting applies to all files uploaded
** previously was only present on the 'Edit Details' form

The linked PR also includes refactoring existing copyright code, removing old and unused copyright sakai.properties, and improved documentation of the current state of valid copyright sakai.properties in default.sakai.properties.
The following sakai.properties have been added:
# SAK-39953 - use custom copyright options rather than the predefined list
# NOTE: define your custom copyright options in /content/content-copyright/impl/src/bundle/org/sakaiproject/content/copyright/copyright.properties
# NOTE: examples are defined in the above file, with the keys 'custom.copyright.#'; define as many or as few as needed by your institution
# DEFAULT: false
# copyright.useCustom=true

# SAK-39953 - require users to explicity define the copyright status for uploaded files in the Resources tool
# NOTE: does not require any other copyright sakai.properties to be set (works with defaults, copyright.types and custom copyright)
# DEFAULT: false
# copyright.requireChoice=true

The following sakai.properties have been removed:
## NOTE: these copyright properties may not be valid anymore - 8 Sept 2011
# default.copyright=Copyright status is not yet determined.
# default.copyright.alert=true
# fairuse.url=http://fairuse.stanford.edu
# newcopyrightinput=true

default.copyright was made obsolete via KNL-1399 (and re-implemented in this PR)
default.copyright.alert was some legacy property, not really sure what it once did
fairuse.url from sakai.properties was not being used; the functionality of overriding the default value was moved into message bundles (/content/content-tool/tool/src/bundle/right.properties) some time ago, so I provided some more documentation there about what it does and how to customize it properly
newcopyrightinput was another legacy property not being used; not sure what it once did
** for all of the above: removed some lingering code in /content/ project that was still referencing these and sticking them in the STATE but never actually using it

All comments from Paul's review have been addressed.

The remaining Codacy flags are either false positives (2), or issues with existing code which is not being touched (10).

Merging this one, @bjones86 is going to add a property change so this can be tested on experimental.


Missing DialogStateOut.supplemental_display_text GRPC messages

Hi,
I've written my own client for the GRPC service where I am submitting text based requests. I am receiving GRPC messages containing audio and supplemental_display_text but I only ever receive one supplemental_display_text message per response. This is generally ok and provides a transcript of the assistant response but there are some queries which result in the single supplemental_display_text only containing the last part of the response. e.g.
If you ask the Google Assistant App on iOS the Question "What do you think of Alexa?" one of the available responses is split over 2 speech bubbles as below:-
Q> What to you think of Alexa?
A> Alexa has such a soothing voice
A> I like it
Running the same question and response through the GRPC service you receive the full audio response but only a single supplemental_display_text message just containing the second response "I like it", where as I would expect 2 messages one containing "Alexa has such a soothing voice" and a second containing "I like it", or a single message containing a concatenated response

Also following this one.
It would be great to get all the messages and not just the last one. Some important use cases that we came across include tell me a joke or tell me a riddle. These ones will always send multi message responses.
@Fleker can you share any updates on this? Is it something that is expected to be handled in the future or is it something that can't be controlled at the service level?
Thanks a lot!

Right now I do not have an update, but we are aware of it.

@Fleker  any update on this issue? I am using C# compiled grpc v1alpha2 library of google assistant.
my user has Philips hue and thermostat. When he allows me to access his google assistant through oauth, I am using his access token to control his devices.
if I send message like "Turn Lamp 4 Off"  it works
but if I ask a question, "Is My Lamp 4 Off ? " am not getting any supplemental text from DialogStateOut
is this bug fixed?


Target Android 13 or higher

Checklist

[X] I have used the search function to see if someone else has already submitted the same feature request.
[X] I will describe the problem with as much detail as possible.
[X] This issue only contains a request for one single feature, not multiple (related) features.

App version
6.711
Problem you are trying to solve
Android 13 has been here for a while and Android 14 is already on the verge of rolling out.
Suggested solution
Can you please target Android 13 or higher?
Screenshots / Drawings / Technical details
No response

We are working on Android 13 support and will soon publish an update.

I'm curious. Why are you asking us to target Android 13? It shouldn't make a difference to users.


chore: declarative JS toolchain as code - via volta  --- reduces dev env variations (v1)

Pinned v14.18.3 LTS using volta, for using this, users must have volta installed. This can be achieved using this command - curl https://get.volta.sh | bash
audited and updated packages as required, now /app/ has 0 vulnerability from 4 and /cms/ has 14 vulnerabilities from 17
Added .nvmrc file for managing node versions
deleted redundant /node_modules/ and /package-lock.json from root

Preview
https://user-images.githubusercontent.com/73601258/169660879-09598924-c59a-4223-888f-110dc12e7cce.mp4

@Sing-Li please let me know if this is fine

@Sing-Li

Nodejs versioning is managed by volta. You can install it by running curl https://get.volta.sh | bash in your terminal. This is needed to ensure that Nodejs v14 and npm v6 are used for compatibility for all distributed development team members.

Can you please check, if this line is descriptive enough?

@Sing-Li done :+1: , please check if I need to do some other changes.
Thank you!

@Sing-Li sure


about dice

How do you calculate the dice? I add label image into Test_SYMNet.py and apply warped flow to get warped_label ,but the dice I caclulated is very low.

1.zip

@1164094277
It is not about the Dice score calculation.
This is the displacement field generated with my provided pre-trained model.

This is the displacement field generated with your trained model.

The deformation model used in SYMNet is called the stationary velocity field. The diffeomorphic properties only hold if and only if the velocity field is smooth. Apparently, the weight of smoothness regularization in your training setting is not sufficient to safeguard the smoothness's assumption.
Here is my advice:

Center-crop the data to match the data dimension with the one reported in our paper, and train the parameters mentioned in our paper (This avoid the complex parameter tuning process.)
OR
Set a higher weight for smoothness regularization (both smoothness regularization loss and orientation consistency loss). Then, add validation code to the training code (right after the code of model saving) to keep track of the model performance at different iterations, i.e. Dice score, std(Jacobian determinant) etc. You can stop the training once you observe that the smoothness of the deformation field is abnormal or the model coverage.

@cwmok @cwmok I've tried training to crop the image to the same size as your image, but the results aren't good either, as I mentioned in the previous question.(dice only 0.5369... ).
I've tried to set a higher weight , but the result is still poor.

@1164094277
Could you attach the trained model and training parameters for reference?
Also, I want to clarify that we only used 26 anatomical structures for evaluation in our paper, including the Brain stem, thalamus, cerebellum cortex etc. But your evaluation script, it includes 35 anatomical structures.
Due to popular requests on the full-size OASIS dataset, I will upload the results as well as the pre-trained model on the full-size OASIS dataset next week.

@cwmok cwmok I checked the code and found that I was using "mode = ‘bilinear’ "(in SpatialTransform) when I applied the warpped flow to the label. I changed it to  "mode = ‘nearest' " to got better results（Pixel  in the warpped label is integer）.   I wonder if it‘s right .

@1164094277
Yes, you are correct. I actually implemented two spatial transformation functions in Models.py: SpatialTransform and SpatialTransformNearest. The  SpatialTransform is for warping the image and the SpatialTransformNearest is for warping the label, so that you don't have to modify the SpatialTransform's mode.
I am glad you have solved your problem.

@1164094277
I have added an example showing how to train on the preprocessed OASIS dataset. For details, please refer to the section "(Example) Training on the preprocessed OASIS dataset" in the readme file.


Add blueprint id to manager endpoint workdir

It seems that multiple deployments named the same could potentially
clash, for example if one was deleted and another created later?

Closed: As this PR is more than six months old without having been merged. Please reopen (and rebase if necessary) if it is still relevant.


Unable to start virtual machine with command when not logged in

Describe the issue
After I boot up the Mac, connect to the Mac via ssh without logging into the desktop, I can't start the virtual machine by entering the following command.
/Applications/UTM.app/Contents/MacOS/utmctl start uc-dev

2023-02-24 11:19:18.155 utmctl[1560:8615] warning: failed to get scripting definition from /Applications/UTM.app; it may not be scriptable.
2023-02-24 11:19:18.155 utmctl[1560:8615] -[SBApplication virtualMachines]: unrecognized selector sent to instance 0x6000029b1080
2023-02-24 11:19:18.155 utmctl[1560:8615] *** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '-[SBApplication virtualMachines]: unrecognized selector sent to instance 0x6000029b1080'
*** First throw call stack:
(
        0   CoreFoundation                      0x00000001940543e8 __exceptionPreprocess + 176
        1   libobjc.A.dylib                     0x0000000193b9eea8 objc_exception_throw + 60
        2   CoreFoundation                      0x00000001940f6c0c -[NSObject(NSObject) __retain_OA] + 0
        3   ScriptingBridge                     0x00000001d1215f54 -[SBObject forwardInvocation:] + 116
        4   CoreFoundation                      0x0000000193fba3f0 ___forwarding___ + 976
        5   CoreFoundation                      0x0000000193fb9f60 _CF_forwarding_prep_0 + 96
        6   utmctl                              0x0000000100744cb8 utmctl + 36024
        7   utmctl                              0x0000000100742004 utmctl + 24580
        8   utmctl                              0x00000001007450ec utmctl + 37100
        9   utmctl                              0x000000010077a238 utmctl + 254520
        10  utmctl                              0x000000010074718c utmctl + 45452
        11  dyld                                0x0000000193bcfe50 start + 2544
)
libc++abi: terminating with uncaught exception of type NSException
zsh: abort      /Applications/UTM.app/Contents/MacOS/utmctl start uc-dev

Configuration

UTM Version: 4.1.5
macOS Version: 13.2.1
Mac Chip (Intel, M1, ...): M1 Pro

The scripting interface still requires the app to the running and I don’t think that works without being logged in. All else aside, the app sandbox is per-user so it’s hard to see how it can work without being logged in.

The scripting interface still requires the app to the running and I don’t think that works without being logged in. All else aside, the app sandbox is per-user so it’s hard to see how it can work without being logged in.

Thank you for your reply. I used multipass to manage the virtual machine before. After switching to utm, I found that utm cannot be started without being on duty.
Unfortunately, I can only continue to use multipass at this stage.


Uncaught TypeError: Cannot read property 'prototype' of undefined

Short description of the problem:
A code that compile very well with the 0.0.47 app-script version  fail  with 1.0.0  in this part of code.
mapToClass: function (constructor, structure) {             /// <summary>             ///     Map table to a javascript constructor function. Objects returned from the database will be instances of this class, making             ///     it possible to the instanceOf operator as well as extending the class using constructor.prototype.method = function(){...}.             /// </summary>             /// <param name="constructor">Constructor function representing the class.</param>             /// <param name="structure" optional="true">Helps IDE code completion by knowing the members that objects contain and not just the indexes. Also             /// know what type each member has. Example: {name: String, emailAddresses: [String], password}</param>             this.schema.mappedClass = constructor;             var instanceTemplate = Object.create(constructor.prototype);             if (structure) {                 // structure and instanceTemplate is for IDE code competion only while constructor.prototype is for actual inheritance.                 applyStructure(instanceTemplate, structure);             }
I think that it is the app-script problem.  this comme after upgrading from IONIC RC4 to IONIC RC5
the problem is related to the maping for classes of the dexie database(IndexDB).
When i come back to the ionic app-script 0.0.47, i can use ionic run android --target=xxxxxxx --prod  and run corectly my code in a device  and that is not the case with the 1.0.0  app-script version
What behavior are you expecting?
I was expecting that my code will not bloc itself in a white screen and give the  Uncaught TypeError: Cannot read property 'prototype' of undefined  message.
As i said previously this behavior not happend with app-script 0.0.47 and the program compile and corectly
Steps to reproduce:

create new projet  with IONIC RC5 and install dexie db library
create a database with at least one table that is mapped with one class
use ionic run android --target=xxxxxxx --prod or ionic run android --target=xxxxxxx --dev
and you will get a white screen.  look for a console when debuging with chrome an you will get the error    Uncaught TypeError: Cannot read property 'prototype' of undefined

insert any relevant code between the above and below backticks

here is a class that faill when mapping
export class PhoneNumber {
id?: number;
type: string;
value: string;
simSerialNumber:string;
displayName:string;
subscriberId:string;
constructor(id?:number) {
    if (id) this.id = id;
}

}
here is a db
import Dexie from 'dexie'; export class DataBase extends Dexie {  phone: Dexie.Table<PhoneNumber, number>;    constructor() {            super("MyDBName");         var db = this;        db.version(1).stores({             phone: '++id, type, value,simSerialNumber,subscriberId,displayName',  }); db.phone.mapToClass(PhoneNumber);    } } export var db = new DataBase();
Which @ionic/app-scripts version are you using?
1.0.0
Other information: (e.g. stacktraces, related issues, suggestions how to fix, stackoverflow links, forum links, etc)

Please provide a minimal example demonstrating the issue so I can recreate and validate it.
Thanks,
Dan

@stchoukeu hey maybe you have the same issue which i had? https://github.com/driftyco/ionic-app-scripts/issues/633
try to avoid barrel imports and see if it solves the issue for you

Hi danbucholtz,
I'm sorry but i was not connected. Please here is a link with a code that show an error with app-script 1.0.0 and compile very well with app-script 0.0.47.  https://github.com/stchoukeu/IONIC2-RC4-with-DEXIE-Database
as showing in https://github.com/stchoukeu/IONIC2-RC4-with-DEXIE-Database/blob/master/Capture.jpg you will remarque that when compiling with app-script 0.0.47.  The application run and go till the home page as desired  with database created  but it faill with the white screen  and provide an error
Uncaught TypeError: Cannot read property 'prototype' of undefined   in the chrome dev tools.
thank you.

I just encountered this.  My solution was to have fewer ongoing saves at once.
instead of
whenjs.all([
  item1.save()
  item2.save()
  item3.save()
  ...
  item100.save()
])

I did
sequence([
  => item1.save()
  => item2.save()
  ...
  => item100.save()
])

And now I get the actual error, WITH the stack trace, rather than a needle in a haystack.

In my code, what i done was only item.save() in a transaction. The problem
that i'm facing come from app-script 1.0.0  my code create a database and
work very Well when i use app-script 0.0.47. the build go till the end and
the execution fail with that message arround mapping database classe.
Le 7 févr. 2017 1:13 AM, "danschumann"<EMAIL_ADDRESS>a écrit :

I just encountered this. My solution was to have fewer ongoing saves at
once.
instead of
whenjs.all([
item1.save()
item2.save()
item3.save()
...
item100.save()
])
I did
sequence([
=> item1.save()
=> item2.save()
...
=> item100.save()
])
And now I get the actual error, WITH the stack trace, rather than a needle
in a haystack.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/driftyco/ionic-app-scripts/issues/688#issuecomment-277857442,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AIvkptU8-7bS2ezPznXYHN4wfFxGoGVwks5rZ7cjgaJpZM4Lu5Bl
.

Please create a minimal repository demonstrating the issue.
Thanks,
Dan

Please Dan i create it and i put in my github repository. It seem that you
have not read my last post.
Le 7 févr. 2017 07:39, "Dan Bucholtz"<EMAIL_ADDRESS>a écrit :
Please create a minimal repository demonstrating the issue.
Thanks,
Dan
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/driftyco/ionic-app-scripts/issues/688#issuecomment-277914681,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AIvkpo5PEaEOv0qfDoubppYVgQ_1B4ZHks5raBGygaJpZM4Lu5Bl
.

Thanks you again for all
Le 7 févr. 2017 07:43, "Simplice TCHOUKEU"<EMAIL_ADDRESS>a écrit :

Please Dan i create it and i put in my github repository. It seem that
you have not read my last post.
Le 7 févr. 2017 07:39, "Dan Bucholtz"<EMAIL_ADDRESS>a écrit :
Please create a minimal repository demonstrating the issue.
Thanks,
Dan
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/driftyco/ionic-app-scripts/issues/688#issuecomment-277914681,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AIvkpo5PEaEOv0qfDoubppYVgQ_1B4ZHks5raBGygaJpZM4Lu5Bl
.

Hi DAN,
please this is the message that i posted on github 5 days ago.
to @danbucholtz https://github.com/danbucholtz ,
I'm sorry but i was not connected. Please here is a link with a code that
show an error with app-script 1.0.0 and compile very well with app-script
0.0.47. https://github.com/stchoukeu/IONIC2-RC4-with-DEXIE-Database
as showing in
https://github.com/stchoukeu/IONIC2-RC4-with-DEXIE-Database/blob/master/Capture.jpg
https://github.com/driftyco/ionic-app-scripts/issues/url you will
remarque that when compiling with app-script 0.0.47. The application run
and go till the home page as desired with database created but it faill
with the white screen and provide an error
Uncaught TypeError: Cannot read property 'prototype' of undefined in the
chrome dev tools. when we use app-script 1.0.0
thank you.
2017-02-07 7:44 GMT+01:00 Simplice TCHOUKEU<EMAIL_ADDRESS>
Thanks you again for all
Le 7 févr. 2017 07:43, "Simplice TCHOUKEU"<EMAIL_ADDRESS>a écrit :

Please Dan i create it and i put in my github repository. It seem that
you have not read my last post.
Le 7 févr. 2017 07:39, "Dan Bucholtz"<EMAIL_ADDRESS>a
écrit :
Please create a minimal repository demonstrating the issue.
Thanks,
Dan
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/driftyco/ionic-app-scripts/issues/688#issuecomment-277914681,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AIvkpo5PEaEOv0qfDoubppYVgQ_1B4ZHks5raBGygaJpZM4Lu5Bl
.

--
Avec mes sincères salutations

TCHOUKEU Simplice Aimé
Architecte des Systèmes d'informations
tel: +237 75 38 35 76
skype: stchoukeu

This seems like an issue with Dexie or Webpack, not app-scripts.
I can log the value of Dexie:
Dexie:  function Dexie(dbName, options) {
    /// <param name="options" type="Object" optional="true">Specify only if you wich to control which addons that should run on this instance</param>
    var deps = D…

And with a prod build:
exie:  function pt(e,n){function a(){ie.on("versionchange",function(t){t.newVersion>0?console.warn("Another connection wants to upgrade database '"+ie.name+"'. Closing db now to resume the upgrade."):console

So it is bundling correctly. I recommend investigating further and opening an issue with Webpack or Dexie if a legitimate issue is found. Our Forum is a good place to go for help.
Thanks,
Dan

Hi DAN,
Since my Dexie library have not change because i just have to change
app-script 1.0.0 for app-script 0.0.47 to have all thing  working
perfectly, i can said that the problem can not come from Dexie.
From the two, it is only Webpack  witch is used by app-script in the build
process.
if there is a change between version of Webpack used in app-script 0.0.47
and the one used in app-script 1.0.0 we can say the this problem come from
the newer version of Webpack.
Can you give for us some information about version of Webpack used by
app-script 0.0.47 and the one used by app-script 1.0.0?
I will open an issue in Webpack project if you confirm my dianostic.

We upgraded from a beta version to a general release version. It should be more stable. I'm not sure what the changes are.
Can you check on the forum and see if anyone else is having issues? If you log the Dexie import, it's there, so something in the code itself is what is triggering the null pointer.
Thanks,
Dan

Thank you a lot for all your job. I posted the problem in the forums.
Le 8 févr. 2017 16:02, "Dan Bucholtz"<EMAIL_ADDRESS>a écrit :

We upgraded from a beta version to a general release version. It should be
more stable. I'm not sure what the changes are.
Can you check on the forum and see if anyone else is having issues? If you
log the Dexie import, it's there, so something in the code itself is what
is triggering the null pointer.
Thanks,
Dan
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/driftyco/ionic-app-scripts/issues/688#issuecomment-278352308,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AIvkpjS0LJ0bd5fXF9pZfalM6juW-Wtvks5radjwgaJpZM4Lu5Bl
.

Oh, yea my issue was w/ dexie.  Not sure how I got onto this ticket, must have googled it.


Support Puppet 5

Upped supported Puppet versions to include Puppet 5
Bumped version to 2.0.2

Coverage decreased (-0.08%) to 72.329% when pulling 2202f315761480fc237986367abfedbe50f50c4a on jeefberkey:puppet5 into 72fccf10b532f06fc81cf491614e7119c72ee981 on hercules-team:master.

Coverage decreased (-0.08%) to 72.329% when pulling 2202f315761480fc237986367abfedbe50f50c4a on jeefberkey:puppet5 into 72fccf10b532f06fc81cf491614e7119c72ee981 on hercules-team:master.

Coverage increased (+0.2%) to 72.629% when pulling d2001dcf4c7e5f11449f714fbe8b6047fec31888 on jeefberkey:puppet5 into 72fccf10b532f06fc81cf491614e7119c72ee981 on hercules-team:master.


Wrong protocol version in the Via header

[bcall@homer ats_ssl_config]$ nghttp -v https://<IP_ADDRESS>:4443/200.php
[  0.000] Connected
The negotiated protocol: h2
...
[from ATS going to the origin]
Via: https/1.1 homer.bryancall.com[aa274815-0002-4b4a-a1b2-058c8a2e0829] (ApacheTrafficServer/7.2.0)

Just FYI:
https://issues.apache.org/jira/browse/TS-4457
https://github.com/apache/trafficserver/pull/1066

interesting. That's done in the response "Via" header. But not in the request "Via" header.
https://github.com/apache/trafficserver/blob/master/proxy/http/HttpTransactHeaders.cc#L754-L763

The fix is merged