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rcsb / py-rcsb_utils_targets

RCSB module containing methods for target data management
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IMGTTargetProvider producing multiple errors #1

Open piehld opened 2 years ago

piehld commented 2 years ago

Just noticed a series of errors produced by IMGTTargetProvider when running the testIMGTTargetFeatureProvider tests. Needs digging into.

Note that this has been occurring for quite some time (unsure of how long exactly, but at least several months), and it does not cause the Azure build to fail, so may not be a critical error.

2022-07-03T12:07:59.7353099Z testBuildIMGTTargetsFeatures (testIMGTTargetFeatureProvider.IMGTTargetFeatureProviderTests) ... INFO:root:Starting testIMGTTargetFeatureProvider.IMGTTargetFeatureProviderTests.testBuildIMGTTargetsFeatures at 2022 07 03 12:07:59
2022-07-03T12:07:59.7354741Z INFO:rcsb.utils.targets.IMGTTargetFeatureProvider:useCache False featurePath '/home/vsts/work/1/s/rcsb/utils/tests-targets/test-output/CACHE/IMGT-features/IMGT-feature-data.json'
2022-07-03T12:07:59.7355752Z INFO:rcsb.utils.targets.IMGTTargetFeatureProvider:Completed reload (useCache False) at 2022 07 03 12:07:59 (0.0001 seconds)
2022-07-03T12:07:59.7356497Z INFO:rcsb.utils.targets.IMGTTargetFeatureProvider:IMGT feature count 0
2022-07-03T12:07:59.7357511Z INFO:rcsb.utils.targets.IMGTTargetProvider:useCache True imgtFeaturePath '/home/vsts/work/1/s/rcsb/utils/tests-targets/test-output/CACHE/IMGT-targets/imgt-data.json'
2022-07-03T12:07:59.7358836Z INFO:rcsb.utils.targets.IMGTTargetProvider:Fetching url http://www.imgt.org/download/3Dstructure-DB/IMGT3DFlatFiles.tgz path /home/vsts/work/1/s/rcsb/utils/tests-targets/test-output/CACHE/IMGT-targets/IMGT3DFlatFiles.tgz
2022-07-03T12:09:21.4990102Z INFO:rcsb.utils.targets.IMGTTargetProvider:Completed fetch (True) at 2022 07 03 12:09:21 (81.7630 seconds)
2022-07-03T12:09:21.4991911Z INFO:rcsb.utils.targets.IMGTTargetProvider:IMGT version '202226-0'
2022-07-03T12:09:21.4992995Z INFO:rcsb.utils.targets.IMGTTargetProvider:Collecting flat files with pattern '/home/vsts/work/1/s/rcsb/utils/tests-targets/test-output/CACHE/IMGT-targets/IMGT3DFlatFiles/*.pdb.gz'
2022-07-03T12:09:24.2968809Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '445'
2022-07-03T12:09:24.2969825Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'4c10' determining alignment boundaries fails
2022-07-03T12:09:30.4258336Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '446'
2022-07-03T12:09:30.4259358Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'4c0y' determining alignment boundaries fails
2022-07-03T12:09:30.4260207Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '446'
2022-07-03T12:09:30.4261068Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'4c0y' determining alignment boundaries fails
2022-07-03T12:09:35.5797167Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '126'
2022-07-03T12:09:35.5798130Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'1yjd' determining alignment boundaries fails
2022-07-03T12:09:56.7599734Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '65'
2022-07-03T12:09:56.7601422Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6e4z' determining alignment boundaries fails
2022-07-03T12:10:02.0155580Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'4xvs' parsing boundaries fails with 'list index out of range' for '(NAG)(NAG)(NAG)               ...'
2022-07-03T12:10:03.2118878Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '446'
2022-07-03T12:10:03.2120636Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6njn' determining alignment boundaries fails
2022-07-03T12:10:03.2121811Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '446'
2022-07-03T12:10:03.2122897Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6njn' determining alignment boundaries fails
2022-07-03T12:10:14.0452207Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'5n2k' parsing boundaries fails with 'list index out of range' for 'MGILPSPGMPALLSLVSLLSVLLMGCVA(P...'
2022-07-03T12:10:14.3889867Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6ana' parsing boundaries fails with 'list index out of range' for '(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)...'
2022-07-03T12:10:36.6677879Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '446'
2022-07-03T12:10:36.6679320Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'4c0u' determining alignment boundaries fails
2022-07-03T12:10:36.6680458Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '446'
2022-07-03T12:10:36.6681447Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'4c0u' determining alignment boundaries fails
2022-07-03T12:10:40.4780098Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '65'
2022-07-03T12:10:41.4392431Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6mv5' determining alignment boundaries fails
2022-07-03T12:10:43.4546753Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'7cz0' parsing boundaries fails with 'list index out of range' for '(CAD)                         ...'
2022-07-03T12:10:50.4625796Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6s8i' parsing boundaries fails with 'list index out of range' for '(NAG)(NAG)                    ...'
2022-07-03T12:10:50.9898024Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6o2a' parsing boundaries fails with 'list index out of range' for '(UNK)VQL(UNK)(UNK)SGGG(UNK)VQ(...'
2022-07-03T12:10:50.9899968Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6o2a' parsing boundaries fails with 'list index out of range' for '(UNK)VQL(UNK)(UNK)SGGG(UNK)VQ(...'
2022-07-03T12:10:50.9901852Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6o2a' parsing boundaries fails with 'list index out of range' for '(UNK)VQL(UNK)(UNK)SGGG(UNK)VQ(...'
2022-07-03T12:10:57.5834725Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '446'
2022-07-03T12:10:57.5835761Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6njm' determining alignment boundaries fails
2022-07-03T12:10:57.5836598Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '446'
2022-07-03T12:10:57.5837467Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6njm' determining alignment boundaries fails
2022-07-03T12:10:57.5838947Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '446'
2022-07-03T12:10:57.5839769Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6njm' determining alignment boundaries fails
2022-07-03T12:10:57.5840597Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '446'
2022-07-03T12:10:57.5841406Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6njm' determining alignment boundaries fails
2022-07-03T12:10:58.2179188Z ERROR:rcsb.utils.targets.IMGTTargetProvider:No matching closing group at position: '65'
2022-07-03T12:10:58.2180240Z ERROR:rcsb.utils.targets.IMGTTargetProvider:'6e4y' determining alignment boundaries fails
2022-07-03T12:11:13.4921789Z INFO:rcsb.utils.targets.IMGTTargetProvider:ID List (7057)
2022-07-03T12:11:13.4923660Z INFO:rcsb.utils.targets.IMGTTargetProvider:Successes (7057) chains (22427)
2022-07-03T12:11:13.4924256Z INFO:rcsb.utils.targets.IMGTTargetProvider:Exceptions (0) []
2022-07-03T12:11:13.4946010Z INFO:rcsb.utils.targets.IMGTTargetProvider:Missing (0) []
2022-07-03T12:11:15.3283250Z INFO:rcsb.utils.targets.IMGTTargetProvider:Completed flatfile prep (True) at 2022 07 03 12:11:15 (195.5926 seconds)
2022-07-03T12:11:17.4010125Z INFO:rcsb.utils.targets.IMGTTargetFeatureProvider:IMGT antibody chain features (22427)
2022-07-03T12:11:23.1363221Z INFO:rcsb.utils.targets.IMGTTargetFeatureProvider:useCache True featurePath '/home/vsts/work/1/s/rcsb/utils/tests-targets/test-output/CACHE/IMGT-features/IMGT-feature-data.json'
2022-07-03T12:11:26.5812074Z INFO:rcsb.utils.targets.IMGTTargetFeatureProvider:Completed reload (useCache True) at 2022 07 03 12:11:26 (3.4450 seconds)
2022-07-03T12:11:26.5813279Z INFO:rcsb.utils.targets.IMGTTargetFeatureProvider:IMGT feature count 22427
2022-07-03T12:11:26.7947263Z INFO:root:Maximum resident memory size 1.2009 GB
2022-07-03T12:11:26.7948818Z INFO:root:Completed testIMGTTargetFeatureProvider.IMGTTargetFeatureProviderTests.testBuildIMGTTargetsFeatures at 2022 07 03 12:11:26 (207.0594 seconds)
2022-07-03T12:11:26.7949490Z ok

FYI @brindakv

aliciaaevans commented 1 year ago

@piehld Confirmed in the log from the stash update from October 13, 2021 that this was happening at least since then.