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To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/bgen/InternalRowToBgenRowConverter.scala"},"region":{"startLine":116}}}],"partialFingerprints":{"codehealthFindingId/v1":"30500128fedd6789ed103668cc9a52793b2e776bf2cc317501ef144f933b47e9"}},{"ruleId":"D2","level":"warning","message":{"text":"VariantQcExprs.callStatsBase (cognitive 34): VariantQcExprs.callStatsBase has cognitive complexity 34 (threshold 15). Drivers by points: if/else 9 (20 pts), loops 6 (12 pts), boolean chains 2 (nesting depth added 17). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/sql/expressions/VariantQcExprs.scala"},"region":{"startLine":73}}}],"partialFingerprints":{"codehealthFindingId/v1":"14eb347cb4b12f7806daf9b6cf61429707a38029b84a712828bfc9ae800aafde"}},{"ruleId":"D2","level":"warning","message":{"text":"VariantNormalizer.normalizeVariant (cognitive 28): VariantNormalizer.normalizeVariant has cognitive complexity 28 (threshold 15). Drivers by points: if/else 11 (21 pts), loops 2 (4 pts), boolean chains 3 (nesting depth added 12). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/transformers/normalizevariants/VariantNormalizer.scala"},"region":{"startLine":55}}}],"partialFingerprints":{"codehealthFindingId/v1":"41b9829e802be8ea405d88f8e49d95ba4180c9ebdd5524cf83f11793b3ad8a60"}},{"ruleId":"D2","level":"warning","message":{"text":"TabixIndexHelper.getFileRangeToRead (cognitive 27): TabixIndexHelper.getFileRangeToRead has cognitive complexity 27 (threshold 15). Drivers by points: if/else 14 (23 pts), boolean chains 3, match/switch 1 (nesting depth added 9). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body. This file is where this pass\u0027s cognitive complexity CONCENTRATES: core/src/main/scala/io/projectglow/vcf/TabixIndexHelper.scala holds 2 of the 16 methods over the threshold \u2014 including the worst \u2014 and 84 of the 200 points over it (42%), 3.4\u00D7 the next-largest file (core/src/main/scala/io/projectglow/sql/expressions/SampleCallSummaryStats.scala at 25). No single row can show this, because each is measured only against the threshold: reducing this one file moves this dimension further than any other file in the repository."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/vcf/TabixIndexHelper.scala"},"region":{"startLine":448}}}],"partialFingerprints":{"codehealthFindingId/v1":"8853646f5f4ee389de36c5a11ab875ac3a0faec06f60a20cf0be3838fb8add2f"}},{"ruleId":"D2","level":"warning","message":{"text":"HardCalls.getHardCalls (cognitive 23): HardCalls.getHardCalls has cognitive complexity 23 (threshold 15). Drivers by points: if/else 6 (14 pts), loops 3 (7 pts), boolean chains 2 (nesting depth added 12). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/sql/expressions/VariantUtilExprs.scala"},"region":{"startLine":298}}}],"partialFingerprints":{"codehealthFindingId/v1":"32b961e97b1568e3d1ec342b300200bd767d04ba975e8a934d1d4c0f3a6db1f7"}},{"ruleId":"D2","level":"warning","message":{"text":"QuinaryOptionalExpression.eval (cognitive 22): QuinaryOptionalExpression.eval has cognitive complexity 22 (threshold 15). Drivers by points: if/else 7 (22 pts) (nesting depth added 15). To reduce it, flatten the nesting: this score is depth rather than breadth \u2014 most of its points come from checks stacked inside one another, so the work sits several levels in. Invert each enclosing check into an early exit (a return, or the language\u0027s equivalent) so the happy path stays at one level, and where a level cannot be exited early, lift the block it encloses into its own named function."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/org/apache/spark/sql/catalyst/expressions/QuinaryOptionalExpression.scala"},"region":{"startLine":37}}}],"partialFingerprints":{"codehealthFindingId/v1":"e5c80a32cc270ea3bf0acadc66e164682cfba7aceb9dd6dcbd9a2cbc70c896c9"}},{"ruleId":"D2","level":"warning","message":{"text":"SenaryExpression.eval (cognitive 21): SenaryExpression.eval has cognitive complexity 21 (threshold 15). Drivers by points: if/else 6 (21 pts) (nesting depth added 15). To reduce it, flatten the nesting: this score is depth rather than breadth \u2014 most of its points come from checks stacked inside one another, so the work sits several levels in. Invert each enclosing check into an early exit (a return, or the language\u0027s equivalent) so the happy path stays at one level, and where a level cannot be exited early, lift the block it encloses into its own named function."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/org/apache/spark/sql/catalyst/expressions/SenaryExpression.scala"},"region":{"startLine":37}}}],"partialFingerprints":{"codehealthFindingId/v1":"23b2596dd2e4d6b9ceaf909a1ea6920a912c3c095e0d71605185801c7222c053"}},{"ruleId":"D2","level":"warning","message":{"text":"BgenRecordWriter.getCompressedGenotypeProbabilityData (cognitive 20): BgenRecordWriter.getCompressedGenotypeProbabilityData has cognitive complexity 20 (threshold 15). Drivers by points: if/else 10 (13 pts), loops 4 (7 pts) (nesting depth added 6). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/bgen/BgenRecordWriter.scala"},"region":{"startLine":167}}}],"partialFingerprints":{"codehealthFindingId/v1":"418450a1d9715378145128c2f33463fc16b1bc04833ea30107b06f5978ef611a"}},{"ruleId":"D2","level":"warning","message":{"text":"functions._prepare_sql_args (cognitive 19): functions._prepare_sql_args has cognitive complexity 19 (threshold 15). Drivers by points: if/else 14 (18 pts), boolean chains 1 (nesting depth added 4). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"python/glow/sql/functions.py"},"region":{"startLine":28}}}],"partialFingerprints":{"codehealthFindingId/v1":"8e5b3ae768298b14b51f0a7b18defc70e1c0dae89dc71fecdc7135427fdfb117"}},{"ruleId":"D2","level":"warning","message":{"text":"InternalRowToVariantContextConverter.createAnnotationArray (cognitive 18): InternalRowToVariantContextConverter.createAnnotationArray has cognitive complexity 18 (threshold 15). Drivers by points: match/switch 2 (9 pts), if/else 2 (6 pts), loops 2 (3 pts) (nesting depth added 12). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/vcf/InternalRowToVariantContextConverter.scala"},"region":{"startLine":327}}}],"partialFingerprints":{"codehealthFindingId/v1":"b9f56e47b26aac6f52309352aea910b9f1dd39b2dd6e4cb39847c72e659f331d"}},{"ruleId":"D2","level":"warning","message":{"text":"VCFLineToInternalRowConverter.parseGenotypes (cognitive 17): VCFLineToInternalRowConverter.parseGenotypes has cognitive complexity 17 (threshold 15). Drivers by points: if/else 6 (11 pts), loops 3 (4 pts), boolean chains 2 (nesting depth added 6). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/vcf/VCFLineToInternalRowConverter.scala"},"region":{"startLine":226}}}],"partialFingerprints":{"codehealthFindingId/v1":"b8c780a448ddfffdc23eceebff33f3cc99b6771f9daa27fdb8d68dd85e020298"}},{"ruleId":"D2","level":"warning","message":{"text":"render_template.prepare_definitions (cognitive 17): render_template.prepare_definitions has cognitive complexity 17 (threshold 15). Drivers by points: loops 4 (9 pts), if/else 2 (8 pts) (nesting depth added 11). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"python/render_template.py"},"region":{"startLine":97}}}],"partialFingerprints":{"codehealthFindingId/v1":"ae911a26a9832a2a3e2ddaeebbb82f27c2fc649ca18f29cec1474e411c7d3d9c"}},{"ruleId":"D2","level":"warning","message":{"text":"VariantContextToInternalRowConverter.getAnnotationArray (cognitive 16): VariantContextToInternalRowConverter.getAnnotationArray has cognitive complexity 16 (threshold 15). Drivers by points: match/switch 2 (9 pts), if/else 2 (4 pts), loops 2 (3 pts) (nesting depth added 10). To reduce it, keep the dispatch but shrink the arms: move each non-trivial case body into its own named function (or onto the value being matched) so the dispatch reads one line per case, and group related cases into a sub-dispatch. Keep every case explicit, and make the behaviour for cases you do not list a deliberate choice rather than an accident."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/vcf/VariantContextToInternalRowConverter.scala"},"region":{"startLine":613}}}],"partialFingerprints":{"codehealthFindingId/v1":"d6c5e7a85e83e407c5c04a5b6768f7b49349dcc860aef9096a9f0565eb359321"}},{"ruleId":"D2","level":"warning","message":{"text":"functions._validate_offset (cognitive 16): functions._validate_offset has cognitive complexity 16 (threshold 15). Drivers by points: if/else 6 (13 pts), loops 1 (3 pts) (nesting depth added 9). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"python/glow/gwas/functions.py"},"region":{"startLine":111}}}],"partialFingerprints":{"codehealthFindingId/v1":"9835fdaefce1445f456f799c25b0a01193b841a410eafc6ca065cbe2b9888adf"}},{"ruleId":"D3","level":"warning","message":{"text":"TooManyMethods: VariantContextToInternalRowConverter: TooManyMethods \u2014 32 methods. The bar is 30 methods; this is 2 over it, 1.07\u00D7 the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/vcf/VariantContextToInternalRowConverter.scala"},"region":{"startLine":50}}}],"partialFingerprints":{"codehealthFindingId/v1":"db3f37658091cb0d88781a174ab30b9b583285c2ce695f5cf8f5160a1d8d949d"}},{"ruleId":"D3","level":"warning","message":{"text":"TooManyMethods: functions: TooManyMethods \u2014 31 methods. The bar is 30 methods; this is 1 over it, 1.03\u00D7 the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/functions.scala"},"region":{"startLine":35}}}],"partialFingerprints":{"codehealthFindingId/v1":"035ef64486991a2c0824f6158a0ac1f5a582745150647f00afa1837782279644"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): core/src/main/scala/io/projectglow/sql/LeftOverlapJoin.scala:55-63 | core/src/main/scala/io/projectglow/sql/LeftOverlapJoin.scala:91-99 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/sql/LeftOverlapJoin.scala"},"region":{"startLine":55}}}],"partialFingerprints":{"codehealthFindingId/v1":"4d80109e686fc56e7fe583561f2f00477a6cf0d7534518c4c9b8588157a0020f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 2): core/src/main/scala/io/projectglow/vcf/TabixIndexHelper.scala:260-267 | core/src/main/scala/io/projectglow/vcf/TabixIndexHelper.scala:275-282 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060core/src/main/scala/io/projectglow/vcf/TabixIndexHelper.scala:260\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/vcf/TabixIndexHelper.scala"},"region":{"startLine":260}}}],"partialFingerprints":{"codehealthFindingId/v1":"78d06d4da6b4ec698f1136d0dc3d63fe3b495b0dd2c3c9db39f525663ba67844"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (26 lines \u00D7 3): core/src/main/shim/3.4/SparkShim.scala:36-61 | core/src/main/shim/3.5/SparkShim.scala:37-62 | core/src/main/shim/4/SparkShim.scala:36-61 \u2014 \u0060core/src/main/shim/3.4/SparkShim.scala\u0060 and \u0060core/src/main/shim/3.5/SparkShim.scala\u0060 are one unit implemented once per sibling directory, so they are most likely parallel implementations of one contract rather than a copy of each other \u2014 this scan matched 1 separate duplicated blocks between them, totalling at least 26 lines. If both are selected at run time, neither can be retired in favour of the other, and the lines that DIFFER between them are the reason both exist. The move that pays here is to hoist the identical part into a shared location the whole family can reach and give what differs a parameter or a seam, so a change lands once instead of once per sibling; extracting one helper per block leaves every sibling to drift on its own. Read the line range as the matched WINDOW rather than a finished unit: at \u0060core/src/main/shim/3.4/SparkShim.scala:36\u0060 it runs out through the closing brace of the declaration holding it and carries on into the declaration that follows \u2014 the window is the tail of one member plus the head of the next, so no call can be substituted for those exact lines, and the smallest declaration that contains all of them is the type they sit in. The repeated unit is the member each site sits in: where those members\u0027 bodies are the same, move one whole member to the shared location and have the others delegate to it; where the copies are a run of near-identical overloads or wrappers that differ only in their signatures, the repetition IS the run \u2014 a one-line delegation has no helper inside it to lift \u2014 so generate the run from the set it enumerates, or accept it and keep each member\u0027s own documentation with it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/shim/3.4/SparkShim.scala"},"region":{"startLine":36}}}],"partialFingerprints":{"codehealthFindingId/v1":"bf9f242d7046c9f341349ba33f4e71dc9a9415b3d377ba4baf1ebddab2d5a38d"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): core/src/main/scala/org/apache/spark/sql/catalyst/expressions/QuinaryOptionalExpression.scala:117-122 | core/src/main/scala/org/apache/spark/sql/catalyst/expressions/SenaryExpression.scala:120-125 \u2014 the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach \u2014 a file they already depend on, or a new one alongside them \u2014 and call it from both call sites, so a change lands once. Read the line range as the matched WINDOW rather than a finished unit: at \u0060core/src/main/scala/org/apache/spark/sql/catalyst/expressions/QuinaryOptionalExpression.scala:117\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/org/apache/spark/sql/catalyst/expressions/QuinaryOptionalExpression.scala"},"region":{"startLine":117}}}],"partialFingerprints":{"codehealthFindingId/v1":"fb26e371ec05166b635f94d0e492c80c7232a0beb50e0574a9d9efc787bdf99d"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (27\u201330 lines \u00D7 2): python/glow/wgr/logistic_ridge_regression.py:261-290 | python/glow/wgr/ridge_regression.py:200-226 \u2014 the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach \u2014 a file they already depend on, or a new one alongside them \u2014 and call it from both call sites, so a change lands once."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"python/glow/wgr/logistic_ridge_regression.py"},"region":{"startLine":261}}}],"partialFingerprints":{"codehealthFindingId/v1":"6fb760b53dedc33607033705ae19b9b6684011e0745a16d931f241dbf2f5917f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): python/glow/gwas/lin_reg.py:135-144 | python/glow/gwas/log_reg.py:119-128 \u2014 the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach \u2014 a file they already depend on, or a new one alongside them \u2014 and call it from both call sites, so a change lands once."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"python/glow/gwas/lin_reg.py"},"region":{"startLine":135}}}],"partialFingerprints":{"codehealthFindingId/v1":"fef968ec6057374b84ef09298b84ad73daf169822a5331e310b34c2bca4e855f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): docs/source/_static/zzz_GENERATED_NOTEBOOK_SOURCE/tertiary/9_compare_hail_to_glow.py:42-47 | docs/source/_static/zzz_GENERATED_NOTEBOOK_SOURCE/tertiary/9_compare_hail_to_glow.py:85-90 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060docs/source/_static/zzz_GENERATED_NOTEBOOK_SOURCE/tertiary/9_compare_hail_to_glow.py:42\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"docs/source/_static/zzz_GENERATED_NOTEBOOK_SOURCE/tertiary/9_compare_hail_to_glow.py"},"region":{"startLine":42}}}],"partialFingerprints":{"codehealthFindingId/v1":"debcdaa4383591047d99c69feb8edcec7dea113b27b7feca819be5d87bc24b40"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (21 lines \u00D7 2): python/glow/wgr/logistic_ridge_regression.py:44-64 | python/glow/wgr/ridge_regression.py:51-71 \u2014 the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach \u2014 a file they already depend on, or a new one alongside them \u2014 and call it from both call sites, so a change lands once."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"python/glow/wgr/logistic_ridge_regression.py"},"region":{"startLine":44}}}],"partialFingerprints":{"codehealthFindingId/v1":"e49d35b494cefb698b810d7c1d3112cde118e4dc9530e04db28b32946b0b55a4"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): python/glow/wgr/ridge_reduction.py:126-130 | python/glow/wgr/ridge_regression.py:150-154 \u2014 the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach \u2014 a file they already depend on, or a new one alongside them \u2014 and call it from both call sites, so a change lands once."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"python/glow/wgr/ridge_reduction.py"},"region":{"startLine":126}}}],"partialFingerprints":{"codehealthFindingId/v1":"99d40f13b2576b616e15f45170025dd0f240589d8696d892ba41c8321d6d05b2"}},{"ruleId":"D6","level":"warning","message":{"text":"Low cohesion: InternalRowToVariantContextConverter (LCOM4 9): InternalRowToVariantContextConverter\u0027s methods fall into 9 groups that share no field and call none of each other, against a bar of more than 3 for this run (LCOM4, configurable \u2014 your repository\u0027s bar is the one quoted here). Each group is a set of methods reachable from one another through shared fields or direct calls, so 9 groups means the type has that many internally-connected clusters with nothing tying them together. Types whose shape makes a high count expected \u2014 and which would otherwise dominate this list \u2014 are excluded before this row is raised, so this is a genuine split candidate rather than a metric reading. It is still a shape, not a defect: confirm the groups match responsibilities you can name before splitting."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/vcf/InternalRowToVariantContextConverter.scala"},"region":{"startLine":46}}}],"partialFingerprints":{"codehealthFindingId/v1":"da48439fc76873b6edca5a2c76a3a768ea734c1a42b1414d289736d2e29011be"}},{"ruleId":"D6","level":"warning","message":{"text":"Low cohesion: VariantContextToInternalRowConverter (LCOM4 8): VariantContextToInternalRowConverter\u0027s methods fall into 8 groups that share no field and call none of each other, against a bar of more than 3 for this run (LCOM4, configurable \u2014 your repository\u0027s bar is the one quoted here). Each group is a set of methods reachable from one another through shared fields or direct calls, so 8 groups means the type has that many internally-connected clusters with nothing tying them together. Types whose shape makes a high count expected \u2014 and which would otherwise dominate this list \u2014 are excluded before this row is raised, so this is a genuine split candidate rather than a metric reading. It is still a shape, not a defect: confirm the groups match responsibilities you can name before splitting."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/vcf/VariantContextToInternalRowConverter.scala"},"region":{"startLine":50}}}],"partialFingerprints":{"codehealthFindingId/v1":"3008b6a8e8deeb4a09b3527896031fec957887ac3fc7b9b8e9d0c6d174c841c4"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: Remove this after upgrade to Spark 2.4.5 and above \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/gff/GffDataSource.scala"},"region":{"startLine":154}}}],"partialFingerprints":{"codehealthFindingId/v1":"228dd46f19aae27005e9439077cdc4b2117a0d82ca0d18c592f6c69d46ca8c48"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO(hhd): Spark 3.0 allows extensions to register functions. After Spark 3.0 is released, \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/sql/SqlExtensionProvider.scala"},"region":{"startLine":34}}}],"partialFingerprints":{"codehealthFindingId/v1":"eaef2c19a95d2f999ff8c90bfed14590854a74c89f2aead9725d884c171cab66"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: Implement Locality \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/sql/util/HadoopLineIterator.scala"},"region":{"startLine":53}}}],"partialFingerprints":{"codehealthFindingId/v1":"d12d8771a5bcec142138ef9ba7a7d500cdc2d79a4454a8a77e68c50931ab0ebe"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: Log splitter usage \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/transformers/normalizevariants/NormalizeVariantsTransformer.scala"},"region":{"startLine":114}}}],"partialFingerprints":{"codehealthFindingId/v1":"3e45f2035135512e55c17893da7a8b965cc7ff9e03001eaf8db08cbc9709b021"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: Log splitter usage \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/transformers/normalizevariants/NormalizeVariantsTransformer.scala"},"region":{"startLine":118}}}],"partialFingerprints":{"codehealthFindingId/v1":"e0dde44f66a9bdb65adf7289f6657cc8ada6b1f74f7319e54cdc36bab6ac2995"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: Log splitter usage \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/transformers/splitmultiallelics/SplitMultiallelicsTransformer.scala"},"region":{"startLine":35}}}],"partialFingerprints":{"codehealthFindingId/v1":"67bed4303bc542b8958077d5314a3b13756054f6d10e7054189cca5aa67ca516"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: More tools to be added \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/transformers/pipe/PipeTransformer.scala"},"region":{"startLine":93}}}],"partialFingerprints":{"codehealthFindingId/v1":"6622e3afade4a77d91221f930810db3ac011b2f491447742c15ccf47c08e974a"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO: Unflattened INFO field splitting \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/transformers/splitmultiallelics/VariantSplitter.scala"},"region":{"startLine":75}}}],"partialFingerprints":{"codehealthFindingId/v1":"6c148b271cc98a43f2036fc544460db955d3b31cd5cf90110bf3fe7e78763ca8"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: // TODO(hhd): Fix the BGEN reader to properly insert nulls \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060// REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/vcf/VCFLineToInternalRowConverter.scala"},"region":{"startLine":447}}}],"partialFingerprints":{"codehealthFindingId/v1":"f5699234bf93ae337d112648c7f57a867ea6cbd121806d5c9f86b053a3390a30"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: # MAGIC TODO, add other steps in the pipeline \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060# REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"docs/source/_static/zzz_GENERATED_NOTEBOOK_SOURCE/tertiary/8_pipeline_runs_comparison.py"},"region":{"startLine":61}}}],"partialFingerprints":{"codehealthFindingId/v1":"0e46a83681eb12a6203bc286cf05c18673ecebb3c1b962725e29ee3ebf37253a"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: # TODO(hhd): Remove this and start using applyInPandas once we only support Spark 3.x. \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060# REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"python/glow/wgr/ridge_regression.py"},"region":{"startLine":28}}}],"partialFingerprints":{"codehealthFindingId/v1":"273439a6d2b1cb67fd2d09a911042b994696f7cab56fe68c579004bee21ecfe0"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: # TODO(hhd): Remove this and start using applyInPandas once we only support Spark 3.x. \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060# REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"python/glow/wgr/ridge_reduction.py"},"region":{"startLine":27}}}],"partialFingerprints":{"codehealthFindingId/v1":"59d282fecfb1dffcd8d45ce22fc3b2f28f5003ebfd2a913452df1a449477ff38"}},{"ruleId":"D19","level":"note","message":{"text":"Documentation: no installation or build instructions: The README does not state how to install or build the project. Add an installation section covering cloning from GitHub, setting up dependencies, and any required environment variables for Databricks container services."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"docs/source/customizing/index.rst"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"e0766993e413c9b5c68728ab1883f890d22248d8da55378dabc73c591c8c58dc"}},{"ruleId":"D19","level":"note","message":{"text":"Documentation: no usage examples: The README does not show how to run or invoke the custom-patches workflow. Add a usage section with an example of cloning the OSS repo, adding private patches, squashing changes, and pushing them."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"docs/source/customizing/index.rst"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"19900cd382415051841c0a8ba118607e060f9e25f9a4ce647e628e413d3870f5"}},{"ruleId":"D26","level":"note","message":{"text":"Projects may be oversized for their cohesion: 1 of 2 project(s) overshoot their size bounds, lowering Project Cohesion to 0.0/10. The most over is \u0060(repository root)\u0060 (17475 LoC, 290 module-visible types across 39 directories). Review these for cohesion \u2014 draw the boundary inside the module first (group each responsibility into its own package or directory and keep the cross-boundary members non-public), since splitting a published package moves types between packages and breaks consumers."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"d5a94650dc74886a0f1f08eb9fb6775f1fc395279ef7e901c970c9d26f767a72"}},{"ruleId":"D28","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"9c7182a25295e9c2ba0275ce53eaa18f26d35d70da2757fe36adcd5948205aa1"},"properties":{"commitSha":"ad765e6163b9b6e8ebaacefeed9df2559314c6b2"}},{"ruleId":"D28","level":"note","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"3cdfd7beb31b791ae18dcb425e21eb157c842e7bbcd522cc330573c1a6538db1"}},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"d5b8f11381d61a58459ffc7c595fd52d09c03c711894a63a9578043d2338412b"},"taxa":[{"id":"CWE-829","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"A08:2025","toolComponent":{"name":"OWASP Top 10","guid":"7d1f0c2e-4b6a-4e39-9a51-0b2e8c3d5f61"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"708fa4dd338e80ac70618e25b9aea92b81a67fd07a5e27b8960da1ef23d34900"},"taxa":[{"id":"CWE-1357","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-353","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"A03:2025","toolComponent":{"name":"OWASP Top 10","guid":"7d1f0c2e-4b6a-4e39-9a51-0b2e8c3d5f61"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. 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Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"f354ba325f97d9886c979cea9bd9dce9128b7bf07f7842e3fb829e22f05e641b"},"taxa":[{"id":"CWE-78","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"A05:2025","toolComponent":{"name":"OWASP Top 10","guid":"7d1f0c2e-4b6a-4e39-9a51-0b2e8c3d5f61"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"d482aa5e1b11165ce12f14ca75305402d9710e25fbf200aab1b08d98d53332fd"},"taxa":[{"id":"CWE-78","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"A05:2025","toolComponent":{"name":"OWASP Top 10","guid":"7d1f0c2e-4b6a-4e39-9a51-0b2e8c3d5f61"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"e2496d94d83f2b49f80810b27d129f3ff00478ed582467d89ff6a6140cfaf225"},"taxa":[{"id":"CWE-78","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"A05:2025","toolComponent":{"name":"OWASP Top 10","guid":"7d1f0c2e-4b6a-4e39-9a51-0b2e8c3d5f61"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"a620f5fb3c5e3ae83bcd785b36ada37e847907cf96d0b836deb5ba70b0ea93df"},"taxa":[{"id":"CWE-78","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"A05:2025","toolComponent":{"name":"OWASP Top 10","guid":"7d1f0c2e-4b6a-4e39-9a51-0b2e8c3d5f61"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"347ec001573d347ef5732d238468f3f82ef4aa6a40d3e0ae0deaa7a44f3dce86"},"taxa":[{"id":"CWE-1357","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-353","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"A03:2025","toolComponent":{"name":"OWASP Top 10","guid":"7d1f0c2e-4b6a-4e39-9a51-0b2e8c3d5f61"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"0df93a7400aca2ac5603a72afd39dbb83c90cb082e2c93eaea6fc9fc519744af"},"taxa":[{"id":"CWE-1357","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-353","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"A03:2025","toolComponent":{"name":"OWASP Top 10","guid":"7d1f0c2e-4b6a-4e39-9a51-0b2e8c3d5f61"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"7c0b68e337c45e1417b4e9c4a2fce0d8a9a92331feb8f35d30cb6092d2d19044"},"taxa":[{"id":"CWE-1357","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-353","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"A03:2025","toolComponent":{"name":"OWASP Top 10","guid":"7d1f0c2e-4b6a-4e39-9a51-0b2e8c3d5f61"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. 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A reasonable place to start a read-through before the aggregate risk above bites."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/vcf/VariantContextToInternalRowConverter.scala"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"16a97fec1530aab75c0e0c1167e1ae61fc96e2902ab1f9b69814d2b132d4aeb3"}},{"ruleId":"D34","level":"note","message":{"text":"Most significant orphaned file: One of the orphaned files carrying the most lost knowledge \u2014 ranked by size weighted by the file\u0027s role in the codebase, the same weighting behind the score above, so core code outranks equally large plumbing. 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Bound \u0060genotypesLen\u0060 against the bytes actually remaining and a maximum the format allows before allocating."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/bgen/BgenGenotypeReader.scala"},"region":{"startLine":46}}}],"partialFingerprints":{"codehealthFindingId/v1":"093ca37e2cf595b376c129280564b69e84b89374f2ef94557aeb1046e3f41964"}},{"ruleId":"X15","level":"warning","message":{"text":"Length read from the parsed input is spent without ever being bounded: \u0060decompressedGenotypesLen\u0060 is read from the bytes being parsed at line 55 (\u0060readInt\u0060), then used to size a \u0060new Array[Byte]\u0060 at line 57 \u2014 and nowhere in its scope is \u0060decompressedGenotypesLen\u0060 bounded from above \u2014 compared to a limit, clamped, or checked against the input that remains (a zero or sign test, or the loop that counts up to it, bounds nothing). 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Bound \u0060decompressedGenotypesLen\u0060 against the bytes actually remaining and a maximum the format allows before allocating."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"core/src/main/scala/io/projectglow/bgen/BgenGenotypeReader.scala"},"region":{"startLine":57}}}],"partialFingerprints":{"codehealthFindingId/v1":"3d37cf500db5c8aa3ed7bca8d11834ef16e266b7ccc0b10ce2ab9e509ef9ee65"}},{"ruleId":"X5","level":"note","message":{"text":"Scala\u0027s null is not held to the type system everywhere: No build over this repository\u0027s 101 Scala product file(s) passes \u0060-Yexplicit-nulls\u0060, enables WartRemover\u0027s \u0060Null\u0060 wart or runs Scalafix\u0027s \u0060DisableSyntax.noNulls\u0060, so every reference type admits null and nothing reports a \u0060null\u0060 written into the code or returned from a Java API \u2014 the first one to reach a method call is a \u0060NullPointerException\u0060. \u0060Option\u0060 by convention is a habit no tool here holds the code to."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"23e7c3c6da50151f07723c64ca4f881fd5903e713d143161a7c0594ad7ba29cc"}}],"taxonomies":[{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d","organization":"MITRE","informationUri":"https://cwe.mitre.org/","isComprehensive":false,"shortDescription":{"text":"The MITRE Common Weakness Enumeration (CWE)."},"taxa":[{"id":"CWE-1032","guid":"5f21e517-68aa-a650-9a25-5771ef024637","name":"OWASP Top Ten \u2014 Security Misconfiguration category","shortDescription":{"text":"OWASP Top Ten \u2014 Security Misconfiguration category"},"helpUri":"https://cwe.mitre.org/data/definitions/1032.html"},{"id":"CWE-1104","guid":"4c918cb5-b2a6-6c55-9963-a44ee464305e","name":"Use of Unmaintained Third Party Components","shortDescription":{"text":"Use of Unmaintained Third Party Components"},"helpUri":"https://cwe.mitre.org/data/definitions/1104.html"},{"id":"CWE-116","guid":"c0134ca8-adc7-6959-bd17-5253a265d101","name":"Improper 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Resource","shortDescription":{"text":"Incorrect Permission Assignment for Critical Resource"},"helpUri":"https://cwe.mitre.org/data/definitions/732.html"},{"id":"CWE-77","guid":"332c8ade-6612-9f56-a06b-d8d90b1a8750","name":"Improper Neutralization of Special Elements used in a Command (\u0027Command Injection\u0027)","shortDescription":{"text":"Improper Neutralization of Special Elements used in a Command (\u0027Command Injection\u0027)"},"helpUri":"https://cwe.mitre.org/data/definitions/77.html"},{"id":"CWE-78","guid":"2e31ceaf-c7ae-2e5e-9661-cfb1362789cf","name":"Improper Neutralization of Special Elements used in an OS Command (\u0027OS Command Injection\u0027)","shortDescription":{"text":"Improper Neutralization of Special Elements used in an OS Command (\u0027OS Command Injection\u0027)"},"helpUri":"https://cwe.mitre.org/data/definitions/78.html"},{"id":"CWE-79","guid":"fd45580b-e8c4-fc5e-8c2f-aa8fab0b4dbf","name":"Improper Neutralization of Input During Web Page Generation 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Injection\u0027)"},"helpUri":"https://cwe.mitre.org/data/definitions/89.html"},{"id":"CWE-937","guid":"16f316ae-415c-b354-a59b-1f7905f756e9","name":"Using Components with Known Vulnerabilities","shortDescription":{"text":"Using Components with Known Vulnerabilities"},"helpUri":"https://cwe.mitre.org/data/definitions/937.html"},{"id":"CWE-94","guid":"75e7f50c-6c2f-dd52-bf40-bf6c52b861fd","name":"Improper Control of Generation of Code (\u0027Code Injection\u0027)","shortDescription":{"text":"Improper Control of Generation of Code (\u0027Code Injection\u0027)"},"helpUri":"https://cwe.mitre.org/data/definitions/94.html"},{"id":"CWE-95","guid":"400bba4e-483c-5c50-a695-114fa9168003","name":"Improper Neutralization of Directives in Dynamically Evaluated Code (\u0027Eval Injection\u0027)","shortDescription":{"text":"Improper Neutralization of Directives in Dynamically Evaluated Code (\u0027Eval Injection\u0027)"},"helpUri":"https://cwe.mitre.org/data/definitions/95.html"}]},{"name":"OWASP Top 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Findings are listed in full, but the details of SECURITY findings \u2014 which rule fired, in which file, on which line, and how to fix it \u2014 are deliberately withheld, and any secret-scanner results are excluded entirely. Where detail is absent here it was REMOVED FOR PUBLICATION; it is not missing from the analysis. The complete artifact is available from the repository owner.","securityFindingsRedacted":63,"secretScannerRunsExcluded":0}},"redactionTokens":["A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."]}]}