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Structured validation results #1104

Merged
merged 124 commits into from
Oct 28, 2022
Merged

Structured validation results #1104

merged 124 commits into from
Oct 28, 2022

Commits on Oct 27, 2022

  1. Define ValidationResult class

    @jwodder @TheChymera
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  2. RF: Initial steps to start RFing validate-bids to use ValidationResul… 

    …t records
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  3. Improved class usage and added test suite

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  4. Debugging

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  5. Debugging out of place cli invocation error

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  6. Starting to deprecate print_validation_results()

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  7. comment for review

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  8. Incremental deprecation of direct upstream output format

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  9. Review comments

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  10. Fixed test log path

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  11. BIDS root detection

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  12. Assigning dandiset and (BIDS) dataset path

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  13. removed comment lines

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  14. Integrated metadata recording

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  15. Processing input path type

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  16. Indentation fix for lint check

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  17. Printing output based on severity

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  18. Message attribute is empty string when nonexistent — not none

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  19. Force posix path for windows tests

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  20. Debugging windows tests

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  21. Typing fixes

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  22. Trying more typing fixes

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  23. Debugging typing

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  24. Removed unneeded module

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  25. Use assert to ensure that Optional becomes non-optional for type chec… 

    …king

also used more descriptive "result" variable instead of "i". We contemplated some other
name (like vrs - for "validation results") but it was not liked
    @yarikoptic @TheChymera
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  26. Further corrected type

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  27. Filtered download for valid testdata

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  28. Type correction

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  29. Update error tests

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  30. fixing windows fixture removal error

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  31. Debug assertion error fix

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  32. Using error fixture for error tests

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  33. Using correct fixture

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  34. Disabled debugging code

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  35. Debug assertion error

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  36. Ensuring that metadata is non-empty

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  37. Making example invalid dataset truly invalid

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  38. Windows debugging

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  39. Further winerror 5 debugging

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  40. Using base exception instead of specific one

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  41. Not using auto-cleaning temp dir via while

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  42. Removed debugging code

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  43. More verbose error printing

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  44. Using entire valid dataset whitelist for testing

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  45. Log creation test using whitelist instead of hard-coded dataset

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  46. Fixed cmd_validate tests

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  47. Fixed report path test

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  48. Testing the command line for all error cases

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  49. Removed deprecated comments

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  50. Populating dandi and bids dataset paths

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  51. Simple fixes suggested by jwodder

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  52. Fixed typing

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  53. Correcting type

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  54. Using pytest temp path generation

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  55. Corrected function parameters

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  56. More parsimonious error reporting

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  57. Global import

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  58. Using built-in find_parent_directory_containing function

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  59. Dropped unused import

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  60. Re-added placeholder metadata to satisfy assert

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  61. No longer recomputing dandi/data-set path for files in same directory

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  62. Trying to make sure typechecking understands logic

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  63. Removed redundant code 

    and black fixes
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  64. No placeholder metadata

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  65. Unified error reporting across validation types 

    also removed part of error reporting which was reporting valid files,
let me know if you need it back.
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  66. Improve style

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  67. Import dandi.validate.Severity in local scope to prevent heavy dep load

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  68. Unified error reporting logic and draft grouping implementation.

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  69. Corrected warning color

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  70. BROKEN — reusage of generic validator output for NWB

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  71. RF+BF: address circular import, unify more of validations into Valida… 

    …tionResults

TODO: pretty much go through all other instances were "str" is returned for an
error.  Most of them could be caught up via   `tox -e typing`  or just inspecting
other code paths.

We also raised following concerns/topics for possible future development
- do not return error structs for exception handling where we catch
  errors from opening files etc.  But may be there was a reason why
  we decided to work with it this way instead of just handling exceptions.
- there is .location (within .nwb / hdf5 file) to point more specifically
  within nwb file internal structure.  We need to provide location for that
  in our data structure. But as we have asset_paths, we might want to do that
  as a dict.
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  72. ENH: add within_asset_paths to point within files/assets

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  73. BF: map importance to our severity based on enum"s name

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  74. ENH+RF: make sure we issue a warning about nwbinspector only once

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  75. Integrating pydantic error into custom object.

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  76. Corrected function return

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  77. Parsing further errors into the custom dandi validation object

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  78. Trying to fix types

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  79. Type fixing

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  80. New object structure for zarr validation

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  81. Further type fixes

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  82. Attempting to fix typing errors

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  83. Fixed more typing errors

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  84. Fixed list unpacking issue discussed in meeting

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  85. Further typing fixes

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  86. Defined missing and removed unused variable

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  87. Trying to standardize error output

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  88. Fixed syntax

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  89. Expanded list comprehension to assert attribute presence

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  90. No more typing errors

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  91. Removed unused imports

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  92. Fixed weird typing issues only appearing on GH

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  93. Placeholder for undefined variable string

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  94. Fixed assertion in test to match object output

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  95. Integrate OSError into object-based validation reporting

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  96. Standardized dandi import

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  97. General-purpose exception catching

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  98. More standardized error IDs

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  99. Typing fix for exception message

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  100. Description/testing of command line validation --grouping option.

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  101. Workaround e.message typechecking dillema

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  102. Removed unneeded imports, added tests for broken nwb dataset

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  103. Removed deprecated comment

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  104. Added click decorator for grouping parameter in nwb validator

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  105. Standardized CLI NWB validator wrt BIDS validator draft and added tests 

    Still using 2 separate functions, merging of validation functions best
for subsequent PR
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  106. Reporting lack of errors explicitly in CLI validation

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  107. Simplified git command execution

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  108. Using click option specification

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  109. List comprehension for more compact code.

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  110. Removed superfluous list bracketing

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  111. clarified comment, removed commented code

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  112. Extracted validation variant common code into internal function 

    and renamed tests for more consistency
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  113. Importing outside of test functions

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  114. Updated grouping for vanilla validator

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  115. Linting fixes

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  116. Importing cast function from typing

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  117. Type annotations

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  118. Fixed typing

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  119. Removed superfluous print call

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  120. Fixes proposed by Yaro

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  121. Not duplicating code for error subclass

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  122. Orthography

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  123. We need newer bidsschematools

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  124. Type fix

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