brkraw 0.3.11__py3-none-any.whl → 0.5.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (113) hide show
  1. brkraw/__init__.py +9 -3
  2. brkraw/apps/__init__.py +12 -0
  3. brkraw/apps/addon/__init__.py +30 -0
  4. brkraw/apps/addon/core.py +35 -0
  5. brkraw/apps/addon/dependencies.py +402 -0
  6. brkraw/apps/addon/installation.py +500 -0
  7. brkraw/apps/addon/io.py +21 -0
  8. brkraw/apps/hook/__init__.py +25 -0
  9. brkraw/apps/hook/core.py +636 -0
  10. brkraw/apps/loader/__init__.py +10 -0
  11. brkraw/apps/loader/core.py +622 -0
  12. brkraw/apps/loader/formatter.py +288 -0
  13. brkraw/apps/loader/helper.py +797 -0
  14. brkraw/apps/loader/info/__init__.py +11 -0
  15. brkraw/apps/loader/info/scan.py +85 -0
  16. brkraw/apps/loader/info/scan.yaml +90 -0
  17. brkraw/apps/loader/info/study.py +69 -0
  18. brkraw/apps/loader/info/study.yaml +156 -0
  19. brkraw/apps/loader/info/transform.py +92 -0
  20. brkraw/apps/loader/types.py +220 -0
  21. brkraw/cli/__init__.py +5 -0
  22. brkraw/cli/commands/__init__.py +2 -0
  23. brkraw/cli/commands/addon.py +327 -0
  24. brkraw/cli/commands/config.py +205 -0
  25. brkraw/cli/commands/convert.py +903 -0
  26. brkraw/cli/commands/hook.py +348 -0
  27. brkraw/cli/commands/info.py +74 -0
  28. brkraw/cli/commands/init.py +214 -0
  29. brkraw/cli/commands/params.py +106 -0
  30. brkraw/cli/commands/prune.py +288 -0
  31. brkraw/cli/commands/session.py +371 -0
  32. brkraw/cli/hook_args.py +80 -0
  33. brkraw/cli/main.py +83 -0
  34. brkraw/cli/utils.py +60 -0
  35. brkraw/core/__init__.py +13 -0
  36. brkraw/core/config.py +380 -0
  37. brkraw/core/entrypoints.py +25 -0
  38. brkraw/core/formatter.py +367 -0
  39. brkraw/core/fs.py +495 -0
  40. brkraw/core/jcamp.py +600 -0
  41. brkraw/core/layout.py +451 -0
  42. brkraw/core/parameters.py +781 -0
  43. brkraw/core/zip.py +1121 -0
  44. brkraw/dataclasses/__init__.py +14 -0
  45. brkraw/dataclasses/node.py +139 -0
  46. brkraw/dataclasses/reco.py +33 -0
  47. brkraw/dataclasses/scan.py +61 -0
  48. brkraw/dataclasses/study.py +131 -0
  49. brkraw/default/__init__.py +3 -0
  50. brkraw/default/pruner_specs/deid4share.yaml +42 -0
  51. brkraw/default/rules/00_default.yaml +4 -0
  52. brkraw/default/specs/metadata_dicom.yaml +236 -0
  53. brkraw/default/specs/metadata_transforms.py +92 -0
  54. brkraw/resolver/__init__.py +7 -0
  55. brkraw/resolver/affine.py +539 -0
  56. brkraw/resolver/datatype.py +69 -0
  57. brkraw/resolver/fid.py +90 -0
  58. brkraw/resolver/helpers.py +36 -0
  59. brkraw/resolver/image.py +188 -0
  60. brkraw/resolver/nifti.py +370 -0
  61. brkraw/resolver/shape.py +235 -0
  62. brkraw/schema/__init__.py +3 -0
  63. brkraw/schema/context_map.yaml +62 -0
  64. brkraw/schema/meta.yaml +57 -0
  65. brkraw/schema/niftiheader.yaml +95 -0
  66. brkraw/schema/pruner.yaml +55 -0
  67. brkraw/schema/remapper.yaml +128 -0
  68. brkraw/schema/rules.yaml +154 -0
  69. brkraw/specs/__init__.py +10 -0
  70. brkraw/specs/hook/__init__.py +12 -0
  71. brkraw/specs/hook/logic.py +31 -0
  72. brkraw/specs/hook/validator.py +22 -0
  73. brkraw/specs/meta/__init__.py +5 -0
  74. brkraw/specs/meta/validator.py +156 -0
  75. brkraw/specs/pruner/__init__.py +15 -0
  76. brkraw/specs/pruner/logic.py +361 -0
  77. brkraw/specs/pruner/validator.py +119 -0
  78. brkraw/specs/remapper/__init__.py +27 -0
  79. brkraw/specs/remapper/logic.py +924 -0
  80. brkraw/specs/remapper/validator.py +314 -0
  81. brkraw/specs/rules/__init__.py +6 -0
  82. brkraw/specs/rules/logic.py +263 -0
  83. brkraw/specs/rules/validator.py +103 -0
  84. brkraw-0.5.0.dist-info/METADATA +81 -0
  85. brkraw-0.5.0.dist-info/RECORD +88 -0
  86. {brkraw-0.3.11.dist-info → brkraw-0.5.0.dist-info}/WHEEL +1 -2
  87. brkraw-0.5.0.dist-info/entry_points.txt +13 -0
  88. brkraw/lib/__init__.py +0 -4
  89. brkraw/lib/backup.py +0 -641
  90. brkraw/lib/bids.py +0 -0
  91. brkraw/lib/errors.py +0 -125
  92. brkraw/lib/loader.py +0 -1220
  93. brkraw/lib/orient.py +0 -194
  94. brkraw/lib/parser.py +0 -48
  95. brkraw/lib/pvobj.py +0 -301
  96. brkraw/lib/reference.py +0 -245
  97. brkraw/lib/utils.py +0 -471
  98. brkraw/scripts/__init__.py +0 -0
  99. brkraw/scripts/brk_backup.py +0 -106
  100. brkraw/scripts/brkraw.py +0 -744
  101. brkraw/ui/__init__.py +0 -0
  102. brkraw/ui/config.py +0 -17
  103. brkraw/ui/main_win.py +0 -214
  104. brkraw/ui/previewer.py +0 -225
  105. brkraw/ui/scan_info.py +0 -72
  106. brkraw/ui/scan_list.py +0 -73
  107. brkraw/ui/subj_info.py +0 -128
  108. brkraw-0.3.11.dist-info/METADATA +0 -25
  109. brkraw-0.3.11.dist-info/RECORD +0 -28
  110. brkraw-0.3.11.dist-info/entry_points.txt +0 -3
  111. brkraw-0.3.11.dist-info/top_level.txt +0 -2
  112. tests/__init__.py +0 -0
  113. {brkraw-0.3.11.dist-info → brkraw-0.5.0.dist-info/licenses}/LICENSE +0 -0
brkraw/lib/errors.py DELETED
@@ -1,125 +0,0 @@
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- import os
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-
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-
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- def print_internal_error(io_handler=None):
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- import traceback
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- import sys
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- if io_handler is None:
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- io_handler = sys.stderr
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- traceback.print_exception(*sys.exc_info(),
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- file=io_handler)
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-
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-
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- class Error(Exception):
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- """ Base class for other custom exceptions """
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- message = None
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-
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-
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- class FileNotValidError(Error):
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- """ Raised when the file is not valid format """
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-
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- def __init__(self, file_name=None, data_type=None):
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- self.file_name = None
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- self.data_type = None
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-
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- if file_name != None:
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- self.file_name = os.path.basename(file_name)
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- if os.path.isdir(file_name):
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- object_type = 'directory'
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- else:
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- object_type = 'file'
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- if data_type != None:
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- self.data_type = data_type
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- self.message = "The {} '{}' is not valid {}".format(object_type,
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- self.file_name,
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- self.data_type)
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- else:
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- self.message = "The {} '{}' is not valid".format(object_type,
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- self.file_name)
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- else:
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- self.message = "The file is not valid"
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-
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-
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- class ArchiveFailedError(Error):
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- """ Raised when the archive process is failed [designed for brkraw module] """
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- file_name = None
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-
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- def __init__(self, file_name=None):
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- if file_name != None:
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- self.file_name = os.path.basename(file_name)
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- self.message = "The data '{}' is not archived".format(
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- self.file_name)
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- else:
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- self.message = "Archive failed to execute"
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-
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-
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- class RemoveFailedError(Error):
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- """ Raise when the os.remove process is failed """
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- file_name = None
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-
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- def __init__(self, file_name=None):
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- if file_name != None:
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- self.file_name = os.path.basename(file_name)
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- self.message = "The file '{}' is not removed".format(
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- self.file_name)
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- else:
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- self.message = "Remove failed to execute"
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-
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-
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- class RenameFailedError(Error):
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- """ Raised when the os.rename process is failed (OSError)"""
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- file1_name = None
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- file2_name = None
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-
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- def __init__(self, file1_name=None, file2_name=None):
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- if file1_name != None:
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- self.file1_name = os.path.basename(file1_name)
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- if file2_name != None:
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- self.file2_name = os.path.basename(file2_name)
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- if (self.file1_name != None) and (self.file2_name != None):
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- self.message = "Rename failed to execute from:'{}' to:'{}'".format(self.file1_name,
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- self.file2_name)
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- else:
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- self.message = "Rename failed to execute"
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-
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-
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- class UnexpectedError(Error):
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- """ Raised when unexpected error occurred """
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-
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- def __init__(self, message=None):
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- print_internal_error()
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- if message is None:
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- self.message = "Unexpected error"
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- else:
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- self.message = message
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-
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-
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- class ValueConflictInField(Error):
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- """ Raised when input value was conflicted with other """
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-
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- def __init__(self, message=None):
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- if message is None:
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- self.message = "The value is conflicted"
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- else:
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- self.message = message
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-
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-
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- class InvalidValueInField(Error):
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- """ Raise when the invalid value is detected in field """
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-
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- def __init__(self, message=None):
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- if message is None:
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- self.message = "Invalid value is detected"
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- else:
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- self.message = message
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-
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-
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- class InvalidApproach(Error):
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- """ Raise when the user try invalid approach """
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-
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- def __init__(self, message=None):
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- print_internal_error()
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- if message is None:
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- self.message = "Invalid approach!"
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- else:
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- self.message = message