arctrl 3.0.0b13__tar.gz → 3.0.0b14__tar.gz

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 (488) hide show
  1. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/PKG-INFO +1 -1
  2. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/pyproject.toml +43 -43
  3. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/__init__.py +2 -0
  4. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/CWL/cwlprocessing_unit.py +2 -2
  5. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/CWL/cwltypes.py +18 -18
  6. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/CWL/decode.py +2 -2
  7. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/CWL/hash_helpers.py +3 -3
  8. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/CWL/workflow_description.py +2 -2
  9. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Contract/arc_assay.py +9 -9
  10. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Contract/arc_investigation.py +2 -2
  11. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Contract/arc_study.py +9 -9
  12. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Contract/arc_workflow.py +16 -16
  13. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Contract/contract.py +8 -8
  14. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Contract/datamap.py +65 -65
  15. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Contract/git.py +16 -16
  16. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Contract/license.py +6 -6
  17. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Contract/validation_packages_config.py +4 -4
  18. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/ContractIO/contract_io.py +87 -87
  19. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/ContractIO/file_system_helper.py +62 -62
  20. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Conversion/assay.py +15 -15
  21. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Conversion/basic.py +5 -5
  22. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Conversion/column_index.py +28 -7
  23. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Conversion/datamap.py +7 -7
  24. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Conversion/date_time.py +2 -2
  25. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Conversion/investigation.py +18 -18
  26. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Conversion/person.py +4 -4
  27. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Conversion/process.py +127 -127
  28. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Conversion/run.py +19 -19
  29. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Conversion/scholarly_article.py +6 -6
  30. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Conversion/study.py +15 -15
  31. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Conversion/table.py +9 -9
  32. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Conversion/workflow.py +28 -28
  33. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Core/Helper/date_time.py +3 -3
  34. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Core/Process/component.py +2 -2
  35. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Core/Process/process.py +8 -8
  36. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Core/Process/process_sequence.py +18 -18
  37. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Core/Process/protocol_parameter.py +2 -2
  38. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Core/Table/arc_table.py +20 -20
  39. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Core/Table/arc_tables.py +16 -16
  40. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Core/Table/composite_column.py +6 -6
  41. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Core/Table/composite_header.py +6 -6
  42. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Core/arc_types.py +685 -685
  43. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Core/conversion.py +11 -11
  44. arctrl-3.0.0b13/src/ARCtrl/py/Core/data_map.py → arctrl-3.0.0b14/src/ARCtrl/py/Core/datamap.py +57 -57
  45. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/FileSystem/file_system.py +4 -4
  46. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/FileSystem/file_system_tree.py +63 -63
  47. {arctrl-3.0.0b13/src/ARCtrl/py/Json/DataMap → arctrl-3.0.0b14/src/ARCtrl/py/Json/Datamap}/data_context.py +24 -24
  48. arctrl-3.0.0b13/src/ARCtrl/py/Json/DataMap/data_map.py → arctrl-3.0.0b14/src/ARCtrl/py/Json/Datamap/datamap.py +10 -10
  49. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/assay_materials.py +5 -5
  50. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/component.py +22 -22
  51. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/factor.py +19 -19
  52. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/factor_value.py +18 -18
  53. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/material.py +46 -46
  54. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/material_attribute.py +13 -13
  55. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/material_attribute_value.py +18 -18
  56. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/material_type.py +6 -6
  57. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/process.py +70 -70
  58. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/process_input.py +10 -10
  59. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/process_output.py +8 -8
  60. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/process_parameter_value.py +14 -14
  61. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/protocol.py +75 -75
  62. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/protocol_parameter.py +13 -13
  63. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/sample.py +41 -41
  64. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/source.py +35 -35
  65. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/study_materials.py +6 -6
  66. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Process/value.py +11 -11
  67. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/ROCrate/ldgraph.py +18 -18
  68. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/ROCrate/ldnode.py +9 -6
  69. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/ROCrate/ldref.py +10 -10
  70. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Table/arc_table.py +85 -85
  71. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Table/cell_table.py +10 -10
  72. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Table/composite_cell.py +25 -25
  73. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Table/composite_header.py +10 -10
  74. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Table/iotype.py +2 -2
  75. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Table/oatable.py +10 -10
  76. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/Table/templates.py +65 -65
  77. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/assay.py +146 -146
  78. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/comment.py +48 -48
  79. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/context/rocrate/isa_assay_context.py +4 -4
  80. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/context/rocrate/isa_comment_context.py +2 -2
  81. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/context/rocrate/isa_component_context.py +6 -6
  82. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/context/rocrate/isa_data_context.py +4 -4
  83. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/context/rocrate/isa_study_context.py +9 -9
  84. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/context/rocrate/rocrate_context.py +12 -12
  85. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/converter_options.py +2 -2
  86. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/data.py +88 -88
  87. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/data_file.py +8 -8
  88. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/decode.py +4 -4
  89. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/encode.py +16 -16
  90. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/idtable.py +4 -4
  91. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/investigation.py +161 -161
  92. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/ontology_annotation.py +96 -96
  93. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/ontology_source_reference.py +68 -68
  94. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/person.py +164 -164
  95. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/property_value.py +50 -50
  96. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/publication.py +71 -71
  97. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/run.py +77 -77
  98. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/string_table.py +15 -15
  99. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/study.py +197 -197
  100. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Json/workflow.py +89 -89
  101. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/component.py +4 -4
  102. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/factor.py +2 -2
  103. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/factor_value.py +2 -2
  104. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/material.py +4 -4
  105. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/material_attribute.py +2 -2
  106. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/material_attribute_value.py +4 -4
  107. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/material_type.py +2 -2
  108. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/process.py +4 -4
  109. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/process_input.py +2 -2
  110. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/process_output.py +4 -4
  111. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/process_parameter_value.py +4 -4
  112. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/process_sequence.py +6 -6
  113. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/protocol.py +4 -4
  114. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/protocol_parameter.py +2 -2
  115. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/sample.py +4 -4
  116. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/source.py +4 -4
  117. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/study_materials.py +6 -6
  118. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Process/value.py +2 -2
  119. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Table/arc_table.py +12 -12
  120. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Table/composite_cell.py +2 -2
  121. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Table/composite_header.py +2 -2
  122. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Table/iotype.py +2 -2
  123. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/Table/templates.py +6 -6
  124. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/assay.py +8 -8
  125. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/comment.py +6 -6
  126. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/data.py +4 -4
  127. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/data_file.py +4 -4
  128. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/datamap.py +10 -10
  129. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/investigation.py +8 -8
  130. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/ldobject.py +8 -8
  131. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/ontology_annotation.py +6 -6
  132. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/ontology_source_reference.py +6 -6
  133. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/person.py +6 -6
  134. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/publication.py +6 -6
  135. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/run.py +4 -4
  136. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/study.py +8 -8
  137. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/JsonIO/workflow.py +4 -4
  138. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/ROCrate/ISAProfile/data.py +4 -4
  139. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/ROCrate/ISAProfile/lab_protocol.py +2 -2
  140. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/ROCrate/ISAProfile/property_value.py +6 -6
  141. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/ROCrate/ISAProfile/sample.py +2 -2
  142. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/ROCrate/LDTypes/dataset.py +29 -29
  143. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/ROCrate/rocrate_context.py +1 -1
  144. arctrl-3.0.0b13/src/ARCtrl/py/Spreadsheet/DataMapTable/data_map_column.py → arctrl-3.0.0b14/src/ARCtrl/py/Spreadsheet/DatamapTable/datamap_column.py +24 -24
  145. arctrl-3.0.0b13/src/ARCtrl/py/Spreadsheet/DataMapTable/data_map_header.py → arctrl-3.0.0b14/src/ARCtrl/py/Spreadsheet/DatamapTable/datamap_header.py +10 -10
  146. arctrl-3.0.0b13/src/ARCtrl/py/Spreadsheet/DataMapTable/data_map_table.py → arctrl-3.0.0b14/src/ARCtrl/py/Spreadsheet/DatamapTable/datamap_table.py +8 -8
  147. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Spreadsheet/Metadata/assays.py +8 -8
  148. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Spreadsheet/Metadata/contacts.py +10 -10
  149. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Spreadsheet/Metadata/factors.py +6 -6
  150. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Spreadsheet/Metadata/ontology_annotation.py +8 -8
  151. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Spreadsheet/Metadata/protocols.py +9 -9
  152. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Spreadsheet/Metadata/publication.py +10 -10
  153. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Spreadsheet/Metadata/sparse_table.py +15 -15
  154. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Spreadsheet/Metadata/study.py +32 -32
  155. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Spreadsheet/Metadata/workflow.py +4 -4
  156. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Spreadsheet/arc_assay.py +6 -6
  157. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Spreadsheet/arc_run.py +4 -4
  158. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Spreadsheet/arc_study.py +6 -6
  159. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Spreadsheet/arc_workflow.py +4 -4
  160. arctrl-3.0.0b13/src/ARCtrl/py/Spreadsheet/data_map.py → arctrl-3.0.0b14/src/ARCtrl/py/Spreadsheet/datamap.py +10 -10
  161. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/ValidationPackages/validation_package.py +10 -10
  162. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/ValidationPackages/validation_packages_config.py +20 -20
  163. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/WebRequest/web_request_py.py +15 -15
  164. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Yaml/validation_package.py +15 -15
  165. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/Yaml/validation_packages_config.py +16 -16
  166. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/arc.py +317 -317
  167. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/column_index.py +9 -9
  168. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/conversion.py +2 -2
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  481. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/fable_modules/yamlicious/persil.py +0 -0
  482. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/fable_modules/yamlicious/preprocessing.py +0 -0
  483. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/fable_modules/yamlicious/reader.py +0 -0
  484. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/fable_modules/yamlicious/regex.py +0 -0
  485. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/fable_modules/yamlicious/regex_active_patterns.py +0 -0
  486. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/fable_modules/yamlicious/writer.py +0 -0
  487. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/py/fable_modules/yamlicious/yamlicious_types.py +0 -0
  488. {arctrl-3.0.0b13 → arctrl-3.0.0b14}/src/ARCtrl/rocrate.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: arctrl
3
- Version: 3.0.0b13
3
+ Version: 3.0.0b14
4
4
  Summary: Library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtimer agnostic contract systems.
5
5
  License-File: LICENSE
6
6
  Keywords: arc,annotated research context,isa,research data,multi platform
@@ -1,43 +1,43 @@
1
- [project]
2
- name = "arctrl"
3
- version = "3.0.0b13"
4
- description = "Library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtimer agnostic contract systems."
5
- authors = [
6
- { name = "Heinrich Lukas Weil", email = "weil@rptu.de" },
7
- { name = "Kevin Frey", email = "freymaurer@gmx.de" },
8
- ]
9
- requires-python = ">=3.11"
10
- readme = "README.md"
11
- maintainers = [{ name = "Florian Wetzels" }]
12
- keywords = [
13
- "arc",
14
- "annotated research context",
15
- "isa",
16
- "research data",
17
- "multi platform",
18
- ]
19
- dependencies = [
20
- "requests>= 2.28.1, <3.0.0",
21
- "openpyxl>=3.1.5,<4",
22
- ]
23
-
24
- [project.urls]
25
- Repository = "https://github.com/nfdi4plants/ARCtrl"
26
-
27
- [dependency-groups]
28
- dev = [
29
- "pytest>=8.1.1,<9",
30
- "twine>=4.0.2"
31
- ]
32
-
33
- [tool.poetry]
34
- include = [
35
- "src/ARCtrl/py/**/*.py"
36
- ]
37
- packages = [
38
- { include = "**/*.py", from = "src/ARCtrl/", to = "arctrl" }
39
- ]
40
-
41
- [build-system]
42
- requires = ["poetry-core"]
43
- build-backend = "poetry.core.masonry.api"
1
+ [project]
2
+ name = "arctrl"
3
+ version = "3.0.0b14"
4
+ description = "Library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtimer agnostic contract systems."
5
+ authors = [
6
+ { name = "Heinrich Lukas Weil", email = "weil@rptu.de" },
7
+ { name = "Kevin Frey", email = "freymaurer@gmx.de" },
8
+ ]
9
+ requires-python = ">=3.11"
10
+ readme = "README.md"
11
+ maintainers = [{ name = "Florian Wetzels" }]
12
+ keywords = [
13
+ "arc",
14
+ "annotated research context",
15
+ "isa",
16
+ "research data",
17
+ "multi platform",
18
+ ]
19
+ dependencies = [
20
+ "requests>= 2.28.1, <3.0.0",
21
+ "openpyxl>=3.1.5,<4",
22
+ ]
23
+
24
+ [project.urls]
25
+ Repository = "https://github.com/nfdi4plants/ARCtrl"
26
+
27
+ [dependency-groups]
28
+ dev = [
29
+ "pytest>=8.1.1,<9",
30
+ "twine>=4.0.2"
31
+ ]
32
+
33
+ [tool.poetry]
34
+ include = [
35
+ "src/ARCtrl/py/**/*.py"
36
+ ]
37
+ packages = [
38
+ { include = "**/*.py", from = "src/ARCtrl/", to = "arctrl" }
39
+ ]
40
+
41
+ [build-system]
42
+ requires = ["poetry-core"]
43
+ build-backend = "poetry.core.masonry.api"
@@ -2,6 +2,8 @@ from __future__ import annotations
2
2
  from collections.abc import Callable
3
3
  from typing import Any
4
4
  from .py.Contract.contract import Contract
5
+ from .py.Core.data_context import DataContext
6
+ from .py.Core.datamap import Datamap
5
7
  from .py.Core.comment import Comment
6
8
  from .py.Core.ontology_annotation import OntologyAnnotation
7
9
  from .py.Core.person import Person
@@ -4,7 +4,7 @@ from ..fable_modules.fable_library.types import (Array, Union)
4
4
  from .tool_description import CWLToolDescription_reflection
5
5
  from .workflow_description import CWLWorkflowDescription_reflection
6
6
 
7
- def _expr519() -> TypeInfo:
7
+ def _expr518() -> TypeInfo:
8
8
  return union_type("ARCtrl.CWL.CWLProcessingUnit", [], CWLProcessingUnit, lambda: [[("Item", CWLToolDescription_reflection())], [("Item", CWLWorkflowDescription_reflection())]])
9
9
 
10
10
 
@@ -19,7 +19,7 @@ class CWLProcessingUnit(Union):
19
19
  return ["CommandLineTool", "Workflow"]
20
20
 
21
21
 
22
- CWLProcessingUnit_reflection = _expr519
22
+ CWLProcessingUnit_reflection = _expr518
23
23
 
24
24
  __all__ = ["CWLProcessingUnit_reflection"]
25
25
 
@@ -7,7 +7,7 @@ from ..fable_modules.fable_library.reflection import (TypeInfo, class_type, stri
7
7
  from ..fable_modules.fable_library.types import (Record, Array, Union, FSharpRef)
8
8
  from ..fable_modules.fable_library.util import identity_hash
9
9
 
10
- def _expr495() -> TypeInfo:
10
+ def _expr472() -> TypeInfo:
11
11
  return class_type("ARCtrl.CWL.FileInstance", None, FileInstance, DynamicObj_reflection())
12
12
 
13
13
 
@@ -25,13 +25,13 @@ class FileInstance(DynamicObj):
25
25
  return this.StructurallyEquals(o) if isinstance(o, FileInstance) else False
26
26
 
27
27
 
28
- FileInstance_reflection = _expr495
28
+ FileInstance_reflection = _expr472
29
29
 
30
30
  def FileInstance__ctor(__unit: None=None) -> FileInstance:
31
31
  return FileInstance(__unit)
32
32
 
33
33
 
34
- def _expr496() -> TypeInfo:
34
+ def _expr475() -> TypeInfo:
35
35
  return class_type("ARCtrl.CWL.DirectoryInstance", None, DirectoryInstance, DynamicObj_reflection())
36
36
 
37
37
 
@@ -49,13 +49,13 @@ class DirectoryInstance(DynamicObj):
49
49
  return identity_hash(this.DeepCopyProperties())
50
50
 
51
51
 
52
- DirectoryInstance_reflection = _expr496
52
+ DirectoryInstance_reflection = _expr475
53
53
 
54
54
  def DirectoryInstance__ctor(__unit: None=None) -> DirectoryInstance:
55
55
  return DirectoryInstance(__unit)
56
56
 
57
57
 
58
- def _expr497() -> TypeInfo:
58
+ def _expr478() -> TypeInfo:
59
59
  return record_type("ARCtrl.CWL.DirentInstance", [], DirentInstance, lambda: [("Entry", string_type), ("Entryname", option_type(string_type)), ("Writable", option_type(bool_type))])
60
60
 
61
61
 
@@ -65,9 +65,9 @@ class DirentInstance(Record):
65
65
  Entryname: str | None
66
66
  Writable: bool | None
67
67
 
68
- DirentInstance_reflection = _expr497
68
+ DirentInstance_reflection = _expr478
69
69
 
70
- def _expr498() -> TypeInfo:
70
+ def _expr482() -> TypeInfo:
71
71
  return union_type("ARCtrl.CWL.CWLType", [], CWLType, lambda: [[("Item", FileInstance_reflection())], [("Item", DirectoryInstance_reflection())], [("Item", DirentInstance_reflection())], [], [], [], [], [], [], [], [], [("Item", CWLType_reflection())]])
72
72
 
73
73
 
@@ -82,7 +82,7 @@ class CWLType(Union):
82
82
  return ["File", "Directory", "Dirent", "String", "Int", "Long", "Float", "Double", "Boolean", "Stdout", "Null", "Array"]
83
83
 
84
84
 
85
- CWLType_reflection = _expr498
85
+ CWLType_reflection = _expr482
86
86
 
87
87
  def CWLType_file(__unit: None=None) -> CWLType:
88
88
  return CWLType(0, FileInstance__ctor())
@@ -92,7 +92,7 @@ def CWLType_directory(__unit: None=None) -> CWLType:
92
92
  return CWLType(1, DirectoryInstance__ctor())
93
93
 
94
94
 
95
- def _expr500() -> TypeInfo:
95
+ def _expr483() -> TypeInfo:
96
96
  return class_type("ARCtrl.CWL.InputRecordSchema", None, InputRecordSchema, DynamicObj_reflection())
97
97
 
98
98
 
@@ -102,13 +102,13 @@ class InputRecordSchema(DynamicObj):
102
102
  pass
103
103
 
104
104
 
105
- InputRecordSchema_reflection = _expr500
105
+ InputRecordSchema_reflection = _expr483
106
106
 
107
107
  def InputRecordSchema__ctor(__unit: None=None) -> InputRecordSchema:
108
108
  return InputRecordSchema(__unit)
109
109
 
110
110
 
111
- def _expr501() -> TypeInfo:
111
+ def _expr484() -> TypeInfo:
112
112
  return class_type("ARCtrl.CWL.InputEnumSchema", None, InputEnumSchema, DynamicObj_reflection())
113
113
 
114
114
 
@@ -118,13 +118,13 @@ class InputEnumSchema(DynamicObj):
118
118
  pass
119
119
 
120
120
 
121
- InputEnumSchema_reflection = _expr501
121
+ InputEnumSchema_reflection = _expr484
122
122
 
123
123
  def InputEnumSchema__ctor(__unit: None=None) -> InputEnumSchema:
124
124
  return InputEnumSchema(__unit)
125
125
 
126
126
 
127
- def _expr502() -> TypeInfo:
127
+ def _expr486() -> TypeInfo:
128
128
  return class_type("ARCtrl.CWL.InputArraySchema", None, InputArraySchema, DynamicObj_reflection())
129
129
 
130
130
 
@@ -134,13 +134,13 @@ class InputArraySchema(DynamicObj):
134
134
  pass
135
135
 
136
136
 
137
- InputArraySchema_reflection = _expr502
137
+ InputArraySchema_reflection = _expr486
138
138
 
139
139
  def InputArraySchema__ctor(__unit: None=None) -> InputArraySchema:
140
140
  return InputArraySchema(__unit)
141
141
 
142
142
 
143
- def _expr503() -> TypeInfo:
143
+ def _expr488() -> TypeInfo:
144
144
  return class_type("ARCtrl.CWL.SchemaDefRequirementType", None, SchemaDefRequirementType, DynamicObj_reflection())
145
145
 
146
146
 
@@ -153,13 +153,13 @@ class SchemaDefRequirementType(DynamicObj):
153
153
  set_property("types", definitions, this.contents)
154
154
 
155
155
 
156
- SchemaDefRequirementType_reflection = _expr503
156
+ SchemaDefRequirementType_reflection = _expr488
157
157
 
158
158
  def SchemaDefRequirementType__ctor_541DA560(types: Any=None, definitions: Any=None) -> SchemaDefRequirementType:
159
159
  return SchemaDefRequirementType(types, definitions)
160
160
 
161
161
 
162
- def _expr504() -> TypeInfo:
162
+ def _expr489() -> TypeInfo:
163
163
  return record_type("ARCtrl.CWL.SoftwarePackage", [], SoftwarePackage, lambda: [("Package", string_type), ("Version", option_type(array_type(string_type))), ("Specs", option_type(array_type(string_type)))])
164
164
 
165
165
 
@@ -169,7 +169,7 @@ class SoftwarePackage(Record):
169
169
  Version: Array[str] | None
170
170
  Specs: Array[str] | None
171
171
 
172
- SoftwarePackage_reflection = _expr504
172
+ SoftwarePackage_reflection = _expr489
173
173
 
174
174
  __all__ = ["FileInstance_reflection", "DirectoryInstance_reflection", "DirentInstance_reflection", "CWLType_reflection", "CWLType_file", "CWLType_directory", "InputRecordSchema_reflection", "InputEnumSchema_reflection", "InputArraySchema_reflection", "SchemaDefRequirementType_reflection", "SoftwarePackage_reflection"]
175
175
 
@@ -1102,10 +1102,10 @@ def DecodeParameters_cwlParameterReferenceDecoder(get: IGetters, key: str, y_ele
1102
1102
  return CWLParameterReference(key, [v2.Value], Decode_cwlTypeStringMatcher(v1.Value, get)[0])
1103
1103
 
1104
1104
  elif pattern_matching_result == 2:
1105
- def _arrow601(value: YAMLElement, get: Any=get, key: Any=key, y_ele: Any=y_ele) -> str:
1105
+ def _arrow603(value: YAMLElement, get: Any=get, key: Any=key, y_ele: Any=y_ele) -> str:
1106
1106
  return string(value)
1107
1107
 
1108
- return CWLParameterReference(key, resizearray(_arrow601, YAMLElement(2, s)))
1108
+ return CWLParameterReference(key, resizearray(_arrow603, YAMLElement(2, s)))
1109
1109
 
1110
1110
  elif pattern_matching_result == 3:
1111
1111
  raise Exception(("" + str(y_ele)) + "")
@@ -31,15 +31,15 @@ def hash_1(obj: Any | None=None) -> int:
31
31
 
32
32
 
33
33
  def box_hash_option(a: Any | None=None) -> Any:
34
- def _arrow465(__unit: None=None, a: Any=a) -> int:
34
+ def _arrow455(__unit: None=None, a: Any=a) -> int:
35
35
  copy_of_struct: _A = value_1(a)
36
36
  return identity_hash(copy_of_struct)
37
37
 
38
- def _arrow466(__unit: None=None, a: Any=a) -> int:
38
+ def _arrow456(__unit: None=None, a: Any=a) -> int:
39
39
  copy_of_struct_1: int = 0
40
40
  return number_hash(copy_of_struct_1)
41
41
 
42
- return _arrow465() if (a is not None) else _arrow466()
42
+ return _arrow455() if (a is not None) else _arrow456()
43
43
 
44
44
 
45
45
  def box_hash_array(a: Array[Any]) -> Any:
@@ -8,7 +8,7 @@ from .outputs import CWLOutput
8
8
  from .requirements import Requirement
9
9
  from .workflow_steps import WorkflowStep
10
10
 
11
- def _expr518() -> TypeInfo:
11
+ def _expr519() -> TypeInfo:
12
12
  return class_type("ARCtrl.CWL.CWLWorkflowDescription", None, CWLWorkflowDescription, DynamicObj_reflection())
13
13
 
14
14
 
@@ -94,7 +94,7 @@ class CWLWorkflowDescription(DynamicObj):
94
94
  this._metadata = metadata
95
95
 
96
96
 
97
- CWLWorkflowDescription_reflection = _expr518
97
+ CWLWorkflowDescription_reflection = _expr519
98
98
 
99
99
  def CWLWorkflowDescription__ctor_704BBD06(steps: Array[WorkflowStep], inputs: Array[CWLInput], outputs: Array[CWLOutput], cwl_version: str | None=None, requirements: Array[Requirement] | None=None, hints: Array[Requirement] | None=None, metadata: DynamicObj | None=None) -> CWLWorkflowDescription:
100
100
  return CWLWorkflowDescription(steps, inputs, outputs, cwl_version, requirements, hints, metadata)
@@ -14,10 +14,10 @@ from .contract import (Contract, DTOType, DTO)
14
14
 
15
15
  def _007CAssayPath_007C__007C(input: Array[str]) -> str | None:
16
16
  (pattern_matching_result,) = (None,)
17
- def _arrow3723(x: str, y: str, input: Any=input) -> bool:
17
+ def _arrow3724(x: str, y: str, input: Any=input) -> bool:
18
18
  return x == y
19
19
 
20
- if (len(input) == 3) if (not equals_with(_arrow3723, input, None)) else False:
20
+ if (len(input) == 3) if (not equals_with(_arrow3724, input, None)) else False:
21
21
  if input[0] == "assays":
22
22
  if input[2] == "isa.assay.xlsx":
23
23
  pattern_matching_result = 0
@@ -46,20 +46,20 @@ def ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(this: ArcAssay, WithFold
46
46
  with_folder: bool = default_arg(WithFolder, False)
47
47
  path: str = Assay_fileNameFromIdentifier(this.Identifier)
48
48
  c: Contract = Contract.create_create(path, DTOType(0), DTO(0, ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(this)))
49
- def _arrow3727(__unit: None=None, this: Any=this, WithFolder: Any=WithFolder) -> IEnumerable_1[Contract]:
50
- def _arrow3725(__unit: None=None) -> IEnumerable_1[Contract]:
49
+ def _arrow3728(__unit: None=None, this: Any=this, WithFolder: Any=WithFolder) -> IEnumerable_1[Contract]:
50
+ def _arrow3726(__unit: None=None) -> IEnumerable_1[Contract]:
51
51
  folder_fs: FileSystemTree = FileSystemTree.create_assays_folder([FileSystemTree.create_assay_folder(this.Identifier)])
52
- def _arrow3724(p: str) -> IEnumerable_1[Contract]:
52
+ def _arrow3725(p: str) -> IEnumerable_1[Contract]:
53
53
  return singleton(Contract.create_create(p, DTOType(10))) if ((p != "assays/.gitkeep") if (p != path) else False) else empty()
54
54
 
55
- return collect(_arrow3724, folder_fs.ToFilePaths(False))
55
+ return collect(_arrow3725, folder_fs.ToFilePaths(False))
56
56
 
57
- def _arrow3726(__unit: None=None) -> IEnumerable_1[Contract]:
57
+ def _arrow3727(__unit: None=None) -> IEnumerable_1[Contract]:
58
58
  return singleton(c)
59
59
 
60
- return append(_arrow3725() if with_folder else empty(), delay(_arrow3726))
60
+ return append(_arrow3726() if with_folder else empty(), delay(_arrow3727))
61
61
 
62
- return to_array(delay(_arrow3727))
62
+ return to_array(delay(_arrow3728))
63
63
 
64
64
 
65
65
  def ARCtrl_ArcAssay__ArcAssay_ToUpdateContract(this: ArcAssay) -> Contract:
@@ -9,10 +9,10 @@ from .contract import (Contract, DTOType, DTO)
9
9
 
10
10
  def _007CInvestigationPath_007C__007C(input: Array[str]) -> str | None:
11
11
  (pattern_matching_result,) = (None,)
12
- def _arrow3742(x: str, y: str, input: Any=input) -> bool:
12
+ def _arrow3754(x: str, y: str, input: Any=input) -> bool:
13
13
  return x == y
14
14
 
15
- if (len(input) == 1) if (not equals_with(_arrow3742, input, None)) else False:
15
+ if (len(input) == 1) if (not equals_with(_arrow3754, input, None)) else False:
16
16
  if input[0] == "isa.investigation.xlsx":
17
17
  pattern_matching_result = 0
18
18
 
@@ -15,10 +15,10 @@ from .contract import (Contract, DTOType, DTO)
15
15
 
16
16
  def _007CStudyPath_007C__007C(input: Array[str]) -> str | None:
17
17
  (pattern_matching_result,) = (None,)
18
- def _arrow3728(x: str, y: str, input: Any=input) -> bool:
18
+ def _arrow3729(x: str, y: str, input: Any=input) -> bool:
19
19
  return x == y
20
20
 
21
- if (len(input) == 3) if (not equals_with(_arrow3728, input, None)) else False:
21
+ if (len(input) == 3) if (not equals_with(_arrow3729, input, None)) else False:
22
22
  if input[0] == "studies":
23
23
  if input[2] == "isa.study.xlsx":
24
24
  pattern_matching_result = 0
@@ -47,20 +47,20 @@ def ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49(this: ArcStudy, WithFold
47
47
  with_folder: bool = default_arg(WithFolder, False)
48
48
  path: str = Study_fileNameFromIdentifier(this.Identifier)
49
49
  c: Contract = Contract.create_create(path, DTOType(1), DTO(0, ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(this)))
50
- def _arrow3732(__unit: None=None, this: Any=this, WithFolder: Any=WithFolder) -> IEnumerable_1[Contract]:
51
- def _arrow3730(__unit: None=None) -> IEnumerable_1[Contract]:
50
+ def _arrow3733(__unit: None=None, this: Any=this, WithFolder: Any=WithFolder) -> IEnumerable_1[Contract]:
51
+ def _arrow3731(__unit: None=None) -> IEnumerable_1[Contract]:
52
52
  folder_fs: FileSystemTree = FileSystemTree.create_studies_folder([FileSystemTree.create_study_folder(this.Identifier)])
53
- def _arrow3729(p: str) -> IEnumerable_1[Contract]:
53
+ def _arrow3730(p: str) -> IEnumerable_1[Contract]:
54
54
  return singleton(Contract.create_create(p, DTOType(10))) if ((p != "studies/.gitkeep") if (p != path) else False) else empty()
55
55
 
56
- return collect(_arrow3729, folder_fs.ToFilePaths(False))
56
+ return collect(_arrow3730, folder_fs.ToFilePaths(False))
57
57
 
58
- def _arrow3731(__unit: None=None) -> IEnumerable_1[Contract]:
58
+ def _arrow3732(__unit: None=None) -> IEnumerable_1[Contract]:
59
59
  return singleton(c)
60
60
 
61
- return append(_arrow3730() if with_folder else empty(), delay(_arrow3731))
61
+ return append(_arrow3731() if with_folder else empty(), delay(_arrow3732))
62
62
 
63
- return to_array(delay(_arrow3732))
63
+ return to_array(delay(_arrow3733))
64
64
 
65
65
 
66
66
  def ARCtrl_ArcStudy__ArcStudy_ToUpdateContract(this: ArcStudy) -> Contract:
@@ -17,10 +17,10 @@ from .contract import (Contract, DTOType, DTO)
17
17
 
18
18
  def _007CWorkflowPath_007C__007C(input: Array[str]) -> str | None:
19
19
  (pattern_matching_result,) = (None,)
20
- def _arrow3733(x: str, y: str, input: Any=input) -> bool:
20
+ def _arrow3734(x: str, y: str, input: Any=input) -> bool:
21
21
  return x == y
22
22
 
23
- if (len(input) == 3) if (not equals_with(_arrow3733, input, None)) else False:
23
+ if (len(input) == 3) if (not equals_with(_arrow3734, input, None)) else False:
24
24
  if input[0] == "workflows":
25
25
  if input[2] == "isa.workflow.xlsx":
26
26
  pattern_matching_result = 0
@@ -47,10 +47,10 @@ def _007CWorkflowPath_007C__007C(input: Array[str]) -> str | None:
47
47
 
48
48
  def _007CWorkflowCWLPath_007C__007C(input: Array[str]) -> str | None:
49
49
  (pattern_matching_result,) = (None,)
50
- def _arrow3734(x: str, y: str, input: Any=input) -> bool:
50
+ def _arrow3735(x: str, y: str, input: Any=input) -> bool:
51
51
  return x == y
52
52
 
53
- if (len(input) == 3) if (not equals_with(_arrow3734, input, None)) else False:
53
+ if (len(input) == 3) if (not equals_with(_arrow3735, input, None)) else False:
54
54
  if input[0] == "workflows":
55
55
  if input[2] == "workflow.cwl":
56
56
  pattern_matching_result = 0
@@ -79,28 +79,28 @@ def ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49(this: ArcWorkflow,
79
79
  with_folder: bool = default_arg(WithFolder, False)
80
80
  path: str = Workflow_fileNameFromIdentifier(this.Identifier)
81
81
  c: Contract = Contract.create_create(path, DTOType(2), DTO(0, ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E(this)))
82
- def _arrow3740(__unit: None=None, this: Any=this, WithFolder: Any=WithFolder) -> IEnumerable_1[Contract]:
83
- def _arrow3736(__unit: None=None) -> IEnumerable_1[Contract]:
82
+ def _arrow3741(__unit: None=None, this: Any=this, WithFolder: Any=WithFolder) -> IEnumerable_1[Contract]:
83
+ def _arrow3737(__unit: None=None) -> IEnumerable_1[Contract]:
84
84
  folder_fs: FileSystemTree = FileSystemTree.create_workflows_folder([FileSystemTree.create_workflow_folder(this.Identifier)])
85
- def _arrow3735(p: str) -> IEnumerable_1[Contract]:
85
+ def _arrow3736(p: str) -> IEnumerable_1[Contract]:
86
86
  return singleton(Contract.create_create(p, DTOType(10))) if ((p != "workflows/.gitkeep") if (p != path) else False) else empty()
87
87
 
88
- return collect(_arrow3735, folder_fs.ToFilePaths(False))
88
+ return collect(_arrow3736, folder_fs.ToFilePaths(False))
89
89
 
90
- def _arrow3739(__unit: None=None) -> IEnumerable_1[Contract]:
91
- def _arrow3737(__unit: None=None) -> IEnumerable_1[Contract]:
90
+ def _arrow3740(__unit: None=None) -> IEnumerable_1[Contract]:
91
+ def _arrow3738(__unit: None=None) -> IEnumerable_1[Contract]:
92
92
  path_1: str = Workflow_cwlFileNameFromIdentifier(this.Identifier)
93
93
  dto: str = encode_processing_unit(value(this.CWLDescription))
94
94
  return singleton(Contract.create_create(path_1, DTOType(8), DTO(1, dto)))
95
95
 
96
- def _arrow3738(__unit: None=None) -> IEnumerable_1[Contract]:
96
+ def _arrow3739(__unit: None=None) -> IEnumerable_1[Contract]:
97
97
  return singleton(c)
98
98
 
99
- return append(_arrow3737() if (this.CWLDescription is not None) else empty(), delay(_arrow3738))
99
+ return append(_arrow3738() if (this.CWLDescription is not None) else empty(), delay(_arrow3739))
100
100
 
101
- return append(_arrow3736() if with_folder else empty(), delay(_arrow3739))
101
+ return append(_arrow3737() if with_folder else empty(), delay(_arrow3740))
102
102
 
103
- return to_array(delay(_arrow3740))
103
+ return to_array(delay(_arrow3741))
104
104
 
105
105
 
106
106
  def ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract(this: ArcWorkflow) -> Contract:
@@ -170,11 +170,11 @@ def ARCtrl_ArcWorkflow__ArcWorkflow_tryCWLFromReadContract_Static(workflow_ident
170
170
  if c.DTOType.tag == 8:
171
171
  if c.DTO is not None:
172
172
  if c.DTO.tag == 1:
173
- def _arrow3741(__unit: None=None, workflow_identifier: Any=workflow_identifier, c: Any=c) -> bool:
173
+ def _arrow3742(__unit: None=None, workflow_identifier: Any=workflow_identifier, c: Any=c) -> bool:
174
174
  cwl: str = c.DTO.fields[0]
175
175
  return c.Path == p
176
176
 
177
- if _arrow3741():
177
+ if _arrow3742():
178
178
  pattern_matching_result = 0
179
179
  cwl_1 = c.DTO.fields[0]
180
180
 
@@ -5,7 +5,7 @@ from ..fable_modules.fable_library.option import default_arg
5
5
  from ..fable_modules.fable_library.reflection import (TypeInfo, union_type, string_type, array_type, record_type, obj_type, option_type)
6
6
  from ..fable_modules.fable_library.types import (Array, Union, Record)
7
7
 
8
- def _expr3644() -> TypeInfo:
8
+ def _expr3666() -> TypeInfo:
9
9
  return union_type("ARCtrl.Contract.DTOType", [], DTOType, lambda: [[], [], [], [], [], [], [], [], [], [], [], []])
10
10
 
11
11
 
@@ -20,9 +20,9 @@ class DTOType(Union):
20
20
  return ["ISA_Assay", "ISA_Study", "ISA_Workflow", "ISA_Run", "ISA_Investigation", "ISA_Datamap", "JSON", "Markdown", "CWL", "YAML", "PlainText", "Cli"]
21
21
 
22
22
 
23
- DTOType_reflection = _expr3644
23
+ DTOType_reflection = _expr3666
24
24
 
25
- def _expr3647() -> TypeInfo:
25
+ def _expr3669() -> TypeInfo:
26
26
  return record_type("ARCtrl.Contract.CLITool", [], CLITool, lambda: [("Name", string_type), ("Arguments", array_type(string_type))])
27
27
 
28
28
 
@@ -35,9 +35,9 @@ class CLITool(Record):
35
35
  return CLITool(name, arguments)
36
36
 
37
37
 
38
- CLITool_reflection = _expr3647
38
+ CLITool_reflection = _expr3669
39
39
 
40
- def _expr3648() -> TypeInfo:
40
+ def _expr3672() -> TypeInfo:
41
41
  return union_type("ARCtrl.Contract.DTO", [], DTO, lambda: [[("Item", obj_type)], [("Item", string_type)], [("Item", CLITool_reflection())]])
42
42
 
43
43
 
@@ -52,7 +52,7 @@ class DTO(Union):
52
52
  return ["Spreadsheet", "Text", "CLITool"]
53
53
 
54
54
 
55
- DTO_reflection = _expr3648
55
+ DTO_reflection = _expr3672
56
56
 
57
57
  def DTO__get_isSpreadsheet(this: DTO) -> bool:
58
58
  if this.tag == 0:
@@ -108,7 +108,7 @@ def DTO__AsCLITool(this: DTO) -> CLITool:
108
108
 
109
109
 
110
110
 
111
- def _expr3651() -> TypeInfo:
111
+ def _expr3692() -> TypeInfo:
112
112
  return record_type("ARCtrl.Contract.Contract", [], Contract, lambda: [("Operation", string_type), ("Path", string_type), ("DTOType", option_type(DTOType_reflection())), ("DTO", option_type(DTO_reflection()))])
113
113
 
114
114
 
@@ -147,7 +147,7 @@ class Contract(Record):
147
147
  return Contract("RENAME", old_path, None, DTO(1, new_path))
148
148
 
149
149
 
150
- Contract_reflection = _expr3651
150
+ Contract_reflection = _expr3692
151
151
 
152
152
  __all__ = ["DTOType_reflection", "CLITool_reflection", "DTO_reflection", "DTO__get_isSpreadsheet", "DTO__get_isText", "DTO__get_isCLITool", "DTO__AsSpreadsheet", "DTO__AsText", "DTO__AsCLITool", "Contract_reflection"]
153
153