arctrl 3.0.0a3__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.
- arctrl/__init__.py +18 -0
- arctrl/py/CWL/__init__.py +0 -0
- arctrl/py/CWL/cwltypes.py +150 -0
- arctrl/py/CWL/decode.py +973 -0
- arctrl/py/CWL/encode.py +1 -0
- arctrl/py/CWL/inputs.py +88 -0
- arctrl/py/CWL/outputs.py +85 -0
- arctrl/py/CWL/requirements.py +77 -0
- arctrl/py/CWL/tool_description.py +103 -0
- arctrl/py/CWL/workflow_description.py +104 -0
- arctrl/py/CWL/workflow_steps.py +113 -0
- arctrl/py/Contract/__init__.py +0 -0
- arctrl/py/Contract/arc.py +60 -0
- arctrl/py/Contract/arc_assay.py +125 -0
- arctrl/py/Contract/arc_investigation.py +88 -0
- arctrl/py/Contract/arc_run.py +125 -0
- arctrl/py/Contract/arc_study.py +126 -0
- arctrl/py/Contract/arc_workflow.py +125 -0
- arctrl/py/Contract/contract.py +153 -0
- arctrl/py/Contract/datamap.py +372 -0
- arctrl/py/Contract/git.py +118 -0
- arctrl/py/Contract/validation_packages_config.py +107 -0
- arctrl/py/ContractIO/__init__.py +0 -0
- arctrl/py/ContractIO/contract_io.py +344 -0
- arctrl/py/ContractIO/file_system_helper.py +264 -0
- arctrl/py/Core/Helper/__init__.py +0 -0
- arctrl/py/Core/Helper/collections_.py +438 -0
- arctrl/py/Core/Helper/date_time.py +26 -0
- arctrl/py/Core/Helper/hash_codes.py +60 -0
- arctrl/py/Core/Helper/identifier.py +248 -0
- arctrl/py/Core/Helper/orcid.py +42 -0
- arctrl/py/Core/Helper/printer.py +13 -0
- arctrl/py/Core/Helper/regex.py +554 -0
- arctrl/py/Core/Helper/sem_ver.py +71 -0
- arctrl/py/Core/Helper/url.py +148 -0
- arctrl/py/Core/Process/__init__.py +0 -0
- arctrl/py/Core/Process/column_index.py +280 -0
- arctrl/py/Core/Process/component.py +200 -0
- arctrl/py/Core/Process/factor.py +151 -0
- arctrl/py/Core/Process/factor_value.py +182 -0
- arctrl/py/Core/Process/material.py +74 -0
- arctrl/py/Core/Process/material_attribute.py +95 -0
- arctrl/py/Core/Process/material_attribute_value.py +184 -0
- arctrl/py/Core/Process/material_type.py +45 -0
- arctrl/py/Core/Process/process.py +477 -0
- arctrl/py/Core/Process/process_input.py +265 -0
- arctrl/py/Core/Process/process_output.py +235 -0
- arctrl/py/Core/Process/process_parameter_value.py +200 -0
- arctrl/py/Core/Process/process_sequence.py +435 -0
- arctrl/py/Core/Process/protocol.py +175 -0
- arctrl/py/Core/Process/protocol_parameter.py +98 -0
- arctrl/py/Core/Process/sample.py +82 -0
- arctrl/py/Core/Process/source.py +62 -0
- arctrl/py/Core/Table/__init__.py +0 -0
- arctrl/py/Core/Table/arc_table.py +1264 -0
- arctrl/py/Core/Table/arc_table_aux.py +575 -0
- arctrl/py/Core/Table/arc_tables.py +591 -0
- arctrl/py/Core/Table/composite_cell.py +319 -0
- arctrl/py/Core/Table/composite_column.py +73 -0
- arctrl/py/Core/Table/composite_header.py +739 -0
- arctrl/py/Core/__init__.py +0 -0
- arctrl/py/Core/arc_types.py +5064 -0
- arctrl/py/Core/comment.py +128 -0
- arctrl/py/Core/comment_list.py +127 -0
- arctrl/py/Core/conversion.py +1313 -0
- arctrl/py/Core/data.py +245 -0
- arctrl/py/Core/data_context.py +157 -0
- arctrl/py/Core/data_file.py +112 -0
- arctrl/py/Core/data_map.py +225 -0
- arctrl/py/Core/identifier_setters.py +31 -0
- arctrl/py/Core/iproperty_value.py +36 -0
- arctrl/py/Core/ontology_annotation.py +299 -0
- arctrl/py/Core/ontology_source_reference.py +114 -0
- arctrl/py/Core/person.py +259 -0
- arctrl/py/Core/publication.py +161 -0
- arctrl/py/Core/template.py +231 -0
- arctrl/py/Core/templates.py +148 -0
- arctrl/py/Core/uri.py +11 -0
- arctrl/py/Core/value.py +188 -0
- arctrl/py/FileSystem/__init__.py +0 -0
- arctrl/py/FileSystem/commit.py +21 -0
- arctrl/py/FileSystem/default_gitattributes.py +5 -0
- arctrl/py/FileSystem/default_gitignore.py +5 -0
- arctrl/py/FileSystem/file_system.py +58 -0
- arctrl/py/FileSystem/file_system_tree.py +426 -0
- arctrl/py/FileSystem/path.py +64 -0
- arctrl/py/Json/DataMap/__init__.py +0 -0
- arctrl/py/Json/DataMap/data_context.py +101 -0
- arctrl/py/Json/DataMap/data_map.py +53 -0
- arctrl/py/Json/Process/__init__.py +0 -0
- arctrl/py/Json/Process/assay_materials.py +46 -0
- arctrl/py/Json/Process/component.py +79 -0
- arctrl/py/Json/Process/factor.py +107 -0
- arctrl/py/Json/Process/factor_value.py +101 -0
- arctrl/py/Json/Process/material.py +226 -0
- arctrl/py/Json/Process/material_attribute.py +79 -0
- arctrl/py/Json/Process/material_attribute_value.py +101 -0
- arctrl/py/Json/Process/material_type.py +53 -0
- arctrl/py/Json/Process/process.py +296 -0
- arctrl/py/Json/Process/process_input.py +83 -0
- arctrl/py/Json/Process/process_output.py +67 -0
- arctrl/py/Json/Process/process_parameter_value.py +81 -0
- arctrl/py/Json/Process/protocol.py +354 -0
- arctrl/py/Json/Process/protocol_parameter.py +79 -0
- arctrl/py/Json/Process/sample.py +277 -0
- arctrl/py/Json/Process/source.py +214 -0
- arctrl/py/Json/Process/study_materials.py +52 -0
- arctrl/py/Json/Process/value.py +56 -0
- arctrl/py/Json/ROCrate/__init__.py +0 -0
- arctrl/py/Json/ROCrate/ldcontext.py +133 -0
- arctrl/py/Json/ROCrate/ldgraph.py +111 -0
- arctrl/py/Json/ROCrate/ldnode.py +290 -0
- arctrl/py/Json/ROCrate/ldref.py +44 -0
- arctrl/py/Json/ROCrate/ldvalue.py +102 -0
- arctrl/py/Json/Table/__init__.py +0 -0
- arctrl/py/Json/Table/arc_table.py +393 -0
- arctrl/py/Json/Table/cell_table.py +83 -0
- arctrl/py/Json/Table/composite_cell.py +136 -0
- arctrl/py/Json/Table/composite_header.py +67 -0
- arctrl/py/Json/Table/iotype.py +24 -0
- arctrl/py/Json/Table/oatable.py +82 -0
- arctrl/py/Json/Table/templates.py +281 -0
- arctrl/py/Json/__init__.py +0 -0
- arctrl/py/Json/assay.py +600 -0
- arctrl/py/Json/comment.py +206 -0
- arctrl/py/Json/context/rocrate/__init__.py +0 -0
- arctrl/py/Json/context/rocrate/isa_assay_context.py +101 -0
- arctrl/py/Json/context/rocrate/isa_comment_context.py +60 -0
- arctrl/py/Json/context/rocrate/isa_component_context.py +77 -0
- arctrl/py/Json/context/rocrate/isa_data_context.py +74 -0
- arctrl/py/Json/context/rocrate/isa_factor_context.py +74 -0
- arctrl/py/Json/context/rocrate/isa_factor_value_context.py +84 -0
- arctrl/py/Json/context/rocrate/isa_investigation_context.py +110 -0
- arctrl/py/Json/context/rocrate/isa_material_attribute_context.py +64 -0
- arctrl/py/Json/context/rocrate/isa_material_attribute_value_context.py +80 -0
- arctrl/py/Json/context/rocrate/isa_material_context.py +71 -0
- arctrl/py/Json/context/rocrate/isa_ontology_annotation_context.py +68 -0
- arctrl/py/Json/context/rocrate/isa_ontology_source_reference_context.py +75 -0
- arctrl/py/Json/context/rocrate/isa_organization_context.py +55 -0
- arctrl/py/Json/context/rocrate/isa_person_context.py +131 -0
- arctrl/py/Json/context/rocrate/isa_process_context.py +94 -0
- arctrl/py/Json/context/rocrate/isa_process_parameter_value_context.py +80 -0
- arctrl/py/Json/context/rocrate/isa_protocol_context.py +97 -0
- arctrl/py/Json/context/rocrate/isa_protocol_parameter_context.py +64 -0
- arctrl/py/Json/context/rocrate/isa_publication_context.py +78 -0
- arctrl/py/Json/context/rocrate/isa_sample_context.py +65 -0
- arctrl/py/Json/context/rocrate/isa_source_context.py +66 -0
- arctrl/py/Json/context/rocrate/isa_study_context.py +125 -0
- arctrl/py/Json/context/rocrate/property_value_context.py +73 -0
- arctrl/py/Json/context/rocrate/rocrate_context.py +81 -0
- arctrl/py/Json/converter_options.py +23 -0
- arctrl/py/Json/data.py +356 -0
- arctrl/py/Json/data_file.py +63 -0
- arctrl/py/Json/decode.py +155 -0
- arctrl/py/Json/encode.py +92 -0
- arctrl/py/Json/idtable.py +44 -0
- arctrl/py/Json/investigation.py +695 -0
- arctrl/py/Json/ontology_annotation.py +404 -0
- arctrl/py/Json/ontology_source_reference.py +255 -0
- arctrl/py/Json/person.py +658 -0
- arctrl/py/Json/property_value.py +359 -0
- arctrl/py/Json/publication.py +279 -0
- arctrl/py/Json/string_table.py +76 -0
- arctrl/py/Json/study.py +793 -0
- arctrl/py/JsonIO/DataMap/__init__.py +0 -0
- arctrl/py/JsonIO/DataMap/data_map.py +53 -0
- arctrl/py/JsonIO/Process/__init__.py +0 -0
- arctrl/py/JsonIO/Process/component.py +60 -0
- arctrl/py/JsonIO/Process/factor.py +36 -0
- arctrl/py/JsonIO/Process/factor_value.py +38 -0
- arctrl/py/JsonIO/Process/material.py +60 -0
- arctrl/py/JsonIO/Process/material_attribute.py +38 -0
- arctrl/py/JsonIO/Process/material_attribute_value.py +60 -0
- arctrl/py/JsonIO/Process/material_type.py +36 -0
- arctrl/py/JsonIO/Process/process.py +60 -0
- arctrl/py/JsonIO/Process/process_input.py +38 -0
- arctrl/py/JsonIO/Process/process_output.py +60 -0
- arctrl/py/JsonIO/Process/process_parameter_value.py +60 -0
- arctrl/py/JsonIO/Process/process_sequence.py +71 -0
- arctrl/py/JsonIO/Process/protocol.py +60 -0
- arctrl/py/JsonIO/Process/protocol_parameter.py +36 -0
- arctrl/py/JsonIO/Process/sample.py +60 -0
- arctrl/py/JsonIO/Process/source.py +60 -0
- arctrl/py/JsonIO/Process/study_materials.py +52 -0
- arctrl/py/JsonIO/Process/value.py +32 -0
- arctrl/py/JsonIO/Table/__init__.py +0 -0
- arctrl/py/JsonIO/Table/arc_table.py +121 -0
- arctrl/py/JsonIO/Table/composite_cell.py +36 -0
- arctrl/py/JsonIO/Table/composite_header.py +36 -0
- arctrl/py/JsonIO/Table/compression.py +85 -0
- arctrl/py/JsonIO/Table/iotype.py +36 -0
- arctrl/py/JsonIO/Table/templates.py +113 -0
- arctrl/py/JsonIO/__init__.py +0 -0
- arctrl/py/JsonIO/assay.py +113 -0
- arctrl/py/JsonIO/comment.py +80 -0
- arctrl/py/JsonIO/data.py +60 -0
- arctrl/py/JsonIO/data_file.py +58 -0
- arctrl/py/JsonIO/decode.py +9 -0
- arctrl/py/JsonIO/encode.py +1 -0
- arctrl/py/JsonIO/investigation.py +113 -0
- arctrl/py/JsonIO/ldobject.py +106 -0
- arctrl/py/JsonIO/ontology_annotation.py +80 -0
- arctrl/py/JsonIO/ontology_source_reference.py +80 -0
- arctrl/py/JsonIO/person.py +82 -0
- arctrl/py/JsonIO/publication.py +82 -0
- arctrl/py/JsonIO/study.py +114 -0
- arctrl/py/ROCrate/Generic/__init__.py +0 -0
- arctrl/py/ROCrate/Generic/comment.py +131 -0
- arctrl/py/ROCrate/Generic/dataset.py +817 -0
- arctrl/py/ROCrate/Generic/defined_term.py +131 -0
- arctrl/py/ROCrate/Generic/file.py +237 -0
- arctrl/py/ROCrate/Generic/lab_process.py +324 -0
- arctrl/py/ROCrate/Generic/lab_protocol.py +338 -0
- arctrl/py/ROCrate/Generic/organization.py +83 -0
- arctrl/py/ROCrate/Generic/person.py +484 -0
- arctrl/py/ROCrate/Generic/postal_address.py +195 -0
- arctrl/py/ROCrate/Generic/property_value.py +696 -0
- arctrl/py/ROCrate/Generic/sample.py +202 -0
- arctrl/py/ROCrate/Generic/scholarly_article.py +229 -0
- arctrl/py/ROCrate/ISAProfile/__init__.py +0 -0
- arctrl/py/ROCrate/ISAProfile/assay.py +70 -0
- arctrl/py/ROCrate/ISAProfile/data.py +65 -0
- arctrl/py/ROCrate/ISAProfile/dataset.py +24 -0
- arctrl/py/ROCrate/ISAProfile/investigation.py +73 -0
- arctrl/py/ROCrate/ISAProfile/lab_process.py +162 -0
- arctrl/py/ROCrate/ISAProfile/lab_protocol.py +37 -0
- arctrl/py/ROCrate/ISAProfile/person.py +72 -0
- arctrl/py/ROCrate/ISAProfile/property_value.py +98 -0
- arctrl/py/ROCrate/ISAProfile/sample.py +64 -0
- arctrl/py/ROCrate/ISAProfile/scholarly_article.py +98 -0
- arctrl/py/ROCrate/ISAProfile/study.py +74 -0
- arctrl/py/ROCrate/__init__.py +0 -0
- arctrl/py/ROCrate/arc_rocrate_metadata.py +39 -0
- arctrl/py/ROCrate/dyn_obj_extensions.py +1 -0
- arctrl/py/ROCrate/helper.py +8 -0
- arctrl/py/ROCrate/ldcontext.py +362 -0
- arctrl/py/ROCrate/ldobject.py +1247 -0
- arctrl/py/ROCrate/rocrate_context.py +51 -0
- arctrl/py/Spreadsheet/AnnotationTable/__init__.py +0 -0
- arctrl/py/Spreadsheet/AnnotationTable/arc_table.py +193 -0
- arctrl/py/Spreadsheet/AnnotationTable/composite_cell.py +78 -0
- arctrl/py/Spreadsheet/AnnotationTable/composite_column.py +210 -0
- arctrl/py/Spreadsheet/AnnotationTable/composite_header.py +623 -0
- arctrl/py/Spreadsheet/DataMapTable/__init__.py +0 -0
- arctrl/py/Spreadsheet/DataMapTable/data_map_column.py +114 -0
- arctrl/py/Spreadsheet/DataMapTable/data_map_header.py +618 -0
- arctrl/py/Spreadsheet/DataMapTable/data_map_table.py +119 -0
- arctrl/py/Spreadsheet/Metadata/__init__.py +0 -0
- arctrl/py/Spreadsheet/Metadata/assays.py +125 -0
- arctrl/py/Spreadsheet/Metadata/comment.py +77 -0
- arctrl/py/Spreadsheet/Metadata/contacts.py +134 -0
- arctrl/py/Spreadsheet/Metadata/conversions.py +190 -0
- arctrl/py/Spreadsheet/Metadata/design_descriptors.py +34 -0
- arctrl/py/Spreadsheet/Metadata/factors.py +107 -0
- arctrl/py/Spreadsheet/Metadata/ontology_annotation.py +88 -0
- arctrl/py/Spreadsheet/Metadata/ontology_source_reference.py +96 -0
- arctrl/py/Spreadsheet/Metadata/protocols.py +146 -0
- arctrl/py/Spreadsheet/Metadata/publication.py +122 -0
- arctrl/py/Spreadsheet/Metadata/run.py +122 -0
- arctrl/py/Spreadsheet/Metadata/sparse_table.py +508 -0
- arctrl/py/Spreadsheet/Metadata/study.py +312 -0
- arctrl/py/Spreadsheet/Metadata/workflow.py +151 -0
- arctrl/py/Spreadsheet/__init__.py +0 -0
- arctrl/py/Spreadsheet/arc_assay.py +233 -0
- arctrl/py/Spreadsheet/arc_investigation.py +418 -0
- arctrl/py/Spreadsheet/arc_run.py +190 -0
- arctrl/py/Spreadsheet/arc_study.py +144 -0
- arctrl/py/Spreadsheet/arc_workflow.py +176 -0
- arctrl/py/Spreadsheet/assembly_info.py +1 -0
- arctrl/py/Spreadsheet/collection_aux.py +167 -0
- arctrl/py/Spreadsheet/data_map.py +44 -0
- arctrl/py/Spreadsheet/template.py +460 -0
- arctrl/py/ValidationPackages/__init__.py +0 -0
- arctrl/py/ValidationPackages/validation_package.py +82 -0
- arctrl/py/ValidationPackages/validation_packages_config.py +132 -0
- arctrl/py/WebRequest/__init__.py +0 -0
- arctrl/py/WebRequest/web_request.py +9 -0
- arctrl/py/WebRequest/web_request_py.py +135 -0
- arctrl/py/Yaml/__init__.py +0 -0
- arctrl/py/Yaml/decode.py +1 -0
- arctrl/py/Yaml/encode.py +10 -0
- arctrl/py/Yaml/validation_package.py +77 -0
- arctrl/py/Yaml/validation_packages_config.py +86 -0
- arctrl/py/__init__.py +0 -0
- arctrl/py/arc.py +1400 -0
- arctrl/py/column_index.py +280 -0
- arctrl/py/conversion.py +2184 -0
- arctrl/py/cross_async.py +76 -0
- arctrl/py/fable_modules/dynamic_obj/__init__.py +0 -0
- arctrl/py/fable_modules/dynamic_obj/dyn_obj.py +136 -0
- arctrl/py/fable_modules/dynamic_obj/dynamic_obj.py +415 -0
- arctrl/py/fable_modules/dynamic_obj/fable_js.py +1 -0
- arctrl/py/fable_modules/dynamic_obj/fable_py.py +288 -0
- arctrl/py/fable_modules/dynamic_obj/hash_codes.py +82 -0
- arctrl/py/fable_modules/dynamic_obj/property_helper.py +25 -0
- arctrl/py/fable_modules/dynamic_obj/reflection_utils.py +87 -0
- arctrl/py/fable_modules/fable_library/__init__.py +0 -0
- arctrl/py/fable_modules/fable_library/array_.py +1528 -0
- arctrl/py/fable_modules/fable_library/async_.py +377 -0
- arctrl/py/fable_modules/fable_library/async_builder.py +379 -0
- arctrl/py/fable_modules/fable_library/big_int.py +330 -0
- arctrl/py/fable_modules/fable_library/bit_converter.py +131 -0
- arctrl/py/fable_modules/fable_library/boolean.py +26 -0
- arctrl/py/fable_modules/fable_library/char.py +237 -0
- arctrl/py/fable_modules/fable_library/choice.py +212 -0
- arctrl/py/fable_modules/fable_library/date.py +779 -0
- arctrl/py/fable_modules/fable_library/date_offset.py +79 -0
- arctrl/py/fable_modules/fable_library/decimal_.py +190 -0
- arctrl/py/fable_modules/fable_library/diagnostics.py +54 -0
- arctrl/py/fable_modules/fable_library/double.py +87 -0
- arctrl/py/fable_modules/fable_library/encoding.py +41 -0
- arctrl/py/fable_modules/fable_library/event.py +206 -0
- arctrl/py/fable_modules/fable_library/file.py +107 -0
- arctrl/py/fable_modules/fable_library/fsharp_collections.py +52 -0
- arctrl/py/fable_modules/fable_library/fsharp_core.py +123 -0
- arctrl/py/fable_modules/fable_library/global_.py +63 -0
- arctrl/py/fable_modules/fable_library/guid.py +41 -0
- arctrl/py/fable_modules/fable_library/int32.py +73 -0
- arctrl/py/fable_modules/fable_library/list.py +1788 -0
- arctrl/py/fable_modules/fable_library/long.py +240 -0
- arctrl/py/fable_modules/fable_library/mailbox_processor.py +179 -0
- arctrl/py/fable_modules/fable_library/map.py +1854 -0
- arctrl/py/fable_modules/fable_library/map_util.py +148 -0
- arctrl/py/fable_modules/fable_library/mutable_map.py +397 -0
- arctrl/py/fable_modules/fable_library/mutable_set.py +279 -0
- arctrl/py/fable_modules/fable_library/native.py +45 -0
- arctrl/py/fable_modules/fable_library/numeric.py +46 -0
- arctrl/py/fable_modules/fable_library/observable.py +222 -0
- arctrl/py/fable_modules/fable_library/option.py +128 -0
- arctrl/py/fable_modules/fable_library/path.py +62 -0
- arctrl/py/fable_modules/fable_library/range.py +117 -0
- arctrl/py/fable_modules/fable_library/reflection.py +463 -0
- arctrl/py/fable_modules/fable_library/reg_exp.py +137 -0
- arctrl/py/fable_modules/fable_library/resize_array.py +31 -0
- arctrl/py/fable_modules/fable_library/result.py +212 -0
- arctrl/py/fable_modules/fable_library/seq.py +1979 -0
- arctrl/py/fable_modules/fable_library/seq2.py +221 -0
- arctrl/py/fable_modules/fable_library/set.py +2414 -0
- arctrl/py/fable_modules/fable_library/singleton_local_time_zone.py +36 -0
- arctrl/py/fable_modules/fable_library/string_.py +573 -0
- arctrl/py/fable_modules/fable_library/system_collections_generic.py +462 -0
- arctrl/py/fable_modules/fable_library/system_text.py +237 -0
- arctrl/py/fable_modules/fable_library/task.py +116 -0
- arctrl/py/fable_modules/fable_library/task_builder.py +122 -0
- arctrl/py/fable_modules/fable_library/thread.py +5 -0
- arctrl/py/fable_modules/fable_library/time_span.py +283 -0
- arctrl/py/fable_modules/fable_library/timer.py +24 -0
- arctrl/py/fable_modules/fable_library/types.py +401 -0
- arctrl/py/fable_modules/fable_library/uri.py +109 -0
- arctrl/py/fable_modules/fable_library/util.py +2735 -0
- arctrl/py/fable_modules/fable_openpyxl/__init__.py +0 -0
- arctrl/py/fable_modules/fable_openpyxl/openpyxl.py +362 -0
- arctrl/py/fable_modules/fable_python/cognite-sdk/__init__.py +0 -0
- arctrl/py/fable_modules/fable_python/cognite-sdk/cognite_sdk.py +22 -0
- arctrl/py/fable_modules/fable_python/flask/__init__.py +0 -0
- arctrl/py/fable_modules/fable_python/flask/flask.py +34 -0
- arctrl/py/fable_modules/fable_python/jupyter/__init__.py +0 -0
- arctrl/py/fable_modules/fable_python/jupyter/ipy_widgets.py +47 -0
- arctrl/py/fable_modules/fable_python/jupyter/ipython.py +13 -0
- arctrl/py/fable_modules/fable_python/stdlib/__init__.py +0 -0
- arctrl/py/fable_modules/fable_python/stdlib/ast.py +1 -0
- arctrl/py/fable_modules/fable_python/stdlib/asyncio/__init__.py +0 -0
- arctrl/py/fable_modules/fable_python/stdlib/asyncio/events.py +17 -0
- arctrl/py/fable_modules/fable_python/stdlib/asyncio/futures.py +52 -0
- arctrl/py/fable_modules/fable_python/stdlib/asyncio/tasks.py +38 -0
- arctrl/py/fable_modules/fable_python/stdlib/base64_.py +1 -0
- arctrl/py/fable_modules/fable_python/stdlib/builtins_.py +38 -0
- arctrl/py/fable_modules/fable_python/stdlib/html.py +1 -0
- arctrl/py/fable_modules/fable_python/stdlib/json.py +1 -0
- arctrl/py/fable_modules/fable_python/stdlib/math_.py +1 -0
- arctrl/py/fable_modules/fable_python/stdlib/os_.py +1 -0
- arctrl/py/fable_modules/fable_python/stdlib/queue_.py +1 -0
- arctrl/py/fable_modules/fable_python/stdlib/string_.py +1 -0
- arctrl/py/fable_modules/fable_python/stdlib/sys_.py +30 -0
- arctrl/py/fable_modules/fable_python/stdlib/time_.py +1 -0
- arctrl/py/fable_modules/fable_python/stdlib/tk_inter.py +1 -0
- arctrl/py/fable_modules/fs_spreadsheet/Cells/__init__.py +0 -0
- arctrl/py/fable_modules/fs_spreadsheet/Cells/fs_cell.py +338 -0
- arctrl/py/fable_modules/fs_spreadsheet/Cells/fs_cells_collection.py +469 -0
- arctrl/py/fable_modules/fs_spreadsheet/DSL/__init__.py +0 -0
- arctrl/py/fable_modules/fs_spreadsheet/DSL/cell_builder.py +214 -0
- arctrl/py/fable_modules/fs_spreadsheet/DSL/column_builder.py +139 -0
- arctrl/py/fable_modules/fs_spreadsheet/DSL/dsl.py +50 -0
- arctrl/py/fable_modules/fs_spreadsheet/DSL/expression.py +65 -0
- arctrl/py/fable_modules/fs_spreadsheet/DSL/operators.py +9 -0
- arctrl/py/fable_modules/fs_spreadsheet/DSL/row_builder.py +139 -0
- arctrl/py/fable_modules/fs_spreadsheet/DSL/sheet_builder.py +118 -0
- arctrl/py/fable_modules/fs_spreadsheet/DSL/table_builder.py +122 -0
- arctrl/py/fable_modules/fs_spreadsheet/DSL/transform.py +464 -0
- arctrl/py/fable_modules/fs_spreadsheet/DSL/types.py +314 -0
- arctrl/py/fable_modules/fs_spreadsheet/DSL/workbook_builder.py +106 -0
- arctrl/py/fable_modules/fs_spreadsheet/Json/__init__.py +0 -0
- arctrl/py/fable_modules/fs_spreadsheet/Json/cell.py +103 -0
- arctrl/py/fable_modules/fs_spreadsheet/Json/column.py +70 -0
- arctrl/py/fable_modules/fs_spreadsheet/Json/row.py +70 -0
- arctrl/py/fable_modules/fs_spreadsheet/Json/table.py +57 -0
- arctrl/py/fable_modules/fs_spreadsheet/Json/value.py +93 -0
- arctrl/py/fable_modules/fs_spreadsheet/Json/workbook.py +71 -0
- arctrl/py/fable_modules/fs_spreadsheet/Json/worksheet.py +217 -0
- arctrl/py/fable_modules/fs_spreadsheet/Ranges/__init__.py +0 -0
- arctrl/py/fable_modules/fs_spreadsheet/Ranges/fs_range.py +47 -0
- arctrl/py/fable_modules/fs_spreadsheet/Ranges/fs_range_address.py +186 -0
- arctrl/py/fable_modules/fs_spreadsheet/Ranges/fs_range_base.py +90 -0
- arctrl/py/fable_modules/fs_spreadsheet/Ranges/fs_range_column.py +78 -0
- arctrl/py/fable_modules/fs_spreadsheet/Ranges/fs_range_row.py +48 -0
- arctrl/py/fable_modules/fs_spreadsheet/Tables/__init__.py +0 -0
- arctrl/py/fable_modules/fs_spreadsheet/Tables/fs_table.py +393 -0
- arctrl/py/fable_modules/fs_spreadsheet/Tables/fs_table_field.py +127 -0
- arctrl/py/fable_modules/fs_spreadsheet/Tables/fs_table_row.py +23 -0
- arctrl/py/fable_modules/fs_spreadsheet/__init__.py +0 -0
- arctrl/py/fable_modules/fs_spreadsheet/fs_address.py +218 -0
- arctrl/py/fable_modules/fs_spreadsheet/fs_column.py +172 -0
- arctrl/py/fable_modules/fs_spreadsheet/fs_row.py +183 -0
- arctrl/py/fable_modules/fs_spreadsheet/fs_workbook.py +180 -0
- arctrl/py/fable_modules/fs_spreadsheet/fs_worksheet.py +600 -0
- arctrl/py/fable_modules/fs_spreadsheet/sheet_builder.py +330 -0
- arctrl/py/fable_modules/fs_spreadsheet_py/__init__.py +0 -0
- arctrl/py/fable_modules/fs_spreadsheet_py/cell.py +63 -0
- arctrl/py/fable_modules/fs_spreadsheet_py/cell_type.py +50 -0
- arctrl/py/fable_modules/fs_spreadsheet_py/fs_extension.py +60 -0
- arctrl/py/fable_modules/fs_spreadsheet_py/json.py +47 -0
- arctrl/py/fable_modules/fs_spreadsheet_py/table.py +53 -0
- arctrl/py/fable_modules/fs_spreadsheet_py/workbook.py +40 -0
- arctrl/py/fable_modules/fs_spreadsheet_py/worksheet.py +54 -0
- arctrl/py/fable_modules/fs_spreadsheet_py/xlsx.py +37 -0
- arctrl/py/fable_modules/thoth_json_core/__init__.py +0 -0
- arctrl/py/fable_modules/thoth_json_core/decode.py +1588 -0
- arctrl/py/fable_modules/thoth_json_core/encode.py +261 -0
- arctrl/py/fable_modules/thoth_json_core/types.py +181 -0
- arctrl/py/fable_modules/thoth_json_python/__init__.py +0 -0
- arctrl/py/fable_modules/thoth_json_python/decode.py +112 -0
- arctrl/py/fable_modules/thoth_json_python/encode.py +72 -0
- arctrl/py/fable_modules/thoth_json_python/python.py +1 -0
- arctrl/py/fable_modules/yamlicious/Interop/__init__.py +0 -0
- arctrl/py/fable_modules/yamlicious/Interop/js_interop.py +1 -0
- arctrl/py/fable_modules/yamlicious/Interop/py_interop.py +7 -0
- arctrl/py/fable_modules/yamlicious/__init__.py +0 -0
- arctrl/py/fable_modules/yamlicious/decode.py +1784 -0
- arctrl/py/fable_modules/yamlicious/encode.py +84 -0
- arctrl/py/fable_modules/yamlicious/library.py +10 -0
- arctrl/py/fable_modules/yamlicious/persil.py +57 -0
- arctrl/py/fable_modules/yamlicious/preprocessing.py +99 -0
- arctrl/py/fable_modules/yamlicious/reader.py +665 -0
- arctrl/py/fable_modules/yamlicious/regex.py +21 -0
- arctrl/py/fable_modules/yamlicious/regex_active_patterns.py +256 -0
- arctrl/py/fable_modules/yamlicious/writer.py +175 -0
- arctrl/py/fable_modules/yamlicious/yamlicious_types.py +128 -0
- arctrl/py/json.py +213 -0
- arctrl/py/rocrate_io.py +72 -0
- arctrl/py/template_web.py +23 -0
- arctrl/py/xlsx.py +148 -0
- arctrl/rocrate.py +21 -0
- arctrl-3.0.0a3.dist-info/LICENSE +21 -0
- arctrl-3.0.0a3.dist-info/METADATA +119 -0
- arctrl-3.0.0a3.dist-info/RECORD +456 -0
- arctrl-3.0.0a3.dist-info/WHEEL +4 -0
arctrl/py/CWL/encode.py
ADDED
|
@@ -0,0 +1 @@
|
|
|
1
|
+
|
arctrl/py/CWL/inputs.py
ADDED
|
@@ -0,0 +1,88 @@
|
|
|
1
|
+
from __future__ import annotations
|
|
2
|
+
from dataclasses import dataclass
|
|
3
|
+
from typing import Any
|
|
4
|
+
from ..fable_modules.dynamic_obj.dynamic_obj import (DynamicObj, DynamicObj_reflection)
|
|
5
|
+
from ..fable_modules.dynamic_obj.dyn_obj import set_optional_property
|
|
6
|
+
from ..fable_modules.fable_library.option import value
|
|
7
|
+
from ..fable_modules.fable_library.reflection import (TypeInfo, string_type, option_type, int32_type, bool_type, record_type, class_type)
|
|
8
|
+
from ..fable_modules.fable_library.types import (Record, FSharpRef)
|
|
9
|
+
from .cwltypes import CWLType
|
|
10
|
+
|
|
11
|
+
def _expr3159() -> TypeInfo:
|
|
12
|
+
return record_type("ARCtrl.CWL.InputBinding", [], InputBinding, lambda: [("Prefix", option_type(string_type)), ("Position", option_type(int32_type)), ("ItemSeparator", option_type(string_type)), ("Separate", option_type(bool_type))])
|
|
13
|
+
|
|
14
|
+
|
|
15
|
+
@dataclass(eq = False, repr = False, slots = True)
|
|
16
|
+
class InputBinding(Record):
|
|
17
|
+
Prefix: str | None
|
|
18
|
+
Position: int | None
|
|
19
|
+
ItemSeparator: str | None
|
|
20
|
+
Separate: bool | None
|
|
21
|
+
|
|
22
|
+
InputBinding_reflection = _expr3159
|
|
23
|
+
|
|
24
|
+
def _expr3160() -> TypeInfo:
|
|
25
|
+
return class_type("ARCtrl.CWL.CWLInput", None, CWLInput, DynamicObj_reflection())
|
|
26
|
+
|
|
27
|
+
|
|
28
|
+
class CWLInput(DynamicObj):
|
|
29
|
+
def __init__(self, name: str, type_: CWLType | None=None, input_binding: InputBinding | None=None, optional: bool | None=None) -> None:
|
|
30
|
+
super().__init__()
|
|
31
|
+
this: FSharpRef[CWLInput] = FSharpRef(None)
|
|
32
|
+
self.name: str = name
|
|
33
|
+
this.contents = self
|
|
34
|
+
self.init_004014: int = 1
|
|
35
|
+
set_optional_property("type", type_, this.contents)
|
|
36
|
+
set_optional_property("inputBinding", input_binding, this.contents)
|
|
37
|
+
set_optional_property("optional", optional, this.contents)
|
|
38
|
+
|
|
39
|
+
@property
|
|
40
|
+
def Name(self, __unit: None=None) -> str:
|
|
41
|
+
this: CWLInput = self
|
|
42
|
+
return this.name
|
|
43
|
+
|
|
44
|
+
@property
|
|
45
|
+
def Type_(self, __unit: None=None) -> CWLType | None:
|
|
46
|
+
this: CWLInput = self
|
|
47
|
+
match_value: Any | None = this.TryGetPropertyValue("type")
|
|
48
|
+
if match_value is not None:
|
|
49
|
+
o: Any = value(match_value)
|
|
50
|
+
return o if isinstance(o, CWLType) else None
|
|
51
|
+
|
|
52
|
+
else:
|
|
53
|
+
return None
|
|
54
|
+
|
|
55
|
+
|
|
56
|
+
@property
|
|
57
|
+
def InputBinding(self, __unit: None=None) -> InputBinding | None:
|
|
58
|
+
this: CWLInput = self
|
|
59
|
+
match_value: Any | None = this.TryGetPropertyValue("inputBinding")
|
|
60
|
+
if match_value is not None:
|
|
61
|
+
o: Any = value(match_value)
|
|
62
|
+
return o if isinstance(o, InputBinding) else None
|
|
63
|
+
|
|
64
|
+
else:
|
|
65
|
+
return None
|
|
66
|
+
|
|
67
|
+
|
|
68
|
+
@property
|
|
69
|
+
def Optional(self, __unit: None=None) -> bool | None:
|
|
70
|
+
this: CWLInput = self
|
|
71
|
+
match_value: Any | None = this.TryGetPropertyValue("optional")
|
|
72
|
+
if match_value is not None:
|
|
73
|
+
o: Any = value(match_value)
|
|
74
|
+
return o if (str(type(o)) == "<class \'bool\'>") else None
|
|
75
|
+
|
|
76
|
+
else:
|
|
77
|
+
return None
|
|
78
|
+
|
|
79
|
+
|
|
80
|
+
|
|
81
|
+
CWLInput_reflection = _expr3160
|
|
82
|
+
|
|
83
|
+
def CWLInput__ctor_Z3A15BEDB(name: str, type_: CWLType | None=None, input_binding: InputBinding | None=None, optional: bool | None=None) -> CWLInput:
|
|
84
|
+
return CWLInput(name, type_, input_binding, optional)
|
|
85
|
+
|
|
86
|
+
|
|
87
|
+
__all__ = ["InputBinding_reflection", "CWLInput_reflection"]
|
|
88
|
+
|
arctrl/py/CWL/outputs.py
ADDED
|
@@ -0,0 +1,85 @@
|
|
|
1
|
+
from __future__ import annotations
|
|
2
|
+
from dataclasses import dataclass
|
|
3
|
+
from typing import Any
|
|
4
|
+
from ..fable_modules.dynamic_obj.dynamic_obj import (DynamicObj, DynamicObj_reflection)
|
|
5
|
+
from ..fable_modules.dynamic_obj.dyn_obj import set_optional_property
|
|
6
|
+
from ..fable_modules.fable_library.option import value
|
|
7
|
+
from ..fable_modules.fable_library.reflection import (TypeInfo, string_type, option_type, record_type, class_type)
|
|
8
|
+
from ..fable_modules.fable_library.types import (Record, FSharpRef)
|
|
9
|
+
from .cwltypes import CWLType
|
|
10
|
+
|
|
11
|
+
def _expr3157() -> TypeInfo:
|
|
12
|
+
return record_type("ARCtrl.CWL.OutputBinding", [], OutputBinding, lambda: [("Glob", option_type(string_type))])
|
|
13
|
+
|
|
14
|
+
|
|
15
|
+
@dataclass(eq = False, repr = False, slots = True)
|
|
16
|
+
class OutputBinding(Record):
|
|
17
|
+
Glob: str | None
|
|
18
|
+
|
|
19
|
+
OutputBinding_reflection = _expr3157
|
|
20
|
+
|
|
21
|
+
def _expr3158() -> TypeInfo:
|
|
22
|
+
return class_type("ARCtrl.CWL.CWLOutput", None, CWLOutput, DynamicObj_reflection())
|
|
23
|
+
|
|
24
|
+
|
|
25
|
+
class CWLOutput(DynamicObj):
|
|
26
|
+
def __init__(self, name: str, type_: CWLType | None=None, output_binding: OutputBinding | None=None, output_source: str | None=None) -> None:
|
|
27
|
+
super().__init__()
|
|
28
|
+
this: FSharpRef[CWLOutput] = FSharpRef(None)
|
|
29
|
+
self.name: str = name
|
|
30
|
+
this.contents = self
|
|
31
|
+
self.init_004011: int = 1
|
|
32
|
+
set_optional_property("type", type_, this.contents)
|
|
33
|
+
set_optional_property("outputBinding", output_binding, this.contents)
|
|
34
|
+
set_optional_property("outputSource", output_source, this.contents)
|
|
35
|
+
|
|
36
|
+
@property
|
|
37
|
+
def Name(self, __unit: None=None) -> str:
|
|
38
|
+
this: CWLOutput = self
|
|
39
|
+
return this.name
|
|
40
|
+
|
|
41
|
+
@property
|
|
42
|
+
def Type_(self, __unit: None=None) -> CWLType | None:
|
|
43
|
+
this: CWLOutput = self
|
|
44
|
+
match_value: Any | None = this.TryGetPropertyValue("type")
|
|
45
|
+
if match_value is not None:
|
|
46
|
+
o: Any = value(match_value)
|
|
47
|
+
return o if isinstance(o, CWLType) else None
|
|
48
|
+
|
|
49
|
+
else:
|
|
50
|
+
return None
|
|
51
|
+
|
|
52
|
+
|
|
53
|
+
@property
|
|
54
|
+
def OutputBinding(self, __unit: None=None) -> OutputBinding | None:
|
|
55
|
+
this: CWLOutput = self
|
|
56
|
+
match_value: Any | None = this.TryGetPropertyValue("outputBinding")
|
|
57
|
+
if match_value is not None:
|
|
58
|
+
o: Any = value(match_value)
|
|
59
|
+
return o if isinstance(o, OutputBinding) else None
|
|
60
|
+
|
|
61
|
+
else:
|
|
62
|
+
return None
|
|
63
|
+
|
|
64
|
+
|
|
65
|
+
@property
|
|
66
|
+
def OutputSource(self, __unit: None=None) -> str | None:
|
|
67
|
+
this: CWLOutput = self
|
|
68
|
+
match_value: Any | None = this.TryGetPropertyValue("outputSource")
|
|
69
|
+
if match_value is not None:
|
|
70
|
+
o: Any = value(match_value)
|
|
71
|
+
return o if (str(type(o)) == "<class \'str\'>") else None
|
|
72
|
+
|
|
73
|
+
else:
|
|
74
|
+
return None
|
|
75
|
+
|
|
76
|
+
|
|
77
|
+
|
|
78
|
+
CWLOutput_reflection = _expr3158
|
|
79
|
+
|
|
80
|
+
def CWLOutput__ctor_744035D(name: str, type_: CWLType | None=None, output_binding: OutputBinding | None=None, output_source: str | None=None) -> CWLOutput:
|
|
81
|
+
return CWLOutput(name, type_, output_binding, output_source)
|
|
82
|
+
|
|
83
|
+
|
|
84
|
+
__all__ = ["OutputBinding_reflection", "CWLOutput_reflection"]
|
|
85
|
+
|
|
@@ -0,0 +1,77 @@
|
|
|
1
|
+
from __future__ import annotations
|
|
2
|
+
from dataclasses import dataclass
|
|
3
|
+
from typing import Any
|
|
4
|
+
from ..fable_modules.dynamic_obj.dynamic_obj import (DynamicObj, DynamicObj_reflection)
|
|
5
|
+
from ..fable_modules.dynamic_obj.dyn_obj import set_optional_property
|
|
6
|
+
from ..fable_modules.fable_library.reflection import (TypeInfo, string_type, option_type, class_type, record_type, array_type, float64_type, union_type)
|
|
7
|
+
from ..fable_modules.fable_library.types import (Record, FSharpRef, Array, Union)
|
|
8
|
+
from .cwltypes import (SchemaDefRequirementType_reflection, SoftwarePackage_reflection, CWLType_reflection)
|
|
9
|
+
|
|
10
|
+
def _expr3142() -> TypeInfo:
|
|
11
|
+
return record_type("ARCtrl.CWL.DockerRequirement", [], DockerRequirement, lambda: [("DockerPull", option_type(string_type)), ("DockerFile", option_type(class_type("Microsoft.FSharp.Collections.FSharpMap`2", [string_type, string_type]))), ("DockerImageId", option_type(string_type))])
|
|
12
|
+
|
|
13
|
+
|
|
14
|
+
@dataclass(eq = False, repr = False, slots = True)
|
|
15
|
+
class DockerRequirement(Record):
|
|
16
|
+
DockerPull: str | None
|
|
17
|
+
DockerFile: Any | None
|
|
18
|
+
DockerImageId: str | None
|
|
19
|
+
|
|
20
|
+
DockerRequirement_reflection = _expr3142
|
|
21
|
+
|
|
22
|
+
def _expr3143() -> TypeInfo:
|
|
23
|
+
return record_type("ARCtrl.CWL.EnvironmentDef", [], EnvironmentDef, lambda: [("EnvName", string_type), ("EnvValue", string_type)])
|
|
24
|
+
|
|
25
|
+
|
|
26
|
+
@dataclass(eq = False, repr = False, slots = True)
|
|
27
|
+
class EnvironmentDef(Record):
|
|
28
|
+
EnvName: str
|
|
29
|
+
EnvValue: str
|
|
30
|
+
|
|
31
|
+
EnvironmentDef_reflection = _expr3143
|
|
32
|
+
|
|
33
|
+
def _expr3147() -> TypeInfo:
|
|
34
|
+
return class_type("ARCtrl.CWL.ResourceRequirementInstance", None, ResourceRequirementInstance, DynamicObj_reflection())
|
|
35
|
+
|
|
36
|
+
|
|
37
|
+
class ResourceRequirementInstance(DynamicObj):
|
|
38
|
+
def __init__(self, cores_min: Any | None=None, cores_max: Any | None=None, ram_min: Any | None=None, ram_max: Any | None=None, tmpdir_min: Any | None=None, tmpdir_max: Any | None=None, outdir_min: Any | None=None, outdir_max: Any | None=None) -> None:
|
|
39
|
+
super().__init__()
|
|
40
|
+
this: FSharpRef[ResourceRequirementInstance] = FSharpRef(None)
|
|
41
|
+
this.contents = self
|
|
42
|
+
self.init_004024: int = 1
|
|
43
|
+
set_optional_property("coresMin", cores_min, this.contents)
|
|
44
|
+
set_optional_property("coresMax", cores_max, this.contents)
|
|
45
|
+
set_optional_property("ramMin", ram_min, this.contents)
|
|
46
|
+
set_optional_property("ramMax", ram_max, this.contents)
|
|
47
|
+
set_optional_property("tmpdirMin", tmpdir_min, this.contents)
|
|
48
|
+
set_optional_property("tmpdirMax", tmpdir_max, this.contents)
|
|
49
|
+
set_optional_property("outdirMin", outdir_min, this.contents)
|
|
50
|
+
set_optional_property("outdirMax", outdir_max, this.contents)
|
|
51
|
+
|
|
52
|
+
|
|
53
|
+
ResourceRequirementInstance_reflection = _expr3147
|
|
54
|
+
|
|
55
|
+
def ResourceRequirementInstance__ctor_D76FC00(cores_min: Any | None=None, cores_max: Any | None=None, ram_min: Any | None=None, ram_max: Any | None=None, tmpdir_min: Any | None=None, tmpdir_max: Any | None=None, outdir_min: Any | None=None, outdir_max: Any | None=None) -> ResourceRequirementInstance:
|
|
56
|
+
return ResourceRequirementInstance(cores_min, cores_max, ram_min, ram_max, tmpdir_min, tmpdir_max, outdir_min, outdir_max)
|
|
57
|
+
|
|
58
|
+
|
|
59
|
+
def _expr3148() -> TypeInfo:
|
|
60
|
+
return union_type("ARCtrl.CWL.Requirement", [], Requirement, lambda: [[], [("Item", array_type(SchemaDefRequirementType_reflection()))], [("Item", DockerRequirement_reflection())], [("Item", array_type(SoftwarePackage_reflection()))], [("Item", array_type(CWLType_reflection()))], [("Item", array_type(EnvironmentDef_reflection()))], [], [("Item", ResourceRequirementInstance_reflection())], [], [], [], [("Item", float64_type)], [], [], [], []])
|
|
61
|
+
|
|
62
|
+
|
|
63
|
+
class Requirement(Union):
|
|
64
|
+
def __init__(self, tag: int, *fields: Any) -> None:
|
|
65
|
+
super().__init__()
|
|
66
|
+
self.tag: int = tag or 0
|
|
67
|
+
self.fields: Array[Any] = list(fields)
|
|
68
|
+
|
|
69
|
+
@staticmethod
|
|
70
|
+
def cases() -> list[str]:
|
|
71
|
+
return ["InlineJavascriptRequirement", "SchemaDefRequirement", "DockerRequirement", "SoftwareRequirement", "InitialWorkDirRequirement", "EnvVarRequirement", "ShellCommandRequirement", "ResourceRequirement", "WorkReuseRequirement", "NetworkAccessRequirement", "InplaceUpdateRequirement", "ToolTimeLimitRequirement", "SubworkflowFeatureRequirement", "ScatterFeatureRequirement", "MultipleInputFeatureRequirement", "StepInputExpressionRequirement"]
|
|
72
|
+
|
|
73
|
+
|
|
74
|
+
Requirement_reflection = _expr3148
|
|
75
|
+
|
|
76
|
+
__all__ = ["DockerRequirement_reflection", "EnvironmentDef_reflection", "ResourceRequirementInstance_reflection", "Requirement_reflection"]
|
|
77
|
+
|
|
@@ -0,0 +1,103 @@
|
|
|
1
|
+
from __future__ import annotations
|
|
2
|
+
from ..fable_modules.dynamic_obj.dynamic_obj import (DynamicObj, DynamicObj_reflection)
|
|
3
|
+
from ..fable_modules.fable_library.option import default_arg
|
|
4
|
+
from ..fable_modules.fable_library.reflection import (TypeInfo, class_type)
|
|
5
|
+
from ..fable_modules.fable_library.types import Array
|
|
6
|
+
from .inputs import CWLInput
|
|
7
|
+
from .outputs import CWLOutput
|
|
8
|
+
from .requirements import Requirement
|
|
9
|
+
|
|
10
|
+
def _expr3164() -> TypeInfo:
|
|
11
|
+
return class_type("ARCtrl.CWL.CWLToolDescription", None, CWLToolDescription, DynamicObj_reflection())
|
|
12
|
+
|
|
13
|
+
|
|
14
|
+
class CWLToolDescription(DynamicObj):
|
|
15
|
+
def __init__(self, outputs: Array[CWLOutput], cwl_version: str | None=None, base_command: Array[str] | None=None, requirements: Array[Requirement] | None=None, hints: Array[Requirement] | None=None, inputs: Array[CWLInput] | None=None, metadata: DynamicObj | None=None) -> None:
|
|
16
|
+
super().__init__()
|
|
17
|
+
self._cwlVersion: str = default_arg(cwl_version, "v1.2")
|
|
18
|
+
self._outputs: Array[CWLOutput] = outputs
|
|
19
|
+
self._baseCommand: Array[str] | None = base_command
|
|
20
|
+
self._requirements: Array[Requirement] | None = requirements
|
|
21
|
+
self._hints: Array[Requirement] | None = hints
|
|
22
|
+
self._inputs: Array[CWLInput] | None = inputs
|
|
23
|
+
self._metadata: DynamicObj | None = metadata
|
|
24
|
+
|
|
25
|
+
@property
|
|
26
|
+
def CWLVersion(self, __unit: None=None) -> str:
|
|
27
|
+
this: CWLToolDescription = self
|
|
28
|
+
return this._cwlVersion
|
|
29
|
+
|
|
30
|
+
@CWLVersion.setter
|
|
31
|
+
def CWLVersion(self, version: str) -> None:
|
|
32
|
+
this: CWLToolDescription = self
|
|
33
|
+
this._cwlVersion = version
|
|
34
|
+
|
|
35
|
+
@property
|
|
36
|
+
def Outputs(self, __unit: None=None) -> Array[CWLOutput]:
|
|
37
|
+
this: CWLToolDescription = self
|
|
38
|
+
return this._outputs
|
|
39
|
+
|
|
40
|
+
@Outputs.setter
|
|
41
|
+
def Outputs(self, outputs: Array[CWLOutput]) -> None:
|
|
42
|
+
this: CWLToolDescription = self
|
|
43
|
+
this._outputs = outputs
|
|
44
|
+
|
|
45
|
+
@property
|
|
46
|
+
def BaseCommand(self, __unit: None=None) -> Array[str] | None:
|
|
47
|
+
this: CWLToolDescription = self
|
|
48
|
+
return this._baseCommand
|
|
49
|
+
|
|
50
|
+
@BaseCommand.setter
|
|
51
|
+
def BaseCommand(self, base_command: Array[str] | None=None) -> None:
|
|
52
|
+
this: CWLToolDescription = self
|
|
53
|
+
this._baseCommand = base_command
|
|
54
|
+
|
|
55
|
+
@property
|
|
56
|
+
def Requirements(self, __unit: None=None) -> Array[Requirement] | None:
|
|
57
|
+
this: CWLToolDescription = self
|
|
58
|
+
return this._requirements
|
|
59
|
+
|
|
60
|
+
@Requirements.setter
|
|
61
|
+
def Requirements(self, requirements: Array[Requirement] | None=None) -> None:
|
|
62
|
+
this: CWLToolDescription = self
|
|
63
|
+
this._requirements = requirements
|
|
64
|
+
|
|
65
|
+
@property
|
|
66
|
+
def Hints(self, __unit: None=None) -> Array[Requirement] | None:
|
|
67
|
+
this: CWLToolDescription = self
|
|
68
|
+
return this._hints
|
|
69
|
+
|
|
70
|
+
@Hints.setter
|
|
71
|
+
def Hints(self, hints: Array[Requirement] | None=None) -> None:
|
|
72
|
+
this: CWLToolDescription = self
|
|
73
|
+
this._hints = hints
|
|
74
|
+
|
|
75
|
+
@property
|
|
76
|
+
def Inputs(self, __unit: None=None) -> Array[CWLInput] | None:
|
|
77
|
+
this: CWLToolDescription = self
|
|
78
|
+
return this._inputs
|
|
79
|
+
|
|
80
|
+
@Inputs.setter
|
|
81
|
+
def Inputs(self, inputs: Array[CWLInput] | None=None) -> None:
|
|
82
|
+
this: CWLToolDescription = self
|
|
83
|
+
this._inputs = inputs
|
|
84
|
+
|
|
85
|
+
@property
|
|
86
|
+
def Metadata(self, __unit: None=None) -> DynamicObj | None:
|
|
87
|
+
this: CWLToolDescription = self
|
|
88
|
+
return this._metadata
|
|
89
|
+
|
|
90
|
+
@Metadata.setter
|
|
91
|
+
def Metadata(self, metadata: DynamicObj | None=None) -> None:
|
|
92
|
+
this: CWLToolDescription = self
|
|
93
|
+
this._metadata = metadata
|
|
94
|
+
|
|
95
|
+
|
|
96
|
+
CWLToolDescription_reflection = _expr3164
|
|
97
|
+
|
|
98
|
+
def CWLToolDescription__ctor_Z3224DB85(outputs: Array[CWLOutput], cwl_version: str | None=None, base_command: Array[str] | None=None, requirements: Array[Requirement] | None=None, hints: Array[Requirement] | None=None, inputs: Array[CWLInput] | None=None, metadata: DynamicObj | None=None) -> CWLToolDescription:
|
|
99
|
+
return CWLToolDescription(outputs, cwl_version, base_command, requirements, hints, inputs, metadata)
|
|
100
|
+
|
|
101
|
+
|
|
102
|
+
__all__ = ["CWLToolDescription_reflection"]
|
|
103
|
+
|
|
@@ -0,0 +1,104 @@
|
|
|
1
|
+
from __future__ import annotations
|
|
2
|
+
from ..fable_modules.dynamic_obj.dynamic_obj import (DynamicObj, DynamicObj_reflection)
|
|
3
|
+
from ..fable_modules.fable_library.option import default_arg
|
|
4
|
+
from ..fable_modules.fable_library.reflection import (TypeInfo, class_type)
|
|
5
|
+
from ..fable_modules.fable_library.types import Array
|
|
6
|
+
from .inputs import CWLInput
|
|
7
|
+
from .outputs import CWLOutput
|
|
8
|
+
from .requirements import Requirement
|
|
9
|
+
from .workflow_steps import WorkflowStep
|
|
10
|
+
|
|
11
|
+
def _expr3169() -> TypeInfo:
|
|
12
|
+
return class_type("ARCtrl.CWL.CWLWorkflowDescription", None, CWLWorkflowDescription, DynamicObj_reflection())
|
|
13
|
+
|
|
14
|
+
|
|
15
|
+
class CWLWorkflowDescription(DynamicObj):
|
|
16
|
+
def __init__(self, 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) -> None:
|
|
17
|
+
super().__init__()
|
|
18
|
+
self._cwlVersion: str = default_arg(cwl_version, "v1.2")
|
|
19
|
+
self._steps: Array[WorkflowStep] = steps
|
|
20
|
+
self._inputs: Array[CWLInput] = inputs
|
|
21
|
+
self._outputs: Array[CWLOutput] = outputs
|
|
22
|
+
self._requirements: Array[Requirement] | None = requirements
|
|
23
|
+
self._hints: Array[Requirement] | None = hints
|
|
24
|
+
self._metadata: DynamicObj | None = metadata
|
|
25
|
+
|
|
26
|
+
@property
|
|
27
|
+
def CWLVersion(self, __unit: None=None) -> str:
|
|
28
|
+
this: CWLWorkflowDescription = self
|
|
29
|
+
return this._cwlVersion
|
|
30
|
+
|
|
31
|
+
@CWLVersion.setter
|
|
32
|
+
def CWLVersion(self, version: str) -> None:
|
|
33
|
+
this: CWLWorkflowDescription = self
|
|
34
|
+
this._cwlVersion = version
|
|
35
|
+
|
|
36
|
+
@property
|
|
37
|
+
def Steps(self, __unit: None=None) -> Array[WorkflowStep]:
|
|
38
|
+
this: CWLWorkflowDescription = self
|
|
39
|
+
return this._steps
|
|
40
|
+
|
|
41
|
+
@Steps.setter
|
|
42
|
+
def Steps(self, steps: Array[WorkflowStep]) -> None:
|
|
43
|
+
this: CWLWorkflowDescription = self
|
|
44
|
+
this._steps = steps
|
|
45
|
+
|
|
46
|
+
@property
|
|
47
|
+
def Inputs(self, __unit: None=None) -> Array[CWLInput]:
|
|
48
|
+
this: CWLWorkflowDescription = self
|
|
49
|
+
return this._inputs
|
|
50
|
+
|
|
51
|
+
@Inputs.setter
|
|
52
|
+
def Inputs(self, inputs: Array[CWLInput]) -> None:
|
|
53
|
+
this: CWLWorkflowDescription = self
|
|
54
|
+
this._inputs = inputs
|
|
55
|
+
|
|
56
|
+
@property
|
|
57
|
+
def Outputs(self, __unit: None=None) -> Array[CWLOutput]:
|
|
58
|
+
this: CWLWorkflowDescription = self
|
|
59
|
+
return this._outputs
|
|
60
|
+
|
|
61
|
+
@Outputs.setter
|
|
62
|
+
def Outputs(self, outputs: Array[CWLOutput]) -> None:
|
|
63
|
+
this: CWLWorkflowDescription = self
|
|
64
|
+
this._outputs = outputs
|
|
65
|
+
|
|
66
|
+
@property
|
|
67
|
+
def Requirements(self, __unit: None=None) -> Array[Requirement] | None:
|
|
68
|
+
this: CWLWorkflowDescription = self
|
|
69
|
+
return this._requirements
|
|
70
|
+
|
|
71
|
+
@Requirements.setter
|
|
72
|
+
def Requirements(self, requirements: Array[Requirement] | None=None) -> None:
|
|
73
|
+
this: CWLWorkflowDescription = self
|
|
74
|
+
this._requirements = requirements
|
|
75
|
+
|
|
76
|
+
@property
|
|
77
|
+
def Hints(self, __unit: None=None) -> Array[Requirement] | None:
|
|
78
|
+
this: CWLWorkflowDescription = self
|
|
79
|
+
return this._hints
|
|
80
|
+
|
|
81
|
+
@Hints.setter
|
|
82
|
+
def Hints(self, hints: Array[Requirement] | None=None) -> None:
|
|
83
|
+
this: CWLWorkflowDescription = self
|
|
84
|
+
this._hints = hints
|
|
85
|
+
|
|
86
|
+
@property
|
|
87
|
+
def Metadata(self, __unit: None=None) -> DynamicObj | None:
|
|
88
|
+
this: CWLWorkflowDescription = self
|
|
89
|
+
return this._metadata
|
|
90
|
+
|
|
91
|
+
@Metadata.setter
|
|
92
|
+
def Metadata(self, metadata: DynamicObj | None=None) -> None:
|
|
93
|
+
this: CWLWorkflowDescription = self
|
|
94
|
+
this._metadata = metadata
|
|
95
|
+
|
|
96
|
+
|
|
97
|
+
CWLWorkflowDescription_reflection = _expr3169
|
|
98
|
+
|
|
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
|
+
return CWLWorkflowDescription(steps, inputs, outputs, cwl_version, requirements, hints, metadata)
|
|
101
|
+
|
|
102
|
+
|
|
103
|
+
__all__ = ["CWLWorkflowDescription_reflection"]
|
|
104
|
+
|
|
@@ -0,0 +1,113 @@
|
|
|
1
|
+
from __future__ import annotations
|
|
2
|
+
from dataclasses import dataclass
|
|
3
|
+
from ..fable_modules.dynamic_obj.dynamic_obj import (DynamicObj, DynamicObj_reflection)
|
|
4
|
+
from ..fable_modules.fable_library.reflection import (TypeInfo, string_type, option_type, record_type, array_type, class_type)
|
|
5
|
+
from ..fable_modules.fable_library.types import (Record, Array)
|
|
6
|
+
from .requirements import Requirement
|
|
7
|
+
|
|
8
|
+
def _expr3161() -> TypeInfo:
|
|
9
|
+
return record_type("ARCtrl.CWL.StepInput", [], StepInput, lambda: [("Id", string_type), ("Source", option_type(string_type)), ("DefaultValue", option_type(string_type)), ("ValueFrom", option_type(string_type))])
|
|
10
|
+
|
|
11
|
+
|
|
12
|
+
@dataclass(eq = False, repr = False, slots = True)
|
|
13
|
+
class StepInput(Record):
|
|
14
|
+
Id: str
|
|
15
|
+
Source: str | None
|
|
16
|
+
DefaultValue: str | None
|
|
17
|
+
ValueFrom: str | None
|
|
18
|
+
|
|
19
|
+
StepInput_reflection = _expr3161
|
|
20
|
+
|
|
21
|
+
def _expr3162() -> TypeInfo:
|
|
22
|
+
return record_type("ARCtrl.CWL.StepOutput", [], StepOutput, lambda: [("Id", array_type(string_type))])
|
|
23
|
+
|
|
24
|
+
|
|
25
|
+
@dataclass(eq = False, repr = False, slots = True)
|
|
26
|
+
class StepOutput(Record):
|
|
27
|
+
Id: Array[str]
|
|
28
|
+
|
|
29
|
+
StepOutput_reflection = _expr3162
|
|
30
|
+
|
|
31
|
+
def _expr3163() -> TypeInfo:
|
|
32
|
+
return class_type("ARCtrl.CWL.WorkflowStep", None, WorkflowStep, DynamicObj_reflection())
|
|
33
|
+
|
|
34
|
+
|
|
35
|
+
class WorkflowStep(DynamicObj):
|
|
36
|
+
def __init__(self, id: str, in_: Array[StepInput], out_: StepOutput, run: str, requirements: Array[Requirement] | None=None, hints: Array[Requirement] | None=None) -> None:
|
|
37
|
+
super().__init__()
|
|
38
|
+
self._id: str = id
|
|
39
|
+
self._in: Array[StepInput] = in_
|
|
40
|
+
self._out: StepOutput = out_
|
|
41
|
+
self._run: str = run
|
|
42
|
+
self._requirements: Array[Requirement] | None = requirements
|
|
43
|
+
self._hints: Array[Requirement] | None = hints
|
|
44
|
+
|
|
45
|
+
@property
|
|
46
|
+
def Id(self, __unit: None=None) -> str:
|
|
47
|
+
this: WorkflowStep = self
|
|
48
|
+
return this._id
|
|
49
|
+
|
|
50
|
+
@Id.setter
|
|
51
|
+
def Id(self, id: str) -> None:
|
|
52
|
+
this: WorkflowStep = self
|
|
53
|
+
this._id = id
|
|
54
|
+
|
|
55
|
+
@property
|
|
56
|
+
def In(self, __unit: None=None) -> Array[StepInput]:
|
|
57
|
+
this: WorkflowStep = self
|
|
58
|
+
return this._in
|
|
59
|
+
|
|
60
|
+
@In.setter
|
|
61
|
+
def In(self, in_: Array[StepInput]) -> None:
|
|
62
|
+
this: WorkflowStep = self
|
|
63
|
+
this._in = in_
|
|
64
|
+
|
|
65
|
+
@property
|
|
66
|
+
def Out(self, __unit: None=None) -> StepOutput:
|
|
67
|
+
this: WorkflowStep = self
|
|
68
|
+
return this._out
|
|
69
|
+
|
|
70
|
+
@Out.setter
|
|
71
|
+
def Out(self, out_: StepOutput) -> None:
|
|
72
|
+
this: WorkflowStep = self
|
|
73
|
+
this._out = out_
|
|
74
|
+
|
|
75
|
+
@property
|
|
76
|
+
def Run(self, __unit: None=None) -> str:
|
|
77
|
+
this: WorkflowStep = self
|
|
78
|
+
return this._run
|
|
79
|
+
|
|
80
|
+
@Run.setter
|
|
81
|
+
def Run(self, run: str) -> None:
|
|
82
|
+
this: WorkflowStep = self
|
|
83
|
+
this._run = run
|
|
84
|
+
|
|
85
|
+
@property
|
|
86
|
+
def Requirements(self, __unit: None=None) -> Array[Requirement] | None:
|
|
87
|
+
this: WorkflowStep = self
|
|
88
|
+
return this._requirements
|
|
89
|
+
|
|
90
|
+
@Requirements.setter
|
|
91
|
+
def Requirements(self, requirements: Array[Requirement] | None=None) -> None:
|
|
92
|
+
this: WorkflowStep = self
|
|
93
|
+
this._requirements = requirements
|
|
94
|
+
|
|
95
|
+
@property
|
|
96
|
+
def Hints(self, __unit: None=None) -> Array[Requirement] | None:
|
|
97
|
+
this: WorkflowStep = self
|
|
98
|
+
return this._hints
|
|
99
|
+
|
|
100
|
+
@Hints.setter
|
|
101
|
+
def Hints(self, hints: Array[Requirement] | None=None) -> None:
|
|
102
|
+
this: WorkflowStep = self
|
|
103
|
+
this._hints = hints
|
|
104
|
+
|
|
105
|
+
|
|
106
|
+
WorkflowStep_reflection = _expr3163
|
|
107
|
+
|
|
108
|
+
def WorkflowStep__ctor_4159DCB0(id: str, in_: Array[StepInput], out_: StepOutput, run: str, requirements: Array[Requirement] | None=None, hints: Array[Requirement] | None=None) -> WorkflowStep:
|
|
109
|
+
return WorkflowStep(id, in_, out_, run, requirements, hints)
|
|
110
|
+
|
|
111
|
+
|
|
112
|
+
__all__ = ["StepInput_reflection", "StepOutput_reflection", "WorkflowStep_reflection"]
|
|
113
|
+
|
|
File without changes
|
|
@@ -0,0 +1,60 @@
|
|
|
1
|
+
from __future__ import annotations
|
|
2
|
+
from ..fable_modules.fable_library.types import Array
|
|
3
|
+
from ..FileSystem.path import split as split_1
|
|
4
|
+
from .arc_assay import _007CAssayPath_007C__007C
|
|
5
|
+
from .arc_investigation import _007CInvestigationPath_007C__007C
|
|
6
|
+
from .arc_run import _007CRunPath_007C__007C
|
|
7
|
+
from .arc_study import _007CStudyPath_007C__007C
|
|
8
|
+
from .arc_workflow import _007CWorkflowPath_007C__007C
|
|
9
|
+
from .contract import (Contract, DTOType)
|
|
10
|
+
from .datamap import _007CDatamapPath_007C__007C
|
|
11
|
+
|
|
12
|
+
def try_isaread_contract_from_path(path: str) -> Contract | None:
|
|
13
|
+
split: Array[str] = split_1(path)
|
|
14
|
+
active_pattern_result: str | None = _007CInvestigationPath_007C__007C(split)
|
|
15
|
+
if active_pattern_result is not None:
|
|
16
|
+
p: str = active_pattern_result
|
|
17
|
+
return Contract.create_read(p, DTOType(4))
|
|
18
|
+
|
|
19
|
+
else:
|
|
20
|
+
active_pattern_result_1: str | None = _007CAssayPath_007C__007C(split)
|
|
21
|
+
if active_pattern_result_1 is not None:
|
|
22
|
+
p_1: str = active_pattern_result_1
|
|
23
|
+
return Contract.create_read(p_1, DTOType(0))
|
|
24
|
+
|
|
25
|
+
else:
|
|
26
|
+
active_pattern_result_2: str | None = _007CStudyPath_007C__007C(split)
|
|
27
|
+
if active_pattern_result_2 is not None:
|
|
28
|
+
p_2: str = active_pattern_result_2
|
|
29
|
+
return Contract.create_read(p_2, DTOType(1))
|
|
30
|
+
|
|
31
|
+
else:
|
|
32
|
+
active_pattern_result_3: str | None = _007CWorkflowPath_007C__007C(split)
|
|
33
|
+
if active_pattern_result_3 is not None:
|
|
34
|
+
p_3: str = active_pattern_result_3
|
|
35
|
+
return Contract.create_read(p_3, DTOType(2))
|
|
36
|
+
|
|
37
|
+
else:
|
|
38
|
+
active_pattern_result_4: str | None = _007CRunPath_007C__007C(split)
|
|
39
|
+
if active_pattern_result_4 is not None:
|
|
40
|
+
p_4: str = active_pattern_result_4
|
|
41
|
+
return Contract.create_read(p_4, DTOType(3))
|
|
42
|
+
|
|
43
|
+
else:
|
|
44
|
+
active_pattern_result_5: str | None = _007CDatamapPath_007C__007C(split)
|
|
45
|
+
if active_pattern_result_5 is not None:
|
|
46
|
+
p_5: str = active_pattern_result_5
|
|
47
|
+
return Contract.create_read(p_5, DTOType(5))
|
|
48
|
+
|
|
49
|
+
else:
|
|
50
|
+
return None
|
|
51
|
+
|
|
52
|
+
|
|
53
|
+
|
|
54
|
+
|
|
55
|
+
|
|
56
|
+
|
|
57
|
+
|
|
58
|
+
|
|
59
|
+
__all__ = ["try_isaread_contract_from_path"]
|
|
60
|
+
|