arctrl 3.0.0b16__tar.gz → 3.0.1__tar.gz

arctrl-3.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: arctrl
+Version: 3.0.1
+Summary: Library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtimer agnostic contract systems.
+License-File: LICENSE
+Keywords: arc,annotated research context,isa,research data,multi platform
+Author: Heinrich Lukas Weil
+Author-email: weil@rptu.de
+Maintainer: Florian Wetzels
+Requires-Python: >=3.11
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Dist: openpyxl (>=3.1.5,<4)
+Requires-Dist: requests (>=2.28.1,<3.0.0)
+Project-URL: Repository, https://github.com/nfdi4plants/ARCtrl
+Description-Content-Type: text/markdown
+
+
+![logo](logos/ARCtrl_horizontal.png)
+
+# ARCtrl
+
+[![DOI](https://img.shields.io/badge/Cite%20Us-10.5281%2Fzenodo.15194394-008273?logo=zenodo&logoColor=C70039)](https://doi.org/10.5281/zenodo.15194394)
+
+> **ARCtrl** the easy way to read, manipulate and write ARCs in __.NET__, __JavaScript__ and __Python__! ❤️
+
+| Version | Downloads |
+| :--------|-----------:|
+|<a href="https://www.nuget.org/packages/ARCtrl/"><img alt="Nuget" src="https://img.shields.io/nuget/v/ARCtrl?logo=nuget&color=%234fb3d9"></a>|<a href="https://www.nuget.org/packages/ARCtrl/"><img alt="Nuget" src="https://img.shields.io/nuget/dt/ARCtrl?color=%234FB3D9"></a>|
+|<a href="https://www.npmjs.com/package/@nfdi4plants/arctrl"><img alt="NPM" src="https://img.shields.io/npm/v/%40nfdi4plants/arctrl?logo=npm&color=%234fb3d9"></a>|<a href="https://www.npmjs.com/package/@nfdi4plants/arctrl"><img alt="NPM" src="https://img.shields.io/npm/dt/%40nfdi4plants%2Farctrl?color=%234fb3d9"></a>|
+|<a href="https://pypi.org/project/ARCtrl/"><img alt="PyPI" src="https://img.shields.io/pypi/v/arctrl?logo=pypi&color=%234fb3d9"></a>|<a href="https://pypi.org/project/ARCtrl/"><img alt="PyPI" src="https://img.shields.io/pepy/dt/arctrl?color=%234fb3d9"></a>|
+
+## Install
+
+#### .NET
+
+```fsharp
+#r "nuget: ARCtrl"
+```
+
+```bash
+<PackageReference Include="ARCtrl" Version="1.1.0" />
+```
+
+#### JavaScript
+
+```bash
+npm i @nfdi4plants/arctrl
+```
+
+#### Python
+
+```bash
+pip install arctrl
+```
+
+## Docs
+
+Documentation can be found [here](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/arctrl/)
+
+## Development
+
+#### Requirements
+
+- [nodejs and npm](https://nodejs.org/en/download)
+    - verify with `node --version` (Tested with v18.16.1)
+    - verify with `npm --version` (Tested with v9.2.0)
+- [.NET SDK](https://dotnet.microsoft.com/en-us/download)
+    - verify with `dotnet --version` (Tested with 7.0.306)
+- [Python](https://www.python.org/downloads/)
+    - verify with `py --version` (Tested with 3.12.2, known to work only for >=3.11)
+
+#### Local Setup
+
+##### Windows
+
+On windows you can use the `setup.cmd` to run the following steps automatically!
+
+1. Setup dotnet tools
+
+   `dotnet tool restore`
+
+
+2. Install NPM dependencies
+
+    `npm install`
+
+3. Setup python environment
+
+    `py -m venv .venv`
+
+4. Install [uv](https://docs.astral.sh/uv/) and dependencies
+
+   1. `.\.venv\Scripts\python.exe -m pip install -U pip setuptools`
+   2. `.\.venv\Scripts\python.exe -m pip install uv`
+   3. `.\.venv\Scripts\python.exe -m uv pip install -r pyproject.toml --group dev`
+
+Verify correct setup with `./build.cmd runtests` ✨
+
+##### Linux / macOS
+
+On unix you can use the `setup.sh` to run the following steps automatically!
+
+1. Setup dotnet tools
+
+   `dotnet tool restore`
+
+
+2. Install NPM dependencies
+
+    `npm install`
+
+3. Setup python environment
+
+    `python -m venv .venv`
+
+4. Install [uv](https://docs.astral.sh/uv/) and dependencies
+
+   1. `.venv/bin/python -m pip install -U pip setuptools`
+   2. `.venv/bin/python -m pip install uv`
+   3. `.venv/bin/python -m uv pip install -r pyproject.toml --group dev`
+
+Verify correct setup with `bash build.sh runtests` ✨
+
+## Branding
+
+Feel free to reference `ARCtrl` on slides or elsewhere using our logos:
+
+|Square | Horizontal | Vertical |
+| - | - | - |
+| ![square](logos/ARCtrl_square.png) | ![horizontal](logos/ARCtrl_horizontal.png) |  ![vertical](logos/ARCtrl_vertical.png) |
+
+## Performance
+
+Measured on 13th Gen Intel(R) Core(TM) i7-13800H
+
+| Name | Description | FSharp Time (ms) | JavaScript Time (ms) | Python Time (ms) |
+| --- | --- | --- | --- | --- |
+| Table_GetHashCode | From a table with 1 column and 10000 rows, retrieve the Hash Code | 0 ± 0 | 0 ± 1 | 91 ± 12 |
+| Table_AddDistinctRows | Add 10000 distinct rows to a table with 4 columns. | 13 ± 2 | 14 ± 4 | 119 ± 12 |
+| Table_AddIdenticalRows | Add 10000 identical rows to a table with 4 columns. | 6 ± 2 | 6 ± 1 | 104 ± 6 |
+| Table_AddColumnsWithDistinctValues | Add 4 columns with 10000 distinct values each. | 8 ± 3 | 10 ± 1 | 53 ± 1 |
+| Table_AddColumnsWithIdenticalValues | Add 4 columns with 10000 identical values each. | 5 ± 1 | 4 ± 0 | 47 ± 1 |
+| Table_fillMissingCells | For a table 6 columns and 20000 rows, where each row has one missing value, fill those values with default values. | 0 ± 0 |  2 ± 1 | 6 ± 4 |
+| Table_ToJson | Serialize a table with 5 columns and 10000 rows to json, with 3 fixed and 2 variable columns. | 227 ± 64 | 68 ± 18 | 7851 ± 1411 |
+| Table_ToCompressedJson | Serialize a table with 5 columns and 10000 rows to compressed json, with 3 fixed and 2 variable columns. | 147 ± 15 | 2878 ± 135 | 6303 ± 1798 |
+| Assay_toJson | Parse an assay with one table with 10000 rows and 6 columns to json, with 3 fixed and 3 variable columns. | 330 ± 36 | 88 ± 9 | 12644 ± 550 |
+| Assay_fromJson | Parse an assay with one table with 10000 rows and 6 columns from json, with 3 fixed and 3 variable columns. | 355 ± 66 | 61 ± 6 | 6499 ± 1068 |
+| Assay_toISAJson | Parse an assay with one table with 10000 rows and 6 columns to json, with 3 fixed and 3 variable columns | 487 ± 36 | 959 ± 36 | 15618 ± 482 |
+| Assay_fromISAJson | Parse an assay with one table with 10000 rows and 6 columns from json, with 3 fixed and 3 variable columns | 359 ± 29 | 706 ± 46 | 9587 ± 621 |
+| Study_FromWorkbook | Parse a workbook with one study with 10000 rows and 6 columns to an ArcStudy | 29 ± 14 | 62 ± 5 | 818 ± 36 |
+| Investigation_ToWorkbook_ManyStudies | Parse an investigation with 1500 studies to a workbook | 240 ± 31 | 284 ± 24 | 3657 ± 199 |
+| Investigation_FromWorkbook_ManyStudies | Parse a workbook with 1500 studies to an ArcInvestigation | 127 ± 20 | 498 ± 21 | 9469 ± 412 |
+| ARC_ToROCrate | Parse an ARC with one assay with 10000 rows and 6 columns to a RO-Crate metadata file. | 1431 ± 99 | 3526 ± 264 | 61224 ± 728 |

arctrl-3.0.1/pyproject.toml

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+[project]
+name = "arctrl"
+version = "3.0.1"
+description = "Library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtimer agnostic contract systems."
+authors = [
+    { name = "Heinrich Lukas Weil", email = "weil@rptu.de" },
+    { name = "Kevin Frey", email = "freymaurer@gmx.de" },
+]
+requires-python = ">=3.11"
+readme = "README.md"
+maintainers = [{ name = "Florian Wetzels" }]
+keywords = [
+    "arc",
+    "annotated research context",
+    "isa",
+    "research data",
+    "multi platform",
+]
+dependencies = [
+    "requests>= 2.28.1, <3.0.0",
+    "openpyxl>=3.1.5,<4",
+]
+
+[project.urls]
+Repository = "https://github.com/nfdi4plants/ARCtrl"
+
+[dependency-groups]
+dev = [
+    "pytest>=8.1.1,<9",
+    "twine>=4.0.2"
+]
+
+[tool.poetry]
+include = [
+    "src/ARCtrl/py/**/*.py"
+]
+packages = [
+    { include = "**/*.py", from = "src/ARCtrl/", to = "arctrl" }
+]
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

arctrl-3.0.1/src/ARCtrl/__init__.py

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+from __future__ import annotations
+from collections.abc import Callable
+from typing import Any
+from .py.Contract.contract import Contract
+from .py.Core.data_context import DataContext
+from .py.Core.datamap import Datamap
+from .py.Core.comment import Comment
+from .py.Core.ontology_annotation import OntologyAnnotation
+from .py.Core.person import Person
+from .py.Core.publication import Publication
+from .py.Core.Table.composite_header import IOType, CompositeHeader
+from .py.Core.Table.composite_cell import CompositeCell
+from .py.Core.Table.composite_column import CompositeColumn
+from .py.Core.Table.arc_table import ArcTable
+from .py.Core.Table.arc_tables import ArcTables
+from .py.Core.arc_types import ArcAssay, ArcStudy, ArcRun, ArcWorkflow, ArcInvestigation
+from .py.Core.template import Template
+from .py.FileSystem.file_system import FileSystem
+from .py.FileSystem.file_system_tree import FileSystemTree
+from .py.json import JsonController
+from .py.yaml import YamlController
+from .py.xlsx import XlsxController
+from .py.arc import ARC

arctrl-3.0.1/src/ARCtrl/cwl.py

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+from __future__ import annotations
+from collections.abc import Callable
+from typing import Any
+from .py.CWL.cwlprocessing_unit import CWLProcessingUnit
+from .py.CWL.cwltypes import CWLType, FileInstance, DirectoryInstance, DirentInstance, InputEnumSchema, InputRecordField, InputRecordSchema, InputArraySchema, SchemaDefRequirementType, SoftwarePackage
+from .py.CWL.parameter_reference import CWLParameterReference
+from .py.CWL.inputs import CWLInput, InputBinding
+from .py.CWL.outputs import CWLOutput, OutputBinding
+from .py.CWL.tool_description import CWLToolDescription
+from .py.CWL.workflow_description import CWLWorkflowDescription
+from .py.CWL.workflow_steps import WorkflowStep, StepInput, StepOutput
+from .py.CWL.requirements import Requirement, DockerRequirement, EnvironmentDef, ResourceRequirementInstance

arctrl-3.0.1/src/ARCtrl/py/CWL/cwlprocessing_unit.py

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+from __future__ import annotations
+from typing import Any
+from ..fable_modules.fable_library.reflection import (TypeInfo, union_type)
+from ..fable_modules.fable_library.seq import choose
+from ..fable_modules.fable_library.types import (Array, Union)
+from ..fable_modules.fable_library.util import IEnumerable_1
+from .expression_tool_description import (CWLExpressionToolDescription_reflection, CWLExpressionToolDescription)
+from .inputs import CWLInput
+from .operation_description import (CWLOperationDescription_reflection, CWLOperationDescription)
+from .outputs import CWLOutput
+from .requirements import (Requirement, HintEntry, HintEntry_get_tryAsRequirement)
+from .tool_description import (CWLToolDescription_reflection, CWLToolDescription)
+from .workflow_description import (CWLWorkflowDescription_reflection, CWLWorkflowDescription)
+from .workflow_steps import WorkflowStepRun
+
+def _expr818() -> TypeInfo:
+    return union_type("ARCtrl.CWL.CWLProcessingUnit", [], CWLProcessingUnit, lambda: [[("Item", CWLToolDescription_reflection())], [("Item", CWLWorkflowDescription_reflection())], [("Item", CWLExpressionToolDescription_reflection())], [("Item", CWLOperationDescription_reflection())]])
+
+
+class CWLProcessingUnit(Union):
+    def __init__(self, tag: int, *fields: Any) -> None:
+        super().__init__()
+        self.tag: int = tag or 0
+        self.fields: Array[Any] = list(fields)
+
+    @staticmethod
+    def cases() -> list[str]:
+        return ["CommandLineTool", "Workflow", "ExpressionTool", "Operation"]
+
+
+CWLProcessingUnit_reflection = _expr818
+
+def CWLProcessingUnit_getInputs_30922B92(processing_unit: CWLProcessingUnit) -> Array[CWLInput]:
+    if processing_unit.tag == 1:
+        return CWLWorkflowDescription.get_inputs(processing_unit.fields[0])
+
+    elif processing_unit.tag == 2:
+        return CWLExpressionToolDescription.get_inputs_or_empty(processing_unit.fields[0])
+
+    elif processing_unit.tag == 3:
+        return CWLOperationDescription.get_inputs(processing_unit.fields[0])
+
+    else: 
+        return CWLToolDescription.get_inputs_or_empty(processing_unit.fields[0])
+
+
+
+def CWLProcessingUnit_getOutputs_30922B92(processing_unit: CWLProcessingUnit) -> Array[CWLOutput]:
+    if processing_unit.tag == 1:
+        return CWLWorkflowDescription.get_outputs(processing_unit.fields[0])
+
+    elif processing_unit.tag == 2:
+        return CWLExpressionToolDescription.get_outputs(processing_unit.fields[0])
+
+    elif processing_unit.tag == 3:
+        return CWLOperationDescription.get_outputs(processing_unit.fields[0])
+
+    else: 
+        return CWLToolDescription.get_outputs(processing_unit.fields[0])
+
+
+
+def CWLProcessingUnit_getRequirements_30922B92(processing_unit: CWLProcessingUnit) -> Array[Requirement]:
+    if processing_unit.tag == 1:
+        return CWLWorkflowDescription.get_requirements_or_empty(processing_unit.fields[0])
+
+    elif processing_unit.tag == 2:
+        return CWLExpressionToolDescription.get_requirements_or_empty(processing_unit.fields[0])
+
+    elif processing_unit.tag == 3:
+        return CWLOperationDescription.get_requirements_or_empty(processing_unit.fields[0])
+
+    else: 
+        return CWLToolDescription.get_requirements_or_empty(processing_unit.fields[0])
+
+
+
+def CWLProcessingUnit_getHints_30922B92(processing_unit: CWLProcessingUnit) -> Array[HintEntry]:
+    if processing_unit.tag == 1:
+        return CWLWorkflowDescription.get_hints_or_empty(processing_unit.fields[0])
+
+    elif processing_unit.tag == 2:
+        return CWLExpressionToolDescription.get_hints_or_empty(processing_unit.fields[0])
+
+    elif processing_unit.tag == 3:
+        return CWLOperationDescription.get_hints_or_empty(processing_unit.fields[0])
+
+    else: 
+        return CWLToolDescription.get_hints_or_empty(processing_unit.fields[0])
+
+
+
+def CWLProcessingUnit_getIntent_30922B92(processing_unit: CWLProcessingUnit) -> Array[str]:
+    if processing_unit.tag == 1:
+        return CWLWorkflowDescription.get_intent_or_empty(processing_unit.fields[0])
+
+    elif processing_unit.tag == 2:
+        return CWLExpressionToolDescription.get_intent_or_empty(processing_unit.fields[0])
+
+    elif processing_unit.tag == 3:
+        return CWLOperationDescription.get_intent_or_empty(processing_unit.fields[0])
+
+    else: 
+        return CWLToolDescription.get_intent_or_empty(processing_unit.fields[0])
+
+
+
+def CWLProcessingUnit_getKnownHints_30922B92(processing_unit: CWLProcessingUnit) -> Array[Requirement]:
+    def _arrow819(__unit: None=None, processing_unit: Any=processing_unit) -> IEnumerable_1[Requirement]:
+        source: Array[HintEntry] = CWLProcessingUnit_getHints_30922B92(processing_unit)
+        return choose(HintEntry_get_tryAsRequirement(), source)
+
+    return list(_arrow819())
+
+
+def WorkflowStepRunOps_fromTool(tool: CWLToolDescription) -> WorkflowStepRun:
+    return WorkflowStepRun(1, tool)
+
+
+def WorkflowStepRunOps_fromWorkflow(workflow: CWLWorkflowDescription) -> WorkflowStepRun:
+    return WorkflowStepRun(2, workflow)
+
+
+def WorkflowStepRunOps_fromExpressionTool(expression_tool: CWLExpressionToolDescription) -> WorkflowStepRun:
+    return WorkflowStepRun(3, expression_tool)
+
+
+def WorkflowStepRunOps_fromOperation(operation: CWLOperationDescription) -> WorkflowStepRun:
+    return WorkflowStepRun(4, operation)
+
+
+def WorkflowStepRunOps_tryGetTool(run: WorkflowStepRun) -> CWLToolDescription | None:
+    (pattern_matching_result, tool) = (None, None)
+    if run.tag == 1:
+        if isinstance(run.fields[0], CWLToolDescription):
+            pattern_matching_result = 0
+            tool = run.fields[0]
+
+        else: 
+            pattern_matching_result = 1
+
+
+    else: 
+        pattern_matching_result = 1
+
+    if pattern_matching_result == 0:
+        return tool
+
+    elif pattern_matching_result == 1:
+        return None
+
+
+
+def WorkflowStepRunOps_tryGetWorkflow(run: WorkflowStepRun) -> CWLWorkflowDescription | None:
+    (pattern_matching_result, workflow) = (None, None)
+    if run.tag == 2:
+        if isinstance(run.fields[0], CWLWorkflowDescription):
+            pattern_matching_result = 0
+            workflow = run.fields[0]
+
+        else: 
+            pattern_matching_result = 1
+
+
+    else: 
+        pattern_matching_result = 1
+
+    if pattern_matching_result == 0:
+        return workflow
+
+    elif pattern_matching_result == 1:
+        return None
+
+
+
+def WorkflowStepRunOps_tryGetExpressionTool(run: WorkflowStepRun) -> CWLExpressionToolDescription | None:
+    (pattern_matching_result, expression_tool) = (None, None)
+    if run.tag == 3:
+        if isinstance(run.fields[0], CWLExpressionToolDescription):
+            pattern_matching_result = 0
+            expression_tool = run.fields[0]
+
+        else: 
+            pattern_matching_result = 1
+
+
+    else: 
+        pattern_matching_result = 1
+
+    if pattern_matching_result == 0:
+        return expression_tool
+
+    elif pattern_matching_result == 1:
+        return None
+
+
+
+def WorkflowStepRunOps_tryGetOperation(run: WorkflowStepRun) -> CWLOperationDescription | None:
+    (pattern_matching_result, operation) = (None, None)
+    if run.tag == 4:
+        if isinstance(run.fields[0], CWLOperationDescription):
+            pattern_matching_result = 0
+            operation = run.fields[0]
+
+        else: 
+            pattern_matching_result = 1
+
+
+    else: 
+        pattern_matching_result = 1
+
+    if pattern_matching_result == 0:
+        return operation
+
+    elif pattern_matching_result == 1:
+        return None
+
+
+
+__all__ = ["CWLProcessingUnit_reflection", "CWLProcessingUnit_getInputs_30922B92", "CWLProcessingUnit_getOutputs_30922B92", "CWLProcessingUnit_getRequirements_30922B92", "CWLProcessingUnit_getHints_30922B92", "CWLProcessingUnit_getIntent_30922B92", "CWLProcessingUnit_getKnownHints_30922B92", "WorkflowStepRunOps_fromTool", "WorkflowStepRunOps_fromWorkflow", "WorkflowStepRunOps_fromExpressionTool", "WorkflowStepRunOps_fromOperation", "WorkflowStepRunOps_tryGetTool", "WorkflowStepRunOps_tryGetWorkflow", "WorkflowStepRunOps_tryGetExpressionTool", "WorkflowStepRunOps_tryGetOperation"]
+