rocratepcc 0.0.2__tar.gz

rocratepcc-0.0.2/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 DataPLANT
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

rocratepcc-0.0.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: rocratepcc
+Version: 0.0.2
+Summary: Polyglot library (.NET, Python, Javascript) for creation of RO-Crate Profile Crates.
+License-File: LICENSE
+Keywords: ro-crate,profile crate
+Author: Heinrich Lukas Weil
+Author-email: weil@rptu.de
+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: arctrl (>=3.0.0b11,<4)
+Project-URL: Repository, https://github.com/nfdi4plants/ROCratePCC
+Description-Content-Type: text/markdown
+
+# RO-Crate Profile Crate Creator
+
+Polyglot library for creation of RO-Crate Profile Crates according to [the official documentation](https://www.researchobject.org/ro-crate/specification/1.2/profiles.html#profile-crate), and based on the examples of [profile run crate](https://www.researchobject.org/workflow-run-crate/profiles/workflow_run_crate/ro-crate-metadata.json) and [workflow crate](https://about.workflowhub.eu/Workflow-RO-Crate/ro-crate-metadata.json).
+
+# Documentation
+
+## FSharp
+
+```fsharp
+open ROCratePCC
+
+let types : ResizeArray<UsedType> = ResizeArray [
+    UsedType(iri = "https://schema.org/CreativeWork", name = "CreativeWork");
+    UsedType(iri = "http://www.w3.org/ns/dx/prof/Profile", name = "Profile");
+]
+
+let authors : ResizeArray<Author> = ResizeArray [
+    Author(orcid = "0000-0002-5526-71389", name = "Florian Wetzels");
+    Author(orcid = "0000-0003-1945-6342", name = "Heinrich Lukas Weil");
+]
+
+let version = "1.0.0-draft.2"
+
+let id = $"https://github.com/nfdi4plants/isa-ro-crate-profile/tree/{version}/profile"
+
+let name = "ISA RO-Crate Profile"
+
+let description = "An RO-Crate profile for representing ISA data in Research Object Crates (RO-Crates). This profile defines how to represent ISA Investigation, Study, and Assay data using RO-Crate metadata."
+
+let license = License(iri = "https://mit-license.org/", name = "MIT License")
+
+let specifications = ResizeArray[
+    TextualResource(
+        name = "ISA RO-Crate Profile description",
+        filePath = "isa_ro_crate.md",
+        encodingFormat = "text/markdown",
+        rootDataEntityId = id
+    )
+]
+
+
+let resourceDescriptors = ResizeArray [
+    Specification(specifications) :> ResourceDescriptor
+]
+
+let rootEntity = 
+    RootDataEntity(
+        id = id,
+        name = name,
+        description = description,
+        license = license,
+        usedTypes = types,
+        resourceDescriptors = resourceDescriptors,
+        authors = ResizeArray authors
+    )
+
+let profile = 
+    Profile(
+        rootEntity,
+        license = license
+    )
+
+let string = profile.ToROCrateJsonString(spaces = 2)
+
+System.IO.File.WriteAllText("profile/ro-crate-metadata.json", string)
+```
+## 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
+
+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` ✨

rocratepcc-0.0.2/README.md

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+# RO-Crate Profile Crate Creator
+
+Polyglot library for creation of RO-Crate Profile Crates according to [the official documentation](https://www.researchobject.org/ro-crate/specification/1.2/profiles.html#profile-crate), and based on the examples of [profile run crate](https://www.researchobject.org/workflow-run-crate/profiles/workflow_run_crate/ro-crate-metadata.json) and [workflow crate](https://about.workflowhub.eu/Workflow-RO-Crate/ro-crate-metadata.json).
+
+# Documentation
+
+## FSharp
+
+```fsharp
+open ROCratePCC
+
+let types : ResizeArray<UsedType> = ResizeArray [
+    UsedType(iri = "https://schema.org/CreativeWork", name = "CreativeWork");
+    UsedType(iri = "http://www.w3.org/ns/dx/prof/Profile", name = "Profile");
+]
+
+let authors : ResizeArray<Author> = ResizeArray [
+    Author(orcid = "0000-0002-5526-71389", name = "Florian Wetzels");
+    Author(orcid = "0000-0003-1945-6342", name = "Heinrich Lukas Weil");
+]
+
+let version = "1.0.0-draft.2"
+
+let id = $"https://github.com/nfdi4plants/isa-ro-crate-profile/tree/{version}/profile"
+
+let name = "ISA RO-Crate Profile"
+
+let description = "An RO-Crate profile for representing ISA data in Research Object Crates (RO-Crates). This profile defines how to represent ISA Investigation, Study, and Assay data using RO-Crate metadata."
+
+let license = License(iri = "https://mit-license.org/", name = "MIT License")
+
+let specifications = ResizeArray[
+    TextualResource(
+        name = "ISA RO-Crate Profile description",
+        filePath = "isa_ro_crate.md",
+        encodingFormat = "text/markdown",
+        rootDataEntityId = id
+    )
+]
+
+
+let resourceDescriptors = ResizeArray [
+    Specification(specifications) :> ResourceDescriptor
+]
+
+let rootEntity = 
+    RootDataEntity(
+        id = id,
+        name = name,
+        description = description,
+        license = license,
+        usedTypes = types,
+        resourceDescriptors = resourceDescriptors,
+        authors = ResizeArray authors
+    )
+
+let profile = 
+    Profile(
+        rootEntity,
+        license = license
+    )
+
+let string = profile.ToROCrateJsonString(spaces = 2)
+
+System.IO.File.WriteAllText("profile/ro-crate-metadata.json", string)
+```
+## 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
+
+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` ✨

rocratepcc-0.0.2/pyproject.toml

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+[project]
+name = "rocratepcc"
+version = "0.0.2"
+description = "Polyglot library (.NET, Python, Javascript) for creation of RO-Crate Profile Crates."
+authors = [
+    { name = "Heinrich Lukas Weil", email = "weil@rptu.de" },
+    { name = "Eli Chadwick", email = "eli.chadwick@manchester.ac.uk" },
+]
+requires-python = ">=3.11"
+readme = "README.md"
+keywords = [
+    "ro-crate",
+    "profile crate"
+]
+dependencies = [
+    "arctrl>=3.0.0b11,<4",
+]
+
+[project.urls]
+Repository = "https://github.com/nfdi4plants/ROCratePCC"
+
+[dependency-groups]
+dev = [
+    "pytest>=8.1.1,<9",
+    "twine>=4.0.2"
+]
+
+[tool.poetry]
+include = [
+    "src/ROCratePCC/py/**/*.py"
+]
+packages = [
+    { include = "**/*.py", from = "src/ROCratePCC/", to = "ROCratePCC" }
+]
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

rocratepcc-0.0.2/src/ROCratePCC/__init__.py

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+from __future__ import annotations
+from collections.abc import Callable
+from typing import Any
+from .py.main import Author, Constraint, Profile, License, CustomResourceDescriptor, Specification, Example, Guidance, UsedType, TextualResource, ResourceDescriptor, RootDataEntity

rocratepcc-0.0.2/src/ROCratePCC/py/fable_modules/arctrl_contract/arc.py

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+from __future__ import annotations
+from ..arctrl_file_system.path import split as split_1
+from ..fable_library.types import Array
+from .arc_assay import _007CAssayPath_007C__007C
+from .arc_investigation import _007CInvestigationPath_007C__007C
+from .arc_run import _007CRunPath_007C__007C
+from .arc_study import _007CStudyPath_007C__007C
+from .arc_workflow import _007CWorkflowPath_007C__007C
+from .contract import (Contract, DTOType)
+from .datamap import _007CDatamapPath_007C__007C
+from .license import LicenseContractExtensions__007CLicensePath_007C__007C
+
+def try_isaread_contract_from_path(path: str) -> Contract | None:
+    split: Array[str] = split_1(path)
+    active_pattern_result: str | None = _007CInvestigationPath_007C__007C(split)
+    if active_pattern_result is not None:
+        p: str = active_pattern_result
+        return Contract.create_read(p, DTOType(4))
+
+    else: 
+        active_pattern_result_1: str | None = _007CAssayPath_007C__007C(split)
+        if active_pattern_result_1 is not None:
+            p_1: str = active_pattern_result_1
+            return Contract.create_read(p_1, DTOType(0))
+
+        else: 
+            active_pattern_result_2: str | None = _007CStudyPath_007C__007C(split)
+            if active_pattern_result_2 is not None:
+                p_2: str = active_pattern_result_2
+                return Contract.create_read(p_2, DTOType(1))
+
+            else: 
+                active_pattern_result_3: str | None = _007CWorkflowPath_007C__007C(split)
+                if active_pattern_result_3 is not None:
+                    p_3: str = active_pattern_result_3
+                    return Contract.create_read(p_3, DTOType(2))
+
+                else: 
+                    active_pattern_result_4: str | None = _007CRunPath_007C__007C(split)
+                    if active_pattern_result_4 is not None:
+                        p_4: str = active_pattern_result_4
+                        return Contract.create_read(p_4, DTOType(3))
+
+                    else: 
+                        active_pattern_result_5: str | None = _007CDatamapPath_007C__007C(split)
+                        if active_pattern_result_5 is not None:
+                            p_5: str = active_pattern_result_5
+                            return Contract.create_read(p_5, DTOType(5))
+
+                        else: 
+                            active_pattern_result_6: str | None = LicenseContractExtensions__007CLicensePath_007C__007C(split)
+                            if active_pattern_result_6 is not None:
+                                p_6: str = active_pattern_result_6
+                                return Contract.create_read(p_6, DTOType(10))
+
+                            else: 
+                                return None
+
+
+
+
+
+
+
+
+
+__all__ = ["try_isaread_contract_from_path"]
+

rocratepcc-0.0.2/src/ROCratePCC/py/fable_modules/arctrl_contract/arc_assay.py

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+from __future__ import annotations
+from typing import Any
+from ..arctrl_core.arc_types import ArcAssay
+from ..arctrl_core.Helper.identifier import Assay_fileNameFromIdentifier
+from ..arctrl_file_system.file_system_tree import FileSystemTree
+from ..arctrl_file_system.path import (combine_many, get_assay_folder_path)
+from ..arctrl_spreadsheet.arc_assay import (ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F, ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D)
+from ..fable_library.array_ import equals_with
+from ..fable_library.option import default_arg
+from ..fable_library.seq import (to_array, delay, append, collect, singleton, empty)
+from ..fable_library.types import Array
+from ..fable_library.util import IEnumerable_1
+from .contract import (Contract, DTOType, DTO)
+
+def _007CAssayPath_007C__007C(input: Array[str]) -> str | None:
+    (pattern_matching_result,) = (None,)
+    def _arrow3626(x: str, y: str, input: Any=input) -> bool:
+        return x == y
+
+    if (len(input) == 3) if (not equals_with(_arrow3626, input, None)) else False:
+        if input[0] == "assays":
+            if input[2] == "isa.assay.xlsx":
+                pattern_matching_result = 0
+
+            else: 
+                pattern_matching_result = 1
+
+
+        else: 
+            pattern_matching_result = 1
+
+
+    else: 
+        pattern_matching_result = 1
+
+    if pattern_matching_result == 0:
+        any_assay_name: str = input[1]
+        return combine_many(input)
+
+    elif pattern_matching_result == 1:
+        return None
+
+
+
+def ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(this: ArcAssay, WithFolder: bool | None=None) -> Array[Contract]:
+    with_folder: bool = default_arg(WithFolder, False)
+    path: str = Assay_fileNameFromIdentifier(this.Identifier)
+    c: Contract = Contract.create_create(path, DTOType(0), DTO(0, ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(this)))
+    def _arrow3630(__unit: None=None, this: Any=this, WithFolder: Any=WithFolder) -> IEnumerable_1[Contract]:
+        def _arrow3628(__unit: None=None) -> IEnumerable_1[Contract]:
+            folder_fs: FileSystemTree = FileSystemTree.create_assays_folder([FileSystemTree.create_assay_folder(this.Identifier)])
+            def _arrow3627(p: str) -> IEnumerable_1[Contract]:
+                return singleton(Contract.create_create(p, DTOType(10))) if ((p != "assays/.gitkeep") if (p != path) else False) else empty()
+
+            return collect(_arrow3627, folder_fs.ToFilePaths(False))
+
+        def _arrow3629(__unit: None=None) -> IEnumerable_1[Contract]:
+            return singleton(c)
+
+        return append(_arrow3628() if with_folder else empty(), delay(_arrow3629))
+
+    return to_array(delay(_arrow3630))
+
+
+def ARCtrl_ArcAssay__ArcAssay_ToUpdateContract(this: ArcAssay) -> Contract:
+    path: str = Assay_fileNameFromIdentifier(this.Identifier)
+    return Contract.create_update(path, DTOType(0), DTO(0, ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(this)))
+
+
+def ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(this: ArcAssay) -> Contract:
+    path: str = get_assay_folder_path(this.Identifier)
+    return Contract.create_delete(path)
+
+
+def ARCtrl_ArcAssay__ArcAssay_toDeleteContract_Static_1501C0F8(assay: ArcAssay) -> Contract:
+    return ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(assay)
+
+
+def ARCtrl_ArcAssay__ArcAssay_toCreateContract_Static_Z2508BE4F(assay: ArcAssay, WithFolder: bool | None=None) -> Array[Contract]:
+    return ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(assay, WithFolder)
+
+
+def ARCtrl_ArcAssay__ArcAssay_toUpdateContract_Static_1501C0F8(assay: ArcAssay) -> Contract:
+    return ARCtrl_ArcAssay__ArcAssay_ToUpdateContract(assay)
+
+
+def ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F(c: Contract) -> ArcAssay | None:
+    (pattern_matching_result, fsworkbook) = (None, None)
+    if c.Operation == "READ":
+        if c.DTOType is not None:
+            if c.DTOType.tag == 0:
+                if c.DTO is not None:
+                    if c.DTO.tag == 0:
+                        pattern_matching_result = 0
+                        fsworkbook = c.DTO.fields[0]
+
+                    else: 
+                        pattern_matching_result = 1
+
+
+                else: 
+                    pattern_matching_result = 1
+
+
+            else: 
+                pattern_matching_result = 1
+
+
+        else: 
+            pattern_matching_result = 1
+
+
+    else: 
+        pattern_matching_result = 1
+
+    if pattern_matching_result == 0:
+        return ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D(fsworkbook)
+
+    elif pattern_matching_result == 1:
+        return None
+
+
+
+__all__ = ["_007CAssayPath_007C__007C", "ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49", "ARCtrl_ArcAssay__ArcAssay_ToUpdateContract", "ARCtrl_ArcAssay__ArcAssay_ToDeleteContract", "ARCtrl_ArcAssay__ArcAssay_toDeleteContract_Static_1501C0F8", "ARCtrl_ArcAssay__ArcAssay_toCreateContract_Static_Z2508BE4F", "ARCtrl_ArcAssay__ArcAssay_toUpdateContract_Static_1501C0F8", "ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F"]
+

rocratepcc-0.0.2/src/ROCratePCC/py/fable_modules/arctrl_contract/arc_investigation.py

@@ -0,0 +1,88 @@
+from __future__ import annotations
+from typing import Any
+from ..arctrl_core.arc_types import ArcInvestigation
+from ..arctrl_file_system.path import combine_many
+from ..arctrl_spreadsheet.arc_investigation import (ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF, ARCtrl_ArcInvestigation__ArcInvestigation_fromFsWorkbook_Static_32154C9D)
+from ..fable_library.array_ import equals_with
+from ..fable_library.types import Array
+from .contract import (Contract, DTOType, DTO)
+
+def _007CInvestigationPath_007C__007C(input: Array[str]) -> str | None:
+    (pattern_matching_result,) = (None,)
+    def _arrow3693(x: str, y: str, input: Any=input) -> bool:
+        return x == y
+
+    if (len(input) == 1) if (not equals_with(_arrow3693, input, None)) else False:
+        if input[0] == "isa.investigation.xlsx":
+            pattern_matching_result = 0
+
+        else: 
+            pattern_matching_result = 1
+
+
+    else: 
+        pattern_matching_result = 1
+
+    if pattern_matching_result == 0:
+        return combine_many(input)
+
+    elif pattern_matching_result == 1:
+        return None
+
+
+
+def ARCtrl_ArcInvestigation__ArcInvestigation_ToCreateContract(this: ArcInvestigation) -> Contract:
+    return Contract.create_create("isa.investigation.xlsx", DTOType(4), DTO(0, ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(this)))
+
+
+def ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(this: ArcInvestigation) -> Contract:
+    return Contract.create_update("isa.investigation.xlsx", DTOType(4), DTO(0, ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(this)))
+
+
+def ARCtrl_ArcInvestigation__ArcInvestigation_toCreateContract_Static_Z720BD3FF(inv: ArcInvestigation) -> Contract:
+    return ARCtrl_ArcInvestigation__ArcInvestigation_ToCreateContract(inv)
+
+
+def ARCtrl_ArcInvestigation__ArcInvestigation_toUpdateContract_Static_Z720BD3FF(inv: ArcInvestigation) -> Contract:
+    return ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract(inv)
+
+
+def ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F(c: Contract) -> ArcInvestigation | None:
+    (pattern_matching_result, fsworkbook) = (None, None)
+    if c.Operation == "READ":
+        if c.DTOType is not None:
+            if c.DTOType.tag == 4:
+                if c.DTO is not None:
+                    if c.DTO.tag == 0:
+                        pattern_matching_result = 0
+                        fsworkbook = c.DTO.fields[0]
+
+                    else: 
+                        pattern_matching_result = 1
+
+
+                else: 
+                    pattern_matching_result = 1
+
+
+            else: 
+                pattern_matching_result = 1
+
+
+        else: 
+            pattern_matching_result = 1
+
+
+    else: 
+        pattern_matching_result = 1
+
+    if pattern_matching_result == 0:
+        return ARCtrl_ArcInvestigation__ArcInvestigation_fromFsWorkbook_Static_32154C9D(fsworkbook)
+
+    elif pattern_matching_result == 1:
+        return None
+
+
+
+__all__ = ["_007CInvestigationPath_007C__007C", "ARCtrl_ArcInvestigation__ArcInvestigation_ToCreateContract", "ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract", "ARCtrl_ArcInvestigation__ArcInvestigation_toCreateContract_Static_Z720BD3FF", "ARCtrl_ArcInvestigation__ArcInvestigation_toUpdateContract_Static_Z720BD3FF", "ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F"]
+