ghga-transpiler 1.4.0__py3-none-any.whl → 2.1.0__py3-none-any.whl

ghga_transpiler/__init__.py

@@ -1,20 +1,26 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
-#
+
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+#
+
+"""GHGA metadata transpiler"""
 
-"""Short description of package"""  # Please adapt to package
+from openpyxl.xml import DEFUSEDXML
 
-from importlib.metadata import version
+__version__ = "2.1.0"
 
-__version__ = version(__package__)
+if not DEFUSEDXML:
+    raise RuntimeError(
+        "The 'defusedxml' package must be present to safely run ghga-transpiler."
+    )

ghga_transpiler/__main__.py

@@ -1,17 +1,18 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
-#
+
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+#
 
 """Entrypoint of the package"""
 

ghga_transpiler/cli.py

@@ -1,28 +1,29 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
-#
+
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 """CLI-specific wrappers around core functions."""
+
 import sys
 from pathlib import Path
-from typing import Optional
 
 import typer
 
 from . import __version__, io
 from .config.exceptions import UnknownVersionError
-from .core import convert_workbook
+from .core import InvalidSematicVersion, convert_workbook
 
 cli = typer.Typer()
 
@@ -43,7 +44,7 @@ def transpile(
         dir_okay=False,
         readable=True,
     ),
-    output_file: Optional[Path] = typer.Argument(
+    output_file: Path | None = typer.Argument(
         None, help="The path to output file (JSON).", dir_okay=False
     ),
     force: bool = typer.Option(
@@ -66,7 +67,7 @@ def transpile(
     """
     try:
         ghga_workbook = io.read_workbook(spread_sheet)
-    except (SyntaxError, UnknownVersionError) as exc:
+    except (SyntaxError, UnknownVersionError, InvalidSematicVersion) as exc:
         sys.exit(f"Unable to parse input file '{spread_sheet}': {exc}")
 
     converted = convert_workbook(ghga_workbook)

ghga_transpiler/config/__init__.py

@@ -1,18 +1,20 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
-#
+
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
+
+"""Module to load workbook configurations and convert it to transpiler config"""
 
-"""Module to load workbook configurations and convert it to transpiler config """
 from .config import Config, load_config  # noqa

ghga_transpiler/config/config.py

@@ -1,24 +1,25 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
-#
+
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 
 """Module to process config file"""
 
 from collections import Counter
+from collections.abc import Callable
 from importlib import resources
-from typing import Callable, Optional
 
 import yaml
 from pydantic import BaseModel, model_validator
@@ -40,18 +41,18 @@ class WorksheetSettings(BaseModel):
     """A data model for the per-worksheet settings of a transpiler config"""
 
     name: str
-    header_row: Optional[int] = None
-    start_row: Optional[int] = None
-    start_column: Optional[int] = None
-    end_column: Optional[int] = None
-    transformations: Optional[dict[str, Callable]] = None
+    header_row: int | None = None
+    start_row: int | None = None
+    start_column: int | None = None
+    end_column: int | None = None
+    transformations: dict[str, Callable] | None = None
 
 
 class Worksheet(BaseModel):
     """A data model for worksheets in the transpiler config"""
 
     sheet_name: str
-    settings: Optional[WorksheetSettings]
+    settings: WorksheetSettings | None
 
 
 class Config(BaseModel):

ghga_transpiler/config/exceptions.py

@@ -1,18 +1,19 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
-#
+
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 
 """Module to collect custom exceptions"""
 

ghga_transpiler/configs/__init__.py

@@ -1,15 +1,16 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
-#
+
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#

ghga_transpiler/core.py

@@ -1,30 +1,33 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
-#
+
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 
 """This module contains functionalities for processing excel sheets into json object."""
-import re
+
+from collections.abc import Callable
 from importlib import resources
-from typing import Callable, Optional, Union
 
+import semver
 from openpyxl import Workbook
 
 from . import config
 
-# pylint: disable=line-too-long
-SEMVER_REGEX = r"^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$"
+
+class InvalidSematicVersion(Exception):
+    """Raised when a version string is invalid."""
 
 
 class GHGAWorkbook:
@@ -33,27 +36,35 @@ class GHGAWorkbook:
     def __init__(self, workbook: Workbook, configs_package: resources.Package):
         """Create a new GHGAWorkbook object from an XLSX workbook"""
         self.workbook = workbook
-        self.version = GHGAWorkbook._get_version(workbook)
-        self.config = config.load_config(self.version, configs_package)
+        self.wb_version = GHGAWorkbook._get_version(workbook)
+        self.config = config.load_config(self.major_minor_version, configs_package)
 
     @staticmethod
     def _get_version(workbook):
         """Function to get workbook version from the worksheet _properties"""
         if "__properties" in workbook.sheetnames:
-            version = str(workbook["__properties"].cell(1, 1).value)
-            if re.fullmatch(SEMVER_REGEX, version):
-                return version
+            try:
+                return semver.Version.parse(workbook["__properties"].cell(1, 1).value)
+            except ValueError:
+                raise InvalidSematicVersion(
+                    "Unable to extract metadata model version from the provided workbook (not a valid semantic version)."
+                ) from None
         raise SyntaxError(
-            "Unable to extract metadata version from the provided workbook."
+            "Unable to extract metadata model version from the provided workbook (missing)."
         )
 
+    @property
+    def major_minor_version(self):
+        """Returns only major and minor version numbers"""
+        return f"{self.wb_version.major}.{self.wb_version.minor}"
+
 
 def get_worksheet_rows(
     worksheet,
-    min_row: Union[int, None],
+    min_row: int | None,
     max_row: int,
-    min_col: Union[int, None],
-    max_col: Union[int, None],
+    min_col: int | None,
+    max_col: int | None,
 ) -> list:
     """Function to create a list of rows of a worksheet"""
     return list(
@@ -67,9 +78,9 @@ def get_worksheet_rows(
 
 def get_header(
     worksheet,
-    header_row: Union[int, None],
-    min_col: Union[int, None],
-    max_col: Union[int, None],
+    header_row: int | None,
+    min_col: int | None,
+    max_col: int | None,
 ) -> list[str]:
     """Function to return a list column names of a worksheet"""
     return list(
@@ -86,7 +97,7 @@ def convert_rows(header, rows) -> list[dict]:
     return [
         {
             key: value
-            for key, value in zip(header, row)
+            for key, value in zip(header, row, strict=False)
             if value is not None and value != ""
         }
         for row in rows
@@ -94,7 +105,7 @@ def convert_rows(header, rows) -> list[dict]:
 
 
 def transform_rows(
-    rows: list[dict], transformations: Optional[dict[str, Callable]]
+    rows: list[dict], transformations: dict[str, Callable] | None
 ) -> list[dict]:
     """Transforms row values if it is applicable with a given function"""
     transformed = []

ghga_transpiler/io.py

@@ -1,18 +1,19 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
-#
+
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 
 """IO related functionality"""
 
@@ -20,7 +21,7 @@ import json
 import sys
 from importlib import resources
 from pathlib import Path
-from typing import Optional, TextIO
+from typing import TextIO
 
 from openpyxl import load_workbook
 
@@ -39,7 +40,7 @@ def _write_json(data: dict, file: TextIO):
     json.dump(obj=data, fp=file, ensure_ascii=False, indent=4)
 
 
-def write_json(data: dict, path: Optional[Path], force: bool) -> None:
+def write_json(data: dict, path: Path | None, force: bool) -> None:
     """Write the data provided as a dictionary to the specified output path or
     to stdout if the path is None.
     """

ghga_transpiler/transformations.py

@@ -1,22 +1,23 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
-#
+
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 
 """Module containing transformation functions"""
 
-from typing import Callable
+from collections.abc import Callable
 
 
 def split_by_semicolon(value: str) -> list[str]:
@@ -35,10 +36,31 @@ def to_attributes() -> Callable:
     def split_one(value: str) -> dict:
         """Returns a dictionary with key, value as keys, splitted string as values"""
         splitted = (elem.strip() for elem in value.split("="))
-        return dict(zip(("key", "value"), splitted))
+        return dict(zip(("key", "value"), splitted, strict=False))
 
     def split_mult(value: str) -> list[dict]:
-        """Function to convert string to attributes"""
+        """Converts string to attributes"""
         return [split_one(elem) for elem in split_by_semicolon(value)]
 
     return split_mult
+
+
+def snake_case(cv: str) -> str:
+    """Converts format of a string to SNAKE_CASE"""
+    return cv.replace(" ", "_").upper()
+
+
+def to_snake_case() -> Callable:
+    """Returns a function that converts a string to SNAKE_CASE"""
+    return snake_case
+
+
+def snake_case_list(value: str) -> list[str]:
+    """Combines the functions to split_by_semicolon and convert_to_snake_case"""
+    list_to_convert = split_by_semicolon(value)
+    return [snake_case(elem) for elem in list_to_convert]
+
+
+def to_snake_case_list() -> Callable:
+    """Returns a function that converts a semicolon separated string into a list of snake-cased strings"""
+    return snake_case_list

{ghga_transpiler-1.4.0.dist-info → ghga_transpiler-2.1.0.dist-info}/LICENSE

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+   Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
    for the German Human Genome-Phenome Archive (GHGA)
 
    Licensed under the Apache License, Version 2.0 (the "License");

{ghga_transpiler-1.4.0.dist-info → ghga_transpiler-2.1.0.dist-info}/METADATA

@@ -1,27 +1,27 @@
 Metadata-Version: 2.1
-Name: ghga-transpiler
-Version: 1.4.0
+Name: ghga_transpiler
+Version: 2.1.0
 Summary: GHGA-Transpiler - excel to JSON converter
 Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
 License: Apache 2.0
 Project-URL: Repository, https://github.com/ghga-de/ghga-transpiler
 Classifier: Development Status :: 1 - Planning
 Classifier: Operating System :: POSIX :: Linux
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Topic :: Internet :: WWW/HTTP :: HTTP Servers
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Intended Audience :: Developers
-Requires-Python: >=3.9
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: typer ~=0.9.0
+Requires-Dist: typer >=0.12
 Requires-Dist: openpyxl ==3.*,>=3.1.2
-Requires-Dist: defusedxml
+Requires-Dist: defusedxml ==0.*,>=0.7
 Requires-Dist: pydantic <3,>=2
 Requires-Dist: PyYAML ~=6.0
+Requires-Dist: semver ==3.*
 
 
 [![tests](https://github.com/ghga-de/ghga-transpiler/actions/workflows/tests.yaml/badge.svg)](https://github.com/ghga-de/ghga-transpiler/actions/workflows/unit_and_int_tests.yaml)

ghga_transpiler-2.1.0.dist-info/RECORD

@@ -0,0 +1,16 @@
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+ghga_transpiler/__main__.py,sha256=EVGi0SsK--oaDF_c6PhVvNyPDnItrJzVapNAsKhgBmM,847
+ghga_transpiler/cli.py,sha256=AzIWDZaRzyREzGmV2az7OXVwzT33ijroot-dHwIdzUA,2491
+ghga_transpiler/core.py,sha256=A2MKKNEwxRViCquU0pbuk7KjXCg8y-F_QJpICvSS-IE,5213
+ghga_transpiler/io.py,sha256=ln997FIjVHyZKeJLkvGeo35hx6ZE4CtPIpoPcu23vGI,1769
+ghga_transpiler/transformations.py,sha256=o-6qJHB-5ptrnMhi-q-3kXrrVdy_XwqLUjTVIg-SH0o,2236
+ghga_transpiler/config/__init__.py,sha256=f8b3Le48ZrbOwRA5MVf6V6zqKFtxii9SQZMvvx1ulz8,817
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+ghga_transpiler-2.1.0.dist-info/LICENSE,sha256=fBYaxYJmvm_AQEYU4gRvUAWbqhO0bgqPj9Yl6f8RXuU,11452
+ghga_transpiler-2.1.0.dist-info/METADATA,sha256=mwfApRxtzL1CvNhD7FJ8UySErjIee1gNTrxhVaP2d4k,4407
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+ghga_transpiler-2.1.0.dist-info/entry_points.txt,sha256=Fr_VQJynZZl95NXjrQW2gE0bCocgjKVNEZQpaLls8po,65
+ghga_transpiler-2.1.0.dist-info/top_level.txt,sha256=TksRpDO3Y4mvK-B09UhQU3ceZpG19fljNlVDGTfjg8o,16
+ghga_transpiler-2.1.0.dist-info/RECORD,,

{ghga_transpiler-1.4.0.dist-info → ghga_transpiler-2.1.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.3)
+Generator: bdist_wheel (0.43.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

ghga_transpiler-1.4.0.dist-info/RECORD

@@ -1,16 +0,0 @@
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-ghga_transpiler/core.py,sha256=ZFGQOlX7EB5du4xAYgJQh0N_MBVdq6cUySIpktRfUj4,4996
-ghga_transpiler/io.py,sha256=MJwXmFC2xsgq7exlG623pnKhCxiJ-EBI9uIV0G46frU,1783
-ghga_transpiler/transformations.py,sha256=qI6vKq3gJPPBE2msUm-DMdVNeLrfJIkbga8l45tS7ek,1567
-ghga_transpiler/config/__init__.py,sha256=IKlzAd82ta9a0_aEps3f4I3GLRSJeyV1QImFcHvBLE0,818
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-ghga_transpiler-1.4.0.dist-info/LICENSE,sha256=a2nPPnhGY9QGdkfGrseHGDVj62fh8o5DoHsUpQp3GzA,11452
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-ghga_transpiler-1.4.0.dist-info/RECORD,,