ghga-transpiler 1.2.0__tar.gz → 2.0.0__tar.gz

{ghga_transpiler-1.2.0 → ghga_transpiler-2.0.0}/PKG-INFO

@@ -1,28 +1,36 @@
 Metadata-Version: 2.1
 Name: ghga_transpiler
-Version: 1.2.0
-Summary: GHGA-Transpiler - GHGA metadata XLSX to JSON transpilation
-Home-page: https://github.com/ghga-de/ghga-transpiler
-Author: German Human Genome Phenome Archive (GHGA)
-Author-email: contact@ghga.de
+Version: 2.0.0
+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: License :: OSI Approved :: Apache Software License
 Classifier: Topic :: Internet :: WWW/HTTP :: HTTP Servers
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Intended Audience :: Developers
 Requires-Python: >=3.9
-Description-Content-Type: text/markdown; charset=UTF-8
-Provides-Extra: all
+Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: typer~=0.9.0
+Requires-Dist: openpyxl==3.*,>=3.1.2
+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/unit_and_int_tests.yaml/badge.svg)](https://github.com/ghga-de/ghga-transpiler/actions/workflows/unit_and_int_tests.yaml)
+[![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)
 [![Coverage Status](https://coveralls.io/repos/github/ghga-de/ghga-transpiler/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/ghga-transpiler?branch=main)
 
 # Ghga Transpiler
 
-GHGA-Transpiler - GHGA metadata XLSX to JSON transpilation
+GHGA-Transpiler - excel to JSON converter
 
 ## Description
 

{ghga_transpiler-1.2.0 → ghga_transpiler-2.0.0}/README.md

@@ -1,10 +1,10 @@
 
-[![tests](https://github.com/ghga-de/ghga-transpiler/actions/workflows/unit_and_int_tests.yaml/badge.svg)](https://github.com/ghga-de/ghga-transpiler/actions/workflows/unit_and_int_tests.yaml)
+[![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)
 [![Coverage Status](https://coveralls.io/repos/github/ghga-de/ghga-transpiler/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/ghga-transpiler?branch=main)
 
 # Ghga Transpiler
 
-GHGA-Transpiler - GHGA metadata XLSX to JSON transpilation
+GHGA-Transpiler - excel to JSON converter
 
 ## Description
 

ghga_transpiler-2.0.0/pyproject.toml

@@ -0,0 +1,45 @@
+[build-system]
+requires = ["setuptools>=67.7.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+# please adapt to package name
+name = "ghga_transpiler"
+version = "2.0.0"
+description = "GHGA-Transpiler - excel to JSON converter"
+readme = "README.md"
+authors = [
+    { name = "German Human Genome Phenome Archive (GHGA)", email = "contact@ghga.de" },
+]
+requires-python = ">=3.9"
+license = { text = "Apache 2.0" }
+classifiers = [
+    "Development Status :: 1 - Planning",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "License :: OSI Approved :: Apache Software License",
+    "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
+    "Topic :: Software Development :: Libraries",
+    "Intended Audience :: Developers",
+]
+dependencies = [
+    "typer ~= 0.9.0",
+    "openpyxl >= 3.1.2, == 3.*",
+    "defusedxml >= 0.7, == 0.*",
+    "pydantic >=2, <3",
+    "PyYAML ~= 6.0",
+    "semver == 3.*"
+]
+
+[project.urls]
+# please adapt to package name
+Repository = "https://github.com/ghga-de/ghga-transpiler"
+
+[project.scripts]
+# please adapt to package name
+ghga-transpiler = "ghga_transpiler.__main__:run"
+
+[tool.setuptools.packages.find]
+where = ["src"]

ghga_transpiler-2.0.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

{ghga_transpiler-1.2.0 → ghga_transpiler-2.0.0/src}/ghga_transpiler/__init__.py

@@ -15,4 +15,13 @@
 
 """Short description of package"""  # Please adapt to package
 
-__version__ = "1.2.0"
+from importlib.metadata import version
+
+from openpyxl.xml import DEFUSEDXML
+
+__version__ = version(__package__)
+
+if not DEFUSEDXML:
+    raise RuntimeError(
+        "The 'defusedxml' package must be present to safely run ghga-transpiler."
+    )

{ghga_transpiler-1.2.0 → ghga_transpiler-2.0.0/src}/ghga_transpiler/cli.py

@@ -13,21 +13,27 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-""" CLI-specific wrappers around core functions."""
+"""CLI-specific wrappers around core functions."""
 import sys
 from pathlib import Path
 from typing import Optional
 
 import typer
 
-from ghga_transpiler import io
-
+from . import __version__, io
 from .config.exceptions import UnknownVersionError
-from .core import convert_workbook
+from .core import InvalidSematicVersion, convert_workbook
 
 cli = typer.Typer()
 
 
+def version_callback(value: bool):
+    """Prints the package version"""
+    if value:
+        print(__version__)
+        raise typer.Exit()
+
+
 @cli.command()
 def transpile(
     spread_sheet: Path = typer.Argument(
@@ -43,15 +49,24 @@ def transpile(
     force: bool = typer.Option(
         False, "--force", "-f", help="Override output file if it exists."
     ),
+    version: bool = typer.Option(
+        False,
+        "--version",
+        "-v",
+        callback=version_callback,
+        is_eager=True,
+        help="Print package version",
+    ),
 ):
     """ghga-transpiler is a command line utility to transpile the official GHGA
     metadata XLSX workbooks to JSON. Please note that ghga-transpiler does not
     validate that the provided metadata is compliant with the GHGA Metadata
     Schema. This can be achieved by running ghga-validator on the JSON data
-    generated by the ghga-transpiler."""
+    generated by the ghga-transpiler.
+    """
     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-1.2.0 → ghga_transpiler-2.0.0/src}/ghga_transpiler/config/config.py

@@ -21,7 +21,7 @@ from importlib import resources
 from typing import Callable, Optional
 
 import yaml
-from pydantic import BaseModel, root_validator
+from pydantic import BaseModel, model_validator
 
 from .exceptions import DuplicatedName, UnknownVersionError
 
@@ -40,11 +40,11 @@ class WorksheetSettings(BaseModel):
     """A data model for the per-worksheet settings of a transpiler config"""
 
     name: str
-    header_row: Optional[int]
-    start_row: Optional[int]
-    start_column: Optional[int]
-    end_column: Optional[int]
-    transformations: Optional[dict[str, Callable]]
+    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
 
 
 class Worksheet(BaseModel):
@@ -61,21 +61,21 @@ class Config(BaseModel):
     default_settings: DefaultSettings
     worksheets: list[Worksheet]
 
-    @root_validator(pre=False)
-    def get_param(cls, values):  # pylint: disable=no-self-argument
+    @model_validator(mode="after")
+    def get_param(cls, values):  # noqa
         """Function to manage parameters of global and worksheet specific configuration"""
-        for sheet in values.get("worksheets"):
-            for key in values.get("default_settings").__dict__:
+        for sheet in values.worksheets:
+            for key in values.default_settings.__dict__:
                 if getattr(sheet.settings, key) is None:
-                    val = getattr(values.get("default_settings"), key)
+                    val = getattr(values.default_settings, key)
                     setattr(sheet.settings, key, val)
         return values
 
-    @root_validator(pre=False)
-    def check_name(cls, values):  # pylint: disable=no-self-argument
+    @model_validator(mode="after")
+    def check_name(cls, values):  # noqa
         """Function to ensure that each worksheets has a unique sheet_name and name attributes."""
         # Check for duplicate attribute names
-        attrs_counter = Counter(ws.settings.name for ws in values["worksheets"])
+        attrs_counter = Counter(ws.settings.name for ws in values.worksheets)
         dup_attrs = [name for name, count in attrs_counter.items() if count > 1]
         if dup_attrs:
             raise DuplicatedName(
@@ -83,7 +83,7 @@ class Config(BaseModel):
             )
 
         # Check for duplicate worksheet names
-        attrs_counter = Counter(ws.sheet_name for ws in values["worksheets"])
+        attrs_counter = Counter(ws.sheet_name for ws in values.worksheets)
         dup_ws_names = [name for name, count in attrs_counter.items() if count > 1]
         if dup_ws_names:
             raise DuplicatedName(
@@ -94,11 +94,10 @@ class Config(BaseModel):
 
 def load_config(version: str, package: resources.Package) -> Config:
     """Reads configuration yaml file from default location and creates a Config object"""
-
     config_resource = resources.files(package).joinpath(f"{version}.yaml")
     try:
         config_str = config_resource.read_text(encoding="utf8")
     except FileNotFoundError:
         # pylint: disable=raise-missing-from
-        raise UnknownVersionError(f"Unknown metadata version: {version}")
-    return Config.parse_obj(yaml.load(config_str, yaml.Loader))  # nosec
+        raise UnknownVersionError(f"Unknown metadata version: {version}") from None
+    return Config.model_validate(yaml.load(config_str, yaml.Loader))  # noqa # nosec

{ghga_transpiler-1.2.0 → ghga_transpiler-2.0.0/src}/ghga_transpiler/core.py

@@ -15,16 +15,17 @@
 #
 
 """This module contains functionalities for processing excel sheets into json object."""
-import re
 from importlib import resources
 from typing import Callable, Optional, Union
 
+import semver
 from openpyxl import Workbook
 
-from ghga_transpiler import config
+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:
@@ -33,20 +34,28 @@ 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,
@@ -81,7 +90,8 @@ def get_header(
 
 def convert_rows(header, rows) -> list[dict]:
     """Function to return list of dictionaries, rows as worksheet row values and
-    column names as keys"""
+    column names as keys
+    """
     return [
         {
             key: value

{ghga_transpiler-1.2.0 → ghga_transpiler-2.0.0/src}/ghga_transpiler/io.py

@@ -24,15 +24,13 @@ from typing import Optional, TextIO
 
 from openpyxl import load_workbook
 
-from ghga_transpiler.core import GHGAWorkbook
+from .core import GHGAWorkbook
 
 
 def read_workbook(
     path: Path, configs_package: resources.Package = "ghga_transpiler.configs"
 ) -> GHGAWorkbook:
-    """
-    Function to read-in a workbook
-    """
+    """Function to read-in a workbook"""
     return GHGAWorkbook(load_workbook(path), configs_package=configs_package)
 
 
@@ -43,7 +41,8 @@ def _write_json(data: dict, file: TextIO):
 
 def write_json(data: dict, path: Optional[Path], force: bool) -> None:
     """Write the data provided as a dictionary to the specified output path or
-    to stdout if the path is None."""
+    to stdout if the path is None.
+    """
     if path is None:
         _write_json(data, sys.stdout)
     elif path.exists() and not force:

{ghga_transpiler-1.2.0 → ghga_transpiler-2.0.0/src}/ghga_transpiler/transformations.py

@@ -38,7 +38,28 @@ def to_attributes() -> Callable:
         return dict(zip(("key", "value"), splitted))
 
     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-1.2.0 → ghga_transpiler-2.0.0/src}/ghga_transpiler.egg-info/PKG-INFO

@@ -1,28 +1,36 @@
 Metadata-Version: 2.1
 Name: ghga-transpiler
-Version: 1.2.0
-Summary: GHGA-Transpiler - GHGA metadata XLSX to JSON transpilation
-Home-page: https://github.com/ghga-de/ghga-transpiler
-Author: German Human Genome Phenome Archive (GHGA)
-Author-email: contact@ghga.de
+Version: 2.0.0
+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: License :: OSI Approved :: Apache Software License
 Classifier: Topic :: Internet :: WWW/HTTP :: HTTP Servers
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Intended Audience :: Developers
 Requires-Python: >=3.9
-Description-Content-Type: text/markdown; charset=UTF-8
-Provides-Extra: all
+Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: typer~=0.9.0
+Requires-Dist: openpyxl==3.*,>=3.1.2
+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/unit_and_int_tests.yaml/badge.svg)](https://github.com/ghga-de/ghga-transpiler/actions/workflows/unit_and_int_tests.yaml)
+[![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)
 [![Coverage Status](https://coveralls.io/repos/github/ghga-de/ghga-transpiler/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/ghga-transpiler?branch=main)
 
 # Ghga Transpiler
 
-GHGA-Transpiler - GHGA metadata XLSX to JSON transpilation
+GHGA-Transpiler - excel to JSON converter
 
 ## Description
 

ghga_transpiler-2.0.0/src/ghga_transpiler.egg-info/SOURCES.txt

@@ -0,0 +1,23 @@
+LICENSE
+README.md
+pyproject.toml
+src/ghga_transpiler/__init__.py
+src/ghga_transpiler/__main__.py
+src/ghga_transpiler/cli.py
+src/ghga_transpiler/core.py
+src/ghga_transpiler/io.py
+src/ghga_transpiler/transformations.py
+src/ghga_transpiler.egg-info/PKG-INFO
+src/ghga_transpiler.egg-info/SOURCES.txt
+src/ghga_transpiler.egg-info/dependency_links.txt
+src/ghga_transpiler.egg-info/entry_points.txt
+src/ghga_transpiler.egg-info/requires.txt
+src/ghga_transpiler.egg-info/top_level.txt
+src/ghga_transpiler/config/__init__.py
+src/ghga_transpiler/config/config.py
+src/ghga_transpiler/config/exceptions.py
+src/ghga_transpiler/configs/__init__.py
+tests/test_convert_workbook.py
+tests/test_create_config.py
+tests/test_io.py
+tests/test_process_workbook.py

ghga_transpiler-2.0.0/src/ghga_transpiler.egg-info/requires.txt

@@ -0,0 +1,6 @@
+typer~=0.9.0
+openpyxl==3.*,>=3.1.2
+defusedxml==0.*,>=0.7
+pydantic<3,>=2
+PyYAML~=6.0
+semver==3.*

{ghga_transpiler-1.2.0 → ghga_transpiler-2.0.0/src}/ghga_transpiler.egg-info/top_level.txt

@@ -1,3 +1 @@
 ghga_transpiler
-scripts
-tests

{ghga_transpiler-1.2.0 → ghga_transpiler-2.0.0}/tests/test_convert_workbook.py

@@ -13,6 +13,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+
+"""Tests for converting the workbook"""
+
 from ghga_transpiler import io
 from ghga_transpiler.core import convert_workbook
 
@@ -22,7 +25,6 @@ from .fixtures.utils import get_project_root
 
 def test_convert_workbook() -> None:
     """Function to test workbook to json conversion"""
-
     workbook_path = (
         get_project_root() / "tests" / "fixtures" / "workbooks" / "a_workbook.xlsx"
     )

{ghga_transpiler-1.2.0 → ghga_transpiler-2.0.0}/tests/test_create_config.py

@@ -13,6 +13,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+
+"""Tests for creating the config"""
+
 from ghga_transpiler.config.config import (
     Config,
     DefaultSettings,
@@ -23,7 +26,6 @@ from ghga_transpiler.config.config import (
 
 def test_config_params() -> None:
     """Testing if default parameters of config yaml are used in the absence of worksheet settings"""
-
     books_sheet = Worksheet(
         sheet_name="books", settings=WorksheetSettings(name="books", end_column=3)
     )

{ghga_transpiler-1.2.0 → ghga_transpiler-2.0.0}/tests/test_io.py

@@ -30,7 +30,7 @@ def test_write_json_file(tmp_path):
     out_path = tmp_path.joinpath("out.json")
     io.write_json(data=EXPECTED_CONVERSION, path=out_path, force=False)
 
-    with open(file=out_path, mode="r", encoding="utf8") as in_file:
+    with open(file=out_path, encoding="utf8") as in_file:
         data = json.load(fp=in_file)
     assert data == EXPECTED_CONVERSION
 

{ghga_transpiler-1.2.0 → ghga_transpiler-2.0.0}/tests/test_process_workbook.py

@@ -16,27 +16,31 @@
 """Unit tests for core functions"""
 
 import pytest
+import semver
 
-from ghga_transpiler.core import GHGAWorkbook
+from ghga_transpiler.core import GHGAWorkbook, InvalidSematicVersion
 
 from .fixtures.utils import create_workbook
 
 
 def test_extract_good_version() -> None:
     """Function to check if the version extraction correctly gets workbook
-    version from _properties worksheet"""
+    version from _properties worksheet
+    """
     workbook = create_workbook("__properties")
     value = workbook["__properties"].cell(row=1, column=1, value="10.3.1-rc2").value
     # pylint: disable=protected-access
     version = GHGAWorkbook._get_version(workbook)
-    assert version == value
+    assert version == semver.Version.parse(str(value))
 
 
 def test_extract_bad_version() -> None:
     """Function to check if the version extraction correctly fails when an non
-    semver string is specified in the _properties worksheet"""
+    semver string is specified in the _properties worksheet
+    """
     workbook = create_workbook("__properties")
     workbook["__properties"].cell(row=1, column=1, value="20.10.3.1")
-    with pytest.raises(SyntaxError):
+
+    with pytest.raises(InvalidSematicVersion):
         # pylint: disable=protected-access
         GHGAWorkbook._get_version(workbook)