ghga-transpiler 2.1.4__tar.gz → 2.2.0__tar.gz

{ghga_transpiler-2.1.4/src/ghga_transpiler.egg-info → ghga_transpiler-2.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ghga_transpiler
-Version: 2.1.4
+Version: 2.2.0
 Summary: GHGA-Transpiler - excel to JSON converter
 Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
 License: Apache 2.0
@@ -13,15 +13,18 @@ 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: >=3.12
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: typer>=0.12
 Requires-Dist: openpyxl==3.*,>=3.1.2
 Requires-Dist: defusedxml==0.*,>=0.7
-Requires-Dist: pydantic<3,>=2
+Requires-Dist: pydantic<3,>=2.6
 Requires-Dist: PyYAML~=6.0
 Requires-Dist: semver==3.*
+Requires-Dist: exceptiongroup>=1.0.0; python_version < "3.11"
+Requires-Dist: tomli>=2.0.0; python_version < "3.11"
+Requires-Dist: eval-type-backport==0.2.0; python_version < "3.10"
 
 
 [![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-2.1.4 → ghga_transpiler-2.2.0}/pyproject.toml

@@ -9,7 +9,7 @@ readme = "README.md"
 authors = [
     { name = "German Human Genome Phenome Archive (GHGA)", email = "contact@ghga.de" },
 ]
-requires-python = ">=3.12"
+requires-python = ">=3.9"
 classifiers = [
     "Development Status :: 1 - Planning",
     "Operating System :: POSIX :: Linux",
@@ -21,15 +21,18 @@ classifiers = [
     "Intended Audience :: Developers",
 ]
 name = "ghga_transpiler"
-version = "2.1.4"
+version = "2.2.0"
 description = "GHGA-Transpiler - excel to JSON converter"
 dependencies = [
     "typer >= 0.12",
     "openpyxl >= 3.1.2, == 3.*",
     "defusedxml >= 0.7, == 0.*",
-    "pydantic >=2, <3",
+    "pydantic >=2.6, <3",
     "PyYAML ~= 6.0",
     "semver == 3.*",
+    "exceptiongroup>=1.0.0; python_version < \"3.11\"",
+    "tomli>= 2.0.0; python_version < \"3.11\"",
+    "eval-type-backport==0.2.0; python_version < \"3.10\"",
 ]
 
 [project.license]
@@ -66,7 +69,6 @@ src = [
     "examples",
     "scripts",
 ]
-target-version = "py312"
 
 [tool.ruff.lint]
 fixable = [

{ghga_transpiler-2.1.4 → ghga_transpiler-2.2.0}/src/ghga_transpiler/__init__.py

@@ -18,7 +18,7 @@
 
 from openpyxl.xml import DEFUSEDXML
 
-__version__ = "2.1.4"
+__version__ = "2.2.0"
 
 if not DEFUSEDXML:
     raise RuntimeError(

{ghga_transpiler-2.1.4 → ghga_transpiler-2.2.0}/src/ghga_transpiler/cli.py

@@ -45,7 +45,7 @@ def transpile(
         dir_okay=False,
         readable=True,
     ),
-    output_file: Optional[Path] = typer.Argument(  # noqa: UP007 (typer issue #461)
+    output_file: Optional[Path] = typer.Argument(
         None, help="The path to output file (JSON).", dir_okay=False
     ),
     force: bool = typer.Option(

{ghga_transpiler-2.1.4 → ghga_transpiler-2.2.0}/src/ghga_transpiler/config/config.py

@@ -17,6 +17,8 @@
 
 """Module to process config file"""
 
+from __future__ import annotations
+
 from collections import Counter
 from collections.abc import Callable
 from importlib import resources

ghga_transpiler-2.2.0/src/ghga_transpiler/configs/2.0.yaml

@@ -0,0 +1,162 @@
+ghga_metadata_version: 2.0.0
+default_settings:
+  header_row: 1
+  start_row: 7
+  start_column: 1
+  transformations:
+    attributes:
+      !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+    format:
+      !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+worksheets:
+  - settings:
+      end_column: 7
+      name: analyses
+      transformations:
+        research_data_files:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+    sheet_name: Analysis
+  - settings:
+      end_column: 11
+      name: analysis_methods
+      transformations:
+        parameters:
+          !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+        software_versions:
+          !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+    sheet_name: AnalysisMethod
+  - settings:
+      end_column: 7
+      name: analysis_method_supporting_files
+    sheet_name: AnalysisMethodSupportingFile
+  - settings:
+      end_column: 7
+      name: studies
+      transformations:
+        affiliations:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        attributes:
+          !!python/object/apply:ghga_transpiler.transformations.to_attributes []
+        types:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
+    sheet_name: Study
+  - settings:
+      end_column: 10
+      name: individuals
+      transformations:
+        phenotypic_features_terms:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        phenotypic_features_ids:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        diagnosis_ids:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        diagnosis_terms:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        sex:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        ancestry_terms:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        ancestry_ids:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+    sheet_name: Individual
+  - settings:
+      end_column: 7
+      name: individual_supporting_files
+    sheet_name: IndividualSupportingFile
+  - settings:
+      end_column: 21
+      name: samples
+      transformations:
+        type:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        storage:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        disease_or_healthy:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        case_control_status:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
+        biospecimen_age_at_sampling:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        biospecimen_vital_status_at_sampling:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        biospecimen_isolation:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        biospecimen_storage:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+    sheet_name: Sample
+  - settings:
+      end_column: 23
+      name: experiment_methods
+      transformations:
+        library_type:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        library_selection_methods:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
+        library_preparation_kit_retail_name:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        primer:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        end_bias:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        target_regions:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+        rnaseq_strandedness:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        instrument_model:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        sequencing_layout:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        flow_cell_type:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        sample_barcode_read:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        sequencing_layout:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+    sheet_name: ExperimentMethod
+  - settings:
+      end_column: 7
+      name: experiment_method_supporting_files
+    sheet_name: ExperimentMethodSupportingFile
+  - settings:
+      end_column: 8
+      name: experiments
+    sheet_name: Experiment
+  - settings:
+      end_column: 9
+      name: research_data_files
+      transformations:
+        experiments:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+    sheet_name: ResearchDataFile
+  - settings:
+      end_column: 7
+      name: process_data_files
+    sheet_name: ProcessDataFile
+  - settings:
+      end_column: 7
+      name: datasets
+      transformations:
+        types: !!python/object/apply:ghga_transpiler.transformations.to_list []
+    sheet_name: Dataset
+  - settings:
+      end_column: 11
+      name: data_access_policies
+      transformations:
+        data_use_modifier_terms:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case_list []
+        data_use_permission_term:
+          !!python/object/apply:ghga_transpiler.transformations.to_snake_case []
+        data_use_modifier_ids:
+          !!python/object/apply:ghga_transpiler.transformations.to_list []
+    sheet_name: DataAccessPolicy
+  - settings:
+      end_column: 4
+      name: data_access_committees
+    sheet_name: DataAccessCommittee
+  - settings:
+      end_column: 9
+      name: publications
+      transformations:
+        xref: !!python/object/apply:ghga_transpiler.transformations.to_list []
+    sheet_name: Publication

{ghga_transpiler-2.1.4 → ghga_transpiler-2.2.0}/src/ghga_transpiler/core.py

@@ -17,6 +17,8 @@
 
 """This module contains functionalities for processing excel sheets into json object."""
 
+from __future__ import annotations
+
 from collections.abc import Callable
 from importlib import resources
 
@@ -97,7 +99,7 @@ def convert_rows(header, rows) -> list[dict]:
     return [
         {
             key: value
-            for key, value in zip(header, row, strict=False)
+            for key, value in zip(header, row)
             if value is not None and value != ""
         }
         for row in rows

{ghga_transpiler-2.1.4 → ghga_transpiler-2.2.0}/src/ghga_transpiler/io.py

@@ -17,6 +17,8 @@
 
 """IO related functionality"""
 
+from __future__ import annotations
+
 import json
 import sys
 from importlib import resources

{ghga_transpiler-2.1.4 → ghga_transpiler-2.2.0}/src/ghga_transpiler/transformations.py

@@ -36,7 +36,7 @@ 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, strict=False))
+        return dict(zip(("key", "value"), splitted))
 
     def split_mult(value: str) -> list[dict]:
         """Converts string to attributes"""

{ghga_transpiler-2.1.4 → ghga_transpiler-2.2.0/src/ghga_transpiler.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ghga_transpiler
-Version: 2.1.4
+Version: 2.2.0
 Summary: GHGA-Transpiler - excel to JSON converter
 Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
 License: Apache 2.0
@@ -13,15 +13,18 @@ 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: >=3.12
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: typer>=0.12
 Requires-Dist: openpyxl==3.*,>=3.1.2
 Requires-Dist: defusedxml==0.*,>=0.7
-Requires-Dist: pydantic<3,>=2
+Requires-Dist: pydantic<3,>=2.6
 Requires-Dist: PyYAML~=6.0
 Requires-Dist: semver==3.*
+Requires-Dist: exceptiongroup>=1.0.0; python_version < "3.11"
+Requires-Dist: tomli>=2.0.0; python_version < "3.11"
+Requires-Dist: eval-type-backport==0.2.0; python_version < "3.10"
 
 
 [![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-2.1.4 → ghga_transpiler-2.2.0}/src/ghga_transpiler.egg-info/SOURCES.txt

@@ -19,6 +19,7 @@ src/ghga_transpiler/config/exceptions.py
 src/ghga_transpiler/configs/0.10.yaml
 src/ghga_transpiler/configs/1.0.yaml
 src/ghga_transpiler/configs/1.1.yaml
+src/ghga_transpiler/configs/2.0.yaml
 src/ghga_transpiler/configs/__init__.py
 tests/test_convert_workbook.py
 tests/test_create_config.py

ghga_transpiler-2.2.0/src/ghga_transpiler.egg-info/requires.txt

@@ -0,0 +1,13 @@
+typer>=0.12
+openpyxl==3.*,>=3.1.2
+defusedxml==0.*,>=0.7
+pydantic<3,>=2.6
+PyYAML~=6.0
+semver==3.*
+
+[:python_version < "3.10"]
+eval-type-backport==0.2.0
+
+[:python_version < "3.11"]
+exceptiongroup>=1.0.0
+tomli>=2.0.0

ghga_transpiler-2.1.4/src/ghga_transpiler.egg-info/requires.txt

@@ -1,6 +0,0 @@
-typer>=0.12
-openpyxl==3.*,>=3.1.2
-defusedxml==0.*,>=0.7
-pydantic<3,>=2
-PyYAML~=6.0
-semver==3.*