Tokay Gecko models (#39)

.github/workflows/pypi_publish.yaml

@@ -61,12 +61,12 @@ jobs:
           pytest .
 
       - name: Publish distribution package to PyPI (test)
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-          repository_url: https://test.pypi.org/legacy/
+          repository-url: https://test.pypi.org/legacy/
 
       - name: Publish distribution package to PyPI (production)
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}

.static_files

@@ -15,6 +15,7 @@
 scripts/script_utils/__init__.py
 scripts/script_utils/cli.py
 
+scripts/__init__.py
 scripts/license_checker.py
 scripts/get_package_name.py
 scripts/update_config_docs.py

ghga_event_schemas/__init__.py

@@ -15,4 +15,4 @@
 
 """A package that collects schemas used for events exchanges between GHGA service."""
 
-__version__ = "0.13.2"
+__version__ = "0.13.3"

ghga_event_schemas/pydantic_.py

@@ -20,7 +20,7 @@
 """
 
 from enum import Enum
-from typing import Optional
+from typing import Any, Optional
 
 from pydantic import BaseModel, EmailStr, Field, validator
 
@@ -53,13 +53,30 @@ class Config:
         extra = "allow"
 
 
-class MetadataDatasetOverview(BaseModel):
+class MetadataDatasetID(BaseModel):
+    """Simplified model to pass artifact/dataset ID to claims repository for deletion"""
+
+    accession: str = Field(..., description="The dataset accession.")
+
+
+class MetadataDataset(MetadataDatasetID):
+    """Model to populate MASS from metldata artifacts"""
+
+    class_name: str = Field(
+        ...,
+        description="The name of the class this dataset/artifact resource corresponds to.",
+    )
+    content: dict[str, Any] = Field(
+        ..., description="The metadata content of this dataset/artifact resource."
+    )
+
+
+class MetadataDatasetOverview(MetadataDatasetID):
     """
     Overview of files contained in a dataset.
     Only fields relevant to the WPS are included for now. May be extended.
     """
 
-    accession: str = Field(..., description="The dataset accession.")
     title: str = Field(..., description="The title of the dataset.")
     stage: MetadataDatasetStage = Field(
         ..., description="The current stage of this dataset."

scripts/__init__.py

@@ -0,0 +1,17 @@
+# Copyright 2021 - 2023 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.
+#
+
+"""Scripts and utils used during development or in CI pipelines."""

scripts/update_template_files.py

@@ -33,7 +33,7 @@
 try:
     from script_utils.cli import echo_failure, echo_success, run
 except ImportError:
-    echo_failure = echo_success = print  # type: ignore
+    echo_failure = echo_success = print
 
     def run(main_fn):
         """Run main function without cli tools (typer)."""

setup.cfg

@@ -38,6 +38,7 @@ packages = find:
 install_requires =
     jsonschema>=4.17.3,<5.0.0
     pydantic[email]>=1.0.0,<2.0.0
+    dnspython<2.4.0
 
 python_requires = >= 3.9