Gen3SchemaDev 2.0.11__tar.gz

gen3schemadev-2.0.11/LICENSE

@@ -0,0 +1,201 @@
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gen3schemadev-2.0.11/PKG-INFO

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+Metadata-Version: 2.4
+Name: Gen3SchemaDev
+Version: 2.0.11
+Summary: Tool for data modelling in Gen3
+License: Apache 2.0
+License-File: LICENSE
+Author: JoshuaHarris391
+Author-email: harjo391@gmail.com
+Requires-Python: >=3.12.10,<4.0
+Classifier: License :: Other/Proprietary License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Dist: check-jsonschema (>=0.34.1,<0.35.0)
+Requires-Dist: gen3-validator (>=1.1.1,<2.0.0)
+Requires-Dist: linkml (>=1.9.4,<2.0.0)
+Requires-Dist: pydantic (>=2.11.9,<3.0.0)
+Requires-Dist: setuptools (>=70.0)
+Description-Content-Type: text/markdown
+
+# Developing a Gen3 Data Dictionary
+
+![overview.png](docs/img/overview.png)
+
+This repository aims to provide the documentation, learning materials, and software tools to facilitate the creation of a data model in Gen3.
+
+[Github Repo](https://github.com/AustralianBioCommons/gen3schemadev)
+
+***Pre-Reading**: Please become familiar with some [core data modelling concepts](docs/core_concepts/pre_reading.md) before starting.*
+
+
+## Using Gen3SchemaDev as a data modelling tool
+- [Quickstart](docs/gen3schemadev/quickstart.md)
+- [Guide to creating your first dictionary](docs/gen3schemadev/first_dictionary.md)
+- [Troubleshooting](docs/gen3schemadev/troubleshooting.md)
+
+
+## Deep dive into Gen3 Data Modelling
+*Special Thanks to Marion Shadbolt for providing the [source material](https://github.com/AustralianBioCommons/umccr-dictionary/tree/main/docs/schemas)*
+1. [Gen3 Dictionary Overview](docs/gen3_data_modelling/dictionary_structure.md)
+1. [Gen3 Schema Explained](docs/gen3_data_modelling/schemas.md)
+   1. [Descriptors](docs/gen3_data_modelling/descriptors.md)
+   2. [Links](docs/gen3_data_modelling/links.md)
+   3. [Properties](docs/gen3_data_modelling/properties.md)
+2. [Example of a Gen3 Schema yaml](docs/gen3_data_modelling/explainer_schema.yaml)
+3. [Handy tips](docs/gen3_data_modelling/handy_tips.md)
+4. [FAIR Concepts for Data Modelling](docs/core_concepts/fair.md)
+
+## For Developers
+
+### Installation and testing
+```bash
+# To install
+pip install poetry
+poetry install
+source $(poetry env info --path)/bin/activate
+gen3schemadev --version
+
+# To run tests
+poetry run pytest
+```
+
+### Contributing
+Gen3SchemaDev is an open source project, and we highly encourage any contributions and PRs. Specifically we need the community to help with the following:
+1. Keeping the [gen3 metaschema](src/gen3schemadev/schema/schema_templates/gen3_metaschema.yml) up to date 
+2. Adding business rule logic to the [rule validator](src/gen3schemadev/validators/rule_validator.py) module. 
+   1. For example, a node with the category `data_file` should have a collection of required data file properties such as md5sum, filesize, etc.
+
+For PRs, please follow the [contributing guidelines](CONTRIBUTING.md).
+
+## License
+[Apache 2.0](LICENSE)
+
+

gen3schemadev-2.0.11/README.md

@@ -0,0 +1,53 @@
+# Developing a Gen3 Data Dictionary
+
+![overview.png](docs/img/overview.png)
+
+This repository aims to provide the documentation, learning materials, and software tools to facilitate the creation of a data model in Gen3.
+
+[Github Repo](https://github.com/AustralianBioCommons/gen3schemadev)
+
+***Pre-Reading**: Please become familiar with some [core data modelling concepts](docs/core_concepts/pre_reading.md) before starting.*
+
+
+## Using Gen3SchemaDev as a data modelling tool
+- [Quickstart](docs/gen3schemadev/quickstart.md)
+- [Guide to creating your first dictionary](docs/gen3schemadev/first_dictionary.md)
+- [Troubleshooting](docs/gen3schemadev/troubleshooting.md)
+
+
+## Deep dive into Gen3 Data Modelling
+*Special Thanks to Marion Shadbolt for providing the [source material](https://github.com/AustralianBioCommons/umccr-dictionary/tree/main/docs/schemas)*
+1. [Gen3 Dictionary Overview](docs/gen3_data_modelling/dictionary_structure.md)
+1. [Gen3 Schema Explained](docs/gen3_data_modelling/schemas.md)
+   1. [Descriptors](docs/gen3_data_modelling/descriptors.md)
+   2. [Links](docs/gen3_data_modelling/links.md)
+   3. [Properties](docs/gen3_data_modelling/properties.md)
+2. [Example of a Gen3 Schema yaml](docs/gen3_data_modelling/explainer_schema.yaml)
+3. [Handy tips](docs/gen3_data_modelling/handy_tips.md)
+4. [FAIR Concepts for Data Modelling](docs/core_concepts/fair.md)
+
+## For Developers
+
+### Installation and testing
+```bash
+# To install
+pip install poetry
+poetry install
+source $(poetry env info --path)/bin/activate
+gen3schemadev --version
+
+# To run tests
+poetry run pytest
+```
+
+### Contributing
+Gen3SchemaDev is an open source project, and we highly encourage any contributions and PRs. Specifically we need the community to help with the following:
+1. Keeping the [gen3 metaschema](src/gen3schemadev/schema/schema_templates/gen3_metaschema.yml) up to date 
+2. Adding business rule logic to the [rule validator](src/gen3schemadev/validators/rule_validator.py) module. 
+   1. For example, a node with the category `data_file` should have a collection of required data file properties such as md5sum, filesize, etc.
+
+For PRs, please follow the [contributing guidelines](CONTRIBUTING.md).
+
+## License
+[Apache 2.0](LICENSE)
+

gen3schemadev-2.0.11/pyproject.toml

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+[project]
+name = "Gen3SchemaDev"
+version = "2.0.11"
+description = "Tool for data modelling in Gen3"
+authors = [
+    {name = "JoshuaHarris391",email = "harjo391@gmail.com"}
+]
+license = {text = "Apache 2.0"}
+readme = "README.md"
+requires-python = ">=3.12.10,<4.0"
+dependencies = [
+    "setuptools>=70.0",
+    "gen3-validator (>=1.1.1,<2.0.0)",
+    "linkml (>=1.9.4,<2.0.0)",
+    "check-jsonschema (>=0.34.1, <0.35.0)",
+    "pydantic (>=2.11.9,<3.0.0)"
+]
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.4.2"
+ipykernel = "^6.30.1"
+
+[build-system]
+requires = ["poetry-core>=2.0.0,<3.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[project.scripts]
+gen3schemadev = "gen3schemadev.cli:main"

gen3schemadev-2.0.11/src/gen3schemadev/__init__.py

@@ -0,0 +1,18 @@
+# Expose main submodules for convenient import
+from .schema import *
+from .validators import *
+from .cli import *
+from .utils import *
+from .converter import *
+from .ddvis import *
+
+try:
+    from importlib.metadata import version, PackageNotFoundError
+except ImportError:
+    from importlib_metadata import version, PackageNotFoundError  # for Python<3.8
+
+try:
+    from importlib.metadata import version
+    __version__ = version('gen3schemadev')
+except Exception:
+    __version__ = 'unknown'

gen3schemadev-2.0.11/src/gen3schemadev/cli.py

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+import argparse
+import logging
+import sys
+import os
+
+from gen3schemadev.schema.gen3_template import (
+    get_metaschema,
+    generate_gen3_template,
+    generate_def_template,
+    generate_setting_template,
+    generate_terms_template,
+    generate_core_metadata_template,
+)
+from gen3schemadev.utils import write_yaml, load_yaml, bundle_yamls, write_json
+from gen3schemadev.schema.input_schema import DataModel
+from gen3schemadev.converter import get_node_names, populate_template
+from gen3schemadev.utils import bundled_schema_to_list_dict, resolve_schema
+from gen3schemadev.validators.metaschema_validator import validate_schema_with_metaschema
+from importlib.metadata import version
+from gen3schemadev.ddvis import visualise_with_docker
+
+# def get_version():
+#     return "2.0.6"
+
+
+def main():
+    version_parser = argparse.ArgumentParser(add_help=False)
+    version_parser.add_argument(
+        '--version',
+        action='version',
+        version=f"gen3schemadev {version('gen3schemadev')}"
+    )
+
+    version_parser.parse_known_args()
+
+    parser = argparse.ArgumentParser(
+        description="Gen3 Schema Development Tool"
+    )
+    parser.add_argument(
+        '--version',
+        action='version',
+        version=f"%(prog)s {version('gen3schemadev')}"
+    )
+
+    subparsers = parser.add_subparsers(dest="command", required=False)
+
+    # Create 'generate' subcommand
+    generate_parser = subparsers.add_parser(
+        "generate",
+        help="Generate schemas"
+    )
+    generate_parser.add_argument(
+        "-i", "--input",
+        required=True,
+        help="Input YAML file"
+    )
+    generate_parser.add_argument(
+        "-o", "--output",
+        required=True,
+        help="Output directory"
+    )
+    generate_parser.add_argument(
+        "--debug",
+        action="store_true",
+        help="Set logging level to DEBUG"
+    )
+
+    # Create 'bundle' subcommand
+    bundle_parser = subparsers.add_parser(
+        "bundle",
+        help="Bundle YAML files"
+    )
+    bundle_parser.add_argument(
+        "-i", "--input",
+        required=True,
+        help="Input directory"
+    )
+    bundle_parser.add_argument(
+        "-f", "--filename",
+        required=True,
+        help="Output Filename"
+    )
+    bundle_parser.add_argument(
+        "--debug",
+        action="store_true",
+        help="Set logging level to DEBUG"
+    )
+
+    # Create 'validate' subcommand
+    validate_parser = subparsers.add_parser(
+        "validate",
+        help="Validate schemas"
+    )
+    validate_parser.add_argument(
+        "-b", "--bundled",
+        required=False,
+        help="Bundled JsonSchema file"
+    )
+    validate_parser.add_argument(
+        "-y", "--yamls",
+        required=False,
+        help="Directory of Gen3 Yaml files"
+    )
+    validate_parser.add_argument(
+        "--debug",
+        action="store_true",
+        help="Set logging level to DEBUG"
+    )
+    
+    # Create 'visualise' subcomand
+    visualise_parser = subparsers.add_parser(
+        "visualise",
+        help="Visualise schemas"
+    )
+    visualise_parser.add_argument(
+        "-i", "--input",
+        required=True,
+        help="Path to Bundled Gen3 JsonSchema file"
+    )
+    visualise_parser.add_argument(
+        "--debug",
+        action="store_true",
+        help="Set logging level to DEBUG"
+    )
+
+    args = parser.parse_args()
+    
+    # Handle case where no command is provided
+    if args.command is None:
+        parser.print_help(sys.stderr)
+        sys.exit(0)
+
+    # Set up basic logging configuration
+    # If the subcommand has --debug, set to DEBUG, else INFO
+    log_level = logging.ERROR
+    if hasattr(args, "debug") and getattr(args, "debug", False):
+        log_level = logging.DEBUG
+    logging.basicConfig(
+        level=log_level,
+        format="%(asctime)s [%(levelname)s] %(message)s"
+    )
+    logger = logging.getLogger(__name__)
+
+
+    if args.command == "generate":
+        print("Starting schema generation process...")
+        metaschema = get_metaschema()
+        converter_template = generate_gen3_template(metaschema)
+        print(f"Loading input YAML from: {args.input}")
+        data = load_yaml(args.input)
+        print("Validating input data model...")
+        validated_model = DataModel.model_validate(data)
+        node_names = get_node_names(validated_model)
+        print(f"Found nodes: {node_names}")
+
+        for node in node_names:
+            print(f"Populating template for node: '{node}'")
+            out_template = populate_template(node, validated_model, converter_template)
+            print(f"Writing output YAML to: {args.output}/{node}.yaml")
+            write_yaml(out_template, f"{args.output}/{node}.yaml")
+
+        print('Writing auxiliary files')
+        write_yaml(generate_def_template(), f"{args.output}/_definitions.yaml")
+        setting_dict = generate_setting_template()
+        setting_dict['_dict_version'] = validated_model.version
+        write_yaml(setting_dict, f"{args.output}/_settings.yaml")
+        write_yaml(generate_terms_template(), f"{args.output}/_terms.yaml")
+        write_yaml(generate_core_metadata_template(), f"{args.output}/core_metadata_collection.yaml")
+
+        print("Schema generation process complete.")
+
+    elif args.command == "bundle":
+        print(f"Bundling YAML files from directory: {args.input}")
+        bundle_dict = bundle_yamls(args.input)
+        print(f"Writing bundled schema to file: {args.filename}")
+        write_json(bundle_dict, args.filename)
+        print("Bundling process complete.")
+
+    elif args.command == "validate":
+        print("Starting validation process...")
+        metaschema = get_metaschema()
+
+        resolve_schema_obj = None
+        if args.bundled:
+            print(f"Resolving schema from bundled file: {args.bundled}")
+            resolve_schema_obj = resolve_schema(schema_path=args.bundled)
+        elif args.yamls:
+            print(f"Bundling and resolving schemas from directory: {args.yamls}")
+            resolve_schema_obj = resolve_schema(schema_dir=args.yamls)
+
+        if resolve_schema_obj is None:
+            logger.error("You must provide either --bundled or --yamls for validation.")
+            sys.exit(1)
+
+        schema_list = bundled_schema_to_list_dict(resolve_schema_obj)
+        print(f"Found {len(schema_list)} schemas to validate.")
+
+        for schema in schema_list:
+            schema_id = schema.get('id', '<no id>')
+            print(f"Validating schema: {schema_id}")
+            validate_schema_with_metaschema(
+                schema,
+                metaschema=metaschema,
+                verbose=True
+            )
+            print(f"Successfully validated schema: {schema_id}")
+        
+        print("Validation process complete.")
+
+    elif args.command == "visualise":
+        print(f"Visualising schema from file: {args.input}")
+        visualise_with_docker(args.input)
+
+if __name__ == "__main__":
+    main()