Implemented methods within the prepare phase of the runner implementation to write the Exomiser application.properties in the input-dir based on what is contained in the tool_specific_configurations in the config.yaml contained in the input directory.
May look to be a large PR at first glance but the changes are focused on writing the application.properties and removing clashing methods in different run steps:
tool_specific_configurations.py -> Defined the fields expected in the config.yaml for creating the application.properties
write_application_properties.py -> All writing methods for writing specific data locations for the application.properties, handling optional extra databases
run.py -> Removed all editing methods of the application.properties as it should be properly configured in the prepare step
runner.py -> Added method within the prepare step to write the application.properties
test_run.py -> Removed all tests for editing the application.properties
test_write_application_properties.py -> Added tests for all methods for writing the application.properties
README.md -> Added pointers as to how the input directory config should be formatted
poetry.lock -> added pydantic library for reading in a nested dictionary to a nested data class
pyproject.toml -> added pydantic library for reading in a nested dictionary to a nested data class
Implemented methods within the
preparephase of the runner implementation to write the Exomiserapplication.propertiesin theinput-dirbased on what is contained in thetool_specific_configurationsin theconfig.yamlcontained in the input directory.May look to be a large PR at first glance but the changes are focused on writing the application.properties and removing clashing methods in different run steps:
tool_specific_configurations.py-> Defined the fields expected in theconfig.yamlfor creating the application.propertieswrite_application_properties.py-> All writing methods for writing specific data locations for the application.properties, handling optional extra databasesrun.py-> Removed all editing methods of the application.properties as it should be properly configured in the prepare steprunner.py-> Added method within thepreparestep to write the application.propertiestest_run.py-> Removed all tests for editing the application.propertiestest_write_application_properties.py-> Added tests for all methods for writing the application.propertiesREADME.md-> Added pointers as to how the input directory config should be formattedpoetry.lock-> added pydantic library for reading in a nested dictionary to a nested data classpyproject.toml-> added pydantic library for reading in a nested dictionary to a nested data class