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chore(repository): Use builders to load proper dictionary (#11)
Use builder pattern to load dictionary to allow support for more dictionary schema locations in the future
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@@ -30,7 +30,7 @@ install_requires = | |
| attrs | ||
| click | ||
| colored | ||
| dulwich | ||
| dulwich>=0.20.31 | ||
| graphviz | ||
| Jinja2 | ||
| jsonschema | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,112 @@ | ||
| import logging | ||
| import os | ||
| from pathlib import Path | ||
| from typing import Optional, cast | ||
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| from psqlgml.dictionaries import repository, schemas | ||
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| __all__ = ["load", "load_local", "DictionaryReader"] | ||
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| logger = logging.getLogger(__name__) | ||
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| class DictionaryReader: | ||
| def __init__(self, name: str, version: str) -> None: | ||
| self.name = name | ||
| self.version = version | ||
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| self._url: Optional[str] = None | ||
| self._is_tag: bool = True | ||
| self._overwrite: bool = False | ||
| self._schema_path: str = "gdcdictionary/schemas" | ||
| self._base_dir: Path = Path( | ||
| os.getenv("GML_DICTIONARY_HOME", f"{Path.home()}/.gml/dictionaries") | ||
| ) | ||
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| self.reader: Optional[repository.Repository] = None | ||
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| def local(self, base_directory: Optional[Path] = None) -> "DictionaryReader": | ||
| logger.debug(f"Reading local Dictionary {self.name}: {self.version} @ {base_directory}") | ||
| self._base_dir = base_directory or self._base_dir | ||
| return self | ||
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| def git( | ||
| self, | ||
| url: str, | ||
| overwrite: bool, | ||
| schema_path: str = "gdcdictionary/schemas", | ||
| is_tag: bool = True, | ||
| ) -> "DictionaryReader": | ||
| logger.debug(f"Reading remote Dictionary {self.name}: {self.version} @ {url}") | ||
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| self._url = url | ||
| self._is_tag = is_tag | ||
| self._overwrite = overwrite | ||
| self._schema_path = schema_path | ||
| return self | ||
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| def is_preloaded_dictionary(self) -> bool: | ||
| """Checks if a dictionary with name and version has been previously loaded""" | ||
| return Path(f"{self._base_dir}/{self.name}/{self.version}").exists() | ||
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| def read(self) -> schemas.Dictionary: | ||
| if self.is_preloaded_dictionary() and not self._overwrite: | ||
| return repository.LocalRepository(name=self.name, base_directory=self._base_dir).read( | ||
| self.version | ||
| ) | ||
| return repository.GitRepository( | ||
| name=self.name, | ||
| url=cast(str, self._url), | ||
| schema_path=self._schema_path, | ||
| force=self._overwrite, | ||
| is_tag=self._is_tag, | ||
| ).read(self.version) | ||
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| def load_local( | ||
| name: str, version: str, dictionary_location: Optional[str] = None | ||
| ) -> schemas.Dictionary: | ||
| """Attempts to load a previously downloaded dictionary from a local location | ||
| Args: | ||
| name: name/label used to save the dictionary locally | ||
| version: version number of the saved dictionary | ||
| dictionary_location: base directory where all dictionaries are dumped | ||
| Returns: | ||
| A Dictionary instance if dictionary files were previously downloaded, else None | ||
| """ | ||
| base_path = Path(dictionary_location) if dictionary_location else None | ||
| return DictionaryReader(name, version).local(base_path).read() | ||
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| def load( | ||
| version: str, | ||
| overwrite: bool = False, | ||
| name: str = "gdcdictionary", | ||
| schema_path: str = "gdcdictionary/schemas", | ||
| git_url: str = "https://github.com/NCI-GDC/gdcdictionary.git", | ||
| is_tag: bool = True, | ||
| ) -> schemas.Dictionary: | ||
| """Downloads and loads a dictionary instance based on the input parameters | ||
| Args: | ||
| version: dictionary version number | ||
| overwrite: force a re-download of the dictionary files, defaults to false | ||
| name: name/label used to save the dictionary locally, defaults to gdcdictionary | ||
| schema_path: path to the dictionary files with the dictionary git repository | ||
| git_url: URL to the git repository | ||
| is_tag: tag or commit | ||
| Returns: | ||
| A Dictionary instance | ||
| """ | ||
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| return ( | ||
| DictionaryReader(name, version) | ||
| .git( | ||
| url=git_url, | ||
| is_tag=is_tag, | ||
| overwrite=overwrite, | ||
| schema_path=schema_path, | ||
| ) | ||
| .read() | ||
| ) |
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