Do not hardcode list of available catalogues

meteor/downloader.py

@@ -22,12 +22,16 @@
 from time import time
 import tarfile
 import json
+from typing import ClassVar
 
 
 @dataclass
 class Downloader(Session):
     """Download and prepare catalogues"""
 
+    CONFIG_DATA_FILE: ClassVar[Path] = Path("data/zenodo.json")
+    TEST_CATALOGUE: ClassVar[str] = "test"
+
     meteor: type[Component]
     choice: str
     taxonomy: bool
@@ -36,14 +40,25 @@ class Downloader(Session):
     catalogues_config: dict = field(default_factory=dict)
     start_time: float = field(default_factory=float)
 
-    def __post_init__(self) -> None:
+    @staticmethod
+    def load_catalogues_config() -> dict:
         try:
-            config_data = importlib.resources.files("meteor") / "data/zenodo.json"
+            config_data = importlib.resources.files("meteor") / str(Downloader.CONFIG_DATA_FILE)
             with importlib.resources.as_file(config_data) as configuration_path:
                 with configuration_path.open("rt", encoding="UTF-8") as config:
-                    self.catalogues_config = json.load(config)
+                    return json.load(config)
         except AssertionError:
-            logging.error("The file zenodo.json is missing in meteor source")
+            logging.error("The file %s is missing in meteor source", Downloader.CONFIG_DATA_FILE.name)
+
+    @staticmethod
+    def get_available_catalogues() -> list[str]:
+        catalogues_config = Downloader.load_catalogues_config()
+        available_catalogues = list(catalogues_config.keys())
+        available_catalogues.remove(Downloader.TEST_CATALOGUE)
+        return available_catalogues
+
+    def __post_init__(self) -> None:
+        self.catalogues_config = Downloader.load_catalogues_config()
         self.meteor.ref_dir.mkdir(exist_ok=True, parents=True)
         if self.taxonomy:
             self.data_type = "taxonomy_info"
@@ -111,7 +126,7 @@ def execute(self) -> None:
             )
             urlretrieve(url, filename=catalogue, reporthook=self.show_progress)
             print(flush=True)
-            if self.choice == "test":
+            if self.choice == Downloader.TEST_CATALOGUE:
                 for sample in self.catalogues_config[self.choice]["samples"]:
                     logging.info(f"Download {sample} fastq file")
                     url_fastq = self.catalogues_config[self.choice]["samples"][sample][

meteor/meteor.py

@@ -148,18 +148,7 @@ def get_arguments() -> Namespace:  # pragma: no cover
         dest="user_choice",
         type=str,
         required=True,
-        choices=[
-            "cat_gut",
-            "chicken_caecal",
-            "dog_gut",
-            "human_gut",
-            "human_oral",
-            "human_skin",
-            "mouse_gut",
-            "rabbit_gut",
-            "rat_gut",
-            "pig_gut",
-        ],
+        choices=Downloader.get_available_catalogues(),
         help="Select the catalogue to download.",
     )
     download_parser.add_argument(