Merge pull request #816 from malariagen/fix/phenotype-path-construction

fix(phenotypes): Correct GCS path construction

Author: jonbrenas

malariagen_data/anoph/phenotypes.py

@@ -1,6 +1,6 @@
 import pandas as pd
 import xarray as xr
-from typing import Callable, Optional, List, Any
+from typing import Callable, Optional, List, Any, TYPE_CHECKING
 import warnings
 import fsspec
 from numpydoc_decorator import doc  # type: ignore
@@ -15,14 +15,20 @@ class AnophelesPhenotypeData:
     Inherited by AnophelesDataResource subclasses (e.g., Ag3).
     """
 
-    # Type annotations for MyPy
-    _url: str
-    _fs: fsspec.AbstractFileSystem
-    sample_metadata: Callable[..., pd.DataFrame]
-    sample_sets: list[str]
-    _prep_sample_sets_param: Callable[..., Any]
-    snp_calls: Callable[..., Any]
-    haplotypes: Callable[..., Any]
+    if TYPE_CHECKING:
+        # Type annotations for MyPy
+        _url: str
+        _fs: fsspec.AbstractFileSystem
+        sample_metadata: Callable[..., pd.DataFrame]
+        _base_path: str
+        _major_version_path: str
+        _release_to_path: Callable[[str], str]
+        lookup_release: Callable[..., str]
+        _prep_sample_sets_param: Callable[..., Any]
+
+        sample_sets: Callable[..., pd.DataFrame]
+        snp_calls: Callable[..., Any]
+        haplotypes: Callable[..., Any]
 
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
@@ -35,11 +41,14 @@ def _load_phenotype_data(
         Load raw phenotypic data from GCS for given sample sets.
         """
         phenotype_dfs = []
-        base_phenotype_path = f"{self._url}v3.2/phenotypes/all"
 
         for sample_set in sample_sets:
-            phenotype_path = f"{base_phenotype_path}/{sample_set}/phenotypes.csv"
             try:
+                release = self.lookup_release(sample_set=sample_set)
+                release_path = self._release_to_path(release)
+
+                phenotype_path = f"{self._base_path}/{release_path}/phenotypes/all/{sample_set}/phenotypes.csv"
+
                 if not self._fs.exists(phenotype_path):
                     warnings.warn(
                         f"Phenotype data file not found for {sample_set} at {phenotype_path}"
@@ -61,14 +70,9 @@ def _load_phenotype_data(
                 df_pheno["sample_set"] = sample_set
                 phenotype_dfs.append(df_pheno)
 
-            except FileNotFoundError:
-                warnings.warn(
-                    f"Phenotype data file not found for {sample_set} at {phenotype_path}"
-                )
-                continue
             except Exception as e:
                 warnings.warn(
-                    f"Unexpected error loading phenotype data for {sample_set} from {phenotype_path}: {e}"
+                    f"Unexpected error loading phenotype data for {sample_set}: {e}"
                 )
                 continue
 
@@ -480,11 +484,14 @@ def phenotype_sample_sets(self) -> List[str]:
 
         all_sample_sets = self.sample_sets()["sample_set"].tolist()  # type: ignore[operator]
         phenotype_sample_sets = []
-        base_phenotype_path = f"{self._url}v3.2/phenotypes/all"
 
         for sample_set in all_sample_sets:
             try:
-                phenotype_path = f"{base_phenotype_path}/{sample_set}/phenotypes.csv"
+                release = self.lookup_release(sample_set=sample_set)
+                release_path = self._release_to_path(release)
+
+                phenotype_path = f"{self._base_path}/{release_path}/phenotypes/all/{sample_set}/phenotypes.csv"
+
                 if self._fs.exists(phenotype_path):
                     phenotype_sample_sets.append(sample_set)
             except Exception: