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Fix phenotype data path construction and remove hardcoded release version #818

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Fix phenotype data path construction and remove hardcoded release version #818

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11 changes: 8 additions & 3 deletions malariagen_data/anoph/phenotypes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
from typing import Callable, Optional, List, Any
import warnings
import fsspec
import posixpath
from numpydoc_decorator import doc # type: ignore

from ..util import check_types
Expand Down Expand Up @@ -35,10 +36,12 @@ 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"
#base_phenotype_path = f"{self._url}v3.2/phenotypes/all"
release = getattr(self, "release", "v3.2")
base_phenotype_path = posixpath.join(self._url, release, "phenotypes", "all")

for sample_set in sample_sets:
phenotype_path = f"{base_phenotype_path}/{sample_set}/phenotypes.csv"
phenotype_path = posixpath.join(base_phenotype_path,sample_set,"phenotypes.csv")
try:
if not self._fs.exists(phenotype_path):
warnings.warn(
Expand Down Expand Up @@ -480,7 +483,9 @@ 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"
#base_phenotype_path = f"{self._url}v3.2/phenotypes/all"
release = getattr(self,"release","v3.2")
base_phenotype_path = posixpath.join(self._url,release,"phenotypes","all")

for sample_set in all_sample_sets:
try:
Expand Down