From e40642186989d1051030cf2d6a16c4a1eb8eff28 Mon Sep 17 00:00:00 2001 From: tn Date: Mon, 26 Jan 2026 21:59:18 -0500 Subject: [PATCH 1/2] public method --- src/pyrecount/accessor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pyrecount/accessor.py b/src/pyrecount/accessor.py index e539b5f..d67480b 100644 --- a/src/pyrecount/accessor.py +++ b/src/pyrecount/accessor.py @@ -78,7 +78,7 @@ def __post_init__(self): root_url=self.root_url, organism=self.organism ) - def _get_project_urls(self, dtype) -> List[str]: + def get_project_urls(self, dtype) -> List[str]: project = ProjectLocator( root_organism_url=self.endpoints.root_organism_url, data_sources=self.endpoints.data_sources, From 91af2ed2de3a2849e07830bc6bd70fec33bbabc6 Mon Sep 17 00:00:00 2001 From: tn Date: Mon, 26 Jan 2026 22:02:13 -0500 Subject: [PATCH 2/2] public method --- src/pyrecount/accessor.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/pyrecount/accessor.py b/src/pyrecount/accessor.py index d67480b..1aa0da1 100644 --- a/src/pyrecount/accessor.py +++ b/src/pyrecount/accessor.py @@ -99,7 +99,7 @@ async def cache(self) -> None: if dtype not in CACHEABLE_DTYPES: continue - for url in self._get_project_urls(dtype): + for url in self.get_project_urls(dtype): fpath = urlparse(url).path.lstrip("/") if path.exists(fpath): continue @@ -139,7 +139,7 @@ def _valid_metadata_url(self, url: str, project_id: str) -> bool: def _metadata_load(self) -> pl.DataFrame: cache_meta: list[pl.DataFrame] = [] join_cols = ["rail_id", "external_id", "study"] - urls = self._get_project_urls(Dtype.METADATA) + urls = self.get_project_urls(Dtype.METADATA) for project_id in self.project_ids: dfs_for_project: list[pl.DataFrame] = [] @@ -210,7 +210,7 @@ def _jxn_load(self) -> Tuple[pl.DataFrame, pl.DataFrame]: cache_mm: List[pl.DataFrame] = [] cache_meta: List[pl.DataFrame] = [] - urls = self._get_project_urls(Dtype.JXN) + urls = self.get_project_urls(Dtype.JXN) for project_id in self.project_ids: project_urls = [ @@ -261,7 +261,7 @@ def _jxn_load(self) -> Tuple[pl.DataFrame, pl.DataFrame]: ) def _bw_load(self) -> pl.DataFrame: - urls = self._get_project_urls(Dtype.BW) + urls = self.get_project_urls(Dtype.BW) for project_id in self.project_ids: project_urls = [ @@ -328,7 +328,7 @@ def _read_counts(self, rname: str): return counts_dataframe def _gene_load(self) -> pl.DataFrame: - for url in self._get_project_urls(Dtype.GENE): + for url in self.get_project_urls(Dtype.GENE): fpath = urlparse(url).path.lstrip("/") if self.annotation.value in fpath: if any(fpath.endswith(ext) for ext in Extensions.GENE.value): @@ -338,7 +338,7 @@ def _gene_load(self) -> pl.DataFrame: return annotation, counts def _exon_load(self) -> pl.DataFrame: - for url in self._get_project_urls(Dtype.EXON): + for url in self.get_project_urls(Dtype.EXON): fpath = urlparse(url).path.lstrip("/") if self.annotation.value in fpath: if any(url.endswith(ext) for ext in Extensions.EXON.value):