fix: rdata_path

metagenomic_curated.py

@@ -12,7 +12,8 @@ import json
 #%%
 sqlite_url = "https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3"
 DATA_URL = "https://bioconductorhubs.blob.core.windows.net/experimenthub/curatedMetagenomicData/"
-    
+RDATA_URL = "https://huggingface.co/datasets/wwydmanski/metagenomic_curated/resolve/main/sampleMetadata.rda"
+
 CITATION = """\
 Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong D, Beghini F, Malik F, Ramos M, Dowd J, Huttenhower C, Morgan M, Segata N, Waldron L (2017). Accessible, curated metagenomic data through ExperimentHub. Nat. Methods, 14 (11), 1023-1024. ISSN 1548-7091, 1548-7105, doi: 10.1038/nmeth.4468.
 """
@@ -76,19 +77,20 @@ class MetagenomicCurated(datasets.GeneratorBasedBuilder):
         url = metadata['location_prefix']+metadata['rdatapaths'][0]['rdatapath']
 
         data_fname: str = dl_manager.download(url)
+        rdata_path: str = dl_manager.download(RDATA_URL)
 
         return [
-            datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": data_fname}),
+            datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": data_fname, "rdata_path": rdata_path}),
         ]
 
-    def _generate_examples(self, filepath):
+    def _generate_examples(self, filepath, rdata_path):
         parsed = rdata.parser.parse_file(filepath)
         converted = rdata.conversion.convert(parsed)
         expressions = list(converted.values())[0].assayData['exprs']
         data_df = expressions.to_pandas().T
         study_name = list(converted.keys())[0].split(".")[0]
 
-        meta = pyreadr.read_r("sampleMetadata.rda")['sampleMetadata']
+        meta = pyreadr.read_r(rdata_path)['sampleMetadata']
         metadata = meta.loc[meta['study_name'] == study_name].set_index('sample_id')
 
         for idx, (i, row) in enumerate(data_df.iterrows()):