fix: fix dataset errors

README.md

@@ -9,8 +9,8 @@ Please refer to the [study list](https://experimenthub.bioconductor.org/package/
 
 ## Sample usage
 ```python
-ds = datasets.load_dataset("wwydmanski/metagenomic_curated", "EH1914")
-X = np.array(ds['train']['features'])
+ds = datasets.load_dataset("./metagenomic_curated.py", "EH1726")
+X = np.array([list(i.values()) for i in ds['train']['features']])
 y = np.array([x['study_condition'] for x in ds['train']['metadata']])
 ```
 

metagenomic_curated.py

@@ -1,4 +1,5 @@
 #%%
+from typing import Any
 import pyreadr
 import pandas as pd
 import numpy as np
@@ -8,6 +9,7 @@ import datasets
 import tempfile
 import rdata
 import json
+from typing import Any
 
 #%%
 sqlite_url = "https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3"
@@ -19,22 +21,6 @@ Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong D, Beghini F, Mal
 """
 
 # %%
-# def get_metadata():
-#     with tempfile.NamedTemporaryFile(delete=False) as tmpfname:
-#         r = requests.get(sqlite_url, allow_redirects=True)
-#         open(tmpfname.name, 'wb').write(r.content)
-
-#     db = sqlite3.connect(tmpfname.name)
-#     cursor = db.cursor()
-#     cur = cursor.execute("""SELECT * FROM resources""")
-
-#     ehid = []
-#     descriptions = []
-#     for row in cur.fetchall():
-#         if "curatedMetagenomicData" in str(row[-1]):
-#             ehid.append(row[1])
-#             descriptions.append(row[7])
-#     return ehid, descriptions
 
 def get_metadata():
     ehids = []
@@ -62,12 +48,22 @@ class MetagenomicCurated(datasets.GeneratorBasedBuilder):
         for ehid, d in zip(ehids, descriptions)
     ]
 
+    def __call__(self, *args: Any, **kwds: Any) -> Any:
+        return super().__call__(*args, **kwds)
+
     def _info(self):
+        try:
+            features = {
+                i: datasets.Value("float32") for i in self.features
+            }
+        except:
+            features = {}
         return datasets.DatasetInfo(
             description=self.config.description,
             citation=CITATION,
             homepage="https://waldronlab.io/curatedMetagenomicData/index.html",
             license="https://www.r-project.org/Licenses/Artistic-2.0",
+            # features=features
         )
     
     def _split_generators(self, dl_manager):
@@ -87,22 +83,29 @@ class MetagenomicCurated(datasets.GeneratorBasedBuilder):
         parsed = rdata.parser.parse_file(filepath)
         converted = rdata.conversion.convert(parsed)
         expressions = list(converted.values())[0].assayData['exprs']
+
         data_df = expressions.to_pandas().T
+        self.features = data_df.columns
+
         study_name = list(converted.keys())[0].split(".")[0]
 
         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()):
+            try:
+                md = {i: str(j) for i, j in metadata.loc[i].to_dict().items()}
+            except KeyError:
+                md = {}
             yield idx, {
-                "features": row.values,
-                "metadata": {i: str(j) for i, j in metadata.loc[i].to_dict().items()}
+                "features": row.to_dict(),
+                "metadata": md
             }
 
 # %%
 if __name__=="__main__":
-    ds = datasets.load_dataset("./metagenomic_curated.py", "EH1914")
-    X = np.array(ds['train']['features'])
+    ds = datasets.load_dataset("./metagenomic_curated.py", "EH1726")
+    X = np.array([list(i.values()) for i in ds['train']['features']])
     y = np.array([x['study_condition'] for x in ds['train']['metadata']])
 
 # %%