fix dataset loading script

binding_affinity.py

@@ -15,7 +15,6 @@
 """TODO: A dataset of protein sequences, ligand SMILES and binding affinities."""
 
 import huggingface_hub
-import pandas as pd
 import os
 import pyarrow.parquet as pq
 import datasets
@@ -92,8 +91,10 @@ class BindingAffinity(datasets.ArrowBasedBuilder):
         features = datasets.Features(
             {
                 "seq": datasets.Value("string"),
-                "smiles_can": datasets.Value("string"),
+                "smiles": datasets.Value("string"),
+                "affinity_uM": datasets.Value("float"),
                 "neg_log10_affinity_M": datasets.Value("float"),
+                "smiles_can": datasets.Value("string"),
                 "affinity": datasets.Value("float"),
                 # These are the features of your dataset like images, labels ...
             }
@@ -124,16 +125,17 @@ class BindingAffinity(datasets.ArrowBasedBuilder):
         # It can accept any type or nested list/dict and will give back the same structure with the url replaced with path to local files.
         # By default the archives will be extracted and a path to a cached folder where they are extracted is returned instead of the archive
         files = dl_manager.download_and_extract(_URLs)
+        print(files)
         return [
             datasets.SplitGenerator(
-                name=datasets.Split.TRAIN,
                 # These kwargs will be passed to _generate_examples
+                name=datasets.Split.TRAIN,
                 gen_kwargs={
-                    "filepath": files["default"],
+                    'filepath': files["default"],
                 },
             ),
             datasets.SplitGenerator(
-                name=datasets.Split.TRAIN+"_no_kras",
+                name='no_kras',
                 # These kwargs will be passed to _generate_examples
                 gen_kwargs={
                     "filepath": files["no_kras"],
@@ -142,24 +144,12 @@ class BindingAffinity(datasets.ArrowBasedBuilder):
 
         ]
 
-    def _generate_examples(
-        self, filepath, split  # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
-    ):
-        """ Yields examples as (key, example) tuples. """
-        # This method handles input defined in _split_generators to yield (key, example) tuples from the dataset.
-        # The `key` is here for legacy reason (tfds) and is not important in itself.
-
-        df = pd.read_parquet(filepath)
-        for k, row in df.iterrows():
-            yield k, {
-                "seq": row["seq"],
-                "smiles_can": row["smiles_can"],
-                "neg_log10_affinity_M": row["neg_log10_affinity_M"],
-                "affinity_uM": row["affinity_uM"],
-            }
-
     def _generate_tables(
-        self, filepath, split  # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
+        self, filepath
     ):
-        df = pq.read_table(filepath)
-        yield split, df
+        from pyarrow import fs
+        local = fs.LocalFileSystem()
+
+        for i, f in enumerate([filepath]):
+            print(f)
+            yield i, pq.read_table(f,filesystem=local)