Update testdataset.py

testdataset.py

@@ -14,14 +14,9 @@
 # limitations under the License.
 
 """
-This is inpsired from the mednil implementation: https://huggingface.co/datasets/bigbio/mednli/blob/main/mednli.py
-
-The files comprising this dataset must be on the users local machine in a single directory that is
-passed to `datasets.load_datset` via the `data_dir` kwarg. This loader script will read the archive
-files directly (i.e. the user should not uncompress, untar or unzip any of the files). For example,
-if `data_dir` is `"testdataset"` it should contain the following files:
-testdataset
-├── testdataset.zip
+This implementation specifies a custom synapse download function that allows
+users to leverage the HF datasets API to download files through the Synapse API given
+Synapse authentication
 """
 
 import csv
@@ -45,7 +40,7 @@ Test Dataset
 
 _CITATION = ""
 
-_HOMEPAGE = "https://www.synapse.org/"
+_HOMEPAGE = "https://www.synapse.org/#!Synapse:syn51520471"
 
 _LICENSE = "other"
 
@@ -54,20 +49,21 @@ _URLS = {}
 _SOURCE_VERSION = "1.0.0"
 _BIGBIO_VERSION = "1.0.0"
 
+# This must be a synapse id of a synapse folder or project
 _SYN_ID = "syn51520473"
 
-@dataclass
-class BigBioConfig(datasets.BuilderConfig):
-    """BuilderConfig for BigBio."""
+# @dataclass
+# class BigBioConfig(datasets.BuilderConfig):
+#     """BuilderConfig for BigBio."""
 
-    name: str = None
-    version: datasets.Version = None
-    description: str = None
-    schema: str = None
-    subset_id: str = None
+#     name: str = None
+#     version: datasets.Version = None
+#     description: str = None
+#     schema: str = None
+#     subset_id: str = None
 
 
-def download_from_synapse(syn_id, path):
+def download_from_synapse(syn_id: str, path: str):
     """Download files from a Synapse folder or project containing test, train, dev csv files
 
     Args:
@@ -79,17 +75,23 @@ def download_from_synapse(syn_id, path):
         import synapseutils
     except ModuleNotFoundError as e:
         raise ModuleNotFoundError("synapseclient must be installed. pip install synapseclient")
-    syn = synapseclient.login()
+
+    try:
+        syn = synapseclient.login()
+    except Exception:
+        raise Exception("Please create a Synapse personal access token and either set up ~/.synapseConfig or `export SYNAPSE_AUTH_TOKEN=<PAT>`")
+
     synapseutils.syncFromSynapse(syn, syn_id, path=path)
     # syn.get(entity=syn_id, downloadLocation=path)
 
 
 class TestDataset(datasets.GeneratorBasedBuilder):
-    """MedNLI"""
+    """Test Dataset"""
 
     SOURCE_VERSION = datasets.Version(_SOURCE_VERSION)
-    BIGBIO_VERSION = datasets.Version(_BIGBIO_VERSION)
+    # BIGBIO_VERSION = datasets.Version(_BIGBIO_VERSION)
 
+    # TODO: Add in builder configs
     # BUILDER_CONFIGS = [
     #     BigBioConfig(
     #         name="default",
@@ -110,6 +112,7 @@ class TestDataset(datasets.GeneratorBasedBuilder):
     DEFAULT_CONFIG_NAME = "testdataset_source"
 
     def _info(self) -> datasets.DatasetInfo:
+        # TODO: This method specifies the datasets.DatasetInfo object which contains informations and typings for the dataset
         features = datasets.Features(
             {
                 "id": datasets.Value("string"),
@@ -122,25 +125,32 @@ class TestDataset(datasets.GeneratorBasedBuilder):
         )
 
         return datasets.DatasetInfo(
+            # This is the description that will appear on the datasets page.
             description=_DESCRIPTION,
+            # This defines the different columns of the dataset and their types
             features=features,
+            # Here we define them above because they are different between the two configurations
+            # If there's a common (input, target) tuple from the features, uncomment supervised_keys line below and
+            # specify them. They'll be used if as_supervised=True in builder.as_dataset.
+            # supervised_keys=("sentence", "label"),
+            # Homepage of the dataset for documentation
             homepage=_HOMEPAGE,
+            # License for the dataset if available
             license=str(_LICENSE),
             citation=_CITATION,
         )
 
     def _split_generators(self, dl_manager) -> List[datasets.SplitGenerator]:
+        # TODO: This method is tasked with downloading/extracting the data and defining the splits depending on the configuration
+        # If several configurations are possible (listed in BUILDER_CONFIGS), the configuration selected by the user is in self.config.name
+
         # This is where we can call the custom download function for Synapse
+        # https://huggingface.co/docs/datasets/v2.12.0/en/package_reference/builder_classes#datasets.DownloadManager.download_custom
         data_dir = dl_manager.download_custom(_SYN_ID, download_from_synapse)
-        # data_dir = self.config.data_dir
-        if data_dir is None:
-            raise ValueError(
-                "This is a local dataset. Please pass the data_dir kwarg to load_dataset."
-            )
-
         return [
             datasets.SplitGenerator(
                 name=datasets.Split.TRAIN,
+                # These kwargs will be passed to _generate_examples
                 gen_kwargs={
                     "filepath": os.path.join(data_dir, "train.csv"),
                     "split": "train",
@@ -163,6 +173,8 @@ class TestDataset(datasets.GeneratorBasedBuilder):
         ]
 
     def _generate_examples(self, filepath, split: str) -> Tuple[int, Dict]:
+        # TODO: This method handles input defined in _split_generators to yield (key, example) tuples from the dataset.
+        # The `row['id']` is for legacy reasons (tfds) and is not important in itself, but must be unique for each example.
         with open(filepath, "r") as f:
             test = csv.DictReader(f)
             for row in test: