Update data URL in pubmed dataset (#3692)

* Update data URL in pubmed dataset

* Update config name and version

* Update dummy data

* Delete metadata JSON

* Delete dummy data

* Add citation acknowledgement and clean

* Update hardcoded exception in CI test for pubmed dataset

* Revert "Delete dummy data"

This reverts commit 9d12f05c1dca14a14100075d598c20e7c3637b56.

Commit from https://github.com/huggingface/datasets/commit/5437925190ffc7ec532396e771e715e9fbd32a48

dummy/{2021/1.0.0 → 2022/2.0.0}/dummy_data.zip

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:e0ef6fe2745e3d8469ea99bdb1eecf97d87d75c93055c051c80912c6ab51885e
-size 1920
+oid sha256:f434e2dda488f7c1cee83060a2500904d9773fb9bdb2d2ff2774b82fe69b2f71
+size 1960

pubmed.py

@@ -12,7 +12,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""TODO: Add a description here."""
+"""MEDLINE/PubMed data."""
 
 
 import copy
@@ -24,11 +24,10 @@ import datasets
 logger = datasets.logging.get_logger(__name__)
 
 
-# Find for instance the citation on arxiv or on the dataset repo/website
 _CITATION = """\
+Courtesy of the U.S. National Library of Medicine.
 """
 
-# You can copy an official description
 _DESCRIPTION = """\
 NLM produces a baseline set of MEDLINE/PubMed citation records in XML format for download on an annual basis. The annual baseline is released in December of each year. Each day, NLM produces update files that include new, revised and deleted citations. See our documentation page for more information.
 """
@@ -37,10 +36,10 @@ _HOMEPAGE = "https://www.nlm.nih.gov/databases/download/pubmed_medline.html"
 
 _LICENSE = ""
 
-# TODO: Add link to the official dataset URLs here
 # The HuggingFace dataset library don't host the datasets but only point to the original files
 # This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
-_URLs = [f"ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed21n{i:04d}.xml.gz" for i in range(1, 1063)]
+# Note these URLs here are used by MockDownloadManager.create_dummy_data_list
+_URLs = [f"ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed22n{i:04d}.xml.gz" for i in range(1, 1115)]
 
 
 # Copyright Ferry Boender, released under the MIT license.
@@ -147,7 +146,7 @@ class Pubmed(datasets.GeneratorBasedBuilder):
     """Pubmed citations records"""
 
     BUILDER_CONFIGS = [
-        datasets.BuilderConfig(name="2021", description="The 2021 annual record", version=datasets.Version("1.0.0")),
+        datasets.BuilderConfig(name="2022", description="The 2022 annual record", version=datasets.Version("2.0.0")),
     ]
 
     # FILLED automatically from features
@@ -307,19 +306,10 @@ class Pubmed(datasets.GeneratorBasedBuilder):
         )
         self.fill_keys_from_features(features)
         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,
-            # specify them here. They'll be used if as_supervised=True in
-            # builder.as_dataset.
-            supervised_keys=None,
-            # Homepage of the dataset for documentation
+            features=features,
             homepage=_HOMEPAGE,
-            # License for the dataset if available
             license=_LICENSE,
-            # Citation for the dataset
             citation=_CITATION,
         )
 
@@ -329,7 +319,6 @@ class Pubmed(datasets.GeneratorBasedBuilder):
         return [
             datasets.SplitGenerator(
                 name=datasets.Split.TRAIN,
-                # These kwargs will be passed to _generate_examples
                 gen_kwargs={"filenames": dl_dir},
             ),
         ]