Uncompress data files on the fly

pubmed.py

@@ -16,6 +16,7 @@
 
 
 import copy
+import gzip
 import xml.etree.ElementTree as ET
 
 import datasets
@@ -312,7 +313,7 @@ class Pubmed(datasets.GeneratorBasedBuilder):
 
     def _split_generators(self, dl_manager):
         """Returns SplitGenerators."""
-        dl_dir = dl_manager.download_and_extract(_URLs)
+        dl_dir = dl_manager.download(_URLs)
         return [
             datasets.SplitGenerator(
                 name=datasets.Split.TRAIN,
@@ -355,28 +356,29 @@ class Pubmed(datasets.GeneratorBasedBuilder):
         """Yields examples."""
         id_ = 0
         for filename in filenames:
-            try:
-                tree = ET.parse(filename)
-                root = tree.getroot()
-                xmldict = self.xml_to_dictionnary(root)
-            except ET.ParseError:
-                logger.warning(f"Ignoring file {filename}, it is malformed")
-                continue
-
-            for article in xmldict["PubmedArticleSet"]["PubmedArticle"]:
-                self.update_citation(article)
-                new_article = default_article()
-
+            with gzip.open(filename) as f:
                 try:
-                    deepupdate(new_article, article)
-                except Exception:
-                    logger.warning(f"Ignoring article {article}, it is malformed")
+                    tree = ET.parse(f)
+                    root = tree.getroot()
+                    xmldict = self.xml_to_dictionnary(root)
+                except ET.ParseError:
+                    logger.warning(f"Ignoring file {filename}, it is malformed")
                     continue
 
-                try:
-                    _ = self.info.features.encode_example(new_article)
-                except Exception as e:
-                    logger.warning(f"Ignore example because {e}")
-                    continue
-                yield id_, new_article
-                id_ += 1
+                for article in xmldict["PubmedArticleSet"]["PubmedArticle"]:
+                    self.update_citation(article)
+                    new_article = default_article()
+
+                    try:
+                        deepupdate(new_article, article)
+                    except Exception:
+                        logger.warning(f"Ignoring article {article}, it is malformed")
+                        continue
+
+                    try:
+                        _ = self.info.features.encode_example(new_article)
+                    except Exception as e:
+                        logger.warning(f"Ignore example because {e}")
+                        continue
+                    yield id_, new_article
+                    id_ += 1