Parallelize with zipped file_list and archive

open_access.py

@@ -59,7 +59,7 @@ _BASELINE_DATE = "2022-12-17"
 _BASELINE_MAX_RANGE = 10
 _BASELINE_RANGES = {
     "commercial": range(_BASELINE_MAX_RANGE),
-    "non_commercial": range(1, _BASELINE_MAX_RANGE),
+    "non_commercial": range(1, _BASELINE_MAX_RANGE),  # non-commercial PMC000xxxxxx baseline does not exist
     "other": range(_BASELINE_MAX_RANGE),
 }
 
@@ -76,7 +76,8 @@ class OpenAccessConfig(datasets.BuilderConfig):
         """
         subsets = [subsets] if isinstance(subsets, str) else subsets
         super().__init__(
-            name="+".join(subsets), **kwargs,
+            name="+".join(subsets),
+            **kwargs,
         )
         self.subsets = subsets if self.name != "all" else list(_SUBSETS.keys())
 
@@ -111,27 +112,18 @@ class OpenAccess(datasets.GeneratorBasedBuilder):
 
     def _split_generators(self, dl_manager):
 
-        baseline_paths = {
-            "baseline_file_lists": [],
-            "baseline_archives": [],
-        }
-        incremental_paths = {
-            "incremental_file_lists": [],
-            "incremental_archives": [],
-        }
-
+        baseline_paths = []
+        incremental_paths = []
         for subset in self.config.subsets:
             url = _URL.format(subset=_SUBSETS[subset])
             basename = f"{_SUBSETS[subset]}_txt."
             # Baselines
             baselines = [f"PMC00{i}xxxxxx.baseline.{_BASELINE_DATE}" for i in _BASELINE_RANGES[subset]]
-            baseline_urls = {
-                "baseline_file_lists": [f"{url}{basename}{baseline}.filelist.csv" for baseline in baselines],
-                "baseline_archives": [f"{url}{basename}{baseline}.tar.gz" for baseline in baselines],
-            }
-            paths = dl_manager.download(baseline_urls)
-            baseline_paths["baseline_file_lists"].extend(paths["baseline_file_lists"])
-            baseline_paths["baseline_archives"].extend(paths["baseline_archives"])
+            baseline_urls = [
+                (f"{url}{basename}{baseline}.filelist.csv", f"{url}{basename}{baseline}.tar.gz")
+                for baseline in baselines
+            ]
+            baseline_paths += dl_manager.download(baseline_urls)
             # Incremental
             date_delta = datetime.date.today() - datetime.date.fromisoformat(_BASELINE_DATE)
             incremental_dates = [
@@ -139,36 +131,30 @@ class OpenAccess(datasets.GeneratorBasedBuilder):
                 for i in range(date_delta.days)
             ]
             incrementals = [f"incr.{date}" for date in incremental_dates]
-            incremental_urls = {
-                "incremental_file_lists": [
-                    f"{url}{basename}{incremental}.filelist.csv" for incremental in incrementals
-                ],
-                "incremental_archives": [f"{url}{basename}{incremental}.tar.gz" for incremental in incrementals],
-            }
-            paths = dl_manager.download(incremental_urls)
-            incremental_paths["incremental_file_lists"].extend(paths["incremental_file_lists"])
-            incremental_paths["incremental_archives"].extend(paths["incremental_archives"])
+            incremental_urls = [
+                (f"{url}{basename}{incremental}.filelist.csv", f"{url}{basename}{incremental}.tar.gz")
+                for incremental in incrementals
+            ]
+            incremental_paths += dl_manager.download(incremental_urls)
 
         return [
             datasets.SplitGenerator(
                 name=datasets.Split.TRAIN,
                 gen_kwargs={
-                    "baseline_file_lists": baseline_paths["baseline_file_lists"],
-                    "baseline_archives": [
-                        dl_manager.iter_archive(archive) for archive in baseline_paths["baseline_archives"]
+                    "baseline_paths": [
+                        (file_list, dl_manager.iter_archive(archive)) for file_list, archive in baseline_paths
                     ],
-                    "incremental_file_lists": incremental_paths["incremental_file_lists"],
-                    "incremental_archives": [
-                        dl_manager.iter_archive(archive) for archive in incremental_paths["incremental_archives"]
+                    "incremental_paths": [
+                        (file_list, dl_manager.iter_archive(archive)) for file_list, archive in incremental_paths
                     ],
                 },
             ),
         ]
 
-    def _generate_examples(self, baseline_file_lists, baseline_archives, incremental_file_lists, incremental_archives):
+    def _generate_examples(self, baseline_paths, incremental_paths):
         key = 0
         # Baselines
-        for baseline_file_list, baseline_archive in zip(baseline_file_lists, baseline_archives):
+        for baseline_file_list, baseline_archive in baseline_paths:
             baselines = pd.read_csv(baseline_file_list, index_col="Article File").to_dict(orient="index")
             for path, file in baseline_archive:
                 data = baselines.pop(path)
@@ -189,8 +175,8 @@ class OpenAccess(datasets.GeneratorBasedBuilder):
                 yield key, data
                 key += 1
         # Incrementals
-        if incremental_file_lists:
-            for incremental_file_list, incremental_archive in zip(incremental_file_lists, incremental_archives):
+        if incremental_paths:
+            for incremental_file_list, incremental_archive in incremental_paths:
                 incrementals = pd.read_csv(incremental_file_list, index_col="Article File").to_dict(orient="index")
                 for path, file in incremental_archive:
                     data = incrementals.pop(path)