Join baseline and incremental paths

open_access.py

@@ -112,8 +112,7 @@ class OpenAccess(datasets.GeneratorBasedBuilder):
 
     def _split_generators(self, dl_manager):
 
-        baseline_paths = []
-        incremental_paths = []
+        paths = []
         for subset in self.config.subsets:
             url = _URL.format(subset=_SUBSETS[subset])
             basename = f"{_SUBSETS[subset]}_txt."
@@ -123,7 +122,6 @@ class OpenAccess(datasets.GeneratorBasedBuilder):
                 (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 = [
@@ -135,29 +133,23 @@ class OpenAccess(datasets.GeneratorBasedBuilder):
                 (f"{url}{basename}{incremental}.filelist.csv", f"{url}{basename}{incremental}.tar.gz")
                 for incremental in incrementals
             ]
-            incremental_paths += dl_manager.download(incremental_urls)
+            paths += dl_manager.download(baseline_urls + incremental_urls)
 
         return [
             datasets.SplitGenerator(
                 name=datasets.Split.TRAIN,
                 gen_kwargs={
-                    "baseline_paths": [
-                        (file_list, dl_manager.iter_archive(archive)) for file_list, archive in baseline_paths
-                    ],
-                    "incremental_paths": [
-                        (file_list, dl_manager.iter_archive(archive)) for file_list, archive in incremental_paths
-                    ],
+                    "paths": [(file_list, dl_manager.iter_archive(archive)) for file_list, archive in paths],
                 },
             ),
         ]
 
-    def _generate_examples(self, baseline_paths, incremental_paths):
+    def _generate_examples(self, paths):
         key = 0
-        # Baselines
-        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)
+        for file_list, archive in paths:
+            file_list_data = pd.read_csv(file_list, index_col="Article File").to_dict(orient="index")
+            for path, file in archive:
+                data = file_list_data.pop(path)
                 content = file.read()
                 try:
                     text = content.decode("utf-8").strip()
@@ -174,25 +166,3 @@ class OpenAccess(datasets.GeneratorBasedBuilder):
                 }
                 yield key, data
                 key += 1
-        # Incrementals
-        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)
-                    content = file.read()
-                    try:
-                        text = content.decode("utf-8").strip()
-                    except UnicodeDecodeError as e:
-                        text = content.decode("latin-1").strip()
-                    data = {
-                        "text": text,
-                        "pmid": data["PMID"],
-                        "accession_id": data["AccessionID"],
-                        "license": data["License"],
-                        "last_updated": data["LastUpdated (YYYY-MM-DD HH:MM:SS)"],
-                        "retracted": data["Retracted"],
-                        "citation": data["Article Citation"],
-                    }
-                    yield key, data
-                    key += 1