Refactor code with baseline ranges

open_access.py

@@ -111,36 +111,27 @@ 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_file_lists = []
-        baseline_archives = []
+            "incremental_archives": [],
+        }
 
         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],
-            # }
-            # baseline_paths = dl_manager.download(baseline_urls)
-            for baseline in baselines:
-                baseline_file_list_url = f"{url}{basename}{baseline}.filelist.csv"
-                try:
-                    baseline_file_list = dl_manager.download(baseline_file_list_url)
-                except FileNotFoundError:  # non-commercial PMC000xxxxxx baseline does not exist
-                    continue
-                baseline_archive_url = f"{url}{basename}{baseline}.tar.gz"
-                try:
-                    baseline_archive = dl_manager.download(baseline_archive_url)
-                except FileNotFoundError:
-                    continue
-                baseline_file_lists.append(baseline_file_list)
-                baseline_archives.append(baseline_archive)
+            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"])
             # Incremental
             date_delta = datetime.date.today() - datetime.date.fromisoformat(_BASELINE_DATE)
             incremental_dates = [
@@ -162,8 +153,10 @@ class OpenAccess(datasets.GeneratorBasedBuilder):
             datasets.SplitGenerator(
                 name=datasets.Split.TRAIN,
                 gen_kwargs={
-                    "baseline_file_lists": baseline_file_lists,
-                    "baseline_archives": [dl_manager.iter_archive(archive) for archive in baseline_archives],
+                    "baseline_file_lists": baseline_paths["baseline_file_lists"],
+                    "baseline_archives": [
+                        dl_manager.iter_archive(archive) for archive in baseline_paths["baseline_archives"]
+                    ],
                     "incremental_file_lists": incremental_paths["incremental_file_lists"],
                     "incremental_archives": [
                         dl_manager.iter_archive(archive) for archive in incremental_paths["incremental_archives"]
@@ -176,28 +169,25 @@ class OpenAccess(datasets.GeneratorBasedBuilder):
         key = 0
         # Baselines
         for baseline_file_list, baseline_archive in zip(baseline_file_lists, baseline_archives):
-            try:
-                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)
-                    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
-            except FileNotFoundError:  # non-commercial PMC000xxxxxx baseline does not exist
-                continue
+            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)
+                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
         # Incrementals
         if incremental_file_lists:
             for incremental_file_list, incremental_archive in zip(incremental_file_lists, incremental_archives):