Added download of increments

pmc_open_access_xml.py

@@ -488,15 +488,13 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
 
             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_file_list = dl_manager.download(baseline_file_list_url)
                     baseline_archive = dl_manager.download(baseline_archive_url)
-                except FileNotFoundError:
+                except FileNotFoundError:  # non-commercial PMC000xxxxxx baseline does not exist
                     continue
+                
                 baseline_file_lists.append(baseline_file_list)
                 baseline_archives.append(baseline_archive)
 
@@ -505,21 +503,22 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
             # Incremental commented because some articles are already in the main parts (updates?)
             # Need to find a way to add them to the dataset without duplicating the articles.
             # Also adding them would mean that each new day the dataset is loaded, the whole dataset is recreated.
-            # date_delta = datetime.date.today() - datetime.date.fromisoformat(_BASELINE_DATE)
-            # incremental_dates = [
-                # (datetime.date.fromisoformat(_BASELINE_DATE) + datetime.timedelta(days=i + 1)).isoformat()
-                # 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"])
+            date_delta = datetime.date.today() - datetime.date.fromisoformat(_BASELINE_DATE)
+            incremental_dates = [
+                (datetime.date.fromisoformat(_BASELINE_DATE) + datetime.timedelta(days=i + 1)).isoformat()
+                for i in range(date_delta.days)
+            ]
+            incrementals = [f"incr.{date}" for date in incremental_dates]
+            for incremental in incrementals:
+                incremental_file_list_url = f"{url}{basename}{incremental}.filelist.csv"
+                incremental_archive_url = f"{url}{basename}{incremental}.tar.gz"
+                try:
+                    incremental_file_list = dl_manager.download(incremental_file_list_url)
+                    incremental_archive = dl_manager.download(incremental_archive_url)
+                except FileNotFoundError:  # Some increment might not exist
+                    continue
+                incremental_paths["incremental_file_lists"].append(incremental_file_list)
+                incremental_paths["incremental_archives"].append(incremental_archive)
 
         return [
             datasets.SplitGenerator(
@@ -528,15 +527,13 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
                     "baseline_file_lists": baseline_file_lists,
                     "baseline_archives": [dl_manager.iter_archive(archive) for archive in baseline_archives],
                     "baseline_package_list": baseline_package_list,
-                    # "incremental_file_lists": incremental_paths["incremental_file_lists"],
-                    # "incremental_archives": [
-                        # dl_manager.iter_archive(archive) for archive in incremental_paths["incremental_archives"]
-                    # ],
+                    "incremental_file_lists": incremental_paths["incremental_file_lists"],
+                    "incremental_archives": [dl_manager.iter_archive(archive) for archive in incremental_paths["incremental_archives"]],
                 },
             ),
         ]
 
-    def _generate_examples(self, baseline_file_lists, baseline_archives, baseline_package_list): #, incremental_file_lists, incremental_archives
+    def _generate_examples(self, baseline_file_lists, baseline_archives, baseline_package_list, incremental_file_lists, incremental_archives):
         #Loading the file listing folders of individual PMC Article package (with medias and graphics)
         oa_package_list = pd.read_csv(baseline_package_list, index_col="Accession ID")
         oa_package_list = oa_package_list[["File"]]