Disabled incrementals and put iter archive into a generator

pmc_open_access_figure.py

@@ -158,47 +158,39 @@ class OpenAccessFigure(datasets.GeneratorBasedBuilder):
             baseline_file_list_urls = [f"{url}{basename}PMC00{i}xxxxxx.baseline.{_BASELINE_DATE}.filelist.csv" for i in range(9) if (subset!="non_commercial" or i>0)]
             baseline_file_list_l.extend(dl_manager.download(baseline_file_list_urls))
 
-            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)
-                                ]
-            incremental_urls = [f"{url}{basename}incr.{date}.filelist.csv" for date in incremental_dates]
-            for url in incremental_urls:
-                try:
-                    incremental_file_list_l.append(dl_manager.download(url))
-                except FileNotFoundError:  # Some increment don't exist
-                    continue
+            #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)
+            #                    ]
+            #incremental_urls = [f"{url}{basename}incr.{date}.filelist.csv" for date in incremental_dates]
+            #for url in incremental_urls:
+            #    try:
+            #        incremental_file_list_l.append(dl_manager.download(url))
+            #    except FileNotFoundError:  # Some increment don't exist
+            #        continue
 
         oa_package_list = pd.read_csv(baseline_package_list, index_col="Accession ID")
         oa_package_list = oa_package_list[["File"]]
         figure_archives = []
         df_l = []
         set_article = set()
-        for l, baseline_file_list in enumerate(incremental_file_list_l[::-1] + baseline_file_list_l):
+        for l, baseline_file_list in enumerate(baseline_file_list_l): # incremental_file_list_l[::-1] + 
             try:
                 file_list = pd.read_csv(baseline_file_list, index_col="AccessionID")
             except FileNotFoundError:  # File not found can happen here in stream mode
                 continue
             file_list = file_list.join(oa_package_list).reset_index().set_index("Article File")
             file_list.File = file_list.File.fillna('')
-            mask = (~file_list.File.isin(set_article)) & (file_list.File!="")
-            file_list = file_list[mask]
+            #mask = (~file_list.File.isin(set_article)) & (file_list.File!="")
+            #file_list = file_list[mask]
             figure_url_l = [f"{_URL_ROOT}{figure_path}" for figure_path in file_list.File]
             
-            n_file = len(file_list.File)
-            n_step = 1000
-            #for low_lim in range(0, n_file+n_step, n_step):
-            #    up_lim = min(low_lim + n_step, n_file)
-            #    if up_lim <= low_lim:
-            #        break
-            #   slc_ = slice(low_lim, up_lim)
-            slc_ = slice(0, n_file)
             try:
-                figure_archives.extend(dl_manager.download(figure_url_l[slc_]))
-                if l < len(incremental_file_list_l): # Only adding the incrementals to the list, the rest don't have overlap in pmid
-                    set_article.union(file_list.File[slc_])
-                df_l.append(file_list[slc_])
+                figure_archives.extend(dl_manager.download(figure_url_l))
+                #if l < len(incremental_file_list_l): # Only adding the incrementals to the list, the rest don't have overlap in pmid
+                #    set_article.union(file_list.File[slc_])
+                df_l.append(file_list)
             except FileNotFoundError:
                 continue
                 
@@ -208,25 +200,37 @@ class OpenAccessFigure(datasets.GeneratorBasedBuilder):
             datasets.SplitGenerator(
                 name=datasets.Split.TRAIN,
                 gen_kwargs={
-                    "figure_archive_lists": [dl_manager.iter_archive(archive) for k, archive in enumerate(figure_archives) if k%10 < 8],
+                    "figure_archive_lists": self.archive_generator(dl_manager, figure_archives, "train"),
                     "package_df": package_df[np.arange(len(package_df))%10 < 8],
                     },
             ),
             datasets.SplitGenerator(
                 name=datasets.Split.TEST,
                 gen_kwargs={
-                    "figure_archive_lists": [dl_manager.iter_archive(archive) for k, archive in enumerate(figure_archives) if k%10 == 8],
+                    "figure_archive_lists": self.archive_generator(dl_manager, figure_archives, "test"),
                     "package_df": package_df[np.arange(len(package_df))%10 == 8],
                     },
             ),
             datasets.SplitGenerator(
                 name=datasets.Split.VALIDATION,
                 gen_kwargs={
-                    "figure_archive_lists": [dl_manager.iter_archive(archive) for k, archive in enumerate(figure_archives) if k%10 == 9],
+                    "figure_archive_lists": self.archive_generator(dl_manager, figure_archives, "validation"),
                     "package_df": package_df[np.arange(len(package_df))%10 == 9],
                     },
             ),
         ]
+        
+    def archive_generator(self, dl_manager, figure_archives, name):
+        if name == "train":
+            for k, archive in enumerate(figure_archives):
+                if k%10 < 8:
+                    yield dl_manager.iter_archive(archive)
+        elif name == "test":
+            for k, archive in enumerate(figure_archives[8::10]):
+                yield dl_manager.iter_archive(archive)
+        elif name == "validation":
+            for k, archive in enumerate(figure_archives[9::10]):
+                yield dl_manager.iter_archive(archive)
 
     def _generate_examples(self, figure_archive_lists, package_df):
         #Loading the file listing folders of individual PMC Article package (with medias and graphics)