Update code and bump baseline date

pmc_open_access_figure.py

@@ -34,6 +34,9 @@ import tarfile
 import datasets
 from datasets.tasks import LanguageModeling
 
+from PIL import ImageFile # Important for error: UserWarning: Corrupt EXIF data.  Expecting to read 4 bytes but only got 0
+import mimetypes
+ImageFile.LOAD_TRUNCATED_IMAGES = True
 
 # TODO: Add BibTeX citation
 # Find for instance the citation on arxiv or on the dataset repo/website
@@ -71,7 +74,7 @@ _SUBSETS = {
     "non_commercial": "oa_noncomm",
     "other": "oa_other",
 }
-_BASELINE_DATE = "2022-09-03"
+_BASELINE_DATE = "2022-12-18"
 
 begin_doc_rgx = re.compile("""<!DOCTYPE.*""")
 def clean_raw(xml_text):
@@ -89,6 +92,13 @@ def clean_raw(xml_text):
 
     return xml_text
 
+def get_extensions_for_type(general_type):
+    for ext in mimetypes.types_map:
+        if mimetypes.types_map[ext].split('/')[0] == general_type:
+            yield ext
+
+IMAGE_EXT = list(get_extensions_for_type('image'))
+
 def extract_captions(article_tree):
     ref_el_l = article_tree.xpath(".//fig")
     figure_captions = []
@@ -134,7 +144,8 @@ class OpenAccessFigure(datasets.GeneratorBasedBuilder):
                 {
                     "accession_id": datasets.Value("string"),
                     "pmid":         datasets.Value("string"),
-                    "figure_idx":    datasets.Value("string"),
+                    "figure_idx":    datasets.Value("int16"),
+					"figure_fn":    datasets.Value("string"),
                     "figure":  datasets.Image(),
                     "caption": datasets.Value("string"),
                     "license": datasets.Value("string"),
@@ -156,7 +167,7 @@ class OpenAccessFigure(datasets.GeneratorBasedBuilder):
         for subset in self.config.subsets:
             url = _URL.format(subset=_SUBSETS[subset])
             basename = f"{_SUBSETS[subset]}_xml."
-            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_urls = [f"{url}{basename}PMC00{i}xxxxxx.baseline.{_BASELINE_DATE}.filelist.csv" for i in range(10) 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)
@@ -176,7 +187,7 @@ class OpenAccessFigure(datasets.GeneratorBasedBuilder):
         figure_archives = []
         df_l = []
         set_article = set()
-        for l, baseline_file_list in enumerate(baseline_file_list_l): # incremental_file_list_l[::-1] + 
+        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
@@ -186,14 +197,14 @@ class OpenAccessFigure(datasets.GeneratorBasedBuilder):
             #mask = (~file_list.File.isin(set_article)) & (file_list.File!="")
             #file_list = file_list[mask]
             figure_url_l = list(_URL_ROOT + file_list.File) #[f"{_URL_ROOT}{figure_path}" for figure_path in file_list.File]
-            
-            try:
-                figure_archives.append(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
+
+            #try
+            figure_archives.append(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
                 
         package_df = pd.concat(df_l).reset_index()
         figure_archives = list(chain(*figure_archives))
@@ -243,7 +254,7 @@ class OpenAccessFigure(datasets.GeneratorBasedBuilder):
             try:
                 for path, file in figure_archive:
                     bn, ext = os.path.splitext(os.path.basename(path))
-                    if ext in [".tif", ".gif", ".jpg", ".png"]:
+                    if ext in IMAGE_EXT:
                         f_d[ext][bn] = Image.open(file, mode="r")
     
                     if ext in [".nxml", ".xml"]:
@@ -257,7 +268,7 @@ class OpenAccessFigure(datasets.GeneratorBasedBuilder):
                         figure_captions, graphic_names = extract_captions(article_tree)
     
                 image_d = {}
-                for ext in [".tif", ".jpg", ".png", ".gif"]:
+                for ext in [".tif", ".jpg", ".png", ".gif"]: #Focussing the dataset only on these four types
                     for bn, image in f_d[ext].items():
                         if bn not in image_d.keys():
                             image_d[bn] = image
@@ -269,7 +280,8 @@ class OpenAccessFigure(datasets.GeneratorBasedBuilder):
                                 "caption":caption,
                                 "pmid": data["PMID"],
                                 "accession_id": data['AccessionID'],
-                                "figure_idx": str(j+1),
+                                "figure_idx": j+1,
+								"figure_fn": graph_name,
                                 "license": data["License"],
                                 "last_updated": data["LastUpdated (YYYY-MM-DD HH:MM:SS)"],
                                 "retracted": data["Retracted"],