Datasets:

TomTBT
/

pmc_open_access_xml

Tasks:

Text Classification

Modalities:

Formats:

Languages:

Size:

Tags:

research papers

Libraries:

License:

Dataset card Data Studio Files Files and versions

TomTBT commited on Oct 17, 2022

Commit

c7c0b81

·

1 Parent(s): 3675966

Stream mode FileNotFound exception handling

Files changed (1) hide show

pmc_open_access_xml.py +4 -1

pmc_open_access_xml.py CHANGED Viewed

@@ -533,7 +533,10 @@ class OpenAccessXML(datasets.GeneratorBasedBuilder):
         # Incrementals
         if incremental_file_lists:
             for incremental_file_list, incremental_archive in zip(incremental_file_lists[::-1], incremental_archives[::-1]):
-                incrementals = pd.read_csv(incremental_file_list, index_col="AccessionID")
                 incrementals = incrementals.join(oa_package_list).reset_index().set_index("Article File")
                 incrementals.File = incrementals.File.fillna('')
                 incrementals = incrementals.to_dict(orient="index")

         # Incrementals
         if incremental_file_lists:
             for incremental_file_list, incremental_archive in zip(incremental_file_lists[::-1], incremental_archives[::-1]):
+                try:
+                    incrementals = pd.read_csv(incremental_file_list, index_col="AccessionID")
+                except FileNotFoundError:  # File not found can happen here in stream mode
+                    continue
                 incrementals = incrementals.join(oa_package_list).reset_index().set_index("Article File")
                 incrementals.File = incrementals.File.fillna('')
                 incrementals = incrementals.to_dict(orient="index")