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textract failure #1

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textract failure #1

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9 changes: 7 additions & 2 deletions zodo/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -251,8 +251,13 @@ def download_supplemental(raw_json):
def extract_text_from_files(pmcdir):
supp_files = [x for x in listdir(pmcdir) if x.split(".")[-1] in SUPPLEMENTAL_DATA_FILETYPES]
logging.debug("Files for extraction in %s : %s", pmcdir, ",".join(supp_files))
# For now just extract all text the same way using textract
supp_file_contents = {x:str(textract.process(join(pmcdir, x))).replace("\\n", "\n") for x in supp_files}
# For now just extract all text the same way using textract (textract may fail)
supp_file_contents = {}
for suppfile in supp_files:
try:
supp_file_contents[suppfile] = str(textract.process(join(pmcdir, suppfile))).replace("\\n", "\n")
except Exception as e:
logging.error("Error in textract: %s", e)
supp_contents = ""
for suppfile, content in supp_file_contents.items():
supp_contents += "\n\n*** " + str(suppfile) + " ***\n" + str(content)
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