def arxiv_refextract(obj, eng):
"""Extract references from arXiv PDF.
:param obj: Workflow Object to process
:param eng: Workflow Engine processing the object
"""
arxiv_id = get_clean_arXiv_id(obj.data)
filename = secure_filename("{0}.pdf".format(arxiv_id))
if filename not in obj.files:
pdf = download_file_to_workflow(
workflow=obj,
name=filename,
url=current_app.config['ARXIV_PDF_URL'].format(
arxiv_id=arxiv_id
)
)
else:
pdf = obj.files[filename]
if pdf:
mapped_references = extract_references(pdf.file.uri)
if mapped_references:
obj.data["references"] = mapped_references
obj.log.info("Extracted {0} references".format(
len(mapped_references)
))
else:
obj.log.info("No references extracted")
else:
obj.log.error("Not able to download and process the PDF")
def arxiv_refextract(obj, eng):
"""Extract references from arXiv PDF.
:param obj: Workflow Object to process
:param eng: Workflow Engine processing the object
"""
arxiv_id = get_clean_arXiv_id(obj.data)
filename = secure_filename("{0}.pdf".format(arxiv_id))
if filename not in obj.files:
pdf = download_file_to_record(
record=obj,
name=filename,
url=current_app.config['ARXIV_PDF_URL'].format(
arxiv_id=arxiv_id
)
)
else:
pdf = obj.files[filename]
if pdf:
mapped_references = extract_references(pdf.file.uri)
if mapped_references:
# FIXME For now we do not add these references to the final record.
obj.extra_data["references"] = mapped_references
obj.log.info("Extracted {0} references".format(
len(mapped_references)
))
else:
obj.log.info("No references extracted")
else:
obj.log.error("Not able to download and process the PDF")
def arxiv_refextract(obj, eng):
"""Perform the reference extraction step.
:param obj: Bibworkflow Object to process
:param eng: BibWorkflowEngine processing the object
"""
model = eng.workflow_definition.model(obj)
record = get_record_from_model(model)
arxiv_id = get_arxiv_id_from_record(record)
existing_file = get_file_by_name(model, "{0}.pdf".format(arxiv_id))
if not existing_file:
# We download it
pdf = get_pdf_for_model(eng, arxiv_id)
if pdf is None:
obj.log.error("No pdf found")
return
add_file_by_name(model, pdf)
else:
pdf = existing_file.get_syspath()
if pdf and os.path.isfile(pdf):
mapped_references = extract_references(pdf)
if mapped_references:
record["references"] = mapped_references
obj.log.info("Extracted {0} references".format(
len(mapped_references)
))
obj.update_task_results(
"References",
[{"name": "References",
"result": mapped_references,
"template": "workflows/results/refextract.html"}]
)
model.update()
else:
obj.log.info("No references extracted")
else:
obj.log.error("Not able to download and process the PDF")
