def extract(self, data, dependency_results):
results_dir = tempfile.mkdtemp() + '/'
temp_pdf_file = extraction.utils.temp_file(data)
try:
command_args = [
'java', '-jar', config.ALGORITHMS_JAR_PATH,
config.ALGORITHMS_PERL_PATH, 'f', temp_pdf_file, results_dir
]
status, stdout, stderr = extraction.utils.external_process(
command_args, timeout=20)
except subprocess.TimeoutExpired:
shutil.rmtree(results_dir)
raise RunnableError(
'Algorithms Jar timed out while processing document')
finally:
os.remove(temp_pdf_file)
if status != 0:
raise RunnableError('Algorithms Jar Failure. Possible error:\n' +
stderr)
paths = glob.glob(results_dir + '*.xml')
if len(paths) != 1:
raise RunnableError(
'Wrong number of results files from Algorithms Jar.')
tree = safeET.parse(paths[0])
xml_root = tree.getroot()
shutil.rmtree(results_dir)
return ExtractorResult(xml_result=xml_root)
def extract(self, data, dependency_results):
results_dir = tempfile.mkdtemp() + '/'
temp_pdf_file = extraction.utils.temp_file(data)
try:
command_args = [config.PDFFIGURES_PATH, '-o', results_dir, '-j', results_dir, temp_pdf_file]
status, stdout, stderr = extraction.utils.external_process(command_args, timeout=20)
except subprocess.TimeoutExpired:
shutil.rmtree(results_dir)
raise RunnableError('PDFFigures timed out while processing document')
finally:
os.remove(temp_pdf_file)
if status != 0:
raise RunnableError('PDFFigures Failure. Possible error:\n' + stderr)
# Handle png results
files = {}
for path in glob.glob(results_dir + '*.png'):
# basename looks something like this: -Figure-X.png
# remove the hyphen and replace with a '.', because framework will add filename prefix later
filename = '.' + os.path.basename(path)[1:]
with open(path, 'rb') as f:
files[filename] = f.read()
# Handle json results
for path in glob.glob(results_dir + '*.json'):
filename = '.' + os.path.basename(path)[1:]
with open(path, 'r') as f:
files[filename] = f.read()
shutil.rmtree(results_dir)
return ExtractorResult(xml_result=None, files=files)
def extract(self, data, dep_results):
# Write the pdf data to a temporary location so PDFBox can process it
file_path = extraction.utils.temp_file(data, suffix='.pdf')
try:
command_args = [
'java', '-jar', config.PDF_BOX_JAR, 'ExtractText', '-console',
'-encoding', 'UTF-8', file_path
]
status, stdout, stderr = extraction.utils.external_process(
command_args, timeout=30)
except subprocess.TimeoutExpired:
raise RunnableError('PDFBox timed out while processing document')
finally:
os.remove(file_path)
if status != 0:
raise RunnableError(
'PDFBox returned error status code {0}.\nPossible error:\n{1}'.
format(status, stderr))
# We can use result from PDFBox directly, no manipulation needed
pdf_plain_text = stdout
files = {'.txt': pdf_plain_text}
return ExtractorResult(xml_result=None, files=files)
def extract(self, data, dep_results):
url = '{0}/processFulltextDocument'.format(config.GROBID_HOST)
files = {'input': data}
vars = {}
try:
resp = requests.post(url, files=files, data=vars)
except requests.exceptions.RequestException as ex:
raise RunnableError('Request to Grobid server failed')
if resp.status_code != 200:
raise RunnableError(
'Grobid returned status {0} instead of 200\nPossible Error:\n{1}'
.format(resp.status_code, resp.text))
xml_text = resp.content
# remove namespace info from xml string
# this is hacky but makes parsing it much much nicer down the road
remove_xmlns = re.compile(r'\sxmlns[^"]+"[^"]+"')
xml_text = remove_xmlns.sub('', xml_text)
xml = safeET.fromstring(xml_text)
# grobid returns TEI xml file
return ExtractorResult(xml_result=xml)
def extract(self, data, deps):
emails = re.findall(r'\b[A-Z0-9._%+-]+@[A-Z0-9.-]+\.[A-Z]{2,4}\b',
data, re.IGNORECASE | re.UNICODE)
root = ET.Element('extraction')
for email in emails:
ele = ET.SubElement(root, 'email')
ele.text = email
return ExtractorResult(xml_result=root)
def extract(self, data, deps):
try:
(status, stdout, stderr) = utils.external_process(
['awk', '/^[0-9]/ {print;}', '-'], input_data=data, timeout=5)
except subprocess.TimeoutExpired:
raise RunnableError('awk timed out')
lines = [line for line in stdout.split("\n") if line]
root = ET.Element('extraction')
for line in lines:
ele = ET.SubElement(root, 'line')
ele.text = line
return ExtractorResult(xml_result=root)
def extract(self, data, dependency_results):
xml_root = dependency_results[
interfaces.FullTextTEIExtractor].xml_result
body_node = xml_root.find('./text/body')
if body_node is None:
return RunnableError('Could not find body text in TEI xml file')
xml_string = ET.tostring(body_node).decode('utf-8')
plain_text = utils.xml_to_plain_text(xml_string)
plain_text = plain_text.encode('utf-8')
files = {'.txt': plain_text}
return ExtractorResult(xml_result=None, files=files)
def extract(self, data, dependency_results):
# Get the plain text file of the PDF and write it to a temporary location
pdf_text = dependency_results[
interfaces.PlainTextExtractor].files['.txt']
text_file_path = extraction.utils.temp_file(pdf_text)
# Run parscit on the text file to extract citations
try:
status, stdout, stderr = extraction.utils.external_process(
['perl', config.PARSCIT_PATH, text_file_path], timeout=20)
except subprocess.TimeoutExpired as te:
raise RunnableError('ParsCit timed out while processing document')
finally:
os.remove(text_file_path)
if status != 0:
raise RunnableError('ParsCit Failure. Possible error:\n' + stderr)
# ParsCit will give us a string representing an xml doc
# convert from string type into an xml object
xml = safeET.fromstring(stdout)
return ExtractorResult(xml_result=xml)
def extract(self, data, dep_results):
file_path = utils.temp_file(data, suffix='.pdf')
try:
status, stdout, stderr = utils.external_process(['java', '-jar', config.PDF_BOX_JAR, 'ExtractText', '-console', '-encoding', 'UTF-8', file_path],
timeout=30)
except subprocess.TimeoutExpired as te:
raise RunnableError('PDFBox timed out while processing document')
finally:
os.remove(file_path)
if status != 0:
raise RunnableError('PDFBox returned error status code {0}.\nPossible error:\n{1}'.format(status, stderr))
plain_text = stdout
# create xml result file that just points towards the file with plain text results
root=ET.Element('file')
root.text = 'plain_text.txt'
files = {'plain_text.txt': stdout}
return ExtractorResult(xml_result=root, files=files)
def extract(self, data, dep_results):
tei_root = dep_results[interfaces.HeaderTEIExtractor].xml_result
result_root = ET.Element('algorithm', {
'name': 'Grobid Header Extraction',
'version': '0.1'
})
# Retrieve title from TEI doc
title = tei_root.find('./teiHeader//titleStmt/title')
if title is not None:
ET.SubElement(result_root, 'title').text = title.text
else:
raise RunnableError('No title found in TEI document')
# Find document-level affiliations
affiliations = tei_root.findall(
'./teiHeader//sourceDesc/biblStruct/analytic/affiliation')
if affiliations:
affiliation_str = " | ".join(
map(_get_affiliation_str, affiliations))
ET.SubElement(result_root, 'affiliation').text = affiliation_str
# Retreive author names from TEI doc
authors = tei_root.findall('./teiHeader//biblStruct//author')
authors_node = ET.SubElement(result_root, 'authors')
if authors is not None and len(authors):
for author in authors:
author_node = ET.SubElement(authors_node, 'author')
# Find and output name-related info
name_tags = []
name_tags.extend(author.findall("./persName/forename"))
name_tags.extend(author.findall('./persName/surname'))
name_parts = [
name.text for name in name_tags if name is not None
]
name = ' '.join(name_parts)
ET.SubElement(author_node, 'name').text = name
# Find and output affilliation-related info
affiliations = author.findall('./affiliation')
if affiliations:
# Use a pipe to delimit seperate affiliations
affiliation_str = " | ".join(
map(_get_affiliation_str, affiliations))
ET.SubElement(author_node,
'affiliation').text = affiliation_str
else:
self.log('No authors found')
# Retreive keywords from TEI doc
keywords = tei_root.findall('./teiHeader//keywords//item/term')
keywords_node = ET.SubElement(result_root, 'keywords')
if keywords is not None and len(keywords):
for term in keywords:
ET.SubElement(keywords_node, 'keyword').text = term.text
else:
self.log('No keywords found')
# Try and find an abstract
divs = tei_root.findall('./text//div')
abstracts = [div for div in divs if div.get('type') == 'abstract']
if abstracts:
abstract = abstracts[0]
xml_string = ET.tostring(abstract)
remove_heading = re.compile(r'\s*<head.*?>.*?<\s*/\s*head>',
re.DOTALL | re.UNICODE)
xml_string = remove_heading.sub('', xml_string)
abstract_string = utils.xml_to_plain_text(xml_string)
ET.SubElement(result_root, 'abstract').text = abstract_string
else:
self.log('No abstract found')
# CSX style xml document of header information
return ExtractorResult(xml_result=result_root)
def extract(self, data, dep_results):
xml = _call_grobid_method(data, 'processReferences')
return ExtractorResult(xml_result=xml)
def extract(self, data, dep_results):
xml = _call_grobid_method(data, 'processHeaderDocument')
return ExtractorResult(xml_result=xml)
def extract(self, data, dep_results):
ele = ET.Element('file')
ele.text = 'test.txt'
files = {'test.txt': 'test test'}
return ExtractorResult(ele, files=files)
def extract(self, data, dep_results):
ele = ET.Element('result')
ele.text = data
return ExtractorResult(ele)
def extract(self, data, dep_results):
return ExtractorResult(xml_result=None)
