def call_pdflatex(src_tex: str,
src_dir: str,
dest_dir: str,
timeout: int = 1200) -> str:
"""
Call pdflatex on the tex source file src_tex, save its output to dest_dir, and return the path of the
resulting pdf.
"""
# Need to be in the same directory as the file to compile it
file_util.safe_makedirs(dest_dir)
# Shell-escape required due to https://www.scivision.co/pdflatex-error-epstopdf-output-filename-not-allowed-in-restricted-mode/
cmd = [
'pdflatex', '-interaction=nonstopmode', '-shell-escape',
'-output-directory=' + dest_dir, src_tex
]
# Run twice so that citations are built correctly
# Had some issues getting latexmk to work
try:
subprocess.run(cmd,
stdout=subprocess.PIPE,
cwd=src_dir,
timeout=timeout)
res = subprocess.run(cmd,
stdout=subprocess.PIPE,
cwd=src_dir,
timeout=timeout)
except subprocess.TimeoutExpired:
raise LatexException(' '.join(cmd), -1,
'Timeout exception after %d' % timeout)
if res.returncode != 0:
raise LatexException(' '.join(cmd), res.returncode, res.stdout)
paperid = os.path.splitext(os.path.basename(src_tex))[0]
return dest_dir + paperid + '.pdf'
def process_paper_tar(paper_tarname: str) -> None:
parts = paper_tarname.split('/')
partition_name = parts[-2]
paper_name = os.path.splitext(parts[-1])[0]
result_path = os.path.join(ARXIV_FIGURE_JSON_DIR, partition_name,
paper_name + '.json')
paper_dir = os.path.join(ARXIV_SRC_DIR, partition_name, paper_name)
if os.path.isfile(result_path):
return
print('.', end='', flush=True)
try:
file_util.extract_tarfile(paper_tarname, paper_dir)
except tarfile.ReadError:
logging.debug('File %s is not a tar' % paper_tarname)
return
diffs = generate_diffs(paper_dir)
if diffs is None:
return
figures_by_page = dict()
for diff in diffs:
figures = consume_diff_generate_figures(diff)
if figures is None:
continue
page_name = os.path.dirname(
diff) + '/' + diff[diff.find('black.pdf-'):]
figures_by_page[page_name] = figures
file_util.safe_makedirs(os.path.dirname(result_path))
file_util.write_json_atomic(
result_path,
config.JsonSerializable.serialize(figures_by_page),
sort_keys=True)
def process_paper_tar(self):
print("------Processing paper_tarname : {}--------".format(
self.paper_tarname))
parts = self.paper_tarname.split('/')
partition_name = parts[-2]
paper_name = os.path.splitext(parts[-1])[0]
result_path = os.path.join(self.ARXIV_FIGURE_JSON_DIR, partition_name,
paper_name + '.json')
paper_dir = os.path.join(self.ARXIV_SRC_DIR, partition_name,
paper_name)
if os.path.isfile(result_path):
return
print('.', end='', flush=True)
try:
file_util.extract_tarfile(self.paper_tarname, paper_dir)
except tarfile.ReadError:
logging.debug('File %s is not a tar' % self.paper_tarname)
return
try:
diffs, black_ims_paths = self.generate_diffs(paper_dir)
except TypeError:
return
if diffs is None:
return
figures_by_page = dict()
for idx, diff in enumerate(diffs):
figures = self.consume_diff_generate_figures(diff)
if figures is None:
continue
try:
figures = self.augment_images(black_ims_paths[idx], figures)
except Exception as e:
print(
"Error augmenting images for image path: {}. Exception message: {}"
.format(black_ims_paths[idx], e))
page_name = os.path.dirname(
diff) + '/' + diff[diff.find('black.pdf-'):]
figures_by_page[page_name] = figures
file_util.safe_makedirs(os.path.dirname(result_path))
file_util.write_json_atomic(
result_path,
config.JsonSerializable.serialize(figures_by_page),
sort_keys=True)
figure_boundaries, caption_boundaries = transform_figure_json(
result_path, self.ignore_pages_with_no_figures)
return result_path, figure_boundaries, caption_boundaries
def run_full_pipeline(
tarpath: str, skip_done: bool=True, save_intermediate: bool=False
) -> None:
foldername = str(os.path.basename(tarpath).split('.')[0])
result_path = LOCAL_FIGURE_JSON_DIR + get_bin(
tarpath
) + foldername + '.json'
if skip_done and file_util.exists(result_path):
return
d = LOCAL_INTERMEDIATE_DIR + get_bin(tarpath)
while True:
try:
file_util.extract_tarfile(tarpath, d, streaming=False)
# botocore.vendored.requests.packages.urllib3.exceptions.ReadTimeoutError can't be caught because it doesn't
# inherit from BaseException, so don't use streaming
break
except FileNotFoundError as e:
logging.exception('Failure reading %s, retrying' % tarpath)
except ReadTimeout as e:
logging.exception('Timeout reading %s, retrying' % tarpath)
pdfs = glob.glob(d + foldername + '/' + '*.pdf')
res = dict()
for pdf in pdfs:
sha1sum = file_util.compute_sha1(pdf)
with open(pdf + '.sha1', 'w') as f:
print(sha1sum, file=f)
paper_figures = match_figures(pdf)
if paper_figures is not None:
res.update(paper_figures)
if save_intermediate:
intermediate_path = PUBMED_INTERMEDIATE_DIR + get_bin(
tarpath
) + foldername + '/'
for file in glob.glob(d + '/' + foldername + '/' + '*'):
file_util.copy(file, intermediate_path + os.path.basename(file))
file_util.safe_makedirs(os.path.dirname(result_path))
file_util.write_json_atomic(
result_path,
config.JsonSerializable.serialize(res),
indent=2,
sort_keys=True
)
