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# Python logging config (passed to dictConfig)
version: 1
formatters:
default:
format: '[%(asctime)s] %(levelname)s in %(name)s:%(lineno)s: %(message)s'
handlers:
console:
level: INFO
formatter: default
class: logging.StreamHandler
stream: ext://sys.stdout
log_file:
level: INFO
formatter: default
class: logging.handlers.RotatingFileHandler
filename: 'logs/server.log'
mode: 'a'
maxBytes: 67108864 # 64 MB
backupCount: 10
loggers:
# root logger
'':
level: INFO
handlers:
- console
- log_file
sciencebeam_parser:
level: DEBUG
__main__:
level: DEBUG
delft:
level: INFO
sciencebeam_trainer_delft:
level: INFO
# The download directory for ScienceBeam Parser resources
# Note: the CV model may download resources to `~/.torch/iopath_cache`,
# unless FVCORE_CACHE is set. (See `iopath.common.file_io.get_cache_dir`)
download_dir: '/data/.sciencebeam-parser/.cache'
pdfalto:
path: https://github.com/kermitt2/pdfalto/files/6104204/pdfalto-4b4e983413278a07bb4cc4b2836de03adc8ca6dc-dockcross-linux-64.gz
wapiti:
install_source: 'https://github.com/kermitt2/Wapiti/archive/a9c25d2bcccd60f1a54a7019689bd5229e866f00.tar.gz'
xslt:
tei_to_jats:
parameters:
# parameters for tei-to-jats.xsl
output_parameters: 'false'
output_bold: 'false'
output_italic: 'false'
output_empty_figure_graphic: 'true'
acknowledgement_target: 'ack'
annex_target: 'back'
lookup:
country:
paths:
- https://raw.githubusercontent.com/kermitt2/grobid/0.8.2/grobid-home/lexicon/countries/CountryCodes.xml
first_name:
paths:
- https://raw.githubusercontent.com/kermitt2/grobid/0.8.2/grobid-home/lexicon/names/firstname.5k
- https://raw.githubusercontent.com/kermitt2/grobid/0.8.2/grobid-home/lexicon/names/names.female
- https://raw.githubusercontent.com/kermitt2/grobid/0.8.2/grobid-home/lexicon/names/names.male
last_name:
paths:
- https://raw.githubusercontent.com/kermitt2/grobid/0.8.2/grobid-home/lexicon/names/lastname.5k
- https://raw.githubusercontent.com/kermitt2/grobid/0.8.2/grobid-home/lexicon/names/names.family
processors:
fulltext:
merge_raw_authors: false
use_cv_model: false
cv_render_dpi: 100
use_ocr_model: false
replace_text_by_cv_graphic: false
max_graphic_distance: 0.3
models:
segmentation:
path: 'https://github.com/kermitt2/grobid/raw/refs/tags/0.6.2/grobid-home/models/segmentation'
engine: 'wapiti'
use_first_token_of_block: false
header:
path: 'https://github.com/elifesciences/sciencebeam-models/releases/download/v0.0.1/2020-10-04-delft-grobid-header-biorxiv-no-word-embedding.tar.gz'
name_header:
# path: 'https://github.com/elifesciences/sciencebeam-models/releases/download/grobid-0.6.1/2021-06-21-grobid-0.6.1-name-header-no-word-embedding-no-layout-features-e800.tar.gz'
path: 'https://github.com/kermitt2/grobid/raw/0.6.0/grobid-home/models/name/header'
engine: 'wapiti'
name_citation:
# path: 'https://github.com/elifesciences/sciencebeam-models/releases/download/grobid-0.6.1/2021-06-28-grobid-0.6.1-name-citation-no-word-embedding-no-layout-features-e500.tar.gz'
path: 'https://github.com/kermitt2/grobid/raw/0.6.2/grobid-home/models/name/citation'
engine: 'wapiti'
affiliation_address:
path: 'https://github.com/elifesciences/sciencebeam-models/releases/download/v0.0.1/2020-10-04-delft-grobid-affiliation-address-biorxiv-no-word-embedding.tar.gz'
fulltext:
path: 'https://github.com/elifesciences/sciencebeam-models/releases/download/biorxiv-grobid/2021-05-11-delft-grobid-fulltext-biorxiv-10k-auto-v0.0.21-train-1986-e159.tar.gz'
figure:
path: 'https://github.com/elifesciences/sciencebeam-models/releases/download/biorxiv-grobid/2021-05-11-delft-grobid-figure-biorxiv-10k-auto-v0.0.18-train-1865-e219.tar.gz'
table:
path: 'https://github.com/elifesciences/sciencebeam-models/releases/download/biorxiv-grobid/2021-05-11-delft-grobid-table-biorxiv-10k-auto-v0.0.18-train-1865-e569.tar.gz'
reference_segmenter:
path: 'https://github.com/elifesciences/sciencebeam-models/releases/download/v0.0.1/2020-10-04-delft-grobid-reference-segmenter-biorxiv-no-word-embedding.tar.gz'
citation:
path: 'https://github.com/elifesciences/sciencebeam-models/releases/download/v0.0.1/2020-10-04-delft-grobid-citation-biorxiv-no-word-embedding.tar.gz'
cv_models:
default:
path: 'lp://efficientdet/PubLayNet'
engine: 'layout_parser'
score_threshold: 0.1
ocr_models:
default:
engine: 'tesserocr'
lang: 'eng'
# see https://github.com/sirfz/tesserocr/blob/v2.5.2/tesserocr.pyx#L75-L90
# (specify literal or int value)
oem: 'DEFAULT'
# see https://github.com/sirfz/tesserocr/blob/v2.5.2/tesserocr.pyx#L102-L121
# (specify literal or int value)
psm: 'SPARSE_TEXT'
doc_to_pdf:
enabled: true
listener:
port: 2003
process_timeout: 600
max_uptime: 10
convert:
remove_line_no: true
remove_header_footer: true
remove_redline: true
# preload resources and models on startup
preload_on_startup: true
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