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from dataclasses import asdict, dataclass
from typing import List, Optional
@dataclass
class GrobidAddress:
addr_line: Optional[str] = None
post_code: Optional[str] = None
settlement: Optional[str] = None
country: Optional[str] = None
country_code: Optional[str] = None # XXX
@dataclass
class GrobidAffiliation:
institution: Optional[str] = None
department: Optional[str] = None
laboratory: Optional[str] = None
address: Optional[GrobidAddress] = None
@dataclass
class GrobidAuthor:
full_name: Optional[str]
given_name: Optional[str] = None
middle: Optional[str] = None # XXX
surname: Optional[str] = None
suffix: Optional[str] = None # XXX
email: Optional[str] = None # XXX
affiliation: Optional[GrobidAffiliation] = None
def to_csl_dict(self) -> dict:
d = dict(
given=self.given_name,
family=self.surname,
suffix=self.suffix,
)
return _simplify_dict(d)
def _csl_date(s: Optional[str]) -> Optional[list]:
if not s:
return None
# YYYY
if len(s) >= 4 and s[0:4].isdigit():
year = int(s[0:4])
else:
return None
# YYYY-MM
if len(s) >= 7 and s[4] == '-' and s[5:7].isdigit():
month = int(s[5:7])
else:
return [[year]]
# YYYY-MM-DD
if len(s) == 10 and s[7] == '-' and s[8:10].isdigit():
day = int(s[8:10])
return [[year, month, day]]
else:
return [[year, month]]
def test_csl_date() -> None:
assert _csl_date("1998") == [[1998]]
assert _csl_date("1998-03") == [[1998, 3]]
assert _csl_date("1998-03-12") == [[1998, 3, 12]]
assert _csl_date("1998-blah") == [[1998]]
assert _csl_date("asdf") is None
@dataclass
class GrobidCitation:
authors: List[GrobidAuthor]
index: Optional[int] = None
id: Optional[str] = None
date: Optional[str] = None
issue: Optional[str] = None
journal: Optional[str] = None # XXX: venue? other?
publisher: Optional[str] = None
title: Optional[str] = None
url: Optional[str] = None
volume: Optional[str] = None
pages: Optional[str] = None
first_page: Optional[str] = None # XXX
last_page: Optional[str] = None # XXX
unstructured: Optional[str] = None
arxiv_id: Optional[str] = None
doi: Optional[str] = None
pmid: Optional[str] = None
pmcid: Optional[str] = None
oa_url: Optional[str] = None
note: Optional[str] = None
def to_dict(self) -> dict:
return _simplify_dict(asdict(self))
def to_csl_dict(self, default_type: str = "article-journal") -> dict:
"""
Transforms in to Citation Style Language (CSL) JSON schema
"""
csl = dict(
type=default_type,
author=[a.to_csl_dict() for a in self.authors],
issued=_csl_date(self.date),
publisher=self.publisher,
title=self.title,
page=self.pages,
URL=self.url,
DOI=self.doi,
PMID=self.pmid,
PMCID=self.pmcid,
note=self.note,
# fields with '-' in the key name
**{
"container-title": self.journal,
"page-first": self.first_page,
})
# numeric fields
if self.issue and self.issue.isdigit():
csl['issue'] = int(self.issue)
if self.volume and self.volume.isdigit():
csl['volume'] = int(self.volume)
return _simplify_dict(csl)
@dataclass
class GrobidJournal:
name: Optional[str] = None
abbrev: Optional[str] = None
publisher: Optional[str] = None
volume: Optional[str] = None
issue: Optional[str] = None
issn: Optional[str] = None
eissn: Optional[str] = None
@dataclass
class GrobidHeader:
authors: List[GrobidAuthor]
title: Optional[str] = None
date: Optional[str] = None
doi: Optional[str] = None
journal: Optional[GrobidJournal] = None
@dataclass
class GrobidDocument:
grobid_version: str
grobid_timestamp: str
header: GrobidHeader
pdf_md5: Optional[str] = None
language_code: Optional[str] = None
citations: Optional[List[GrobidCitation]] = None
abstract: Optional[str] = None
body: Optional[str] = None
acknowledgement: Optional[str] = None
annex: Optional[str] = None
def to_dict(self) -> dict:
"""
Returns a dict version of this object which has no 'None' fields
(recursively), and is appropriate for serializing to JSON with
json.dumps().
If you did want all the fields, you could use dataclasses.asdict()
directly on thing object.
"""
return _simplify_dict(asdict(self))
def to_legacy_dict(self) -> dict:
"""
Returns a dict in the old "grobid2json" format.
"""
d = self.to_dict()
# all header fields at top-level
d.update(d.pop('header', {}))
# files not in the old schema
d.pop('pdf_md5', None)
for c in d.get('citations', []):
c.pop('note', None)
# author changes
for a in d['authors']:
a['name'] = a.pop('full_name')
addr = a.get('affiliation', {}).get('address')
if addr and addr.get('post_code'):
addr['postCode'] = addr.pop('post_code')
for c in d['citations'] or []:
for a in c['authors']:
a['name'] = a.pop('full_name')
return d
def remove_encumbered(self) -> None:
"""
This helper function removes fields from this object which might raise
copyright concerns.
"""
self.abstract = None
self.body = None
self.acknowledgement = None
self.annex = None
def _simplify_dict(d: dict) -> dict:
"""
Recursively remove empty dict values from a dict and all sub-lists and
sub-dicts.
TODO: should this return Optional[dict]?
"""
if d in [None, {}, '']:
return {}
for k in list(d.keys()):
if isinstance(d[k], dict):
d[k] = _simplify_dict(d[k])
elif isinstance(d[k], list):
for i in range(len(d[k])):
if isinstance(d[k][i], dict):
d[k][i] = _simplify_dict(d[k][i])
if d[k] in [None, {}, '']:
d.pop(k)
return d
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