class JatsParser(object):
"""Parser for the JATS format.
It can be used directly by invoking the :func:`JatsParser.parse` method, or be
subclassed to customize its behavior.
Args:
jats_record (Union[str, scrapy.selector.Selector]): the record in JATS format to parse.
source (Optional[str]): if provided, sets the ``source`` everywhere in
the record. Otherwise, the source is extracted from the JATS metadata.
"""
def __init__(self, jats_record, source=None):
self.root = self.get_root_node(jats_record)
if not source:
source = self.publisher
self.builder = LiteratureBuilder(source)
def parse(self):
"""Extract a JATS record into an Inspire HEP record.
Returns:
dict: the same record in the Inspire Literature schema.
"""
self.builder.add_abstract(self.abstract)
self.builder.add_title(self.title, subtitle=self.subtitle)
self.builder.add_copyright(**self.copyright)
self.builder.add_document_type(self.document_type)
self.builder.add_license(**self.license)
for author in self.authors:
self.builder.add_author(author)
self.builder.add_number_of_pages(self.number_of_pages)
self.builder.add_publication_info(**self.publication_info)
for collab in self.collaborations:
self.builder.add_collaboration(collab)
for doi in self.dois:
self.builder.add_doi(**doi)
for keyword in self.keywords:
self.builder.add_keyword(**keyword)
self.builder.add_imprint_date(self.publication_date.dumps())
for reference in self.references:
self.builder.add_reference(reference)
return self.builder.record
@property
def references(self):
"""Extract a JATS record into an Inspire HEP references record.
Returns:
List[dict]: an array of reference schema records, representing
the references in the record
"""
ref_nodes = self.root.xpath('./back/ref-list/ref')
return list(
itertools.chain.from_iterable(
self.get_reference(node) for node in ref_nodes
)
)
remove_tags_config_abstract = {
'allowed_tags': ['sup', 'sub'],
'allowed_trees': ['math'],
'strip': 'self::pub-id|self::issn'
}
@property
def abstract(self):
abstract_nodes = self.root.xpath('./front//abstract[1]')
if not abstract_nodes:
return
abstract = remove_tags(abstract_nodes[0], **self.remove_tags_config_abstract).strip()
return abstract
@property
def article_type(self):
article_type = self.root.xpath('./@article-type').extract_first()
return article_type
@property
def artid(self):
artid = self.root.xpath('./front/article-meta//elocation-id//text()').extract_first()
return artid
@property
def authors(self):
author_nodes = self.root.xpath('./front//contrib[@contrib-type="author"]')
authors = [self.get_author(author) for author in author_nodes]
return authors
@property
def collaborations(self):
collab_nodes = self.root.xpath(
'./front//collab |'
'./front//contrib[@contrib-type="collaboration"] |'
'./front//on-behalf-of'
)
collaborations = set(
collab.xpath('string(.)').extract_first() for collab in collab_nodes
)
return collaborations
@property
def copyright(self):
copyright = {
'holder': self.copyright_holder,
'material': self.material,
'statement': self.copyright_statement,
'year': self.copyright_year,
}
return copyright
@property
def copyright_holder(self):
copyright_holder = self.root.xpath('./front//copyright-holder/text()').extract_first()
return copyright_holder
@property
def copyright_statement(self):
copyright_statement = self.root.xpath('./front//copyright-statement/text()').extract_first()
return copyright_statement
@property
def copyright_year(self):
copyright_year = self.root.xpath('./front//copyright-year/text()').extract_first()
return maybe_int(copyright_year)
@property
def dois(self):
doi_values = self.root.xpath('./front/article-meta//article-id[@pub-id-type="doi"]/text()').extract()
dois = [
{'doi': value, 'material': self.material} for value in doi_values
]
if self.material != 'publication':
doi_values = self.root.xpath(
'./front/article-meta//related-article[@ext-link-type="doi"]/@href'
).extract()
related_dois = ({'doi': value} for value in doi_values)
dois.extend(related_dois)
return dois
@property
def document_type(self):
if self.is_conference_paper:
document_type = 'conference paper'
else:
document_type = 'article'
return document_type
@property
def is_conference_paper(self):
"""Decide whether the article is a conference paper."""
conference_node = self.root.xpath('./front//conference').extract_first()
return bool(conference_node)
@property
def journal_title(self):
journal_title = self.root.xpath(
'./front/journal-meta//abbrev-journal-title/text() |'
'./front/journal-meta//journal-title/text()'
).extract_first()
return journal_title
@property
def journal_issue(self):
journal_issue = self.root.xpath('./front/article-meta/issue/text()').extract_first()
return journal_issue
@property
def journal_volume(self):
journal_volume = self.root.xpath('./front/article-meta/volume/text()').extract_first()
return journal_volume
@property
def keywords(self):
keyword_groups = self.root.xpath('./front//kwd-group')
keywords = itertools.chain.from_iterable(self.get_keywords(group) for group in keyword_groups)
return keywords
@property
def license(self):
license = {
'license': self.license_statement,
'material': self.material,
'url': self.license_url,
}
return license
@property
def license_statement(self):
license_statement = self.root.xpath('string(./front/article-meta//license)').extract_first().strip()
return license_statement
@property
def license_url(self):
url_nodes = (
'./front/article-meta//license_ref/text() |'
'./front/article-meta//license/@href |'
'./front/article-meta//license//ext-link/@href'
)
license_url = self.root.xpath(url_nodes).extract_first()
return license_url
@property
def material(self):
if self.article_type.startswith('correc'):
material = 'erratum'
elif self.article_type in ('erratum', 'translation', 'addendum', 'reprint'):
material = self.article_type
else:
material = 'publication'
return material
@property
def number_of_pages(self):
number_of_pages = maybe_int(self.root.xpath('./front/article-meta//page-count/@count').extract_first())
return number_of_pages
@property
def page_start(self):
page_start = self.root.xpath('./front/article-meta/fpage/text()').extract_first()
return page_start
@property
def page_end(self):
page_end = self.root.xpath('./front/article-meta/lpage/text()').extract_first()
return page_end
@property
def publication_date(self):
date_nodes = self.root.xpath(
'./front//pub-date[@pub-type="ppub"] |'
'./front//pub-date[@pub-type="epub"] |'
'./front//pub-date[starts-with(@date-type,"pub")] |'
'./front//date[starts-with(@date-type,"pub")]'
)
publication_date = min(
self.get_date(date_node) for date_node in date_nodes
)
return publication_date
@property
def publication_info(self):
publication_info = {
'artid': self.artid,
'journal_title': self.journal_title,
'journal_issue': self.journal_issue,
'journal_volume': self.journal_volume,
'material': self.material,
'page_start': self.page_start,
'page_end': self.page_end,
'year': self.year,
}
return publication_info
@property
def publisher(self):
publisher = self.root.xpath('./front//publisher-name/text()').extract_first()
return publisher
@property
def subtitle(self):
subtitle = self.root.xpath('string(./front//subtitle)').extract_first()
return subtitle
@property
def title(self):
title = self.root.xpath('string(./front//article-title)').extract_first()
return title
def get_affiliation(self, id_):
"""Get the affiliation with the specified id.
Args:
id_(str): the value of the ``id`` attribute of the affiliation.
Returns:
Optional[str]: the affiliation with that id or ``None`` if there is
no match.
"""
affiliation_node = self.root.xpath("//aff[@id=$id_]", id_=id_)
if affiliation_node:
affiliation = remove_tags(
affiliation_node[0], strip="self::label | self::email"
).strip()
return affiliation
def get_emails_from_refs(self, id_):
"""Get the emails from the node with the specified id.
Args:
id_(str): the value of the ``id`` attribute of the node.
Returns:
List[str]: the emails from the node with that id or [] if none found.
"""
email_nodes = self.root.xpath('//aff[@id=$id_]/email/text()', id_=id_)
return email_nodes.extract()
@property
def year(self):
not_online = (
'not(starts-with(@publication-format, "elec"))'
' and not(starts-with(@publication-format, "online")'
)
date_nodes = self.root.xpath(
'./front//pub-date[@pub-type="ppub"] |'
'./front//pub-date[starts-with(@date-type,"pub") and $not_online] |'
'./front//date[starts-with(@date-type,"pub") and $not_online]',
not_online=not_online
)
year = min(
self.get_date(date_node) for date_node in date_nodes
).year
return year
def get_author_affiliations(self, author_node):
"""Extract an author's affiliations."""
raw_referred_ids = author_node.xpath('.//xref[@ref-type="aff"]/@rid').extract()
# Sometimes the rid might have more than one ID (e.g. rid="id0 id1")
referred_ids = set()
for raw_referred_id in raw_referred_ids:
referred_ids.update(set(raw_referred_id.split(' ')))
affiliations = [
self.get_affiliation(rid) for rid in referred_ids
if self.get_affiliation(rid)
]
return affiliations
def get_author_emails(self, author_node):
"""Extract an author's email addresses."""
emails = author_node.xpath('.//email/text()').extract()
referred_ids = author_node.xpath('.//xref[@ref-type="aff"]/@rid').extract()
for referred_id in referred_ids:
emails.extend(self.get_emails_from_refs(referred_id))
return emails
@staticmethod
def get_author_name(author_node):
"""Extract an author's name."""
surname = author_node.xpath('.//surname/text()').extract_first()
if not surname:
# the author name is unstructured
author_name = author_node.xpath('string(./string-name)').extract_first()
given_names = author_node.xpath('.//given-names/text()').extract_first()
suffix = author_node.xpath('.//suffix/text()').extract_first()
author_name = ', '.join(el for el in (surname, given_names, suffix) if el)
return author_name
@staticmethod
def get_date(date_node):
"""Extract a date from a date node.
Returns:
PartialDate: the parsed date.
"""
iso_string = date_node.xpath('./@iso-8601-date').extract_first()
iso_date = PartialDate.loads(iso_string) if iso_string else None
year = date_node.xpath('string(./year)').extract_first()
month = date_node.xpath('string(./month)').extract_first()
day = date_node.xpath('string(./day)').extract_first()
date_from_parts = PartialDate.from_parts(year, month, day) if year else None
string_date = date_node.xpath('string(./string-date)').extract_first()
try:
parsed_date = PartialDate.parse(string_date)
except ValueError:
parsed_date = None
date = get_first([iso_date, date_from_parts, parsed_date])
return date
@staticmethod
def get_keywords(group_node):
"""Extract keywords from a keyword group."""
schema = None
if 'pacs' in group_node.xpath('@kwd-group-type').extract_first(default='').lower():
schema = 'PACS'
keywords = (kwd.xpath('string(.)').extract_first() for kwd in group_node.xpath('.//kwd'))
keyword_dicts = ({'keyword': keyword, 'schema': schema} for keyword in keywords)
return keyword_dicts
@staticmethod
def get_root_node(jats_record):
"""Get a selector on the root ``article`` node of the record.
This can be overridden in case some preprocessing needs to be done on
the XML.
Args:
jats_record(Union[str, scrapy.selector.Selector]): the record in JATS format.
Returns:
scrapy.selector.Selector: a selector on the root ``<article>``
node.
"""
if isinstance(jats_record, six.string_types):
root = get_node(jats_record)
else:
root = jats_record
root.remove_namespaces()
return root
def get_author(self, author_node):
"""Extract one author.
Args:
author_node(scrapy.selector.Selector): a selector on a single
author, e.g. a ``<contrib contrib-type="author">``.
Returns:
dict: the parsed author, conforming to the Inspire schema.
"""
author_name = self.get_author_name(author_node)
emails = self.get_author_emails(author_node)
affiliations = self.get_author_affiliations(author_node)
return self.builder.make_author(author_name, raw_affiliations=affiliations, emails=emails)
@staticmethod
def get_reference_authors(ref_node, role):
"""Extract authors of `role` from a reference node.
Args:
ref_node(scrapy.selector.Selector): a selector on a single reference.
role(str): author role
Returns:
List[str]: list of names
"""
return ref_node.xpath(
'./person-group[@person-group-type=$role]/string-name/text()',
role=role
).extract()
def get_reference(self, ref_node):
"""Extract one reference.
Args:
ref_node(scrapy.selector.Selector): a selector on a single
reference, i.e. ``<ref>``.
Returns:
dict: the parsed reference, as generated by
:class:`inspire_schemas.api.ReferenceBuilder`
"""
for citation_node in ref_node.xpath('./mixed-citation'):
builder = ReferenceBuilder()
builder.add_raw_reference(
ref_node.extract().strip(),
source=self.builder.source,
ref_format='JATS'
)
fields = [
(
(
'self::node()[@publication-type="journal" '
'or @publication-type="eprint"]/source/text()'
),
builder.set_journal_title,
),
(
'self::node()[@publication-type="book"]/source/text()',
builder.add_parent_title,
),
('./publisher-name/text()', builder.set_publisher),
('./volume/text()', builder.set_journal_volume),
('./issue/text()', builder.set_journal_issue),
('./year/text()', builder.set_year),
('./pub-id[@pub-id-type="arxiv"]/text()', builder.add_uid),
('./pub-id[@pub-id-type="doi"]/text()', builder.add_uid),
(
'pub-id[@pub-id-type="other"]'
'[contains(preceding-sibling::text(),"Report No")]/text()',
builder.add_report_number
),
('./article-title/text()', builder.add_title),
('../label/text()', lambda x: builder.set_label(x.strip('[].')))
]
for xpath, field_handler in fields:
value = citation_node.xpath(xpath).extract_first()
citation_node.xpath(xpath)
if value:
field_handler(value)
remainder = remove_tags(
citation_node,
strip='self::person-group'
'|self::pub-id'
'|self::article-title'
'|self::volume'
'|self::issue'
'|self::year'
'|self::label'
'|self::publisher-name'
'|self::source[../@publication-type!="proc"]'
'|self::object-id'
'|self::page-range'
'|self::issn'
).strip('"\';,. \t\n\r').replace('()', '')
if remainder:
builder.add_misc(remainder)
for editor in self.get_reference_authors(citation_node, 'editor'):
builder.add_author(editor, 'editor')
for author in self.get_reference_authors(citation_node, 'author'):
builder.add_author(author, 'author')
page_range = citation_node.xpath('./page-range/text()').extract_first()
if page_range:
page_artid = split_page_artid(page_range)
builder.set_page_artid(*page_artid)
yield builder.obj
def attach_fulltext_document(self, file_name, url):
self.builder.add_document(file_name, url, fulltext=True, hidden=True)
def hepcrawl_to_hep(crawler_record):
"""
Args:
crawler_record(dict): dictionary representing the hepcrawl formatted
record.
Returns:
dict: The hep formatted record.
"""
def _filter_affiliation(affiliations):
return [
affilation.get('value')
for affilation in affiliations
if affilation.get('value')
]
builder = LiteratureBuilder(
source=crawler_record['acquisition_source']['source']
)
for author in crawler_record.get('authors', []):
builder.add_author(builder.make_author(
full_name=author['full_name'],
raw_affiliations=_filter_affiliation(author['affiliations']),
))
for title in crawler_record.get('titles', []):
builder.add_title(
title=title.get('title'),
subtitle=title.get('subtitle'),
source=title.get('source')
)
for abstract in crawler_record.get('abstracts', []):
builder.add_abstract(
abstract=abstract.get('value'),
source=abstract.get('source')
)
for arxiv_eprint in crawler_record.get('arxiv_eprints', []):
builder.add_arxiv_eprint(
arxiv_id=arxiv_eprint.get('value'),
arxiv_categories=arxiv_eprint.get('categories')
)
for doi in crawler_record.get('dois', []):
builder.add_doi(
doi=doi.get('value'),
material=doi.get('material'),
)
for private_note in crawler_record.get('private_notes', []):
builder.add_private_note(
private_notes=private_note
)
for public_note in crawler_record.get('public_notes', []):
builder.add_public_note(
public_note=public_note.get('value'),
source=public_note.get('source')
)
for license in crawler_record.get('license', []):
builder.add_license(
url=license.get('url'),
license=license.get('license'),
material=license.get('material'),
)
for collaboration in crawler_record.get('collaborations', []):
builder.add_collaboration(
collaboration=collaboration.get('value')
)
for imprint in crawler_record.get('imprints', []):
builder.add_imprint_date(
imprint_date=imprint.get('date')
)
for copyright in crawler_record.get('copyright', []):
builder.add_copyright(
holder=copyright.get('holder'),
material=copyright.get('material'),
statement=copyright.get('statement')
)
builder.add_preprint_date(
preprint_date=crawler_record.get('preprint_date')
)
acquisition_source = crawler_record.get('acquisition_source', {})
builder.add_acquisition_source(
method=acquisition_source['method'],
date=acquisition_source['datetime'],
source=acquisition_source['source'],
submission_number=acquisition_source['submission_number'],
)
try:
builder.add_number_of_pages(
number_of_pages=int(crawler_record.get('page_nr', [])[0])
)
except (TypeError, ValueError, IndexError):
pass
publication_types = [
'introductory',
'lectures',
'review',
'manual',
]
document_types = [
'book',
'note',
'report',
'proceedings',
'thesis',
]
added_doc_type = False
for collection in crawler_record.get('collections', []):
collection = collection['primary'].strip().lower()
if collection == 'arxiv':
continue # ignored
elif collection == 'citeable':
builder.set_citeable(True)
elif collection == 'core':
builder.set_core(True)
elif collection == 'noncore':
builder.set_core(False)
elif collection == 'published':
builder.set_refereed(True)
elif collection == 'withdrawn':
builder.set_withdrawn(True)
elif collection in publication_types:
builder.add_publication_type(collection)
elif collection == 'bookchapter':
added_doc_type = True
builder.add_document_type('book chapter')
elif collection == 'conferencepaper':
added_doc_type = True
builder.add_document_type('conference paper')
elif collection in document_types:
added_doc_type = True
builder.add_document_type(collection)
if not added_doc_type:
builder.add_document_type('article')
_pub_info = crawler_record.get('publication_info', [{}])[0]
builder.add_publication_info(
year=_pub_info.get('year'),
artid=_pub_info.get('artid'),
page_end=_pub_info.get('page_end'),
page_start=_pub_info.get('page_start'),
journal_issue=_pub_info.get('journal_issue'),
journal_title=_pub_info.get('journal_title'),
journal_volume=_pub_info.get('journal_volume'),
pubinfo_freetext=_pub_info.get('pubinfo_freetext'),
material=_pub_info.get('pubinfo_material'),
)
for report_number in crawler_record.get('report_numbers', []):
builder.add_report_number(
report_number=report_number.get('value'),
source=report_number.get('source')
)
for url in crawler_record.get('urls', []):
builder.add_url(url=url.get('value'))
for document in crawler_record.get('documents', []):
builder.add_document(
description=document.get('description'),
fulltext=document.get('fulltext'),
hidden=document.get('hidden'),
key=document['key'],
material=document.get('material'),
original_url=document.get('original_url'),
url=document['url'],
)
return builder.record
def crawler2hep(crawler_record):
def _filter_affiliation(affiliations):
return [
affilation.get('value') for affilation in affiliations
if affilation.get('value')
]
builder = LiteratureBuilder('hepcrawl')
for author in crawler_record.get('authors', []):
builder.add_author(
builder.make_author(
author['full_name'],
affiliations=_filter_affiliation(author['affiliations']),
))
for title in crawler_record.get('titles', []):
builder.add_title(title=title.get('title'), source=title.get('source'))
for abstract in crawler_record.get('abstracts', []):
builder.add_abstract(abstract=abstract.get('value'),
source=abstract.get('source'))
for arxiv_eprint in crawler_record.get('arxiv_eprints', []):
builder.add_arxiv_eprint(
arxiv_id=arxiv_eprint.get('value'),
arxiv_categories=arxiv_eprint.get('categories'))
for doi in crawler_record.get('dois', []):
builder.add_doi(doi=doi.get('value'))
for public_note in crawler_record.get('public_notes', []):
builder.add_public_note(public_note=public_note.get('value'),
source=public_note.get('source'))
for license in crawler_record.get('license', []):
builder.add_license(url=license.get('url'),
license=license.get('license'))
for collaboration in crawler_record.get('collaborations', []):
builder.add_collaboration(collaboration=collaboration.get('value'))
for imprint in crawler_record.get('imprints', []):
builder.add_imprint_date(imprint_date=imprint.get('date'))
for copyright in crawler_record.get('copyright', []):
builder.add_copyright(holder=copyright.get('holder'),
material=copyright.get('material'),
statement=copyright.get('statement'))
builder.add_preprint_date(
preprint_date=crawler_record.get('preprint_date'))
acquisition_source = crawler_record.get('acquisition_source', {})
builder.add_acquisition_source(
method='hepcrawl',
date=acquisition_source.get('date'),
source=acquisition_source.get('source'),
submission_number=acquisition_source.get('submission_number'))
try:
builder.add_number_of_pages(
number_of_pages=int(crawler_record.get('page_nr', [])[0]))
except (TypeError, ValueError, IndexError):
pass
publication_types = [
'introductory',
'lectures',
'review',
]
special_collections = [
'cdf-internal-note',
'cdf-note',
'cds',
'd0-internal-note',
'd0-preliminary-note',
'h1-internal-note',
'h1-preliminary-note',
'halhidden',
'hephidden',
'hermes-internal-note',
'larsoft-internal-note',
'larsoft-note',
'zeus-internal-note',
'zeus-preliminary-note',
]
document_types = [
'book',
'note',
'report',
'proceedings',
'thesis',
]
added_doc_type = False
for collection in crawler_record.get('collections', []):
collection = collection['primary'].strip().lower()
if collection == 'arxiv':
continue # ignored
elif collection == 'citeable':
builder.set_citeable(True)
elif collection == 'core':
builder.set_core(True)
elif collection == 'noncore':
builder.set_core(False)
elif collection == 'published':
builder.set_refereed(True)
elif collection == 'withdrawn':
builder.set_withdrawn(True)
elif collection in publication_types:
builder.add_publication_type(collection)
elif collection in special_collections:
builder.add_special_collection(collection.upper())
elif collection == 'bookchapter':
added_doc_type = True
builder.add_document_type('book chapter')
elif collection == 'conferencepaper':
added_doc_type = True
builder.add_document_type('conference paper')
elif collection in document_types:
added_doc_type = True
builder.add_document_type(collection)
if not added_doc_type:
builder.add_document_type('article')
_pub_info = crawler_record.get('publication_info', [{}])[0]
builder.add_publication_info(
year=_pub_info.get('year'),
artid=_pub_info.get('artid'),
page_end=_pub_info.get('page_end'),
page_start=_pub_info.get('page_start'),
journal_issue=_pub_info.get('journal_issue'),
journal_title=_pub_info.get('journal_title'),
journal_volume=_pub_info.get('journal_volume'),
pubinfo_freetext=_pub_info.get('pubinfo_freetext'),
)
for report_number in crawler_record.get('report_numbers', []):
builder.add_report_number(report_number=report_number.get('value'),
source=report_number.get('source'))
builder.validate_record()
return builder.record
class ArxivParser(object):
"""Parser for the arXiv format.
It can be used directly by invoking the :func:`ArxivParser.parse` method, or be
subclassed to customize its behavior.
Args:
arxiv_record (Union[str, scrapy.selector.Selector]): the record in arXiv format to parse.
source (Optional[str]): if provided, sets the ``source`` everywhere in
the record. Otherwise, the source is extracted from the arXiv metadata.
"""
_l2t = LatexNodes2Text(
latex_context=get_arxiv_latex_context_db(),
math_mode="verbatim",
strict_latex_spaces="based-on-source",
keep_comments=True,
keep_braced_groups=True,
keep_braced_groups_minlen=2,
)
def __init__(self, arxiv_record, source=None):
self.root = self.get_root_node(arxiv_record)
if not source:
source = 'arXiv'
self.builder = LiteratureBuilder(source)
def parse(self):
"""Extract an arXiv record into an Inspire HEP record.
Returns:
dict: the same record in the Inspire Literature schema.
"""
self.builder.add_abstract(abstract=self.abstract, source=self.source)
self.builder.add_title(title=self.title, source=self.source)
for license in self.licenses:
self.builder.add_license(**license)
for author in self.authors:
self.builder.add_author(author)
self.builder.add_number_of_pages(self.number_of_pages)
self.builder.add_publication_info(**self.publication_info)
for collab in self.collaborations:
self.builder.add_collaboration(collab)
for doi in self.dois:
self.builder.add_doi(**doi)
self.builder.add_preprint_date(self.preprint_date)
if self.public_note:
self.builder.add_public_note(self.public_note, self.source)
for rep_number in self.report_numbers:
self.builder.add_report_number(rep_number, self.source)
self.builder.add_arxiv_eprint(self.arxiv_eprint, self.arxiv_categories)
self.builder.add_private_note(self.private_note)
self.builder.add_document_type(self.document_type)
normalized_categories = [
classify_field(arxiv_cat) for arxiv_cat in self.arxiv_categories
]
self.builder.add_inspire_categories(dedupe_list(normalized_categories),
'arxiv')
return self.builder.record
def _get_authors_and_collaborations(self, node):
"""Parse authors, affiliations and collaborations from the record node.
Heuristics are used to detect collaborations. In case those are not
reliable, a warning is returned for manual checking.
Args:
node (Selector): a selector on a record
Returns:
tuple: a tuple of (authors, collaborations, warning)
"""
author_selectors = node.xpath('.//authors//author')
# take 'for the' out of the general phrases and dont use it in
# affiliations
collab_phrases = [
'consortium',
' collab ',
'collaboration',
' team',
'group',
' on behalf of ',
' representing ',
]
inst_phrases = ['institute', 'university', 'department', 'center']
authors = []
collaborations = []
warning_tags = []
some_affiliation_contains_collaboration = False
authors_and_affiliations = (
self._get_author_names_and_affiliations(author)
for author in author_selectors)
next_author_and_affiliations = (
self._get_author_names_and_affiliations(author)
for author in author_selectors)
next(next_author_and_affiliations)
for (forenames, keyname,
affiliations), (next_forenames, next_keyname,
_) in six.moves.zip_longest(
authors_and_affiliations,
next_author_and_affiliations,
fillvalue=('end of author-list', '', None)):
name_string = " %s %s " % (forenames, keyname)
# collaborations in affiliation field? Cautious with 'for the' in
# Inst names
affiliations_with_collaborations = []
affiliations_without_collaborations = []
for aff in affiliations:
affiliation_contains_collaboration = any(
phrase in aff.lower()
for phrase in collab_phrases) and not any(
phrase in aff.lower() for phrase in inst_phrases)
if affiliation_contains_collaboration:
affiliations_with_collaborations.append(aff)
some_affiliation_contains_collaboration = True
else:
affiliations_without_collaborations.append(aff)
for aff in affiliations_with_collaborations:
coll, author_name = coll_cleanforthe(aff)
if coll and coll not in collaborations:
collaborations.append(coll)
# Check if name is a collaboration, else append to authors
collaboration_in_name = ' for the ' in name_string.lower() or any(
phrase in name_string.lower() for phrase in collab_phrases)
if collaboration_in_name:
coll, author_name = coll_cleanforthe(name_string)
if author_name:
surname, given_names = split_fullname(author_name)
authors.append({
'full_name': surname + ', ' + given_names,
'surname': surname,
'given_names': given_names,
'affiliations': [],
})
if coll and coll not in collaborations:
collaborations.append(coll)
elif name_string.strip() == ':':
# DANGERZONE : this might not be correct - add a warning for the cataloger
warning_tags.append(' %s %s ' % (next_forenames, next_keyname))
if not some_affiliation_contains_collaboration:
# everything up to now seems to be collaboration info
for author_info in authors:
name_string = " %s %s " % \
(author_info['given_names'], author_info['surname'])
coll, author_name = coll_cleanforthe(name_string)
if coll and coll not in collaborations:
collaborations.append(coll)
authors = []
else:
authors.append({
'full_name':
keyname + ', ' + forenames,
'surname':
keyname,
'given_names':
forenames,
'affiliations':
affiliations_without_collaborations
})
if warning_tags:
warning = 'WARNING: Colon in authors before %s: Check author list for collaboration names!' % ', '.join(
warning_tags)
else:
warning = ''
return authors, collaborations, warning
@staticmethod
def _get_author_names_and_affiliations(author_node):
forenames = u' '.join(
author_node.xpath('.//forenames//text()').extract())
keyname = u' '.join(author_node.xpath('.//keyname//text()').extract())
affiliations = author_node.xpath('.//affiliation//text()').extract()
return forenames, keyname, affiliations
@property
def preprint_date(self):
preprint_date = self.root.xpath('.//created/text()').extract_first()
return preprint_date
@property
def abstract(self):
abstract = self.root.xpath('.//abstract/text()').extract_first()
long_text_fixed = self.fix_long_text(abstract)
return self.latex_to_unicode(long_text_fixed)
@property
def authors(self):
authors, _, _ = self.authors_and_collaborations
parsed_authors = [
self.builder.make_author(full_name=auth["full_name"],
raw_affiliations=auth["affiliations"])
for auth in authors
]
return parsed_authors
@property
def collaborations(self):
_, collaborations, _ = self.authors_and_collaborations
return collaborations
@property
def dois(self):
doi_values = self.root.xpath('.//doi/text()').extract()
doi_values_splitted = chain.from_iterable(
[re.split(RE_DOIS, doi) for doi in doi_values])
dois = [{
'doi': value,
'material': 'publication'
} for value in doi_values_splitted]
return dois
@property
def licenses(self):
licenses = self.root.xpath('.//license/text()').extract()
return [{
'url': license,
'material': self.material
} for license in licenses]
@property
def material(self):
return 'preprint'
@property
def number_of_pages(self):
comments = '; '.join(self.root.xpath('.//comments/text()').extract())
found_pages = RE_PAGES.search(comments)
if found_pages:
pages = found_pages.group(1)
return maybe_int(pages)
return None
@property
def publication_info(self):
publication_info = {
'material': 'publication',
'pubinfo_freetext': self.pubinfo_freetext,
}
return publication_info
@property
def pubinfo_freetext(self):
return self.root.xpath('.//journal-ref/text()').extract_first()
@property
def title(self):
long_text_fixed = self.fix_long_text(
self.root.xpath('.//title/text()').extract_first())
return self.latex_to_unicode(long_text_fixed)
@staticmethod
def fix_long_text(text):
return re.sub(r'\s+', ' ', text).strip()
@staticmethod
def get_root_node(arxiv_record):
"""Get a selector on the root ``article`` node of the record.
This can be overridden in case some preprocessing needs to be done on
the XML.
Args:
arxiv_record(Union[str, scrapy.selector.Selector]): the record in arXiv format.
Returns:
scrapy.selector.Selector: a selector on the root ``<article>``
node.
"""
if isinstance(arxiv_record, six.string_types):
root = get_node(arxiv_record)
else:
root = arxiv_record
root.remove_namespaces()
return root
@property
def public_note(self):
comments = '; '.join(self.root.xpath('.//comments/text()').extract())
return self.latex_to_unicode(comments)
@property
def private_note(self):
_, _, warning = self.authors_and_collaborations
return warning
@property
def report_numbers(self):
report_numbers = self.root.xpath('.//report-no/text()').extract()
rns = []
for rn in report_numbers:
rns.extend(rn.split(', '))
return rns
@property
def arxiv_eprint(self):
return self.root.xpath('.//id/text()').extract_first()
@property
def arxiv_categories(self):
categories = self.root.xpath('.//categories/text()').extract_first(
default='[]')
categories = categories.split()
categories_without_old = [
normalize_arxiv_category(arxiv_cat) for arxiv_cat in categories
]
return dedupe_list(categories_without_old)
@property
def document_type(self):
comments = '; '.join(self.root.xpath('.//comments/text()').extract())
doctype = 'article'
if RE_THESIS.search(comments):
doctype = 'thesis'
elif RE_CONFERENCE.search(comments):
doctype = 'conference paper'
return doctype
@property
def source(self):
return 'arXiv'
@property
def authors_and_collaborations(self):
if not hasattr(self, '_authors_and_collaborations'):
self._authors_and_collaborations = self._get_authors_and_collaborations(
self.root)
return self._authors_and_collaborations
@classmethod
def latex_to_unicode(cls, latex_string):
try:
return cls._l2t.latex_to_text(latex_string).replace(" ", " ")
except Exception as e:
return latex_string
class JatsParser(object):
"""Parser for the JATS format.
It can be used directly by invoking the :func:`JatsParser.parse` method, or be
subclassed to customize its behavior.
Args:
jats_record (Union[str, scrapy.selector.Selector]): the record in JATS format to parse.
source (Optional[str]): if provided, sets the ``source`` everywhere in
the record. Otherwise, the source is extracted from the JATS metadata.
"""
def __init__(self, jats_record, source=None):
self.root = self.get_root_node(jats_record)
if not source:
source = self.publisher
self.builder = LiteratureBuilder(source)
def parse(self):
"""Extract a JATS record into an Inspire HEP record.
Returns:
dict: the same record in the Inspire Literature schema.
"""
self.builder.add_abstract(self.abstract)
self.builder.add_title(self.title, subtitle=self.subtitle)
self.builder.add_copyright(**self.copyright)
self.builder.add_document_type(self.document_type)
self.builder.add_license(**self.license)
for author in self.authors:
self.builder.add_author(author)
self.builder.add_number_of_pages(self.number_of_pages)
self.builder.add_publication_info(**self.publication_info)
for collab in self.collaborations:
self.builder.add_collaboration(collab)
for doi in self.dois:
self.builder.add_doi(**doi)
for keyword in self.keywords:
self.builder.add_keyword(**keyword)
self.builder.add_imprint_date(self.publication_date.dumps())
for reference in self.references:
self.builder.add_reference(reference)
return self.builder.record
@property
def references(self):
"""Extract a JATS record into an Inspire HEP references record.
Returns:
List[dict]: an array of reference schema records, representing
the references in the record
"""
ref_nodes = self.root.xpath('./back/ref-list/ref')
return list(
itertools.chain.from_iterable(
self.get_reference(node) for node in ref_nodes
)
)
remove_tags_config_abstract = {
'allowed_tags': ['sup', 'sub'],
'allowed_trees': ['math'],
'strip': 'self::pub-id|self::issn'
}
@property
def abstract(self):
abstract_nodes = self.root.xpath('./front//abstract[1]')
if not abstract_nodes:
return
abstract = remove_tags(abstract_nodes[0], **self.remove_tags_config_abstract).strip()
return abstract
@property
def article_type(self):
article_type = self.root.xpath('./@article-type').extract_first()
return article_type
@property
def artid(self):
artid = self.root.xpath('./front/article-meta//elocation-id//text()').extract_first()
return artid
@property
def authors(self):
author_nodes = self.root.xpath('./front//contrib[@contrib-type="author"]')
authors = [self.get_author(author) for author in author_nodes]
return authors
@property
def collaborations(self):
collab_nodes = self.root.xpath(
'./front//collab |'
'./front//contrib[@contrib-type="collaboration"] |'
'./front//on-behalf-of'
)
collaborations = set(
collab.xpath('string(.)').extract_first() for collab in collab_nodes
)
return collaborations
@property
def copyright(self):
copyright = {
'holder': self.copyright_holder,
'material': self.material,
'statement': self.copyright_statement,
'year': self.copyright_year,
}
return copyright
@property
def copyright_holder(self):
copyright_holder = self.root.xpath('./front//copyright-holder/text()').extract_first()
return copyright_holder
@property
def copyright_statement(self):
copyright_statement = self.root.xpath('./front//copyright-statement/text()').extract_first()
return copyright_statement
@property
def copyright_year(self):
copyright_year = self.root.xpath('./front//copyright-year/text()').extract_first()
return maybe_int(copyright_year)
@property
def dois(self):
doi_values = self.root.xpath('./front/article-meta//article-id[@pub-id-type="doi"]/text()').extract()
dois = [
{'doi': value, 'material': self.material} for value in doi_values
]
if self.material != 'publication':
doi_values = self.root.xpath(
'./front/article-meta//related-article[@ext-link-type="doi"]/@href'
).extract()
related_dois = ({'doi': value} for value in doi_values)
dois.extend(related_dois)
return dois
@property
def document_type(self):
if self.is_conference_paper:
document_type = 'conference paper'
else:
document_type = 'article'
return document_type
@property
def is_conference_paper(self):
"""Decide whether the article is a conference paper."""
conference_node = self.root.xpath('./front//conference').extract_first()
return bool(conference_node)
@property
def journal_title(self):
journal_title = self.root.xpath(
'./front/journal-meta//abbrev-journal-title/text() |'
'./front/journal-meta//journal-title/text()'
).extract_first()
return journal_title
@property
def journal_issue(self):
journal_issue = self.root.xpath('./front/article-meta/issue/text()').extract_first()
return journal_issue
@property
def journal_volume(self):
journal_volume = self.root.xpath('./front/article-meta/volume/text()').extract_first()
return journal_volume
@property
def keywords(self):
keyword_groups = self.root.xpath('./front//kwd-group')
keywords = itertools.chain.from_iterable(self.get_keywords(group) for group in keyword_groups)
return keywords
@property
def license(self):
license = {
'license': self.license_statement,
'material': self.material,
'url': self.license_url,
}
return license
@property
def license_statement(self):
license_statement = self.root.xpath('string(./front/article-meta//license)').extract_first().strip()
return license_statement
@property
def license_url(self):
url_nodes = (
'./front/article-meta//license_ref/text() |'
'./front/article-meta//license/@href |'
'./front/article-meta//license//ext-link/@href'
)
license_url = self.root.xpath(url_nodes).extract_first()
return license_url
@property
def material(self):
if self.article_type.startswith('correc'):
material = 'erratum'
elif self.article_type in ('erratum', 'translation', 'addendum', 'reprint'):
material = self.article_type
else:
material = 'publication'
return material
@property
def number_of_pages(self):
number_of_pages = maybe_int(self.root.xpath('./front/article-meta//page-count/@count').extract_first())
return number_of_pages
@property
def page_start(self):
page_start = self.root.xpath('./front/article-meta/fpage/text()').extract_first()
return page_start
@property
def page_end(self):
page_end = self.root.xpath('./front/article-meta/lpage/text()').extract_first()
return page_end
@property
def publication_date(self):
date_nodes = self.root.xpath(
'./front//pub-date[@pub-type="ppub"] |'
'./front//pub-date[@pub-type="epub"] |'
'./front//pub-date[starts-with(@date-type,"pub")] |'
'./front//date[starts-with(@date-type,"pub")]'
)
publication_date = min(
self.get_date(date_node) for date_node in date_nodes
)
return publication_date
@property
def publication_info(self):
publication_info = {
'artid': self.artid,
'journal_title': self.journal_title,
'journal_issue': self.journal_issue,
'journal_volume': self.journal_volume,
'material': self.material,
'page_start': self.page_start,
'page_end': self.page_end,
'year': self.year,
}
return publication_info
@property
def publisher(self):
publisher = self.root.xpath('./front//publisher-name/text()').extract_first()
return publisher
@property
def subtitle(self):
subtitle = self.root.xpath('string(./front//subtitle)').extract_first()
return subtitle
@property
def title(self):
title = self.root.xpath('string(./front//article-title)').extract_first()
return title
def get_affiliation(self, id_):
"""Get the affiliation with the specified id.
Args:
id_(str): the value of the ``id`` attribute of the affiliation.
Returns:
Optional[str]: the affiliation with that id or ``None`` if there is
no match.
"""
affiliation_node = self.root.xpath('//aff[@id=$id_]', id_=id_)[0]
affiliation = remove_tags(
affiliation_node,
strip='self::label | self::email'
).strip()
return affiliation
def get_emails_from_refs(self, id_):
"""Get the emails from the node with the specified id.
Args:
id_(str): the value of the ``id`` attribute of the node.
Returns:
List[str]: the emails from the node with that id or [] if none found.
"""
email_nodes = self.root.xpath('//aff[@id=$id_]/email/text()', id_=id_)
return email_nodes.extract()
@property
def year(self):
not_online = (
'not(starts-with(@publication-format, "elec"))'
' and not(starts-with(@publication-format, "online")'
)
date_nodes = self.root.xpath(
'./front//pub-date[@pub-type="ppub"] |'
'./front//pub-date[starts-with(@date-type,"pub") and $not_online] |'
'./front//date[starts-with(@date-type,"pub") and $not_online]',
not_online=not_online
)
year = min(
self.get_date(date_node) for date_node in date_nodes
).year
return year
def get_author_affiliations(self, author_node):
"""Extract an author's affiliations."""
raw_referred_ids = author_node.xpath('.//xref[@ref-type="aff"]/@rid').extract()
# Sometimes the rid might have more than one ID (e.g. rid="id0 id1")
referred_ids = set()
for raw_referred_id in raw_referred_ids:
referred_ids.update(set(raw_referred_id.split(' ')))
affiliations = [
self.get_affiliation(rid) for rid in referred_ids
if self.get_affiliation(rid)
]
return affiliations
def get_author_emails(self, author_node):
"""Extract an author's email addresses."""
emails = author_node.xpath('.//email/text()').extract()
referred_ids = author_node.xpath('.//xref[@ref-type="aff"]/@rid').extract()
for referred_id in referred_ids:
emails.extend(self.get_emails_from_refs(referred_id))
return emails
@staticmethod
def get_author_name(author_node):
"""Extract an author's name."""
surname = author_node.xpath('.//surname/text()').extract_first()
if not surname:
# the author name is unstructured
author_name = author_node.xpath('string(./string-name)').extract_first()
given_names = author_node.xpath('.//given-names/text()').extract_first()
suffix = author_node.xpath('.//suffix/text()').extract_first()
author_name = ', '.join(el for el in (surname, given_names, suffix) if el)
return author_name
@staticmethod
def get_date(date_node):
"""Extract a date from a date node.
Returns:
PartialDate: the parsed date.
"""
iso_string = date_node.xpath('./@iso-8601-date').extract_first()
iso_date = PartialDate.loads(iso_string) if iso_string else None
year = date_node.xpath('string(./year)').extract_first()
month = date_node.xpath('string(./month)').extract_first()
day = date_node.xpath('string(./day)').extract_first()
date_from_parts = PartialDate.from_parts(year, month, day) if year else None
string_date = date_node.xpath('string(./string-date)').extract_first()
try:
parsed_date = PartialDate.parse(string_date)
except ValueError:
parsed_date = None
date = get_first([iso_date, date_from_parts, parsed_date])
return date
@staticmethod
def get_keywords(group_node):
"""Extract keywords from a keyword group."""
schema = None
if 'pacs' in group_node.xpath('@kwd-group-type').extract_first(default='').lower():
schema = 'PACS'
keywords = (kwd.xpath('string(.)').extract_first() for kwd in group_node.xpath('.//kwd'))
keyword_dicts = ({'keyword': keyword, 'schema': schema} for keyword in keywords)
return keyword_dicts
@staticmethod
def get_root_node(jats_record):
"""Get a selector on the root ``article`` node of the record.
This can be overridden in case some preprocessing needs to be done on
the XML.
Args:
jats_record(Union[str, scrapy.selector.Selector]): the record in JATS format.
Returns:
scrapy.selector.Selector: a selector on the root ``<article>``
node.
"""
if isinstance(jats_record, six.string_types):
root = get_node(jats_record)
else:
root = jats_record
root.remove_namespaces()
return root
def get_author(self, author_node):
"""Extract one author.
Args:
author_node(scrapy.selector.Selector): a selector on a single
author, e.g. a ``<contrib contrib-type="author">``.
Returns:
dict: the parsed author, conforming to the Inspire schema.
"""
author_name = self.get_author_name(author_node)
emails = self.get_author_emails(author_node)
affiliations = self.get_author_affiliations(author_node)
return self.builder.make_author(author_name, raw_affiliations=affiliations, emails=emails)
@staticmethod
def get_reference_authors(ref_node, role):
"""Extract authors of `role` from a reference node.
Args:
ref_node(scrapy.selector.Selector): a selector on a single reference.
role(str): author role
Returns:
List[str]: list of names
"""
return ref_node.xpath(
'./person-group[@person-group-type=$role]/string-name/text()',
role=role
).extract()
def get_reference(self, ref_node):
"""Extract one reference.
Args:
ref_node(scrapy.selector.Selector): a selector on a single
reference, i.e. ``<ref>``.
Returns:
dict: the parsed reference, as generated by
:class:`inspire_schemas.api.ReferenceBuilder`
"""
for citation_node in ref_node.xpath('./mixed-citation'):
builder = ReferenceBuilder()
builder.add_raw_reference(
ref_node.extract().strip(),
source=self.builder.source,
ref_format='JATS'
)
fields = [
(
(
'self::node()[@publication-type="journal" '
'or @publication-type="eprint"]/source/text()'
),
builder.set_journal_title,
),
(
'self::node()[@publication-type="book"]/source/text()',
builder.add_parent_title,
),
('./publisher-name/text()', builder.set_publisher),
('./volume/text()', builder.set_journal_volume),
('./issue/text()', builder.set_journal_issue),
('./year/text()', builder.set_year),
('./pub-id[@pub-id-type="arxiv"]/text()', builder.add_uid),
('./pub-id[@pub-id-type="doi"]/text()', builder.add_uid),
(
'pub-id[@pub-id-type="other"]'
'[contains(preceding-sibling::text(),"Report No")]/text()',
builder.add_report_number
),
('./article-title/text()', builder.add_title),
('../label/text()', lambda x: builder.set_label(x.strip('[].')))
]
for xpath, field_handler in fields:
value = citation_node.xpath(xpath).extract_first()
citation_node.xpath(xpath)
if value:
field_handler(value)
remainder = remove_tags(
citation_node,
strip='self::person-group'
'|self::pub-id'
'|self::article-title'
'|self::volume'
'|self::issue'
'|self::year'
'|self::label'
'|self::publisher-name'
'|self::source[../@publication-type!="proc"]'
'|self::object-id'
'|self::page-range'
'|self::issn'
).strip('"\';,. \t\n\r').replace('()', '')
if remainder:
builder.add_misc(remainder)
for editor in self.get_reference_authors(citation_node, 'editor'):
builder.add_author(editor, 'editor')
for author in self.get_reference_authors(citation_node, 'author'):
builder.add_author(author, 'author')
page_range = citation_node.xpath('./page-range/text()').extract_first()
if page_range:
page_artid = split_page_artid(page_range)
builder.set_page_artid(*page_artid)
yield builder.obj
def attach_fulltext_document(self, file_name, url):
self.builder.add_document(file_name, url, fulltext=True, hidden=True)
