class Link(Parser):
url = tools.RunPython('format_doi', ctx)
# identifier will always be DOI
type = tools.Static('doi')
def format_doi(self, doi):
return format_doi_as_url(self, doi)
class Link(Parser):
url = tools.RunPython('format_url', ctx)
type = tools.Static('provider')
def format_url(self, ctx):
return 'https://www.nsf.gov/awardsearch/showAward?AWD_ID={}'.format(
ctx['id'])
class FunderAgent(Parser):
schema = tools.GuessAgentType(tools.OneOf(ctx.funderName,
ctx.contributorName),
default='organization')
name = tools.OneOf(ctx.funderName, ctx.contributorName)
identifiers = tools.Map(
tools.Delegate(AgentIdentifier),
tools.Try(tools.IRI(
tools.OneOf(ctx.funderIdentifier,
tools.RunPython(force_text, ctx.nameIdentifier),
tools.Static(None))),
exceptions=(ValueError, )))
class Extra:
name_identifier = tools.Try(ctx.nameIdentifier)
name_identifier_scheme = tools.Try(
ctx.nameIdentifier['@nameIdentifierScheme'])
name_identifier_scheme_uri = tools.Try(
ctx.nameIdentifier['@schemeURI'])
funder_identifier = tools.Try(ctx.funderIdentifier)
funder_identifier_type = tools.Try(ctx.funderIdentifierType)
contributor_type = tools.Try(ctx.contributorType)
class Extra:
name_identifier = tools.Try(ctx.nameIdentifier)
name_identifier_scheme = tools.Try(
ctx.nameIdentifier['@nameIdentifierScheme'])
name_identifier_scheme_uri = tools.Try(
ctx.nameIdentifier['@schemeURI'])
contributor_type = tools.Try(ctx.contributorType)
# v.4 new givenName and familyName properties
given_name = tools.OneOf(ctx.creatorName['@givenName'],
ctx.contributorName['@givenName'],
tools.Static(None))
family_name = tools.OneOf(ctx.creatorName['@familyName'],
ctx.contributorName['@familyName'],
tools.Static(None))
class CreativeWork(Parser):
schema = tools.RunPython('get_type', ctx)
title = tools.RunPython('get_title', ctx)
description = Soup(ctx, 'p', class_='genericfile_description')['#text']
date_published = tools.ParseDate(
Soup(ctx, itemprop='datePublished')['#text'])
date_updated = tools.ParseDate(Soup(ctx, itemprop='dateModified')['#text'])
rights = tools.OneOf(tools.RunPython('get_rights_url', ctx),
tools.RunPython('get_dd', ctx, 'Rights')['#text'],
tools.Static(None))
language = tools.Try(
tools.ParseLanguage(Soup(ctx, itemprop='inLanguage')['#text']))
tags = tools.Map(tools.Delegate(ThroughTags), Soup(ctx,
itemprop='keywords'))
identifiers = tools.Map(
tools.Delegate(WorkIdentifier),
tools.Try(tools.RunPython('get_dd', ctx, 'Permanent Link')),
)
related_agents = tools.Concat(
tools.Map(tools.Delegate(Creator), Soup(ctx, itemprop='creator')),
tools.Map(tools.Delegate(Contributor), Soup(ctx,
itemprop='contributor')),
tools.Map(tools.Delegate(Publisher), Soup(ctx, itemprop='publisher')),
)
class Extra:
gwu_unit = tools.RunPython('get_dd', ctx, 'GW Unit')['#text']
related_url = tools.RunPython('get_dd', ctx, 'Related URL')['#text']
previous_publication_information = tools.RunPython(
'get_dd', ctx, 'Previous Publication Information')['#text']
depositor = tools.RunPython('get_dd', ctx, 'Depositor')['#text']
characterization = tools.RunPython('get_dd', ctx,
'Characterization')['#text']
def get_type(self, obj):
return {
'http://schema.org/CreativeWork': 'CreativeWork',
'http://schema.org/Article': 'Article',
'http://schema.org/Book': 'Book',
}.get(obj.soup.find('div')['itemtype'], 'CreativeWork')
def get_title(self, obj):
title = obj.h1.soup
title.find('span', class_='label').decompose()
return title.get_text()
def get_dd(self, obj, dt):
dt_tag = obj.soup.find('dt', string=dt)
if dt_tag:
return SoupXMLDict(soup=dt_tag.find_next_sibling('dd'))
return None
def get_rights_url(self, obj):
dd = self.get_dd(obj, 'Rights')
return dd.soup.find('i', class_='glyphicon-new-window').parent['href']
class Preprint(Parser):
title = tools.Try(ctx['DC.Title'])
description = tools.Try(ctx['DC.Description'])
# is_deleted
date_published = tools.ParseDate(tools.Try(ctx['article:published_time']))
date_updated = tools.ParseDate(tools.Try(ctx['DC.Date']))
# free_to_read_type
# free_to_read_date
rights = tools.Try(ctx['DC.Rights'])
language = tools.Try(ctx['DC.Language'])
subjects = tools.Map(tools.Delegate(ThroughSubjects),
tools.Static('Biology'),
tools.Subjects(tools.Try(ctx['subject-areas'])))
tags = tools.Map(tools.Delegate(ThroughTags), tools.Try(ctx['category']),
tools.Try(ctx['subject-areas']))
identifiers = tools.Map(tools.Delegate(WorkIdentifier),
tools.Try(ctx['og:url']),
ctx['citation_public_url'], ctx['citation_doi'])
related_agents = tools.Concat(
tools.Map(tools.Delegate(Publisher), tools.Try(ctx['DC.Publisher'])),
tools.Map(tools.Delegate(Creator),
tools.RunPython('get_contributors', ctx)))
# related_works
class Extra:
identifiers = ctx['DC.Identifier']
access_rights = ctx['DC.AccessRights']
def get_contributors(self, link):
authors = link.get('citation_author', []) if isinstance(
link.get('citation_author', []),
list) else [link['citation_author']]
institutions = link.get(
'citation_author_institution', []) if isinstance(
link.get('citation_author_institution', []),
list) else [link['citation_author_institution']]
emails = link.get('citation_author_email', []) if isinstance(
link.get('citation_author_email', []),
list) else [link['citation_author_email']]
contribs = []
for author, email, institution in itertools.zip_longest(
authors, emails, institutions):
contrib = {
'author': author,
'institution': institution,
'email': email,
}
contribs.append(contrib)
return contribs
class Preprint(Parser):
title = ctx.item['dc:title']
description = ctx.item.description
contributors = tools.Map(tools.Delegate(Contributor),
ctx.item['dc:creator'])
date_published = ctx.item['dc:date']
publishers = tools.Map(
tools.Delegate(Association.using(entity=tools.Delegate(Publisher))),
ctx.item['dc:publisher'])
links = tools.Map(tools.Delegate(ThroughLinks), ctx.item['dc:identifier'])
subjects = tools.Map(
tools.Delegate(ThroughSubjects),
tools.Concat(tools.Static('Biology and life sciences')))
class Preprint(Parser):
title = ctx.item['dc:title']
description = ctx.item.description
date_published = tools.ParseDate(ctx.item['dc:date'])
date_updated = tools.ParseDate(ctx.item['dc:date'])
subjects = tools.Map(
tools.Delegate(ThroughSubjects),
tools.Concat(tools.Static('Biology'))
)
identifiers = tools.Map(tools.Delegate(WorkIdentifier), ctx.item['dc:identifier'])
related_agents = tools.Concat(
tools.Delegate(Publisher, ctx.item['dc:publisher']),
tools.Map(tools.Delegate(Creator), ctx.item['dc:creator']),
)
class Preprint(Parser):
title = ctx.attributes.title
description = ctx.attributes.description
contributors = tools.Map(tools.Delegate(Contributor), ctx.contributors)
institutions = tools.Map(
tools.Delegate(Association.using(entity=tools.Delegate(Institution))),
ctx.embeds.affiliated_institutions.data)
# rights = tools.Try(ctx.attributes.node_license)
date_updated = tools.ParseDate(ctx.attributes.date_modified)
links = tools.Map(tools.Delegate(ThroughLinks), ctx.links.html)
tags = tools.Map(tools.Delegate(ThroughTags), ctx.attributes.category,
ctx.attributes.tags)
subjects = tools.Map(tools.Delegate(ThroughSubjects),
tools.Static('Engineering and technology'))
class Extra:
date_created = tools.ParseDate(ctx.attributes.date_created)
date_modified = ctx.attributes.date_modified
class CreativeWork(Parser):
title = ctx.attributes.title
description = ctx.attributes.description
is_deleted = tools.Static(False)
# date_published =
date_updated = tools.ParseDate(ctx.attributes.date_modified)
# free_to_read_type =
# free_to_read_date =
# rights = tools.Try(ctx.attributes.node_license) Doesn't seem to have an useful information
# language =
identifiers = tools.Map(tools.Delegate(WorkIdentifier), ctx.links.html,
ctx.links.self)
tags = tools.Map(tools.Delegate(ThroughTags), ctx.attributes.category,
ctx.attributes.tags)
class Extra:
date_created = tools.ParseDate(ctx.attributes.date_created)
class Preprint(osf.Project):
description = tools.Try(ctx.attributes.abstract)
date_updated = tools.ParseDate(ctx.attributes.date_modified)
date_published = tools.ParseDate(ctx.attributes.date_created)
# NOTE: OSF has a direct mapping to SHARE's taxonomy. Subjects() is not needed
subjects = tools.Map(tools.Delegate(ThroughSubjects),
ctx.attributes.subjects)
identifiers = tools.Map(tools.Delegate(WorkIdentifier), ctx.links.self,
ctx.links.html, tools.Try(ctx.links.doi))
tags = tools.Map(tools.Delegate(ThroughTags),
tools.Try(ctx.attributes.tags))
rights = tools.Try(ctx.attributes.node_license)
related_works = tools.Static([])
related_agents = tools.Concat(
tools.Map(
tools.Delegate(osf.Creator),
tools.Filter(lambda x: x['attributes']['bibliographic'],
ctx.contributors)),
tools.Map(
tools.Delegate(osf.Contributor),
tools.Filter(lambda x: not x['attributes']['bibliographic'],
ctx.contributors)),
)
class OAICreativeWork(Parser):
default_type = None
type_map = None
schema = tools.RunPython(
'get_schema',
tools.OneOf(ctx.record.metadata.dc['dc:type'], tools.Static(None)))
title = tools.Join(
tools.RunPython('force_text',
tools.Try(ctx.record.metadata.dc['dc:title'])))
description = tools.Join(
tools.RunPython('force_text',
tools.Try(ctx.record.metadata.dc['dc:description'])))
identifiers = tools.Map(
tools.Delegate(OAIWorkIdentifier),
tools.Unique(
tools.Map(
tools.Try(tools.IRI(), exceptions=(ValueError, )),
tools.Filter(
not_citation,
tools.RunPython(
'force_text',
tools.Concat(
tools.Try(ctx.record.metadata.dc['dc:identifier']),
tools.Try(ctx.record.header['identifier'])))))))
related_works = tools.Concat(
tools.Map(
tools.Delegate(OAIWorkRelation),
tools.Unique(
tools.Map(tools.Try(tools.IRI(), exceptions=(ValueError, )),
tools.RunPython('get_relation', ctx)))))
related_agents = tools.Concat(
tools.Map(tools.Delegate(OAICreator),
tools.Try(ctx.record.metadata.dc['dc:creator'])),
tools.Map(tools.Delegate(OAIContributor),
tools.Try(ctx.record.metadata.dc['dc:contributor'])),
tools.Map(
tools.Delegate(OAIPublisher),
tools.RunPython('force_text',
tools.Try(
ctx.record.metadata.dc['dc:publisher']))),
)
rights = tools.Join(tools.Try(ctx.record.metadata.dc['dc:rights']))
# Note: this is only taking the first language in the case of multiple languages
language = tools.ParseLanguage(
tools.Try(ctx.record.metadata.dc['dc:language'][0]), )
subjects = tools.Map(
tools.Delegate(OAIThroughSubjects),
tools.Subjects(
tools.Map(
tools.RunPython('tokenize'),
tools.RunPython(
'force_text',
tools.Concat(
tools.Try(ctx.record.header.setSpec),
tools.Try(ctx.record.metadata.dc['dc:type']),
tools.Try(ctx.record.metadata.dc['dc:format']),
tools.Try(ctx.record.metadata.dc['dc:subject']),
)))))
tags = tools.Map(
tools.Delegate(OAIThroughTags),
tools.Concat(tools.Map(
tools.RunPython('tokenize'),
tools.RunPython(
'force_text',
tools.Concat(
tools.Try(ctx.record.header.setSpec),
tools.Try(ctx.record.metadata.dc['dc:type']),
tools.Try(ctx.record.metadata.dc['dc:format']),
tools.Try(ctx.record.metadata.dc['dc:subject']),
))),
deep=True))
date_updated = tools.ParseDate(ctx.record.header.datestamp)
is_deleted = tools.RunPython('check_status',
tools.Try(ctx.record.header['@status']))
class Extra:
"""
Fields that are combined in the base parser are relisted as singular elements that match
their original entry to preserve raw data structure.
"""
# An agent responsible for making contributions to the resource.
contributor = tools.Try(ctx.record.metadata.dc['dc:contributor'])
# The spatial or temporal topic of the resource, the spatial applicability of the resource,
# or the jurisdiction under which the resource is relevant.
coverage = tools.Try(ctx.record.metadata.dc['dc:coverage'])
# An agent primarily responsible for making the resource.
creator = tools.Try(ctx.record.metadata.dc['dc:creator'])
# A point or period of time associated with an event in the lifecycle of the resource.
dates = tools.Try(ctx.record.metadata.dc['dc:date'])
# The file format, physical medium, or dimensions of the resource.
resource_format = tools.Try(ctx.record.metadata.dc['dc:format'])
# An unambiguous reference to the resource within a given context.
identifiers = tools.Concat(
tools.Try(ctx.record.metadata.dc['dc:identifier']),
tools.Try(ctx.record.header['identifier']))
# A related resource.
relation = tools.RunPython('get_relation', ctx)
# A related resource from which the described resource is derived.
source = tools.Try(ctx.record.metadata.dc['dc:source'])
# The nature or genre of the resource.
resource_type = tools.Try(ctx.record.metadata.dc['dc:type'])
set_spec = tools.Try(ctx.record.header.setSpec)
# Language also stored in the Extra class in case the language reported cannot be parsed by ParseLanguage
language = tools.Try(ctx.record.metadata.dc['dc:language'])
# Status in the header, will exist if the resource is deleted
status = tools.Try(ctx.record.header['@status'])
def check_status(self, status):
if status == 'deleted':
return True
return False
def get_schema(self, types):
if not types or not self.type_map:
return self.default_type
if isinstance(types, str):
types = [types]
for t in types:
if isinstance(t, dict):
t = t['#text']
t = t.lower()
if t in self.type_map:
return self.type_map[t]
return self.default_type
def force_text(self, data):
if isinstance(data, dict):
return data['#text']
if isinstance(data, str):
return data
fixed = []
for datum in (data or []):
if datum is None:
continue
if isinstance(datum, dict):
if '#text' not in datum:
logger.warn('Skipping %s, no #text key exists', datum)
continue
fixed.append(datum['#text'])
elif isinstance(datum, str):
fixed.append(datum)
else:
raise Exception(datum)
return fixed
def tokenize(self, data):
if isinstance(data, str):
data = [data]
tokens = []
for item in data:
tokens.extend(
[x.strip() for x in re.split(r'(?: - )|\.|,', item) if x])
return tokens
def get_relation(self, ctx):
if not ctx['record'].get('metadata'):
return []
relation = ctx['record']['metadata']['dc'].get('dc:relation') or []
identifiers = ctx['record']['metadata']['dc'].get(
'dc:identifier') or []
if isinstance(identifiers, dict):
identifiers = (identifiers, )
identifiers = ''.join(i['#text'] if isinstance(i, dict) else i
for i in identifiers if i)
identifiers = re.sub(
'http|:|/', '',
identifiers + ctx['record']['header']['identifier'])
if isinstance(relation, dict):
relation = (relation['#text'], )
return [
r for r in relation
if r and re.sub('http|:|/', '', r) not in identifiers
]
class Preprint(EngrxivPreprint):
subjects = tools.Map(tools.Delegate(ThroughSubjects),
tools.Static('Social and behavioral sciences'))
class Preprint(Parser):
title = tools.Try(ctx['DC.Title'])
description = tools.Try(ctx['DC.Description'])
contributors = tools.Map(tools.Delegate(Contributor),
tools.RunPython('get_contributors', ctx))
links = tools.Concat(
tools.Map(tools.Delegate(ThroughLinks),
tools.Concat(ctx['og:url'], ctx['citation_public_url'])),
tools.Map(tools.Delegate(DoiThroughLinks),
tools.Concat(ctx['citation_doi'])))
publishers = tools.Map(
tools.Delegate(Association.using(entity=tools.Delegate(Publisher))),
ctx['DC.Publisher'])
date_updated = tools.ParseDate(ctx['DC.Date'])
date_published = tools.ParseDate(ctx['article:published_time'])
language = tools.Try(ctx['DC.Language'])
rights = tools.Try(ctx['DC.Rights'])
tags = tools.Map(tools.Delegate(ThroughTags),
tools.Concat(tools.Try(ctx['category'])))
subjects = tools.Map(
tools.Delegate(ThroughSubjects),
tools.Static('Biology and life sciences'),
ctx['subject-areas'],
)
class Extra:
identifiers = ctx['DC.Identifier']
access_rights = ctx['DC.AccessRights']
record_type = ctx['type']
contributors = ctx['DC.Contributor']
citation_author = ctx['citation_author']
citation_author_institution = ctx['citation_author_institution']
citation_author_email = ctx['citation_author_email']
def get_contributors(self, link):
authors = link['citation_author'] if isinstance(
link['citation_author'], list) else [link['citation_author']]
institutions = link['citation_author_institution'] if isinstance(
link['citation_author_institution'],
list) else [link['citation_author_institution']]
emails = link['citation_author_email'] if isinstance(
link['citation_author_email'],
list) else [link['citation_author_email']]
contribs = []
for author, email, institution in itertools.zip_longest(
authors, emails, institutions):
contrib = {
'author': author,
'institution': institution,
'email': email,
}
contribs.append(contrib)
return contribs
class Link(Parser):
url = tools.RunPython('format_link', tools.RunPython(force_text, ctx))
type = tools.Static('doi')
def format_link(self, link):
return format_doi_as_url(self, link)
class AlternateLink(Parser):
schema = 'Link'
url = tools.RunPython(force_text, ctx)
type = tools.Static('misc')
class Link(Parser):
url = ctx
type = tools.Static('provider')
class Identifier(Parser):
url = ctx
base_url = tools.Static('https://osf.io/')
class Preprint(normalizer.Project):
subjects = tools.Map(
tools.Delegate(ThroughSubjects),
tools.Concat(tools.Static({'text': 'Social and behavioral sciences'})))
