def test_replace_refs_correct_sources(get_db_rec, get_es_rec):
with_es_record = {'ES': 'ES'}
with_db_record = {'DB': 'DB'}
get_es_rec.return_value = with_es_record
get_db_rec.return_value = with_db_record
db_rec = replace_refs({'$ref': _build_url()}, 'db')
es_rec = replace_refs({'$ref': _build_url()}, 'es')
assert db_rec == with_db_record
assert es_rec == with_es_record
def test_replace_refs_correct_sources(get_db_rec, get_es_rec):
with_es_record = {'ES': 'ES'}
with_db_record = {'DB': 'DB'}
get_es_rec.return_value = with_es_record
get_db_rec.return_value = with_db_record
db_rec = replace_refs({'$ref': _build_url()}, 'db')
es_rec = replace_refs({'$ref': _build_url()}, 'es')
assert db_rec == with_db_record
assert es_rec == with_es_record
def test_replace_refs_correct_sources(get_db_rec, get_es_rec, app):
with_es_record = {'ES': 'ES'}
with_db_record = {'DB': 'DB'}
get_es_rec.return_value = with_es_record
get_db_rec.return_value = with_db_record
with app.app_context():
db_rec = replace_refs({'$ref': _build_url(app)}, 'db')
es_rec = replace_refs({'$ref': _build_url(app)}, 'es')
# Lazy objects need to be evaluated in app_context.
assert db_rec == with_db_record
assert es_rec == with_es_record
def populate_journal_coverage(obj, eng):
"""Populate ``journal_coverage`` from the Journals DB.
Searches in the Journals DB if the current article was published in a
journal that we harvest entirely, then populates the ``journal_coverage``
key in ``extra_data`` with ``'full'`` if it was, ``'partial' otherwise.
Args:
obj: a workflow object.
eng: a workflow engine.
Returns:
None
"""
journals = replace_refs(
get_value(obj.data, 'publication_info.journal_record'), 'db')
if not journals:
return
if any(
get_value(journal, '_harvesting_info.coverage') == 'full'
for journal in journals):
obj.extra_data['journal_coverage'] = 'full'
else:
obj.extra_data['journal_coverage'] = 'partial'
def get_conference_record(record, default=None):
"""Return the first Conference record associated with a record.
Queries the database to fetch the first Conference record referenced
in the ``publication_info`` of the record.
Args:
record(InspireRecord): a record.
default: value to be returned if no conference record present/found
Returns:
InspireRecord: the first Conference record associated with the record.
Examples:
>>> record = {
... 'publication_info': [
... {
... 'conference_record': {
... '$ref': '/api/conferences/972464',
... },
... },
... ],
... }
>>> conference_record = get_conference_record(record)
>>> conference_record['control_number']
972464
"""
replaced = replace_refs(get_value(record, 'publication_info.conference_record[0]'), 'db')
if replaced:
return replaced
else:
return default
def get_conference_record(record):
"""Return the first Conference record associated with a record.
Queries the database to fetch the first Conference record referenced
in the ``publication_info`` of the record.
Args:
record(InspireRecord): a record.
Returns:
InspireRecord: the first Conference record associated with the record.
Examples:
>>> record = {
... 'publication_info': [
... {
... 'conference_record': {
... '$ref': '/api/conferences/972464',
... },
... },
... ],
... }
>>> conference_record = get_conference_record(record)
>>> conference_record['control_number']
972464
"""
return replace_refs(
get_value(record,
'publication_info.conference_record[0]',
default=None), 'db')
def conference_information(self):
"""Conference information.
Returns a list with information about conferences related to the
record.
"""
conf_info = []
for pub_info in self['publication_info']:
conference_recid = None
parent_recid = None
parent_rec = {}
conference_rec = {}
if 'conference_record' in pub_info:
conference_rec = replace_refs(pub_info['conference_record'],
'es')
if conference_rec and conference_rec.get('control_number'):
conference_recid = conference_rec['control_number']
else:
conference_rec = {}
if 'parent_record' in pub_info:
parent_rec = replace_refs(pub_info['parent_record'], 'es')
if parent_rec and parent_rec.get('control_number'):
parent_recid = parent_rec['control_number']
else:
parent_rec = {}
conf_info.append({
"conference_recid":
conference_recid,
"conference_title":
LiteratureReader(conference_rec).title,
"parent_recid":
parent_recid,
"parent_title":
LiteratureReader(parent_rec).title.replace(
"Proceedings, ", "", 1),
"page_start":
pub_info.get('page_start'),
"page_end":
pub_info.get('page_end'),
"artid":
pub_info.get('artid'),
})
return conf_info
def set_refereed_and_fix_document_type(obj, eng):
"""Set the ``refereed`` field using the Journals DB.
Searches in the Journals DB if the current article was published in journals
that we know for sure to be peer-reviewed, or that publish both peer-reviewed
and non peer-reviewed content but for which we can infer that it belongs to
the former category, and sets the ``refereed`` key in ``data`` to ``True`` if
that was the case. If instead we know for sure that all journals in which it
published are **not** peer-reviewed we set it to ``False``.
Also replaces the ``article`` document type with ``conference paper`` if the
paper was only published in non refereed proceedings.
Args:
obj: a workflow object.
eng: a workflow engine.
Returns:
None
"""
journals = replace_refs(
get_value(obj.data, 'publication_info.journal_record'), 'db')
if not journals:
return
is_published_in_a_refereed_journal_that_does_not_publish_proceedings = any(
journal.get('refereed') and not journal.get('proceedings')
for journal in journals)
is_published_in_a_refereed_journal_that_also_publishes_proceedings = any(
journal.get('refereed') and journal.get('proceedings')
for journal in journals)
is_not_a_conference_paper = 'conference paper' not in obj.data[
'document_type']
is_published_exclusively_in_non_refereed_journals = all(
not journal.get('refereed', True) for journal in journals)
if is_published_in_a_refereed_journal_that_does_not_publish_proceedings:
obj.data['refereed'] = True
elif is_not_a_conference_paper and is_published_in_a_refereed_journal_that_also_publishes_proceedings:
obj.data['refereed'] = True
elif is_published_exclusively_in_non_refereed_journals:
obj.data['refereed'] = False
is_published_only_in_proceedings = all(
journal.get('proceedings') for journal in journals)
is_published_only_in_non_refereed_journals = all(
not journal.get('refereed') for journal in journals)
if is_published_only_in_proceedings and is_published_only_in_non_refereed_journals:
try:
obj.data['document_type'].remove('article')
obj.data['document_type'].append('conference paper')
except ValueError:
pass
def get_journal_coverage(obj, eng):
"""Return the journal coverage that this article belongs to."""
journals = replace_refs(get_value(obj.data, 'publication_info.journal_record'), 'db')
if not journals:
return
if any(journal['_harvesting_info'].get('coverage') == 'full' for journal in journals):
obj.extra_data['journal_coverage'] = 'full'
else:
obj.extra_data['journal_coverage'] = 'partial'
def conference_information(self):
"""Conference information.
Returns a list with information about conferences related to the
record.
"""
conf_info = []
for pub_info in self['publication_info']:
conference_recid = None
parent_recid = None
parent_rec = {}
conference_rec = {}
if 'conference_record' in pub_info:
conference_rec = replace_refs(pub_info['conference_record'],
'es')
if conference_rec and conference_rec.get('control_number'):
conference_recid = conference_rec['control_number']
else:
conference_rec = {}
if 'parent_record' in pub_info:
parent_rec = replace_refs(pub_info['parent_record'], 'es')
if parent_rec and parent_rec.get('control_number'):
parent_recid = parent_rec['control_number']
else:
parent_rec = {}
conf_info.append(
{
"conference_recid": conference_recid,
"conference_title": get_title(conference_rec),
"parent_recid": parent_recid,
"parent_title":
get_title(parent_rec).replace(
"Proceedings, ", "", 1
),
"page_start": pub_info.get('page_start'),
"page_end": pub_info.get('page_end'),
"artid": pub_info.get('artid'),
}
)
return conf_info
def set_refereed_and_fix_document_type(obj, eng):
"""Set the ``refereed`` field using the Journals DB.
Searches in the Journals DB if the current article was published in journals
that we know for sure to be peer-reviewed, or that publish both peer-reviewed
and non peer-reviewed content but for which we can infer that it belongs to
the former category, and sets the ``refereed`` key in ``data`` to ``True`` if
that was the case. If instead we know for sure that all journals in which it
published are **not** peer-reviewed we set it to ``False``.
Also replaces the ``article`` document type with ``conference paper`` if the
paper was only published in non refereed proceedings.
Args:
obj: a workflow object.
eng: a workflow engine.
Returns:
None
"""
journals = replace_refs(get_value(obj.data, 'publication_info.journal_record'), 'db')
if not journals:
return
is_published_in_a_refereed_journal_that_does_not_publish_proceedings = any(
journal.get('refereed') and not journal.get('proceedings') for journal in journals)
is_published_in_a_refereed_journal_that_also_publishes_proceedings = any(
journal.get('refereed') and journal.get('proceedings') for journal in journals)
is_not_a_conference_paper = 'conference paper' not in obj.data['document_type']
is_published_exclusively_in_non_refereed_journals = all(
not journal.get('refereed', True) for journal in journals)
if is_published_in_a_refereed_journal_that_does_not_publish_proceedings:
obj.data['refereed'] = True
elif is_not_a_conference_paper and is_published_in_a_refereed_journal_that_also_publishes_proceedings:
obj.data['refereed'] = True
elif is_published_exclusively_in_non_refereed_journals:
obj.data['refereed'] = False
is_published_only_in_proceedings = all(journal.get('proceedings') for journal in journals)
is_published_only_in_non_refereed_journals = all(not journal.get('refereed') for journal in journals)
if is_published_only_in_proceedings and is_published_only_in_non_refereed_journals:
try:
obj.data['document_type'].remove('article')
obj.data['document_type'].append('conference paper')
except ValueError:
pass
def _conference_data(conf):
ref = replace_refs(conf, 'db')
# FIXME: Add conference city, country, and country code fields
if ref:
return {'type': "conference",
'name': get_value(ref, "titles[0].title", ""),
'acronym': get_value(ref, "acronym[0]", ""),
'opening_date': get_value(ref, "opening_date", ""),
'closing_date': get_value(ref, "closing_date", "")}
else:
return {'type': "conference",
'name': "",
'acronym': "",
'opening_date': "",
'closing_date': ""}
def _conference_data(conf):
ref = replace_refs(conf, 'db')
# FIXME: Add conference city, country, and country code fields
if ref:
return {
'type': "conference",
'name': get_value(ref, "titles[0].title", ""),
'acronym': get_value(ref, "acronym[0]", ""),
'opening_date': get_value(ref, "opening_date", ""),
'closing_date': get_value(ref, "closing_date", "")
}
else:
return {
'type': "conference",
'name': "",
'acronym': "",
'opening_date': "",
'closing_date': ""
}
def _conference_data(conf_record):
#sys.stderr.write(str(conf_record))
ref = replace_refs(conf_record, 'db')
#sys.stderr.write(str(ref))
o_addr = ref['address'][0]['original_address'].split(" ")
city = o_addr[0][:-1] # trim off comma
country = o_addr[1]
date = ref['date'].split(" ")
month = date[1]
year = date[2]
return {'type': "conference",
'name': ref['titles'][0]['title'],
'acronym': ref['acronym'][0],
'opening_date': ref['opening_date'],
'closing_date': ref['closing_date'],
'month': month,
'year': year,
'city': city,
'country': country,
'country_code': ref['address'][0]['country_code']}
def populate_journal_coverage(obj, eng):
"""Populate ``journal_coverage`` from the Journals DB.
Searches in the Journals DB if the current article was published in a
journal that we harvest entirely, then populates the ``journal_coverage``
key in ``extra_data`` with ``'full'`` if it was, ``'partial' otherwise.
Args:
obj: a workflow object.
eng: a workflow engine.
Returns:
None
"""
journals = replace_refs(get_value(obj.data, 'publication_info.journal_record'), 'db')
if not journals:
return
if any(get_value(journal, '_harvesting_info.coverage') == 'full' for journal in journals):
obj.extra_data['journal_coverage'] = 'full'
else:
obj.extra_data['journal_coverage'] = 'partial'
def tei_response(record):
data = record
env = Environment(loader=PackageLoader('inspirehep.modules.converttohal',
'templates'), trim_blocks=True, lstrip_blocks=True)
template = env.get_template(TEMPLATE)
#import ipdb; ipdb.set_trace()
authors = data['authors']
for author in data['authors']:
if 'full_name' in author and author['full_name']:
# handle first/last name
#scan = scan_author_string_for_phrases(author['full_name'])
#parsed = parse_scanned_author_for_phrases(scan)
#author['parsed_name'] = parsed
parsed = HumanName(author['full_name'])
author['parsed_name'] = parsed
#sys.stderr.write(str(scan) + '\n' + str(parsed) + '\n')
#sys.exit(0)
'''
auth_spl = author['full_name'].split(",")
if len(auth_spl) == 2:
last = auth_spl[0].strip()
first = auth_spl[1].strip()
else:
last = author['full_name']
first = ""
authors.append({'last': last,
'first': first,
'affiliation_id': (author['affiliations'][0]
['recid'])
if 'affiliations' in author
and 'recid' in author['affiliations'][0]
else ""
})'''
titles = data.get('titles', [])
# TODO: update the following line
doi = data['dois'][0]['value'] if 'dois' in data else ""
if 'publication_info' in data:
pub_info = data['publication_info'][0]
if 'journal_title' in pub_info:
if 'page_artid' in pub_info:
pp = pub_info['page_artid']
elif 'page_start' and 'page_end' in pub_info:
pp = pub_info['page_start'] + "-" + pub_info['page_end']
elif 'page_start' in pub_info or 'page_end' in pub_info:
pp = pub_info['page_start'] or pub_info['page_end']
else:
pp = ""
publication = {'type': "journal",
'name': pub_info['journal_title'],
'year': pub_info['year'],
'volume': pub_info['journal_volume']
if 'journal_volume' in pub_info
else "",
'issue': pub_info['journal_issue']
if 'journal_issue' in pub_info
else "",
'pp': pp}
elif 'conference_record' in pub_info:
publication = _conference_data(pub_info['conference_record'])
else:
publication = None
else:
publication = None
my_affiliations = []
recids = []
structures = []
for author in (data.get('authors') or []):
for affiliation in (author.get('affiliations') or []):
if 'recid' in affiliation and affiliation['recid'] not in recids:
my_affiliations.append(affiliation)
recids.append(affiliation['recid'])
for affiliation in my_affiliations:
ref = replace_refs(affiliation, 'db')
#import ipdb; ipdb.set_trace()
#sys.stderr.write(str(ref) + '\n')
#sys.stderr.write(str(ref['record']) + '\n')
#sys.stderr.write(str(ref['record']['collections']) + '\n')
#sys.stderr.write(str(ref['record']['collections'][1]['primary']) + '\n\n')
if ('record' in ref and 'collections' in ref['record']):
structures.append({'type': ref['record']['collections'][1]['primary'].lower()
if len(ref['record']['collections']) >= 2 else "",
'name': ref['record']['institution'][0],
'address': ref['record']['address'][0]['original_address'],
'country': ref['record']['address'][0]['country_code'],
'recid': ref['record']['oai_pmh'][0]['id'].split(":")[-1]
})
print template.render(titles=titles, doi=doi, authors=authors,
publication=publication, structures=structures)
def publication_info(record):
"""Displays inline publication and conference information"""
result = {}
out = []
if 'publication_info' in record:
journal_title, journal_volume, year, journal_issue, pages = \
('', '', '', '', '')
for pub_info in record['publication_info']:
if 'journal_title' in pub_info:
journal_title = '<i>' + pub_info['journal_title'] + '</i>'
if 'journal_volume' in pub_info:
journal_volume = ' ' + pub_info['journal_volume']
if 'year' in pub_info:
year = ' (' + str(pub_info['year']) + ')'
if 'journal_issue' in pub_info:
journal_issue = ' ' + pub_info['journal_issue'] + ', '
if 'page_start' in pub_info and 'page_end' in pub_info:
pages = ' ' + '{page_start}-{page_end}'.format(**pub_info)
elif 'page_start' in pub_info:
pages = ' ' + '{page_start}'.format(**pub_info)
elif 'artid' in pub_info:
pages = ' ' + '{artid}'.format(**pub_info)
out.append(journal_title + journal_volume +
year + journal_issue + pages)
if out:
result['pub_info'] = out
if not result:
for field in record['publication_info']:
if 'pubinfo_freetext' in field:
out.append(field['pubinfo_freetext'])
result['pub_info'] = out
break
# Conference info line
for pub_info in record['publication_info']:
conference_recid = None
parent_recid = None
if 'conference_record' in pub_info:
conference_rec = replace_refs(pub_info['conference_record'],
'es')
if conference_rec and conference_rec.get('control_number'):
conference_recid = conference_rec['control_number']
if 'parent_record' in pub_info:
parent_rec = replace_refs(pub_info['parent_record'], 'es')
if parent_rec and parent_rec.get('control_number'):
parent_recid = parent_rec['control_number']
if conference_recid and parent_recid:
try:
ctx = {
"parent_recid": parent_recid,
"conference_recid": conference_recid,
"conference_title": get_title(conference_rec)
}
if result:
result['conf_info'] = render_macro_from_template(
name="conf_with_pub_info",
template="inspirehep_theme/format/record/Conference_info_macros.tpl",
ctx=ctx)
break
else:
ctx.update(dict(
page_start=pub_info.get('page_start'),
page_end=pub_info.get('page_end'),
artid=pub_info.get('artid')
))
result['conf_info'] = render_macro_from_template(
name="conf_without_pub_info",
template="inspirehep_theme/format/record/Conference_info_macros.tpl",
ctx=ctx)
break
except TypeError:
pass
elif conference_recid and not parent_recid:
try:
ctx = {
"conference_recid": conference_recid,
"conference_title": get_title(conference_rec),
"pub_info": bool(result.get('pub_info', ''))
}
result['conf_info'] = render_macro_from_template(
name="conference_only",
template="inspirehep_theme/format/record/Conference_info_macros.tpl",
ctx=ctx)
except TypeError:
pass
elif parent_recid and not conference_recid:
try:
ctx = {
"parent_recid": parent_recid,
"parent_title":
parent_rec['titles'][0]['title'].replace(
"Proceedings, ", "", 1),
"pub_info": bool(result.get('pub_info', ''))
}
result['conf_info'] = render_macro_from_template(
name="proceedings_only",
template="inspirehep_theme/format/record/Conference_info_macros.tpl",
ctx=ctx)
except TypeError:
pass
return result
