def test_citation_string_serializer_records_list(
running_app,
client,
es_clear,
minimal_record,
superuser_identity,
):
"""Test Citation String Serializer for a list of records."""
service = current_rdm_records.records_service
default_style = StringCitationSerializer._default_style
default_locale = StringCitationSerializer._default_locale
headers = {"Accept": "text/x-bibliography"}
expected_data = []
for _ in range(3):
draft = service.create(superuser_identity, minimal_record)
record = service.publish(draft.id, superuser_identity)
expected_record_data = get_citation_string(
CSLJSONSchema().dump(record),
record.id,
locale=default_locale,
style=get_style_filepath(default_style),
)
expected_data.append(expected_record_data)
RDMRecord.index.refresh()
response = client.get("/records", headers=headers)
response_data = response.get_data(as_text=True)
assert response.status_code == 200
assert response.headers["content-type"] == "text/plain"
for citation in expected_data:
assert citation in response_data
def format_bibliography(json_data):
""" Format CSL-JSON to HTML APA format """
json_data = _uniqueify(_flatten(json_data))
bib_source = CiteProcJSON(json_data)
style_path = get_style_filepath('apa')
bib_style = CitationStylesStyle(style_path, validate=False)
# Create the citeproc-py bibliography, passing it the:
# * CitationStylesStyle,
# * BibliographySource (CiteProcJSON in this case), and
# * a formatter (plain, html, or you can write a custom formatter)
bibliography = CitationStylesBibliography(bib_style, bib_source,
formatter.html)
# Processing citations in a document needs to be done in two passes as for
# some CSL styles, a citation can depend on the order of citations in the
# bibliography and thus on citations following the current one.
# For this reason, we first need to register all citations with the
# CitationStylesBibliography.
for c in json_data:
bibliography.register(Citation([CitationItem(c['id'])]))
items = []
for item in bibliography.bibliography():
items.append(str(item))
return items
def test_style_filepath():
"""Test style filepath retrieval."""
filepath = get_style_filepath('apa')
assert os.path.exists(filepath)
assert 'styles/apa.csl' in filepath
filepath = get_style_filepath('nature-digest')
assert os.path.exists(filepath)
assert 'styles/nature.csl' in filepath
filepath = get_style_filepath('nature-digest', resolve_dependencies=False)
assert os.path.exists(filepath)
assert 'styles/dependent/nature-digest.csl' in filepath
with pytest.raises(StyleNotFoundError):
filepath = get_style_filepath('non-existent-style')
def retrieve_csl_style(style=CSL_STYLE):
"""Returns file path to CSL style definition for ``style``.
This function searches for the CSL definition file in the ``csl``
subdirectory of the ``BASE_DIR`` defined in the projects ``settings.py``
file and then in the ``csl`` subdirectory of the application directory
(i.e., ``cv``).
If a file with the style name cannot be found in one of those two
directories, the function will use the ``get_style_filepath()``
method from the :mod:`citeproc_styles` module. The method will return
a ``StyleNotFoundError`` if no match exists in the
:mod:`citeproc_styles` style repository.
"""
file_locations = [
os.path.abspath(settings.BASE_DIR),
os.path.abspath(apps.get_app_config('cv').path)
]
for file_location in file_locations:
style_path = Path(
os.path.join(file_location, "csl", "{}.csl".format(style)))
if style_path.is_file():
return (style_path)
return get_style_filepath(style)
def get_style_location(style):
"""Return the path to the CSL style if exists or throw."""
try:
return get_style_filepath(style.lower())
except StyleNotFoundError as ex:
current_app.logger.warning(f"CSL style {style} not found.")
raise ex
def test_style_filepath():
"""Test style filepath retrieval."""
filepath = get_style_filepath('apa')
assert os.path.exists(filepath)
assert 'styles/apa.csl' in filepath
filepath = get_style_filepath('nature-digest')
assert os.path.exists(filepath)
assert 'styles/nature.csl' in filepath
filepath = get_style_filepath('nature-digest', resolve_dependencies=False)
assert os.path.exists(filepath)
assert 'styles/dependent/nature-digest.csl' in filepath
with pytest.raises(StyleNotFoundError):
filepath = get_style_filepath('non-existent-style')
def __init__(self, bib_stylename):
# valid style names: plos, apa, pnas, nature, bmj, harvard1
# full list is here: https://github.com/citation-style-language/styles
self.style_path = get_style_filepath(bib_stylename)
super(EnhancedCitationStyle, self).__init__(self.style_path,
validate=False)
def test_citation_string_serializer_record(
running_app,
vocabulary_clear,
client,
es_clear,
minimal_record,
superuser_identity,
):
"""Test Citation String Serializer for single records."""
service = current_rdm_records.records_service
draft = service.create(superuser_identity, minimal_record)
record = service.publish(draft.id, superuser_identity)
_id = record.id
_url = f"/records/{_id}"
headers = {"Accept": "text/x-bibliography"}
default_style = StringCitationSerializer._default_style
default_locale = StringCitationSerializer._default_locale
test_cases = [
(
f"{_url}?style=3d-printing-in-medicine&locale=es-ES",
"3d-printing-in-medicine",
"es-ES",
200,
),
(f"{_url}?locale=es-ES", default_style, "es-ES", 200),
(
f"{_url}?style=3d-printing-in-medicine",
"3d-printing-in-medicine",
default_locale,
200,
),
(f"{_url}", default_style, default_locale, 200),
(f"{_url}?style=Unknown_style", "Unknown_style", default_locale, 400),
(f"{_url}?locale=Unknown_locale", default_style, default_locale, 200),
]
for url, expected_style, expected_locale, expected_status in test_cases:
response = client.get(url, headers=headers)
assert response.status_code == expected_status
body = response.get_data(as_text=True)
if expected_status == 200:
assert response.headers["content-type"] == "text/plain"
expected_data = get_citation_string(
CSLJSONSchema().dump(record),
_id,
locale=expected_locale,
style=get_style_filepath(expected_style),
)
assert expected_data == body
elif expected_status == 400:
# in case of error, the response is JSON
assert response.headers["content-type"] == "application/json"
assert f"Citation string style not found." in body
def cite(self):
style_path = get_style_filepath(CSL_STYLE)
print(style_path)
bib_style = CitationStylesStyle(style_path, validate=False)
bibliography = CitationStylesBibliography(bib_style,
CiteProcJSON([self.fields]),
formatter.html)
citation = Citation([CitationItem(self.instance.slug)])
bibliography.register(citation)
return str(bibliography.bibliography()[0])
def bibToCite(bibfile, ID):
bib_source = BibTeX(bibfile)
style_path = get_style_filepath('modern-language-association')
bib_style = CitationStylesStyle(style_path, validate=False)
bibliography = CitationStylesBibliography(bib_style, bib_source,
formatter.plain)
citation1 = Citation([CitationItem(ID)])
bibliography.register(citation1)
with open('out.txt', 'w') as f:
for item in bibliography.bibliography():
print(str(item), file=f)
def _get_args(cls, **kwargs):
"""Parse style and locale.
Argument location precedence: kwargs > view_args > query
"""
csl_args = {'style': cls._default_style, 'locale': cls._default_locale}
if has_request_context():
parser = FlaskParser(locations=('view_args', 'query'))
csl_args.update(parser.parse(cls._user_args, request))
csl_args.update(
{k: kwargs[k]
for k in ('style', 'locale') if k in kwargs})
try:
csl_args['style'] = get_style_filepath(csl_args['style'].lower())
except StyleNotFoundError:
if has_request_context():
raise StyleNotFoundRESTError(csl_args['style'])
raise
return csl_args
def citeproc_csl(csl_json: Dict[str, Any],
style: str,
html: bool = False) -> str:
"""
Renders a release entity to a styled citation.
Notable styles include:
- 'csl-json': special case to JSON encode the structured CSL object (via
release_to_csl())
- bibtext: multi-line bibtext format (used with LaTeX)
Returns a string; if the html flag is set, and the style isn't 'csl-json'
or 'bibtex', it will be HTML. Otherwise plain text.
"""
if not csl_json.get("id"):
csl_json["id"] = "unknown"
if style == "csl-json":
return json.dumps(csl_json)
bib_src = CiteProcJSON([csl_json])
form = formatter.plain
if html:
form = formatter.html
style_path = get_style_filepath(style)
bib_style = CitationStylesStyle(style_path, validate=False)
bib = CitationStylesBibliography(bib_style, bib_src, form)
bib.register(Citation([CitationItem(csl_json["id"])]))
lines = bib.bibliography()[0]
if style == "bibtex":
out = ""
for line in lines:
if line.startswith(" @"):
out += "@"
elif line.startswith(" "):
out += "\n " + line
else:
out += line
return "".join(out)
else:
return "".join(lines)
def run_citeproc_releases(args):
for line in args.json_input:
line = line.strip()
if not line:
continue
entity = entity_from_json(line, ReleaseEntity, api_client=args.api.api_client)
csl_json = release_to_csl(entity)
# XXX:
csl_json['id'] = "release:" + (entity.ident or "unknown")
if args.style == "csl-json":
args.json_output.write(json.dumps(csl_json) + "\n")
continue
bib_src = CiteProcJSON([csl_json])
form = formatter.plain
if args.html:
form = formatter.html
style_path = get_style_filepath(args.style)
bib_style = CitationStylesStyle(style_path, validate=False)
bib = CitationStylesBibliography(bib_style, bib_src, form)
bib.register(Citation([CitationItem(csl_json['id'])]))
# XXX:
#args.json_output.write(
# json.dumps(release_to_csl(entity)) + '\n')
lines = bib.bibliography()[0]
if args.style == "bibtex":
for l in lines:
if l.startswith(" @"):
args.json_output.write("\n@")
elif l.startswith(" "):
#print("line: START|{}|END".format(l))
args.json_output.write("\n " + l)
else:
args.json_output.write(l)
else:
args.json_output.write(''.join(lines) + "\n")
print()
def _get_args(cls, **kwargs):
"""Parse style and locale.
Argument location precedence: kwargs > view_args > query
"""
csl_args = {
'style': cls._default_style,
'locale': cls._default_locale
}
if has_request_context():
parser = FlaskParser(locations=('view_args', 'query'))
csl_args.update(parser.parse(cls._user_args, request))
csl_args.update({k: kwargs[k]
for k in ('style', 'locale') if k in kwargs})
try:
csl_args['style'] = get_style_filepath(csl_args['style'].lower())
except StyleNotFoundError:
if has_request_context():
raise StyleNotFoundRESTError(csl_args['style'])
raise
return csl_args
