def setUp(self):
# ignore suspect key "version"
suspect_keys = ["version"]
fixture = os.path.join("fixtures", "6", "CITATION.cff")
with open(fixture, "r") as f:
cffstr = f.read()
self.citation = Citation(cffstr=cffstr, ignore_suspect_keys=True, suspect_keys=suspect_keys)
def setUp(self):
# trying to ignore a key that doesn't exist
suspect_keys = ["hjjshbdjsu3933"]
fixture = os.path.join("fixtures", "1", "CITATION.cff")
with open(fixture, "r") as f:
cffstr = f.read()
self.citation = Citation(cffstr=cffstr, ignore_suspect_keys=True, suspect_keys=suspect_keys)
def setUp(self):
# with removal of suspect key "version"
remove = ["version"]
fixture = os.path.join("fixtures", "6", "CITATION.cff")
with open(fixture, "r") as f:
cffstr = f.read()
self.citation = Citation(cffstr=cffstr, instantiate_empty=True, remove=remove)
self.citation._parse_yaml()
self.citation._remove_suspect_keys()
def setUp(self):
# trying to remove a key that doesn't exist
remove = ["hjjshbdjsu3933"]
fixture = os.path.join("fixtures", "1", "CITATION.cff")
with open(fixture, "r") as f:
cffstr = f.read()
self.citation = Citation(cffstr=cffstr, instantiate_empty=True, remove=remove)
self.citation._parse_yaml()
self.citation._remove_suspect_keys()
def setUp(self):
# with override
override = {
"doi": "thebestdoi.23678237",
"date-released": datetime.datetime.strptime("2018-03-05", "%Y-%m-%d").date()
}
fixture = os.path.join("fixtures", "1", "CITATION.cff")
with open(fixture, "r") as f:
cffstr = f.read()
self.citation = Citation(cffstr=cffstr, instantiate_empty=True, override=override)
self.citation._parse_yaml()
self.citation._override_suspect_keys()
class CitationTest4(unittest.TestCase):
def setUp(self):
fixture = os.path.join("fixtures", "4", "CITATION.cff")
with open(fixture, "r") as f:
cffstr = f.read()
self.citation = Citation(cffstr=cffstr, instantiate_empty=True)
def test_conversion_to_yaml(self):
with self.assertRaises(ValueError) as context:
self.citation._parse_yaml()
self.assertTrue('Provided CITATION.cff does not seem valid YAML.' in str(context.exception))
def test_on_github_but_over_http(self):
url = "http://github.com"
with self.assertRaises(Exception) as context:
self.citation = Citation(url)
self.assertTrue(
"Only 'https://github.com' URLs are supported at the moment." ==
str(context.exception))
def test_on_github_but_no_repo_specified(self):
url = "https://github.com/citation-file-format"
with self.assertRaises(Exception) as context:
self.citation = Citation(url)
self.assertTrue('Error extracting (user|organization) and/or repository ' +\
'information from the provided URL' in str(context.exception))
def test_google(self):
url = "www.google.com"
with self.assertRaises(Exception) as context:
self.citation = Citation(url=url)
self.assertTrue(
"Only 'https://github.com' URLs are supported at the moment." ==
str(context.exception))
def test_on_github_with_url_without_tree_element(self):
url = "https://github.com/xenon-middleware/xenon/sha/134624562456"
with self.assertRaises(ValueError) as context:
self.citation = Citation(url)
self.assertTrue(
str(context.exception).startswith(
"Expected 'https://github.com/" +
"<org>/<repo>/tree/...' but instead found"))
def test_retrieval_via_tag(self):
# https://github.com/<org>/<repo>/tree/<tagname>
url = "https://github.com/citation-file-format/cff-converter-python/tree/0.0.1"
citation = Citation(url=url)
fixture = os.path.join("fixtures", "1", "CITATION.cff")
with open(fixture) as f:
expected_cffstr = f.read()
actual_cffstr = citation.cffstr
self.assertEqual(expected_cffstr, actual_cffstr)
def test_retrieval_of_latest_master(self):
# https://github.com/<org>/<repo>
url = "https://github.com/citation-file-format/cff-converter-python"
citation = Citation(url=url)
fixture = os.path.join("fixtures", "7", "CITATION.cff")
with open(fixture) as f:
expected_cffstr = f.read()
actual_cffstr = citation.cffstr
self.assertEqual(expected_cffstr, actual_cffstr)
def test_retrieval_via_sha(self):
# https://github.com/<org>/<repo>/tree/<sha>
url = "https://github.com/citation-file-format/cff-converter-python/tree/" + \
"b7505591cf421ab33156ec0bffb0af43fd7d2cd1"
citation = Citation(url=url)
fixture = os.path.join("fixtures", "1", "CITATION.cff")
with open(fixture) as f:
expected_cffstr = f.read()
actual_cffstr = citation.cffstr
self.assertEqual(expected_cffstr, actual_cffstr)
class CitationTest3(unittest.TestCase):
def setUp(self):
fixture = os.path.join("fixtures", "3", "CITATION.cff")
with open(fixture, "r") as f:
cffstr = f.read()
self.citation = Citation(cffstr=cffstr, suspect_keys=[])
def test_printing_as_bibtex(self):
fixture = os.path.join("fixtures", "3", "bibtex.bib")
with open(fixture, "r") as f:
expected_bibtex = f.read()
actual_bibtex = self.citation.as_bibtex()
self.assertEqual(expected_bibtex, actual_bibtex)
def test_printing_as_codemeta(self):
fixture = os.path.join("fixtures", "3", "codemeta.json")
with open(fixture, "r") as f:
expected_codemeta = f.read()
actual_codemeta = self.citation.as_codemeta()
self.assertEqual(expected_codemeta, actual_codemeta)
def test_printing_as_enw(self):
fixture = os.path.join("fixtures", "3", "endnote.enw")
with open(fixture, "r") as f:
expected_endnote = f.read()
actual_endnote = self.citation.as_enw()
self.assertEqual(expected_endnote, actual_endnote)
def test_printing_as_ris(self):
fixture = os.path.join("fixtures", "3", "ris.txt")
with open(fixture, "r") as f:
expected_ris = f.read()
actual_ris = self.citation.as_ris()
self.assertEqual(expected_ris, actual_ris)
def test_printing_as_zenodojson(self):
fixture = os.path.join("fixtures", "3", "zenodo.json")
with open(fixture, "r") as f:
expected_zenodojson = f.read()
actual_zenodojson = self.citation.as_zenodojson()
self.assertEqual(expected_zenodojson, actual_zenodojson)
def get_bibtex_from_citation_file(package_name):
"""
Fetch BibTeX information directly from the package if available in either
of the files CITATION.cff or CITATION (if installed).
Parameters
----------
package_name : str
Name of the package.
Returns
-------
bibtex : str or None
Returns the BibTeX string or None if the package is not installed or doesn't provide one.
"""
package = importlib.import_module(package_name)
cff_file = os.path.join(package.__path__[0], 'CITATION.cff')
citation_file = os.path.join(package.__path__[0], 'CITATION')
if os.path.exists(cff_file):
with open(cff_file) as f:
cffstr = f.read()
citation = Citation(cffstr=cffstr)
bibtex = citation.as_bibtex()
elif os.path.exists(citation_file):
with open(citation_file) as f:
citestr = f.read()
match = re.search(cite_tag_pattr, citestr)
if match is None:
raise ValueError(
'Could not find any BibTeX entries in CITATION file')
for i_end in range(match.end(), len(citestr)):
bibtex = citestr[match.start():i_end]
if bibtex.count('{') == bibtex.count('}'):
break
else:
raise ValueError(
'Mismatched braces in BibTeX entry in CITATION file')
else:
bibtex = None
return bibtex
class CitationTestIgnoreSuspectKeyVersion(unittest.TestCase):
def setUp(self):
# ignore suspect key "version"
suspect_keys = ["version"]
fixture = os.path.join("fixtures", "6", "CITATION.cff")
with open(fixture, "r") as f:
cffstr = f.read()
self.citation = Citation(cffstr=cffstr, ignore_suspect_keys=True, suspect_keys=suspect_keys)
def test_printing_as_bibtex(self):
fixture = os.path.join("fixtures", "6", "bibtex-no-version.bib")
with open(fixture, "r") as f:
expected_bibtex = f.read()
actual_bibtex = self.citation.as_bibtex()
self.assertEqual(expected_bibtex, actual_bibtex)
def test_printing_as_codemeta(self):
fixture = os.path.join("fixtures", "6", "codemeta-no-version.json")
with open(fixture, "r") as f:
expected_codemeta = f.read()
actual_codemeta = self.citation.as_codemeta()
self.assertEqual(expected_codemeta, actual_codemeta)
def test_printing_as_enw(self):
fixture = os.path.join("fixtures", "6", "endnote-no-version.enw")
with open(fixture, "r") as f:
expected_endnote = f.read()
actual_endnote = self.citation.as_enw()
self.assertEqual(expected_endnote, actual_endnote)
def test_printing_as_ris(self):
fixture = os.path.join("fixtures", "6", "ris-no-version.txt")
with open(fixture, "r") as f:
expected_ris = f.read()
actual_ris = self.citation.as_ris()
self.assertEqual(expected_ris, actual_ris)
class CitationTestIgnoreNonExistentKey(unittest.TestCase):
def setUp(self):
# trying to ignore a key that doesn't exist
suspect_keys = ["hjjshbdjsu3933"]
fixture = os.path.join("fixtures", "1", "CITATION.cff")
with open(fixture, "r") as f:
cffstr = f.read()
self.citation = Citation(cffstr=cffstr, ignore_suspect_keys=True, suspect_keys=suspect_keys)
def test_printing_as_bibtex(self):
fixture = os.path.join("fixtures", "1", "bibtex.bib")
with open(fixture, "r") as f:
expected_bibtex = f.read()
actual_bibtex = self.citation.as_bibtex()
self.assertEqual(expected_bibtex, actual_bibtex)
def test_printing_as_codemeta(self):
fixture = os.path.join("fixtures", "1", "codemeta.json")
with open(fixture, "r") as f:
expected_codemeta = f.read()
actual_codemeta = self.citation.as_codemeta()
self.assertEqual(expected_codemeta, actual_codemeta)
def test_printing_as_enw(self):
fixture = os.path.join("fixtures", "1", "endnote.enw")
with open(fixture, "r") as f:
expected_endnote = f.read()
actual_endnote = self.citation.as_enw()
self.assertEqual(expected_endnote, actual_endnote)
def test_printing_as_ris(self):
fixture = os.path.join("fixtures", "1", "ris.txt")
with open(fixture, "r") as f:
expected_ris = f.read()
actual_ris = self.citation.as_ris()
self.assertEqual(expected_ris, actual_ris)
class CitationTestOverride(unittest.TestCase):
def setUp(self):
# with override
override = {
"doi": "thebestdoi.23678237",
"date-released": datetime.datetime.strptime("2018-03-05", "%Y-%m-%d").date()
}
fixture = os.path.join("fixtures", "1", "CITATION.cff")
with open(fixture, "r") as f:
cffstr = f.read()
self.citation = Citation(cffstr=cffstr, instantiate_empty=True, override=override)
self.citation._parse_yaml()
self.citation._override_suspect_keys()
def test_printing_as_bibtex(self):
fixture = os.path.join("fixtures", "5", "bibtex.bib")
with open(fixture, "r") as f:
expected_bibtex = f.read()
actual_bibtex = self.citation.as_bibtex()
self.assertEqual(expected_bibtex, actual_bibtex)
def test_printing_as_codemeta(self):
fixture = os.path.join("fixtures", "5", "codemeta.json")
with open(fixture, "r") as f:
expected_codemeta = f.read()
actual_codemeta = self.citation.as_codemeta()
self.assertEqual(expected_codemeta, actual_codemeta)
def test_printing_as_enw(self):
fixture = os.path.join("fixtures", "5", "endnote.enw")
with open(fixture, "r") as f:
expected_endnote = f.read()
actual_endnote = self.citation.as_enw()
self.assertEqual(expected_endnote, actual_endnote)
def test_printing_as_ris(self):
fixture = os.path.join("fixtures", "5", "ris.txt")
with open(fixture, "r") as f:
expected_ris = f.read()
actual_ris = self.citation.as_ris()
self.assertEqual(expected_ris, actual_ris)
def generate_files(self):
for release in self.releases:
try:
override = {
"doi":
release["doi"],
"date-released":
datetime.strptime(release["datePublished"],
"%Y-%m-%d").date(),
"version":
release["tag"]
}
remove = ["commit"]
citation = Citation(url=release["url"],
override=override,
remove=remove)
try:
release["files"] = dict({
"bibtex":
citation.as_bibtex(),
"codemeta":
citation.as_codemeta(),
"cff":
citation.cffstr,
"schema_dot_org":
citation.as_schema_dot_org(),
"endnote":
citation.as_enw(),
"ris":
citation.as_ris()
})
release["citability"] = "full"
except Exception:
continue
except Exception as e:
if str(e).startswith("Error requesting file: "):
continue
elif str(e).startswith(
"Provided CITATION.cff does not seem valid YAML."):
continue
elif type(e).__name__ == "ScannerError":
continue
else:
raise e
return self
class CitationTestRemoveSuspectKeyVersion(unittest.TestCase):
def setUp(self):
# with removal of suspect key "version"
remove = ["version"]
fixture = os.path.join("fixtures", "6", "CITATION.cff")
with open(fixture, "r") as f:
cffstr = f.read()
self.citation = Citation(cffstr=cffstr, instantiate_empty=True, remove=remove)
self.citation._parse_yaml()
self.citation._remove_suspect_keys()
def test_printing_as_bibtex(self):
fixture = os.path.join("fixtures", "6", "bibtex-no-version.bib")
with open(fixture, "r") as f:
expected_bibtex = f.read()
actual_bibtex = self.citation.as_bibtex()
self.assertEqual(expected_bibtex, actual_bibtex)
def test_printing_as_codemeta(self):
fixture = os.path.join("fixtures", "6", "codemeta-no-version.json")
with open(fixture, "r") as f:
expected_codemeta = f.read()
actual_codemeta = self.citation.as_codemeta()
self.assertEqual(expected_codemeta, actual_codemeta)
def test_printing_as_enw(self):
fixture = os.path.join("fixtures", "6", "endnote-no-version.enw")
with open(fixture, "r") as f:
expected_endnote = f.read()
actual_endnote = self.citation.as_enw()
self.assertEqual(expected_endnote, actual_endnote)
def test_printing_as_ris(self):
fixture = os.path.join("fixtures", "6", "ris-no-version.txt")
with open(fixture, "r") as f:
expected_ris = f.read()
actual_ris = self.citation.as_ris()
self.assertEqual(expected_ris, actual_ris)
def test1(cffstr):
citation = Citation(cffstr=cffstr,
suspect_keys=[],
validate=True,
raise_exception=True)
assert citation.yaml is not None
def cffconvert(request):
"""Responds to any HTTP request.
Args:
request (flask.Request): HTTP request object.
Returns:
The response text or any set of values that can be turned into a
Response object using
`make_response <http://flask.pocoo.org/docs/1.0/api/#flask.Flask.make_response>`.
"""
cffstr = None
outputformat = None
url = None
validate = False
ignore_suspect_keys = False
verbose = False
version = False
outstr = ''
if request.args:
if 'cffstr' in request.args:
cffstr = request.args.get('cffstr')
if 'outputformat' in request.args:
outputformat = request.args.get('outputformat')
if 'url' in request.args:
url = request.args.get('url')
if 'validate' in request.args:
validate = True
if 'ignore_suspect_keys' in request.args:
ignore_suspect_keys = True
if 'verbose' in request.args:
verbose = True
if 'version' in request.args:
version = True
else:
return Response(get_help_text(), mimetype='text/html')
if version is True:
outstr += "{0}\n".format(cffconvert_version.__version__)
return Response(outstr, mimetype='text/plain')
if verbose is True:
outstr += "{0} = {1}\n".format("cffstr", cffstr)
outstr += "{0} = {1}\n".format("outputformat", outputformat)
outstr += "{0} = {1}\n".format("url", url)
outstr += "{0} = {1}\n".format("validate", validate)
outstr += "{0} = {1}\n".format("ignore_suspect_keys",
ignore_suspect_keys)
outstr += "{0} = {1}\n".format("verbose", verbose)
outstr += "{0} = {1}\n".format("version", version)
if url is not None and cffstr is not None:
outstr += "\n\n{0}\n".format("Error: can't have both url and cffstr.")
return Response(outstr, mimetype='text/plain')
remove = None
override = None
suspect_keys = None
try:
citation = Citation(url=url,
cffstr=cffstr,
ignore_suspect_keys=ignore_suspect_keys,
override=override,
remove=remove,
suspect_keys=suspect_keys,
validate=validate,
raise_exception=True)
except Exception as e:
if str(e) == "Provided CITATION.cff does not seem valid YAML.":
outstr += "\n\nError: Provided 'cffstr' does not seem valid YAML."
else:
outstr += "\n\nError: " + str(e)
return Response(outstr, mimetype='text/plain')
acceptable_output_formats = [
"bibtex", "cff", "codemeta", "endnote", "schema.org", "ris", "zenodo"
]
if validate:
# when validating, there's no need to convert to anything yet
pass
elif outputformat not in acceptable_output_formats:
outstr += "\n\n'outputformat' should be one of [{0}]".format(
", ".join(acceptable_output_formats))
return Response(outstr, mimetype='text/plain')
if outputformat is None:
return
elif outputformat == "bibtex":
outstr += citation.as_bibtex()
elif outputformat == "cff":
outstr += citation.cffstr
elif outputformat == "codemeta":
outstr += citation.as_codemeta()
elif outputformat == "endnote":
outstr += citation.as_enw()
elif outputformat == "ris":
outstr += citation.as_ris()
elif outputformat == "schema.org":
outstr += citation.as_schema_dot_org()
elif outputformat == "zenodo":
outstr += citation.as_zenodojson()
return Response(outstr, mimetype='text/plain')
def test_retrieval_of_latest_master(self):
# this test checks if cffconvert can behave similar to a simple curl or wget
# https://github.com/<org>/<repo>
url = "https://github.com/citation-file-format/cff-converter-python"
citation = Citation(url=url)
self.assertIsNotNone(citation)
def test_retrieval_via_branchname(self):
# https://github.com/<org>/<repo>/tree/<branchname>
# this test checks if cffconvert can behave similar to a simple curl or wget
url = "https://github.com/citation-file-format/cff-converter-python/tree/master"
citation = Citation(url=url)
self.assertIsNotNone(citation)
def setUp(self):
fixture = os.path.join("fixtures", "3", "CITATION.cff")
with open(fixture, "r") as f:
cffstr = f.read()
self.citation = Citation(cffstr=cffstr, suspect_keys=[])
def test_neither_url_nor_cffstr(self):
with self.assertRaises(ValueError):
self.citation = Citation()
def test_both_url_and_cffstr(self):
with self.assertRaises(ValueError) as context:
self.citation = Citation(url="some url", cffstr="some cffstr")
assert "You should specify either \'url\' or \'cffstr\'." in str(context.exception)
def test_on_github_but_repo_doesnt_exist(self):
url = "https://github.com/org_1122334455/repo_0123456789"
with self.assertRaises(Exception) as context:
self.citation = Citation(url)
self.assertTrue('Error requesting file: ' in str(context.exception))
def cli(infile, outfile, outputformat, url, validate, ignore_suspect_keys, verbose, version):
if version is True:
print("{0}".format(cffconvert_version.__version__))
return
if verbose is True:
click.echo("{0} = {1}".format("infile", infile))
click.echo("{0} = {1}".format("outfile", outfile))
click.echo("{0} = {1}".format("outputformat", outputformat))
click.echo("{0} = {1}".format("url", url))
click.echo("{0} = {1}".format("validate", validate))
click.echo("{0} = {1}".format("ignore_suspect_keys", ignore_suspect_keys))
click.echo("{0} = {1}".format("verbose", verbose))
click.echo("{0} = {1}".format("version", version))
if infile is None and url is None:
infile = "CITATION.cff"
elif infile is not None and url is not None:
raise ValueError("You need to specify either \'--infile\' or \'url\' but not both.")
if infile is None:
cffstr = None
elif infile == '-':
cffstr = sys.stdin.read()
else:
with open(infile, "r") as f:
cffstr = f.read()
# TODO currently there is no way to provide values for these 3 arguments from the command line
remove = None
override = None
suspect_keys = None
citation = Citation(url=url, cffstr=cffstr, ignore_suspect_keys=ignore_suspect_keys, override=override,
remove=remove, suspect_keys=suspect_keys, validate=validate)
acceptable_output_formats = ["bibtex", "cff", "codemeta", "endnote", "ris", "schema.org", "zenodo"]
if validate:
# when validating, there's no need to convert to anything yet
pass
elif outputformat not in acceptable_output_formats:
raise ValueError("'--outputformat' should be one of [{0}]".format(", ".join(acceptable_output_formats)))
if outputformat is None:
return
elif outputformat == "bibtex":
outstr = citation.as_bibtex()
elif outputformat == "cff":
outstr = citation.as_cff()
elif outputformat == "codemeta":
outstr = citation.as_codemeta()
elif outputformat == "endnote":
outstr = citation.as_enw()
elif outputformat == "ris":
outstr = citation.as_ris()
elif outputformat == "schema.org":
outstr = citation.as_schema_dot_org()
elif outputformat == "zenodo":
outstr = citation.as_zenodojson()
if outfile is None:
print(outstr, end='')
else:
with open(outfile, "w") as f:
f.write(outstr)
def setUp(self):
fixture = os.path.join("fixtures", "4", "CITATION.cff")
with open(fixture, "r") as f:
cffstr = f.read()
self.citation = Citation(cffstr=cffstr, instantiate_empty=True)