def test_04_detect_verify_type_error(self):
doi = DOIPlugin()
# create an invalid doi and assert it is a doi
bjid = {"id" : "a;lkdsjfjdsajadskja", "type" : "doi"}
with self.assertRaises(model_exceptions.LookupException):
doi.type_detect_verify(bjid)
def test_06_canonicalise_ignore(self):
doi = DOIPlugin()
bjid = {"id" : "whatever", "type" : "pmid"}
record = models.MessageObject(record={"identifier" : bjid})
doi.canonicalise(record)
assert not bjid.has_key("canonical")
def _resolve_doi(self, canonical_pmid):
xml_url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=" + canonical_pmid[5:] + "&retmode=xml"
# now dereference it and find out the target of the (chain of) 303(s)
response = util.http_get(xml_url)
if response.status_code != requests.codes.ok:
raise plugin.PluginException(plugin.PluginException.HTTP, "unable to retrieve record from PubMed")
try:
xml = etree.fromstring(response.text.encode("utf-8"))
except:
log.error("Error parsing the XML from " + xml_url)
return None, None
xp = "/PubmedArticleSet/PubmedArticle/PubmedData/ArticleIdList/ArticleId[@IdType='doi']"
els = xml.xpath(xp)
if len(els) == 0:
# we didn't find a DOI
return None, None
# FIXME: we assume there is only one DOI in the record - is this really true?
doi_string = els[0].text
doi = DOIPlugin()
canonical_doi = doi.canonical_form(doi_string)
loc = doi.dereference(canonical_doi)
return canonical_doi, loc
def test_04_detect_verify_type_error(self):
doi = DOIPlugin()
# create an invalid doi and assert it is a doi
bjid = {"id" : "a;lkdsjfjdsajadskja", "type" : "doi"}
record = models.MessageObject(record={"identifier" : bjid})
with self.assertRaises(models.LookupException):
doi.type_detect_verify(record)
def test_03_detect_verify_type_ignores(self):
doi = DOIPlugin()
bjid = {"id" : "whatever", "type" : "pmid"}
doi.type_detect_verify(bjid)
assert bjid['type'] == "pmid"
bjid = {"key" : "value"}
doi.type_detect_verify(bjid)
assert not bjid.has_key("type")
def test_12_dereference_fail(self):
oldget = requests.get
requests.get = get_fail
doi = DOIPlugin()
record = {"identifier" : {"id" : "123", "type" : "doi", "canonical" : "doi:123"}}
record = models.MessageObject(record=record)
with self.assertRaises(plugin.PluginException):
doi.detect_provider(record)
requests.get = oldget
def test_07_canonicalise_error(self):
doi = DOIPlugin()
# create an invalid doi and assert it is a doi
bjid = {"id" : "a;lkdsjfjdsajadskja", "type" : "doi"}
with self.assertRaises(model_exceptions.LookupException):
doi.canonicalise(bjid)
bjid = {"key" : "value"}
with self.assertRaises(model_exceptions.LookupException):
doi.canonicalise(bjid)
def test_01_detect_verify_type_real_dois(self):
doi = DOIPlugin()
counter = 0
for d in DOIS:
bjid = {'id' : d}
doi.type_detect_verify(bjid)
assert bjid.has_key("type")
assert bjid["type"] == "doi"
counter += 1
assert counter == len(DOIS)
assert counter > 0
def test_05_canonicalise_real(self):
doi = DOIPlugin()
counter = 0
for d in CANONICAL.keys():
bjid = {'id' : d, 'type' : 'doi'}
doi.canonicalise(bjid)
assert bjid.has_key("canonical")
assert bjid["canonical"] == CANONICAL[d]
counter += 1
assert counter == len(CANONICAL.keys())
assert counter > 0
def test_01_detect_verify_type_real_dois(self):
doi = DOIPlugin()
counter = 0
for d in DOIS:
bjid = {'id' : d}
record = models.MessageObject(record={"identifier" : bjid})
doi.type_detect_verify(record)
assert bjid.has_key("type")
assert bjid["type"] == "doi"
counter += 1
assert counter == len(DOIS)
assert counter > 0
def test_03_detect_verify_type_ignores(self):
doi = DOIPlugin()
bjid = {"id" : "whatever", "type" : "pmid"}
record = models.MessageObject(record={"identifier" : bjid})
doi.type_detect_verify(record)
assert bjid['type'] == "pmid"
bjid = {"key" : "value"}
record = models.MessageObject(record={"identifier" : bjid})
doi.type_detect_verify(record)
assert not bjid.has_key("type")
def test_11_dereference_success_via_detect_provider(self):
oldget = requests.get
requests.get = get_success
doi = DOIPlugin()
record = {"identifier" : {"id" : "123", "type" : "doi", "canonical" : "doi:123"}}
doi.detect_provider(record)
assert "provider" in record
assert "url" in record["provider"]
assert record['provider']['url'][0] == "http://location"
assert record["provider"]["doi"] == "doi:123"
requests.get = oldget
def test_09_dereference_no_location(self):
oldget = requests.get
requests.get = get_no_location
doi = DOIPlugin()
record = {"identifier" : {"id" : "123", "type" : "doi", "canonical" : "doi:123"}}
doi.provider_dereference(record)
assert "provider" in record
assert "url" not in record["provider"]
assert "doi" in record["provider"]
assert record["provider"]["doi"] == "doi:123"
requests.get = oldget
def test_05_canonicalise_real(self):
doi = DOIPlugin()
counter = 0
for d in CANONICAL.keys():
bjid = {'id' : d, 'type' : 'doi'}
record = models.MessageObject(record={"identifier" : bjid})
doi.canonicalise(record)
assert bjid.has_key("canonical")
assert bjid["canonical"] == CANONICAL[d]
counter += 1
assert counter == len(CANONICAL.keys())
assert counter > 0
def test_07_canonicalise_error(self):
doi = DOIPlugin()
# create an invalid doi and assert it is a doi
bjid = {"id" : "a;lkdsjfjdsajadskja", "type" : "doi"}
record = models.MessageObject(record={"identifier" : bjid})
with self.assertRaises(models.LookupException):
doi.canonicalise(record)
bjid = {"key" : "value"}
record = models.MessageObject(record={"identifier" : bjid})
with self.assertRaises(models.LookupException):
doi.canonicalise(record)
def test_09_dereference_no_location(self):
oldget = util.http_get
util.http_get = get_no_location
doi = DOIPlugin()
record = {"identifier" : {"id" : "123", "type" : "doi", "canonical" : "doi:123"}}
record = models.MessageObject(record=record)
doi.provider_dereference(record)
record = record.record
assert "provider" in record
assert "url" not in record["provider"]
assert "doi" in record["provider"]
assert record["provider"]["doi"] == "doi:123"
util.http_get = oldget
def test_11_dereference_success_via_detect_provider(self):
oldget = util.http_get
util.http_get = get_success
doi = DOIPlugin()
record = {"identifier" : {"id" : "123", "type" : "doi", "canonical" : "doi:123"}}
record = models.MessageObject(record=record)
doi.detect_provider(record)
record = record.record
assert "provider" in record
assert "url" in record["provider"]
assert record['provider']['url'][0] == "http://location"
assert record["provider"]["doi"] == "doi:123"
util.http_get = oldget
def test_10_dereference_success(self):
oldget = requests.get
requests.get = get_success
doi = DOIPlugin()
record = {"identifier" : {"id" : "123", "type" : "doi", "canonical" : "doi:123"}}
record = models.MessageObject(record=record)
doi.provider_dereference(record)
record = record.record
assert "provider" in record
assert "url" in record["provider"]
assert record['provider']['url'][0] == "http://location"
assert record["provider"]["doi"] == "doi:123"
requests.get = oldget
def test_08_dereference_not_relevant(self):
doi = DOIPlugin()
record = {}
doi.provider_dereference(record)
assert len(record.keys()) == 0
record['identifier'] = {}
doi.provider_dereference(record)
assert len(record['identifier'].keys()) == 0
record['identifier']['id'] = "123"
record['identifier']['type'] = "pmid"
record['identifier']['canonical'] = "pmid:123"
doi.provider_dereference(record)
assert not "provider" in record
record['identifier']['type'] = "doi"
del record['identifier']['canonical']
doi.provider_dereference(record)
assert not "provider" in record
def test_08_dereference_not_relevant(self):
doi = DOIPlugin()
record = models.MessageObject(record={})
doi.provider_dereference(record)
assert len(record.record.keys()) == 0
record.id = "123"
record.identifier_type = "pmid"
record.canonical = "pmid:123"
doi.provider_dereference(record)
assert not "provider" in record.record
record.identifier_type = "doi"
record.canonical = None
doi.provider_dereference(record)
assert not "provider" in record.record
def test_02_detect_verify_type_not_dois(self):
#Test the various erroneous DOI possibilities, which will include:
#- prefixes without dois attached
#- random strings
doi = DOIPlugin()
# try some prefixes
bjid = {'id' : 'doi:'}
record = models.MessageObject(record={"identifier" : bjid})
doi.type_detect_verify(record)
assert not bjid.has_key("type")
bjid = {'id' : 'http://dx.doi.org/'}
record = models.MessageObject(record={"identifier" : bjid})
doi.type_detect_verify(record)
assert not bjid.has_key("type")
# try some random strings
bjid = {'id' : 'qp23u4ehjkjewfiuwqr'}
record = models.MessageObject(record={"identifier" : bjid})
doi.type_detect_verify(record)
assert not bjid.has_key("type")
bjid = {'id' : 'qp23u410.jewfiuwqr'} # has the 10. substring in it
record = models.MessageObject(record={"identifier" : bjid})
doi.type_detect_verify(record)
assert not bjid.has_key("type")
bjid = {'id' : 'doi:qp23u4ehjkjewfiuwqr'} # starts with a doi prefix, but isn't one
record = models.MessageObject(record={"identifier" : bjid})
doi.type_detect_verify(record)
assert not bjid.has_key("type")
def test_06_canonicalise_ignore(self):
doi = DOIPlugin()
bjid = {"id" : "whatever", "type" : "pmid"}
doi.canonicalise(bjid)
assert not bjid.has_key("canonical")
