def test_04_detect_verify_type_error(self):
# create an invalid pmid and assert it is a pmid
pmid = PMIDPlugin()
bjid = {"id" : "a;lkdsjfjdsajadskja", "type" : "pmid"}
record = models.MessageObject(bid=bjid)
with self.assertRaises(models.LookupException):
pmid.type_detect_verify(record)
def test_07_canonicalise_error(self):
pmid = PMIDPlugin()
# create an invalid pmid and assert it is a pmid
bjid = {"id" : "a;lkdsjfjdsajadskja", "type" : "pmid"}
with self.assertRaises(model_exceptions.LookupException):
pmid.canonicalise(bjid)
bjid = {"key" : "value"}
with self.assertRaises(model_exceptions.LookupException):
pmid.canonicalise(bjid)
def test_03_detect_verify_type_ignores(self):
pmid = PMIDPlugin()
bjid = {"id" : "whatever", "type" : "doi"}
pmid.type_detect_verify(bjid)
assert bjid['type'] == "doi"
bjid = {"key" : "value"}
pmid.type_detect_verify(bjid)
assert not bjid.has_key("type")
def test_02_detect_verify_type_not_pmids(self):
#Test the various erroneous PMID possibilities, which will include:
#- less than 1 and more than 8 digits
#- random strings (i.e. not just digits)
pmid = PMIDPlugin()
# some random digits
bjid = {'id' : 'qp23u4ehjkjewfiuwqr'} # random numbers and digits
record = models.MessageObject(bid=bjid)
pmid.type_detect_verify(record)
assert not bjid.has_key("type")
bjid = {'id' : 'qp23u4.10238765.jewfiuwqr'} # has an 8 digit substring in it
# (therefore also has a 1,2..7-digit substring in it)
record = models.MessageObject(bid=bjid)
pmid.type_detect_verify(record)
assert not bjid.has_key("type")
# less than 1 and more than 8 digits
bjid = {'id' : ''} # well, less than 1 digit doesn't exist
# and letters are covered elsewhere...
record = models.MessageObject(bid=bjid)
pmid.type_detect_verify(record)
assert not bjid.has_key("type")
bjid = {'id' : '123456789'}
record = models.MessageObject(bid=bjid)
pmid.type_detect_verify(record)
assert not bjid.has_key("type")
def test_05_canonicalise_real(self):
pmid = PMIDPlugin()
counter = 0
for d in CANONICAL.keys():
bjid = {'id' : d, 'type' : 'pmid'}
pmid.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_pmids(self):
pmid = PMIDPlugin()
counter = 0
for d in PMIDS:
bjid = {'id' : d}
pmid.type_detect_verify(bjid)
assert bjid.has_key("type")
assert bjid["type"] == "pmid"
counter += 1
assert counter == len(PMIDS)
assert counter > 0
def test_12_provider_resolve_fail_doi(self):
old_get = util.http_get
util.http_get = get_doi_fail
pmid = PMIDPlugin()
record = {"identifier" : {"id" : "23175652", "type" : "pmid", "canonical" : "pmid:23175652"}}
record = models.MessageObject(record=record)
with self.assertRaises(plugin.PluginException):
pmid.detect_provider(record)
util.http_get = old_get
def test_01_detect_verify_type_real_pmids(self):
pmid = PMIDPlugin()
counter = 0
for d in PMIDS:
bjid = {'id' : d}
record = models.MessageObject(bid=bjid)
pmid.type_detect_verify(record)
assert bjid.has_key("type")
assert bjid["type"] == "pmid"
counter += 1
assert counter == len(PMIDS)
assert counter > 0
def test_07_canonicalise_error(self):
pmid = PMIDPlugin()
# create an invalid pmid and assert it is a pmid
bjid = {"id" : "a;lkdsjfjdsajadskja", "type" : "pmid"}
record = models.MessageObject(bid=bjid)
with self.assertRaises(models.LookupException):
pmid.canonicalise(record)
bjid = {"key" : "value"}
record = models.MessageObject(record={"identifier" : bjid})
with self.assertRaises(models.LookupException):
pmid.canonicalise(record)
def test_05_canonicalise_real(self):
pmid = PMIDPlugin()
counter = 0
for d in CANONICAL.keys():
bjid = {'id' : d, 'type' : 'pmid'}
record = models.MessageObject(bid=bjid)
pmid.canonicalise(record)
assert bjid.has_key("canonical")
assert bjid["canonical"] == CANONICAL[d]
counter += 1
assert counter == len(CANONICAL.keys())
assert counter > 0
def test_03_detect_verify_type_ignores(self):
pmid = PMIDPlugin()
bjid = {"id" : "whatever", "type" : "doi"}
record = models.MessageObject(bid=bjid)
pmid.type_detect_verify(record)
assert bjid['type'] == "doi"
bjid = {"key" : "value"}
record = models.MessageObject(record={"identifier" : bjid})
pmid.type_detect_verify(record)
assert not bjid.has_key("type")
def test_10_provider_resolve_from_icon(self):
old_get = requests.get
requests.get = get_icon
pmid = PMIDPlugin()
record = {"identifier" : {"id" : "23175652", "type" : "pmid", "canonical" : "pmid:23175652"}}
pmid.provider_resolver(record)
assert "provider" in record
assert "url" in record["provider"]
assert record['provider']["url"][0] == "http://jb.asm.org/cgi/pmidlookup?view=long&pmid=23175652", record['provider']["url"][0]
requests.get = old_get
def test_09_provider_resolve_doi(self):
old_get = requests.get
requests.get = get_doi
pmid = PMIDPlugin()
record = {"identifier" : {"id" : "23175652", "type" : "pmid", "canonical" : "pmid:23175652"}}
pmid.provider_resolver(record)
assert "provider" in record
assert "url" in record["provider"]
assert record['provider']["url"][0] == "http://jb.asm.org/content/195/3/502", record['provider']['url']
assert record["provider"]["doi"] == "doi:10.1128/JB.01321-12"
requests.get = old_get
def test_11_provider_resolve_from_resources(self):
old_get = requests.get
requests.get = get_linkout
pmid = PMIDPlugin()
record = {"identifier" : {"id" : "1234567", "type" : "pmid", "canonical" : "pmid:1234567"}}
pmid.provider_resolver(record)
assert "provider" in record
assert "url" in record["provider"]
assert "http://www.nlm.nih.gov/medlineplus/menopause.html" in record["provider"]["url"], record["provider"]["url"]
assert "http://toxnet.nlm.nih.gov/cgi-bin/sis/search/r?dbs+hsdb:@term+@rn+50-28-2" in record["provider"]["url"], record["provider"]["url"]
assert len(record['provider']['url']) == 2
requests.get = old_get
def test_10_provider_resolve_from_icon(self):
old_get = util.http_get
util.http_get = get_icon
pmid = PMIDPlugin()
record = {"identifier" : {"id" : "23175652", "type" : "pmid", "canonical" : "pmid:23175652"}}
record = models.MessageObject(record=record)
pmid.detect_provider(record)
record = record.record
assert "provider" in record
assert "url" in record["provider"]
assert record['provider']["url"][0] == "http://jb.asm.org/cgi/pmidlookup?view=long&pmid=23175652", record['provider']["url"][0]
util.http_get = old_get
def test_09_provider_resolve_doi(self):
old_get = util.http_get
util.http_get = get_doi
pmid = PMIDPlugin()
record = {"identifier" : {"id" : "23175652", "type" : "pmid", "canonical" : "pmid:23175652"}}
record = models.MessageObject(record=record)
pmid.detect_provider(record)
record = record.record
assert "provider" in record
assert "url" in record["provider"]
assert record['provider']["url"][0] == "http://jb.asm.org/content/195/3/502", record['provider']['url']
assert record["provider"]["doi"] == "doi:10.1128/JB.01321-12"
util.http_get = old_get
def test_08_provider_resolve_not_relevant(self):
pmid = PMIDPlugin()
record = {}
pmid.provider_resolver(record)
assert len(record.keys()) == 0
record['identifier'] = {}
pmid.provider_resolver(record)
assert len(record['identifier'].keys()) == 0
record['identifier']['id'] = "123"
record['identifier']['type'] = "doi"
record['identifier']['canonical'] = "doi:123"
pmid.provider_resolver(record)
assert not "provider" in record
record['identifier']['type'] = "pmid"
del record['identifier']['canonical']
pmid.provider_resolver(record)
assert not "provider" in record
def test_08_provider_resolve_not_relevant(self):
pmid = PMIDPlugin()
record = models.MessageObject()
pmid.detect_provider(record)
assert len(record.record.keys()) == 0
record.id = "123"
record.identifier_type = "doi"
record.canonical = "doi:123"
pmid.detect_provider(record)
assert not "provider" in record.record
record.identifier_type = "pmid"
record.canonical = None
pmid.detect_provider(record)
assert not "provider" in record.record
def test_06_canonicalise_ignore(self):
pmid = PMIDPlugin()
bjid = {"id" : "whatever", "type" : "doi"}
record = models.MessageObject(bid=bjid)
pmid.canonicalise(record)
assert not bjid.has_key("canonical")
def test_06_canonicalise_ignore(self):
pmid = PMIDPlugin()
bjid = {"id" : "whatever", "type" : "doi"}
pmid.canonicalise(bjid)
assert not bjid.has_key("canonical")
def test_04_detect_verify_type_error(self):
# create an invalid pmid and assert it is a pmid
pmid = PMIDPlugin()
bjid = {"id" : "a;lkdsjfjdsajadskja", "type" : "pmid"}
with self.assertRaises(model_exceptions.LookupException):
pmid.type_detect_verify(bjid)
