class ResolverTests(TestCase):
context = Context()
OCLC_GATEWAY_URL = 'http://worldcatlibraries.org/registry/gateway'
def test_default(self):
r = find_resolver(self.context, '999.9.9.9')
self.assertEqual(self.OCLC_GATEWAY_URL, r.base_url)
def test_default_text(self):
r = find_resolver(self.context, '999.9.9.9')
self.assertEqual('Find in a library', r.link_text)
def test_simple(self):
# curtis.med.yale.edu
r = find_resolver(self.context, '128.36.123.51')
self.failIfEqual(self.OCLC_GATEWAY_URL, r.base_url)
def test_yale(self):
# NOTE: this will fail if YUL's resolver location changes
r = find_resolver(self.context, '128.36.123.51')
self.assertEqual('http://sfx.library.yale.edu/sfx_local', r.base_url)
def test_umich(self):
# NOTE: this will fail if UMich resolver location changes
r = find_resolver(self.context, '141.211.2.202')
self.assertEqual('http://sfx.lib.umich.edu:9003/sfx_locater',
r.base_url)
class UserFunctionTests(TestCase):
context = Context()
def test_userset(self):
set = user.UserSet()
set.user_id = 6
set.name = 'test'
set.save(self.context)
loaded_set = user.UserSet(self.context, set.uid)
self.assertEquals(loaded_set.name, set.name)
def context(self):
"""After you've called parse_args() you should be able
to fetch a canary.context.Context object.
context = cmdline.context()
"""
if not self.options.config:
self.guess_canary_config()
from canary.context import CanaryConfig, Context
config = CanaryConfig()
config.read_file(self.options.config)
return Context(config)
class SearchTests(TestCase):
context = Context()
def test_context(self):
self.assertEquals(isinstance(self.context, Context), True)
def test_simple_search(self):
try:
search_index = SearchIndex(self.context)
hits, searcher = search_index.search('test')
for i, doc in hits:
foo, bar = doc.get('uid'), hits.score(i)
if searcher:
searcher.close()
except Exception, e:
self.fail('Error searching: %s' % e)
class ParserTests(TestCase):
"""A fixture for setting up common tangle of objects used during parsing.
Hopefully this will change (or go away) as parsing is refactored.
"""
context = Context()
def __init__(self, name, source_name):
TestCase.__init__(self, name)
source_catalog = self.context.get_source_catalog()
source = source_catalog.get_source_by_name(source_name)
self.mapped_terms = source_catalog.get_mapped_terms(source.uid)
self.parser = Parser(source)
def parse(self, file_name):
return self.parser.parse(file_name, self.mapped_terms, False)
def parse_email(self, file_name):
return self.parser.parse(file_name, self.mapped_terms, True)
def get_mapped_metadata(self, record):
return record.get_mapped_metadata(self.mapped_terms)
#!/usr/bin/env python
# $Id$
from canary.context import Context
from canary.loader import QueuedRecord
from canary.study import Study
context = Context()
cursor = context.get_cursor()
cursor.execute("""
SELECT studies.record_id, study_history.study_id, study_history.modified
FROM study_history, studies
WHERE study_history.message = 'Set record status to curated'
AND study_history.study_id = studies.uid
ORDER BY studies.record_id ASC, study_history.modified ASC
""")
for row in cursor:
print "record_id:%i; study_id:%i; curated:%s" % row
# update either QUEUED_RECORDS or STUDIES with curated time
# r = QueuedRecord(con,row[0])
# r.date_curated = row[2]
# r.save
s = Study(context, row[1])
s.date_curated = row[2]
s.save(context)
#!/usr/bin/env python
# $Id$
from canary.context import Context
from canary.loader import QueuedRecord
from canary.study import Study
context = Context()
cursor = context.get_cursor()
cursor.execute("""
SELECT studies.record_id, study_history.study_id, study_history.modified
FROM study_history, studies
WHERE study_history.message = 'Set record status to curated'
AND study_history.study_id = studies.uid
ORDER BY studies.record_id ASC, study_history.modified ASC
""")
for row in cursor:
print "record_id:%i; study_id:%i; curated:%s" % row
# update either QUEUED_RECORDS or STUDIES with curated time
# r = QueuedRecord(con,row[0])
# r.date_curated = row[2]
# r.save
s = Study(context, row[1])
s.date_curated = row[2]
s.save(context)
legend(
(p_exp[0], p_coh[0], p_csec[0], p_desc[0], precords[0], pstudies[0]),
('Experimental', 'Cohort', 'Cross-Sectional', 'Descriptive',
'# Studies Total', '# Records w/Linkage'))
## legend((p_exp[0], p_desc[0], p_agg[0], p_csec[0], p_coh[0],
## p_cc[0], p_dm[0], precords[0], pstudies[0]),
## ('Experimental', 'Descriptive', 'Aggregate',
## 'Cross-Sectional', 'Cohort', 'Case-Control', 'Disease Model',
#savefig(('%s' % token.replace(' ', '_')))
show()
cla()
if __name__ == '__main__':
context = Context()
search_index = SearchIndex(context)
searches = (
'Lead [exposure]',
'Hantavirus [exposure]',
'peromyscus [species]',
'Michigan [location]',
'DDT [exposure]',
'2003 [year]',
'cats and dogs',
'"Burger J" [author]',
'cross-sectional [methodology]',
'case-control [methodology] and cattle [species]',
'disease-model [methodology]',
'"age factors" [risk_factors]',
'Sarin [exposure]',
class StatsTests (TestCase):
context = Context()
def setUp (self):
# each test gets a new collector
self.collector = StatCollector(self.context)
# get some records for statistics generation once
searcher = RecordSearcher(self.context)
self.records = searcher.search('environment')
def test_curators (self):
handler = ArticleTypeHandler()
self.collector.add_handler(handler)
self.collector.process(self.records)
self.assertEquals(len(handler.stats.keys()) > 0, True)
def test_article_types (self):
handler = ArticleTypeHandler()
self.collector.add_handler(handler)
self.collector.process(self.records)
self.assertEquals(len(handler.stats.keys()) > 0, True)
def test_methodology_samplings (self):
handler = MethodologySamplingHandler()
self.collector.add_handler(handler)
self.collector.process(self.records)
self.assertEquals(len(handler.stats.keys()) > 0, True)
def test_methology_types (self):
handler = MethodologyTypeHandler()
self.collector.add_handler(handler)
self.collector.process(self.records)
self.assertEquals(len(handler.stats.keys()) > 0, True)
def test_methology_timings (self):
handler = MethodologyTimingHandler()
self.collector.add_handler(handler)
self.collector.process(self.records)
self.assertEquals(len(handler.stats.keys()) > 0, True)
def test_methology_controls (self):
handler = MethodologyControlHandler()
self.collector.add_handler(handler)
self.collector.process(self.records)
self.assertEquals(len(handler.stats.keys()) > 0, True)
def test_exposure_routes (self):
handler = ExposureRouteHandler()
self.collector.add_handler(handler)
self.collector.process(self.records)
self.assertEquals(len(handler.stats.keys()) > 0, True)
def test_exposures (self):
handler = ExposureHandler()
self.collector.add_handler(handler)
self.collector.process(self.records)
self.assertEquals(len(handler.stats.keys()) > 0, True)
def test_risk_factors (self):
handler = RiskFactorHandler()
self.collector.add_handler(handler)
self.collector.process(self.records)
self.assertEquals(len(handler.stats.keys()) > 0, True)
def test_outcomes (self):
handler = OutcomeHandler()
self.collector.add_handler(handler)
self.collector.process(self.records)
self.assertEquals(len(handler.stats.keys()) > 0, True)
def test_species (self):
handler = SpeciesHandler()
self.collector.add_handler(handler)
self.collector.process(self.records)
self.assertEquals(len(handler.stats.keys()) > 0, True)
def test_locations (self):
handler = LocationHandler()
self.collector.add_handler(handler)
self.collector.process(self.records)
self.assertEquals(len(handler.stats.keys()) > 0, True)