def _move_label_properties_for_otu(otu, syntax_version):
ol = find_val_literal_meta_first(otu, 'ot:originalLabel', syntax_version)
assert ol is not None
label_att = otu.get('@label')
if label_att is not None:
del otu['@label']
if label_att != ol:
ml = find_val_literal_meta_first(otu, 'ot:ottTaxonName', syntax_version)
if (not ml) or (ml != label_att):
add_literal_meta(otu, 'ot:altLabel', label_att, syntax_version)
def testExternalURL(self):
pa = PhylesystemAPI(self.domains, get_from='api')
u = pa.get_external_url('pg_10')
re = requests.get(u).json()
sid = find_val_literal_meta_first(re['nexml'], 'ot:studyId',
detect_nexson_version(re))
self.assertTrue(sid in ['10', 'pg_10'])
def _do_sugar_tests(self, pa):
x = pa.get('pg_10')['data']
sid = find_val_literal_meta_first(x['nexml'], 'ot:studyId',
detect_nexson_version(x))
self.assertTrue(sid in ['10', 'pg_10'])
y = pa.get('pg_10', tree_id='tree3', format='newick')
self.assertTrue(y.startswith('('))
def test_phylesystem_api_for_study(test_case_instance, phylesystem_wrapper, study_id='pg_10'):
from peyotl.nexson_syntax.helper import detect_nexson_version, find_val_literal_meta_first
x = phylesystem_wrapper.get(study_id)['data']
sid = find_val_literal_meta_first(x['nexml'], 'ot:studyId', detect_nexson_version(x))
test_case_instance.assertTrue(sid in [study_id])
y = phylesystem_wrapper.get(study_id, tree_id='tree3', format='newick')
test_case_instance.assertTrue(y.startswith('('))
def add_or_replace_annotation(
self, #pylint: disable=R0201
obj,
annotation,
agent,
add_agent_only=False):
'''Takes an `annotation` dictionary which is
expected to have a string as the value of annotation['author']['name']
This function will remove all annotations from obj that:
1. have the same author/name, and
2. have no messages that are flagged as messages to be preserved (values for 'preserve'
that evaluate to true)
'''
nex = get_nexml_el(obj)
nvers = detect_nexson_version(obj)
_LOG.debug('detected version as ' + nvers)
agents_obj = find_val_literal_meta_first(nex, 'ot:agents', nvers)
if not agents_obj:
agents_obj = add_literal_meta(nex, 'ot:agents', {'agent': []},
nvers)
agents_list = agents_obj.setdefault('agent', [])
found_agent = False
aid = agent['@id']
for a in agents_list:
if a.get('@id') == aid:
found_agent = True
break
if not found_agent:
agents_list.append(agent)
if add_agent_only:
delete_same_agent_annotation(obj, annotation)
else:
replace_same_agent_annotation(obj, annotation)
def add_or_replace_annotation(self, # pylint: disable=R0201
obj,
annotation,
agent,
add_agent_only=False):
"""Takes an `annotation` dictionary which is
expected to have a string as the value of annotation['author']['name']
This function will remove all annotations from obj that:
1. have the same author/name, and
2. have no messages that are flagged as messages to be preserved (values for 'preserve'
that evaluate to true)
"""
nex = get_nexml_el(obj)
nvers = detect_nexson_version(obj)
_LOG.debug('detected version as ' + nvers)
agents_obj = find_val_literal_meta_first(nex, 'ot:agents', nvers)
if not agents_obj:
agents_obj = add_literal_meta(nex, 'ot:agents', {'agent': []}, nvers)
agents_list = agents_obj.setdefault('agent', [])
found_agent = False
aid = agent['@id']
for a in agents_list:
if a.get('@id') == aid:
found_agent = True
break
if not found_agent:
agents_list.append(agent)
if add_agent_only:
delete_same_agent_annotation(obj, annotation)
else:
replace_same_agent_annotation(obj, annotation)
def testFetchStudy(self):
try:
x = self.phylografter.fetch_study('252')
except:
_LOG.exception('GET from phylografter failed!')
else:
sid = find_val_literal_meta_first(x['nexml'], 'ot:studyId', detect_nexson_version(x))
self.assertTrue(sid in ['252', 'pg_252'])
def testExternalURL(self):
# N.B. that the URL for this API call is an odd one, e.g.
# http://devapi.opentreeoflife.org/phylesystem/external_url/pg_10
pa = PhylesystemAPI(self.domains, get_from='api')
u = pa.get_external_url('pg_10')
re = requests.get(u).json()
sid = find_val_literal_meta_first(re['nexml'], 'ot:studyId', detect_nexson_version(re))
self.assertTrue(sid in ['10', 'pg_10'])
def testFetchStudy(self):
try:
x = self.phylografter.fetch_study('252')
except:
_LOG.exception('GET from phylografter failed!')
else:
sid = find_val_literal_meta_first(x['nexml'], 'ot:studyId',
detect_nexson_version(x))
self.assertTrue(sid in ['252', 'pg_252'])
def testExternalURL(self):
# N.B. that the URL for this API call is an odd one, e.g.
# http://devapi.opentreeoflife.org/phylesystem/external_url/pg_10
pa = PhylesystemAPI(self.domains, get_from='api')
u = pa.get_external_url('pg_10')
re = requests.get(u).json()
sid = find_val_literal_meta_first(re['nexml'], 'ot:studyId',
detect_nexson_version(re))
self.assertTrue(sid in ['10', 'pg_10'])
def test_phylesystem_api_for_study(test_case_instance,
phylesystem_wrapper,
study_id='pg_10'):
from peyotl.nexson_syntax.helper import detect_nexson_version, find_val_literal_meta_first
x = phylesystem_wrapper.get(study_id)['data']
sid = find_val_literal_meta_first(x['nexml'], 'ot:studyId',
detect_nexson_version(x))
test_case_instance.assertTrue(sid in [study_id])
y = phylesystem_wrapper.get(study_id, tree_id='tree3', format='newick')
test_case_instance.assertTrue(y.startswith('('))
def _fill_otu_ottid_maps(self, otus_group_id):
if self._otuid2ottid_byogid.get(otus_group_id) is None:
otuid2ottid = {}
ottid2otuid_list = {}
self._otuid2ottid_byogid[otus_group_id] = otuid2ottid
self._ottid2otuid_list_byogid[otus_group_id] = ottid2otuid_list
otu_dict = self._otu_by_otug[otus_group_id]
for otuid, otu in otu_dict.items():
ottid = find_val_literal_meta_first(otu, 'ot:ottId', self._nexson_version)
otuid2ottid[otuid] = ottid
ottid2otuid_list.setdefault(ottid, []).append(otuid)
return otuid2ottid, ottid2otuid_list
return self._otuid2ottid_byogid[otus_group_id], self._ottid2otuid_list_byogid[otus_group_id]
def _fill_otu_ottid_maps(self, otus_group_id):
if self._otuid2ottid_byogid.get(otus_group_id) is None:
otuid2ottid = {}
ottid2otuid_list = {}
self._otuid2ottid_byogid[otus_group_id] = otuid2ottid
self._ottid2otuid_list_byogid[otus_group_id] = ottid2otuid_list
otu_dict = self._otu_by_otug[otus_group_id]
for otuid, otu in otu_dict.items():
ottid = find_val_literal_meta_first(otu, 'ot:ottId',
self._nexson_version)
otuid2ottid[otuid] = ottid
ottid2otuid_list.setdefault(ottid, []).append(otuid)
return otuid2ottid, ottid2otuid_list
return self._otuid2ottid_byogid[
otus_group_id], self._ottid2otuid_list_byogid[otus_group_id]
def testStudy(self):
x = self.ot.study.get('pg_10')['data']
sid = find_val_literal_meta_first(x['nexml'], 'ot:studyId', detect_nexson_version(x))
self.assertTrue(sid in ['10', 'pg_10'])
y = self.ot.study.get('pg_10', tree_id='tree3', format='newick')
self.assertTrue(y.startswith('('))
def testFetchStudyRemote(self):
pa = PhylesystemAPI(self.domains, get_from='api')
x = pa.get_study('pg_10')['data']
sid = find_val_literal_meta_first(x['nexml'], 'ot:studyId',
detect_nexson_version(x))
self.assertTrue(sid in ['10', 'pg_10'])
def testExternalURL(self):
pa = PhylesystemAPI(self.domains, get_from='api')
u = pa.get_external_url('pg_10')
re = requests.get(u).json()
sid = find_val_literal_meta_first(re['nexml'], 'ot:studyId', detect_nexson_version(re))
self.assertTrue(sid in ['10', 'pg_10'])
def testFetchStudyRemote(self):
pa = PhylesystemAPI(self.domains, get_from='api')
x = pa.get_study('pg_10')['data']
sid = find_val_literal_meta_first(x['nexml'], 'ot:studyId', detect_nexson_version(x))
self.assertTrue(sid in ['10', 'pg_10'])
