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 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 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 phyleystem_api(self):
if self._phylesystem_api is None:
# trigger helpful message if config is not found
self._get_config_var('phylesystem_api_parent', 'phylesystem', 'parent', None)
pa = PhylesystemAPI(get_from='local')
self._phylesystem_api = pa
return self._phylesystem_api
def testRemoteTransSugar(self):
pa = PhylesystemAPI(self.domains, get_from='api', transform='server')
self._do_sugar_tests(pa)
def testConfig(self):
pa = PhylesystemAPI(self.domains, get_from='api')
x = pa.phylesystem_config
self.assertTrue('repo_nexml2json' in x.keys())
def testLocalSugar(self):
pa = PhylesystemAPI(self.domains, get_from='local')
self._do_sugar_tests(pa)
def testExternalSugar(self):
pa = PhylesystemAPI(self.domains, get_from='external')
self._do_sugar_tests(pa)
def testRemoteStudyList(self):
pa = PhylesystemAPI(self.domains, get_from='api')
sl = pa.study_list
# dev/production repos should have hundreds of studies
self.assertTrue(len(sl) > 100)
parser.add_argument('collection',
default=None,
type=str,
help='filepath for the collections JSON')
args = parser.parse_args(sys.argv[1:])
if not os.path.isfile(args.collection):
sys.exit('Input collection "{}" does not exist.\n'.format(args.collection))
try:
# get the list of trees that are 'included'
included = collection_to_included_trees(args.collection)
except:
sys.stderr.write('JSON parse error when reading collection "{}".\n'.format(args.collection))
raise
# work off the local copy of the phylesystem
phy = PhylesystemAPI(get_from='local')
# looking for the tree properties: ot:unrootedTree, ot:inGroupClade
# and the study property ot:candidateTreeForSynthesis
print("studyid,treeid,preferred,ingroup,unrooted")
for d in included:
studyid = d['studyID']
treeid = d['treeID']
# expect these defaults for synthesis trees
unrootedTree = False
ingroupSpecified = True
preferredTree = True
check = True
nx = phy.get_study(studyid)['data']
#!/usr/bin/env python
from peyotl.api import PhylesystemAPI
pa = PhylesystemAPI(get_from='external')
print(pa.get('pg_10', tree_id='tree3', subtree_id='ingroup', format='newick'))
def addStudy(session, study_id):
# get latest version of nexson
print "adding study {s}".format(s=study_id)
phy = PhylesystemAPI(get_from="local")
studyobj = phy.get_study(study_id)["data"]
nexml = get_nexml_el(studyobj)
year = nexml.get("^ot:studyYear")
proposedTrees = nexml.get("^ot:candidateTreeForSynthesis")
if proposedTrees is None:
proposedTrees = []
# create a new Study object
new_study = Study(id=study_id, year=year)
session.add(new_study)
# session.commit()
# get curator(s), noting that ot:curators might be a
# string or a list
c = nexml.get("^ot:curatorName")
print " ot:curatorName: ", c
# create list of curator objects
curator_list = []
if isinstance(c, basestring):
curator_list.append(c)
else:
curator_list = c
for curator in curator_list:
test_c = session.query(Curator).filter(Curator.name == curator).first()
if test_c:
print "curator {c} already exists".format(c=curator)
# session.add(curator)
new_study.curators.append(test_c)
else:
print "curator {c} does no exist".format(c=curator)
new_study.curators.append(Curator(name=curator))
# mapped otus in this study
otu_dict = gen_otu_dict(studyobj)
# iterate over the OTUs in the study, collecting the mapped
# ones (oid to ott_id mapping held at the study level)
mapped_otus = {}
for oid, o in otu_dict.items():
ottID = o.get("^ot:ottId")
if ottID is not None:
mapped_otus[oid] = ottID
# iterate over trees and insert tree data
for trees_group_id, tree_id, tree in iter_trees(studyobj):
print " tree :", tree_id
proposedForSynth = False
if tree_id in proposedTrees:
proposedForSynth = True
treejson = json.dumps(tree)
new_tree = Tree(tree_id=tree_id, study_id=study_id, proposed=proposedForSynth, data=treejson)
# get otus
ottIDs = set() # ott ids for this tree
ntips = 0
for node_id, node in iter_node(tree):
oid = node.get("@otu")
# no @otu property on internal nodes
if oid is not None:
ntips += 1
# ottID = mapped_otus[oid]
if oid in mapped_otus:
ottID = mapped_otus[oid]
# check that this exists in the taxonomy
# (it might not, if the ID has been deprecated)
taxon = session.query(Taxonomy).filter(Taxonomy.id == ottID).first()
if taxon:
new_tree.otus.append(taxon)
ottIDs.add(ottID)
new_tree.ntips = ntips
# need to write function for recursive query of Taxonomy table
# ottIDs = parent_closure(ottIDs,taxonomy)
# update with treebase id, if exists
datadeposit = nexml.get("^ot:dataDeposit")
if datadeposit:
url = datadeposit["@href"]
pattern = re.compile(u".+TB2:(.+)$")
matchobj = re.match(pattern, url)
if matchobj:
tb_id = matchobj.group(1)
new_tree.treebase_id = tb_id
session.add(new_tree)
# now that we have added the tree info, update the study record
# with the json data (minus the tree info)
del nexml["treesById"]
studyjson = json.dumps(nexml)
new_study.data = studyjson
session.commit()
#!/usr/bin/env python
"""Takes meta properties for a tree requested"""
from __future__ import absolute_import, division, print_function, unicode_literals
from peyotl.api import PhylesystemAPI
from peyotl.utility import propinquity_fn_to_study_tree
import codecs
import sys
out = codecs.getwriter('utf-8')(sys.stdout)
NON_META = frozenset([u'^ot:rootNodeId',
u'nodeById',
u'edgeBySourceId',
u'^ot:inGroupClade',
u'@xsi:type',
u'^ot:branchLengthTimeUnit',
u'^ot:branchLengthDescription',
u'^ot:tag',
u'^ot:branchLengthMode'])
for arg in sys.argv[1:]:
study_id, tree_id = propinquity_fn_to_study_tree(arg, strip_extension=False)
pa = PhylesystemAPI(get_from='local')
try:
tree = pa.get(study_id, tree_id=tree_id)[tree_id]
print('Tree "{}" in study "{}":'.format(tree_id, study_id))
for k, v in tree.items():
if (v is not None) and (v is not '') and (k not in NON_META):
print(k, v)
except:
sys.stderr.write('WARNING: did not find tree "{}" in study "{}"'.format(tree_id, study_id))
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'])
def testExternalSugar(self):
pa = PhylesystemAPI(self.domains, get_from='external')
test_phylesystem_api_for_study(self, pa)
def testRemoteSugar(self):
pa = PhylesystemAPI(self.domains, get_from='api')
test_phylesystem_api_for_study(self, pa)
def testStudyList(self):
pa = PhylesystemAPI(self.domains, get_from='local')
sl = pa.study_list
self.assertTrue(len(sl) > 100)
def testPushFailureState(self):
pa = PhylesystemAPI(self.domains, get_from='api')
sl = pa.push_failure_state
self.assertTrue(sl[0] is True)
def scream_about_new_failure(resp, OAUTH_TOKEN):
params = {'access_token': OAUTH_TOKEN}
template = "A push to GitHub has failed:\n date: {d}\n study: {s}\n commit: {c}"
msg = template.format(d=resp['date'], s=resp['study'], c=resp['commit'])
payload = {"body": msg}
resp = requests.post(URL, params=params, data=json.dumps(payload))
resp.raise_for_status()
def write_known_failures(fail_list):
with codecs.open(KNOWN_FAILURE_FILE, 'w', encoding='utf-8') as kff:
json.dump(fail_list, kff, sort_keys=True, indent=2)
if __name__ == '__main__':
if len(sys.argv) < 2:
sys.exit(
'expecting a GitHub OAUTH token as the first (and only) argument')
OAUTH_TOKEN = sys.argv[1]
pa = PhylesystemAPI()
succeeding, push_fail_dict = pa.push_failure_state
if not succeeding:
known_failures_d, kf_list = read_known_failures()
c = push_fail_dict['commit']
if c not in known_failures_d:
scream_about_new_failure(push_fail_dict, OAUTH_TOKEN)
kf_list.append(push_fail_dict)
write_known_failures(kf_list)
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'])
#!/usr/bin/env python
from peyotl.api import PhylesystemAPI
pa = PhylesystemAPI(get_from='api',
transform='client')
print(pa.get('pg_10',
tree_id='tree3',
subtree_id='ingroup',
format='newick'))
def testRemoteSugar(self):
pa = PhylesystemAPI(self.domains, get_from='api')
self._do_sugar_tests(pa)
def setUp(self):
self.pa = PhylesystemAPI(None, get_from='local', locals_repos_dict=test_repos)
def testRemoteTransSugar(self):
pa = PhylesystemAPI(self.domains, get_from='api', transform='server')
test_phylesystem_api_for_study(self, pa)
