def simple_test(path, input, check=None, expected_status=200, is_right=(lambda x:True)):
DOMAIN = config('host', 'apihost')
url = DOMAIN + path
try:
# print 'checking', url
(win, output) = test_http_json_method(url, verb='POST', data=input,
expected_status=expected_status,
return_bool_data=True)
if not win:
# Error message already printed
print '** http lose'
return 1
if isinstance(output, dict) and 'error' in output:
# Should be 400, not 200
print '** error', output
return 1
elif check == None:
return 0
elif check(output, ''):
if is_right(output):
return 0
else:
print '** result is not right', output
return 1
else:
return 1
except Exception, e:
print '** exception', e
traceback.print_exc()
return 1
def check_node_info(parameters):
DOMAIN = config('host', 'apihost')
SUBMIT_URI = DOMAIN + '/v3/tree_of_life/node_info'
test, result, _ = test_http_json_method(SUBMIT_URI, "POST",
data=parameters,
expected_status=200,
return_bool_data=True)
if not test: sys.exit(1)
node_id_key = u'node_id'
check_node_result(result, node_id_key)
# check_node_expectation(parameters, result, node_id_key, ...name...)
valid_keys = [node_id_key, u'taxon', u'nearest_taxon', u'synth_id']
check_result_keys(result, valid_keys)
sys.exit(exit_status[0])
def check_node_info(parameters):
DOMAIN = config('host', 'apihost')
SUBMIT_URI = DOMAIN + '/v3/tree_of_life/node_info'
test, result, _ = test_http_json_method(SUBMIT_URI,
"POST",
data=parameters,
expected_status=200,
return_bool_data=True)
if not test: sys.exit(1)
node_id_key = u'node_id'
check_node_result(result, node_id_key)
# check_node_expectation(parameters, result, node_id_key, ...name...)
valid_keys = [node_id_key, u'taxon', u'nearest_taxon', u'synth_id']
check_result_keys(result, valid_keys)
sys.exit(exit_status[0])
def simple_test(path, input, check, is_right=(lambda x:True)):
DOMAIN = config('host', 'apihost')
url = DOMAIN + path
try:
# print 'checking', url
output = get_obj_from_http(url, verb='POST', data=input)
if isinstance(output, dict) and 'error' in output:
# Should be 400, not 200
print '** error', output
return 1
elif check(output, ''):
if is_right(output):
return 0
else:
print '** result is not right', output
return 1
else:
return 1
except Exception, e:
print '** exception', e
traceback.print_exc()
return 1
def simple_test(path, input, check, is_right=(lambda x: True)):
DOMAIN = config('host', 'apihost')
url = DOMAIN + path
try:
# print 'checking', url
output = get_obj_from_http(url, verb='POST', data=input)
if isinstance(output, dict) and 'error' in output:
# Should be 400, not 200
print '** error', output
return 1
elif check(output, ''):
if is_right(output):
return 0
else:
print '** result is not right', output
return 1
else:
return 1
except Exception, e:
print '** exception', e
traceback.print_exc()
return 1
def simple_test(path,
input,
check=None,
expected_status=200,
is_right=(lambda x: True)):
DOMAIN = config('host', 'apihost')
url = DOMAIN + path
try:
# print 'checking', url
(win, output) = test_http_json_method(url,
verb='POST',
data=input,
expected_status=expected_status,
return_bool_data=True)
if not win:
# Error message already printed
print '** http lose'
return 1
if isinstance(output, dict) and 'error' in output:
# Should be 400, not 200
print '** error', output
return 1
elif check == None:
return 0
elif check(output, ''):
if is_right(output):
return 0
else:
print '** result is not right', output
return 1
else:
return 1
except Exception, e:
print '** exception', e
traceback.print_exc()
return 1
#!/usr/bin/env python
import sys, os
from opentreetesting import test_http_json_method, config
DOMAIN = config('host', 'apihost')
SUBMIT_URI = DOMAIN + '/v3/amendments/list_all'
r = test_http_json_method(SUBMIT_URI,
'GET',
expected_status=200,
return_bool_data=True)
if not r[0]:
sys.exit(1)
#print r[1]
#!/usr/bin/env python
import sys
import requests
import json
from opentreetesting import config, summarize_json_response
DOMAIN = config('host', 'golshost')
p = '/ext/GoLS/graphdb/getStudyIngestMessagesForNexSON'
if DOMAIN.startswith('http://127.0.0.1'):
p = '/db/data' + p
SUBMIT_URI = DOMAIN + p
payload = {
'nexsonBlob': open('data/359', 'rU').read()
}
headers = {
'content-type' : 'application/json',
'accept' : 'application/json',
}
d = json.dumps(payload)
resp = requests.post(SUBMIT_URI,
headers=headers,
data=d,
allow_redirects=True)
summarize_json_response(resp) or sys.exit(1)
#!/usr/bin/env python
import sys, os, re
from opentreetesting import test_http_json_method, config
DOMAIN = config("host", "apihost")
SUBMIT_URI = DOMAIN + "/v2/taxonomy/subtree"
test, result = test_http_json_method(
SUBMIT_URI, "POST", data={"ott_id": 515698}, expected_status=200, return_bool_data=True
)
if not test:
sys.exit(1)
tree = result[u"subtree"]
if tree is None or tree == "":
sys.stderr.write("Expected result to have a tree, but found {}\n".format(result))
sys.exit(1)
# trying to avoid dealing with a newick parser here...
ROOTTAXONSTR = "\)Barnadesia_ott515698;"
namecheck = re.compile(ROOTTAXONSTR)
if re.search(namecheck, tree) is None:
errstr = "requested taxon {} does not appear at root of tree:\n {}"
sys.stderr.write(errstr, ROOTTAXONSTR[1:], tree)
sys.exit(1)
#!/usr/bin/env python
# export PYTHONPATH=~/a/ot/repo/germinator/ws-tests
# python ws-tests/test_v3_addition.py host:apihost="http://localhost:7476" host:translate=true
import sys, requests, opentreetesting, json
from check import *
opentreetesting.exit_if_api_is_readonly('test_v3_addition.py')
# Find an unused OTT id
id = 99000000
DOMAIN = opentreetesting.config('host', 'apihost')
while True:
response = requests.request(
'POST',
opentreetesting.translate(DOMAIN + '/v3/taxonomy/taxon_info'),
headers={'content-type': 'application/json'},
data=json.dumps({'ott_id': id}),
allow_redirects=True)
if response.status_code != 200:
print 'id %s is unused' % id
break
# print 'id %s is in use' % id
id += 10
name1 = "Test taxon 1"
def check_about(parameters):
DOMAIN = config('host', 'apihost')
SUBMIT_URI = DOMAIN + '/v3/tree_of_life/about'
test, result, _ = test_http_json_method(SUBMIT_URI, "POST",
data=parameters,
expected_status=200,
return_bool_data=True)
if not test:
sys.exit(1)
""" Doc says:
"synth_id" : "opentree4.1",
"root_node_id" : "ott93302", # in v2 this was an integer
"num_source_trees" : 484,
"date_completed" : "2016-02-09 18:14:43",
"taxonomy_version" : "2.9draft12",
"num_tips" : 2424255,
"num_source_studies" : 478,
"filtered_flags" : [ "major_rank_conflict", "major_rank_conflict_inherited", "environmental", "unclassified_inherited", "unclassified", "viral", "barren", "not_otu", "incertae_sedis", "incertae_sedis_inherited", "extinct_inherited", "extinct", "hidden", "unplaced", "unplaced_inherited", "was_container", "inconsistent", "hybrid", "merged" ],
"root_ott_id" : 93302
"root_taxon_name" : "cellular organisms",
maybe: "root_taxon" : { ... }
"""
code = [0]
def lose(): code[0] = 1
def check_result_type(name, typo):
value = result.get(name)
if not isinstance(value, typo):
if value == None:
sys.stderr.write('{} missing\n'.format(name))
print result.keys()
else:
sys.stderr.write('{} is not a {}\n'.format(name, typo))
lose()
return None
return value
check_result_type(u'root_node_id', unicode)
num_source_trees = check_result_type(u'num_source_trees', int)
if num_source_trees != None and num_source_trees < 2:
sys.stderr.write('not very many source trees: {}\n'.format(num_source_trees))
lose()
check_result_type(u'date_completed', unicode)
num_tips = check_result_type(u'num_tips', int)
if num_tips != None and num_tips < 3:
sys.stderr.write('not very many tips: {}\n'.format(num_tips))
lose()
check_result_type(u'taxonomy_version', unicode)
num_source_trees = check_result_type(u'num_source_trees', int)
if num_source_trees != None and num_source_trees < 2:
sys.stderr.write('not very trees: {}\n'.format(num_source_trees))
lose()
num_source_studies = check_result_type(u'num_source_studies', int)
if num_source_studies != None and num_source_studies < 2:
sys.stderr.write('not very studies: {}\n'.format(num_source_studies))
lose()
check_result_type(u'filtered_flags', list)
if u'root_ott_id' in result:
check_result_type(u'root_ott_id', int)
check_result_type(u'root_taxon_name', unicode)
source_list = parameters.get(u'source_list')
if source_list == None or not source_list:
if u'sources' in result:
sys.stderr.write('source_list false but there are sources in result: {}\n'.format(source_list))
lose()
else:
sources = check_result_type(u'sources', list)
metas = check_result_type(u'source_id_map', dict)
if sources != None:
for source in sources:
if not isinstance(source, unicode):
sys.stderr.write('ill-formed source: {} should be a string\n'.format(source))
lose()
break
if metas != None:
for label in metas.keys():
meta = metas[label]
if label == u'taxonomy':
True
elif (isinstance(meta, dict) and
u'study_id' in meta and
u'tree_id' in meta):
True
else:
sys.stderr.write('ill-formed meta: {} should be {}"study_id": ..., "tree_id": ...{}\n'.format(meta, '{', '}'))
lose()
break
sys.exit(code[0])
#!/usr/bin/env python
from opentreetesting import test_http_json_method, config
from peyotl import convert_nexson_format
import datetime
import codecs
import json
import sys
import os
# this makes it easier to test concurrent pushes to different branches
study_id = 12
DOMAIN = config('host', 'apihost')
starting_commit_SHA = config('host', 'parentsha')
SUBMIT_URI = DOMAIN + '/v1/study/%s' % study_id
fn = 'data/{s}.json'.format(s=study_id)
inpf = codecs.open(fn, 'rU', encoding='utf-8')
n = json.load(inpf)
# refresh a timestamp so that the test generates a commit
m = n['nexml']['meta']
short_list = [i for i in m if i.get('@property') == 'bogus_timestamp']
if short_list:
el = short_list[0]
else:
el = {'@property': 'bogus_timestamp', '@xsi:type': 'nex:LiteralMeta'}
m.append(el)
el['$'] = datetime.datetime.utcnow().isoformat()
n = convert_nexson_format(n, '1.2')
data = { 'nexson' : n,
#!/usr/bin/env python
# export PYTHONPATH=~/a/ot/repo/germinator/ws-tests
# python ws-tests/test_v3_addition.py host:apihost="http://localhost:7476" host:translate=true
import sys, requests, opentreetesting, json
from check import *
opentreetesting.exit_if_api_is_readonly('test_v3_addition.py')
# Find an unused OTT id
id = 99000000
DOMAIN = opentreetesting.config('host', 'apihost')
while True:
response = requests.request('POST',
opentreetesting.translate(DOMAIN + '/v3/taxonomy/taxon_info'),
headers={'content-type' : 'application/json'},
data=json.dumps({'ott_id': id}),
allow_redirects=True)
if response.status_code != 200:
print 'id %s is unused' % id
break
# print 'id %s is in use' % id
id += 10
name1 = "Test taxon 1"
name2 = "Test taxon 2"
#!/usr/bin/env python
import sys
import requests
import json
#curl -X POST http://opentree-dev.bio.ku.edu:7474/ext/TNRS/graphdb/doTNRSForNames -H "Content-Type: Application/json" -d '{"queryString": "Pan trodlogytes, H**o sapphire, Plantago, Morpho peleides, Eleocharis"}'
from opentreetesting import config
DOMAIN = config('host', 'tnrshost')
SUBMIT_URI = DOMAIN + '/ext/TNRS/graphdb/doTNRSForNames'
payload = {
"queryString": "Pan trodlogytes, H**o sapphire, Plantago, Morpho peleides, Eleocharis",
"contextName": "All life"
}
if len(sys.argv) > 1:
payload['queryString'] = ', '.join(sys.argv[1:])
headers = {
'content-type' : 'application/json',
'accept' : 'application/json',
}
resp = requests.post(SUBMIT_URI,
headers=headers,
data=json.dumps(payload),
allow_redirects=True)
sys.stderr.write('Sent POST to %s\n' %(resp.url))
resp.raise_for_status()
try:
results = resp.json()
print 'results =', str(results)
def check_about(parameters):
DOMAIN = config('host', 'apihost')
SUBMIT_URI = DOMAIN + '/v3/tree_of_life/about'
test, result, _ = test_http_json_method(SUBMIT_URI,
"POST",
data=parameters,
expected_status=200,
return_bool_data=True)
if not test:
sys.exit(1)
""" Doc says:
"synth_id" : "opentree4.1",
"root_node_id" : "ott93302", # in v2 this was an integer
"num_source_trees" : 484,
"date_completed" : "2016-02-09 18:14:43",
"taxonomy_version" : "2.9draft12",
"num_tips" : 2424255,
"num_source_studies" : 478,
"filtered_flags" : [ "major_rank_conflict", "major_rank_conflict_inherited", "environmental", "unclassified_inherited", "unclassified", "viral", "barren", "not_otu", "incertae_sedis", "incertae_sedis_inherited", "extinct_inherited", "extinct", "hidden", "unplaced", "unplaced_inherited", "was_container", "inconsistent", "hybrid", "merged" ],
"root_ott_id" : 93302
"root_taxon_name" : "cellular organisms",
maybe: "root_taxon" : { ... }
"""
code = [0]
def lose():
code[0] = 1
def check_result_type(name, typo):
value = result.get(name)
if not isinstance(value, typo):
if value == None:
sys.stderr.write('{} missing\n'.format(name))
print result.keys()
else:
sys.stderr.write('{} is not a {}\n'.format(name, typo))
lose()
return None
return value
check_result_type(u'root_node_id', unicode)
num_source_trees = check_result_type(u'num_source_trees', int)
if num_source_trees != None and num_source_trees < 2:
sys.stderr.write(
'not very many source trees: {}\n'.format(num_source_trees))
lose()
check_result_type(u'date_completed', unicode)
num_tips = check_result_type(u'num_tips', int)
if num_tips != None and num_tips < 3:
sys.stderr.write('not very many tips: {}\n'.format(num_tips))
lose()
check_result_type(u'taxonomy_version', unicode)
num_source_trees = check_result_type(u'num_source_trees', int)
if num_source_trees != None and num_source_trees < 2:
sys.stderr.write('not very trees: {}\n'.format(num_source_trees))
lose()
num_source_studies = check_result_type(u'num_source_studies', int)
if num_source_studies != None and num_source_studies < 2:
sys.stderr.write('not very studies: {}\n'.format(num_source_studies))
lose()
check_result_type(u'filtered_flags', list)
if u'root_ott_id' in result:
check_result_type(u'root_ott_id', int)
check_result_type(u'root_taxon_name', unicode)
source_list = parameters.get(u'source_list')
if source_list == None or not source_list:
if u'sources' in result:
sys.stderr.write(
'source_list false but there are sources in result: {}\n'.
format(source_list))
lose()
else:
sources = check_result_type(u'sources', list)
metas = check_result_type(u'source_id_map', dict)
if sources != None:
for source in sources:
if not isinstance(source, unicode):
sys.stderr.write(
'ill-formed source: {} should be a string\n'.format(
source))
lose()
break
if metas != None:
for label in metas.keys():
meta = metas[label]
if label == u'taxonomy':
True
elif (isinstance(meta, dict) and u'study_id' in meta
and u'tree_id' in meta):
True
else:
sys.stderr.write(
'ill-formed meta: {} should be {}"study_id": ..., "tree_id": ...{}\n'
.format(meta, '{', '}'))
lose()
break
sys.exit(code[0])