def testCachedValidation(self):
try:
import dogpile.cache
except:
pass
else:
r = pathmap.get_test_repos()
p = Phylesystem(r)
nexson, sha = p.return_study('xy_10')
r = p.add_validation_annotation(nexson, sha)
cache_hits = p._cache_hits
r1 = p.add_validation_annotation(nexson, sha)
self.assertEqual(1 + cache_hits, p._cache_hits)
self.assertEqual(r, r1)
import sys; from peyotl import write_as_json;
write_as_json(nexson, sys.stdout)
def testCachedValidation(self):
try:
# noinspection PyPackageRequirements
import dogpile.cache
except:
pass
else:
r = pathmap.get_test_repos()
p = Phylesystem(r)
nexson, sha = p.return_study('xy_10')
r = p.add_validation_annotation(nexson, sha)
cache_hits = p._cache_hits
r1 = p.add_validation_annotation(nexson, sha)
self.assertEqual(1 + cache_hits, p._cache_hits)
self.assertEqual(r, r1)
write_as_json(nexson, sys.stdout)
def testCachedValidation(self):
try:
import dogpile.cache
except:
pass
else:
r = pathmap.get_test_repos()
p = Phylesystem(r)
nexson, sha = p.return_study('xy_10')
r = p.add_validation_annotation(nexson, sha)
cache_hits = p._cache_hits
r1 = p.add_validation_annotation(nexson, sha)
self.assertEqual(1 + cache_hits, p._cache_hits)
self.assertEqual(r, r1)
import sys
from peyotl import write_as_json
write_as_json(nexson, sys.stdout)
#! /usr/bin/env python
import unittest
from peyotl.api import PhylesystemAPI
from peyotl.test.support import test_phylesystem_api_for_study
from peyotl.test.support.pathmap import get_test_repos
from peyotl.utility import get_logger
_LOG = get_logger(__name__)
test_repos = get_test_repos(['mini_phyl', 'mini_system'])
@unittest.skipIf(not test_repos,
'See the documentation about the maintainers test to configure your '
'machine to run tests that require the mini_phyl and mini_system repos')
class TestPhylesystemAPI(unittest.TestCase):
def setUp(self):
self.pa = PhylesystemAPI(None, get_from='local', locals_repos_dict=test_repos)
def testLocalStudyList(self):
sl = self.pa.study_list
# local repo should have just a few studies
# @TODO we need a better test, I changed it from 10 to 10000.
# because I use my own fork of a large phylesystem in my tests
# I'm not sure what invariants we should check for, but
# length of study list is probably not one.
self.assertTrue(len(sl) < 10000)
def testLocalSugar(self):
test_phylesystem_api_for_study(self, self.pa, 'xy_10')
#! /usr/bin/env python
# coding=utf-8
from peyotl.collections_store.collections_umbrella import _TreeCollectionStore
import unittest
from peyotl.test.support import pathmap
import os
from peyotl.utility import get_logger
_LOG = get_logger(__name__)
_repos = pathmap.get_test_repos()
mc = _repos['mini_collections']
# TODO: filter repo list to just tree-collection shards? or rely on smart (failed) shard creation?
# _repos = {'mini_collections': mc}
@unittest.skipIf(
not os.path.isdir(mc),
'Peyotl not configured for maintainer test of mini_collections.'
'Skipping this test is normal (for everyone other than maintainers).\n'
'See http://opentreeoflife.github.io/peyotl/maintainer/')
class TestTreeCollections(unittest.TestCase):
def setUp(self):
self.r = dict(_repos)
def testSlugify(self):
from peyotl.utility.str_util import slugify
self.assertEqual('simple-test', slugify('Simple Test'))
self.assertEqual('no-punctuation-allowed',
from peyotl.phylesystem.git_workflows import acquire_lock_raise, \
commit_and_try_merge2master, \
delete_study, \
GitWorkflowError, \
merge_from_master
from peyotl.phylesystem.phylesystem_umbrella import Phylesystem
from peyotl.utility.input_output import read_as_json
import unittest
import codecs
import json
import copy
from peyotl.test.support import pathmap
from peyotl.utility import get_logger
_LOG = get_logger(__name__)
phylesystem = Phylesystem(pathmap.get_test_repos())
_MINI_PHYL_SHA1 = '2d59ab892ddb3d09d4b18c91470b8c1c4cca86dc'
_SID = 'xy_10'
_AUTH = {
'name': 'test_name',
'email': '*****@*****.**',
'login': '******',
}
class TestPhylesystemDel(unittest.TestCase):
def testDelStudy(self):
ga = phylesystem.create_git_action(_SID)
ga.acquire_lock()
try:
#! /usr/bin/env python
import unittest
from peyotl.api import TreeCollectionsAPI
from peyotl.test.support import test_collections_api
from peyotl.test.support.pathmap import get_test_repos
from peyotl.utility import get_logger
_LOG = get_logger(__name__)
test_repos = get_test_repos(['mini_collections'])
@unittest.skipIf(
not test_repos,
'See the documentation about the maintainers test to configure your '
'machine to run tests that require the mini_collections repos')
class TestTreeCollectionsAPI(unittest.TestCase):
def setUp(self):
self.tca = TreeCollectionsAPI(None,
get_from='local',
locals_repos_dict=test_repos)
def testCollectionList(self):
cl = self.tca.collection_list
# We assume there's always at least one collection.
self.assertTrue(len(cl) > 0)
def testLocalSugar(self):
test_collections_api(self, self.tca)
from peyotl.phylesystem.git_workflows import acquire_lock_raise, \
commit_and_try_merge2master, \
delete_study, \
GitWorkflowError, \
merge_from_master
from peyotl.phylesystem.phylesystem_umbrella import Phylesystem
from peyotl.utility.input_output import read_as_json
import unittest
import codecs
import json
import copy
from peyotl.test.support import pathmap
from peyotl.utility import get_logger
_LOG = get_logger(__name__)
phylesystem = Phylesystem(pathmap.get_test_repos())
_MINI_PHYL_SHA1 = '2d59ab892ddb3d09d4b18c91470b8c1c4cca86dc'
_SID = 'xy_10'
_AUTH = {
'name': 'test_name',
'email': '*****@*****.**',
'login': '******',
}
class TestPhylesystem(unittest.TestCase):
def xtestSimple(self):
ga = phylesystem.create_git_action(_SID)
ga.acquire_lock()
try:
curr, sha, wip_map = ga.return_study(_SID, return_WIP_map=True)
#! /usr/bin/env python
import unittest
from peyotl.api import TreeCollectionsAPI
from peyotl.test.support import test_collections_api
from peyotl.test.support.pathmap import get_test_repos
from peyotl.utility import get_logger
_LOG = get_logger(__name__)
test_repos = get_test_repos(['mini_collections'])
@unittest.skipIf(not test_repos,
'See the documentation about the maintainers test to configure your '
'machine to run tests that require the mini_collections repos')
class TestTreeCollectionsAPI(unittest.TestCase):
def setUp(self):
self.tca = TreeCollectionsAPI(None, get_from='local', locals_repos_dict=test_repos)
def testCollectionList(self):
cl = self.tca.collection_list
# We assume there's always at least one collection.
self.assertTrue(len(cl) > 0)
def testLocalSugar(self):
test_collections_api(self, self.tca)
if __name__ == "__main__":
unittest.main()
#! /usr/bin/env python
# coding=utf-8
import unittest
from peyotl.amendments.amendments_umbrella import _TaxonomicAmendmentStore
from peyotl.test.support import pathmap
from peyotl.utility import get_logger
_LOG = get_logger(__name__)
test_repos = pathmap.get_test_repos(['mini_amendments'])
@unittest.skipIf(not test_repos,
'See the documentation about the maintainers test to configure your '
'machine to run tests that require the mini_amendments repos')
class TestTaxonomicAmendments(unittest.TestCase):
def setUp(self):
self.c = _TaxonomicAmendmentStore(repos_dict=dict(test_repos))
def testInit(self):
self.assertEqual(1, len(self.c._shards))
def testAmendmentIndexing(self):
k = list(self.c._doc2shard_map.keys())
k.sort()
expected = ['additions-5000000-5000003']
# TODO: populate with more test data?
self.assertEqual(k, expected)
def testURL(self):
#! /usr/bin/env python
import unittest
from peyotl.api import TaxonomicAmendmentsAPI
from peyotl.test.support import test_amendments_api
from peyotl.test.support.pathmap import get_test_repos
from peyotl.utility import get_logger
_LOG = get_logger(__name__)
test_repos = get_test_repos(['mini_amendments'])
@unittest.skipIf(not test_repos,
'See the documentation about the maintainers test to configure your '
'machine to run tests that require the mini_amendments repos')
class TestTaxonomicAmendmentsAPI(unittest.TestCase):
def setUp(self):
self.taa = TaxonomicAmendmentsAPI(None, get_from='local', locals_repos_dict=test_repos)
def testAmendmentList(self):
al = self.taa.amendment_list
# We assume there's always at least one amendment.
self.assertTrue(len(al) > 0)
def testLocalSugar(self):
test_amendments_api(self, self.taa)
if __name__ == "__main__":
unittest.main()
#! /usr/bin/env python
# put tests here that use local phylesystem
# see http://opentreeoflife.github.io/peyotl/maintainer/ for setup
from peyotl.utility.input_output import read_as_json
from peyotl.phylesystem.phylesystem_umbrella import _Phylesystem
import unittest
from peyotl.test.support import pathmap
import os
from peyotl.utility import get_logger
_LOG = get_logger(__name__)
_repos = pathmap.get_test_repos()
ms, mp = _repos['mini_system'], _repos['mini_phyl']
# TODO: filter repo list to just phylesystem shards? or rely on smart (failed) shard creation?
# _repos = {s: _repos[s] for s in _repos if s in ('mini_system', 'mini_phyl',)}
# pylint: disable=W0212
@unittest.skipIf((not os.path.isdir(ms)) or (not os.path.isdir(mp)),
'Peyotl not configured for maintainer test of mini_phyl/system.'
'Skipping this test is normal (for everyone other than MTH and EJBM).\n'
'See http://opentreeoflife.github.io/peyotl/maintainer/ ')
class TestPhylesystem(unittest.TestCase):
def setUp(self):
self.r = dict(_repos)
