def testDeleteCollectionRemote(self):
# drive RESTful API via wrapper
tca = TreeCollectionsAPI(self.domains, get_from='api')
# remove any prior clones of our tests collection? or let them pile up for now?
cl = tca.collection_list
cid = 'jimallman/doomed-collection'
if cid not in cl:
# add our dummy collection so just we can delete it
cjson = get_empty_collection()
commit_msg = 'Creating temporary collection via API wrapper'
result = tca.post_collection(cjson,
cid,
commit_msg)
cl = tca.collection_list
self.assertEqual(result['error'], 0)
self.assertEqual(result['merge_needed'], False)
self.assertEqual(result['resource_id'], cid)
self.assertTrue(cid in cl)
# now try to clobber it
try:
c = tca.get_collection(cid)
except HTTPError as err:
raise_http_error_with_more_detail(err)
except Exception as err:
raise err
else:
tca.delete_collection(cid, c['sha'])
# is it really gone?
cl = tca.collection_list
self.assertTrue(cid not in cl)
def testCreateCollectionRemote(self):
# drive RESTful API via wrapper
tca = TreeCollectionsAPI(self.domains, get_from='api')
# remove any prior clones of our tests collection? or let them pile up for now?
cl = tca.collection_list
test_collection_name = 'My test collection'
test_collection_id_base = 'jimallman/my-test-collection'
expected_id = test_collection_id_base
while expected_id in cl:
# keep generating ids until we find a new one
expected_id = increment_slug(expected_id)
# generate a new collection and name it
cjson = get_empty_collection()
cjson['name'] = test_collection_name
# N.B. this name already exists! should force a new, serial id
cslug = slugify(cjson['name'])
cid = 'jimallman/{}'.format(cslug)
# TODO: generate a unique URL based on this json, and modify it internally?
commit_msg = 'Test of creating collections via API wrapper'
result = tca.post_collection(cjson,
cid,
commit_msg)
cl = tca.collection_list
self.assertEqual(result['error'], 0)
self.assertEqual(result['merge_needed'], False)
self.assertEqual(result['resource_id'], expected_id)
self.assertTrue(expected_id in cl)
def testDeleteCollectionRemote(self):
# drive RESTful API via wrapper
tca = TreeCollectionsAPI(self.domains, get_from='api')
# remove any prior clones of our tests collection? or let them pile up for now?
cl = tca.collection_list
cid = 'jimallman/doomed-collection'
if cid not in cl:
# add our dummy collection so just we can delete it
cjson = get_empty_collection()
commit_msg = 'Creating temporary collection via API wrapper'
result = tca.post_collection(cjson, cid, commit_msg)
cl = tca.collection_list
self.assertEqual(result['error'], 0)
self.assertEqual(result['merge_needed'], False)
self.assertEqual(result['resource_id'], cid)
self.assertTrue(cid in cl)
# now try to clobber it
try:
c = tca.get_collection(cid)
except HTTPError as err:
raise_http_error_with_more_detail(err)
except Exception as err:
raise err
else:
tca.delete_collection(cid, c['sha'])
# is it really gone?
cl = tca.collection_list
self.assertTrue(cid not in cl)
def testCreateCollectionRemote(self):
# drive RESTful API via wrapper
tca = TreeCollectionsAPI(self.domains, get_from='api')
# remove any prior clones of our tests collection? or let them pile up for now?
cl = tca.collection_list
test_collection_name = 'My test collection'
test_collection_id_base = 'jimallman/my-test-collection'
expected_id = test_collection_id_base
while expected_id in cl:
# keep generating ids until we find a new one
expected_id = increment_slug(expected_id)
# generate a new collection and name it
cjson = get_empty_collection()
cjson['name'] = test_collection_name
# N.B. this name already exists! should force a new, serial id
cslug = slugify(cjson['name'])
cid = 'jimallman/{}'.format(cslug)
# TODO: generate a unique URL based on this json, and modify it internally?
commit_msg = 'Test of creating collections via API wrapper'
result = tca.post_collection(cjson, cid, commit_msg)
cl = tca.collection_list
self.assertEqual(result['error'], 0)
self.assertEqual(result['merge_needed'], False)
self.assertEqual(result['resource_id'], expected_id)
self.assertTrue(expected_id in cl)
def testCreated(self):
c = get_empty_collection()
aa = validate_collection(c)
errors = aa[0]
self.assertTrue(len(errors) == 0)
from peyotl.collections_store.validation import validate_collection
from peyotl import write_as_json
import sys
# Expecting a lot of lines like pg_2359_4962 for 'pg_2359', 'tree4962'
inp_fn = sys.argv[1]
with open(inp_fn, 'rU') as inp:
lines = []
for line in inp:
line = line.strip()
if (not line) or (line == 'taxonomy'):
continue
assert line.endswith('.tre')
frag = line[:-4]
s = frag.split('_')
study_id, tree_frag = '_'.join(s[:-1]), s[-1]
tree_id = 'tree' + tree_frag
lines.append((study_id, tree_id))
c = get_empty_collection()
d = c['decisions']
for pair in lines:
d.append({'SHA': '',
'decision': 'INCLUDED',
'name': '',
'studyID': pair[0],
'treeID': pair[1]
})
assert not (validate_collection(c)[0])
write_as_json(c, sys.stdout)
selected_study_found = True
else:
continue
ga = ps.create_git_action(study_id)
with ga.lock():
ga.checkout(sha)
if copy_phylesystem_file_if_differing(ga,
sha,
inc,
out_dir,
generic2concrete):
num_moved += 1
ga.checkout_master()
debug('{} total trees'.format(len(included)))
debug('{} JSON files copied'.format(num_moved))
if selected_study is not None:
if selected_study_found:
sys.exit(0)
error('The selected tree {}_{}.json was not found in the collection\n.'.format(selected_study, selected_tree))
sys.exit(1)
# now we write a "concrete" version of this snapshot
coll_name = os.path.split(args.collection)[-1]
concrete_collection = get_empty_collection()
concrete_collection['description'] = 'Concrete form of collection "{}"'.format(coll_name)
cd_list = concrete_collection['decisions']
for inc in included:
concrete = generic2concrete[id(inc)]
cd_list.append(concrete)
concrete_fn = os.path.join(out_dir, 'concrete_' + coll_name)
write_as_json(concrete_collection, concrete_fn)
def testCreated(self):
c = get_empty_collection()
aa = validate_collection(c)
errors = aa[0]
self.assertTrue(len(errors) == 0)
selected_study_found = True
else:
continue
ga = ps.create_git_action(study_id)
with ga.lock():
ga.checkout(sha)
if copy_phylesystem_file_if_differing(ga, sha, inc, out_dir,
generic2concrete):
num_moved += 1
ga.checkout_master()
debug('{} total trees'.format(len(included)))
debug('{} JSON files copied'.format(num_moved))
if selected_study is not None:
if selected_study_found:
sys.exit(0)
error(
'The selected tree {}_{}.json was not found in the collection\n.'.
format(selected_study, selected_tree))
sys.exit(1)
# now we write a "concrete" version of this snapshot
coll_name = os.path.split(args.collection)[-1]
concrete_collection = get_empty_collection()
concrete_collection[
'description'] = 'Concrete form of collection "{}"'.format(coll_name)
cd_list = concrete_collection['decisions']
for inc in included:
concrete = generic2concrete[id(inc)]
cd_list.append(concrete)
concrete_fn = os.path.join(out_dir, 'concrete_' + coll_name)
write_as_json(concrete_collection, concrete_fn)
