def test_get_linked_items_w_type_in_no_children(auth, mocker):
mocker.patch('functions.script_utils.get_metadata',
side_effect=[{
'status': 'current'
}, {
'@type': ['Publication']
}])
iids = scu.get_linked_items(auth, 'test_id')
assert iids['test_id'] == 'Publication'
def test_get_linked_items_w_no_type(auth, mocker):
mocker.patch('functions.script_utils.get_metadata',
side_effect=[{
'status': 'released'
}, {
'field': 'value'
}])
iids = scu.get_linked_items(auth, 'test_id')
assert not iids
def main(): # pragma: no cover
args = get_args()
try:
auth = get_authentication_with_server(args.key, args.env)
except Exception:
print("Authentication failed")
sys.exit(1)
itemids = scu.get_item_ids_from_args(args.input, auth, args.search)
taggable = scu.get_types_that_can_have_field(auth, 'tags')
if args.types2exclude is not None:
# remove explicitly provide types not to tag
taggable = [t for t in taggable if t not in args.types2exclude]
seen = [
] # only need to add tag once so this keeps track of what's been seen
to_patch = {} # keep track of those to patch
# main loop through the top level item ids
for itemid in itemids:
items2tag = {}
if args.taglinked:
# need to get linked items and tag them
linked = scu.get_linked_items(auth, itemid, {})
items2tag = scu.filter_dict_by_value(linked,
taggable,
include=True)
else:
# only want to tag provided items
itype = scu.get_item_type(auth, itemid)
if itype in taggable:
items2tag = {itemid: itype}
for i, t in items2tag.items():
if i not in seen:
seen.append(i)
item = get_metadata(i, auth)
if not scu.has_field_value(item, 'tags', args.tag):
# not already tagged with this tag so make a patch and add 2 dict
to_patch[i] = make_tag_patch(item, args.tag)
# now do the patching or reporting
for pid, patch in to_patch.items():
if args.dbupdate:
pres = patch_metadata(patch, pid, auth)
print(pres['status'])
else:
print("DRY RUN: patch ", pid, " with ", patch)
def test_get_linked_items_w_no_linked_foundids(auth, mocker):
goodids = ['test_id']
badids = ['6256801c-9c6e-4563-a97a-a295fccf5f07']
resp1 = {
'status': 'released',
'@type': ['Biosample', 'Item'],
'biosource': '7256801c-9c6e-4563-a97a-a295fccf5f07',
'attachment': '6256801c-9c6e-4563-a97a-a295fccf5f07'
}
found = {}
mocker.patch('functions.script_utils.get_metadata',
side_effect=[resp1, {
'@type': ['Biosample']
}])
mocker.patch('functions.script_utils.find_uuids', return_value=None)
iids = scu.get_linked_items(auth, 'test_id', found)
for i in iids:
assert i in goodids
assert i not in badids
def test_get_linked_item_ids_w_recursive(auth, mocker):
goodids = [
'test_id', '7256801c-9c6e-4563-a97a-a295fccf5f07',
'5256801c-9c6e-4563-a97a-a295fccf5f07'
]
badids = ['6256801c-9c6e-4563-a97a-a295fccf5f07']
resp1 = {
'status': 'released',
'@type': ['Biosample', 'Item'],
'biosource': '7256801c-9c6e-4563-a97a-a295fccf5f07',
'attachment': '6256801c-9c6e-4563-a97a-a295fccf5f07'
}
resp1 = OrderedDict(sorted(resp1.items(), key=lambda t: t[0]))
resp2 = {
'status': 'released',
'@type': ['Biosource', 'Item'],
'biosource_vendor': '5256801c-9c6e-4563-a97a-a295fccf5f07'
}
resp2 = OrderedDict(sorted(resp2.items(), key=lambda t: t[0]))
resp3 = {
'status': 'released',
}
mocker.patch('functions.script_utils.get_metadata',
side_effect=[
resp1, {
'@type': ['Biosample']
}, resp2, {
'@type': ['Biosource']
}, resp3, {
'@type': ['Vendor']
}
])
mocker.patch('functions.script_utils.find_uuids',
side_effect=[
None, ['7256801c-9c6e-4563-a97a-a295fccf5f07'], None,
None, ['5256801c-9c6e-4563-a97a-a295fccf5f07'], None, None
])
iids = scu.get_linked_items(auth, 'test_id')
for i in iids:
assert i in goodids
assert i not in badids
def main():
args = get_args(sys.argv[1:])
try:
auth = get_authentication_with_server(args.key, args.env)
except Exception:
print("Authentication failed")
sys.exit(1)
itemids = scu.get_item_ids_from_args(args.input, auth, args.search)
excluded_types = get_excluded(args.types2exclude, args.types2include)
no_child = ['Publication', 'Lab', 'User', 'Award'] # default no_childs
if args.no_children:
no_child.extend(args.no_children)
no_child = list(set(no_child))
all_linked_ids = []
# main loop through the top level item ids
for itemid in itemids:
linked = scu.get_linked_items(auth, itemid, {})
if excluded_types is not None:
linked = scu.filter_dict_by_value(linked,
excluded_types,
include=False)
ll = [(k, linked[k]) for k in sorted(linked, key=linked.get)]
for i, t in ll:
suff = ''
if i == itemid:
suff = '\tINPUT'
if is_released(i, auth):
suff = '\tRELEASED' + suff
if not args.include_released:
print(i, '\t', t, '\tSKIPPING', suff)
continue
if i not in all_linked_ids:
all_linked_ids.append(i)
else:
suff = suff + '\tSEEN'
print(i, '\t', t, suff)
for a in all_linked_ids:
print(a)
def test_get_linked_items_w_error_status(auth, mocker):
mocker.patch('functions.script_utils.get_metadata',
return_value={'status': 'error'})
iids = scu.get_linked_items(auth, 'test_id')
assert not iids
def test_get_linked_items_w_item_in_found(auth):
itemid = 'itemid'
found_items = {itemid: 1}
iid = scu.get_linked_items(auth, itemid, found_items)
assert itemid in iid