def test_has_field_value_check_for_field_and_value(eset_json):
fields_w_values = {
"schema_version": "2",
"accession": "4DNES4GSP9S4",
"aliases": "ren:HG00512_repset"
}
for f, v in fields_w_values.items():
assert scu.has_field_value(eset_json, f, v)
def make_tag_patch(item, tag):
if not scu.has_field_value(item, 'tags', tag):
# not already tagged with this tag so make a patch and add 2 dict
if item.get('tags'):
tags = item['tags']
tags.append(tag)
else:
tags = [tag]
return {'tags': tags}
return None
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_has_field_value_value_not_found_as_string(eset_json):
not_found = 'unfound'
assert not scu.has_field_value(eset_json, 'status', not_found)
def test_has_field_value_value_not_found_in_list(eset_json):
not_found = 'unfound'
assert not scu.has_field_value(eset_json, 'experiments_in_set', not_found)
def test_has_field_value_check_for_field_w_item_no_dict():
f = "b"
v = "/labs/david-gilbert-lab/"
assert not scu.has_field_value('blah', f, v, True)
def test_has_field_value_check_for_field_w_item_not_found(bs_embed_json):
f = "lab"
v = "/labs/nobodys-lab/"
assert not scu.has_field_value(bs_embed_json, f, v, True)
def test_has_field_value_check_for_field_w_item(bs_embed_json):
f = "lab"
v = "/labs/david-gilbert-lab/"
assert scu.has_field_value(bs_embed_json, f, v, True)
def test_has_field_value_no_it_doesnt(eset_json):
fieldnames = ['biosample', 'blah', 'bio_rep_no']
for f in fieldnames:
assert not scu.has_field_value(eset_json, f)
def test_has_field_value_check_for_field_only(eset_json):
fieldnames = ['schema_version', 'award', 'alternate_accessions']
for f in fieldnames:
assert scu.has_field_value(eset_json, f)