def patch_and_report(connection, patch_d, skipped, uuid2patch, dryrun):
# report and patch
if dryrun:
print('DRY RUN - nothing will be patched to database')
if skipped:
print('WARNING! - SKIPPING for', uuid2patch)
for f, v in skipped.items():
print('Field: %s\tHAS: %s\tNOT ADDED: %s' %
(f, v['new'], v['old']))
if not patch_d:
print('NOTHING TO PATCH - ALL DONE!')
else:
print('PATCHING -', uuid2patch)
for f, v in patch_d.items():
print(f, '\t', v)
if not dryrun:
# do the patch
res = patch_FDN(uuid2patch, connection, patch_d)
if res['status'] == 'success':
print("SUCCESS!")
return True
else:
print("FAILED TO PATCH", uuid2patch, "RESPONSE STATUS",
res['status'], res['description'])
return False
return True
def main(): # pragma: no cover
start = datetime.now()
print(str(start))
args = get_args()
try:
connection = fdn_connection(args.keyfile, keyname=args.key)
except Exception as e:
print("Connection failed")
sys.exit(1)
# assumes a single line corresponds to json for single term
if not args.dbupdate:
print("DRY RUN - use --dbupdate to update the database")
with open(args.infile) as items:
for i in items:
[iid, payload] = [t.strip() for t in i.split('\t')]
payload = json.loads(payload)
if args.dbupdate:
e = patch_FDN(iid, connection, payload)
else:
print("DRY RUN\n\tPATCH: ", iid, " TO\n", payload)
e = {'status': 'success'}
status = e.get('status')
if status and status == 'success':
print(status)
else:
print('FAILED', e)
end = datetime.now()
print("FINISHED - START: ", str(start), "\tEND: ", str(end))
def do_patch(uid, type, patch, connection, dbupdate, cnts):
if not dbupdate:
print('DRY RUN - will update %s of type %s with %s' % (uid, type, patch))
cnts['not_patched'] += 1
return
# import pdb; pdb.set_trace()
res = patch_FDN(uid, connection, patch)
# res = {'status': 'testing'}
print('UPDATING - %s of type %s with %s' % (uid, type, patch))
rs = res['status']
print(rs)
if rs == 'success':
cnts['patched'] += 1
else:
cnts['errors'] += 1
print(res)
return
def main(): # pragma: no cover
args = get_args()
try:
connection = fdn_connection(args.keyfile, keyname=args.key)
except Exception as e:
print("Connection failed")
sys.exit(1)
itemids = scu.get_item_ids_from_args(args.input, connection, args.search)
taggable = scu.get_types_that_can_have_field(connection, '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(connection, itemid, {})
items2tag = scu.filter_dict_by_value(linked, taggable, include=True)
else:
# only want to tag provided items
itype = scu.get_item_type(connection, itemid)
if itype in taggable:
items2tag = {itemid: itype}
for i, t in items2tag.items():
if i not in seen:
seen.append(i)
item = get_FDN(i, connection)
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_FDN(pid, connection, patch)
print(pres['status'])
else:
print("DRY RUN: patch ", pid, " with ", patch)
def main():
args = get_args()
try:
connection = fdn_connection(args.keyfile, keyname=args.key)
except Exception as e:
print("Connection failed")
sys.exit(1)
id_list = scu.get_item_ids_from_args(args.input, connection, args.search)
val = args.value
if args.isarray:
val = val.split("'")[1::2]
for iid in id_list:
print("PATCHING", iid, "to", args.field, "=", val)
if (args.dbupdate):
# do the patch
res = patch_FDN(iid, connection, {args.field: val})
if res['status'] == 'success':
print("SUCCESS!")
else:
print("FAILED TO PATCH", iid, "RESPONSE STATUS", res['status'],
res['description'])
def main(): # pragma: no cover
start = datetime.now()
print(str(start))
args = get_args()
try:
connection = fdn_connection(args.keyfile, keyname=args.key)
except Exception as e:
print("Connection failed")
sys.exit(1)
phase2 = {}
# assumes a single line corresponds to json for single term
if not args.dbupdate:
print("DRY RUN - use --dbupdate to update the database")
with open(args.infile) as terms:
for t in terms:
phase2json = {}
term = json.loads(t)
id_tag = get_id(term)
if id_tag is None:
print("No Identifier for ", term)
else:
tid = '/ontology-terms/' + id_tag
# look for parents and remove for phase 2 loading if they are there
if 'parents' in term:
phase2json['parents'] = term['parents']
del term['parents']
if 'slim_terms' in term:
phase2json['slim_terms'] = term['slim_terms']
del term['slim_terms']
dbterm = get_FDN(tid, connection)
op = ''
if 'OntologyTerm' in dbterm['@type']:
if args.dbupdate:
e = patch_FDN(dbterm["uuid"], connection, term)
else:
e = {'status': 'dry run'}
op = 'PATCH'
else:
if args.dbupdate:
e = new_FDN(connection, 'OntologyTerm', term)
else:
e = {'status': 'dry run'}
op = 'POST'
status = e.get('status')
if status and status == 'dry run':
print(op, status)
elif status and status == 'success':
print(op, status, e['@graph'][0]['uuid'])
if phase2json:
phase2[e['@graph'][0]['uuid']] = phase2json
else:
print('FAILED', tid, e)
print("START LOADING PHASE2 at ", str(datetime.now()))
for tid, data in phase2.items():
if args.dbupdate:
e = patch_FDN(tid, connection, data)
else:
e = {'status': 'dry run'}
status = e.get('status')
if status and status == 'dry run':
print('PATCH', status)
elif status and status == 'success':
print('PATCH', status, e['@graph'][0]['uuid'])
else:
print('FAILED', tid, e)
end = datetime.now()
print("FINISHED - START: ", str(start), "\tEND: ", str(end))