13682489429

Committed 05 Mar 2025 06:03PM UTC coverage: 33.8%. Remained the same

Build # 13682489429

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #117 from 4dn-dcic/ajs_upd_dependencies

Ajs upd dependencies

Run Details

2 of 2 new or added lines in 1 file covered. (100.0%)

22 existing lines in 14 files now uncovered.

1256 of 3716 relevant lines covered (33.8%)

2.02 hits per line

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0.0

/scripts/tagger.py

import sys
import argparse
from dcicutils.ff_utils import get_metadata, patch_metadata
from functions import script_utils as scu
""" Script to add arbitrary tags to items that can be tagged
"""

def make_tag_patch(item, tag):
    if item.get('tags'):
        tags = item['tags']
        tags.append(tag)
    else:
        tags = [tag]
    return {'tags': tags}


def get_args():  # pragma: no cover
    parser = argparse.ArgumentParser(
        description='Add a tag to provided items (and optionally their children)',
        parents=[scu.create_input_arg_parser(), scu.create_ff_arg_parser()],
        formatter_class=argparse.RawDescriptionHelpFormatter,
    )
    parser.add_argument('tag',
                        help="The tag you want to add - eg. '4DN Standard'")
    parser.add_argument('--taglinked',
                        default=False,
                        action='store_true',
                        help='Tag items linked to items that are input')
    parser.add_argument('--types2exclude',
                        nargs='+',
                        help="List of Item Types to Explicitly Exclude Tagging - \
                        you may have some linked items that can get tags but may \
                        not want to tag them with this tag")
    args = parser.parse_args()
    return args


def main():  # pragma: no cover
    args = get_args()
    auth = scu.authenticate(key=args.key, keyfile=args.keyfile, env=args.env)
    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)


if __name__ == '__main__':  # pragma: no cover
    main()

1	import sys	×
2	import argparse	×
3	from dcicutils.ff_utils import get_metadata, patch_metadata	×
4	from functions import script_utils as scu	×
UNCOV 5	""" Script to add arbitrary tags to items that can be tagged
6	"""
7
8	def make_tag_patch(item, tag):	×
9	if item.get('tags'):	×
10	tags = item['tags']	×
11	tags.append(tag)	×
12	else:
13	tags = [tag]	×
14	return {'tags': tags}	×
15
16
17	def get_args(): # pragma: no cover
18	parser = argparse.ArgumentParser(
19	description='Add a tag to provided items (and optionally their children)',
20	parents=[scu.create_input_arg_parser(), scu.create_ff_arg_parser()],
21	formatter_class=argparse.RawDescriptionHelpFormatter,
22	)
23	parser.add_argument('tag',
24	help="The tag you want to add - eg. '4DN Standard'")
25	parser.add_argument('--taglinked',
26	default=False,
27	action='store_true',
28	help='Tag items linked to items that are input')
29	parser.add_argument('--types2exclude',
30	nargs='+',
31	help="List of Item Types to Explicitly Exclude Tagging - \
32	you may have some linked items that can get tags but may \
33	not want to tag them with this tag")
34	args = parser.parse_args()
35	return args
36
37
38	def main(): # pragma: no cover
39	args = get_args()
40	auth = scu.authenticate(key=args.key, keyfile=args.keyfile, env=args.env)
41	itemids = scu.get_item_ids_from_args(args.input, auth, args.search)
42	taggable = scu.get_types_that_can_have_field(auth, 'tags')
43	if args.types2exclude is not None:
44	# remove explicitly provide types not to tag
45	taggable = [t for t in taggable if t not in args.types2exclude]
46
47	seen = [] # only need to add tag once so this keeps track of what's been seen
48	to_patch = {} # keep track of those to patch
49	# main loop through the top level item ids
50	for itemid in itemids:
51	items2tag = {}
52	if args.taglinked:
53	# need to get linked items and tag them
54	linked = scu.get_linked_items(auth, itemid, {})
55	items2tag = scu.filter_dict_by_value(linked, taggable, include=True)
56	else:
57	# only want to tag provided items
58	itype = scu.get_item_type(auth, itemid)
59	if itype in taggable:
60	items2tag = {itemid: itype}
61	for i, t in items2tag.items():
62	if i not in seen:
63	seen.append(i)
64	item = get_metadata(i, auth)
65	if not scu.has_field_value(item, 'tags', args.tag):
66	# not already tagged with this tag so make a patch and add 2 dict
67	to_patch[i] = make_tag_patch(item, args.tag)
68
69	# now do the patching or reporting
70	for pid, patch in to_patch.items():
71	if args.dbupdate:
72	pres = patch_metadata(patch, pid, auth)
73	print(pres['status'])
74	else:
75	print("DRY RUN: patch ", pid, " with ", patch)
76
77
78	if __name__ == '__main__': # pragma: no cover
79	main()

4dn-dcic / dcicwrangling / 13682489429

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