Coverage for bioimageio/spec/generic/_v0_2_converter.py: 12%

1import collections.abc 

2from typing import Any, Dict, Mapping, Union 

3 

4from .._internal.io import BioimageioYamlContent 

5from .._internal.type_guards import is_mapping 

6 

7 

8def convert_from_older_format(data: BioimageioYamlContent) -> None: 

9 """convert raw RDF data of an older format where possible""" 

10 # check if we have future format version 

11 if "format_version" not in data: 

12 return 

13 

14 fv = data["format_version"] 

15 if isinstance(fv, str) and tuple(map(int, fv.split(".")[:2])) > (0, 2): 

16 return 

17 

18 # we unofficially accept strings as author entries 

19 authors = data.get("authors") 

20 if isinstance(authors, list): 

21 data["authors"] = [{"name": a} if isinstance(a, str) else a for a in authors] 

22 

23 if data.get("format_version") in ("0.2.0", "0.2.1"): 

24 data["format_version"] = "0.2.2" 

25 

26 if data.get("format_version") == "0.2.2": 

27 remove_slashes_from_names(data) 

28 data["format_version"] = "0.2.3" 

29 

30 if data.get("format_version") == "0.2.3": 

31 if isinstance(config := data.get("config"), dict) and isinstance( 

32 bconfig := config.get("bioimageio"), dict 

33 ): 

34 if (nickname := bconfig.get("nickname")) is not None: 

35 data["id"] = nickname 

36 

37 if (nickname_icon := bconfig.get("nickname_icon")) is not None: 

38 data["id_emoji"] = nickname_icon 

39 

40 data["format_version"] = "0.2.4" 

41 

42 remove_doi_prefix(data) 

43 remove_gh_prefix(data) 

44 

45 

46def remove_slashes_from_names(data: Dict[Any, Any]) -> None: 

47 NAME = "name" 

48 if NAME in data and isinstance(data[NAME], str): 

49 data[NAME] = data[NAME].replace("/", "").replace("\\", "") 

50 

51 # update authors and maintainers 

52 def rm_slashes_in_person_name( 

53 person: Union[Any, Mapping[Union[Any, str], Any]], 

54 ) -> Any: 

55 if not is_mapping(person): 

56 return person 

57 

58 new_person = dict(person) 

59 if isinstance(n := person.get(NAME), str): 

60 new_person[NAME] = n.replace("/", "").replace("\\", "") 

61 

62 return new_person 

63 

64 for group in ("authors", "maintainers"): 

65 persons = data.get(group) 

66 if isinstance(persons, collections.abc.Sequence): 

67 data[group] = [rm_slashes_in_person_name(p) for p in persons] # type: ignore 

68 

69 

70DOI_PREFIXES = ("https://doi.org/", "http://dx.doi.org/") 

71 

72 

73def remove_doi_prefix(data: BioimageioYamlContent) -> None: 

74 """we unofficially accept DOIs starting with "https://doi.org/" here we remove this prefix""" 

75 cite = data.get("cite") 

76 if isinstance(cite, collections.abc.Sequence): 

77 new_cite = list(cite) 

78 for i in range(len(new_cite)): 

79 cite_entry = new_cite[i] 

80 if not isinstance(cite_entry, collections.abc.Mapping): 

81 continue 

82 

83 doi = cite_entry.get("doi") 

84 if not isinstance(doi, str): 

85 continue 

86 

87 for doi_prefix in DOI_PREFIXES: 

88 if doi.startswith(doi_prefix): 

89 doi = doi[len(doi_prefix) :] 

90 break 

91 else: 

92 continue 

93 

94 new_cite_entry = dict(cite_entry) 

95 new_cite_entry["doi"] = doi 

96 new_cite[i] = new_cite_entry 

97 

98 data["cite"] = new_cite 

99 

100 

101def remove_gh_prefix(data: BioimageioYamlContent) -> None: 

102 def rm_gh(field_name: str): 

103 authors = data.get(field_name) 

104 if not isinstance(authors, list): 

105 return 

106 

107 for a in authors: 

108 if ( 

109 isinstance(a, dict) 

110 and "github_user" in a 

111 and isinstance(a["github_user"], str) 

112 and a["github_user"].startswith("https://github.com/") 

113 ): 

114 a["github_user"] = a["github_user"][len("https://github.com/") :] 

115 

116 rm_gh("authors") 

117 rm_gh("maintainers")