1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
|
"""
Contains possible interactions with the Galaxy library folders
"""
from typing import (
Any,
Dict,
List,
Optional,
TYPE_CHECKING,
Union,
)
from typing_extensions import Literal
from bioblend.galaxy.client import Client
if TYPE_CHECKING:
from bioblend.galaxy import GalaxyInstance
class FoldersClient(Client):
module = "folders"
def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
super().__init__(galaxy_instance)
def create_folder(self, parent_folder_id: str, name: str, description: Optional[str] = None) -> Dict[str, Any]:
"""
Create a folder.
:type parent_folder_id: str
:param parent_folder_id: Folder's description
:type name: str
:param name: name of the new folder
:type description: str
:param description: folder's description
:rtype: dict
:return: details of the updated folder
"""
payload: Dict[str, str] = {"name": name}
if description:
payload["description"] = description
return self._post(payload=payload, id=parent_folder_id)
def show_folder(self, folder_id: str, contents: bool = False) -> Dict[str, Any]:
"""
Display information about a folder.
:type folder_id: str
:param folder_id: the folder's encoded id, prefixed by 'F'
:type contents: bool
:param contents: True to get the contents of the folder, rather
than just the folder details.
:rtype: dict
:return: dictionary including details of the folder
"""
return self._get(id=folder_id, contents=contents)
def delete_folder(self, folder_id: str, undelete: bool = False) -> Dict[str, Any]:
"""
Marks the folder with the given ``id`` as `deleted` (or removes the
`deleted` mark if the `undelete` param is True).
:type folder_id: str
:param folder_id: the folder's encoded id, prefixed by 'F'
:type undelete: bool
:param undelete: If set to True, the folder will be undeleted
(i.e. the `deleted` mark will be removed)
:return: detailed folder information
:rtype: dict
"""
payload = {"undelete": undelete}
return self._delete(payload=payload, id=folder_id)
def update_folder(self, folder_id: str, name: str, description: Optional[str] = None) -> Dict[str, Any]:
"""
Update folder information.
:type folder_id: str
:param folder_id: the folder's encoded id, prefixed by 'F'
:type name: str
:param name: name of the new folder
:type description: str
:param description: folder's description
:rtype: dict
:return: details of the updated folder
"""
payload = {"name": name}
if description:
payload["description"] = description
return self._put(payload=payload, id=folder_id)
def get_permissions(self, folder_id: str, scope: Literal["current", "available"] = "current") -> Dict[str, Any]:
"""
Get the permissions of a folder.
:type folder_id: str
:param folder_id: the folder's encoded id, prefixed by 'F'
:type scope: str
:param scope: scope of permissions, either 'current' or 'available'
:rtype: dict
:return: dictionary including details of the folder permissions
"""
url = self._make_url(folder_id) + "/permissions"
return self._get(url=url)
def set_permissions(
self,
folder_id: str,
action: Literal["set_permissions"] = "set_permissions",
add_ids: Optional[List[str]] = None,
manage_ids: Optional[List[str]] = None,
modify_ids: Optional[List[str]] = None,
) -> Dict[str, Any]:
"""
Set the permissions of a folder.
:type folder_id: str
:param folder_id: the folder's encoded id, prefixed by 'F'
:type action: str
:param action: action to execute, only "set_permissions" is supported.
:type add_ids: list of str
:param add_ids: list of role IDs which can add datasets to the folder
:type manage_ids: list of str
:param manage_ids: list of role IDs which can manage datasets in the folder
:type modify_ids: list of str
:param modify_ids: list of role IDs which can modify datasets in the folder
:rtype: dict
:return: dictionary including details of the folder
"""
url = self._make_url(folder_id) + "/permissions"
payload: Dict[str, Union[str, List[str]]] = {"action": action}
if add_ids:
payload["add_ids[]"] = add_ids
if manage_ids:
payload["manage_ids[]"] = manage_ids
if modify_ids:
payload["modify_ids[]"] = modify_ids
return self._post(url=url, payload=payload)
|
