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comparison planemo/lib/python3.7/site-packages/bioblend/galaxy/__init__.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 """
2 A base representation of an instance of Galaxy
3 """
4 from bioblend.galaxy import (config, datasets, datatypes, folders, forms,
5 ftpfiles, genomes, groups, histories,
6 invocations, jobs, libraries, quotas, roles,
7 tool_data, tools, toolshed, users, visual,
8 workflows)
9 from bioblend.galaxy.client import Client
10 from bioblend.galaxyclient import GalaxyClient
11
12
13 class GalaxyInstance(GalaxyClient):
14 def __init__(self, url, key=None, email=None, password=None, verify=True):
15 """
16 A base representation of a connection to a Galaxy instance, identified
17 by the server URL and user credentials.
18
19 After you have created a ``GalaxyInstance`` object, access various
20 modules via the class fields. For example, to work with histories and
21 get a list of all the user's histories, the following should be done::
22
23 from bioblend import galaxy
24
25 gi = galaxy.GalaxyInstance(url='http://127.0.0.1:8000', key='your_api_key')
26
27 hl = gi.histories.get_histories()
28
29 :type url: str
30 :param url: A FQDN or IP for a given instance of Galaxy. For example:
31 http://127.0.0.1:8080 . If a Galaxy instance is served under
32 a prefix (e.g., http://127.0.0.1:8080/galaxy/), supply the
33 entire URL including the prefix (note that the prefix must
34 end with a slash). If a Galaxy instance has HTTP Basic
35 authentication with username and password, then the
36 credentials should be included in the URL, e.g.
37 http://user:pass@host:port/galaxy/
38
39 :type key: str
40 :param key: User's API key for the given instance of Galaxy, obtained
41 from the user preferences. If a key is not supplied, an
42 email address and password must be and the key will
43 automatically be created for the user.
44
45 :type email: str
46 :param email: Galaxy e-mail address corresponding to the user.
47 Ignored if key is supplied directly.
48
49 :type password: str
50 :param password: Password of Galaxy account corresponding to the above
51 e-mail address. Ignored if key is supplied directly.
52
53 :param verify: Whether to verify the server's TLS certificate
54 :type verify: bool
55 """
56 super().__init__(url, key, email, password, verify=verify)
57 self.libraries = libraries.LibraryClient(self)
58 self.histories = histories.HistoryClient(self)
59 self.workflows = workflows.WorkflowClient(self)
60 self.invocations = invocations.InvocationClient(self)
61 self.datasets = datasets.DatasetClient(self)
62 self.users = users.UserClient(self)
63 self.genomes = genomes.GenomeClient(self)
64 self.tools = tools.ToolClient(self)
65 self.toolshed = toolshed.ToolShedClient(self)
66 self.toolShed = self.toolshed # historical alias
67 self.config = config.ConfigClient(self)
68 self.visual = visual.VisualClient(self)
69 self.quotas = quotas.QuotaClient(self)
70 self.groups = groups.GroupsClient(self)
71 self.roles = roles.RolesClient(self)
72 self.datatypes = datatypes.DatatypesClient(self)
73 self.jobs = jobs.JobsClient(self)
74 self.forms = forms.FormsClient(self)
75 self.ftpfiles = ftpfiles.FTPFilesClient(self)
76 self.tool_data = tool_data.ToolDataClient(self)
77 self.folders = folders.FoldersClient(self)
78
79 @property
80 def max_get_attempts(self):
81 return Client.max_get_retries()
82
83 @max_get_attempts.setter
84 def max_get_attempts(self, v):
85 Client.set_max_get_retries(v)
86
87 @property
88 def get_retry_delay(self):
89 return Client.get_retry_delay()
90
91 @get_retry_delay.setter
92 def get_retry_delay(self, v):
93 Client.set_get_retry_delay(v)
94
95 def __repr__(self):
96 """
97 A nicer representation of this GalaxyInstance object
98 """
99 return "GalaxyInstance object for Galaxy at {0}".format(self.base_url)