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