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annotate planemo/lib/python3.7/site-packages/bioblend/toolshed/__init__.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
parents d30785e31577
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1 """
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2 A base representation of an instance of Tool Shed
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3 """
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4 from bioblend.galaxyclient import GalaxyClient
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5 from bioblend.toolshed import categories, repositories, tools
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8 class ToolShedInstance(GalaxyClient):
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9 def __init__(self, url, key=None, email=None, password=None, verify=True):
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10 """
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11 A base representation of a connection to a ToolShed instance, identified
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12 by the ToolShed URL and user credentials.
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14 After you have created a ``ToolShedInstance`` object, access various
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15 modules via the class fields. For example, to work with repositories and
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16 get a list of all public repositories, the following should be done::
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17
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18 from bioblend import toolshed
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20 ts = toolshed.ToolShedInstance(url='https://testtoolshed.g2.bx.psu.edu')
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22 rl = ts.repositories.get_repositories()
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23
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24 tools = ts.tools.search_tools('fastq')
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25
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26 :type url: str
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27 :param url: A FQDN or IP for a given instance of ToolShed. For example:
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28 https://testtoolshed.g2.bx.psu.edu . If a ToolShed instance
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29 is served under a prefix (e.g.
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30 http://127.0.0.1:8080/toolshed/), supply the entire URL
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31 including the prefix (note that the prefix must end with a
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32 slash).
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33
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34 :type key: str
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35 :param key: If required, user's API key for the given instance of ToolShed,
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36 obtained from the user preferences.
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37
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38 :type email: str
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39 :param email: ToolShed e-mail address corresponding to the user.
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40 Ignored if key is supplied directly.
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41
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42 :type password: str
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43 :param password: Password of ToolShed account corresponding to the above
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44 e-mail address. Ignored if key is supplied directly.
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45
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46 :param verify: Whether to verify the server's TLS certificate
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47 :type verify: bool
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48 """
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49 super().__init__(url, key, email, password, verify=verify)
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50 self.categories = categories.ToolShedCategoryClient(self)
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51 self.repositories = repositories.ToolShedRepositoryClient(self)
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52 self.tools = tools.ToolShedToolClient(self)