Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/ephemeris/__init__.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1
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2 # -*- coding: utf-8 -*-
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3
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4 import yaml
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5 from bioblend import galaxy
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6
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7 __version__ = '0.10.5'
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8
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9 PROJECT_NAME = "ephemeris"
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10 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
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11 PROJECT_URL = "https://github.com/galaxyproject/ephemeris"
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12 PROJECT_AUTHOR = 'Galaxy Project and Community'
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13 PROJECT_EMAIL = 'jmchilton@gmail.com'
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14 RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
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15 PROJECT_USERAME, PROJECT_NAME
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16 )
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17
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18
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19 def check_url(url, log=None):
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20 if not url.startswith('http'):
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21 if log:
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22 log.warning('URL should start with http:// or https://. https:// chosen by default.')
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23 url = 'https://' + url
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24 return url
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25
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26
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27 def get_galaxy_connection(args, file=None, log=None, login_required=True):
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28 """
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29 Return a Galaxy connection, given a user or an API key.
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30 If not given gets the arguments from the file.
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31 If either is missing raise ValueError.
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32 """
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33 if file:
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34 file_content = load_yaml_file(file)
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35 else:
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36 file_content = dict()
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37
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38 url = args.galaxy or file_content.get('galaxy_instance')
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39 galaxy_url = check_url(url, log)
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40 api_key = args.api_key or file_content.get('api_key')
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41
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42 if args.user and args.password:
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43 return galaxy.GalaxyInstance(url=galaxy_url, email=args.user, password=args.password)
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44 elif api_key:
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45 return galaxy.GalaxyInstance(url=galaxy_url, key=api_key)
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46 elif not login_required:
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47 return galaxy.GalaxyInstance(url=galaxy_url)
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48 else:
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49 raise ValueError("Missing api key or user & password combination, in order to make a galaxy connection.")
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51
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52 def load_yaml_file(filename):
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53 """
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54 Load YAML from the `tool_list_file` and return a dict with the content.
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55 """
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56 with open(filename, 'r') as f:
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57 dictionary = yaml.safe_load(f)
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58 return dictionary
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59
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60
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61 def dump_to_yaml_file(content, file_name):
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62 """
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63 Dump YAML-compatible `content` to `file_name`.
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64 """
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65 with open(file_name, 'w') as f:
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66 yaml.dump(content, f, default_flow_style=False)