Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/ephemeris/install_tool_deps.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 #!/usr/bin/env python
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2 '''Tool to install tool dependencies on a Galaxy instance.'''
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3 import argparse
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4 import logging as log
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5 import os
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6 import xml.etree.ElementTree as ET
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7
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8 import yaml
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9 from bioblend import ConnectionError as ConnErr
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10 from bioblend.galaxy.tools import ToolClient
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11
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12 from ephemeris import get_galaxy_connection
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13 from ephemeris.common_parser import get_common_args
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14
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15 timeout_codes = (408, 502, 504)
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16
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17
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18 def _parser():
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19 parent = get_common_args()
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20 parser = argparse.ArgumentParser(parents=[parent])
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21 parser.add_argument("-t", "--tool", help='Path to a tool file, tool_conf file, or yaml file containing a sequence of tool ids', nargs='*')
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22 parser.add_argument("-i", "--id", help='Space-separated list of tool ids', nargs='*')
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23
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24 return parser
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25
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26
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27 def _install(tool_client, tool_id):
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28 try:
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29 tool_client.install_dependencies(tool_id)
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30 except ConnErr as e:
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31 if e.status_code in timeout_codes:
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32 log.warning(e.body)
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33 else:
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34 raise
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35
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36
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37 def main():
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38 """
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39 This script uses bioblend to trigger dependencies installations for the provided tools
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40 """
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41 args = _parser().parse_args()
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42 gi = get_galaxy_connection(args)
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43 tool_client = ToolClient(gi)
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44
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45 if args.verbose:
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46 log.basicConfig(level=log.DEBUG)
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47
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48 if args.tool:
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49 for tool_conf_path in args.tool: # type: str
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50 _, ext = os.path.splitext(tool_conf_path)
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51 if ext == '.xml':
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52 log.info("tool_conf xml found, parsing..")
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53 # install all
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54 root = ET.ElementTree(file=tool_conf_path).getroot()
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55 if root.tag == "toolbox":
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56 # Install all from tool_conf
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57 tool_path = root.get('tool_path', '')
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58 tool_path = tool_path.replace('${tool_conf_dir}', os.path.abspath(os.path.dirname(tool_conf_path)))
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59 if tool_path:
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60 log.info("Searching for tools relative to " + tool_path)
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61 tools = root.findall(".//tool[@file]")
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62 if len(tools) == 0:
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63 log.warning("No tools found in tool_conf")
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64 continue
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65
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66 for tool in tools:
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67 tool_id = ET.ElementTree(file=os.path.join(tool_path, tool.get('file'))).getroot().get('id')
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68 if tool_id:
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69 log.info("Installing tool dependencies for " + tool_id + " from: " + tool.get('file'))
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70 _install(tool_client, tool_id)
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71 elif root.tag == "tool" and root.get('id'):
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72 # Install from single tool file
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73 log.info("Tool xml found. Installing " + root.get('id') + " dependencies..")
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74 _install(tool_client, root.get('id'))
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75 else:
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76 log.info("YAML tool list found, parsing..")
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77 with open(tool_conf_path) as fh:
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78 tool_ids = yaml.safe_load(fh)
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79 for tool_id in tool_ids:
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80 # Install from yaml file
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81 log.info("Installing " + tool_id + " dependencies..")
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82 _install(tool_client, tool_id)
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83
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84 if args.id:
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85 for tool_id in args.id: # type: str
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86 log.info("Installing " + tool_id + " dependencies..")
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87 _install(tool_client, tool_id.strip())
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88
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89
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90 if __name__ == '__main__':
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91 main()