Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/galaxy/util/plugin_config.py @ 2:6af9afd405e9 draft

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
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1 import collections
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2 from xml.etree import ElementTree
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3
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4 try:
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5 import yaml
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6 except ImportError:
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7 yaml = None
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8
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9 from galaxy.util.submodules import import_submodules
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10
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11
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12 PluginConfigSource = collections.namedtuple('PluginConfigSource', ['type', 'source'])
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14
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15 def plugins_dict(module, plugin_type_identifier):
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16 """ Walk through all classes in submodules of module and find ones labelled
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17 with specified plugin_type_identifier and throw in a dictionary to allow
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18 constructions from plugins by these types later on.
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19 """
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20 plugin_dict = {}
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21
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22 for plugin_module in import_submodules(module, ordered=True):
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23 # FIXME: this is not how one is suppose to use __all__ why did you do
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24 # this past John?
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25 for clazz in getattr(plugin_module, "__all__", []):
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26 try:
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27 clazz = getattr(plugin_module, clazz)
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28 except TypeError:
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29 clazz = clazz
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30 plugin_type = getattr(clazz, plugin_type_identifier, None)
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31 if plugin_type:
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32 plugin_dict[plugin_type] = clazz
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33
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34 return plugin_dict
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35
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36
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37 def load_plugins(plugins_dict, plugin_source, extra_kwds=None, plugin_type_keys=('type',)):
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38 if extra_kwds is None:
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39 extra_kwds = {}
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40 if plugin_source.type == "xml":
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41 return __load_plugins_from_element(plugins_dict, plugin_source.source, extra_kwds)
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42 else:
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43 return __load_plugins_from_dicts(plugins_dict, plugin_source.source, extra_kwds, plugin_type_keys=plugin_type_keys)
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44
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45
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46 def __load_plugins_from_element(plugins_dict, plugins_element, extra_kwds):
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47 plugins = []
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48
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49 for plugin_element in plugins_element:
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50 plugin_type = plugin_element.tag
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51 plugin_kwds = dict(plugin_element.items())
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52 plugin_kwds.update(extra_kwds)
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53 try:
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54 plugin_klazz = plugins_dict[plugin_type]
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55 except KeyError:
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56 template = "Failed to find plugin of type [%s] in available plugin types %s"
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57 message = template % (plugin_type, str(plugins_dict.keys()))
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58 raise Exception(message)
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59
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60 plugin = plugin_klazz(**plugin_kwds)
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61 plugins.append(plugin)
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62
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63 return plugins
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64
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65
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66 def __load_plugins_from_dicts(plugins_dict, configs, extra_kwds, plugin_type_keys):
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67 plugins = []
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68
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69 for config in configs:
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70 plugin_type = None
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71 for plugin_type_key in plugin_type_keys:
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72 if plugin_type_key in config:
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73 plugin_type = config[plugin_type_key]
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74 break
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75 assert plugin_type is not None, "Could not determine plugin type for [%s]" % config
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76 plugin_kwds = config
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77 plugin_kwds.update(extra_kwds)
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78 plugin = plugins_dict[plugin_type](**plugin_kwds)
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79 plugins.append(plugin)
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80
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81 return plugins
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82
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83
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84 def plugin_source_from_path(path):
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85 if path.endswith(".yaml") or path.endswith(".yml") or path.endswith(".yaml.sample") or path.endswith(".yml.sample"):
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86 return PluginConfigSource('dict', __read_yaml(path))
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87 else:
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88 return PluginConfigSource('xml', ElementTree.parse(path).getroot())
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89
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90
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91 def __read_yaml(path):
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92 if yaml is None:
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93 raise ImportError("Attempting to read YAML configuration file - but PyYAML dependency unavailable.")
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94
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95 with open(path, "rb") as f:
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96 return yaml.safe_load(f)