Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/util/plugin_config.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import collections |
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2 |
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3 import yaml |
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4 |
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5 from galaxy.util import parse_xml |
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6 from galaxy.util.submodules import import_submodules |
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7 |
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8 |
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9 PluginConfigSource = collections.namedtuple('PluginConfigSource', ['type', 'source']) |
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10 |
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11 |
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12 def plugins_dict(module, plugin_type_identifier): |
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13 """ Walk through all classes in submodules of module and find ones labelled |
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14 with specified plugin_type_identifier and throw in a dictionary to allow |
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15 constructions from plugins by these types later on. |
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16 """ |
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17 plugin_dict = {} |
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18 |
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19 for plugin_module in import_submodules(module, ordered=True): |
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20 for clazz in __plugin_classes_in_module(plugin_module): |
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21 plugin_type = getattr(clazz, plugin_type_identifier, None) |
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22 if plugin_type: |
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23 plugin_dict[plugin_type] = clazz |
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24 |
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25 return plugin_dict |
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26 |
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27 |
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28 def load_plugins(plugins_dict, plugin_source, extra_kwds=None, plugin_type_keys=('type',), dict_to_list_key=None): |
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29 if extra_kwds is None: |
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30 extra_kwds = {} |
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31 if plugin_source.type == "xml": |
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32 return __load_plugins_from_element(plugins_dict, plugin_source.source, extra_kwds) |
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33 else: |
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34 return __load_plugins_from_dicts( |
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35 plugins_dict, |
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36 plugin_source.source, |
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37 extra_kwds, |
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38 plugin_type_keys=plugin_type_keys, |
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39 dict_to_list_key=dict_to_list_key, |
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40 ) |
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41 |
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42 |
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43 def __plugin_classes_in_module(plugin_module): |
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44 for clazz in getattr(plugin_module, "__all__", []): |
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45 try: |
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46 clazz = getattr(plugin_module, clazz) |
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47 except TypeError: |
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48 clazz = clazz |
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49 yield clazz |
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50 |
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51 |
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52 def __load_plugins_from_element(plugins_dict, plugins_element, extra_kwds): |
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53 plugins = [] |
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54 |
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55 for plugin_element in plugins_element: |
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56 plugin_type = plugin_element.tag |
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57 plugin_kwds = dict(plugin_element.items()) |
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58 plugin_kwds.update(extra_kwds) |
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59 try: |
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60 plugin_klazz = plugins_dict[plugin_type] |
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61 except KeyError: |
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62 template = "Failed to find plugin of type [%s] in available plugin types %s" |
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63 message = template % (plugin_type, str(plugins_dict.keys())) |
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64 raise Exception(message) |
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65 |
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66 plugin = plugin_klazz(**plugin_kwds) |
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67 plugins.append(plugin) |
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68 |
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69 return plugins |
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70 |
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71 |
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72 def __load_plugins_from_dicts(plugins_dict, configs, extra_kwds, plugin_type_keys, dict_to_list_key): |
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73 plugins = [] |
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74 |
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75 if isinstance(configs, dict) and dict_to_list_key is not None: |
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76 configs_as_list = [] |
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77 for key, value in configs.items(): |
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78 config = value.copy() |
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79 config[dict_to_list_key] = key |
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80 configs_as_list.append(config) |
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81 else: |
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82 configs_as_list = configs |
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83 |
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84 for config in configs_as_list: |
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85 plugin_type = None |
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86 for plugin_type_key in plugin_type_keys: |
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87 if plugin_type_key in config: |
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88 plugin_type = config[plugin_type_key] |
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89 break |
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90 assert plugin_type is not None, "Could not determine plugin type for [%s]" % config |
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91 plugin_kwds = config |
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92 plugin_kwds.update(extra_kwds) |
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93 plugin = plugins_dict[plugin_type](**plugin_kwds) |
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94 plugins.append(plugin) |
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95 |
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96 return plugins |
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97 |
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98 |
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99 def plugin_source_from_path(path): |
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100 if path.endswith(".yaml") or path.endswith(".yml") or path.endswith(".yaml.sample") or path.endswith(".yml.sample"): |
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101 return PluginConfigSource('dict', __read_yaml(path)) |
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102 else: |
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103 return PluginConfigSource('xml', parse_xml(path, remove_comments=True).getroot()) |
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104 |
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105 |
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106 def plugin_source_from_dict(as_dict): |
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107 return PluginConfigSource('dict', as_dict) |
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108 |
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109 |
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110 def __read_yaml(path): |
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111 if yaml is None: |
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112 raise ImportError("Attempting to read YAML configuration file - but PyYAML dependency unavailable.") |
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113 |
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114 with open(path, "rb") as f: |
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115 return yaml.safe_load(f) |