Source code for qiime2.sdk.plugin_manager

# ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, QIIME 2 development team.
# Distributed under the terms of the Modified BSD License.
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------

import collections
import os
import pkg_resources
import enum

import qiime2.core.type
from qiime2.core.format import FormatBase
from qiime2.plugin.model import SingleFileDirectoryFormatBase
from qiime2.core.validate import ValidationObject
from qiime2.sdk.util import parse_type
from qiime2.core.type import is_semantic_type

class GetFormatFilters(enum.Flag):

[docs] class UninitializedPluginManagerError(Exception): pass
[docs] class PluginManager: entry_point_group = 'qiime2.plugins' __instance = None @classmethod def iter_entry_points(cls): """Yield QIIME 2 plugin entry points. If the QIIMETEST environment variable is set, only the framework testing plugin entry point (`dummy-plugin`) will be yielded. Otherwise, all available plugin entry points (excluding `dummy-plugin`) will be yielded. """ for entry_point in pkg_resources.iter_entry_points( group=cls.entry_point_group): if 'QIIMETEST' in os.environ: if in ('dummy-plugin', 'other-plugin'): yield entry_point else: if not in ('dummy-plugin', 'other-plugin'): yield entry_point @classmethod def reuse_existing(cls): if cls.__instance is not None: return cls.__instance raise UninitializedPluginManagerError # This class is a singleton as it is slow to create, represents the # state of a qiime2 installation, and is needed *everywhere* def __new__(cls, add_plugins=True): if cls.__instance is None: self = super().__new__(cls) cls.__instance = self try: self._init(add_plugins=add_plugins) except Exception: cls.__instance = None raise else: if add_plugins is False: raise ValueError( 'PluginManager singleton already exists, cannot change ' 'current value for `add_plugins`.') return cls.__instance def forget_singleton(self): """Allows later instatiation of PluginManager to produce new object This is done by clearing class member which saves the instance. This will NOT invalidate or remove the object this method is called on. """ self.__class__.__instance = None def _init(self, add_plugins): self.plugins = {} self.type_fragments = {} self._plugin_by_id = {} self.semantic_types = {} self.transformers = collections.defaultdict(dict) self._reverse_transformers = collections.defaultdict(dict) self.formats = {} self.views = {} self.artifact_classes = {} self._ff_to_sfdf = {} self.validators = {} if add_plugins: # These are all dependent loops, each requires the loop above it to # be completed. for entry_point in self.iter_entry_points(): project_name = entry_point.dist.project_name package = entry_point.module_name.split('.')[0] plugin = entry_point.load() self.add_plugin(plugin, package, project_name, consistency_check=False) self._consistency_check() def _consistency_check(self): for semantic_type, validator_obj in self.validators.items(): validator_obj.assert_transformation_available( self.get_directory_format(semantic_type)) def add_plugin(self, plugin, package=None, project_name=None, consistency_check=True): self.plugins[] = plugin self._plugin_by_id[] = plugin if plugin.package is None: plugin.package = package if plugin.project_name is None: plugin.project_name = project_name # validate _after_ applying arguments if plugin.package is None: raise ValueError( 'No value specified for package - must provide a value for ' '`package` or set `plugin.package`.') if plugin.project_name is None: raise ValueError( 'No value specified for project_name - must proved a value ' 'for `project_name` or set `plugin.project_name`.') self._integrate_plugin(plugin) plugin.freeze() if consistency_check is True: return self._consistency_check() def get_plugin(self, *, id=None, name=None): if id is None and name is None: raise ValueError("No plugin requested.") elif id is not None: try: return self._plugin_by_id[id] except KeyError: raise KeyError('No plugin currently registered ' 'with id: "%s".' % (id,)) else: try: return self.plugins[name] except KeyError: raise KeyError('No plugin currently registered ' 'with name: "%s".' % (name,)) def _integrate_plugin(self, plugin): for type_name, type_record in plugin.type_fragments.items(): if type_name in self.type_fragments: conflicting_type_record = \ self.type_fragments[type_name] raise ValueError("Duplicate semantic type (%r) defined in" " plugins: %r and %r" % (type_name,, self.type_fragments[type_name] = type_record for (input, output), transformer_record in plugin.transformers.items(): if output in self.transformers[input]: raise ValueError("Transformer from %r to %r already exists." % (input, output)) self.transformers[input][output] = transformer_record self._reverse_transformers[output][input] = transformer_record for name, record in plugin.views.items(): if name in self.views: raise NameError( "Duplicate view registration (%r) defined in plugins: %r" " and %r" % (name,, self.formats[name] ) self.views[name] = record for name, record in plugin.formats.items(): fmt = record.format if issubclass( fmt, qiime2.plugin.model.SingleFileDirectoryFormatBase): if fmt.file.format in self._ff_to_sfdf.keys(): self._ff_to_sfdf[fmt.file.format].add(fmt) else: self._ff_to_sfdf[fmt.file.format] = {fmt} # TODO: remove this when `sniff` is removed if hasattr(fmt, 'sniff') and hasattr(fmt, '_validate_'): raise RuntimeError( 'Format %r registered in plugin %r defines sniff and' '_validate_ methods - only one is permitted.' % (name, ) self.formats[name] = record for name, record in plugin.artifact_classes.items(): if name in self.artifact_classes: raise NameError( "Duplicate artifact class registration (%r) defined in " "plugins %r and %r." % (name,, self.artifact_classes[name] ) else: self.artifact_classes[name] = record for semantic_type, validation_object in plugin.validators.items(): if semantic_type not in self.validators: self.validators[semantic_type] = \ ValidationObject(semantic_type) self.validators[semantic_type].add_validation_object( validation_object) def get_semantic_types(self): result = {} for plugin in self.plugins.values(): result.update(plugin.artifact_classes) return result # TODO: Should plugin loading be transactional? i.e. if there's # something wrong, the entire plugin fails to load any piece, like a # databases rollback/commit def get_formats(self, *, filter=None, semantic_type=None): """ get_formats(self, *, filter=None, semantic_type=None) filter : enum | "IMPORTABLE" | "EXPORTABLE" filter is an enum integer that will be used to determine user input to output specified formats semantic_type : TypeExpression | String The semantic type is used to filter the formats associated with that specific semantic type This method will filter out the formats using the filter provided by the user and the semantic type. The return is a dictionary of filtered formats keyed on their string names. """ filter_map = {"IMPORTABLE": GetFormatFilters.IMPORTABLE, "EXPORTABLE": GetFormatFilters.EXPORTABLE} if filter is not None and not isinstance(filter, GetFormatFilters) \ and filter not in filter_map: raise ValueError( f"The provided format filter {filter} is not valid.") if isinstance(filter, str): filter = filter_map[filter] if semantic_type is None: formats = set(f.format for f in self.artifact_classes.values()) else: formats = set() if isinstance(semantic_type, str): semantic_type = parse_type(semantic_type, "semantic") if is_semantic_type(semantic_type): for artifact_class in self.artifact_classes.values(): if semantic_type <= artifact_class.semantic_type: formats.add(artifact_class.format) break if not formats: raise ValueError("No formats associated with the type " f"{semantic_type}.") else: raise ValueError(f"{semantic_type} is not a valid semantic " "type.") transformable_formats = set(formats) if filter is None or GetFormatFilters.IMPORTABLE in filter: transformable_formats.update( self._get_formats_helper(formats, self._reverse_transformers)) if filter is None or GetFormatFilters.EXPORTABLE in filter: transformable_formats.update( self._get_formats_helper(formats, self.transformers)) result_formats = {} for format_ in transformable_formats: format_ = format_.__name__ result_formats[format_] = self.formats[format_] return result_formats def _get_formats_helper(self, formats, transformer_dict): """ _get_formats_helper(self, formats, transformer_dict) formats : Set[DirectoryFormat] We are finding all formats that are one transformer away from formats in this set tranformer_dict : Dict[ str, Dict[str, TransformerReord]] The dictionary of transformers allows the method to get formats that are transformable from the given format This method creates a set utilizing the transformers dictionary and the formats set to get related formats for a specific format. """ query_set = set(formats) for format_ in formats: if issubclass(format_, SingleFileDirectoryFormatBase): if format_.file.format.__name__ in self.formats: query_set.add(format_.file.format) result_formats = set(query_set) for format_ in query_set: for transformed_format in transformer_dict[format_]: if issubclass(transformed_format, FormatBase): result_formats.add(transformed_format) if issubclass(transformed_format, SingleFileDirectoryFormatBase): result_formats.add(transformed_format.file.format) if transformed_format in self._ff_to_sfdf: result_formats.update( self._ff_to_sfdf[transformed_format]) return result_formats @property def type_formats(self): # self.type_formats was replaced with self.artifact_classes - this # property provides backward compatibility return list(self.artifact_classes.values()) @property def importable_formats(self): """Formats that are importable. A format is importable in a QIIME 2 deployment if it can be transformed into at least one of the canonical semantic type formats. """ return self.get_formats(filter=GetFormatFilters.IMPORTABLE) @property def exportable_formats(self): """Formats that are exportable. A format is exportable in a QIIME 2 deployment if it can be transformed from at least one of the canonical semantic type formats. """ return self.get_formats(filter=GetFormatFilters.EXPORTABLE) @property def importable_types(self): """Return set of concrete semantic types that are importable. A concrete semantic type is importable if it has an associated directory format. """ return self.get_semantic_types() def get_directory_format(self, semantic_type): if not qiime2.core.type.is_semantic_type(semantic_type): raise TypeError( "Must provide a semantic type via `semantic_type`, not %r" % semantic_type) # TODO: ideally we could just lookup semantic_type in # self.artifact_classes but properties get in the way. Is there a way # to strip properties so this could be simplified to return # self.artifact_classes[semantic_type] while catching a KeyError? for artifact_class_record in self.artifact_classes.values(): if semantic_type <= artifact_class_record.semantic_type: return artifact_class_record.format # TODO: We need a good way to tell if a semantic type is registered but # does not have a directory format. The previous error was causing a # lot of confusion. # # Reference: raise TypeError( "Semantic type %r is invalid, either because it doesn't have a " "compatible directory format, or because it's not registered." % semantic_type)