Source code for bio2bel.manager.namespace_manager

# -*- coding: utf-8 -*-

"""Provide abstractions over BEL namespace generation procedures."""

import json
import logging
import os
import time
from abc import ABC, abstractmethod
from typing import Iterable, List, Mapping, Optional, Set, TextIO

import click
from sqlalchemy.ext.declarative import DeclarativeMeta
from tqdm import tqdm

from bel_resources import write_annotation, write_namespace
from pybel import BELGraph
from pybel.manager.models import Base, Namespace, NamespaceEntry
from .cli_manager import CliMixin
from .connection_manager import ConnectionManager
from ..constants import directory_option
from ..utils import get_namespace_hash

__all__ = [
    'Bio2BELMissingNamespaceModelError',
    'BELNamespaceManagerMixin',
]

logger = logging.getLogger(__name__)


class Bio2BELMissingNamespaceModelError(TypeError):
    """Raised when the namespace_model class variable is not defined."""


[docs]class BELNamespaceManagerMixin(ABC, ConnectionManager, CliMixin): """A mixin for generating a BEL namespace file and uploading it to the PyBEL database. First, you'll have to make sure that :mod:`pybel` is installed. This can be done with pip like: .. code-block:: bash $ pip install pybel To use this mixin, you need to properly implement the AbstractManager, and add additional class variables and functions. ``namespace_model``: The SQLAlchemy class that represents the entity to serialize into the namespace .. code-block:: python >>> from bio2bel import AbstractManager >>> from bio2bel.namespace_manager import NamespaceManagerMixin >>> from .models import HumanGene >>> >>> class MyManager(AbstractManager, NamespaceManagerMixin): ... module_name = 'hgnc' ... ... ... namespace_model = HumanGene Several fields from Identifiers.org should be populated, including: 1. ``identifiers_recommended`` 2. ``identifiers_pattern`` 3. ``identifiers_miriam`` 4. ``identifiers_namespace`` 5. ``identifiers_url`` .. code-block:: python >>> from bio2bel import AbstractManager >>> from bio2bel.namespace_manager import NamespaceManagerMixin >>> from .models import HumanGene >>> >>> class MyManager(AbstractManager, NamespaceManagerMixin): ... module_name = 'hgnc' ... ... ... namespace_model = HumanGene ... identifiers_recommended = 'HGNC' ... identifiers_pattern = '...' ... identifiers_miriam = 'MIR:00000080' ... identifiers_namespace = 'hgnc' ... identifiers_url = 'http://identifiers.org/hgnc/' Two methods need to be implemented. First, the static method ``_get_identifier`` should take in the namespace model and give back the database identifier. for us, this is easy, since the HumanGene class has an attribute called ``hgnc_id``. Perhaps in the future, we will enfoce the convention that the namespace model should have a field called <module name>_id, but having this method gives lots of flexibility. This is also a good place to add more specific type annotations (not yet tested with MyPy). .. code-block:: python >>> from bio2bel import AbstractManager >>> from bio2bel.namespace_manager import NamespaceManagerMixin >>> from .models import HumanGene >>> >>> class MyManager(AbstractManager, NamespaceManagerMixin): ... module_name = 'hgnc' ... ... ... namespace_model = HumanGene ... identifiers_recommended = 'HGNC' ... identifiers_pattern = '...' ... identifiers_miriam = 'MIR:00000080' ... identifiers_namespace = 'hgnc' ... identifiers_url = 'http://identifiers.org/hgnc/' ... ... @staticmethod ... def _get_identifier(model: HumanGene) -> str: ... return model.hgnc_id Last, we must implement the method ``_create_namespace_entry_from_model``, which encodes the logic of building a :class:`pybel.manager.models.NamespaceEntry` from the Bio2BEL repository's namespace model. For a repository like ChEBI, this is very simple, but for HGNC there is reason to add additional logic to get the proper encodings. .. code-block:: python >>> from bio2bel import AbstractManager >>> from bio2bel.namespace_manager import NamespaceManagerMixin >>> from pybel.manager.models import Namespace, NamespaceEntry >>> from .models import HumanGene >>> >>> class MyManager(AbstractManager, NamespaceManagerMixin): ... module_name = 'hgnc' ... ... ... namespace_model = HumanGene ... identifiers_recommended = 'HGNC' ... identifiers_pattern = '...' ... identifiers_miriam = 'MIR:00000080' ... identifiers_namespace = 'hgnc' ... identifiers_url = 'http://identifiers.org/hgnc/' ... ... @staticmethod ... def _get_identifier(model: HumanGene) -> str: ... return model.hgnc_id ... ... def _create_namespace_entry_from_model(self, model: HumanGene, namespace: Namespace) -> NamespaceEntry: ... return NamespaceEntry( ... encoding=encodings.get(model.locus_type, 'GRP'), ... identifier=model.hgnc_id, ... name=model.hgnc_symbol, ... namespace=namespace, ... ) """ namespace_model: DeclarativeMeta #: Can be set to False for namespaces that don't have labels has_names: bool = True is_namespace: bool = True is_annotation: bool = False identifiers_recommended = None identifiers_pattern = None identifiers_miriam = None identifiers_namespace = None identifiers_url = None def __init__(self, *args, **kwargs): # noqa: D107 if not hasattr(self, 'namespace_model'): raise Bio2BELMissingNamespaceModelError('Class variable `namespace_model` was not defined.') super().__init__(*args, **kwargs) # Ensure that the PyBEL database is ready to go Base.metadata.create_all(self.engine, checkfirst=True) @abstractmethod def _create_namespace_entry_from_model(self, model, namespace: Namespace) -> NamespaceEntry: """Create a PyBEL NamespaceEntry model from a Bio2BEL model. :param model: The model to convert :param namespace: The PyBEL namespace to add to """ @classmethod def _get_identifier(cls, model) -> str: """Extract the identifier from an instance of namespace_model. :param model: The model to convert """ return getattr(model, f'{cls.module_name}_id') @staticmethod def _get_encoding(model) -> str: """Extract the BEL encoding from an instance of a namespace_model. :param model: The model to convert """ return model.bel_encoding @staticmethod def _get_name(model) -> str: """Extract the name from an instance of namespace_model. :param model: The model to convert """ return model.name def _iterate_namespace_models(self, **kwargs) -> Iterable: """Return an iterator over the models to be converted to the namespace.""" return tqdm( self._get_query(self.namespace_model), total=self._count_model(self.namespace_model), **kwargs ) @classmethod def _get_namespace_name(cls) -> str: """Get the nicely formatted name of this namespace.""" return cls.identifiers_recommended or cls.module_name @classmethod def _get_namespace_keyword(cls) -> str: """Get the keyword to use as the reference BEL namespace.""" return cls.identifiers_namespace or cls.module_name.upper() @classmethod def _get_namespace_url(cls) -> str: """Get the URL to use as the reference BEL namespace.""" return cls.identifiers_url or f'_{cls.module_name.upper()}' def _get_default_namespace(self) -> Optional[Namespace]: """Get the reference BEL namespace if it exists.""" return self._get_query(Namespace).filter(Namespace.url == self._get_namespace_url()).one_or_none() def _get_namespace_entries(self, namespace) -> List: return [ namespace_entry for namespace_entry in ( self._create_namespace_entry_from_model(model, namespace) for model in self._iterate_namespace_models() ) if namespace_entry is not None ] def _make_namespace(self) -> Namespace: """Make a namespace.""" namespace = Namespace( name=self._get_namespace_name(), keyword=self._get_namespace_keyword(), url=self._get_namespace_url(), version=str(time.asctime()), ) self.session.add(namespace) entries = self._get_namespace_entries(namespace) self.session.add_all(entries) t = time.time() logger.info('committing models') self.session.commit() logger.info('committed models in %.2f seconds', time.time() - t) return namespace @staticmethod def _get_old_entry_identifiers(namespace: Namespace) -> Set[NamespaceEntry]: """Convert a PyBEL generalized namespace entries to a set. Default to using the identifier, but can be overridden to use the name instead. >>> {term.identifier for term in namespace.entries} """ return {term.identifier for term in namespace.entries} def _update_namespace(self, namespace: Namespace) -> None: """Update an already-created namespace. Note: Only call this if namespace won't be none! """ old_entry_identifiers = self._get_old_entry_identifiers(namespace) new_count = 0 skip_count = 0 for model in self._iterate_namespace_models(): if self._get_identifier(model) in old_entry_identifiers: continue entry = self._create_namespace_entry_from_model(model, namespace=namespace) if entry is None or entry.name is None: skip_count += 1 continue new_count += 1 self.session.add(entry) t = time.time() logger.info('got %d new entries. skipped %d entries missing names. committing models', new_count, skip_count) self.session.commit() logger.info('committed models in %.2f seconds', time.time() - t)
[docs] def add_namespace_to_graph(self, graph: BELGraph) -> Namespace: """Add this manager's namespace to the graph.""" namespace = self.upload_bel_namespace() graph.namespace_url[namespace.keyword] = namespace.url # Add this manager as an annotation, too self._add_annotation_to_graph(graph) return namespace
def _add_annotation_to_graph(self, graph: BELGraph) -> None: """Add this manager as an annotation to the graph.""" if 'bio2bel' not in graph.annotation_list: graph.annotation_list['bio2bel'] = set() graph.annotation_list['bio2bel'].add(self.module_name)
[docs] def upload_bel_namespace(self, update: bool = False) -> Namespace: """Upload the namespace to the PyBEL database. :param update: Should the namespace be updated first? """ if not self.is_populated(): self.populate() namespace = self._get_default_namespace() if namespace is None: logger.info('making namespace for %s', self._get_namespace_name()) return self._make_namespace() if update: self._update_namespace(namespace) return namespace
[docs] def drop_bel_namespace(self) -> Optional[Namespace]: """Remove the default namespace if it exists.""" namespace = self._get_default_namespace() if namespace is not None: for entry in tqdm(namespace.entries, desc=f'deleting entries in {self._get_namespace_name()}'): self.session.delete(entry) self.session.delete(namespace) logger.info('committing deletions') self.session.commit() return namespace
[docs] def write_bel_namespace(self, file: TextIO, use_names: bool = False) -> None: """Write as a BEL namespace file.""" if not self.is_populated(): self.populate() if use_names and not self.has_names: raise ValueError values = ( self._get_namespace_name_to_encoding(desc='writing names') if use_names else self._get_namespace_identifier_to_encoding(desc='writing identifiers') ) write_namespace( namespace_name=self._get_namespace_name(), namespace_keyword=self._get_namespace_keyword(), namespace_query_url=self.identifiers_url, values=values, file=file, )
[docs] def write_bel_annotation(self, file: TextIO) -> None: """Write as a BEL annotation file.""" if not self.is_populated(): self.populate() values = self._get_namespace_name_to_encoding(desc='writing names') write_annotation( keyword=self._get_namespace_keyword(), citation_name=self._get_namespace_name(), description='', values=values, file=file, )
[docs] def write_bel_namespace_mappings(self, file: TextIO, **kwargs) -> None: """Write a BEL namespace mapping file.""" json.dump(self._get_namespace_identifier_to_name(**kwargs), file, indent=2, sort_keys=True)
[docs] def write_directory(self, directory: str) -> bool: """Write a BEL namespace for identifiers, names, name hash, and mappings to the given directory.""" current_md5_hash = self.get_namespace_hash() md5_hash_path = os.path.join(directory, f'{self.module_name}.belns.md5') if not os.path.exists(md5_hash_path): old_md5_hash = None else: with open(md5_hash_path) as file: old_md5_hash = file.read().strip() if old_md5_hash == current_md5_hash: return False with open(md5_hash_path, 'w') as file: print(current_md5_hash, file=file) with open(os.path.join(directory, f'{self.module_name}.belns'), 'w') as file: self.write_bel_namespace(file, use_names=False) if self.has_names: with open(os.path.join(directory, f'{self.module_name}-names.belns'), 'w') as file: self.write_bel_namespace(file, use_names=True) with open(os.path.join(directory, f'{self.module_name}.belns.mapping'), 'w') as file: self.write_bel_namespace_mappings(file, desc='writing mapping') return True
def _get_namespace_name_to_encoding(self, **kwargs) -> Mapping[str, str]: return { self._get_name(model): self._get_encoding(model) for model in self._iterate_namespace_models(**kwargs) } def _get_namespace_identifier_to_encoding(self, **kwargs) -> Mapping[str, str]: return { self._get_identifier(model): self._get_encoding(model) for model in self._iterate_namespace_models(**kwargs) } def _get_namespace_identifier_to_name(self, **kwargs) -> Mapping[str, str]: return { self._get_identifier(model): self._get_name(model) for model in self._iterate_namespace_models(**kwargs) }
[docs] def get_namespace_hash(self, hash_fn=None) -> str: """Get the namespace hash. Defaults to MD5. """ if self.has_names: items = self._get_namespace_name_to_encoding(desc='getting hash').items() else: items = self._get_namespace_identifier_to_encoding(desc='getting hash').items() return get_namespace_hash(items, hash_function=hash_fn)
@staticmethod def _cli_add_to_bel_namespace(main: click.Group) -> click.Group: """Add the export BEL namespace command.""" return add_cli_to_bel_namespace(main) @staticmethod def _cli_add_clear_bel_namespace(main: click.Group) -> click.Group: """Add the clear BEL namespace command.""" return add_cli_clear_bel_namespace(main) @staticmethod def _cli_add_write_bel_namespace(main: click.Group) -> click.Group: """Add the write BEL namespace command.""" return add_cli_write_bel_namespace(main) @staticmethod def _cli_add_write_bel_annotation(main: click.Group) -> click.Group: """Add the write BEL namespace command.""" return add_cli_write_bel_annotation(main)
[docs] @classmethod def get_cli(cls) -> click.Group: """Get a :mod:`click` main function with added BEL namespace commands.""" main = super().get_cli() if cls.is_namespace: @main.group() def belns(): """Manage BEL namespace.""" cls._cli_add_to_bel_namespace(belns) cls._cli_add_clear_bel_namespace(belns) cls._cli_add_write_bel_namespace(belns) if cls.is_annotation: @main.group() def belanno(): """Manage BEL annotation.""" cls._cli_add_write_bel_annotation(belanno) return main
def add_cli_to_bel_namespace(main: click.Group) -> click.Group: # noqa: D202 """Add a ``upload_bel_namespace`` command to main :mod:`click` function.""" @main.command() @click.option('-u', '--update', is_flag=True) @click.pass_obj def upload(manager: BELNamespaceManagerMixin, update): """Upload names/identifiers to terminology store.""" namespace = manager.upload_bel_namespace(update=update) click.echo(f'uploaded [{namespace.id}] {namespace.keyword}') return main def add_cli_clear_bel_namespace(main: click.Group) -> click.Group: # noqa: D202 """Add a ``clear_bel_namespace`` command to main :mod:`click` function.""" @main.command() @click.pass_obj def drop(manager: BELNamespaceManagerMixin): """Clear names/identifiers to terminology store.""" namespace = manager.drop_bel_namespace() if namespace: click.echo(f'namespace {namespace} was cleared') return main def add_cli_write_bel_namespace(main: click.Group) -> click.Group: # noqa: D202 """Add a ``write_bel_namespace`` command to main :mod:`click` function.""" @main.command() @directory_option @click.pass_obj def write(manager: BELNamespaceManagerMixin, directory: str): """Write a BEL namespace names/identifiers to terminology store.""" manager.write_directory(directory) return main def add_cli_write_bel_annotation(main: click.Group) -> click.Group: # noqa: D202 """Add a ``write_bel_annotation`` command to main :mod:`click` function.""" @main.command() @directory_option @click.pass_obj def write(manager: BELNamespaceManagerMixin, directory: str): """Write a BEL annotation.""" with open(os.path.join(directory, manager.identifiers_namespace), 'w') as file: manager.write_bel_annotation(file) return main