# -----------------------------------------------------------------------------

# Copyright (c) 2014--, The Qiita Development Team.

#

# Distributed under the terms of the BSD 3-clause License.

#

# The full license is in the file LICENSE, distributed with this software.

# -----------------------------------------------------------------------------

r"""

Ontology and Controlled Vocabulary objects (:mod:`qiita_db.study`)

==================================================================

.. currentmodule:: qiita_db.ontology

This module provides the encapsulation of an ontology. The resulting object can

be used to interrogate the terms in an ontology.

Classes

-------

.. autosummary::

   :toctree: generated/

   Ontology

"""

import qiita_db as qdb

class Ontology(qdb.base.QiitaObject):

    """Object to access ontologies and associated terms from the database

    Attributes

    ----------

    terms

    shortname

    """

    _table = 'ontology'

    def __contains__(self, value):

        with qdb.sql_connection.TRN:

            sql = """SELECT EXISTS (

                        SELECT *

                        FROM qiita.term t

                            JOIN qiita.{0} o ON t.ontology_id = o.ontology_id

                        WHERE o.ontology_id = %s

                            AND term = %s)""".format(self._table)

            qdb.sql_connection.TRN.add(sql, [self._id, value])

            return qdb.sql_connection.TRN.execute_fetchlast()

    @property

    def terms(self):

        with qdb.sql_connection.TRN:

            sql = """SELECT term

                     FROM qiita.term

                     WHERE ontology_id = %s AND user_defined = false"""

            qdb.sql_connection.TRN.add(sql, [self.id])

            return qdb.sql_connection.TRN.execute_fetchflatten()

    @property

    def user_defined_terms(self):

        with qdb.sql_connection.TRN:

            sql = """SELECT term

                     FROM qiita.term

                     WHERE ontology_id = %s AND user_defined = true"""

            qdb.sql_connection.TRN.add(sql, [self.id])

            return qdb.sql_connection.TRN.execute_fetchflatten()

    @property

    def shortname(self):

        return qdb.util.convert_from_id(self.id, 'ontology')

    def add_user_defined_term(self, term):

        """Add a user defined term to the ontology

        Parameters

        ----------

        term : str

            New user defined term to add into a given ontology

        """

        # we don't need to add an existing term

        terms = self.user_defined_terms + self.terms

        if term not in terms:

            sql = """INSERT INTO qiita.term

                        (ontology_id, term, user_defined)

                     VALUES (%s, %s, true);"""

            qdb.sql_connection.perform_as_transaction(sql, [self.id, term])

    def term_type(self, term):

        """Get the type of a given ontology term

        Parameters

        ----------

        term : str

            String for which the method will check the type

        Returns

        -------

        str

            The term type: 'ontology' if the term is part of the ontology,

            'user_defined' if the term is part of the ontology and was

            user-defined and 'not_ontology' if the term is not part of the

            ontology.

        """

        with qdb.sql_connection.TRN:

            sql = """SELECT user_defined FROM

                     qiita.term

                     WHERE term = %s AND ontology_id = %s"""

            qdb.sql_connection.TRN.add(sql, [term, self.id])

            result = qdb.sql_connection.TRN.execute_fetchindex()

            if not result:

                return 'not_ontology'

            elif result[0][0]:

                return 'user_defined'

            elif not result[0][0]:

                return 'ontology'