Data Models for db interaction

ckanext/rdkit_visuals/models/base.py

@@ -0,0 +1,3 @@
+from sqlalchemy.ext.declarative import declarative_base
+
+Base = declarative_base()

ckanext/rdkit_visuals/models/molecule_rel.py

@@ -1,39 +1,117 @@
 # encoding: utf-8
 
-from six import text_type
-from sqlalchemy import orm, types, Column, Table, ForeignKey
-from sqlalchemy.ext.associationproxy import association_proxy
-
-from ckan.model import (
-    meta,
-    core,
-    package as _package,
-    extension,
-    domain_object,
-    types as _types,
-)
-
-__all__ = [u'MolecularRelationData', u'molecule_rel_data_table']
-
-molecule_rel_data_table = Table(u'molecule_rel_data', meta.metadata,
-                            Column(u'id', types.Integer, primary_key=True, nullable=False),
-                            Column(u'molecule_id', types.UnicodeText, ForeignKey('molecules.id'), nullable = False),
-                            Column(u'package_id', types.UnicodeText, ForeignKey('package.id'), nullable=False),)
-
-
-
-class MolecularRelationData(domain_object.DomainObject):
-    def __init__(self, related_object):
-        self.package_id = related_object.get('package_id')
-        self.molecule_id = related_object.get('molecule_id')
-
-
-meta.mapper(
-    MolecularRelationData,
-    molecule_rel_data_table,
-    properties={
-        u"package": orm.relation(
-            _package, backref=orm.backref(u"molecules", cascade=u"all, delete, delete-orphan")
-        )
-    },
-)
+import datetime
+from sqlalchemy import Column, ForeignKey, func, String, distinct
+from sqlalchemy.orm import relationship
+from sqlalchemy import orm
+
+from ckan.model import meta, Package, domain_object
+from ckanext.rdkit_visuals.models.molecule_tab import Molecules
+from sqlalchemy import types as _types
+from ckan.model import Session
+from ckan.model import meta
+from .base import Base
+
+
+
+class MolecularRelationData(Base):
+    __tablename__ = "molecule_rel_data"
+
+    """
+    Table which contains molecule and package relationship.
+    
+    molecules_id from molecules data table are stored here. 
+    Which internally, relates to the packages and their ids. 
+    
+    These two are combined in this table, for simplier access. 
+    
+    """
+
+    id = Column(u'id', _types.Integer, primary_key=True,autoincrement=True, nullable=False)
+    molecules_id = Column(u'molecules_id', _types.UnicodeText, ForeignKey('molecules.id'), nullable=False)
+    package_id = Column(u'package_id', _types.UnicodeText, ForeignKey('package.id'), nullable=False)
+
+    @classmethod
+    def create(cls, molecules_id, package_id):
+        """
+        Create a new MoleculeRelData entry and store it in the database.
+
+        :param molecules_id: The ID of the molecule
+        :param package_id: The ID of the package
+        :param session: The SQLAlchemy session for database interaction
+        :return: The created MoleculeRelData instance
+        """
+        new_entry = cls(molecules_id=molecules_id, package_id=package_id)
+        Session.add(new_entry)
+        Session.commit()
+        return new_entry
+
+    @classmethod
+    def get_package_list_inchi_key(cls, page_size, current_page):
+        """
+        Get the list of InChIKeys and their associated packages IDs.
+
+        :param page_size: The number of records per page
+        :param current_page: The current page number
+        :return: InChIKeys and their associated packages IDs  (inchi_key, package_ids)
+        """
+        offset_value = (current_page - 1) * page_size
+
+        subquery = Session.query(
+            cls.molecules_id,
+            func.string_agg(cls.package_id.cast(_types.String), ', ').label('package_ids')
+        ).group_by(cls.molecules_id).subquery()
+
+        query = Session.query(
+            Molecules.inchi_key,
+            subquery.c.package_ids
+        ).join(
+            Molecules,
+            Molecules.id == subquery.c.molecules_id
+        ).limit(page_size).offset(offset_value)
+
+        return query.all()
+
+    @classmethod
+    def get_count_rows(cls):
+        """
+        Get the number of rows/molecules with datasets in molecule_rel_data table.
+        :return: Number of rows to display "n Molecules Found"
+        """
+        subquery = Session.query(
+            cls.molecules_id,
+            cls.package_id
+        ).distinct(cls.molecules_id).subquery()
+
+        count = Session.query(func.count()).select_from(subquery).scalar()
+        return count
+
+    @classmethod
+    def get_mol_formula_by_package_id(cls, package_id):
+        """
+
+        :param package_id:
+        :return:
+        """
+
+        molecules_sub_query = Session.query(
+            cls.molecules_id
+        ).filter(cls.package_id == package_id).subquery()
+
+        mol_formula = Session.query(Molecules.mol_formula).filter(Molecules.id.in_(molecules_sub_query)).all()
+
+        return mol_formula
+
+    @classmethod
+    def get_exact_mass_by_package_id(cls, package_id):
+        """
+
+        :param package_id:
+        :return:
+        """
+        molecules_sub_query = Session.query(
+            cls.molecules_id
+        ).filter(cls.package_id == package_id).subquery()
+
+        exact_mass = Session.query(Molecules.exact_mass).filter(Molecules.id.in_(molecules_sub_query)).all()
+        return exact_mass

ckanext/rdkit_visuals/models/molecule_tab.py

@@ -1,50 +1,63 @@
 # encoding: utf-8
 
-from six import text_type
-from sqlalchemy import orm, types, Column, Table, ForeignKey
-from sqlalchemy.ext.associationproxy import association_proxy
-
-from ckan.model import (
-    meta,
-    core,
-    package as _package,
-    extension,
-    domain_object,
-    types as _types,
-)
-
-
-__all__ = [u'MolecularData', u'molecule_data_table']
-
-molecule_data_table = Table(u'molecule_data', meta.metadata,
-                Column(u'id', types.Integer, primary_key = True, nullable = False),
-                Column(u'package_id', types.UnicodeText, ForeignKey('package.id'), nullable = False),
-                Column(u'inchi',types.UnicodeText),
-                Column(u'smiles',types.UnicodeText),
-                Column(u'inchi_key', types.UnicodeText),
-                Column(u'exact_mass', types.UnicodeText)
+from sqlalchemy import Column, ForeignKey, func, String, Float
+from sqlalchemy.orm import relationship
+from sqlalchemy import orm
+
+from ckan.model import meta, Package, domain_object
+from sqlalchemy import types as _types
+from ckan.model import Session
+from ckan.model import meta
+from .base import Base
+
+
+
+class Molecules(Base):
+    __tablename__ = 'molecules'
+
+    """
+    Molecules is an essential table for storing the molecular information in a database using RDKit visuals while
+    harvesting the metadata through CKAN harvesters.
+    
+    """
+
+    id = Column(_types.Integer, primary_key=True, autoincrement=True)
+    package_id = Column(_types.Integer, ForeignKey('package.id'))
+    inchi = Column(_types.String)
+    smiles = Column(_types.String)
+    inchi_key = Column(_types.String)
+    exact_mass = Column(Float)
+    mol_formula = Column(_types.String)
+
+    # Relationship with the Package model
+    #package = relationship('Package')
+
+    # Additional methods can be added here as needed
+
+    @classmethod
+    def create(cls, package_id, inchi, smiles, inchi_key, exact_mass, mol_formula):
+        """
+        Create a new Molecule entry and store it in the database.
+
+        :param package_id: The ID of the package
+        :param inchi: InChI string for the molecule
+        :param smiles: SMILES string for the molecule
+        :param inchi_key: InChI key for the molecule
+        :param exact_mass: The exact mass of the molecule
+        :param mol_formula: The molecular formula of the molecule
+        :param session: The SQLAlchemy session for database interaction
+        :return: The created Molecule instance
+        """
+        new_molecule = cls(
+            package_id=package_id,
+            inchi=inchi,
+            smiles=smiles,
+            inchi_key=inchi_key,
+            exact_mass=exact_mass,
+            mol_formula=mol_formula
         )
+        Session.add(new_molecule)
+        Session.commit()
+        return new_molecule
 
 
-
-class MolecularData(domain_object.DomainObject):
-    def __init__(self, related_object):
-        self.package_id = related_object.get('package_id')
-        self.inchi = related_object.get('inchi')
-        self.smiles = related_object.get('smiles')
-        self.inchi_key = related_object.get('inchi_key')
-        self.exact_mass = related_object.get('exact_mass')
-
-
-
-
-meta.mapper(
-    MolecularData,
-    molecule_data_table,
-    properties={
-        u"package": orm.relation(
-            _package, backref=orm.backref(u"molecule_data", cascade=u"all, delete, delete-orphan")
-        )
-    },
-)
-