molecule tables updated

ckanext/rdkit_visuals/models/molecule_rel.py

@@ -5,11 +5,11 @@
 from sqlalchemy.orm import relationship
 from sqlalchemy import orm
 
-from ckan.model import meta, Package, domain_object
+import ckan.model.package as _package
 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 ckan.model.meta import
 from .base import Base
 
 
@@ -22,14 +22,15 @@ class MolecularRelationData(Base):
     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. 
+    These two are combined in this table, for simpler 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)
 
+    #package = relationship(_package.Package, backref="molecular_relation_data")
+
     @classmethod
     def create(cls, molecules_id, package_id):
         """
@@ -129,3 +130,6 @@ def get_molecule_data_by_package_id(cls, package_id):
         molecule_data = Session.query(Molecules.inchi).filter(Molecules.id.in_(molecules_sub_query)).all()
 
         return molecule_data
+
+
+#meta.registry.map_imperatively(MolecularRelationData, MolecularRelationData.__table__)

ckanext/rdkit_visuals/models/molecule_tab.py

@@ -11,7 +11,6 @@
 from .base import Base
 
 
-
 class Molecules(Base):
     __tablename__ = 'molecules'
 
@@ -22,20 +21,20 @@ class Molecules(Base):
     """
 
     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')
+    # 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):
+    def create(cls, inchi, smiles, inchi_key, exact_mass, mol_formula):
         """
         Create a new Molecule entry and store it in the database.
 
@@ -49,7 +48,6 @@ def create(cls, package_id, inchi, smiles, inchi_key, exact_mass, mol_formula):
         :return: The created Molecule instance
         """
         new_molecule = cls(
-            package_id=package_id,
             inchi=inchi,
             smiles=smiles,
             inchi_key=inchi_key,
@@ -60,4 +58,14 @@ def create(cls, package_id, inchi, smiles, inchi_key, exact_mass, mol_formula):
         Session.commit()
         return new_molecule
 
+    @classmethod
+    def _get_inchi_from_db(cls, inchi_key):
+        """
+
+        :param inchi_key:
+        :return: the id of the molecule
+        """
+
+        molecule_id_result = Session.query(Molecules.id).filter(Molecules.inchi_key == inchi_key).all()
 
+        return molecule_id_result