ddi-fw 0.0.128__tar.gz → 0.0.130__tar.gz

{ddi_fw-0.0.128 → ddi_fw-0.0.130}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ddi_fw
-Version: 0.0.128
+Version: 0.0.130
 Summary: Do not use :)
 Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
 Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>

{ddi_fw-0.0.128 → ddi_fw-0.0.130}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ddi_fw"
-version = "0.0.128"
+version = "0.0.130"
 description = "Do not use :)"
 readme = "README.md"
 authors = [

ddi_fw-0.0.130/src/ddi_fw/datasets/ddi_mdl_text/base.py

@@ -0,0 +1,156 @@
+import pathlib
+
+import numpy as np
+import pandas as pd
+
+from ddi_fw.datasets.feature_vector_generation import SimilarityMatrixGenerator
+from ddi_fw.langchain.embeddings import PoolingStrategy
+from .. import BaseDataset
+from ..db_utils import create_connection
+
+HERE = pathlib.Path(__file__).resolve().parent
+list_of_embedding_columns = ['description',
+                             'indication',
+                             'mechanism_of_action',
+                             'pharmacodynamics', 
+                             'description_indication',
+                             'description_mechanism_of_action',
+                             'description_pharmacodynamics',
+                             'indication_mechanism_of_action',
+                             'indication_pharmacodynamics',
+                             'mechanism_of_action_pharmacodynamics',
+                             'description_indication_mechanism_of_action',
+                             'description_indication_pharmacodynamics',
+                             'description_mechanism_of_action_pharmacodynamics',
+                             'indication_mechanism_of_action_pharmacodynamics'
+                             'description_indication_mechanism_of_action_pharmacodynamics',
+                             ]
+
+list_of_chemical_property_columns = ['enzyme',
+                                     'target',
+                                     'pathway',
+                                     'smile']
+list_of_ner_columns = ['tui', 'cui', 'entities']
+
+
+def indices_to_binary_vector(indices, vector_length=881):
+    # vector_length = len(indices)
+    # Initialize a zero vector of the given length
+    binary_vector = [0] * vector_length
+
+    # Set the positions specified by indices to 1
+    for index in indices:
+        if 0 <= index < vector_length:
+            binary_vector[index] = 1
+
+    return binary_vector
+
+
+class DDIMDLDataset(BaseDataset):
+    def __init__(self, embedding_size,
+                 embedding_dict,
+                 embeddings_pooling_strategy: PoolingStrategy,
+                 ner_df,
+                 chemical_property_columns=['enzyme',
+                                            'target',
+                                            'pathway',
+                                            'smile'],
+                 embedding_columns=[],
+                 ner_columns=[],
+                 **kwargs):
+        columns = kwargs['columns']
+        if columns:
+            chemical_property_columns = []
+            embedding_columns = []
+            ner_columns = []
+            for column in columns:
+                if column in list_of_chemical_property_columns:
+                    chemical_property_columns.append(column)
+                elif column in list_of_embedding_columns:
+                    embedding_columns.append(column)
+                elif column in list_of_ner_columns:
+                    ner_columns.append(column)
+                # elif column == 'smile_2':
+                #     continue
+                else:
+                    raise Exception(f"{column} is not related this dataset")
+
+        super().__init__(embedding_size=embedding_size,
+                         embedding_dict=embedding_dict,
+                         embeddings_pooling_strategy=embeddings_pooling_strategy,
+                         ner_df=ner_df,
+                         chemical_property_columns=chemical_property_columns,
+                         embedding_columns=embedding_columns,
+                         ner_columns=ner_columns,
+                         **kwargs)
+
+        # kwargs = {'index_path': str(HERE.joinpath('indexes'))}
+        kwargs['index_path'] = str(HERE.joinpath('indexes'))
+
+        db = HERE.joinpath('data/event.db')
+        conn = create_connection(db)
+        print("db prep")
+        self.drugs_df = self.__select_all_drugs_as_dataframe__(conn)
+        self.ddis_df = self.__select_all_events__(conn)
+        print("db bitti")
+        self.index_path = kwargs.get('index_path')
+
+        # jaccard_sim_dict = {}
+        # sim_matrix_gen = SimilarityMatrixGenerator()
+        # jaccard_sim_dict["smile_2"] = sim_matrix_gen.create_jaccard_similarity_matrices(
+        #                 self.drugs_df["smile_2"].to_list())
+
+        # similarity_matrices = {}
+        # drugbank_ids = self.drugs_df['id'].to_list()
+        # new_columns = {}
+        # for idx in range(len(drugbank_ids)):
+        #     new_columns[idx] = drugbank_ids[idx]
+        # new_df = pd.DataFrame.from_dict(jaccard_sim_dict["smile_2"])
+        # new_df = new_df.rename(index=new_columns, columns=new_columns)
+        # similarity_matrices["smile_2"] = new_df
+
+        # def lambda_fnc(row, value):
+        #     if row['id1'] in value and row['id2'] in value:
+        #         return np.float16(np.hstack(
+        #             (value[row['id1']], value[row['id2']])))
+        # for key, value in similarity_matrices.items():
+
+        #     print(f'sim matrix: {key}')
+        #     self.ddis_df[key] = self.ddis_df.apply(
+        #         lambda_fnc, args=(value,), axis=1)
+        #     print(self.ddis_df[key].head())
+        # print("init finished")
+
+    def __select_all_drugs_as_dataframe__(self, conn):
+        headers = ['index', 'id', 'name',
+                   'target', 'enzyme', 'pathway', 'smile']
+        cur = conn.cursor()
+        cur.execute(
+            '''select "index", id, name, target, enzyme, pathway, smile from drug''')
+        rows = cur.fetchall()
+        df = pd.DataFrame(columns=headers, data=rows)
+        df['enzyme'] = df['enzyme'].apply(lambda x: x.split('|'))
+        df['target'] = df['target'].apply(lambda x: x.split('|'))
+        df['pathway'] = df['pathway'].apply(lambda x: x.split('|'))
+        # df['smile_2'] = df['smile'].apply(lambda x: indices_to_binary_vector(indices = list(map(int, x.split('|'))), vector_length = 881))
+        df['smile'] = df['smile'].apply(lambda x: x.split('|'))
+
+        return df
+
+    def __select_all_events__(self, conn):
+        """
+        Query all rows in the event table
+        :param conn: the Connection object
+        :return:
+        """
+        cur = conn.cursor()
+        cur.execute('''
+                select ex."index", d1.id, d1.name, d2.id, d2.name,  mechanism || ' ' ||action from extraction ex
+                join drug d1 on  d1.name = ex.drugA
+                join drug d2 on  d2.name = ex.drugB
+        ''')
+
+        rows = cur.fetchall()
+
+        headers = ["index", "id1", "name1", "id2", "name2", "event_category"]
+        return pd.DataFrame(columns=headers, data=rows)