ddi-fw 0.0.145__py3-none-any.whl → 0.0.147__py3-none-any.whl

ddi_fw/datasets/mdf_sa_ddi/base.py

@@ -6,22 +6,63 @@ import pandas as pd
 
 from ddi_fw.utils import ZipHelper
 
-from ..core import BaseDataset
+from .. import BaseDataset
+from ddi_fw.langchain.embeddings import PoolingStrategy
+from ..db_utils import create_connection
 # from ..db_utils import create_connection, select_all_drugs_as_dataframe, select_events_with_category
 
 HERE = pathlib.Path(__file__).resolve().parent
-
-
+list_of_embedding_columns = ['all_text', 'description',
+                     'synthesis_reference', 'indication',
+                     'pharmacodynamics', 'mechanism_of_action',
+                     'toxicity', 'metabolism',
+                     'absorption', 'half_life',
+                     'protein_binding', 'route_of_elimination',
+                     'volume_of_distribution', 'clearance']
+
+list_of_chemical_property_columns = ['enzyme',
+                             'target',
+                             'smile']
+
+list_of_ner_columns = ['tui', 'cui', 'entities']
 class MDFSADDIDataset(BaseDataset):
-    def __init__(self, chemical_property_columns=['enzyme',
+    def __init__(self, embedding_size,
+                 embedding_dict,
+                 embeddings_pooling_strategy: PoolingStrategy,
+                 ner_df,
+                 chemical_property_columns=['enzyme',
                                                   'target',
                                                   'smile'],
                  embedding_columns=[],
                  ner_columns=[],
                  **kwargs):
 
-        super().__init__(chemical_property_columns, 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)
 
         db_zip_path = HERE.joinpath('mdf-sa-ddi.zip')
         db_path = HERE.joinpath('mdf-sa-ddi.db')
@@ -33,7 +74,8 @@ class MDFSADDIDataset(BaseDataset):
             conn = create_connection(db_path)
             self.drugs_df = select_all_drugs_as_dataframe(conn)
             self.ddis_df = select_all_events_as_dataframe(conn)
-        kwargs = {'index_path': str(HERE.joinpath('indexes'))}
+        # kwargs = {'index_path': str(HERE.joinpath('indexes'))}
+        kwargs['index_path'] = str(HERE.joinpath('indexes'))
 
         self.index_path = kwargs.get('index_path')
 
@@ -83,21 +125,6 @@ class MDFSADDIDataset(BaseDataset):
             file_path=db_path, output_path=HERE, name='mdf-sa-ddi')
 
 
-def create_connection(db_file=r"mdf-sa-ddi.db"):
-    """ create a database connection to the SQLite database
-        specified by db_file
-    :param db_file: database file
-    :return: Connection object or None
-    """
-    conn = None
-    try:
-        conn = sqlite3.connect(db_file)
-    except Error as e:
-        print(e)
-
-    return conn
-
-
 def select_all_drugs(conn):
     cur = conn.cursor()
     cur.execute(

{ddi_fw-0.0.145.dist-info → ddi_fw-0.0.147.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ddi_fw
-Version: 0.0.145
+Version: 0.0.147
 Summary: Do not use :)
 Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
 Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>

{ddi_fw-0.0.145.dist-info → ddi_fw-0.0.147.dist-info}/RECORD

@@ -47,7 +47,7 @@ ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_2.txt,sha256=fFJbN0DbKH4mve
 ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_3.txt,sha256=NhiLF_5INQCpjOlE-RIxDKy7rYwksLdx60L6HCmDKoY,81247
 ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_4.txt,sha256=bPvMCJVy7jtcaYbR-5bmdB6s7gT8NSfK2wDC7iJ0O10,81308
 ddi_fw/datasets/mdf_sa_ddi/__init__.py,sha256=UEFBM92y2aJjlMJw4Jx405tOAwJ88r_nHAVgAszSjuo,68
-ddi_fw/datasets/mdf_sa_ddi/base.py,sha256=e56uJEU6ZZlWh9ZZCO-H7Pcqm8gQE9SQtm7ujeDKgIU,4893
+ddi_fw/datasets/mdf_sa_ddi/base.py,sha256=kYNmtg-s0V7mP-wjLMaAstNCG3vckMPQSE651RA_LAE,6502
 ddi_fw/datasets/mdf_sa_ddi/df_extraction_cleanxiaoyu50.csv,sha256=EOOLF_0vVVzShoofcGYlOzpztlM1m9jJdftepHicix4,25787699
 ddi_fw/datasets/mdf_sa_ddi/drug_information_del_noDDIxiaoyu50.csv,sha256=lpuMz5KxPsG6MKNuIIUmT5cZquWHQiIao8tXlmOHzq8,381321
 ddi_fw/datasets/mdf_sa_ddi/mdf-sa-ddi.zip,sha256=DfN8mczGvWba2y45cPqtWtXjUDXy49VOtRfpcb0tn8c,4382827
@@ -106,7 +106,7 @@ ddi_fw/utils/package_helper.py,sha256=erl8_onmhK-41zQoaED2qyDUV9GQxmT9sdoyRp9_q5
 ddi_fw/utils/py7zr_helper.py,sha256=gOqaFIyJvTjUM-btO2x9AQ69jZOS8PoKN0wetYIckJw,4747
 ddi_fw/utils/utils.py,sha256=szwnxMTDRrZoeNRyDuf3aCbtzriwtaRk4mHSH3asLdA,4301
 ddi_fw/utils/zip_helper.py,sha256=YRZA4tKZVBJwGQM0_WK6L-y5MoqkKoC-nXuuHK6CU9I,5567
-ddi_fw-0.0.145.dist-info/METADATA,sha256=sXEGur4T8IymB0S1rMjVy6I4Z5Lyk3JM7djW2WERe48,1965
-ddi_fw-0.0.145.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-ddi_fw-0.0.145.dist-info/top_level.txt,sha256=PMwHICFZTZtcpzQNPV4UQnfNXYIeLR_Ste-Wfc1h810,7
-ddi_fw-0.0.145.dist-info/RECORD,,
+ddi_fw-0.0.147.dist-info/METADATA,sha256=tP6mvgGgtbBX-YxyZOzIaEf2K8vTWh0K0BjC_3c0DPs,1965
+ddi_fw-0.0.147.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+ddi_fw-0.0.147.dist-info/top_level.txt,sha256=PMwHICFZTZtcpzQNPV4UQnfNXYIeLR_Ste-Wfc1h810,7
+ddi_fw-0.0.147.dist-info/RECORD,,