ddi-fw 0.0.30__tar.gz → 0.0.32__tar.gz

{ddi_fw-0.0.30 → ddi_fw-0.0.32}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ddi_fw
-Version: 0.0.30
+Version: 0.0.32
 Summary: Do not use :)
 Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
 Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>

{ddi_fw-0.0.30 → ddi_fw-0.0.32}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ddi_fw"
-version = "0.0.30"
+version = "0.0.32"
 description = "Do not use :)"
 readme = "README.md"
 authors = [

{ddi_fw-0.0.30 → ddi_fw-0.0.32}/src/ddi_fw/datasets/core.py

@@ -9,7 +9,7 @@ from ddi_fw.datasets.idf_helper import IDF
 
 from ddi_fw.utils.zip_helper import ZipHelper
 from .feature_vector_generation import SimilarityMatrixGenerator, VectorGenerator
-from ddi_fw.ner.ner import CTakesNER
+# from ddi_fw.ner.ner import CTakesNER
 from ddi_fw.utils import create_folder_if_not_exists
 from stopwatch import Stopwatch, profile
 
@@ -21,9 +21,10 @@ def stack(df_column):
 
 
 class BaseDataset(ABC):
-    def __init__(self,embedding_dict, chemical_property_columns, embedding_columns, ner_columns,
+    def __init__(self,embedding_dict, ner_df, chemical_property_columns, embedding_columns, ner_columns,
                  **kwargs):
         self.embedding_dict = embedding_dict
+        self.ner_df = ner_df
         self.__similarity_related_columns__ = []
         self.__similarity_related_columns__.extend(chemical_property_columns)
         self.__similarity_related_columns__.extend(ner_columns)
@@ -266,7 +267,7 @@ class BaseDataset(ABC):
         #     x = {k: v for l in d.values.tolist() for k, v in l.items()}
         #     embedding_dict[embedding_column] = x
  
-        self.ner_df = CTakesNER().load()
+        # self.ner_df = CTakesNER().load()
         drug_names = self.drugs_df['name'].to_list()
         drug_ids = self.drugs_df['id'].to_list()
 

{ddi_fw-0.0.30 → ddi_fw-0.0.32}/src/ddi_fw/datasets/ddi_mdl/base.py

@@ -8,7 +8,7 @@ HERE = pathlib.Path(__file__).resolve().parent
 
 
 class DDIMDLDataset(BaseDataset):
-    def __init__(self, embedding_dict, chemical_property_columns=['enzyme',
+    def __init__(self, embedding_dict, ner_def, chemical_property_columns=['enzyme',
                                                    'target',
                                                    'pathway',
                                                    'smile'],
@@ -16,13 +16,13 @@ class DDIMDLDataset(BaseDataset):
                  ner_columns=[],
                  **kwargs):
 
-        super().__init__(embedding_dict, chemical_property_columns, embedding_columns,
+        super().__init__(embedding_dict,ner_def, chemical_property_columns, embedding_columns,
                          ner_columns, **kwargs)
 
         # kwargs = {'index_path': str(HERE.joinpath('indexes'))}
         kwargs['index_path']= str(HERE.joinpath('indexes'))
 
-        db = HERE.joinpath('event.db')
+        db = HERE.joinpath('data/event.db')
         conn = create_connection(db)
         print("db prep")
         self.drugs_df = self.__select_all_drugs_as_dataframe__(conn)

{ddi_fw-0.0.30 → ddi_fw-0.0.32}/src/ddi_fw.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ddi_fw
-Version: 0.0.30
+Version: 0.0.32
 Summary: Do not use :)
 Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
 Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>