ddi-fw 0.0.30__py3-none-any.whl → 0.0.32__py3-none-any.whl

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/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.dist-info → ddi_fw-0.0.32.dist-info}/METADATA

@@ -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.dist-info → ddi_fw-0.0.32.dist-info}/RECORD

@@ -1,12 +1,12 @@
 ddi_fw/datasets/__init__.py,sha256=gkzHCU9-BL_bOU-RvvwdOIp_DhKRfXKU5SvgfQLVTds,505
-ddi_fw/datasets/core.py,sha256=Iv8l2WRM2rNyshdXd8LIz06qIGpz3EwCImEIc_Qr00w,18084
+ddi_fw/datasets/core.py,sha256=AHGFo5dEbvwDt9kQTeiBuVPAGfG6I4cawc-e2wNm04c,18126
 ddi_fw/datasets/db_utils.py,sha256=OTsa3d-Iic7z3HmzSQK9UigedRbHDxYChJk0s4GfLnw,6191
 ddi_fw/datasets/embedding_generator.py,sha256=Jqrlv88RCu0Lg812KsA12X0cSaZuxbckJ4LNRKNy_qw,2173
 ddi_fw/datasets/embedding_generator_new.py,sha256=GExjmBysPWkmFxTZQPs2yEmDdFllZ-qC9lhZeRQAfbQ,4320
 ddi_fw/datasets/feature_vector_generation.py,sha256=dxTHvp6uTkao9PdThs116Q3bWw_WTo9T8WigVL4G01s,3245
 ddi_fw/datasets/idf_helper.py,sha256=_Gd1dtDSLaw8o-o0JugzSKMt9FpeXewTh4wGEaUd4VQ,2571
 ddi_fw/datasets/setup_._py,sha256=khYVJuW5PlOY_i_A16F3UbSZ6s6o_ljw33Byw3C-A8E,1047
-ddi_fw/datasets/ddi_mdl/base.py,sha256=_R9-CE2P2kNoxpkDWWIHfSvsRidmYqTj-Ldp4HZpoPg,2453
+ddi_fw/datasets/ddi_mdl/base.py,sha256=NQl0AM-s7ZpbTdfBkCTNl2_sn0F8IabsgT_B8lxSh_Y,2475
 ddi_fw/datasets/ddi_mdl/readme.md,sha256=WC6lpmsEKvIISnZqENY7TWtzCQr98HPpE3oRsBl8pIw,625
 ddi_fw/datasets/ddi_mdl/data/event.db,sha256=cmlSsf9MYjRzqR-mw3cUDnTnfT6FkpOG2yCl2mMwwew,30580736
 ddi_fw/datasets/ddi_mdl/indexes/test_indexes.txt,sha256=XVlDqYATckrQwNSXqMSKVBqyoN_Hg8SK6CL-XMdLADY,102176
@@ -80,7 +80,7 @@ ddi_fw/utils/enums.py,sha256=19eJ3fX5eRK_xPvkYcukmug144jXPH4X9zQqtsFBj5A,671
 ddi_fw/utils/py7zr_helper.py,sha256=rWhz3Trj6bk6B24hMuff1fKdRbC0yuvaHFlL8-eaAhg,4450
 ddi_fw/utils/utils.py,sha256=Na6Y8mY-CFbQjrgd9xC8agcrjVvTj_7KIXqFm1H_3qU,3549
 ddi_fw/utils/zip_helper.py,sha256=YRZA4tKZVBJwGQM0_WK6L-y5MoqkKoC-nXuuHK6CU9I,5567
-ddi_fw-0.0.30.dist-info/METADATA,sha256=NMiiLuGtxDcvRyvpsWN9HcHGOQOQwYPtLSd5A4UwHuk,1563
-ddi_fw-0.0.30.dist-info/WHEEL,sha256=5Mi1sN9lKoFv_gxcPtisEVrJZihrm_beibeg5R6xb4I,91
-ddi_fw-0.0.30.dist-info/top_level.txt,sha256=PMwHICFZTZtcpzQNPV4UQnfNXYIeLR_Ste-Wfc1h810,7
-ddi_fw-0.0.30.dist-info/RECORD,,
+ddi_fw-0.0.32.dist-info/METADATA,sha256=7D754IM_jrjiv8zoHY6nKAvBP4fiDsgEZPv8WjZr86w,1563
+ddi_fw-0.0.32.dist-info/WHEEL,sha256=5Mi1sN9lKoFv_gxcPtisEVrJZihrm_beibeg5R6xb4I,91
+ddi_fw-0.0.32.dist-info/top_level.txt,sha256=PMwHICFZTZtcpzQNPV4UQnfNXYIeLR_Ste-Wfc1h810,7
+ddi_fw-0.0.32.dist-info/RECORD,,