ddi-fw 0.0.151__py3-none-any.whl → 0.0.153__py3-none-any.whl

ddi_fw/datasets/core.py

@@ -1,5 +1,5 @@
 import glob
-from typing import List, Optional, Type
+from typing import Any, Dict, List, Optional, Type
 import numpy as np
 import pandas as pd
 from pydantic import BaseModel, Field, computed_field
@@ -194,8 +194,8 @@ class BaseDataset(BaseModel):
 
 
 class TextDatasetMixin(BaseDataset):
-    embedding_size: int
-    embedding_dict: dict
+    embedding_size: Optional[int] = None 
+    embedding_dict: Dict[str, Any] = Field(default_factory=dict, description="Dictionary for embeddings")
     embeddings_pooling_strategy: PoolingStrategy | None = None
 
     def process_text(self):

ddi_fw/datasets/ddi_mdl/base.py

@@ -30,6 +30,7 @@ LIST_OF_NER_COLUMNS = ['tui', 'cui', 'entities']
 HERE = pathlib.Path(__file__).resolve().parent
 
 class DDIMDLDataset(TextDatasetMixin):
+    dataset_name: str = "DDIMDLDataset"
     index_path: str = Field(default_factory=lambda: str(
         pathlib.Path(__file__).resolve().parent.joinpath('indexes')))
     # drugs_df: pd.DataFrame = Field(default_factory=pd.DataFrame)

ddi_fw/pipeline/pipeline.py

@@ -35,20 +35,18 @@ class Pipeline(BaseModel):
     model: Optional[Any] = None
     multi_modal:  Optional[Any] = None
     use_mlflow: bool = True
-    _items: List = []
-    _train_idx_arr: List | None = []
-    _val_idx_arr: List | None = []
-
+    _items:List=[]
+    _train_idx_arr:List|None=[]
+    _val_idx_arr:List|None=[]
+    
     @property
     def items(self) -> List:
         return self._items
-
     @property
-    def train_idx_arr(self) -> List | None:
+    def train_idx_arr(self) -> List|None:
         return self._train_idx_arr
-
     @property
-    def val_idx_arr(self) -> List | None:
+    def val_idx_arr(self) -> List|None:
         return self._val_idx_arr
 
     class Config:
@@ -127,15 +125,12 @@ class Pipeline(BaseModel):
                 print(
                     f"Embeddings of {column} are calculated from {vector_db_collection_name}")
 
-            # if metadatas == None or embeddings == None:
-            if 'embeddings' not in dictionary or 'metadatas' not in dictionary or not dictionary['embeddings'] or not dictionary['metadatas']:
-                raise ValueError(
-                    "The collection does not contain embeddings or metadatas.")
-
             # Populate the embedding dictionary with embeddings from the vector database
             metadatas = dictionary["metadatas"]
             embeddings = dictionary["embeddings"]
-
+            if metadatas is None or embeddings is None:
+                raise ValueError(
+                    "The collection does not contain embeddings or metadatas.")
             for metadata, embedding in zip(metadatas, embeddings):
                 embedding_dict[metadata["type"]
                                ][metadata["id"]].append(embedding)
@@ -189,8 +184,7 @@ class Pipeline(BaseModel):
         if issubclass(self.dataset_type, TextDatasetMixin):
             key, value = next(iter(embedding_dict.items()))
             embedding_size = value[next(iter(value))][0].shape[0]
-            pooling_strategy = self.embedding_pooling_strategy_type(
-            ) if self.embedding_pooling_strategy_type else None
+            pooling_strategy = self.embedding_pooling_strategy_type() if self.embedding_pooling_strategy_type  else None
 
             dataset = self.dataset_type(
                 embedding_dict=embedding_dict,

{ddi_fw-0.0.151.dist-info → ddi_fw-0.0.153.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ddi_fw
-Version: 0.0.151
+Version: 0.0.153
 Summary: Do not use :)
 Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
 Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>

{ddi_fw-0.0.151.dist-info → ddi_fw-0.0.153.dist-info}/RECORD

@@ -1,12 +1,12 @@
 ddi_fw/datasets/__init__.py,sha256=yDsRQD_9Ijpm_Rl2wSDwdutG5Q_wca_UBPEvm7nBx04,444
-ddi_fw/datasets/core.py,sha256=JA6WJz3VCUfxI85rYE7ZBqC4pnn7L8NSS9-EgjLw710,7968
+ddi_fw/datasets/core.py,sha256=vRMpUsIHIbOKi-6TuUPNu1Ve3ny3cS9hdsydQxFCNvE,8078
 ddi_fw/datasets/dataset_splitter.py,sha256=lLIelXv-8rCK0tbwLNgHBHYUO_65HT-_kErAlZhRQVE,1662
 ddi_fw/datasets/db_utils.py,sha256=OTsa3d-Iic7z3HmzSQK9UigedRbHDxYChJk0s4GfLnw,6191
 ddi_fw/datasets/embedding_generator.py,sha256=jiDKwLaPMaQkloxQkuCrhl-A-2OdvocmkSzjWtUnk4g,2255
 ddi_fw/datasets/feature_vector_generation.py,sha256=gvjpEzkgVV8dp4V8NMMv59u0v-1tNAJ7v83R-keWGoA,4748
 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=usw3AhBCjdYwZx9MMnyNaUYTEyYXoRSO4fNJJHxnPuk,9312
+ddi_fw/datasets/ddi_mdl/base.py,sha256=sj4WfwNmcTFznVxlND6FYoyqnL7VUrjn0TG24LDYk3w,9353
 ddi_fw/datasets/ddi_mdl/debug.log,sha256=eWz05j8RFqZuHFDTCF7Rck5w4rvtTanFN21iZsgxO7Y,115
 ddi_fw/datasets/ddi_mdl/readme.md,sha256=WC6lpmsEKvIISnZqENY7TWtzCQr98HPpE3oRsBl8pIw,625
 ddi_fw/datasets/ddi_mdl/data/event.db,sha256=cmlSsf9MYjRzqR-mw3cUDnTnfT6FkpOG2yCl2mMwwew,30580736
@@ -88,7 +88,7 @@ ddi_fw/pipeline/__init__.py,sha256=tKDM_rW4vPjlYTeOkNgi9PujDzb4e9O3LK1w5wqnebw,2
 ddi_fw/pipeline/multi_modal_combination_strategy.py,sha256=JSyuP71b1I1yuk0s2ecCJZTtCED85jBtkpwTUxibJvI,1706
 ddi_fw/pipeline/multi_pipeline.py,sha256=D_BZ3ciHbVGuuB7m7cEmVQHESruh1gqhA-vxCMfNKj0,5407
 ddi_fw/pipeline/ner_pipeline.py,sha256=q1aKjb54Ra1HzZ7dARvBw6lB37je9R-POEf2h6QT_nU,6018
-ddi_fw/pipeline/pipeline.py,sha256=NPew1lESAiuXUKR4Ob9R4LwRh2Xe1qfnqZDfmuMuC7k,11253
+ddi_fw/pipeline/pipeline.py,sha256=l-T-QnR_cVD590UovmsUlfjivaaZih7j_KMIJvGDAtA,11073
 ddi_fw/utils/__init__.py,sha256=77563ikqAtdzjjgRlLp5OAsJBbpLA1Cao8iecGaVUXQ,354
 ddi_fw/utils/enums.py,sha256=19eJ3fX5eRK_xPvkYcukmug144jXPH4X9zQqtsFBj5A,671
 ddi_fw/utils/json_helper.py,sha256=BVU6wmJgdXPxyqLPu3Ck_9Es5RrP1PDanKvE-OSj1D4,571
@@ -97,7 +97,7 @@ 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-0.0.151.dist-info/METADATA,sha256=cTz-LpUrPhCU0uKQ2A9oE3lm5uaI3ra3nFHufSoi8hA,2082
-ddi_fw-0.0.151.dist-info/WHEEL,sha256=DK49LOLCYiurdXXOXwGJm6U4DkHkg4lcxjhqwRa0CP4,91
-ddi_fw-0.0.151.dist-info/top_level.txt,sha256=PMwHICFZTZtcpzQNPV4UQnfNXYIeLR_Ste-Wfc1h810,7
-ddi_fw-0.0.151.dist-info/RECORD,,
+ddi_fw-0.0.153.dist-info/METADATA,sha256=Lj5ZaKAa6dL9CvHiGIo1KAUtbB8MA40dVlbpHNUcaHA,2082
+ddi_fw-0.0.153.dist-info/WHEEL,sha256=DK49LOLCYiurdXXOXwGJm6U4DkHkg4lcxjhqwRa0CP4,91
+ddi_fw-0.0.153.dist-info/top_level.txt,sha256=PMwHICFZTZtcpzQNPV4UQnfNXYIeLR_Ste-Wfc1h810,7
+ddi_fw-0.0.153.dist-info/RECORD,,