add docs

docs/api.md

@@ -1,5 +1,22 @@
 # API
 
+## IOs
+
+```{eval-rst}
+.. module:: ehrdata.io
+.. currentmodule:: ehrdata
+
+.. autosummary::
+    :toctree: generated
+
+    io.init_omop
+    io.extract_features
+    io.extract_note
+    io.from_dataframe
+    io.to_dataframe
+
+```
+
 ## Preprocessing
 
 ```{eval-rst}
@@ -9,7 +26,8 @@
 .. autosummary::
     :toctree: generated
 
-    pp.basic_preproc
+    pp.get_feature_statistics
+    pp.qc_lab_measurements
 ```
 
 ## Tools

ehrdata/io/_omop.py

@@ -490,10 +490,11 @@ def to_dataframe(
             df = df.rename(columns={"entry": "visit_occurrence_id"})
             del df["subentry"]
 
+        """
         for col in df.columns:
             if col.endswith("time"):
                 df[col] = pd.to_datetime(df[col])
-
+        """
         df["feature_name"] = feature
         df_concat = pd.concat([df_concat, df], axis=0)
 

ehrdata/utils/_omop_utils.py

@@ -109,6 +109,7 @@ def get_omop_cdm_field_level():
     return df
 
 
+# TODO also check column data type
 def check_with_omop_cdm(folder_path: str, delimiter: str = None, make_filename_lowercase: bool = True) -> dict:
     """Check if the data adheres to the OMOP Common Data Model (CDM) version 5.4 standards
 
@@ -519,15 +520,15 @@ def get_feature_info(
         if isinstance(feature, numbers.Integral):
             feature_id = feature
             feature_id_1, feature_id_2 = map_concept_id(adata_dict=adata_dict, concept_id=feature_id, verbose=False)
-            try:
+            if feature_id_1 in df_concept["concept_id"].values:
                 feature_name = df_concept[df_concept["concept_id"] == feature_id_1]["concept_name"].values[0]
-            except KeyError:
+            else:
                 if ignore_not_shown_in_concept_table:
                     fetures_not_shown_in_concept_table.append(feature)
-                    continue
+                    feature_name = feature_id_1
                 else:
                     rprint(f"Feature ID - [red]{feature_id_1}[/] could not be found in concept table")
-                    raise
+                    raise ValueError
             match_1_ratio = 100
 
         # if the input is feature name