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aphp · Apr 18, 2024 · dc4759f · dc4759f
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Showing 3 changed files with 37 additions and 24 deletions.
diff --git a/eds_scikit/io/omop_explorer_default_config.py b/eds_scikit/io/omop_explorer_default_config.py
@@ -45,7 +45,7 @@
         "mapper": {
             "visit_occurrence_id": {"not NaN": ".*"},
             "condition_source_value": {"not NaN": ".*"},
-        }, 
+        },
     },
     "note": {
         "category_columns": [
@@ -59,7 +59,7 @@
         "mapper": {
             "note_class_source_value": {"CR": r"^CR", "CRH": r"^CRH", "LT": r"^LT"},
             "visit_occurrence_id": {"not NaN": ".*"},
-        }, 
+        },
     },
     "drug_exposure_prescription": {
         "category_columns": [
@@ -72,19 +72,19 @@
             "dose_unit_source_value",
             "drug_ucd_source_value",
             "prescription_type_source_value",
-            "cdm_source"
+            "cdm_source",
         ],
         "date_column": "drug_exposure_start_datetime",
         "mapper": {
             "visit_occurrence_id": {"not NaN": ".*"},
             "drug_type_source_value": {"not NaN": ".*"},
             "drug_source_value": {"not NaN": ".*"},
             "drug_class_source_value": {"not NaN": ".*"},
-            "drug_ucd_source_value" : {"not NaN": ".*"},
-            "route_source_value" : {"not NaN": ".*"},
-            "dose_unit_source_value" : {"not NaN": ".*"},
-            "prescription_type_source_value" : {"not NaN": ".*"},
-        }, 
+            "drug_ucd_source_value": {"not NaN": ".*"},
+            "route_source_value": {"not NaN": ".*"},
+            "dose_unit_source_value": {"not NaN": ".*"},
+            "prescription_type_source_value": {"not NaN": ".*"},
+        },
     },
     "drug_exposure_administration": {
         "category_columns": [
@@ -96,18 +96,17 @@
             "route_source_value",
             "dose_unit_source_value",
             "drug_ucd_source_value",
-            "cdm_source"
+            "cdm_source",
         ],
         "date_column": "drug_exposure_start_datetime",
         "mapper": {
             "visit_occurrence_id": {"not NaN": ".*"},
             "drug_type_source_value": {"not NaN": ".*"},
             "drug_source_value": {"not NaN": ".*"},
             "drug_class_source_value": {"not NaN": ".*"},
-            "drug_ucd_source_value" : {"not NaN": ".*"},
-            "route_source_value" : {"not NaN": ".*"},
-            "dose_unit_source_value" : {"not NaN": ".*"},
-        }, 
+            "drug_ucd_source_value": {"not NaN": ".*"},
+            "route_source_value": {"not NaN": ".*"},
+            "dose_unit_source_value": {"not NaN": ".*"},
+        },
     },
-
 }
diff --git a/eds_scikit/plot/omop_explorer.py b/eds_scikit/plot/omop_explorer.py
@@ -1,3 +1,5 @@
+import os
+
 from loguru import logger
 
 from eds_scikit.io import HiveData
@@ -24,7 +26,7 @@ def generate_omop_explorer(
     output_dir : str, optional
         Output directory path, by default "omop_explorer"
     """
-    
+
     if not os.path.exists(f"{output_dir}/"):
         os.makedirs(f"{output_dir}/")
 
@@ -146,15 +148,19 @@ def generate_omop_explorer(
     chart.save(f"{output_dir}/note_chart.html")
 
     logger.info("notes processing done.")
-    
+
     # Drug Exposure Prescription
 
     logger.info("Starting drug exposure prescription processing.")
 
     drg_exposure = data.drug_exposure_prescription
     config = explorer_config["drug_exposure_prescription"]
-    drg_exposure = drg_exposure.merge(visit_occurrence, on="visit_occurrence_id", how="left")
-    drg_exposure["visit_occurrence_id"] = drg_exposure["visit_occurrence_id"].astype(str)
+    drg_exposure = drg_exposure.merge(
+        visit_occurrence, on="visit_occurrence_id", how="left"
+    )
+    drg_exposure["visit_occurrence_id"] = drg_exposure["visit_occurrence_id"].astype(
+        str
+    )
 
     drg_exposure_count = reduce_table(
         drg_exposure,
@@ -165,19 +171,25 @@ def generate_omop_explorer(
         mapper=config["mapper"],
     )
     drg_exposure_count = drg_exposure_count[~(drg_exposure_count == 0).any(axis=1)]
-    chart = visualize_table(drg_exposure_count, title="drug exposure prescription table dashboard")
+    chart = visualize_table(
+        drg_exposure_count, title="drug exposure prescription table dashboard"
+    )
     chart.save(f"{output_dir}/drug_exposure_prescription.html")
 
     logger.info("drug exposure prescription processing done.")
-    
+
     # Drug Exposure Administration
 
     logger.info("Starting drug exposure administration processing.")
 
     drg_exposure = data.drug_exposure_administration
     config = explorer_config["drug_exposure_administration"]
-    drg_exposure = drg_exposure.merge(visit_occurrence, on="visit_occurrence_id", how="left")
-    drg_exposure["visit_occurrence_id"] = drg_exposure["visit_occurrence_id"].astype(str)
+    drg_exposure = drg_exposure.merge(
+        visit_occurrence, on="visit_occurrence_id", how="left"
+    )
+    drg_exposure["visit_occurrence_id"] = drg_exposure["visit_occurrence_id"].astype(
+        str
+    )
 
     drg_exposure_count = reduce_table(
         drg_exposure,
@@ -188,7 +200,9 @@ def generate_omop_explorer(
         mapper=config["mapper"],
     )
     drg_exposure_count = drg_exposure_count[~(drg_exposure_count == 0).any(axis=1)]
-    chart = visualize_table(drg_exposure_count, title="drug exposure administration table dashboard")
+    chart = visualize_table(
+        drg_exposure_count, title="drug exposure administration table dashboard"
+    )
     chart.save(f"{output_dir}/drug_exposure_administration.html")
 
     logger.info("drug exposure administration processing done.")
diff --git a/eds_scikit/plot/table_viz.py b/eds_scikit/plot/table_viz.py
@@ -3,8 +3,8 @@
 
 import altair as alt
 import pandas as pd
-from eds_scikit.plot.altair_utils import generate_color_map
 
+from eds_scikit.plot.altair_utils import generate_color_map
 from eds_scikit.utils.checks import check_columns
 from eds_scikit.utils.framework import get_framework, to