fix omop_teva

aphp · Apr 25, 2024 · 958a99e · 958a99e
1 parent 7fb049a
commit 958a99e
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Showing 3 changed files with 16 additions and 2 deletions.
diff --git a/eds_scikit/io/omop_teva_default_config.py b/eds_scikit/io/omop_teva_default_config.py
@@ -1,7 +1,8 @@
 default_omop_teva_config = {
     "visit_occurrence": {
         "category_columns": [
-            "visit_occurrence_id" "care_site_short_name",
+            "visit_occurrence_id",
+            "care_site_short_name",
             "stay_source_value",
             "visit_source_value",
             "admission_reason_source_value",

diff --git a/eds_scikit/plot/omop_teva.py b/eds_scikit/plot/omop_teva.py
@@ -1,11 +1,16 @@
 import os
 
 from loguru import logger
+import pickle
 
 from eds_scikit.io import HiveData
 from eds_scikit.io.omop_teva_default_config import default_omop_teva_config
 from eds_scikit.plot.table_viz import reduce_table, visualize_table
 
+def save_pickle(obj, path : str):
+    with open(path, "wb") as outp:
+        pickle.dump(obj, outp)
+
 
 def generate_omop_teva(
     data: HiveData,
@@ -50,6 +55,8 @@ def generate_omop_teva(
         config["date_column"],
         "visit_occurrence_id",
     ]
+    print(visit_columns)
+    print(visit_occurrence.columns)
     visit_occurrence = visit_occurrence[visit_columns]
 
     visit_occurrence_count = reduce_table(
@@ -66,6 +73,7 @@ def generate_omop_teva(
     chart = visualize_table(
         visit_occurrence_count, title="visit_occurrence table dashboard"
     )
+    save_pickle(f"{output_dir}/visit_occurrence_count")
     chart.save(f"{output_dir}/visit_occurrence_chart.html")
 
     logger.info("visit_occurrence processing done.")
@@ -101,6 +109,7 @@ def generate_omop_teva(
     chart = visualize_table(
         procedure_occurrence_count, title="procedure_occurrence table dashboard"
     )
+    save_pickle(f"{output_dir}/procedure_occurrence_count")
     chart.save(f"{output_dir}/procedure_occurrence_chart.html")
 
     logger.info("procedure_occurrence processing done.")
@@ -137,6 +146,7 @@ def generate_omop_teva(
     chart = visualize_table(
         condition_occurrence_count, title="condition_occurrence table dashboard"
     )
+    save_pickle(f"{output_dir}/condition_occurrence_count")
     chart.save(f"{output_dir}/condition_occurrence_chart.html")
 
     logger.info("condition_occurrence processing done.")
@@ -161,6 +171,7 @@ def generate_omop_teva(
         end_date=end_date,
         mapper=config["mapper"],
     )
+    save_pickle(f"{output_dir}/note_count")
     note_count = note_count[~(note_count == 0).any(axis=1)]
     chart = visualize_table(note_count, title="note table dashboard")
     chart.save(f"{output_dir}/note_chart.html")
@@ -197,6 +208,7 @@ def generate_omop_teva(
     chart = visualize_table(
         drg_exposure_count, title="drug exposure prescription table dashboard"
     )
+    save_pickle(f"{output_dir}/drg_exposure_prescription_count")
     chart.save(f"{output_dir}/drug_exposure_prescription.html")
 
     logger.info("drug exposure prescription processing done.")
@@ -231,6 +243,7 @@ def generate_omop_teva(
     chart = visualize_table(
         drg_exposure_count, title="drug exposure administration table dashboard"
     )
+    save_pickle(f"{output_dir}/drug_exposure_administration_count")
     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
@@ -146,7 +146,7 @@ def reduce_table(
 def visualize_table(
     table_count: DataFrame,
     title: str = "table exploration dashboard",
-    description=False,
+    description=True,
 ) -> alt.Chart:
 
     """Generate reduced table dashboard.