fixing tests

aphp · Feb 8, 2024 · 94558a4 · 94558a4
1 parent c415802
commit 94558a4
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Showing 6 changed files with 96 additions and 89 deletions.
diff --git a/eds_scikit/biology/cleaning/main.py b/eds_scikit/biology/cleaning/main.py
@@ -53,7 +53,7 @@ def bioclean(
         concepts_sets = fetch_all_concepts_set()
 
     measurements = prepare_measurement_table(
-        data, start_date, end_date, concepts_sets, convert_units
+        data, start_date, end_date, concepts_sets, False, convert_units
     )
     # Filter Measurement.
     if studied_cohort:
@@ -70,4 +70,6 @@ def bioclean(
     )
     # Plot values
     value_column = "value_as_number_normalized" if convert_units else "value_as_number"
-    plot_biology_summary(measurements, value_column)
+    unit_column = "unit_source_value_normalized" if convert_units else "unit_source_value"
+
+    plot_biology_summary(measurements, value_column, unit_column)
diff --git a/eds_scikit/biology/utils/prepare_measurement.py b/eds_scikit/biology/utils/prepare_measurement.py
@@ -94,7 +94,6 @@ def prepare_measurement_table(
         measurement["value_as_number_normalized"] = (
             measurement["value_as_number"] * measurement["factor"]
         )
-
     if is_koalas(measurement):
         measurement.cache()
         logger.info("Done. Once computed, measurement will be cached.")

diff --git a/eds_scikit/biology/utils/process_concepts.py b/eds_scikit/biology/utils/process_concepts.py
@@ -41,14 +41,18 @@ def add_concept_codes(
             raise TypeError
         if isinstance(concept_codes, str):
             concept_codes = [concept_codes]
-        if isinstance(concept_codes, list):
+        elif isinstance(concept_codes, list):
+            for concept_code in concept_codes:
+                if not(isinstance(concept_code, str)):
+                    logger.error("concept_codes must be string or list of string")
+                    raise TypeError
             if not (terminology in self.concept_codes.keys()):
                 self.concept_codes[terminology] = []
             for concept_code in concept_codes:
                 if concept_code not in self.concept_codes[terminology]:
                     self.concept_codes[terminology].append(concept_code)
         else:
-            logger.error("concept_codes must be string or list")
+            logger.error("concept_codes must be string or list of string")
             raise TypeError
 
     def remove_concept_codes(