Small bugfixes

vantage6 · Jul 26, 2023 · de1fab7 · de1fab7
1 parent 364d43d
commit de1fab7
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Showing 2 changed files with 15 additions and 8 deletions.
diff --git a/feature-extraction/ohdsi/feature_extraction/__init__.py b/feature-extraction/ohdsi/feature_extraction/__init__.py
@@ -1,4 +1,5 @@
 import os
+import json
 
 from rpy2 import robjects
 from rpy2.robjects.methods import RS4
@@ -788,10 +789,11 @@ def create_analysis_details(
         ...     included_covariate_ids = []
         ... )
         """
+        parameters_json = json.dumps(parameters)
         return extractor_r.createAnalysisDetails(
             analysis_id,
             sql_file_name,
-            parameters,
+            parameters_json,
             included_covariate_concept_ids,
             add_descendants_to_include,
             excluded_covariate_concept_ids,
@@ -940,7 +942,7 @@ def create_detailed_temporal_covariate_settings(
 class DefaultTemporalCovariateSettings:
 
     @staticmethod
-    def createTemporalCovariateSettings(
+    def create_temporal_covariate_settings(
         use_demographics_gender: bool = False,
         use_demographics_age: bool = False,
         use_demographics_age_group: bool = False,
@@ -1154,6 +1156,10 @@ def createTemporalCovariateSettings(
         ...     use_demographics_age=True,
         ... )
         """
+
+        temporal_start_days_list = list(temporal_start_days)
+        temporal_end_days_list = list(temporal_end_days)
+
         return extractor_r.createTemporalCovariateSettings(
             use_demographics_gender,
             use_demographics_age,
@@ -1196,8 +1202,8 @@ def createTemporalCovariateSettings(
             use_distinct_observation_count,
             use_visit_count,
             use_visit_concept_count,
-            temporal_start_days,
-            temporal_end_days,
+            temporal_start_days_list,
+            temporal_end_days_list,
             included_covariate_concept_ids,
             add_descendants_to_include,
             excluded_covariate_concept_ids,

diff --git a/sqlrender/ohdsi/sqlrender/__init__.py b/sqlrender/ohdsi/sqlrender/__init__.py
@@ -98,7 +98,7 @@ def render(sql: str, warn_on_missing_parameters: bool = True, **kwargs) \
 
     @staticmethod
     def translate(sql: str, target_dialect: str,
-                  temp_emulation_schema: str | None) -> StrVector:
+                  temp_emulation_schema: str | None = None) -> StrVector:
         """
         ``translate`` translates SQL from one dialect to another.
 
@@ -131,7 +131,7 @@ def translate(sql: str, target_dialect: str,
 
     @staticmethod
     def translate_single_statement(
-        sql: str, target_dialect: str, temp_emulation_schema: str | None
+        sql: str, target_dialect: str, temp_emulation_schema: str | None = None
     ) -> StrVector:
         """
         Translates a single SQL statement from one dialect to another.
@@ -294,7 +294,7 @@ def render_sql_file(
     @staticmethod
     def translate_sql_file(source_file: str | Path, target_file: str | Path,
                            target_dialect: str,
-                           temp_emulation_schema: str | None) -> None:
+                           temp_emulation_schema: str | None = None) -> None:
         """
         Translate a SQL file.
 
@@ -334,7 +334,8 @@ def translate_sql_file(source_file: str | Path, target_file: str | Path,
 
     @staticmethod
     def load_render_translate_sql(sql_file: str | Path, package_name: str,
-                                  dbms: str, temp_emulation_schema: str | None,
+                                  dbms: str,
+                                  temp_emulation_schema: str | None = None,
                                   warn_on_missing_parameters: bool = True) \
             -> StrVector:
         """