support condition_occurrence

theislab · Nov 21, 2024 · 056340e · 056340e
1 parent 5b38706
commit 056340e
Show file tree

Hide file tree

Showing 4 changed files with 85 additions and 6 deletions.
diff --git a/src/ehrdata/io/omop/_check_arguments.py b/src/ehrdata/io/omop/_check_arguments.py
@@ -12,7 +12,7 @@
 VALID_OBSERVATION_TABLES_SINGLE = ["person"]
 VALID_OBSERVATION_TABLES_JOIN = ["person_cohort", "person_observation_period", "person_visit_occurrence"]
 VALID_VARIABLE_TABLES = ["measurement", "observation", "specimen"]
-VALID_INTERVAL_VARIABLE_TABLES = ["drug_exposure"]
+VALID_INTERVAL_VARIABLE_TABLES = ["drug_exposure", "condition_occurrence"]
 VALID_KEEP_DATES = ["start", "end", "interval"]
 
 

diff --git a/src/ehrdata/io/omop/_queries.py b/src/ehrdata/io/omop/_queries.py
@@ -24,7 +24,16 @@
     "observation": "observation",
     "specimen": "specimen",
     "drug_exposure": "drug",
+    "condition_occurrence": "condition",
 }
+DATA_TABLE_DATE_TRUNK = {
+    "measurement": "measurement",
+    "observation": "observation",
+    "specimen": "specimen",
+    "drug_exposure": "drug_exposure",
+    "condition_occurrence": "condition",
+}
+
 
 AGGREGATION_STRATEGY_KEY = {
     "last": "LAST",
@@ -147,7 +156,7 @@ def time_interval_table_query_long_format(
         ) \
         SELECT lfi.person_id, lfi.data_table_concept_id, interval_step, interval_start, interval_end, {_generate_value_query("data_table_with_presence_indicator", data_field_to_keep, AGGREGATION_STRATEGY_KEY[aggregation_strategy])} \
         FROM long_format_intervals as lfi \
-        LEFT JOIN data_table_with_presence_indicator ON lfi.person_id = data_table_with_presence_indicator.person_id AND lfi.data_table_concept_id = data_table_with_presence_indicator.{DATA_TABLE_CONCEPT_ID_TRUNK[data_table]}_concept_id AND data_table_with_presence_indicator.{data_table}_{date_prefix}date BETWEEN lfi.interval_start AND lfi.interval_end \
+        LEFT JOIN data_table_with_presence_indicator ON lfi.person_id = data_table_with_presence_indicator.person_id AND lfi.data_table_concept_id = data_table_with_presence_indicator.{DATA_TABLE_CONCEPT_ID_TRUNK[data_table]}_concept_id AND data_table_with_presence_indicator.{DATA_TABLE_DATE_TRUNK[data_table]}_{date_prefix}date BETWEEN lfi.interval_start AND lfi.interval_end \
         GROUP BY lfi.person_id, lfi.data_table_concept_id, interval_step, interval_start, interval_end
         """
     ).df()
@@ -222,9 +231,9 @@ def time_interval_table_for_interval_tables_query_long_format(
         FROM long_format_intervals as lfi \
         LEFT JOIN data_table_with_presence_indicator ON lfi.person_id = data_table_with_presence_indicator.person_id \
                 AND lfi.data_table_concept_id = data_table_with_presence_indicator.{DATA_TABLE_CONCEPT_ID_TRUNK[data_table]}_concept_id \
-                AND (data_table_with_presence_indicator.{data_table}_start_date BETWEEN lfi.interval_start AND lfi.interval_end \
-                    OR data_table_with_presence_indicator.{data_table}_end_date BETWEEN lfi.interval_start AND lfi.interval_end \
-                    OR (data_table_with_presence_indicator.{data_table}_start_date < lfi.interval_start AND data_table_with_presence_indicator.{data_table}_end_date > lfi.interval_end)) \
+                AND (data_table_with_presence_indicator.{DATA_TABLE_DATE_TRUNK[data_table]}_start_date BETWEEN lfi.interval_start AND lfi.interval_end \
+                    OR data_table_with_presence_indicator.{DATA_TABLE_DATE_TRUNK[data_table]}_end_date BETWEEN lfi.interval_start AND lfi.interval_end \
+                    OR (data_table_with_presence_indicator.{DATA_TABLE_DATE_TRUNK[data_table]}_start_date < lfi.interval_start AND data_table_with_presence_indicator.{DATA_TABLE_DATE_TRUNK[data_table]}_end_date > lfi.interval_end)) \
         GROUP BY lfi.person_id, lfi.data_table_concept_id, interval_step, interval_start, interval_end
         """
     ).df()

diff --git a/tests/data/toy_omop/vanilla/condition_occurrence.csv b/tests/data/toy_omop/vanilla/condition_occurrence.csv
@@ -0,0 +1,10 @@
+condition_occurrence_id,person_id,condition_concept_id,condition_start_date,condition_start_datetime,condition_end_date,condition_end_datetime,condition_type_concept_id,condition_status_concept_id,stop_reason,provider_id,visit_occurrence_id,visit_detail_id,condition_source_value,condition_source_concept_id,condition_status_source_value
+1,1,43530622,2100-01-01,2100-01-01 12:00:00,2100-01-31,2100-01-31 00:00:00,38000175,0,,0,31,,10,1121000119107,
+2,1,43530622,2100-02-01,2100-02-01 12:00:00,2100-02-28,2100-02-28 00:00:00,38000175,0,,0,28,,10,1121000119107,
+3,1,4112343,2100-01-01,2100-01-01 12:00:00,2100-01-31,2100-01-31 00:00:00,38000175,0,,0,31,,15,4112343,
+4,2,43530622,2100-01-01,2100-01-01 12:00:00,2100-01-31,2100-01-31 00:00:00,38000175,0,,0,31,,10,1121000119107,
+5,2,43530622,2100-02-01,2100-02-01 12:00:00,2100-02-28,2100-02-28 00:00:00,38000175,0,,0,28,,10,1121000119107,
+6,2,4112343,2100-01-01,2100-01-01 12:00:00,2100-01-31,2100-01-31 00:00:00,38000175,0,,0,31,,15,4112343,
+7,3,43530622,2100-01-01,2100-01-01 12:00:00,2100-01-31,2100-01-31 00:00:00,38000175,0,,0,31,,10,1121000119107,
+8,3,43530622,2100-02-01,2100-02-01 12:00:00,2100-02-28,2100-02-28 00:00:00,38000175,0,,0,28,,10,1121000119107,
+9,3,4112343,2100-01-01,2100-01-01 12:00:00,2100-01-31,2100-01-31 00:00:00,38000175,0,,0,31,,15,4112343,
diff --git a/tests/test_io/test_omop.py b/tests/test_io/test_omop.py
@@ -16,6 +16,7 @@
     "observation": 2,
     "specimen": 2,
     "drug_exposure": 2,
+    "condition_occurrence": 2,
 }
 
 # constants for setup_variables
@@ -261,7 +262,66 @@ def test_setup_variables(
                 [[1, 1, 1, 1], [1, 1, 1, 1]],
             ],
         ),
-        # (["condition_occurrence"], ["is_present"]), # TODO: write test file
+        (
+            ["condition_occurrence"],
+            ["condition_source_value"],
+            "start",
+            [
+                [[15, np.nan, np.nan, np.nan], [10, np.nan, np.nan, np.nan]],
+                [[15, np.nan, np.nan, np.nan], [10, np.nan, np.nan, np.nan]],
+                [[15, np.nan, np.nan, np.nan], [10, np.nan, np.nan, np.nan]],
+            ],
+        ),
+        (
+            ["condition_occurrence"],
+            ["condition_source_value"],
+            "end",
+            [
+                [[np.nan, np.nan, np.nan, np.nan], [np.nan, np.nan, np.nan, np.nan]],
+                [[np.nan, np.nan, np.nan, np.nan], [np.nan, np.nan, np.nan, np.nan]],
+                [[np.nan, np.nan, np.nan, np.nan], [np.nan, np.nan, np.nan, np.nan]],
+            ],
+        ),
+        (
+            ["condition_occurrence"],
+            ["condition_source_value"],
+            "interval",
+            [
+                [[15, 15, 15, 15], [10, 10, 10, 10]],
+                [[15, 15, 15, 15], [10, 10, 10, 10]],
+                [[15, 15, 15, 15], [10, 10, 10, 10]],
+            ],
+        ),
+        (
+            ["condition_occurrence"],
+            ["is_present"],
+            "start",
+            [
+                [[1, np.nan, np.nan, np.nan], [1, np.nan, np.nan, np.nan]],
+                [[1, np.nan, np.nan, np.nan], [1, np.nan, np.nan, np.nan]],
+                [[1, np.nan, np.nan, np.nan], [1, np.nan, np.nan, np.nan]],
+            ],
+        ),
+        (
+            ["condition_occurrence"],
+            ["is_present"],
+            "end",
+            [
+                [[np.nan, np.nan, np.nan, np.nan], [np.nan, np.nan, np.nan, np.nan]],
+                [[np.nan, np.nan, np.nan, np.nan], [np.nan, np.nan, np.nan, np.nan]],
+                [[np.nan, np.nan, np.nan, np.nan], [np.nan, np.nan, np.nan, np.nan]],
+            ],
+        ),
+        (
+            ["condition_occurrence"],
+            ["is_present"],
+            "interval",
+            [
+                [[1, 1, 1, 1], [1, 1, 1, 1]],
+                [[1, 1, 1, 1], [1, 1, 1, 1]],
+                [[1, 1, 1, 1], [1, 1, 1, 1]],
+            ],
+        ),
         # (["procedure_occurrence"], ["is_present"]), # TODO: write test file
         # (["device_exposure"], ["is_present"]), # TODO: write test file
         # (["note"], ["is_present"]),