support condition_era

theislab · Nov 22, 2024 · e4ad1db · e4ad1db
1 parent 0525855
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diff --git a/src/ehrdata/io/omop/_check_arguments.py b/src/ehrdata/io/omop/_check_arguments.py
@@ -19,6 +19,7 @@
     "device_exposure",
     "drug_era",
     "dose_era",
+    "condition_era",
 ]
 VALID_KEEP_DATES = ["start", "end", "interval"]
 

diff --git a/src/ehrdata/io/omop/_queries.py b/src/ehrdata/io/omop/_queries.py
@@ -19,6 +19,7 @@
     "device_exposure": "device",
     "drug_era": "drug",
     "dose_era": "drug",
+    "condition_era": "condition",
 }
 
 DATA_TABLE_DATE_KEYS = {
@@ -37,6 +38,7 @@
         "device_exposure": "device_exposure_start_date",
         "drug_era": "drug_era_start_date",
         "dose_era": "dose_era_start_date",
+        "condition_era": "condition_era_start_date",
     },
     "end": {
         "visit_occurrence": "visit_end_date",
@@ -48,6 +50,7 @@
         "device_exposure": "device_exposure_end_date",
         "drug_era": "drug_era_end_date",
         "dose_era": "dose_era_end_date",
+        "condition_era": "condition_era_end_date",
     },
 }
 

diff --git a/tests/data/toy_omop/vanilla/condition_era.csv b/tests/data/toy_omop/vanilla/condition_era.csv
@@ -0,0 +1,10 @@
+condition_era_id,person_id,condition_concept_id,condition_era_start_date,condition_era_end_date,condition_occurrence_count
+1,1,4140598,2100-01-01,2100-01-31,256
+2,1,4140598,2100-02-01,2100-02-28,256
+3,1,434610,2100-01-01,2100-01-31,1
+4,2,4140598,2100-01-01,2100-01-31,256
+5,2,4140598,2100-02-01,2100-02-28,256
+6,2,434610,2100-01-01,2100-01-31,1
+7,3,4140598,2100-01-01,2100-01-31,256
+8,3,4140598,2100-02-01,2100-02-28,256
+9,3,434610,2100-01-01,2100-01-31,1
diff --git a/tests/test_io/test_omop.py b/tests/test_io/test_omop.py
@@ -21,6 +21,7 @@
     "device_exposure": 2,
     "drug_era": 2,
     "dose_era": 2,
+    "condition_era": 2,
 }
 
 # constants for setup_variables
@@ -566,6 +567,66 @@ def test_setup_variables(
                 [[1, 1, 1, 1], [1, 1, 1, 1]],
             ],
         ),
+        (
+            ["condition_era"],
+            ["condition_occurrence_count"],
+            "start",
+            [
+                [[1, np.nan, np.nan, np.nan], [256, np.nan, np.nan, np.nan]],
+                [[1, np.nan, np.nan, np.nan], [256, np.nan, np.nan, np.nan]],
+                [[1, np.nan, np.nan, np.nan], [256, np.nan, np.nan, np.nan]],
+            ],
+        ),
+        (
+            ["condition_era"],
+            ["condition_occurrence_count"],
+            "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_era"],
+            ["condition_occurrence_count"],
+            "interval",
+            [
+                [[1, 1, 1, 1], [256, 256, 256, 256]],
+                [[1, 1, 1, 1], [256, 256, 256, 256]],
+                [[1, 1, 1, 1], [256, 256, 256, 256]],
+            ],
+        ),
+        (
+            ["condition_era"],
+            ["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_era"],
+            ["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_era"],
+            ["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]],
+            ],
+        ),
     ],
 )
 @pytest.mark.parametrize(