Merge pull request #6 from VectorInstitute/add_procedures_method_mimiciv

Add custom procedures method that joins on d_procedures
VectorInstitute · Nov 30, 2023 · 15f0b34 · 15f0b34
2 parents 813bdee + d65e53b
commit 15f0b34
Show file tree

Hide file tree

Showing 4 changed files with 173 additions and 154 deletions.
diff --git a/cycquery/mimiciv.py b/cycquery/mimiciv.py
@@ -87,18 +87,11 @@ def patients(
 
         return QueryInterface(self.db, table)
 
-    def diagnoses(
+    def diagnoses_icd(
         self,
     ) -> QueryInterface:
         """Query MIMIC diagnosis data.
 
-        Parameters
-        ----------
-        join
-            Join arguments.
-        ops
-            Additional operations to apply to the query.
-
         Returns
         -------
         cycquery.interface.QueryInterface
@@ -116,6 +109,28 @@ def diagnoses(
 
         return QueryInterface(self.db, table)
 
+    def procedures_icd(
+        self,
+    ) -> QueryInterface:
+        """Query MIMIC procedures data.
+
+        Returns
+        -------
+        cycquery.interface.QueryInterface
+            Constructed query, wrapped in an interface object.
+
+        """
+        table = self.get_table("mimiciv_hosp", "procedures_icd")
+
+        # Join with procedures dimension table.
+        table = qo.Join(
+            join_table=self.get_table("mimiciv_hosp", "d_icd_procedures"),
+            on=["icd_code", "icd_version"],
+            on_to_type=["str", "int"],
+        )(table)
+
+        return QueryInterface(self.db, table)
+
     def labevents(
         self,
     ) -> QueryInterface:

diff --git a/docs/source/tutorials/mimiciv.ipynb b/docs/source/tutorials/mimiciv.ipynb
@@ -107,7 +107,7 @@
     "    qo.ConditionInYears(\"admittime\", \"2015\"),\n",
     ")\n",
     "patient_admissions = patient_admissions.ops(ops)\n",
-    "diagnoses = querier.diagnoses()\n",
+    "diagnoses = querier.diagnoses_icd()\n",
     "diagnoses_ops = qo.Sequential(\n",
     "    qo.ConditionEquals(\"icd_version\", 10),\n",
     "    qo.ConditionSubstring(\"long_title\", \"schizophrenia\"),\n",
@@ -143,7 +143,7 @@
     "    qo.ConditionInYears(\"admittime\", \"2015\"),\n",
     ")\n",
     "patient_admissions = patient_admissions.ops(ops)\n",
-    "diagnoses = querier.diagnoses()\n",
+    "diagnoses = querier.diagnoses_icd()\n",
     "diagnoses_ops = qo.Sequential(\n",
     "    qo.ConditionEquals(\"icd_version\", 9),\n",
     "    qo.ConditionRegexMatch(\"long_title\", r\"(?=.*schizophrenia)(?=.*chronic)\"),\n",