diff --git a/cycquery/mimiciv.py b/cycquery/mimiciv.py index 25f6da7..014274b 100644 --- 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 index 049614a..a05874c 100644 --- 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\", 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assert "patients" in custom_tables - assert "diagnoses" in custom_tables + assert "diagnoses_icd" in custom_tables + assert "procedures_icd" in custom_tables assert "labevents" in custom_tables assert "chartevents" in custom_tables