remove cursors and use schema name in queries

notebooks/crrt-notebook.ipynb

@@ -109,7 +109,6 @@
     "and lower(label) like '%crrt%'\n",
     "\"\"\"\n",
     "df = pd.read_sql_query(query,con)\n",
-    "cur.close()\n",
     "\n",
     "df"
    ]
@@ -141,11 +140,7 @@
    },
    "outputs": [],
    "source": [
-    "cur = con.cursor()\n",
-    "cur.execute('SET search_path to ' + schema_name)\n",
-    "\n",
-    "\n",
-    "query = \"\"\"\n",
+    "query = query_schema + \"\"\"\n",
     "select itemid, label, category, linksto\n",
     "from d_items di\n",
     "where dbsource = 'metavision'\n",
@@ -156,7 +151,6 @@
     "order by linksto, category, label\n",
     "\"\"\"\n",
     "df = pd.read_sql_query(query,con)\n",
-    "cur.close()\n",
     "\n",
     "HTML(df.head().to_html().replace('NaN', ''))"
    ]
@@ -315,11 +309,7 @@
    },
    "outputs": [],
    "source": [
-    "cur = con.cursor()\n",
-    "cur.execute('SET search_path to ' + schema_name)\n",
-    "\n",
-    "\n",
-    "query = \"\"\"\n",
+    "query = query_schema + \"\"\"\n",
     "select\n",
     "  ce.icustay_id, di.label, ce.charttime\n",
     "  , ce.value\n",
@@ -350,7 +340,6 @@
     "order by ce.icustay_id, ce.charttime, di.label;\n",
     "\"\"\"\n",
     "df = pd.read_sql_query(query,con)\n",
-    "cur.close()\n",
     "\n",
     "HTML(df.head().to_html().replace('NaN', ''))"
    ]
@@ -404,7 +393,7 @@
    "source": [
     "def print_itemid_info(con, itemid):\n",
     "    # get name of itemid\n",
-    "    query = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "    query = query_schema + \"\"\"\n",
     "    select label\n",
     "    from d_items\n",
     "    where itemid = \"\"\" + str(itemid)\n",
@@ -413,7 +402,7 @@
     "    print('Values for {} - {}...'.format(itemid, df['label'][0]))\n",
     "    \n",
     "    \n",
-    "    query = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "    query = query_schema + \"\"\"\n",
     "    select value\n",
     "    , count(distinct icustay_id) as number_of_patients\n",
     "    , count(icustay_id) as number_of_observations\n",
@@ -634,7 +623,6 @@
     "from t1\n",
     "\"\"\"\n",
     "df = pd.read_sql_query(query,con)\n",
-    "cur.close()\n",
     "\n",
     "HTML(df.to_html().replace('NaN', ''))"
    ]
@@ -654,7 +642,7 @@
    },
    "outputs": [],
    "source": [
-    "query = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "query = query_schema + \"\"\"\n",
     "with t1 as \n",
     "(\n",
     "select icustay_id, charttime\n",
@@ -874,7 +862,7 @@
    "outputs": [],
    "source": [
     "print(\"Durations from INPUTEVENTS for one patient with KCl...\")\n",
-    "query = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "query = query_schema + \"\"\"\n",
     "select \n",
     "    linkorderid\n",
     "  , orderid\n",
@@ -967,7 +955,7 @@
    "outputs": [],
    "source": [
     "print(\"Durations from INPUTEVENTS_MV, new events noted with time_partition...\")\n",
-    "query = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "query = query_schema + \"\"\"\n",
     "with t1 as\n",
     "(\n",
     "select \n",
@@ -1036,7 +1024,7 @@
    "outputs": [],
    "source": [
     "print(\"Durations from INPUTEVENTS for one patient with KCl...\")\n",
-    "query = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "query = query_schema + \"\"\"\n",
     "with t1 as\n",
     "(\n",
     "select icustay_id\n",
@@ -1106,7 +1094,7 @@
    "outputs": [],
    "source": [
     "print(\"Durations from INPUTEVENTS for one patient with KCl...\")\n",
-    "query = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "query = query_schema + \"\"\"\n",
     "with t1 as\n",
     "(\n",
     "select icustay_id\n",
@@ -1199,7 +1187,7 @@
    "outputs": [],
    "source": [
     "print(\"Durations from INPUTEVENTS for one patient with KCl...\")\n",
-    "query = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "query = query_schema + \"\"\"\n",
     "with t1 as\n",
     "(\n",
     "select icustay_id\n",
@@ -1276,7 +1264,7 @@
    },
    "outputs": [],
    "source": [
-    "query_inputevents = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "query_inputevents = query_schema + \"\"\"\n",
     "with t1 as\n",
     "(\n",
     "select icustay_id\n",
@@ -1353,7 +1341,7 @@
    "outputs": [],
    "source": [
     "print(\"Durations from INPUTEVENTS for one patient given propofol...\")\n",
-    "query = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "query = query_schema + \"\"\"\n",
     "with t1 as\n",
     "(\n",
     "select icustay_id\n",
@@ -1404,7 +1392,7 @@
    "outputs": [],
    "source": [
     "print(\"Grouped durations from INPUTEVENTS for one patient given propofol...\")\n",
-    "query = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "query = query_schema + \"\"\"\n",
     "with t1 as\n",
     "(\n",
     "select icustay_id\n",
@@ -1466,7 +1454,7 @@
     "# convert CHARTEVENTS into durations\n",
     "# NOTE: we only look at a single patient as an exemplar\n",
     "print(\"Durations from CHARTEVENTS...\")\n",
-    "query = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "query = query_schema + \"\"\"\n",
     "with crrt_settings as\n",
     "(\n",
     "select ce.icustay_id, ce.charttime\n",
@@ -1642,7 +1630,7 @@
    "outputs": [],
    "source": [
     "# happy with the above query - repeat it without the isolation to a single ICUSTAY_ID\n",
-    "query_chartevents = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "query_chartevents = query_schema + \"\"\"\n",
     "with crrt_settings as\n",
     "(\n",
     "select ce.icustay_id, ce.charttime\n",
@@ -1833,7 +1821,7 @@
     "# extract the durations from PROCEDUREEVENTS_MV\n",
     "# NOTE: we only look at a single patient as an exemplar\n",
     "print(\"Durations from PROCEDUREEVENTS_MV...\")\n",
-    "query = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "query = query_schema + \"\"\"\n",
     "select icustay_id\n",
     "  , ROW_NUMBER() over (partition by icustay_id order by starttime, endtime) as num\n",
     "  , starttime, endtime\n",
@@ -1869,7 +1857,7 @@
    "outputs": [],
    "source": [
     "# happy with above query\n",
-    "query_procedureevents = 'SET search_path to ' + schema_name + \"\"\";\n",
+    "query_procedureevents = query_schema + \"\"\"\n",
     "select icustay_id\n",
     "  , ROW_NUMBER() over (partition by icustay_id order by starttime, endtime) as num\n",
     "  , starttime, endtime\n",