Merge pull request #765 from OHDSI/location_export

Location table export to ares
OHDSI · Jul 18, 2024 · d519971 · d519971
2 parents b6ff655 + d2e0bfd
commit d519971
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Showing 6 changed files with 101 additions and 55 deletions.
diff --git a/R/exportToAres.R b/R/exportToAres.R
@@ -1915,6 +1915,18 @@ generateDataDensityTotal <- function(connection, resultsDatabaseSchema) {
   return(data)
 }
 
+generateLocationData <- function(connection, resultsDatabaseSchema) {
+  renderedSql <- SqlRender::loadRenderTranslateSql(
+    sqlFilename = "export/location/sqlLocationTable.sql",
+    packageName = "Achilles",
+    dbms = connection@dbms,
+    results_database_schema = resultsDatabaseSchema
+  )
+
+  locationData <- DatabaseConnector::querySql(connection, renderedSql)
+  return(locationData)
+}
+
 generateDataDensityRecordsPerPerson <- function(connection, resultsDatabaseSchema) {
   renderedSql <- SqlRender::loadRenderTranslateSql(
     sqlFilename = "export/datadensity/recordsperperson.sql",
@@ -2292,6 +2304,10 @@ exportToAres <- function(
     filename <- file.path(sourceOutputPath, "death.json")
     write(jsonlite::toJSON(currentTable), filename)
 
+    writeLines("Generating location report")
+    currentTable <- generateLocationData(conn, resultsDatabaseSchema)
+    filename <- file.path(sourceOutputPath, "location.csv")
+    data.table::fwrite(currentTable, file = filename)
     writeLines("Generating domain summary reports")
 
     # domain summary - conditions
@@ -2636,4 +2652,4 @@ exportToAres <- function(
     jsonOutput = jsonlite::toJSON(currentTable)
     write(jsonOutput, file = paste0(sourceOutputPath, "/person.json"))
   }
-}
+}
diff --git a/inst/sql/sql_server/analyses/1100.sql b/inst/sql/sql_server/analyses/1100.sql
@@ -2,23 +2,24 @@
 
 --HINT DISTRIBUTE_ON_KEY(stratum_1)
 WITH rawData AS (
-  select
-    left(l1.zip,3) as stratum_1,
-    COUNT_BIG(distinct person_id) as count_value
-  from @cdmDatabaseSchema.person p1
-    inner join @cdmDatabaseSchema.location l1
-    on p1.location_id = l1.location_id
-  where p1.location_id is not null
-    and l1.zip is not null
-  group by left(l1.zip,3)
+  SELECT
+    LEFT(l1.zip, 3) AS stratum_1,
+    l1.location_id AS stratum_2,
+    COUNT_BIG(DISTINCT p1.person_id) AS count_value
+  FROM @cdmDatabaseSchema.person p1
+  INNER JOIN @cdmDatabaseSchema.location l1
+    ON p1.location_id = l1.location_id
+  WHERE p1.location_id IS NOT NULL
+    AND l1.zip IS NOT NULL
+  GROUP BY LEFT(l1.zip, 3), l1.location_id
 )
 SELECT
-  1100 as analysis_id,
-  CAST(stratum_1 AS VARCHAR(255)) as stratum_1,
-  cast(null as varchar(255)) as stratum_2,
-  cast(null as varchar(255)) as stratum_3,
-  cast(null as varchar(255)) as stratum_4,
-  cast(null as varchar(255)) as stratum_5,
+  1100 AS analysis_id,
+  CAST(stratum_1 AS VARCHAR(255)) AS stratum_1,
+  CAST(stratum_2 AS VARCHAR(255)) AS stratum_2,
+  CAST(NULL AS VARCHAR(255)) AS stratum_3,
+  CAST(NULL AS VARCHAR(255)) AS stratum_4,
+  CAST(NULL AS VARCHAR(255)) AS stratum_5,
   count_value
-into @scratchDatabaseSchema@schemaDelim@tempAchillesPrefix_1100
+INTO @scratchDatabaseSchema@schemaDelim@tempAchillesPrefix_1100
 FROM rawData;
diff --git a/inst/sql/sql_server/analyses/1101.sql b/inst/sql/sql_server/analyses/1101.sql
@@ -1,14 +1,18 @@
 -- 1101	Number of persons by location state
 
 --HINT DISTRIBUTE_ON_KEY(stratum_1)
-select 1101 as analysis_id,  
-	CAST(l1.state AS VARCHAR(255)) as stratum_1, 
-	cast(null as varchar(255)) as stratum_2, cast(null as varchar(255)) as stratum_3, cast(null as varchar(255)) as stratum_4, cast(null as varchar(255)) as stratum_5,
-	COUNT_BIG(distinct person_id) as count_value
-into @scratchDatabaseSchema@schemaDelim@tempAchillesPrefix_1101
-from @cdmDatabaseSchema.person p1
-	inner join @cdmDatabaseSchema.location l1
-	on p1.location_id = l1.location_id
-where p1.location_id is not null
-	and l1.state is not null
-group by l1.state;
+SELECT 
+  1101 AS analysis_id,
+  CAST(l1.state AS VARCHAR(255)) AS stratum_1,
+  CAST(l1.location_id AS VARCHAR(255)) AS stratum_2,
+  CAST(NULL AS VARCHAR(255)) AS stratum_3,
+  CAST(NULL AS VARCHAR(255)) AS stratum_4,
+  CAST(NULL AS VARCHAR(255)) AS stratum_5,
+  COUNT_BIG(DISTINCT p1.person_id) AS count_value
+INTO @scratchDatabaseSchema@schemaDelim@tempAchillesPrefix_1101
+FROM @cdmDatabaseSchema.person p1
+INNER JOIN @cdmDatabaseSchema.location l1
+  ON p1.location_id = l1.location_id
+WHERE p1.location_id IS NOT NULL
+  AND l1.state IS NOT NULL
+GROUP BY l1.state, l1.location_id;
diff --git a/inst/sql/sql_server/analyses/1102.sql b/inst/sql/sql_server/analyses/1102.sql
@@ -2,23 +2,25 @@
 
 --HINT DISTRIBUTE_ON_KEY(stratum_1)
 WITH rawData AS (
-  select
-    left(l1.zip,3) as stratum_1,
-    COUNT_BIG(distinct care_site_id) as count_value
-  from @cdmDatabaseSchema.care_site cs1
-    inner join @cdmDatabaseSchema.location l1
-    on cs1.location_id = l1.location_id
-  where cs1.location_id is not null
-    and l1.zip is not null
-  group by left(l1.zip,3)
+  SELECT
+    LEFT(l1.zip, 3) AS stratum_1,
+    cs1.location_id AS stratum_2,
+    COUNT_BIG(DISTINCT cs1.care_site_id) AS count_value
+  FROM @cdmDatabaseSchema.care_site cs1
+  INNER JOIN @cdmDatabaseSchema.location l1
+    ON cs1.location_id = l1.location_id
+  WHERE cs1.location_id IS NOT NULL
+    AND l1.zip IS NOT NULL
+  GROUP BY LEFT(l1.zip, 3), cs1.location_id
 )
 SELECT
-  1102 as analysis_id,
-  CAST(stratum_1 AS VARCHAR(255)) as stratum_1,
-  cast(null as varchar(255)) as stratum_2,
-  cast(null as varchar(255)) as stratum_3,
-  cast(null as varchar(255)) as stratum_4,
-  cast(null as varchar(255)) as stratum_5,
+  1102 AS analysis_id,
+  CAST(stratum_1 AS VARCHAR(255)) AS stratum_1,
+  CAST(stratum_2 AS VARCHAR(255)) AS stratum_2,
+  CAST(NULL AS VARCHAR(255)) AS stratum_3,
+  CAST(NULL AS VARCHAR(255)) AS stratum_4,
+  CAST(NULL AS VARCHAR(255)) AS stratum_5,
   count_value
-into @scratchDatabaseSchema@schemaDelim@tempAchillesPrefix_1102
+INTO @scratchDatabaseSchema@schemaDelim@tempAchillesPrefix_1102
 FROM rawData;
+
diff --git a/inst/sql/sql_server/analyses/1103.sql b/inst/sql/sql_server/analyses/1103.sql
@@ -1,14 +1,18 @@
 -- 1103	Number of care sites by location state
 
 --HINT DISTRIBUTE_ON_KEY(stratum_1)
-select 1103 as analysis_id,  
-	CAST(l1.state AS VARCHAR(255)) as stratum_1, 
-	cast(null as varchar(255)) as stratum_2, cast(null as varchar(255)) as stratum_3, cast(null as varchar(255)) as stratum_4, cast(null as varchar(255)) as stratum_5,
-	COUNT_BIG(distinct care_site_id) as count_value
-into @scratchDatabaseSchema@schemaDelim@tempAchillesPrefix_1103
-from @cdmDatabaseSchema.care_site cs1
-	inner join @cdmDatabaseSchema.location l1
-	on cs1.location_id = l1.location_id
-where cs1.location_id is not null
-	and l1.state is not null
-group by l1.state;
+SELECT 
+  1103 AS analysis_id,
+  CAST(l1.state AS VARCHAR(255)) AS stratum_1,
+  CAST(cs1.location_id AS VARCHAR(255)) AS stratum_2,
+  CAST(NULL AS VARCHAR(255)) AS stratum_3,
+  CAST(NULL AS VARCHAR(255)) AS stratum_4,
+  CAST(NULL AS VARCHAR(255)) AS stratum_5,
+  COUNT_BIG(DISTINCT cs1.care_site_id) AS count_value
+INTO @scratchDatabaseSchema@schemaDelim@tempAchillesPrefix_1103
+FROM @cdmDatabaseSchema.care_site cs1
+INNER JOIN @cdmDatabaseSchema.location l1
+  ON cs1.location_id = l1.location_id
+WHERE cs1.location_id IS NOT NULL
+  AND l1.state IS NOT NULL
+GROUP BY l1.state, cs1.location_id;
diff --git a/inst/sql/sql_server/export/location/sqlLocationTable.sql b/inst/sql/sql_server/export/location/sqlLocationTable.sql
@@ -0,0 +1,19 @@
+WITH denom AS (
+    SELECT 
+        count_value 
+    FROM 
+        @results_database_schema.achilles_results 
+    WHERE 
+        analysis_id = 1
+)
+SELECT 
+    c.analysis_id AS analysis_id,
+    c.stratum_1 AS location_name,
+    c.stratum_2 AS location_id,
+    c.count_value AS count_persons,
+    1.0 * c.count_value / denom.count_value AS percent_persons
+FROM 
+    @results_database_schema.achilles_results c,
+    denom
+WHERE 
+    c.analysis_id BETWEEN 1100 AND 1103;