Brought back missing analyses, bugfixes for PG/Oracle, Redshift (#321)

* Fix for #317 (more Oracle cast issues), #313 (allow vocabDatabaseSchema parameter in achillesHeel), #312 (convert cdmVersion to character). Also, some strange encoding in the exportToJson.R script. Removed redundant concept_hierarchy.sql file (this was supposed to be removed for 1.6).

* Added analyses 822, 823, 1822, 1823 back. Fixed missing null cast in Heel RD 25. Adjusted analysis_details CSV to match new analyses. Added drop index statements.

* Fixes to analysis_details CSV, analysis 1822 had the wrong field name, added drop if not null statements in dropAllScratchTables

* Removed usage of DatabaseConnector::getTableNames() due to inconsistent effectiveness in Redshift

* Updated version number to 1.6.1

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: Achilles
 Type: Package
 Title: Creates descriptive statistics summary for an entire OMOP CDM instance
-Version: 1.6
-Date: 2018-04-09
+Version: 1.6.1
+Date: 2018-10-02
 Author: Patrick Ryan, Martijn Schuemie, Vojtech Huser, Chris Knoll, Ajit Londhe
 Maintainer: Patrick Ryan <[email protected]>
 LazyData: true
@@ -20,4 +20,4 @@ Suggests:
     R.utils
 License: Apache License
 Roxygen: list(wrap = FALSE)
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0

R/Achilles.R

@@ -105,6 +105,8 @@ achilles <- function (connectionDetails,
     cdmVersion <- .getCdmVersion(connectionDetails, cdmDatabaseSchema)
   }
 
+  cdmVersion <- as.character(cdmVersion)
+
   # Check CDM version is valid ---------------------------------------------------------------------------------------------------
 
   if (compareVersion(a = as.character(cdmVersion), b = "5") < 0) {
@@ -839,9 +841,6 @@ dropAllScratchTables <- function(connectionDetails,
 
   connection <- DatabaseConnector::connect(connectionDetails = connectionDetails)
 
-  scratchTables <- lapply(DatabaseConnector::getTableNames(connection = connection, 
-                                                    databaseSchema = scratchDatabaseSchema), function(t) tolower(t))
-
   if ("achilles" %in% tableTypes) {
 
     # Drop Achilles Scratch Tables ------------------------------------------------------
@@ -856,13 +855,11 @@ dropAllScratchTables <- function(connectionDetails,
       sprintf("%s_dist_%d", tempAchillesPrefix, id)
     })
 
-    dropTables <- c(Reduce(intersect, list(scratchTables, resultsTables)), 
-                    Reduce(intersect, list(scratchTables, resultsDistTables)))
-
-    dropSqls <- lapply(dropTables, function(scratchTable) {
-      SqlRender::renderSql("drop table @scratchDatabaseSchema.@scratchTable;", 
-                           scratchDatabaseSchema = scratchDatabaseSchema,
-                           scratchTable = scratchTable)$sql
+    dropSqls <- lapply(c(resultsTables, resultsDistTables), function(scratchTable) {
+      sql <- SqlRender::renderSql("IF OBJECT_ID('@scratchDatabaseSchema.@scratchTable', 'U') IS NOT NULL DROP TABLE @scratchDatabaseSchema.@scratchTable;", 
+                                  scratchDatabaseSchema = scratchDatabaseSchema,
+                                  scratchTable = scratchTable)$sql
+      sql <- SqlRender::translateSql(sql = sql, targetDialect = connectionDetails$dbms)$sql
     })
 
     cluster <- OhdsiRTools::makeCluster(numberOfThreads = numThreads, singleThreadToMain = TRUE)
@@ -890,13 +887,12 @@ dropAllScratchTables <- function(connectionDetails,
     parallelHeelTables <- lapply(parallelFiles, function(t) tolower(paste(tempHeelPrefix,
                                                                           trimws(tools::file_path_sans_ext(basename(t))),
                                                                     sep = "_")))
-
-    dropTables <- Reduce(intersect, list(scratchTables, parallelHeelTables))
 
-    dropSqls <- lapply(dropTables, function(scratchTable) {
-      SqlRender::renderSql("drop table @scratchDatabaseSchema.@scratchTable;", 
+    dropSqls <- lapply(parallelHeelTables, function(scratchTable) {
+      sql <- SqlRender::renderSql("IF OBJECT_ID('@scratchDatabaseSchema.@scratchTable', 'U') IS NOT NULL DROP TABLE @scratchDatabaseSchema.@scratchTable;", 
                            scratchDatabaseSchema = scratchDatabaseSchema,
                            scratchTable = scratchTable)$sql
+      sql <- SqlRender::translateSql(sql = sql, targetDialect = connectionDetails$dbms)$sql
     })
 
     cluster <- OhdsiRTools::makeCluster(numberOfThreads = numThreads, singleThreadToMain = TRUE)
@@ -924,12 +920,12 @@ dropAllScratchTables <- function(connectionDetails,
     conceptHierarchyTables <- lapply(hierarchySqlFiles, function(t) tolower(paste(tempAchillesPrefix, "ch",
                                                                           trimws(tools::file_path_sans_ext(basename(t))),
                                                                           sep = "_")))
-    dropTables <- Reduce(intersect, list(scratchTables, conceptHierarchyTables))
 
-    dropSqls <- lapply(dropTables, function(scratchTable) {
-      SqlRender::renderSql("drop table @scratchDatabaseSchema.@scratchTable;", 
+    dropSqls <- lapply(conceptHierarchyTables, function(scratchTable) {
+      sql <- SqlRender::renderSql("IF OBJECT_ID('@scratchDatabaseSchema.@scratchTable', 'U') IS NOT NULL DROP TABLE @scratchDatabaseSchema.@scratchTable;", 
                            scratchDatabaseSchema = scratchDatabaseSchema,
                            scratchTable = scratchTable)$sql
+      sql <- SqlRender::translateSql(sql = sql, targetDialect = connectionDetails$dbms)$sql
     })
 
     cluster <- OhdsiRTools::makeCluster(numberOfThreads = numThreads, singleThreadToMain = TRUE)

R/AchillesHeel.R

@@ -38,6 +38,7 @@
 #' @param resultsDatabaseSchema		         string name of database schema that we can write final results to. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, 
 #'                                         so for example 'results.dbo'.
 #' @param scratchDatabaseSchema            (OPTIONAL, multi-threaded mode) Name of a fully qualified schema that is accessible to/from the resultsDatabaseSchema, that can store all of the scratch tables. Default is resultsDatabaseSchema.
+#' @param vocabDatabaseSchema		           String name of database schema that contains OMOP Vocabulary. Default is cdmDatabaseSchema. On SQL Server, this should specifiy both the database and the schema, so for example 'results.dbo'.
 #' @param cdmVersion                       Define the OMOP CDM version used:  currently supports v5 and above.  Default = "5". 
 #' @param numThreads                       (OPTIONAL, multi-threaded mode) The number of threads to use to run Achilles in parallel. Default is 1 thread.
 #' @param tempHeelPrefix                   (OPTIONAL, multi-threaded mode) The prefix to use for the "temporary" (but actually permanent) Heel tables. Default is "tmpheel"
@@ -55,6 +56,7 @@
 #'                                cdmDatabaseSchema = "cdm", 
 #'                                resultsDatabaseSchema = "results", 
 #'                                scratchDatabaseSchema = "scratch",
+#'                                vocabDatabaseSchema = "vocab",
 #'                                cdmVersion = "5.3.0",
 #'                                numThreads = 10)
 #' }
@@ -63,6 +65,7 @@ achillesHeel <- function(connectionDetails,
                          cdmDatabaseSchema, 
                          resultsDatabaseSchema = cdmDatabaseSchema,
                          scratchDatabaseSchema = resultsDatabaseSchema,
+                         vocabDatabaseSchema = cdmDatabaseSchema,
                          cdmVersion = "5",
                          numThreads = 1,
                          tempHeelPrefix = "tmpheel",
@@ -79,6 +82,8 @@ achillesHeel <- function(connectionDetails,
     cdmVersion <- .getCdmVersion(connectionDetails, cdmDatabaseSchema)
   }
 
+  cdmVersion <- as.character(cdmVersion)
+
   # Check CDM version is valid ---------------------------------------------------------------------------------------------------
 
   if (compareVersion(a = cdmVersion, b = "5") < 0) {
@@ -145,6 +150,7 @@ achillesHeel <- function(connectionDetails,
                 cdmDatabaseSchema = cdmDatabaseSchema,
                 resultsDatabaseSchema = resultsDatabaseSchema,
                 scratchDatabaseSchema = scratchDatabaseSchema,
+                vocabDatabaseSchema = vocabDatabaseSchema,
                 schemaDelim = schemaDelim,
                 tempHeelPrefix = tempHeelPrefix,
                 numThreads = numThreads,
@@ -360,6 +366,7 @@ achillesHeel <- function(connectionDetails,
                         cdmDatabaseSchema,
                         resultsDatabaseSchema,
                         scratchDatabaseSchema,
+                        vocabDatabaseSchema,
                         schemaDelim,
                         tempHeelPrefix, 
                         numThreads,
@@ -375,6 +382,7 @@ achillesHeel <- function(connectionDetails,
                                            cdmDatabaseSchema = cdmDatabaseSchema,
                                            resultsDatabaseSchema = resultsDatabaseSchema,
                                            scratchDatabaseSchema = scratchDatabaseSchema,
+                                           vocabDatabaseSchema = vocabDatabaseSchema,
                                            schemaDelim = schemaDelim,
                                            tempHeelPrefix = tempHeelPrefix,
                                            heelName = gsub(pattern = ".sql", replacement = "", x = basename(heelFile)))

R/exportToJson.R

@@ -1482,7 +1482,7 @@ generateObservationPeriodReport <- function(conn, dbms, cdmDatabaseSchema, resul
   # a.	Visualization:  scatterplot
   # b.	X-axis:  length of observation period
   # c.	Y-axis:  % of population observed
-  # d.	Note:  will look like a Kaplan-Meier ‘survival’ plot, but information is the same as shown in ‘length of observation’ barchart, just plotted as cumulative 
+  # d.	Note:  will look like a Kaplan-Meier survival plot, but information is the same as shown in a length of observation barchart, just plotted as cumulative 
 
   renderedSql <- SqlRender::loadRenderTranslateSql(sqlFilename = "export/observationperiod/cumulativeduration.sql",
                                         packageName = "Achilles",

inst/csv/achilles/achilles_analysis_details.csv

@@ -118,6 +118,8 @@ ANALYSIS_ID,DISTRIBUTION,COST,DISTRIBUTED_FIELD,ANALYSIS_NAME,STRATUM_1_NAME,STR
 814,0,0,,"Number of observation records with no value (numeric, string, or concept)",,,,,
 815,1,0,,"Distribution of numeric values, by observation_concept_id and unit_concept_id",,,,,
 820,0,0,,Number of observation records  by observation start month,calendar month,,,,
+822,0,0,,"Number of observation records, by observation_concept_id and value_as_concept_id",observation_concept_id,value_as_concept_id,,,
+823,0,0,,"Number of observation records, by observation_concept_id and qualifier_concept_id",observation_concept_id,qualifier_concept_id,,,
 891,0,0,,Percentage of total persons that have at least x observations,observation_concept_id,observation_person,,,
 900,0,0,,"Number of persons with at least one drug era, by drug_concept_id",drug_concept_id,,,,
 901,0,0,,"Number of drug era records, by drug_concept_id",drug_concept_id,,,,
@@ -197,10 +199,12 @@ ANALYSIS_ID,DISTRIBUTION,COST,DISTRIBUTED_FIELD,ANALYSIS_NAME,STRATUM_1_NAME,STR
 1814,0,0,,"Number of measurement records with no value (numeric, string, or concept)",,,,,
 1815,1,0,,"Distribution of numeric values, by measurement_concept_id and unit_concept_id",,,,,
 1816,1,0,,"Distribution of low range, by measurement_concept_id and unit_concept_id",,,,,
-1817,1,0,,"Distribution of high range, by observation_concept_id and unit_concept_id",,,,,
+1817,1,0,,"Distribution of high range, by measurement_concept_id and unit_concept_id",,,,,
 1818,0,0,,"Number of measurement records below/within/above normal range, by measurement_concept_id and unit_concept_id",,,,,
 1820,0,0,,Number of measurement records  by measurement start month,calendar month,,,,
 1821,0,0,,Number of measurement records with no numeric value,,,,,
+1822,0,0,,"Number of measurement records, by measurement_concept_id and value_as_concept_id",measurement_concept_id,value_as_concept_id,,,
+1823,0,0,,"Number of measurement records, by measurement_concept_id and operator_concept_id",measurement_concept_id,operator_concept_id,,,
 1891,0,0,,Percentage of total persons that have at least x measurements,measurement_concept_id,measurement_person,,,
 1900,0,0,,"Source values mapped to concept_id 0 by table, by source_value",table_name,source_value,,,
 2000,0,0,,Number of patients with at least 1 Dx and 1 Rx,,,,,

inst/sql/sql_server/analyses/1822.sql

@@ -0,0 +1,15 @@
+
+-- 1822	Number of measurement records, by measurement_concept_id and value_as_concept_id
+
+--HINT DISTRIBUTE_ON_KEY(stratum_1)
+select
+	1822 AS analysis_id,
+	cast(measurement_concept_id AS varchar(255)) AS stratum_1,
+	cast(value_as_concept_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(*) AS count_value
+into @scratchDatabaseSchema@schemaDelim@tempAchillesPrefix_1822
+from @cdmDatabaseSchema.measurement
+group by measurement_concept_id, value_as_concept_id;

inst/sql/sql_server/analyses/1823.sql

@@ -0,0 +1,15 @@
+
+-- 1823	Number of measurement records, by measurement_concept_id and operator_concept_id
+
+--HINT DISTRIBUTE_ON_KEY(stratum_1)
+select 
+	1823 AS analysis_id, 
+	cast(measurement_concept_id AS varchar(255)) AS stratum_1, 
+	cast(operator_concept_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(*) AS count_value
+into @scratchDatabaseSchema@schemaDelim@tempAchillesPrefix_1823
+from @cdmDatabaseSchema.measurement
+group by measurement_concept_id, operator_concept_id

inst/sql/sql_server/analyses/822.sql

@@ -0,0 +1,15 @@
+
+-- 822	Number of observation records, by observation_concept_id and value_as_concept_id, observation_concept_id
+
+--HINT DISTRIBUTE_ON_KEY(stratum_1)
+select
+	822 AS analysis_id,
+	cast(observation_concept_id AS varchar(255)) AS stratum_1, 
+	cast(value_as_concept_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(*) AS count_value
+into @scratchDatabaseSchema@schemaDelim@tempAchillesPrefix_822
+from @cdmDatabaseSchema.observation
+group by observation_concept_id, value_as_concept_id;

inst/sql/sql_server/analyses/823.sql

@@ -0,0 +1,15 @@
+
+-- 823	Number of observation records, by observation_concept_id and qualifier_concept_id
+
+--HINT DISTRIBUTE_ON_KEY(stratum_1)
+select 
+	823 AS analysis_id, 
+	cast(observation_concept_id AS varchar(255)) AS stratum_1, 
+	cast(qualifier_concept_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(*) AS count_value
+into @scratchDatabaseSchema@schemaDelim@tempAchillesPrefix_823
+from @cdmDatabaseSchema.observation
+group by observation_concept_id, qualifier_concept_id;

inst/sql/sql_server/heels/parallel/heel_results/rule_10.sql

@@ -16,7 +16,7 @@ from
   FROM @resultsDatabaseSchema.ACHILLES_results or1
   INNER JOIN @resultsDatabaseSchema.ACHILLES_analysis oa1
   	ON or1.analysis_id = oa1.analysis_id
-  INNER JOIN @cdmDatabaseSchema.concept c1
+  INNER JOIN @vocabDatabaseSchema.concept c1
   	ON or1.stratum_1 = CAST(c1.concept_id AS VARCHAR(19))
   WHERE or1.analysis_id IN (202)
   	AND or1.stratum_1 IS NOT NULL

inst/sql/sql_server/heels/parallel/heel_results/rule_11.sql

@@ -16,7 +16,7 @@ from
   FROM @resultsDatabaseSchema.ACHILLES_results or1
   INNER JOIN @resultsDatabaseSchema.ACHILLES_analysis oa1
   	ON or1.analysis_id = oa1.analysis_id
-  INNER JOIN @cdmDatabaseSchema.concept c1
+  INNER JOIN @vocabDatabaseSchema.concept c1
   	ON or1.stratum_1 = CAST(c1.concept_id AS VARCHAR(19))
   WHERE or1.analysis_id IN (301)
   	AND or1.stratum_1 IS NOT NULL

inst/sql/sql_server/heels/parallel/heel_results/rule_12.sql

@@ -16,7 +16,7 @@ from
   FROM @resultsDatabaseSchema.ACHILLES_results or1
   INNER JOIN @resultsDatabaseSchema.ACHILLES_analysis oa1
   	ON or1.analysis_id = oa1.analysis_id
-  INNER JOIN @cdmDatabaseSchema.concept c1
+  INNER JOIN @vocabDatabaseSchema.concept c1
   	ON or1.stratum_1 = CAST(c1.concept_id AS VARCHAR(19))
   WHERE or1.analysis_id IN (
   		400,

inst/sql/sql_server/heels/parallel/heel_results/rule_13.sql

@@ -16,7 +16,7 @@ from
   FROM @resultsDatabaseSchema.ACHILLES_results or1
   INNER JOIN @resultsDatabaseSchema.ACHILLES_analysis oa1
   	ON or1.analysis_id = oa1.analysis_id
-  INNER JOIN @cdmDatabaseSchema.concept c1
+  INNER JOIN @vocabDatabaseSchema.concept c1
   	ON or1.stratum_1 = CAST(c1.concept_id AS VARCHAR(19))
   WHERE or1.analysis_id IN (
   		700,

inst/sql/sql_server/heels/parallel/heel_results/rule_14.sql

@@ -16,7 +16,7 @@ from
   FROM @resultsDatabaseSchema.ACHILLES_results or1
   INNER JOIN @resultsDatabaseSchema.ACHILLES_analysis oa1
   	ON or1.analysis_id = oa1.analysis_id
-  INNER JOIN @cdmDatabaseSchema.concept c1
+  INNER JOIN @vocabDatabaseSchema.concept c1
   	ON or1.stratum_1 = CAST(c1.concept_id AS VARCHAR(19))
   WHERE or1.analysis_id IN (600)
   	AND or1.stratum_1 IS NOT NULL

inst/sql/sql_server/heels/parallel/heel_results/rule_17.sql

@@ -16,7 +16,7 @@ from
   FROM @resultsDatabaseSchema.ACHILLES_results or1
   INNER JOIN @resultsDatabaseSchema.ACHILLES_analysis oa1
   	ON or1.analysis_id = oa1.analysis_id
-  INNER JOIN @cdmDatabaseSchema.concept c1
+  INNER JOIN @vocabDatabaseSchema.concept c1
   	ON or1.stratum_1 = CAST(c1.concept_id AS VARCHAR(19))
   WHERE or1.analysis_id IN (1610)
   	AND or1.stratum_1 IS NOT NULL

inst/sql/sql_server/heels/parallel/heel_results/rule_4.sql

@@ -16,7 +16,7 @@ from
   FROM @resultsDatabaseSchema.ACHILLES_results or1
   INNER JOIN @resultsDatabaseSchema.ACHILLES_analysis oa1
   	ON or1.analysis_id = oa1.analysis_id
-  LEFT JOIN @cdmDatabaseSchema.concept c1
+  LEFT JOIN @vocabDatabaseSchema.concept c1
   	ON or1.stratum_1 = CAST(c1.concept_id AS VARCHAR(19))
   WHERE or1.analysis_id IN (
   		2,

inst/sql/sql_server/heels/parallel/heel_results/rule_5.sql

@@ -19,7 +19,7 @@ from
   FROM @resultsDatabaseSchema.ACHILLES_results or1
   INNER JOIN @resultsDatabaseSchema.ACHILLES_analysis oa1
   	ON or1.analysis_id = oa1.analysis_id
-  LEFT JOIN @cdmDatabaseSchema.concept c1
+  LEFT JOIN @vocabDatabaseSchema.concept c1
   	ON or1.stratum_2 = CAST(c1.concept_id AS VARCHAR(19))
   WHERE or1.analysis_id IN (
   		405,

inst/sql/sql_server/heels/parallel/heel_results/rule_7.sql

@@ -17,7 +17,7 @@ from
   FROM @resultsDatabaseSchema.ACHILLES_results or1
   INNER JOIN @resultsDatabaseSchema.ACHILLES_analysis oa1
   	ON or1.analysis_id = oa1.analysis_id
-  INNER JOIN @cdmDatabaseSchema.concept c1
+  INNER JOIN @vocabDatabaseSchema.concept c1
   	ON or1.stratum_1 = CAST(c1.concept_id AS VARCHAR(19))
   WHERE or1.analysis_id IN (2)
   	AND or1.stratum_1 IS NOT NULL

inst/sql/sql_server/heels/parallel/heel_results/rule_8.sql

@@ -16,7 +16,7 @@ from
   FROM @resultsDatabaseSchema.ACHILLES_results or1
   INNER JOIN @resultsDatabaseSchema.ACHILLES_analysis oa1
   	ON or1.analysis_id = oa1.analysis_id
-  INNER JOIN @cdmDatabaseSchema.concept c1
+  INNER JOIN @vocabDatabaseSchema.concept c1
   	ON or1.stratum_1 = CAST(c1.concept_id AS VARCHAR(19))
   WHERE or1.analysis_id IN (4)
   	AND or1.stratum_1 IS NOT NULL

inst/sql/sql_server/heels/parallel/heel_results/rule_9.sql

@@ -16,7 +16,7 @@ from
   FROM @resultsDatabaseSchema.ACHILLES_results or1
   INNER JOIN @resultsDatabaseSchema.ACHILLES_analysis oa1
   	ON or1.analysis_id = oa1.analysis_id
-  INNER JOIN @cdmDatabaseSchema.concept c1
+  INNER JOIN @vocabDatabaseSchema.concept c1
   	ON or1.stratum_1 = CAST(c1.concept_id AS VARCHAR(19))
   WHERE or1.analysis_id IN (5)
   	AND or1.stratum_1 IS NOT NULL

inst/sql/sql_server/heels/parallel/results_derived/25.sql

@@ -17,7 +17,7 @@ from
 (
   --100000+analysis_id, 
   select
-    NULL as analysis_id,
+    cast(null as int) as analysis_id,
     stratum_2 as stratum_1,
     cast(null as varchar(255)) as stratum_2,
     count_value,

inst/sql/sql_server/post_processing/achilles_indices.sql

@@ -39,10 +39,15 @@ CREATE CLUSTERED COLUMNSTORE INDEX ClusteredIndex_Achilles_results
   ON @resultsDatabaseSchema.ACHILLES_results;
 }
 
+
+DROP INDEX IF EXISTS idx_ar_aid on @resultsDatabaseSchema.ACHILLES_results (analysis_id);
 CREATE INDEX idx_ar_aid
   ON @resultsDatabaseSchema.ACHILLES_results (analysis_id);
+
+DROP INDEX IF EXISTS idx_ar_s1 on @resultsDatabaseSchema.ACHILLES_results (stratum_1);
 CREATE INDEX idx_ar_s1
   ON @resultsDatabaseSchema.ACHILLES_results (stratum_1);
+
 CREATE INDEX idx_ar_s2
   ON @resultsDatabaseSchema.ACHILLES_results (stratum_2);
 CREATE INDEX idx_ar_aid_s1

inst/sql/sql_server/post_processing/concept_hierarchies/condition.sql

@@ -5,7 +5,7 @@
     snomed.concept_id,
     snomed.concept_name AS concept_name,
     'Condition' AS treemap,
-    null as concept_hierarchy_type,
+    cast(null as varchar(20)) as concept_hierarchy_type,
     pt_to_hlt.pt_concept_name as level1_concept_name,
     hlt_to_hlgt.hlt_concept_name as level2_concept_name,
     hlgt_to_soc.hlgt_concept_name as level3_concept_name,

inst/sql/sql_server/post_processing/concept_hierarchies/drug.sql

@@ -5,7 +5,7 @@
     rxnorm.concept_id,
     rxnorm.concept_name AS concept_name,
     'Drug' AS treemap,
-    null as concept_hierarchy_type,    
+    cast(null as varchar(20)) as concept_hierarchy_type,    
     rxnorm.rxnorm_ingredient_concept_name as level1_concept_name,
     atc5_to_atc3.atc5_concept_name as level2_concept_name,
     atc3_to_atc1.atc3_concept_name as level3_concept_name,