Make initializeDatabase call the correct DDL file (#266)

R/dbUtils.R

@@ -161,7 +161,11 @@ initializeDatabase <- function(connectionDetails, overwrite = FALSE, testing = F
       return()
     }
   }
-  DatabaseConnector::executeSql(conn, sql = readr::read_file(system.file("sql", "backbone_ddl.sql", package="gaiaCore")))
+  DatabaseConnector::executeSql(conn, sql = "CREATE SCHEMA IF NOT EXISTS backbone AUTHORIZATION postgres;")
+  # TODO the sequences file is not autogenerated. Add it to the create/writeDdl script?
+  DatabaseConnector::executeSql(conn, sql = readr::read_file(system.file("ddl", "001", "gaiadb_001_sequences.sql", package="gaiaCore")))
+  DatabaseConnector::executeSql(conn, sql = readr::read_file(system.file("ddl", "001", "gaiadb_001_ddl.sql", package="gaiaCore")))
+  # DatabaseConnector::executeSql(conn, sql = readr::read_file(system.file("sql", "backbone_ddl.sql", package="gaiaCore")))
   message("backbone schema created.")
   if (!testing) {
     dataSource <- readr::read_csv(system.file(file.path("csv", paste0("data_source.csv")), package = 'gaiaCore'))

inst/csv/data_source.csv

@@ -11,9 +11,7 @@ data_source_uuid,org_id,org_set_id,dataset_name,dataset_version,geom_type,geom_s
 8888,EPA,AQS,annual_conc_by_cbsa_2018,2018,,,cbsa,1,10184,file,zip,csv,annual_aqi_by_cbsa_2018.csv,https://aqs.epa.gov/aqsweb/airdata/annual_aqi_by_cbsa_2018.zip,,https://www.epa.gov/aqs
 7777,EPA,AQS,annual_conc_by_monitor_2018,2018,point,,,1,7777,file,zip,csv,annual_conc_by_monitor_2018.csv,https://aqs.epa.gov/aqsweb/airdata/annual_conc_by_monitor_2018.zip,,https://www.epa.gov/aqs
 1234,Census,TIGER/Line,us-county-2018,2018,polygon,"{""stage_transform"":[""dplyr::mutate(staged,geom_source_coding='GEOID',geom_source_value=GEOID,geom_name=dplyr::select(sf::st_drop_geometry(staged), n = if('NAME' %in% colnames(staged)) 'NAME' else 'NAMELSAD')$n,geom_local_value=geometry,geom_local_epsg=sf::st_crs(staged, paramaters=TRUE)$epsg)""]}",county,0,,file,zip,shp,tl_2018_us_county.shp,https://www2.census.gov/geo/tiger/TIGER2018/COUNTY/tl_2018_us_county.zip,,https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html
-6666,WaterQualityData.us,WQX,station,,point,,,0,,API,zip,csv,station.csv,https://www.waterqualitydata.us/data/Station/search?mimeType=csv&zip=yes,,https://www.waterqualitydata.us/webservices_documentation
 9999,CDC/ATSDR,SVI,us-county-2018,2018,,,county,1,1234,file,zip,gdb,SVI2018_US_county.gdb,https://svi.cdc.gov/Documents/Data/2018/db/states_counties/SVI_2018_US_county.zip,,https://www.atsdr.cdc.gov/placeandhealth/svi/index.html
-5555,WaterQualityData.us,WQX,result,,,,,1,6666,API,zip,csv,result.csv,https://www.waterqualitydata.us/data/Result/search?characterticName={param1}&mimeType=csv&zip=yes,,https://www.waterqualitydata.us/webservices_documentation
 10148,Census,TIGER/Line,us-zcta5-2014,2014,polygon,"{""stage_transform"":[""dplyr::mutate(staged,geom_source_coding='GEOID',geom_source_value=GEOID10,geom_local_value=geometry,geom_local_epsg=sf::st_crs(staged, paramaters=TRUE)$epsg)""]}",zcta5,0,,file,zip,shp,tl_2014_us_zcta510.shp,https://www2.census.gov/geo/tiger/TIGER2014/ZCTA5/tl_2014_us_zcta510.zip,,https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html
 10159,Census,TIGER/Line,us-zcta5-2015,2015,polygon,"{""stage_transform"":[""dplyr::mutate(staged,geom_source_coding='GEOID',geom_source_value=GEOID10,geom_local_value=geometry,geom_local_epsg=sf::st_crs(staged, paramaters=TRUE)$epsg)""]}",zcta5,0,,file,zip,shp,tl_2015_us_zcta510.shp,https://www2.census.gov/geo/tiger/TIGER2015/ZCTA5/tl_2015_us_zcta510.zip,,https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html
 7878,EPA,AQS,daily_aqi_by_county_2018,2018,,,county,1,1234,file,zip,csv,daily_aqi_by_county_2018.csv,https://aqs.epa.gov/aqsweb/airdata/daily_aqi_by_county_2018.zip,,https://www.epa.gov/aqs

inst/csv/gaia001fieldLevel.csv

@@ -6,7 +6,7 @@ data_source,dataset_name,Yes,varchar(100),,,No,No,,,,,
 data_source,dataset_version,Yes,varchar(100),,,No,No,,,,,
 data_source,geom_type,No,varchar(100),,,No,No,,,,,
 data_source,geom_spec,No,text,,,No,No,,,,,
-data_source,boundary_type,Yes,varchar(100),,,No,No,,,,,
+data_source,boundary_type,No,varchar(100),,,No,No,,,,,
 data_source,has_attributes,No,int4,,,No,No,,,,,
 data_source,geom_dependency_uuid,No,int4,,,No,Yes,data_source,data_source_uuid,,,
 data_source,download_method,Yes,varchar(100),,,No,No,,,,,

inst/ddl/001/gaiadb_001_ddl.sql

@@ -7,7 +7,7 @@ CREATE TABLE backbone.data_source (
 			dataset_version varchar(100) NOT NULL,
 			geom_type varchar(100) NULL,
 			geom_spec text NULL,
-			boundary_type varchar(100) NOT NULL,
+			boundary_type varchar(100) NULL,
 			has_attributes int4 NULL,
 			geom_dependency_uuid int4 NULL,
 			download_method varchar(100) NOT NULL,

inst/ddl/001/gaiadb_001_sequences.sql

@@ -0,0 +1,43 @@
+CREATE SEQUENCE IF NOT EXISTS backbone.attr_index_attr_index_id_seq
+	INCREMENT BY 1
+	MINVALUE 1
+	MAXVALUE 2147483647
+	START 1
+	CACHE 1
+	NO CYCLE;
+-- DROP SEQUENCE backbone.attr_template_attr_record_id_seq;
+
+CREATE SEQUENCE IF NOT EXISTS backbone.attr_template_attr_record_id_seq
+	INCREMENT BY 1
+	MINVALUE 1
+	MAXVALUE 2147483647
+	START 1
+	CACHE 1
+	NO CYCLE;
+-- DROP SEQUENCE backbone.variable_source_variable_source_id_seq;
+
+CREATE SEQUENCE IF NOT EXISTS backbone.variable_source_variable_source_id_seq
+	INCREMENT BY 1
+	MINVALUE 1
+	MAXVALUE 2147483647
+	START 1
+	CACHE 1
+	NO CYCLE;
+-- DROP SEQUENCE backbone.geom_index_geom_index_id_seq;
+
+CREATE SEQUENCE IF NOT EXISTS backbone.geom_index_geom_index_id_seq
+	INCREMENT BY 1
+	MINVALUE 1
+	MAXVALUE 2147483647
+	START 1
+	CACHE 1
+	NO CYCLE;
+-- DROP SEQUENCE backbone.geom_template_geom_record_id_seq;
+
+CREATE SEQUENCE IF NOT EXISTS backbone.geom_template_geom_record_id_seq
+	INCREMENT BY 1
+	MINVALUE 1
+	MAXVALUE 2147483647
+	START 1
+	CACHE 1
+	NO CYCLE;-- backbone.attr_index definition