Merge pull request #57 from NOAA-EDAB/fix_herring_source

Fix herring database source

DESCRIPTION

@@ -23,7 +23,7 @@ Suggests:
     ggforce,
     NEFSCspatial
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Imports: 
     data.table,
     sf,

R/get_gears.R

@@ -62,7 +62,7 @@ get_gears <- function(channel,gears="all") {
   query <- DBI::dbGetQuery(channel,sqlStatement)
 
 # get column names
-  sqlcolName <- "select COLUMN_NAME from ALL_TAB_COLUMNS where TABLE_NAME = 'GEAR' and owner='CFDBS';"
+  sqlcolName <- "select COLUMN_NAME from ALL_TAB_COLUMNS where TABLE_NAME = 'GEAR' and owner='CFDBS'"
   colNames <- DBI::dbGetQuery(channel,sqlcolName)
 
   return (list(data=dplyr::as_tibble(query),sql=sqlStatement, colNames=colNames))

R/get_herring_data.R

@@ -26,7 +26,7 @@ get_herring_data <- function(channel, comland, filterByYear, filterByArea,
 
   herr.qry <- paste0("select year, month, category, stock_area, negear, gearname,
                      keptmt, discmt
-                     from cfdbs.maine_herring_catch
+                     from NEFSC_GARFO.maine_herring_catch
                      where year ", years)
   if(!is.na(filterByArea[1])){
     herr.qry <- paste0(herr.qry, " and stock_area in (", survdat:::sqltext(filterByArea), ")

R/get_locations.R

@@ -47,7 +47,7 @@
 #' @export
 #'
 #
-get_locations <- function(channel,sqlStatement="select * from cfdbs.loc;"){
+get_locations <- function(channel,sqlStatement="select * from cfdbs.loc"){
 
   query <- DBI::dbGetQuery(channel,sqlStatement)
 
@@ -56,7 +56,7 @@ get_locations <- function(channel,sqlStatement="select * from cfdbs.loc;"){
   #save(species,file="data/speciesDefinitions.RData")
 
   # get column names
-  sqlcolName <- "select COLUMN_NAME from ALL_TAB_COLUMNS where TABLE_NAME = 'LOC' and owner='CFDBS';"
+  sqlcolName <- "select COLUMN_NAME from ALL_TAB_COLUMNS where TABLE_NAME = 'LOC' and owner='CFDBS'"
   colNames <- DBI::dbGetQuery(channel,sqlcolName)
 
   return (list(data=dplyr::as_tibble(query),sql=sqlStatement, colNames=colNames))

R/get_species_itis.R

@@ -80,18 +80,18 @@ get_species_itis <- function(channel,species="all",nameType="common_name"){
   sqlStatement <- sub(";","",sqlStatement)
   if (length(species) == 1) {
     if (tolower(species) == "all") {
-      sqlStatement <- paste0(sqlStatement," where NESPP4_FLAG = 1;")
+      sqlStatement <- paste0(sqlStatement," where NESPP4_FLAG = 1")
     } else {
-      sqlStatement <- paste0(sqlStatement," and NESPP4_FLAG = 1;")
+      sqlStatement <- paste0(sqlStatement," and NESPP4_FLAG = 1")
     }
   } else {
-    sqlStatement <- paste0(sqlStatement," and NESPP4_FLAG = 1;")
+    sqlStatement <- paste0(sqlStatement," and NESPP4_FLAG = 1")
   }
 
   query <- DBI::dbGetQuery(channel,sqlStatement)
 
   # get column names
-  sqlcolName <- "select COLUMN_NAME from ALL_TAB_COLUMNS where TABLE_NAME = 'SPECIES_ITIS_NE' and owner='CFDBS';"
+  sqlcolName <- "select COLUMN_NAME from ALL_TAB_COLUMNS where TABLE_NAME = 'SPECIES_ITIS_NE' and owner='CFDBS'"
   colNames <- t(DBI::dbGetQuery(channel,sqlcolName))
 
   return (list(data=dplyr::as_tibble(query),sql=sqlStatement, colNames=colNames))

R/get_vessels.R

@@ -49,7 +49,7 @@ get_vessels <- function(channel,sqlStatement="select * from cfdbs.mstrvess",wher
 
   #appends where
   if (!is.null(where)) {
-    sqlStatement <- paste(sqlStatement,"where",where,";")
+    sqlStatement <- paste(sqlStatement,"where",where)
   }
 
   query <- DBI::dbGetQuery(channel,sqlStatement)
@@ -59,7 +59,7 @@ get_vessels <- function(channel,sqlStatement="select * from cfdbs.mstrvess",wher
   #save(species,file="data/speciesDefinitions.RData")
 
   # get column names
-  sqlcolName <- "select COLUMN_NAME from ALL_TAB_COLUMNS where TABLE_NAME = 'MSTRVESS' and owner='CFDBS';"
+  sqlcolName <- "select COLUMN_NAME from ALL_TAB_COLUMNS where TABLE_NAME = 'MSTRVESS' and owner='CFDBS'"
   colNames <- DBI::dbGetQuery(channel,sqlcolName)
 
   return (list(data=dplyr::as_tibble(query),sql=sqlStatement, colNames=colNames))