Store each plate as a transaction. Add fast mode option for storing screens....

Store each plate as a transaction. Add fast mode option for storing screens. Add optional screen parameter to Well$get_all_by_compound().

R/Compound.R

@@ -67,7 +67,7 @@ Compound <- R6Class(
       cat(paste0(paste0("ID: ", self$ID), "\n",
                  paste0("ChEMBL ID: ", self$ChEMBL_ID), "\n",
                  paste0("ChEBI ID: ", self$ChEBI_ID), "\n",
-                 paste0("Name ", self$name), "\n",
+                 paste0("Name: ", self$name), "\n",
                  paste0("Usage class: ", self$usage_class), "\n",
                  paste0("Dose: ", self$dose), "\n",
                  paste0("Unit: ", self$unit), "\n",

R/PlateHandle.R

@@ -74,6 +74,7 @@ PlateHandle <- R6Class(
       statement <- "INSERT IGNORE INTO Plate (ID, nrows, ncols, name, type, date_prepared, date_used)
                                       VALUES (?, ?, ?, ?, ?, ?, ?)" 
       for(plate in plate.list) {
+        dbBegin(self$dbConnection)
         result <- self$dbConnection$execute(statement, list(plate$ID,
                                                             plate$nrows,
                                                             plate$ncols,
@@ -105,6 +106,7 @@ PlateHandle <- R6Class(
                                                     qc$ID))
           }
         }
+        dbCommit(self$dbConnection)
       }
     }
   )

R/Screen.R

@@ -62,9 +62,11 @@ Screen <- R6Class(
                  paste0("Ended on: ", self$date_ended), "\n"))
     },
     #' @description Store the object into the database
-    store = function() {
+    #' @param fast.mode (optional, default: FALSE) Speeds up data loading by
+    #' disabling integrity checks
+    store = function(fast.mode = FALSE) {
       scrh <- ScreenHandle$new(self$dbConnection)
-      status <- scrh$store(list(self))
+      status <- scrh$store(list(self), fast.mode = fast.mode)
     }
   ),
   private = list(

R/ScreenHandle.R

@@ -109,7 +109,14 @@ ScreenHandle <- R6Class(
     },
     #' @description Store Screen objects in the database
     #' @param screen.list A list of Screen objects
-    store = function(screen.list) {
+    #' @param fast.mode (optional, default: FALSE) Speeds up data loading by
+    #' disabling integrity checks
+    store = function(screen.list, fast.mode = FALSE) {
+      if(fast.mode) { # Disable integrity checks
+        result <- self$dbConnection$execute("SET @@session.unique_checks = 0")
+        result <- self$dbConnection$execute("SET @@session.foreign_key_checks = 0")
+        result <- self$dbConnection$execute("SET @@global.innodb_autoinc_lock_mode = 2")
+      }
       statement <- "INSERT IGNORE INTO Screen (ID, name, description, status, date_started, date_ended)
                                        VALUES (?, ?, ?, ?, ?, ?)" 
       for(screen in screen.list) {
@@ -138,6 +145,11 @@ ScreenHandle <- R6Class(
           }
         }
       }
+      if(fast.mode) { # Re-enable integrity checks
+        result <- self$dbConnection$execute("SET @@session.unique_checks = 1")
+        result <- self$dbConnection$execute("SET @@session.foreign_key_checks = 1")
+        result <- self$dbConnection$execute("SET @@global.innodb_autoinc_lock_mode = 1")
+      }
     }
   )
 )
\ No newline at end of file

R/Well.R

@@ -12,8 +12,8 @@
 #' @field qc List of QC objects
 #' @field datafiles List of Datafile objects representing plate-level data
 #' @field phenotypes List of Phenotype objects
-#' @field replicates List of Well objects from the same screen and having the  
-#' same samples and compounds at the same dose.
+#' @field replicates Retrieves a list of Well objects from the same screen and having the  
+#' same samples and compounds at the same dose. Can't be set.
 #' 
 #' @export
 Well <- R6Class(

R/WellHandle.R

@@ -94,13 +94,23 @@ WellHandle <- R6Class(
     },
     #' @description Retrieve all wells where a compound is found
     #' @param compound A Compound object
+    #' @param screen (optional) a Screen object to limit to wells from this screen
     #' @return List of Well objects
-    get_all_by_compound = function(compound) {
-      query <- "SELECT W.* FROM Well AS W, Well_has_Compound AS WhC
-                WHERE WhC.Compound_ID = ?
-                AND WhC.Plate_ID = W.Plate_ID
-                AND WhC.Well_position = W.position"
-      data <- self$dbConnection$get_data(query, list(compound$ID))
+    get_all_by_compound = function(compound, screen = NULL) {
+      if(is.null(screen)) {
+        query <- "SELECT W.* FROM Well AS W, Well_has_Compound AS WhC
+                  WHERE WhC.Compound_ID = ?
+                  AND WhC.Plate_ID = W.Plate_ID
+                  AND WhC.Well_position = W.position"
+        data <- self$dbConnection$get_data(query, list(compound$ID))
+      } else {
+        query <- "SELECT W.* FROM Well AS W, Well_has_Compound AS WhC, Screen_has_Plate AS ShP
+                  WHERE WhC.Compound_ID = ? AND ShP.Screen_ID = ?
+                  AND ShP.Plate_ID = WhC.Plate_ID
+                  AND WhC.Plate_ID = W.Plate_ID
+                  AND WhC.Well_position = W.position" 
+        data <- self$dbConnection$get_data(query, list(compound$ID, screen$ID))
+      }
       if(length(data$position)>0) {
         wells <- list()
         df.list <- split(data, paste0(data$Plate_ID, data$position))