Don't try to change database variable @@global.innodb_autoinc_lock_mode.

R/ScreenHandle.R

@@ -115,7 +115,6 @@ ScreenHandle <- R6Class(
       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 (?, ?, ?, ?, ?, ?)" 
@@ -148,7 +147,6 @@ 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")
       }
     }
   )

man/Screen.Rd

@@ -98,9 +98,17 @@ Output summary of the object content
 \subsection{Method \code{store()}}{
 Store the object into the database
 \subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{Screen$store()}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{Screen$store(fast.mode = FALSE)}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{fast.mode}}{(optional, default: FALSE) Speeds up data loading by
+disabling integrity checks}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-Screen-clone"></a>}}

man/ScreenHandle.Rd

@@ -159,13 +159,16 @@ A string starting with the prefix SCR:
 \subsection{Method \code{store()}}{
 Store Screen objects in the database
 \subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{ScreenHandle$store(screen.list)}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{ScreenHandle$store(screen.list, fast.mode = FALSE)}\if{html}{\out{</div>}}
 }
 
 \subsection{Arguments}{
 \if{html}{\out{<div class="arguments">}}
 \describe{
 \item{\code{screen.list}}{A list of Screen objects}
+
+\item{\code{fast.mode}}{(optional, default: FALSE) Speeds up data loading by
+disabling integrity checks}
 }
 \if{html}{\out{</div>}}
 }

man/Well.Rd

@@ -37,8 +37,8 @@ and columns by numbers starting with A1 in the top left corner.}
 
 \item{\code{phenotypes}}{List of Phenotype objects}
 
-\item{\code{replicates}}{List of Well objects from the same screen and having the
-same samples and compounds at the same dose.}
+\item{\code{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.}
 }
 \if{html}{\out{</div>}}
 }

man/WellHandle.Rd

@@ -114,13 +114,15 @@ List of Well objects
 \subsection{Method \code{get_all_by_compound()}}{
 Retrieve all wells where a compound is found
 \subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{WellHandle$get_all_by_compound(compound)}\if{html}{\out{</div>}}
+\if{html}{\out{<div class="r">}}\preformatted{WellHandle$get_all_by_compound(compound, screen = NULL)}\if{html}{\out{</div>}}
 }
 
 \subsection{Arguments}{
 \if{html}{\out{<div class="arguments">}}
 \describe{
 \item{\code{compound}}{A Compound object}
+
+\item{\code{screen}}{(optional) a Screen object to limit to wells from this screen}
 }
 \if{html}{\out{</div>}}
 }