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Commit 67dd5369 authored by Jean-Karim Heriche's avatar Jean-Karim Heriche
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Don't try to change database variable @@global.innodb_autoinc_lock_mode.

parent a6d074eb
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......@@ -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")
}
}
)
......
......@@ -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>}}
......
......@@ -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>}}
}
......
......@@ -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>}}
}
......
......@@ -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>}}
}
......
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