Fix a few bugs

R/CompoundHandle.R

@@ -65,8 +65,7 @@ CompoundHandle <- R6Class(
                             name = df$name,
                             usage_class = df$usage_class,
                             dose = df$dose,
-                            unit = df$unit,
-                            well = well)
+                            unit = df$unit)
           compounds <- c(compounds, c)
         }
         return(compounds)

R/Phenotype.R

@@ -38,9 +38,9 @@ Phenotype <- R6Class(
         stop("DB connection obect required to create Phenotype object")
       }
       if(is.na(name)) { stop("Name required to create Phenotype object") }
-      if(is.na(xrefDB) || is.na(xrefID)) { 
-        warning("Consider setting one xrefDB and xrefID crossreference for new Phenotype object")
-      }
+      # if(is.na(xrefDB) || is.na(xrefID)) {
+      #   warning("Consider setting one xrefDB and xrefID crossreference for new Phenotype object")
+      # }
       self$dbConnection <- dbConnection
       if(is.na(ID)) {
         ph <- PhenotypeHandle$new(self$dbConnection)

R/ScreenHandle.R

@@ -31,6 +31,20 @@ ScreenHandle <- R6Class(
         return(screen)
       } else { return(NULL) }
     },
+    #' @description Retrieve all screens
+    #' @return Vector of Screen objects
+    get_all_screens = function() {
+      query <- "SELECT DISTINCT ID FROM Screen"
+      df <- self$dbConnection$get_data(query)
+      if(length(df$ID)>0) {
+        screens <- list()
+        for(id in df$ID) {
+          sc <- self$get_by_id(id)
+          screens <- c(screens, sc)
+        }
+        return(screens)
+      }
+    },
     #' @description Retrieve all screens with the given name
     #' @param name A screen name
     #' @return Vector of Screen objects
@@ -39,7 +53,7 @@ ScreenHandle <- R6Class(
       df <- self$dbConnection$get_data(query, list(name))
       if(length(df$ID)>0) {
         screens <- list()
-        for(id in df$dbID) {
+        for(id in df$ID) {
           sc <- self$get_by_id(id)
           screens <- c(screens, sc)
         }

R/WellHandle.R

@@ -36,10 +36,31 @@ WellHandle <- R6Class(
       data <- self$dbConnection$get_data(query, list(plate$ID))
       if(length(data$Plate_ID)>0) {
         wells <- list()
-        df.list <- split(data, data$ID)
+        df.list <- split(data, data$position)
         for(df in df.list) {
           w <- Well$new(dbConnection = self$dbConnection,
-                        ID = df$Plate_ID, position = df$Well_position, 
+                        ID = df$Plate_ID, position = df$position,
+                        label = df$label, temperature = df$temperature)
+          wells <- c(wells, w)
+        }
+        return(wells)
+      } else { return(NULL) }
+    },
+    #' @description Retrieve all wells where a compound is found
+    #' @param compound A Compound object
+    #' @return Vector 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$ID))
+      if(length(data$position)>0) {
+        wells <- list()
+        df.list <- split(data, paste0(data$Plate_ID, data$position))
+        for(df in df.list) {
+          w <- Well$new(dbConnection = self$dbConnection,
+                        plate_ID = df$Plate_ID, position = df$position,
                         label = df$label, temperature = df$temperature)
           wells <- c(wells, w)
         }

man/ScreenHandle.Rd

@@ -19,6 +19,7 @@ retrieval of Screen objects.
 \itemize{
 \item \href{#method-ScreenHandle-new}{\code{ScreenHandle$new()}}
 \item \href{#method-ScreenHandle-get_by_id}{\code{ScreenHandle$get_by_id()}}
+\item \href{#method-ScreenHandle-get_all_screens}{\code{ScreenHandle$get_all_screens()}}
 \item \href{#method-ScreenHandle-get_all_by_name}{\code{ScreenHandle$get_all_by_name()}}
 \item \href{#method-ScreenHandle-get_all_by_status}{\code{ScreenHandle$get_all_by_status()}}
 \item \href{#method-ScreenHandle-get_new_ID}{\code{ScreenHandle$get_new_ID()}}
@@ -65,6 +66,19 @@ A Screen object
 }
 }
 \if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-ScreenHandle-get_all_screens"></a>}}
+\if{latex}{\out{\hypertarget{method-ScreenHandle-get_all_screens}{}}}
+\subsection{Method \code{get_all_screens()}}{
+Retrieve all screens
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ScreenHandle$get_all_screens()}\if{html}{\out{</div>}}
+}
+
+\subsection{Returns}{
+Vector of Screen objects
+}
+}
+\if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-ScreenHandle-get_all_by_name"></a>}}
 \if{latex}{\out{\hypertarget{method-ScreenHandle-get_all_by_name}{}}}
 \subsection{Method \code{get_all_by_name()}}{

man/WellHandle.Rd

@@ -20,6 +20,7 @@ retrieval of Well objects.
 \item \href{#method-WellHandle-new}{\code{WellHandle$new()}}
 \item \href{#method-WellHandle-get_by_id}{\code{WellHandle$get_by_id()}}
 \item \href{#method-WellHandle-get_all_by_plate}{\code{WellHandle$get_all_by_plate()}}
+\item \href{#method-WellHandle-get_all_by_compound}{\code{WellHandle$get_all_by_compound()}}
 \item \href{#method-WellHandle-store}{\code{WellHandle$store()}}
 \item \href{#method-WellHandle-clone}{\code{WellHandle$clone()}}
 }
@@ -85,6 +86,26 @@ Vector of Well objects
 }
 }
 \if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-WellHandle-get_all_by_compound"></a>}}
+\if{latex}{\out{\hypertarget{method-WellHandle-get_all_by_compound}{}}}
+\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>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{compound}}{A Compound object}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Returns}{
+Vector of Well objects
+}
+}
+\if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-WellHandle-store"></a>}}
 \if{latex}{\out{\hypertarget{method-WellHandle-store}{}}}
 \subsection{Method \code{store()}}{