#' AnalysisHandle
#' @description Object for handling database operations related to the storage and
#' retrieval of Analysis objects.
#' @field dbConnection A dbConnection object
#' @export
AnalysisHandle <- R6Class(
classname = "AnalysisHandle",
lock_class = TRUE,
public = list(
dbConnection = NULL,
#' @description Create an object for handling database operations related to
#' the storage and retrieval of Analysis objects.
#' @param dbConnection A dbConnection object
initialize = function(dbConnection = NA) {
self$dbConnection <- dbConnection
},
#' @description Retrieve an Analysis object using its database ID
#' @param dbID Database ID of the Analysis object to retrieve
#' @return An Analysis object
get_by_id = function(dbID) {
query <- "SELECT * FROM Analysis WHERE ID = ?"
df <- self$dbConnection$get_data(query, list(dbID))
if(nrow(df$ID)>0) {
analysis <- analysis$new(dbConnection = self$dbConnection,
ID = df$ID,
name = df$name,
version = df$version,
description = df$description,
outcome = df$outcome,
status = df$status,
code = df$code)
return(analysis)
} else { return(NULL) }
},
#' @description Retrieve an analysis using an associated data file
#' @param datafile A Datafile object
#' @param data_as_input logical (default = FALSE), whether the data is an
#' input to the analysis workflow
#' @return An Analysis object or a list of Analysis objects if data_as_input = TRUE
get_by_data = function(datafile, data_as_input = FALSE) {
if(data_as_input) {
# Analyses that consumed this data
query <- "SELECT DISTINCT A.* FROM Analysis AS A, Analysis_has_Data AS AhD
WHERE AhD.Parent_ID = ? AND AhD.Analysis_ID = A.ID"
data <- self$dbConnection$get_data(query, list(screen$ID))
if(length(data$ID)>0) {
analyses <- list()
df.list <- split(data, data$ID)
for(df in df.list) {
a <- Analysis$new(dbConnection = self$dbConnection,
ID = df$ID,
name = df$name,
version = df$version,
description = df$description,
outcome = df$outcome,
status = df$status,
code = df$code)
analyses <- c(analyses, a)
}
return(analyses)
} else { return(NULL) }
} else {
# Analysis that produced this data.
# There should be only one.
query <- "SELECT DISTINCT A.* FROM Analysis AS A, Analysis_has_Data AS AhD
WHERE AhD.Child_ID = ? AND AhD.Analysis_ID = A.ID"
df <- self$dbConnection$get_data(query, list(datafile$ID))
if(length(df$ID) == 1) {
analysis <- Analysis$new(dbConnection = self$dbConnection,
ID = df$ID,
name = df$name,
version = df$version,
description = df$description,
outcome = df$outcome,
status = df$status,
code = df$code)
return(analysis)
} else if(length(df$ID) == 0) {
return(NULL)
} else { # Shouldn't happen
stop("Datafile produced by more than one analysis")
}
}
},
#' @description Retrieve all analyses associated with a screen
#' @param screen A Screen object
#' @return List of Analysis objects
get_all_by_screen = function(screen) {
query <- "SELECT A.* FROM Analysis AS A, Screen_has_Analysis AS ShA
WHERE ShA.Screen_ID = ? AND ShA.Analysis_ID = A.ID"
data <- self$dbConnection$get_data(query, list(screen$ID))
if(length(data$ID)>0) {
analyses <- list()
df.list <- split(data, data$ID)
for(df in df.list) {
a <- Analysis$new(dbConnection = self$dbConnection,
ID = df$ID,
name = df$name,
version = df$version,
description = df$description,
outcome = df$outcome,
status = df$status,
code = df$code)
analyses <- c(analyses, a)
}
return(analyses)
} else { return(NULL) }
},
#' @description Retrieve all analyses associated with a screen plate
#' @param plate A Plate object
#' @return List of Analysis objects
get_all_by_plate = function(plate) {
query <- "SELECT A.* FROM Analysis AS A, Analysis_has_Data AS AhD, Plate_has_Data AS PhD
WHERE PhD.Plate_ID = ? AND
(PhD.Datafile_ID = AhD.Parent_ID OR PhD.Datafile_ID = AhD.Child_ID) AND
AhD.Analysis_ID = A.ID"
data <- self$dbConnection$get_data(query, list(plate$ID))
if(length(data$ID)>0) {
analyses <- list()
df.list <- split(data, data$ID)
for(df in df.list) {
a <- Analysis$new(dbConnection = self$dbConnection,
ID = df$ID,
name = df$name,
version = df$version,
description = df$description,
outcome = df$outcome,
status = df$status,
code = df$code)
analyses <- c(analyses, a)
}
return(analyses)
} else { return(NULL) }
},
#' @description Generate a database ID for an Analysis object
#' @return A string starting with the prefix ANA:
get_new_ID = function() {
query <- "SELECT seq FROM Analysis ORDER BY seq DESC LIMIT 1"
df <- self$dbConnection$get_data(query)
if(nrow(df)>0) {
ID <- paste0("ANA:", sprintf("%012d", df$seq+1))
} else { # The table is empty
ID <- paste0("ANA:", sprintf("%012d",1))
}
return(ID)
},
#' @description Store Analysis objects in the database
#' @param analysis.list A list of Analysis objects
store = function(analysis.list) {
statement <- "INSERT IGNORE INTO Analysis (ID, name, version, description, outcome, status, code)
VALUES (?, ?, ?, ?, ?, ?, ?)"
for(analysis in analysis.list) {
result <- self$dbConnection$execute(statement, list(analysis$ID,
analysis$name,
analysis$version,
analysis$description,
analysis$outcome,
analysis$status,
analysis$code))
if(length(analysis$input_datafiles)>0) {
dfh <- DatafileHandle$new(self$dbConnection)
result <- dfh$store(analysis$input_datafiles)
for(datafile in analysis$input_datafiles) {
st <- "INSERT IGNORE INTO Analysis_has_Data (Analysis_ID, Parent_ID)
VALUES (?, ?)"
r <- self$dbConnection$execute(st, list(plate$ID,
datafile$ID))
}
}
if(length(analysis$output_datafiles)>0) {
dfh <- DatafileHandle$new(self$dbConnection)
result <- dfh$store(analysis$output_datafiles)
for(datafile in analysis$output_datafiles) {
st <- "INSERT IGNORE INTO Analysis_has_Data (Analysis_ID, Child_ID)
VALUES (?, ?)"
r <- self$dbConnection$execute(st, list(plate$ID,
datafile$ID))
}
}
}
}
)
)