Remove memory cache (#33)

* up

* up

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MGnifyR
 Type: Package
-Version: 0.99.14
+Version: 0.99.15
 Authors@R:
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "[email protected]",

NAMESPACE

@@ -4,10 +4,8 @@ export("authTok<-")
 export("cacheDir<-")
 export("clearCache<-")
 export("databaseUrl<-")
-export("memCache<-")
 export("showWarnings<-")
 export("useCache<-")
-export("useMemCache<-")
 export("verbose<-")
 export(MgnifyClient)
 export(authTok)
@@ -18,7 +16,6 @@ export(doQuery)
 export(getFile)
 export(getMetadata)
 export(getResult)
-export(memCache)
 export(mgnify_analyses_from_samples)
 export(mgnify_analyses_from_studies)
 export(mgnify_client)
@@ -33,17 +30,14 @@ export(searchAnalysis)
 export(searchFile)
 export(showWarnings)
 export(useCache)
-export(useMemCache)
 export(verbose)
 exportClasses(MgnifyClient)
 exportMethods("authTok<-")
 exportMethods("cacheDir<-")
 exportMethods("clearCache<-")
 exportMethods("databaseUrl<-")
-exportMethods("memCache<-")
 exportMethods("showWarnings<-")
 exportMethods("useCache<-")
-exportMethods("useMemCache<-")
 exportMethods("verbose<-")
 exportMethods(authTok)
 exportMethods(cacheDir)
@@ -53,12 +47,10 @@ exportMethods(doQuery)
 exportMethods(getFile)
 exportMethods(getMetadata)
 exportMethods(getResult)
-exportMethods(memCache)
 exportMethods(searchAnalysis)
 exportMethods(searchFile)
 exportMethods(showWarnings)
 exportMethods(useCache)
-exportMethods(useMemCache)
 exportMethods(verbose)
 import(MultiAssayExperiment)
 import(TreeSummarizedExperiment)

R/MgnifyClient.R

@@ -29,20 +29,11 @@
 #' @param showWarnings A single boolean value specifying whether to print
 #' warnings during invocation of some MGnifyR functions.
 #' (By default: \code{showWarnings = FALSE})
-#' 
+#'
 #' @param verbose A single boolean value specifying whether to print extra
 #' output during invocation of some MGnifyR functions.
 #' (By default: \code{verbose = FALSE})
 #'
-#' @param useMemCache A single boolean value specifying whether to indicate
-#' whether functional results obtained when \code{bulk_dl} is \code{TRUE}
-#' in \code{mgnify_get_analyses_results} should be stored in an in-memory
-#' cache, rather than the cached input being re-read for each accession. this
-#' is currently NOT working properly and should therefore be set \code{FALSE}.
-#' It has the potential to speed up searches considerably though, especially
-#' for studies with a large number of samples, so will be implemented properly
-#' in the future. (By default: \code{useMemCache = FALSE})
-#' 
 #' @param clearCache A single boolean value specifying whether to clear the
 #' cache. (By default: \code{clearCache = FALSE})
 #'
@@ -76,8 +67,7 @@ NULL
 #' @export
 MgnifyClient <- function(
         username = NULL, password = NULL, useCache = FALSE, cacheDir = NULL,
-        showWarnings = FALSE, verbose = TRUE, useMemCache = FALSE,
-        clearCache = FALSE, ...){
+        showWarnings = FALSE, verbose = TRUE, clearCache = FALSE, ...){
     ############################### INPUT CHECK ################################
     if( !(is.null(username) || .is_non_empty_string(username)) ){
         stop(
@@ -111,11 +101,6 @@ MgnifyClient <- function(
             "extra output during invocation of MGnifyR functions.",
             call. = FALSE)
     }
-    if( !.is_a_bool(useMemCache) ){
-        stop(
-            "'useMemCache' must be a boolean value specifying whether use ",
-            "on-disk memory.", call. = FALSE)
-    }
     if( !.is_a_bool(clearCache) ){
         stop(
             "'clearCache' must be a boolean value specifying whether to ",
@@ -161,8 +146,6 @@ MgnifyClient <- function(
         useCache = useCache,
         cacheDir = cachepath,
         showWarnings = showWarnings,
-        memCache = list(),
-        useMemCache = useMemCache,
         clearCache = clearCache,
         verbose = verbose
     )

R/allAccessors.R

@@ -12,7 +12,7 @@
 #'
 #' @examples
 #' mg <- MgnifyClient()
-#' 
+#'
 #' databaseUrl(mg)
 #' showWarnings(mg) <- FALSE
 #'
@@ -52,19 +52,6 @@ setMethod(
     "showWarnings", signature = c(x = "MgnifyClient"),
     function(x){ x@showWarnings })
 
-#' @rdname MgnifyClient-accessors
-#' @include allClasses.R allGenerics.R MgnifyClient.R utils.R
-#' @export
-setMethod(
-    "useMemCache", signature = c(x = "MgnifyClient"),
-    function(x){ x@useMemCache })
-
-#' @rdname MgnifyClient-accessors
-#' @include allClasses.R allGenerics.R MgnifyClient.R utils.R
-#' @export
-setMethod(
-    "memCache", signature = c(x = "MgnifyClient"), function(x){ x@memCache })
-
 #' @rdname MgnifyClient-accessors
 #' @include allClasses.R allGenerics.R MgnifyClient.R utils.R
 #' @export
@@ -114,20 +101,6 @@ setMethod(
     "showWarnings<-", signature = c(x = "MgnifyClient"),
     function(x, value){ BiocGenerics:::replaceSlots(x, showWarnings = value) })
 
-#' @rdname MgnifyClient-accessors
-#' @include allClasses.R allGenerics.R MgnifyClient.R utils.R
-#' @export
-setMethod(
-    "useMemCache<-", signature = c(x = "MgnifyClient"),
-    function(x, value){ BiocGenerics:::replaceSlots(x, useMemCache = value) })
-
-#' @rdname MgnifyClient-accessors
-#' @include allClasses.R allGenerics.R MgnifyClient.R utils.R
-#' @export
-setMethod(
-    "memCache<-", signature = c(x = "MgnifyClient"),
-    function(x, value){ BiocGenerics:::replaceSlots(x, memCache = value) })
-
 #' @rdname MgnifyClient-accessors
 #' @include allClasses.R allGenerics.R MgnifyClient.R utils.R
 #' @export

R/allClasses.R

@@ -8,26 +8,21 @@
 #' database.
 #'
 #' @slot authTok A single character value specifying authentication token.
-#' 
+#'
 #' @slot useCache A single boolean value specifying whether to use cache.
 #'
 #' @slot cacheDir A single character value specifying cache directory.
 #'
 #' @slot showWarnings A single boolean value specifying whether to show
 #' warnings.
 #'
-#' @slot useMemCache A single boolean value specifying whether to use on-disk
-#' memory.
-#'
-#' @slot memCache A single character value specifying on-disk memory directory.
-#'
 #' @slot clearCache A single boolean value specifying whether to clear cache.
-#' 
+#'
 #' @slot verbose A single boolean value specifying whether to show messages.
 #'
 #' @section Constructor:
 #' See  \code{\link{MgnifyClient}} for constructor.
-#' 
+#'
 #' @section Accessor:
 #' See \code{\link{MgnifyClient-accessors}} for accessor functions.
 #'
@@ -45,16 +40,12 @@ setClass(
         useCache = "logical",
         cacheDir = "character",
         showWarnings = "logical",
-        useMemCache = "logical",
-        memCache = "list",
         clearCache = "logical",
         verbose = "logical"),
     prototype = list(
         databaseUrl = "https://www.ebi.ac.uk/metagenomics/api/v1",
         authTok = NULL,
         useCache = FALSE,
         cacheDir = NULL,
-        useMemCache = FALSE,
-        memCache = list(),
         clearCache = FALSE,
         verbose = TRUE))

R/allGenerics.R

@@ -27,17 +27,6 @@ setGeneric(
     "showWarnings", signature = c("x"), function(x)
         standardGeneric("showWarnings"))
 
-#' @rdname MgnifyClient-accessors
-#' @export
-setGeneric(
-    "useMemCache", signature = c("x"), function(x)
-        standardGeneric("useMemCache"))
-
-#' @rdname MgnifyClient-accessors
-#' @export
-setGeneric(
-    "memCache", signature = c("x"), function(x) standardGeneric("memCache"))
-
 #' @rdname MgnifyClient-accessors
 #' @export
 setGeneric(
@@ -78,18 +67,6 @@ setGeneric(
     "showWarnings<-", signature = c("x"), function(x, value)
         standardGeneric("showWarnings<-"))
 
-#' @rdname MgnifyClient-accessors
-#' @export
-setGeneric(
-    "useMemCache<-", signature = c("x"), function(x, value)
-        standardGeneric("useMemCache<-"))
-
-#' @rdname MgnifyClient-accessors
-#' @export
-setGeneric(
-    "memCache<-", signature = c("x"), function(x, value)
-        standardGeneric("memCache<-"))
-
 #' @rdname MgnifyClient-accessors
 #' @export
 setGeneric(

R/deprecate.R

@@ -67,7 +67,7 @@ mgnify_client <- function(
         url = url,
         username = username, password = password,
         useCache = usecache, cacheDir = cache_dir, warnings = warnings,
-        useMemCache = use_memcache)
+        use.mem.cache = use_memcache)
 }
 
 #' @rdname deprecate

R/getResult.R

@@ -86,7 +86,7 @@
 #' # Get OTU tables as TreeSE
 #' accession_list <- c("MGYA00377505")
 #' tse <- getResult(mg, accession_list, get.func=FALSE, get.taxa=TRUE)
-#' 
+#'
 #' \donttest{
 #' # Get functional data along with OTU tables as MAE
 #' mae <- getResult(mg, accession_list, get.func=TRUE, get.taxa=TRUE)
@@ -96,7 +96,7 @@
 #'     mg, accession_list, get.func=TRUE, get.taxa=TRUE, output = "list",
 #'     as.df = TRUE, use.cache = TRUE)
 #' }
-#' 
+#'
 #' @name getResult
 NULL
 
@@ -751,7 +751,7 @@ setMethod("getResult", signature = c(x = "MgnifyClient"), function(
 .get_bulk_files <- function(
         cur_type, client, r, metadata_df, downloadDIR,
         use.cache, clear.cache = clearCache(client),
-        use.mem.cache = useMemCache(client), ...){
+        use.mem.cache = FALSE, mem.cache.name = "mgnify_memory_cache", ...){
     # Input check
     if( !.is_a_bool(clear.cache) ){
         stop(
@@ -761,6 +761,18 @@ setMethod("getResult", signature = c(x = "MgnifyClient"), function(
         stop(
             "'use.mem.cache' must be a single boolean value.", call. = FALSE)
     }
+    # Check mem.cache.name
+    if( !( length(mem.cache.name) == 1 && is.character(mem.cache.name) ) ){
+      stop("'mem.cache.name' must be a single character value.", call. = FALSE)
+    }
+    if( exists(mem.cache.name) && use.mem.cache ){
+        mgnify_memory_cache <- get(mem.cache.name)
+        if( !is.list(mgnify_memory_cache) ){
+            stop("'mem.cache.name' must specify a list object.", call. = FALSE)
+        }
+    } else if(use.mem.cache){
+        mgnify_memory_cache <- list()
+    }
     #
     # Get the url
     data_url <- r$links$self
@@ -812,6 +824,8 @@ setMethod("getResult", signature = c(x = "MgnifyClient"), function(
     if( use.mem.cache ){
         mgnify_memory_cache[[cur_type]] <- list(
             data=tmp_df, fname=fname)
+        # Assign to global variable so it is visible for user
+        assign(mem.cache.name, mgnify_memory_cache, envir = .GlobalEnv)
     }
 
     # Because there seem to be "mismatches" between the
@@ -866,9 +880,6 @@ setMethod("getResult", signature = c(x = "MgnifyClient"), function(
     return(tmp_df)
 }
 
-# Result table caching
-mgnify_memory_cache <- list()
-
 # Which parser do you use for which type of output?
 # a list of parsers for each output type. If new output types come, add them to
 # here (and below) so that they are fetched from the database.