diff --git a/NAMESPACE b/NAMESPACE
index 3cfa939c79fa3e3767d965d2849eb0ebca3d3c9a..5c54f9ee486b77912b8b0cb22cdb9d4f1e6837d1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -16,6 +16,7 @@ export(get_rt_interval)
export(get_val_unit)
export(grab_unit)
export(import_project)
+export(init)
export(list2rev)
export(load_compound_input)
export(load_data_input)
diff --git a/R/api.R b/R/api.R
index dd9b24ac187012c276426410bc7857de13278faf..577ec70e53926075912e4b3e82377b278708f923 100644
--- a/R/api.R
+++ b/R/api.R
@@ -11,20 +11,19 @@
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
## See the License for the specific language governing permissions and
## limitations under the License.
-
-##' @export
-##' @param project `character(1)`, a directory containing input data.
-##' @param top_data_dir `character(1)`, a directory contining data
-##' subdirs.
-##' @param metfrag_db_dir `character(1)`, a directory containing
-##' MetFrag DBs.
-##' @param m `state`, a Shinyscreen state.
-##' @param phases `character(n)`, a character vector of Shinyscreen
-##' phases.
-##' @param help `logical(1)`, print help?
-run <- function(project="",
- top_data_dir="",
- metfrag_db_dir="",
+#' @title Run Shinyscreen Pipeline
+#'
+#' @details TODO.
+#'
+#' @param envopts `envopts`, an `envopts` object.
+#' @param project `character(1)`, a directory containing input data.
+#' @param m `state`, a Shinyscreen state.
+#' @param phases `character(n)`, a character vector of Shinyscreen
+#' phases.
+#' @param help `logical(1)`, print help?
+#' @export
+run <- function(envopts,
+ project="",
m=NULL,
phases=NULL,
help=F) {
@@ -53,19 +52,26 @@ run <- function(project="",
}
all_phases[phases]
+
}
- eo = prepare_paths(project=project,
- projects="",
- top_data_dir=top_data_dir,
- metfrag_db_dir=metfrag_db_dir)
-
-
- m <- if (nchar(project)!=0) new_project(project,envopts=eo) else if (!is.null(m)) m else stop("(run): Either the YAML config file (project),\n or the starting state (m) must be provided\n as the argument to the run function.")
- ## m$conf$project <- norm_path(m$conf$project) #FIXME: Test in all workflows!
- m <- withr::with_dir(new=m$run$paths$project,code = Reduce(function (prev,f) f(prev),
- x = the_phases,
- init = m))
+
+ m = if (is.null(m)) {
+ ## A project from scratch.
+ new_project(project,envopts=envopts)
+ } else {
+ ## Regenerate the runtime environment.
+
+ project = if (nchar(project)==0L) m$run$project else project
+ m$run = new_runtime_state(project=project,
+ envopts = envopts,
+ conf=m$conf)
+ m
+ }
+
+ m = withr::with_dir(new=m$run$paths$project,code = Reduce(function (prev,f) f(prev),
+ x = the_phases,
+ init = m))
return(invisible(m))
}
@@ -697,78 +703,12 @@ create_plots <- function(m) {
m
}
-
-prepare_paths <- function(project,
- projects,
- top_data_dir,
- metfrag_db_dir) {
-
- ## Get system-wide config.
- eo = load_envopts()
-
- ## Figure out how to run.
-
-
- if (nchar(top_data_dir)>0) {
- ## Specified `top_data_dir` overrides everything.
- eo$top_data_dir = norm_path(top_data_dir)
- } else {
- ## If no user supplied `top_data_dir`, check if envopts
- ## top_data_dir is empty.
- if (nchar(eo$top_data_dir)==0L) {
- ## If yes, the last attempt is to designate
- ## `project` dir as `top_data_dir` directory.
- if (dir.exists(project)) eo$top_data_dir=norm_path(project)
- }
-
- }
-
-
- ## In case `project` is a not a zero-length string.
- if (nchar(project)!=0) {
- ## The variable `projects` is alwas a super-directory of
- ## `project`.
- withr::with_dir(project,{
- eo$projects=norm_path("..")
- })
- } else {
- if (nchar(projects)!=0) {
- eo$projects=projects
- }
- }
-
-
- ## Override the default `db_dir` if `metfrag_db_dir` supplied.
- if (nchar(metfrag_db_dir)>0) {
- eo$metfrag$db_dir = norm_path(metfrag_db_dir)
- } else {
- ## If no default `db_dir`, try with `project`.
- if (nchar(eo$metfrag$db_dir)==0L) {
- eo$metfrag$db_dir = norm_path(project)
- }
- }
- eo
-}
-
prepare_app <- function(dir_before,
- projects,
- top_data_dir,
- metfrag_db_dir) {
-
+ envopts) {
## Information that needs to be availabe to the shiny server.
init <- list()
init$dir_before <- dir_before
- init$envopts = prepare_paths(project="",
- projects=projects,
- top_data_dir=top_data_dir,
- metfrag_db_dir=metfrag_db_dir)
- init$top_data_dir <- init$envopts$top_data_dir
- init$projects <- init$envopts$projects
-
-
- check_dir_absent(init$top_data_dir,what="top-data-dir")
- check_dir_absent(init$projects,what="projects")
-
+ init$envopts = envopts
## Create independent starting `home' for the server.
dir_start <- tempfile("shinyscreen")
@@ -788,14 +728,10 @@ prepare_app <- function(dir_before,
dir_start
}
+
#' @export
#' @title app
-#' @param projects `character(1)`, a location on the server side
-#' containing project directories.
-#' @param top_data_dir `character(1)`, a location on the server side
-#' containing data directories.
-#' @param metfrag_db_dir `character(1)`, a location on the server side
-#' containing MetFrag databases.
+#' @param envopts `envopts`. Shinyscreen environment options.
#' @param shiny_args `list`, optional list of arguments conveyed to
#' `rmarkdown::run` `shiny_args` argument.
#' @param render_args `list`, optional list of arguments conveyed to
@@ -804,19 +740,15 @@ prepare_app <- function(dir_before,
#' of the MetFrag jar file.
#' @return Nada.
#' @author Todor Kondić
-app <- function(projects="",
- top_data_dir="",
- metfrag_db_dir="",
+app <- function(envopts,
shiny_args=list(launch.browser=F),
render_args=NULL) {
dir_before = getwd()
message("dir_before: ", dir_before)
- message("top_data_dir: ", top_data_dir)
- message("projects: ", projects)
+ message("top_data_dir: ", envopts$top_data_dir)
+ message("projects: ", evnopts$projects)
dir_start = prepare_app(dir_before=dir_before,
- projects=projects,
- top_data_dir=top_data_dir,
- metfrag_db_dir=metfrag_db_dir)
+ envopts=envopts)
on.exit(expr=setwd(dir_before))
setwd(dir_start)
@@ -826,22 +758,21 @@ app <- function(projects="",
#' @export
#' @title serve
-#' @param top_data_dir `character(1)`, a location on the server side
-#' containing data directories.
-#' @param metfrag_db_dir `character(1)`, a location on the server side
-#' containing MetFrag DBs.
-#' @param usersdir `character(1)`, a location on the server side
-#' containing individual user directories.
+#' @param envopts `envopts`, an `envopts` object.
#' @param user `character(1)`, subdir of usersdir.
#' @param host `character(1)`, optional, address where the page is
#' served.
#' @param port `integer(1)`, optional, port at which the page is
#' served.
+#' @param top_data_dir `character(1)`, a location on the server side
+#' containing data directories.
+#' @param metfrag_db_dir `character(1)`, a location on the server side
+#' containing MetFrag DBs.
#' @return Nada.
#' @author Todor Kondić
-serve <- function(top_data_dir,metfrag_db_dir,usersdir,user,host='0.0.0.0',port=7777) {
+serve <- function(envopts,user,host='0.0.0.0',port=7777) {
shiny_args <- c(list(launch.browser=F),list(host=host,port=port))
- projects <- file.path(usersdir,user)
+ projects <- file.path(envopts$users_dir,user)
if (!dir.exists(projects)) {
dir.create(projects)
message('Created projects: ',projects)
@@ -849,9 +780,7 @@ serve <- function(top_data_dir,metfrag_db_dir,usersdir,user,host='0.0.0.0',port=
message('Using existing projects: ', projects)
}
app(shiny_args=shiny_args,
- top_data_dir=top_data_dir,
- projects=projects,
- metfrag_db_dir=metfrag_db_dir)
+ envopts=envopts)
}
@@ -941,24 +870,65 @@ report <- function(m) {
#' @title Initialise Shinyscreen Configuration
#' @details This function is used to inform `shinyscreen` about the
-#' working environment. It is only necessary to call it once. The
-#' parameters will be memorised.
+#' working environment. If argument `save` is T, the configuration
+#' will be memorised. Subsequent calls to `init` without arguments
+#' will just load the configuration. If `merge` argument is T, the
+#' resulting configuration object is going to be a merge between
+#' the new parameters and the memorised ones. Those arguments not
+#' mentioned in the argument list will be remembered from the save
+#' config.
#' @inheritParams envopts
-#' @return Nothing.
+#' @param merge `logical(1)`, optional. If T, merge with saved
+#' configuration.
+#' @param save `logical(1)`, optional. If T, save configuration,
+#' otherwise just return the Shinyscreen environment options.
+#' @return An `envopts` object.
#' @author Todor Kondić
-init <- function(projects="",
- top_data_dir="",
- metfrag_db_dir="",
- metfrag_jar="",
- java_bin=Sys.which("java"),
- metfrag_max_proc=parallel::detectCores()) {
- e = envopts(projects = projects,
- top_data_dir = top_data_dir,
- metfrag_db_dir = metfrag_db_dir,
- metfrag_jar = metfrag_jar,
- java_bin = java_bin,
- metfrag_max_proc = metfrag_max_proc)
- save_envopts(o=e)
+#' @export
+init <- function(projects=NULL,
+ top_data_dir=NULL,
+ metfrag_db_dir=NULL,
+ metfrag_jar=NULL,
+ java_bin=NULL,
+ metfrag_max_proc=NULL,
+ merge=T,
+ save=F) {
+
+
+ env = environment()
+ eargs = list()
+ ## Merge into the untouched (NULLs), only.
+ if (merge) {
+ ## Merge with old values
+ eold = load_envopts()
+ cargs = formalArgs(envopts)
+ if (length(eold)>0L) {
+ for (a in cargs) {
+ if (is.null(env[[a]])) eargs[[a]] = eold[[a]] else eargs[[a]]=env[[a]]
+ }
+ }
+ }
+
+ ## Default values = "" .
+ chrargs = c("projects","top_data_dir","metfrag_db_dir")
+
+ for (ca in chrargs) {
+ if (is.null(eargs[[ca]])) eargs[[ca]]=""
+ }
+
+ if (is.null(java_bin)) {
+ eargs[["java_bin"]]= Sys.which("java")
+ }
+
+ if (is.null(metfrag_max_proc)) {
+ eargs$metfrag_max_proc = parallel::detectCores()
+ }
+
+ e = do.call(envopts,eargs)
+
+
+ if (save) save_envopts(o=e)
+ e
}
#' @title Run MetFrag
diff --git a/R/envopts.R b/R/envopts.R
index cfccd2e41825af8c7521a153e8c5ff4da1c4d598..f4beb664f2f6005a8d1d3935c9c79ffced34b6f0 100644
--- a/R/envopts.R
+++ b/R/envopts.R
@@ -22,6 +22,14 @@
+mk_envopts <- function() {
+ res = list()
+ class(res) = c("envopts","list") #Just to officially make it an
+ #object.
+ res
+}
+
+
#' @title Create a `envopts` Object
#' @details An `envopts` object is Shinyscreen way to store settings
#' related to a specific computing environment. Information such
@@ -37,6 +45,8 @@
#' @param metfrag_db_dir `character(1)`, a path to the directory which
#' contains MetFrag databases.
#' @param metfrag_jar `character(1)`, a path to MetFrag JAR file.
+#' @param users_dir `character(1)`, a location on the server side
+#' containing individual user directories.
#' @param java_bin `character(1)`, a path to jave runtime
#' (optional). We try to detect this.
#' @param metfrag_max_proc `integer(1)`, maximum number of CPU cores
@@ -47,18 +57,22 @@ envopts <- function(projects="",
top_data_dir="",
metfrag_db_dir="",
metfrag_jar="",
+ users_dir="",
java_bin=Sys.which("java"),
metfrag_max_proc = parallel::detectCores()) {
+ res = mk_envopts()
res = list(metfrag=list())
- class(res) = c("envopts","list") #Just to officially make it an
- #object.
-
- check_dir_absent_nz(projects,what="projects-dir")
+
+ check_dir_absent(projects,what="projects-dir")
res$projects = projects
- check_dir_absent_nz(top_data_dir,what="top-data-dir")
+ check_dir_absent(top_data_dir,what="top-data-dir")
res$top_data_dir=top_data_dir
- check_dir_absent_nz(metfrag_db_dir,what="mf-db-dir")
+
+ check_dir_absent(users_dir,what="users-dir")
+ res$users_dir=users_dir
+
+ check_dir_absent(metfrag_db_dir,what="mf-db-dir")
res$metfrag$db_dir = norm_path(metfrag_db_dir)
check_file_absent(metfrag_jar,what="mf-jar")
@@ -94,8 +108,7 @@ get_envopts_fn <- function() {
load_envopts <- function() {
cfgfile = get_envopts_fn()
- check_conf_absent(cfgfile)
- readRDS(cfgfile)
+ if (file.exists(cfgfile)) readRDS(cfgfile) else mk_envopts()
}
diff --git a/R/errors.R b/R/errors.R
index 32e69d91f72a1309bf08fd8e19d85863ca79240f..5d0f71a280e538abbcf10af42c28e9a13047866f 100644
--- a/R/errors.R
+++ b/R/errors.R
@@ -14,13 +14,18 @@
errc_conf_file_absent <- errorCondition("There is no config file in the project directory.",class="conf-file-absent")
-check_notastring <- function(value,what) {
- if (!is.character(value)) stop(errorCondition(paste0("The value (",str(value),") of, ",what," is not a character vector."),class=paste0(what,'-notastring')))
+check_notastring <- function(value, what, strict=F) {
+ cond = !is.character(value)
+ if (strict) cond = cond || is.na(value)
+
+ if (cond) stop(errorCondition(paste0("The value (",value,") of, ",what," is not a character vector (or, it is, maybe, a missing value)."),class=paste0(what,'-notastring')))
}
-check_dir_absent <- function(dir,what) {
- check_notastring(dir,what)
- if (nchar(dir)>0L && !dir.exists(dir)) stop(errorCondition(paste0("The ", what, " directory --- ", dir, "--- does not exist, or cannot be found."), class=paste0(what,'-absent')))
+check_dir_absent <- function(dir,what,strict=F) {
+ check_notastring(dir,what,strict=strict)
+ cond = !dir.exists(dir)
+ if (!strict) cond = cond && nchar(dir)>0L
+ if (cond) stop(errorCondition(paste0("The ", what, " directory --- ", dir, "--- does not exist, or cannot be found."), class=paste0(what,'-absent')))
}
check_dir_absent_nz <- function(dir,what) {
diff --git a/R/shiny-state.R b/R/shiny-state.R
index 43c190d578f68f92ea3ad3d0230b1b665885ca7b..31bf6295557b63bf4f7e2056416e2f67ecd7aac8 100644
--- a/R/shiny-state.R
+++ b/R/shiny-state.R
@@ -251,8 +251,8 @@ unpack_app_state <- function(session,envopts,input,top_data_dir,project_path,pac
gui$datatab$tag <- packed_state$datatab$tag
gui$datatab$set <- packed_state$datatab$set
x <- packed_state$paths$data
- gui$paths$data <- if (length(x)>0 & nchar(x)>0) file.path(top_data_dir,basename(x))
- if (!dir.exists(gui$paths$data)) {warning("Data directory ", gui$paths$data, " does not exist. You must select one.")}
+ gui$paths$data = if (length(x)>0 && nchar(x)>0) basename(x) else ""
+ if (!dir.exists(file.path(top_data_dir,gui$paths$data))) {warning("Data directory ", gui$paths$data, " does not exist. You must select one.")}
gui
})
@@ -271,7 +271,7 @@ input2conf_setup <- function(input,gui,conf=list()) {
conf$compounds$sets <- gui$compounds$sets
- conf$paths$data = gui$paths$data
+ conf$paths$data = basename(gui$paths$data)
conf
}
@@ -362,7 +362,6 @@ app_state2state <- function(input,gui,envopts,m=NULL) {
m$conf = input2conf_setup(input=input,
gui=gui)
-
m = app_update_conf(input=input,
gui=gui,
envopts=envopts,
@@ -373,33 +372,10 @@ app_state2state <- function(input,gui,envopts,m=NULL) {
"metfrag"),
m=m)
- ## m$conf = input2conf_setup(input,gui=gui)
- ## m$conf = input2conf_prescreen(input=input,conf=m$conf)
- ## m$conf = input2conf_figures(input,conf=m$conf)
- ## m$conf = input2conf_report(input,conf=m$conf)
- ## m$conf = input2conf_metfrag(input,conf=m$conf)
-
-
-
- ## m$run <- new_runtime_state(project=gui$paths$project,
- ## envopts = envopts,
- ## conf=m$conf)
-
-
- m$input$tab$mzml <- gui2datatab(gui)
+ m$input$tab$mzml = gui2datatab(gui)
m
}
-
-
-
-
-gen_comp_state <- function(input,gui) {
- m <- app_state2state(input,gui)
- run(m=m,phases=c("setup","mk_comp_tab"))
-
-}
-
get_sets <- function(gui) {
fn_sets <- file.path(gui$paths$project,gui$compounds$sets)
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index 007489ed254cf3e34437e7b2f95c059280fa0329..710e3d8a9d0393a44a07f2eb3a852ac915e17c72 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -708,24 +708,6 @@ mk_shinyscreen_server <- function(projects,init) {
})
- rf_setup_state <- reactive({
- rvs$gui$project
- rvs$gui$datatab$file
- rvs$gui$datatab$tag
- rvs$gui$datatab$adduct
- rvs$gui$datatab$set
- rvs$gui$paths$data
- rvs$gui$paths$project
- isolate({
- req(pre_setup_val_block(rvs$gui))
- q = app_state2state(input,rvs$gui,envopts=init$envopts)
-
- })
- run(m=q,phases=c("setup","comptab"))
- })
-
-
-
## REACTIVE FUNCTIONS: COMPOUND INDEX
rf_get_cindex <- reactive({
@@ -945,7 +927,7 @@ mk_shinyscreen_server <- function(projects,init) {
updateSelectInput(session = session,
inputId = "top_data_dir_list",
selected = basename(top_data_dir),
- choices = list.dirs(path = init$top_data_dir,
+ choices = list.dirs(path = init$envopts$top_data_dir,
full.names = F,
recursive = F))
})
@@ -964,7 +946,7 @@ mk_shinyscreen_server <- function(projects,init) {
observeEvent(rtimer1000(),{
projects = rv_projects()
- curr_projects = list.dirs(path=init$projects, full.names = F, recursive = F)
+ curr_projects = list.dirs(path=init$envopts$projects, full.names = F, recursive = F)
if (length(union(curr_projects,projects)) != length(intersect(curr_projects,projects))) {
updateSelectInput(session=session,
inputId="proj_list",
@@ -983,7 +965,7 @@ mk_shinyscreen_server <- function(projects,init) {
## loaded. Everything else works off rvs$m and rvs$gui.
wd = input$proj_list
req(!is.null(wd) && !is.na(wd) && nchar(wd)>0)
- fullwd = file.path(init$projects,wd)
+ fullwd = file.path(init$envopts$projects,wd)
check_dir_absent(fullwd,what="project")
## Load saved state if existing, create if it does not.
fn_packed_state = file.path(fullwd,FN_GUI_STATE)
@@ -994,7 +976,7 @@ mk_shinyscreen_server <- function(projects,init) {
rvs$gui = unpack_app_state(session=session,
envopt=init$envopts,
input=input,
- top_data_dir=init$top_data_dir,
+ top_data_dir=init$envopts$top_data_dir,
project_path=fullwd,
packed_state=pack)
## Load computational state.
@@ -1050,7 +1032,7 @@ mk_shinyscreen_server <- function(projects,init) {
observeEvent(input$sel_data_dir_b,{
data_dir = input$top_data_dir_list
req(isTruthy(data_dir))
- rvs$gui$paths$data = file.path(init$top_data_dir, data_dir)
+ rvs$gui$paths$data = file.path(init$envopts$top_data_dir, data_dir)
message("Selected data dir:",rvs$gui$paths$data)
@@ -1154,7 +1136,10 @@ mk_shinyscreen_server <- function(projects,init) {
isolate({
if (rv_extr_flag()) {
rv_extr_flag(F)
- rvs$m = run(m=rvs$m,phases=c("setup","comptab","extract"))
+ rvs$m = run(m=rvs$m,
+ top_data_dir=init$envopts$top_data_dir,
+ metfrag_db_dir=init$envopts$metfrag$db_dir,
+ phases=c("setup","comptab","extract"))
rvs$status$is_extracted_stat = "Yes."
rvs$status$is_qa_stat = "No."
fn_c_state = file.path(rvs$m$run$paths$project,
@@ -1202,7 +1187,10 @@ mk_shinyscreen_server <- function(projects,init) {
shinymsg("Prescreening started. Please wait.")
rv_presc_flag(F)
## If user changed prescreening params.
- rvs$m = run(m=rvs$m,phases="prescreen")
+ rvs$m = run(m=rvs$m,
+ top_data_dir=init$envopts$top_data_dir,
+ metfrag_db_dir=init$envopts$metfrag$db_dir,
+ phases="prescreen")
rvs$status$is_qa_stat = "Yes."
shinymsg("Prescreening has been completed.")
}
diff --git a/R/state.R b/R/state.R
index 466f597d1090978f7e195a29118cc0d433fe4d83..54450c7a3e6878383eb64d732f1bac6d69a2f055 100644
--- a/R/state.R
+++ b/R/state.R
@@ -54,21 +54,6 @@ runtime_from_conf <- function(run,conf) {
run
}
-reinit_run_data <- function(projects,top_data_dir,project,run=NULL) {
- if (!is.null(run)) {
- olddata <- run$paths$data
- oldproject <- basename(run$paths$project)
- if (project != oldproject) {
- message("Project has been renamed to: ",project)
- message("Old project name was: ", oldproject)
- }
- if (isTruthy(olddata)) run$paths$data <- file.path(top_user_dir,basename(olddata))
- }
- run$project <- project
- run$paths$project <- file.path(projects,project)
- run
-}
-
#' @title Create Runtime Configuration
#' @details This is a part of the configuration that can only be
#' diagnosed at runtime.
@@ -163,9 +148,9 @@ new_runtime_state <- function(project,envopts,conf=NULL) {
}
## Check if all OK with project name.
- check_notastring(project,"project")
- project_path = norm_path(project)
- check_dir_absent(project_path,"project")
+ check_notastring(project,"project",strict=T)
+ project_path = file.path(envopts$projects,basename(project))
+ check_dir_absent(project_path,"project_path", strict=T)
project = basename(project)
run = list()
run$project = project
@@ -176,7 +161,7 @@ new_runtime_state <- function(project,envopts,conf=NULL) {
run$paths$data = norm_path(file.path(envopts$top_data_dir,conf$paths$data))
- check_dir_absent(run$paths$data,"data-dir")
+ check_dir_absent(run$paths$data,"data-dir", strict=T)
if (!is.null(conf)) runtime_from_conf(run=run,conf=conf) else run
diff --git a/man/app.Rd b/man/app.Rd
index a8967036119890a602e80afeee3afa7889f10dcb..9c2b84dd46b6fbc9c89cd212d71f0b7deff22b31 100644
--- a/man/app.Rd
+++ b/man/app.Rd
@@ -4,19 +4,10 @@
\alias{app}
\title{app}
\usage{
-app(
- projects = getwd(),
- top_data_dir = getwd(),
- shiny_args = list(launch.browser = F),
- render_args = NULL
-)
+app(envopts, shiny_args = list(launch.browser = F), render_args = NULL)
}
\arguments{
-\item{projects}{\code{character(1)}, a location on the server side
-containing project directories.}
-
-\item{top_data_dir}{\code{character(1)}, a location on the server side
-containing data directories.}
+\item{envopts}{\code{envopts}. Shinyscreen environment options.}
\item{shiny_args}{\code{list}, optional list of arguments conveyed to
\code{rmarkdown::run} \code{shiny_args} argument.}
@@ -24,9 +15,6 @@ containing data directories.}
\item{render_args}{\code{list}, optional list of arguments conveyed to
\code{rmarkdown::run} \code{render_args} argument.}
-\item{metfrag_db_dir}{\code{character(1)}, a location on the server side
-containing MetFrag databases.}
-
\item{metfrag_runtime}{\code{character(1)}, a location on the server side
of the MetFrag jar file.}
}
diff --git a/man/envopts.Rd b/man/envopts.Rd
index 336ba3cceb0db73dac2b7b02bafaf7de877fe2d6..38c21b2845b82bb0325fd5b4ab0b143a70921ea7 100644
--- a/man/envopts.Rd
+++ b/man/envopts.Rd
@@ -5,16 +5,34 @@
\title{Create a \code{envopts} Object}
\usage{
envopts(
+ projects = "",
+ top_data_dir = "",
metfrag_db_dir = "",
metfrag_jar = "",
+ users_dir = "",
java_bin = Sys.which("java"),
metfrag_max_proc = parallel::detectCores()
)
}
\arguments{
-\item{metfrag_db_dir}{\code{character(1)}, a path to the directory which contains MetFrag databases}
+\item{projects}{\code{character(1)}, a directory which contains all
+shinyscreen projects directories. A single project directory
+contains input and output files.}
-\item{metfrag_jar}{\code{character(1)}, a path to MetFrag JAR file}
+\item{top_data_dir}{\code{character(1)}, a directory which contains all
+\code{data} directories. A single \code{data} directory contains \code{mzML}
+spectrometry data files.}
+
+\item{metfrag_db_dir}{\code{character(1)}, a path to the directory which
+contains MetFrag databases.}
+
+\item{metfrag_jar}{\code{character(1)}, a path to MetFrag JAR file.}
+
+\item{users_dir}{\code{character(1)}, a location on the server side
+containing individual user directories.}
+
+\item{java_bin}{\code{character(1)}, a path to jave runtime
+(optional). We try to detect this.}
\item{metfrag_max_proc}{\code{integer(1)}, maximum number of CPU cores
available for MetFrag.}
@@ -26,7 +44,7 @@ An \code{envopts} object.
Create a \code{envopts} Object
}
\details{
-A \code{envopts} object is Shinyscreen way to store settings
+An \code{envopts} object is Shinyscreen way to store settings
related to a specific computing environment. Information such
as the run time path to a MetFrag JAR will vary from one to
another setup and we need to convey this to the \code{shinyscreen}
diff --git a/man/init.Rd b/man/init.Rd
index b45624b9db07ee044fcacc1df88925b65e632556..399987dceccdc866225a79f73db11ae3bc41b6f8 100644
--- a/man/init.Rd
+++ b/man/init.Rd
@@ -5,30 +5,57 @@
\title{Initialise Shinyscreen Configuration}
\usage{
init(
+ projects = "",
+ top_data_dir = "",
metfrag_db_dir = "",
metfrag_jar = "",
java_bin = Sys.which("java"),
- metfrag_max_proc = parallel::detectCores()
+ metfrag_max_proc = parallel::detectCores(),
+ merge = T,
+ save = F
)
}
\arguments{
-\item{metfrag_db_dir}{\code{character(1)}, a path to the directory which contains MetFrag databases}
+\item{projects}{\code{character(1)}, a directory which contains all
+shinyscreen projects directories. A single project directory
+contains input and output files.}
-\item{metfrag_jar}{\code{character(1)}, a path to MetFrag JAR file}
+\item{top_data_dir}{\code{character(1)}, a directory which contains all
+\code{data} directories. A single \code{data} directory contains \code{mzML}
+spectrometry data files.}
+
+\item{metfrag_db_dir}{\code{character(1)}, a path to the directory which
+contains MetFrag databases.}
+
+\item{metfrag_jar}{\code{character(1)}, a path to MetFrag JAR file.}
+
+\item{java_bin}{\code{character(1)}, a path to jave runtime
+(optional). We try to detect this.}
\item{metfrag_max_proc}{\code{integer(1)}, maximum number of CPU cores
available for MetFrag.}
+
+\item{merge}{\code{logical(1)}, optional. If T, merge with saved
+configuration.}
+
+\item{save}{\code{logical(1)}, optional. If T, save configuration,
+otherwise just return the Shinyscreen environment options.}
}
\value{
-Nothing.
+An \code{envopts} object.
}
\description{
Initialise Shinyscreen Configuration
}
\details{
This function is used to inform \code{shinyscreen} about the
-working environment. It is only necessary to call it once. The
-parameters will be memorised.
+working environment. If argument \code{save} is T, the configuration
+will be memorised. Subsequent calls to \code{init} without arguments
+will just load the configuration. If \code{merge} argument is T, the
+resulting configuration object is going to be a merge between
+the new parameters and the memorised ones. Those arguments not
+mentioned in the argument list will be remembered from the save
+config.
}
\author{
Todor Kondić
diff --git a/man/metfrag.Rd b/man/metfrag.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..916d5e4f666fe2f0708a62dbe45fc4419752ba83
--- /dev/null
+++ b/man/metfrag.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/api.R
+\name{metfrag}
+\alias{metfrag}
+\title{Run MetFrag}
+\usage{
+metfrag(m)
+}
+\arguments{
+\item{m}{\code{state}, a state object.}
+}
+\value{
+m
+}
+\description{
+Run MetFrag
+}
+\author{
+Todor Kondić
+}
diff --git a/man/run.Rd b/man/run.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..0c376a2be2a6532e4e3655f722b286ee8a718edf
--- /dev/null
+++ b/man/run.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/api.R
+\name{run}
+\alias{run}
+\title{Run Shinyscreen Pipeline}
+\usage{
+run(envopts, project = "", m = NULL, phases = NULL, help = F)
+}
+\arguments{
+\item{envopts}{\code{envopts}, an \code{envopts} object.}
+
+\item{project}{\code{character(1)}, a directory containing input data.}
+
+\item{m}{\code{state}, a Shinyscreen state.}
+
+\item{phases}{\code{character(n)}, a character vector of Shinyscreen
+phases.}
+
+\item{help}{\code{logical(1)}, print help?}
+}
+\description{
+Run Shinyscreen Pipeline
+}
+\details{
+TODO.
+}
diff --git a/man/serve.Rd b/man/serve.Rd
index 531f87eddf9a519154f83c34f56727ad2f0496ed..c9e16ed35e31deda862499472d3007ad139c2738 100644
--- a/man/serve.Rd
+++ b/man/serve.Rd
@@ -4,14 +4,10 @@
\alias{serve}
\title{serve}
\usage{
-serve(top_data_dir, usersdir, user, host = "0.0.0.0", port = 7777)
+serve(envopts, user, host = "0.0.0.0", port = 7777)
}
\arguments{
-\item{top_data_dir}{\code{character(1)}, a location on the server side
-containing data directories.}
-
-\item{usersdir}{\code{character(1)}, a location on the server side
-containing individual user directories.}
+\item{envopts}{\code{envopts}, an \code{envopts} object.}
\item{user}{\code{character(1)}, subdir of usersdir.}
@@ -20,6 +16,12 @@ served.}
\item{port}{\code{integer(1)}, optional, port at which the page is
served.}
+
+\item{top_data_dir}{\code{character(1)}, a location on the server side
+containing data directories.}
+
+\item{metfrag_db_dir}{\code{character(1)}, a location on the server side
+containing MetFrag DBs.}
}
\value{
Nada.