From c03e821d1cff40b1afa252c86b4bbf38ebdd43c8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Tue, 10 Jan 2023 12:48:23 +0100
Subject: [PATCH] api, resources, tests, ... : Add MetFrag related arguments to
`app'.
* DESCRIPTION: New version and doc engine.
* NAMESPACE: Adapted.
* man: Updated.
---
DESCRIPTION | 4 +-
NAMESPACE | 1 -
R/api.R | 81 +++++++++++++++++++++++++++------------
R/resources.R | 9 ++++-
man/app.Rd | 25 ++++++++----
man/serve.Rd | 8 ++--
tests/testthat/test-api.R | 40 +++++++++++++++++++
7 files changed, 127 insertions(+), 41 deletions(-)
create mode 100644 tests/testthat/test-api.R
diff --git a/DESCRIPTION b/DESCRIPTION
index f33b90a..57676cd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: shinyscreen
Title: Pre-screening of Mass Spectrometry Data
-Version: 1.2.9000
+Version: 1.2.9001
Author: Todor Kondić
Maintainer: Todor Kondić <todor.kondic@uni.lu>
Authors@R:
@@ -41,7 +41,7 @@ Description: Pre-screening of Mass Spectrometry Data.
License: Apache License (>= 2.0)
Encoding: UTF-8
LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
Roxygen: list(markdown = TRUE)
Collate:
'base.R'
diff --git a/NAMESPACE b/NAMESPACE
index 9937375..ec49d63 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -52,4 +52,3 @@ importFrom(MSnbase,readMSData)
importFrom(promises,"%...>%")
importFrom(promises,future_promise)
importFrom(shiny,validate)
-importFrom(ggplot2,aes)
diff --git a/R/api.R b/R/api.R
index 03fb257..1b2db95 100644
--- a/R/api.R
+++ b/R/api.R
@@ -673,41 +673,72 @@ create_plots <- function(m) {
m
}
+prepare_app <- function(dir_before,
+ projects,
+ top_data_dir,
+ metfrag_db_dir,
+ metfrag_runtime) {
+ init <- list()
+ init$dir_before <- dir_before
+ init$top_data_dir <- norm_path(top_data_dir)
+ init$projects <- norm_path(projects)
+ init$metfrag_db_dir <- if (nchar(norm_path(metfrag_db_dir))>0L) norm_path(metfrag_db_dir) else ""
+ init$metfrag_runtime <- if (nchar(norm_path(metfrag_runtime))>0L) norm_path(metfrag_runtime) else ""
+ if (!dir.exists(init$top_data_dir)) stop(errorCondition(paste0("Data directory (top_data_dir), currently `",
+ init$top_data_dir,
+ "` does not exist. Abort."),
+ class = "top-data-dir-absent"))
+ if (!dir.exists(init$projects)) stop(errorCondition(paste0("User root directory (projects), currently `",
+ init$projects,"` does not exist.. Abort."),
+ class= "projects-absent"))
+
+ if (nchar(init$metfrag_db_dir)>0L && !dir.exists(init$metfrag_db_dir)) stop(errorCondition("MetFrag DB directory specified, but cannot be found.", class = "mf-db-dir-absent"))
+ if (nchar(init$metfrag_runtime)>0L && !file.exists(init$metfrag_runtime)) stop(errorCondition("MetFrag jar file specified, but cannot be found.", class = "mf-jar-absent"))
+
+ dir_start <- tempfile("shinyscreen")
+ dir.create(dir_start, recursive = T)
+
+ dir.create(file.path(dir_start,'www'), showWarnings=F)
+ saveRDS(object = init,file=file.path(dir_start,"init.rds"))
+ file.copy(system.file(file.path("rmd","app.Rmd"),package = "shinyscreen"),file.path(dir_start,"app_run.Rmd"))
+ file.copy(system.file(file.path("www","custom.css"),package = "shinyscreen"),file.path(dir_start,"www","custom.css"))
+ dir_start
+}
+
#' @export
#' @title app
-#' @param shiny_args `list`, optional list of arguments conveyed to
-#' `rmarkdown::run` `shiny_args` argument.
-#' @param render_args `list`, optional list of arguments conveyed to
-#' `rmarkdown::run` `render_args` argument.
+#' @param projects `character(1)`, a location on the server side
+#' containing project directories.
#' @param top_data_dir `character(1)`, a location on the server side
#' containing data directories.
#' @param metfrag_db_dir `character(1)`, a location on the server side
#' containing MetFrag databases.
-#' @param projects `character(1)`, a location on the server side
-#' containing project directories.
+#' @param metfrag_runtime `character(1)`, a location on the server side
+#' of the MetFrag jar file.
+#' @param shiny_args `list`, optional list of arguments conveyed to
+#' `rmarkdown::run` `shiny_args` argument.
+#' @param render_args `list`, optional list of arguments conveyed to
+#' `rmarkdown::run` `render_args` argument.
#' @return Nada.
#' @author Todor Kondić
-app <- function(shiny_args=list(launch.browser=F),render_args=NULL,top_data_dir=getwd(),projects=getwd(),metfrag_db_dir="") {
- dir_before <- getwd()
- init <- list()
- init$dir_before <- dir_before
- init$top_data_dir <- norm_path(top_data_dir)
- init$metfrag_db_dir <- metfrag_db_dir
- init$projects <- norm_path(projects)
- if (!dir.exists(init$top_data_dir)) stop("Data directory (top_data_dir), currently `",
- init$top_data_dir,
- "` does not exist. Abort.")
- if (!dir.exists(init$projects)) stop("User root directory (projects), currently `",
- init$projects,"` does not exist.. Abort.")
+app <- function(projects=getwd(),
+ top_data_dir=getwd(),
+ metfrag_db_dir="",
+ metfrag_runtime="",
+ 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)
+ dir_start = prepare_app(dir_before=dir_before,
+ projects=projects,
+ top_data_dir=top_data_dir,
+ metfrag_db_dir=metfrag_db_dir,
+ metfrag_runtime=metfrag_runtime)
+
on.exit(expr=setwd(dir_before))
-
- dir_start <- tempfile("shinyscreen")
- dir.create(dir_start, recursive = T)
setwd(dir_start)
- dir.create('www', showWarnings=F)
- saveRDS(object = init,file="init.rds")
- file.copy(system.file(file.path("rmd","app.Rmd"),package = "shinyscreen"),"app_run.Rmd")
- file.copy(system.file(file.path("www","custom.css"),package = "shinyscreen"),file.path("www","custom.css"))
rmarkdown::run(file = "app_run.Rmd", shiny_args = shiny_args, render_args = render_args)
}
diff --git a/R/resources.R b/R/resources.R
index 98b115a..041499a 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -323,4 +323,11 @@ METFRAG_PREPFLT_CHOICES = c("UnconnectedCompoundFilter","IsotopeFilter")
METFRAG_PREPFLT_DEFAULT = c("UnconnectedCompoundFilter","IsotopeFilter")
METFRAG_POSTPFLT_CHOICES = c("InChIKeyFilter")
METFRAG_POSTPFLT_DEFAULT = c("InChIKeyFilter")
-
+METFRAG_STANDARD_SCORES = "FragmenterScore,OfflineIndividualMoNAScore" # AutomatedPeakFingerprintAnnotationScore,
+ # AutomatedLossFingerprintAnnotationScore
+ # supposedly
+ # do
+ # not
+ # work
+ # well.
+METFRAG_STANDARD_WEIGHTS = "1,1"
diff --git a/man/app.Rd b/man/app.Rd
index cf673be..d4ba1d3 100644
--- a/man/app.Rd
+++ b/man/app.Rd
@@ -5,23 +5,32 @@
\title{app}
\usage{
app(
+ projects = getwd(),
+ top_data_dir = getwd(),
+ metfrag_db_dir = "",
+ metfrag_runtime = "",
shiny_args = list(launch.browser = F),
- render_args = NULL,
- indir = getwd(),
- userdir = getwd()
+ 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{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.}
+
\item{shiny_args}{\code{list}, optional list of arguments conveyed to
\code{rmarkdown::run} \code{shiny_args} argument.}
\item{render_args}{\code{list}, optional list of arguments conveyed to
\code{rmarkdown::run} \code{render_args} argument.}
-
-\item{indir}{\code{character(1)}, a location on the server side
-containing data directories.}
-
-\item{userdir}{\code{character(1)}, a location on the server side containing project directories.}
}
\value{
Nada.
diff --git a/man/serve.Rd b/man/serve.Rd
index e653a05..531f87e 100644
--- a/man/serve.Rd
+++ b/man/serve.Rd
@@ -4,16 +4,16 @@
\alias{serve}
\title{serve}
\usage{
-serve(indir, topuserdir, user, host = "0.0.0.0", port = 7777)
+serve(top_data_dir, usersdir, user, host = "0.0.0.0", port = 7777)
}
\arguments{
-\item{indir}{\code{character(1)}, a location on the server side
+\item{top_data_dir}{\code{character(1)}, a location on the server side
containing data directories.}
-\item{topuserdir}{\code{character(1)}, a location on the server side
+\item{usersdir}{\code{character(1)}, a location on the server side
containing individual user directories.}
-\item{user}{\code{character(1)}, subdir of topuserdir.}
+\item{user}{\code{character(1)}, subdir of usersdir.}
\item{host}{\code{character(1)}, optional, address where the page is
served.}
diff --git a/tests/testthat/test-api.R b/tests/testthat/test-api.R
new file mode 100644
index 0000000..6c7ca2e
--- /dev/null
+++ b/tests/testthat/test-api.R
@@ -0,0 +1,40 @@
+test_that("Preparation for app start",{
+ dbef = "bef"
+ dir.create("bef")
+ ddata = "topdata"
+ dir.create(ddata)
+ dproj = "proj"
+ dir.create(dproj)
+ ddbdir = "dbdir"
+ dir.create(ddbdir)
+ mrt = "mrt.fake.jar"
+ saveRDS("",file=mrt)
+ expect_error(prepare_app(dir_before=dbef,
+ projects=dproj,
+ top_data_dir=ddata,
+ metfrag_db_dir=ddbdir,
+ metfrag_runtime="absent.jar"),
+ class="mf-jar-absent")
+
+ expect_error(prepare_app(dir_before=dbef,
+ projects="absent",
+ top_data_dir=ddata,
+ metfrag_db_dir=ddbdir,
+ metfrag_runtime=mrt),
+ class="projects-absent")
+ expect_error(prepare_app(dir_before=dbef,
+ projects=dproj,
+ top_data_dir="absent",
+ metfrag_db_dir=ddbdir,
+ metfrag_runtime=mrt),
+ class="top-data-dir-absent")
+ expect_error(prepare_app(dir_before=dbef,
+ projects=dproj,
+ top_data_dir=ddata,
+ metfrag_db_dir="absent",
+ metfrag_runtime=mrt),
+ class="mf-db-dir-absent")
+
+
+
+})
--
GitLab