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xieguigangxieguigang
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split source file into multiple parrs
1 parent 20431f7 commit 72a6a61

8 files changed

Lines changed: 180 additions & 181 deletions

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‎R/application/reflection.R‎

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Original file line numberDiff line numberDiff line change
@@ -45,47 +45,3 @@ const __build_app = function(f) {
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}
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}
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#' parse the workfile expression
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#'
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const __workfiles = function(files_uri) {
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if (length(files_uri) == 0) {
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NULL;
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} else {
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__workfiles_data(files_uri);
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}
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}
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const __workfiles_data = function(files_uri) {
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let uri = lapply(files_uri, si -> __workfile_uri_parser(si));
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let app = as.character(uri@app);
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let file = as.character(uri@file);
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let app_groups = data.frame(app, file)
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|> as.list(byrow = TRUE)
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|> groupBy("app")
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|> lapply(app -> app@file)
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;
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app_groups;
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}
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#' parse the workfile expression
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#'
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#' @param uri a character vector that contains the workfile
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#' reference expression.
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#'
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#' @return a tuple list object that contains the necessary
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#' parameter value for call ``workfile`` function for gets
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#' the reference file path to the required data files.
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#'
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const __workfile_uri_parser = function(uri) {
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# example as:
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# app_name://file/path/to/file.txt
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let tuple = tagvalue(uri, '://', as.list = TRUE);
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let ref = list(
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app = names(tuple),
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file = unlist(tuple)
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);
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# app, file
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return(ref);
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}

‎R/application/uri_parser.R‎

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#' parse the workfile expression
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#'
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const __workfiles = function(files_uri) {
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if (length(files_uri) == 0) {
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NULL;
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} else {
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__workfiles_data(files_uri);
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}
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}
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const __workfiles_data = function(files_uri) {
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let uri = lapply(files_uri, si -> __workfile_uri_parser(si));
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let app = as.character(uri@app);
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let file = as.character(uri@file);
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let app_groups = data.frame(app, file)
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|> as.list(byrow = TRUE)
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|> groupBy("app")
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|> lapply(app -> app@file)
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;
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app_groups;
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}
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#' parse the workfile expression
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#'
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#' @param uri a character vector that contains the workfile
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#' reference expression.
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#'
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#' @return a tuple list object that contains the necessary
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#' parameter value for call ``workfile`` function for gets
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#' the reference file path to the required data files.
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#'
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const __workfile_uri_parser = function(uri) {
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# example as:
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# app_name://file/path/to/file.txt
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let tuple = tagvalue(uri, '://', as.list = TRUE);
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let ref = list(
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app = names(tuple),
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file = unlist(tuple)
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);
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# app, file
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return(ref);
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}

‎R/context/context.R‎

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Original file line numberDiff line numberDiff line change
@@ -44,43 +44,3 @@ const init_context = function(outputdir = "./", ssid = NULL) {
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invisible(NULL);
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}
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#' create an in-memory context object just used for run debug
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#'
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#' @param ssid the session id for multiple user environment, default NULL means global user environment
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#' @param mounts should be a callable function for mounts the
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#' application modules into the workflow registry.
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#'
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const create_memory_context = function(mounts = NULL,ssid = NULL) {
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set(globalenv(), paste( [__global_ctx,ssid], sep ="-"), list(
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root = NULL, # set all workspace to empty
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analysis = NULL,
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temp_dir = NULL,
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t0 = now(),
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workflow = list(),
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pipeline = [],
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symbols = list()
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));
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if (!is.null(mounts)) {
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mounts();
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}
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}
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const __global_ctx = "&[workflow_render]";
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#' get current workflow environment context
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#'
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#' @param ssid the session id for multiple user environment, default NULL means global user environment
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#'
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#' @return the context object which is generated via the
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#' ``init_context`` function.
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#'
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const .get_context = function(ssid = NULL) {
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const workflow_render as string = paste([__global_ctx, ssid], sep = "-");
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if (exists(workflow_render, globalenv())) {
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get(workflow_render, globalenv());
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} else {
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.Internal::stop("You must initialize the analysis context at first!");
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}
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}

‎R/context/memory_access.R‎

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#' create an in-memory context object just used for run debug
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#'
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#' @param ssid the session id for multiple user environment, default NULL means global user environment
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#' @param mounts should be a callable function for mounts the
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#' application modules into the workflow registry.
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#'
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const create_memory_context = function(mounts = NULL,ssid = NULL) {
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set(globalenv(), paste( [__global_ctx,ssid], sep ="-"), list(
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root = NULL, # set all workspace to empty
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analysis = NULL,
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temp_dir = NULL,
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t0 = now(),
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workflow = list(),
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pipeline = [],
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symbols = list()
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));
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if (!is.null(mounts)) {
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mounts();
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}
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}
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const __global_ctx = "&[workflow_render]";
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#' get current workflow environment context
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#'
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#' @param ssid the session id for multiple user environment, default NULL means global user environment
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#'
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#' @return the context object which is generated via the
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#' ``init_context`` function.
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#'
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const .get_context = function(ssid = NULL) {
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const workflow_render as string = paste([__global_ctx, ssid], sep = "-");
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if (exists(workflow_render, globalenv())) {
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get(workflow_render, globalenv());
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} else {
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.Internal::stop("You must initialize the analysis context at first!");
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}
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}

‎R/context/workspace.R‎

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This file was deleted.

‎R/context/workspace/workdir.R‎

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#' Get workspace root directory
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#'
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#' @param ssid the session id for multiple user environment, default NULL means global user environment
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#' @details actually this function will returns the ``output`` dir
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#' path which is set via the ``init_context`` function
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#'
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const workdir_root = function(ssid = NULL) {
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.get_context(ssid)$root;
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}
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#' get directory folder path for the analysis output result
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#'
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#' @param ssid the session id for multiple user environment, default NULL means global user environment
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#' @details a character vector of the analysis result output directory.
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#'
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const result_dir = function(ssid = NULL) {
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.get_context(ssid)$analysis;
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}
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const workspace_temproot = function(ssid = NULL) {
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const context = .get_context(ssid);
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const temp_root = context$temp_dir;
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temp_root;
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}

‎R/context/workspace/workfile.R‎

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#' Construct of the file path inside an app workspace
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#'
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#' @param app this app parameter value could be in 3 kinds
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#' of data type:
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#'
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#' 1. app tuple list object, which is created via the ``app`` function.
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#' 2. the app name character vector
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#' 3. the workfile path expression, should be in format like: ``app://relpath/to/file.ext``
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#' @param ssid the session id for multiple user environment, default NULL means global user environment
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#'
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#' @return the data file path of the required reference file inside this workflow
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#'
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#' @details the workfile path expression is in format string of: ``app://filepath``,
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#' example as ``getMzSet://mzset.txt``, where we could parse the reference information
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#' from this character string: app name is ``getMzSet``, and the relpath data is
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#' ``mzset.txt``. so, such configuation could be equals to the function invoke
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#' of the workfile function: ``workfile("getMzSet", "/mzset.txt");``.
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#'
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const workfile = function(app, relpath = NULL, ssid = NULL, verbose = FALSE) {
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if (is.empty(relpath)) {
21+
if (is.character(app)) {
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relpath <- __workfile_uri_parser(app);
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# gets the internal workfile reference
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# its physical file path
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file.path(WorkflowRender::workspace(relpath$app, ssid, verbose = verbose), relpath$file);
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} else {
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throw_err("the given expression value should be an internal workfile path reference!");
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}
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} else {
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file.path(WorkflowRender::workspace(app, ssid, verbose = verbose), relpath);
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}
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}

‎R/context/workspace/workspace.R‎

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#' get app workspace location
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#'
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#' @param app the app list object or just the app name its
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#' character text value.
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#' @param ssid the session id for multiple user environment, default NULL means global user environment
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#'
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#' @return a character vector of the workspace directory path
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#' of the specific analysis application.
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#'
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#' @details the verbose option could be config from the
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#' commandline option: ``--verbose``
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#'
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const workspace = function(app, ssid = NULL, verbose = FALSE) {
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const verboseOpt = as.logical(getOption("verbose", default = verbose));
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const context = .get_context(ssid);
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const temp_root = context$temp_dir;
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const app_name = get_app_name(app);
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const workdir = normalizePath(`${temp_root}/workflow_tmp/${app_name}/`);
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const program = context$pipeline;
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if (verboseOpt) {
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print("view of the given app object for get its workspace dir:");
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print("get app_name:");
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str(app_name);
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print("get pipeline workflow components:");
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str(program);
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print("combine the workdir path:");
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print(workdir);
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};
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32+
if (!(app_name in program)) {
33+
echo_warning(`The app(${app_name}) has not been registered in the analysis context yet.`, app);
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};
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workdir;
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}
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