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‎man/.internal_call.1‎

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.TH .INTERNAL_CALL 1 2025-Mar "" "Invoke an analysis application"
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.TH .INTERNAL_CALL 1 2025-Mar "internal" "@title Invoke an Analysis Application (Internal Function)"
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.SH NAME
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.internal_call \- .internal_call(app, context)
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.SH SYNOPSIS
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\fI.internal_call(app, context)\fR
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.SH DESCRIPTION
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.PP
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This internal function executes an analysis application after validating its dependencies. It handles application execution, error reporting, and performance profiling.
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.PP
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.SH OPTIONS
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.PP
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\fBapp\fB \fR\- .
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\fBapp\fB \fR\- . A list defining the analysis application. Must contain: - `name`: (character) Name of the application (for logging). - `call`: (function) The function to execute the application logic. - `profiler`: (list) Stores performance metrics (e.g., execution time).
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.PP
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.PP
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\fBcontext\fB \fR\- . A list or environment providing runtime context, such as input data paths, environment variables, or configuration settings required by the application.
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.PP
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.SH VALUE
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.PP
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Invisibly returns `NULL`. The function primarily updates `app$profiler` with execution time metrics and may modify the `context` during execution.
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.PP
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.SH DETAILS
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.PP
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\fBcontext\fB \fR\- .
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### Key Steps: 1. ​**Dependency Check**: Validates if required context variables and files exist via `check_dependency(app, context)`. - If dependencies are met, proceeds to execute the application. - If dependencies are missing, throws an error with detailed missing resources. 2. ​**Execution**: - Logs start/end timestamps if `options(verbose = TRUE)`. - Executes `app$call` with arguments `app` and `context` using `do.call()`. 3. ​**Error Handling**: - Aggregates missing dependencies into readable error messages. - Calls `throw_err()` to terminate the workflow and report issues. 4. ​**Profiling**: Records total execution time in `app$profiler$time` using `time_span()` for human-readable formatting.
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.SH FILES
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.PP
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SMRUCC/R#.declare_function..internal_call at runner.R:line 3
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SMRUCC/R#.declare_function..internal_call at runner.R:line 57
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.PP
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.SH COPYRIGHT
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Copyright © xieguigang, MIT Licensed 2025

‎man/__runImpl.1‎

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.TH __RUNIMPL 1 2025-Mar "" "An internal function for start the workflow"
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.TH __RUNIMPL 1 2025-Mar "internal" "Internal Workflow Execution Engine"
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.SH NAME
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__runImpl \- __runImpl(context,
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<i>disables</i> = 'list'())
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.SH SYNOPSIS
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\fI__runImpl(context,
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<i>disables</i> = 'list'())\fR
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.SH DESCRIPTION
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.PP
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An internal function that drives the execution of a modular workflow. It sequentially processes analysis modules according to the pipeline configuration while respecting disablement rules.
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.PP
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.SH OPTIONS
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.PP
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\fBcontext\fB \fR\- .
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\fBcontext\fB \fR\- . A workflow context object containing: \itemize{ \item{pipeline - character vector of module execution order} \item{workflow - list of module definitions} }
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.PP
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.PP
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\fBdisables\fB \fR\- 'list'(). A named list specifying module disablement status. Format: `list(module_name = TRUE/FALSE)`. Modules with TRUE will be skipped.
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.PP
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.SH VALUE
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.PP
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Invisibly returns NULL. Modifies the workflow context object in-place through module executions.
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.PP
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.SH DETAILS
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.PP
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\fBdisables\fB \fR\- 'list'().
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This function: \enumerate{ \item Retrieves module execution order from `context$pipeline` \item Checks disablement status through two mechanisms: \itemize{ \item Explicit disablement via `disables` parameter \item Module's own `disable` property (set by upstream modules) } \item Executes non-disabled modules using `.internal_call()` \item Provides verbose logging when `options(verbose=TRUE)` } The workflow context is modified in-place by module execution.
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.SH FILES
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.PP
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SMRUCC/R#.declare_function.__runImpl at workflowRender.R:line 37
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SMRUCC/R#.declare_function.__runImpl at workflowRender.R:line 76
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.PP
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.SH COPYRIGHT
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Copyright © xieguigang, MIT Licensed 2025

‎man/index.json‎

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‎vignettes/R/docs/.internal_call.html‎

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<html>
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<title>Invoke an analysis application</title>
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<title>@title Invoke an Analysis Application (Internal Function)</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
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</table>
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<h2>Invoke an analysis application</h2>
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<h2>@title Invoke an Analysis Application (Internal Function)</h2>
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<h3>Description</h3>
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<p>This internal function executes an analysis application after validating its dependencies. It handles application execution, error reporting, and performance profiling.</p>
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<h3>Usage</h3>
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<h3>Arguments</h3>
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<dt>app</dt>
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<dd><p><p>A list defining the analysis application. Must contain: - `name`: (character) Name of the application (for logging). - `call`: (function) The function to execute the application logic. - `profiler`: (list) Stores performance metrics (e.g., execution time).</p></p></dd>
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<dt>context</dt>
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<dd><p><p>A list or environment providing runtime context, such as input data paths, environment variables, or configuration settings required by the application.</p></p></dd>
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</table>
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<h3 style="display: none;">Details</h3>
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<h3 style="display: block;">Details</h3>
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<h3>Key Steps: 1. ​<strong>Dependency Check<em></em>: Validates if required context variables and files exist via `check<em>dependency(app, context)`. - If dependencies are met, proceeds to execute the application. - If dependencies are missing, throws an error with detailed missing resources. 2. ​**Execution**: - Logs start/end timestamps if `options(verbose = TRUE)`. - Executes `app$call` with arguments `app` and `context` using `do.call()`. 3. ​**Error Handling**: - Aggregates missing dependencies into readable error messages. - Calls `throw</em>err()` to terminate the workflow and report issues. 4. ​<em></em>Profiling</strong>: Records total execution time in `app$profiler$time` using `time_span()` for human-readable formatting.</h3>
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<h3 style="display: block">Authors</h3>
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xieguigang
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<h3>Value</h3>
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This function has no value returns.
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<p>Invisibly returns `NULL`. The function primarily updates `app$profiler` with execution time metrics and may modify the `context` during execution.</p>
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<h3 style="display: none;">Examples</h3>
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‎vignettes/R/docs/__runImpl.html‎

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<html>
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<head>
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<title>An internal function for start the workflow</title>
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<title>Internal Workflow Execution Engine</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
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<link rel="stylesheet" type="text/css" href="https://rdocumentation.rsharp.net/assets/page.css">
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</table>
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<h2>An internal function for start the workflow</h2>
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<h2>Internal Workflow Execution Engine</h2>
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<h3>Description</h3>
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<p>An internal function that drives the execution of a modular workflow. It sequentially processes analysis modules according to the pipeline configuration while respecting disablement rules.</p>
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<h3>Usage</h3>
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<h3>Arguments</h3>
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<dt>context</dt>
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<dd><p><p>A workflow context object containing: \itemize{ \item{pipeline - character vector of module execution order} \item{workflow - list of module definitions} }</p></p></dd>
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<dt>disables</dt>
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<dd><p><p>A named list specifying module disablement status. Format: `list(module_name = TRUE/FALSE)`. Modules with TRUE will be skipped.</p></p></dd>
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<h3 style="display: none;">Details</h3>
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<h3 style="display: block;">Details</h3>
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<p>This function: \enumerate{ \item Retrieves module execution order from `context$pipeline` \item Checks disablement status through two mechanisms: \itemize{ \item Explicit disablement via `disables` parameter \item Module's own `disable` property (set by upstream modules) } \item Executes non-disabled modules using `.internal_call()` \item Provides verbose logging when `options(verbose=TRUE)` } The workflow context is modified in-place by module execution.</p>
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<h3>Value</h3>
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This function has no value returns.
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<p>Invisibly returns NULL. Modifies the workflow context object in-place through module executions.</p>
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<h3 style="display: none;">Examples</h3>
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