Feature/21 edit table entries by arunge · Pull Request #26 · Pandora-IsoMemo/PEITHO

arunge · 2026-03-10T08:11:01Z

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Copilot

Pull request overview

This PR updates the workflow model (steps + inputs) to support editing workflow/inputs in the Shiny app, while refactoring step execution to use command + args (string) and a workflow-level input_list.

Changes:

Refactor workflowstep from operation/params to command/args and add required-field tracking for input/result tags.
Add Shiny table modules (workflow/inputs/results) including UI for editing step fields and input values.
Update workflow file-loading helpers and associated tests/docs; adjust WebText fetching to a structural extraction approach.

Reviewed changes

Copilot reviewed 49 out of 49 changed files in this pull request and generated 16 comments.

Show a summary per file

File	Description
tests/testthat/test-run-workflowstep.R	Updates step/run tests to new `command/args` model (some stale args remain).
tests/testthat/test-run-workflow.R	Updates workflow execution tests to use `input_list`.
tests/testthat/test-fetch_WebText.R	Removes selector-miss warning test; aligns with new fetch behavior.
tests/testthat/test-extract-workflow-from-files.R	Switches to `workflow_steps_from_files()` + explicit input loading.
man/workflow_table_ui.Rd	New docs for workflow table UI module.
man/workflow_table_server.Rd	New docs for workflow table server module.
man/workflow_steps_from_files.Rd	Renamed docs for extracting steps from files (missing `input_list` arg doc).
man/workflow_file_paths.Rd	Updates reference to new loader function.
man/update_input_list.workflow.Rd	New docs for updating workflow input list.
man/update_input_list.Rd	New generic docs for `update_input_list()`.
man/update.workflowstep.Rd	New docs for `update.workflowstep()` (field list is outdated).
man/update.workflow.Rd	New docs for `update.workflow()` (currently describes wrong types/return).
man/update.Rd	Updates generic `update()` documentation.
man/run.workflowstep.Rd	Updates run-step docs for `step_i`/`input_list`.
man/run.workflow.Rd	Updates run-workflow docs wording to “command”.
man/results_table_ui.Rd	New docs for results table UI module.
man/results_table_server.Rd	New docs for results table server module.
man/new_workflowsteprun.Rd	Updates wording from operation→command.
man/new_workflowstep.Rd	Updates constructor docs to `entry/command/args`.
man/new_workflow.Rd	Documents new `input_list` and argument order.
man/inputs_table_ui.Rd	New docs for inputs table UI module.
man/inputs_table_server.Rd	New docs for inputs table server module.
man/get_field.workflowstep.Rd	New docs for step field getter.
man/get_field.workflow.Rd	New docs for workflow field getter.
man/get_field.Rd	New generic docs for `get_field()`.
man/fetch_WebText.Rd	Removes `css_selector` param docs (description still mentions selector).
man/extract_inputs.workflowrun.Rd	Removes extract_inputs docs (feature removed).
man/extract_inputs.workflow.Rd	Removes extract_inputs docs (feature removed).
man/extract_inputs.Rd	Removes extract_inputs generic docs (generic removed).
man/as.data.frame.workflowstep.Rd	New docs for `as.data.frame.workflowstep`.
inst/scripts/example_wf.R	Updates example to use `my_run_1$input_list`.
inst/main.R	Switches to `devtools::load_all()` for launching app.
inst/app/ui.R	Switches from raw tables to module UIs; adds tab id for active-tab logic.
inst/app/server.R	Switches from renderTable to module servers; simplifies `new_workflow()` call.
R/02-workflow_table-module.R	Adds workflow table module + step editing UI/server.
R/02-results_table-module.R	Adds results table module.
R/02-inputs_table-module.R	Adds inputs table module + input editing UI/server.
R/02-WebText-factory.R	Removes `css_selector`; extracts text via main/article/body.
R/01-workflowsteprun-class.R	Updates printing/summary for `entry/command`.
R/01-workflowstep-class.R	Refactors step structure (`entry/command/args/required_*`), adds update/get/as.data.frame.
R/01-workflowstate-class.R	Updates state df + state update to use `entry`.
R/01-workflowrun-class.R	Removes `extract_inputs.workflowrun()`.
R/01-workflow-from-file.R	Adds input loading + required-field parsing; introduces `workflow_steps_from_files()`.
R/01-workflow-class.R	Adds workflow `input_list`, update helpers, and required input/step validation in `run.workflow()`.
R/01-operationparam-class.R	Minor message/comment tweak.
R/00-generics.R	Replaces `extract_inputs` with `get_field` + `update_input_list` generics.
R/00-Namespace.R	Adds `capture.output` import.
NEWS.md	Fixes headings to use `##`.
NAMESPACE	Adds new exports/S3 methods, but still references removed `extract_inputs`.

Comments suppressed due to low confidence (1)

man/workflow_steps_from_files.Rd:18

The workflow_steps_from_files() Rd lists input_list in the usage, but it is missing from the \arguments{} section. Please add an argument description for input_list (what it should contain and how it's used) so the public API docs are complete.

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Copilot · 2026-03-10T08:20:46Z

R/02-results_table-module.R

+results_table_server <- function(id, wf_run, is_active_tab) {
+  moduleServer(id, function(input, output, session) {
+    output$results_table <- renderTable({
+      wfr <- wf_run()
+      if (is.null(wfr)) return(NULL)
+      as.data.frame(wfr)


is_active_tab is accepted by results_table_server() but never used. If you intend to avoid recomputation when the tab is inactive, add a req(isTRUE(is_active_tab())) (or remove the argument to keep the API minimal).

inst/main.R

tests/testthat/test-run-workflowstep.R

Copilot · 2026-03-10T08:20:47Z

NAMESPACE

 S3method(extract_inputs,workflow)
 S3method(extract_inputs,workflowrun)


extract_inputs is still exported and registered as an S3 generic/method here, but the extract_inputs generic and its methods were removed from R/ in this PR. This will cause NAMESPACE/installation errors. Either reintroduce the generic + methods, or remove these S3method(extract_inputs, ...) entries and export(extract_inputs) from NAMESPACE.

Copilot · 2026-03-10T08:20:48Z

man/update.workflow.Rd

+\arguments{
+\item{x}{A `workflowstep` object to update.}
+
+\item{step}{The index of the step to update.}
+
+\item{entry}{The name of the entry to update (one of "name", "label", "comments", "command",
+"params", "loop")}
+
+\item{value}{The new value to assign to the specified entry.}
+
+\item{...}{Additional arguments (not used).}
+}
+\value{
+The updated `workflowstep` object.
+}


The documentation describes x as a workflowstep and says the return value is an updated workflowstep, but update.workflow() is a method for workflow and returns the updated workflow object. Please fix the roxygen docs so generated Rd matches the actual S3 method signature and behavior.

Copilot · 2026-03-10T08:20:48Z

R/01-workflow-from-file.R

+  # return empty wf if no inputs
+  if (length(input_list) == 0) {
+    warn_msg <- sprintf("Empty input list. Returning empty workflow.")
+    PEITHO:::logWarn("%s", warn_msg)
+    warning(warn_msg, immediate. = TRUE, call. = FALSE)
+    return(list())
+  }


workflow_steps_from_files() returns an empty step list whenever length(input_list) == 0. This prevents loading workflows that don't use any @#*I*#@...@#*I*#@ input tags (or have an intentionally empty inputs.json) even though steps with only literal args could still be valid. Consider only requiring input_list when steps actually reference inputs, or treating an empty input_list as valid and relying on the required_inputs check at run-time.

Copilot · 2026-03-10T08:20:49Z

R/02-WebText-factory.R

 #' Fetch and parse web text from a URL
 #'
 #' This function retrieves the HTML content from the specified URL,
 #' extracts text based on the provided CSS selector, and returns a
 #' `WebText` object containing the extracted text and metadata.


The roxygen description still mentions extracting text "based on the provided CSS selector", but css_selector is no longer a parameter and the implementation now uses
//. Please update the docstring to reflect the new extraction approach to avoid misleading users.

R/02-inputs_table-module.R

man/update.workflowstep.Rd

arunge added 14 commits February 18, 2026 15:13

extract modules for tables

0302e4a

UI to edit a workflow field

51e6268

update edit inputs

5de1bbb

logic to edit a workflow

4d4bdb0

validate field to update

e29795a

minor fixes

f0fd57c

rename operation into command, update file when updating commands list

252a1e6

check active tab, rename id into entry, keep input_list in wf object

00516d8

enable update of inputs

8380ded

focus on main text in fetch_WebText

144cef6

option to update input names

672abf2

fix update of inputs ui

3c9ff70

fix update of ui inputs

9d5fc2a

shift param creation into run method

657c15a

arunge self-assigned this Mar 10, 2026

arunge requested a review from Copilot March 10, 2026 08:13

Copilot started reviewing on behalf of arunge March 10, 2026 08:13 View session

Copilot AI reviewed Mar 10, 2026

View reviewed changes

arunge added 6 commits March 10, 2026 09:21

fix docu and namespace

4c867d8

suggest devtools

138295f

fix docu

b5b74a1

fix arg in test

a1f8c4c

remove duplication

6a34e6b

fix import

a7c61ee

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Feature/21 edit table entries#26

Feature/21 edit table entries#26
arunge wants to merge 20 commits intobetafrom
feature/21_edit_table_entries

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