fix: address PR #156 review feedback (round 2)

- Add empty notebook guards to search notebook Conclusions and Research
  Questions presets (prevents modal flash on empty notebooks)
- Redact api_key from verbose OpenAlex log output
- Fix wizard dismissal race by requiring has_seen_wizard input before check
- Fix misplaced roxygen docs on generate_preset() and document custom_prompt
- Remove "Editable prompts" from README (feature not yet implemented)

Author: seanthimons

R/api_openalex.R

@@ -8,7 +8,7 @@ OPENALEX_BASE_URL <- "https://api.openalex.org"
 #' @return httr2 response
 perform_openalex <- function(req) {
   if (isTRUE(getOption("serapeum.verbose_api", FALSE))) {
-    url <- req$url
+    url <- gsub("api_key=[^&]+", "api_key=<REDACTED>", req$url)
     message("[OpenAlex API] ", url)
   }
   req_perform(req)

R/mod_search_notebook.R

@@ -3351,6 +3351,15 @@ mod_search_notebook_server <- function(id, con, notebook_id, config, notebook_re
       }
       req(!is_processing())
       req(has_api_key())
+
+      # Empty notebook guard
+      paper_count <- tryCatch(nrow(list_abstracts(con(), notebook_id())), error = function(e) 0L)
+      if (paper_count == 0L) {
+        showNotification("This notebook has no papers yet. Run a search first, then try again.",
+                         type = "warning", duration = 5)
+        return()
+      }
+
       is_processing(TRUE)
       show_synthesis_modal("Conclusion Synthesis")
 
@@ -3389,6 +3398,15 @@ mod_search_notebook_server <- function(id, con, notebook_id, config, notebook_re
       }
       req(!is_processing())
       req(has_api_key())
+
+      # Empty notebook guard
+      paper_count <- tryCatch(nrow(list_abstracts(con(), notebook_id())), error = function(e) 0L)
+      if (paper_count == 0L) {
+        showNotification("This notebook has no papers yet. Run a search first, then try again.",
+                         type = "warning", duration = 5)
+        return()
+      }
+
       is_processing(TRUE)
       show_synthesis_modal("Research Questions")
 

R/rag.R

@@ -135,13 +135,6 @@ rag_query <- function(con, config, question, notebook_id, session_id = NULL) {
   response
 }
 
-#' Generate preset content (summary, key points, etc.)
-#' @param con Database connection
-#' @param config App config
-#' @param notebook_id Notebook ID
-#' @param preset_type Type of preset ("summarize", "keypoints", "studyguide", "outline")
-#' @param session_id Optional Shiny session ID for cost logging (default NULL)
-#' @return Generated content
 #' Get the task instruction for a preset type
 #' @param preset_type Preset type string
 #' @return Task instruction string, or NULL if unknown
@@ -160,6 +153,15 @@ get_preset_instruction <- function(preset_type) {
   presets[[preset_type]]
 }
 
+#' Generate preset content (summary, key points, etc.)
+#' @param con Database connection
+#' @param config App config
+#' @param notebook_id Notebook ID
+#' @param preset_type Type of preset ("summarize", "keypoints", "studyguide", "outline",
+#'   "overview", "conclusions", "lit_review", "methodology_extractor", "gap_analysis")
+#' @param session_id Optional Shiny session ID for cost logging (default NULL)
+#' @param custom_prompt Optional custom prompt to override the default preset instruction
+#' @return Generated content
 generate_preset <- function(con, config, notebook_id, preset_type, session_id = NULL,
                             custom_prompt = NULL) {
   prompt <- custom_prompt %||% get_preset_instruction(preset_type)

README.md

@@ -17,7 +17,6 @@ Upload PDFs and chat with your documents using RAG (Retrieval-Augmented Generati
 - **Markdown rendering** - Assistant responses display with formatted headers, tables, lists, and code blocks
 - **One-click presets** - Summarize, Key Points, Study Guide, Outline, and more
 - **Synthesis progress feedback** - Status modal with rotating stage indicators for long-running presets
-- **Editable prompts** - Expand the prompt editor to view and customize LLM prompts before sending
 - **Chat export** - Download conversations as Markdown (.md) or styled HTML (.html)
 - **Full-text search** - Vector embeddings for semantic search across documents
 - **Slide generation** - Generate Quarto RevealJS presentations from your research

app.R

@@ -668,6 +668,7 @@ server <- function(input, output, session) {
   observe({
     con <- con_r()
     req(con)
+    req(!is.null(input$has_seen_wizard))
     notebooks <- list_notebooks(con)
     has_seen <- isTRUE(input$has_seen_wizard)
     if (nrow(notebooks) == 0 && !has_seen) {