fix: standalone bugfix batch (6 issues)

[seanthimons]

Summary

• Network graph year filters lower-bounds are wrong #128 (notebook descriptions): Closed as already resolved — tooltips exist on all sidebar buttons
• feat: v16.0 Content & Output Quality milestone #221 (keyword filter return type): Closed as already resolved — caller destructures correctly
• Re-extraction: all-saves-fail after delete leaves no figures #223 (sparkline crash on all-NA): Fixed max(-Inf) guard with is.finite() check
• Add error path tests for vision describe and API response handling #220 (NA guard on api_key): Added is.na() check before nchar() call
• Figure manifest: NA rendered as literal string in LLM prompt #224 (magic number): Extracted cost_usd = 0.01 to named constant OA_CONTENT_DOWNLOAD_COST_USD in config.R
• Heal flow sends base64-inlined QMD to LLM on second attempt #222 (nchar multi-element vector): Wrapped nchar(content) == 0 in all() to prevent if() error on vector input

Test plan

• 5 new tests for build_latency_sparkline edge cases (all-NA, all-zero, mixed, normal, single-row)
• 8 new tests for extract_message_content (normal, NULL+reasoning, NULL-no-reasoning, empty string, multi-element vector, list-of-parts, mixed parts)
• Full test suite passes (0 failures in new/modified tests)
• App startup smoke test passes

[Copilot]

Pull request overview

This PR bundles several small bugfixes across the OpenRouter integration, cost/latency UI, and OpenAlex usage logging, with accompanying test coverage to prevent regressions.

Changes:

• Hardened OpenRouter message parsing and API-key validation edge cases.
• Fixed latency sparkline handling for all-NA / non-finite max latency scenarios, and added tests.
• Replaced a hardcoded OpenAlex content-download cost with a named config constant.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/testthat/test-extract-message-content.R	Adds unit tests covering extract_message_content() shapes and edge cases.
tests/testthat/test-cost-tracking.R	Adds sparkline edge-case tests and imports shiny for tag class assertions.
R/mod_query_builder.R	Adds NA/empty guarding for provider$api_key before calling OpenRouter.
R/mod_cost_tracker.R	Prevents sparkline crash when max() is non-finite or non-positive.
R/import_paper.R	Uses OA_CONTENT_DOWNLOAD_COST_USD constant for OpenAlex usage logging.
R/config.R	Introduces OA_CONTENT_DOWNLOAD_COST_USD constant.
R/api_openrouter.R	Fixes if() crash on multi-element content by wrapping emptiness check in all().

Comments suppressed due to low confidence (2)

R/mod_cost_tracker.R:329

• bar_heights can be NA when trend$avg_latency_ms contains NA, which then makes max(as.integer(bar_heights[i]), 2) return NA (since max() propagates NA by default). This produces invalid CSS like height: NApx for those bars. Consider treating non-finite/NA heights as 0 before applying the minimum height (e.g., use if (!is.finite(h)) h <- 0 or max(..., na.rm = TRUE)).

  bar_heights <- (trend$avg_latency_ms / max_ms) * 40

  tags$div(
    class = "d-flex align-items-end gap-1",
    style = "height: 48px;",
    lapply(seq_len(nrow(trend)), function(i) {
      tags$div(
        style = sprintf(
          "width: 6px; height: %dpx; background: var(--bs-secondary); border-radius: 2px 2px 0 0; opacity: 0.7;",
          max(as.integer(bar_heights[i]), 2)
        ),

R/mod_query_builder.R:86

• The PR description references issue #220 for the API key NA guard, but the linked Issue #220 text is about vision describe error-path tests and an OpenRouter response bounds check in R/api_openrouter.R:60-67. If this PR is intended to close the linked Issue #220, those items don’t appear to be addressed here; consider updating the PR description/issue references to avoid confusion.

      if ((is.null(provider$api_key) || is.na(provider$api_key) || !nzchar(provider$api_key)) && !is_local_provider(provider)) {
        showNotification(
          "OpenRouter API key not configured. Please go to Settings.",
          type = "warning",
          duration = 5

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[Copilot]

OA_CONTENT_DOWNLOAD_COST_USD is defined in config.R, but import_single_paper() is sourced/used in at least one worker context that does not source config.R (e.g., batch_import_task in mod_search_notebook.R sources import_paper.R without config.R). In that path, evaluating cost_usd = OA_CONTENT_DOWNLOAD_COST_USD will fail and silently skip OA usage logging (caught by tryCatch). Consider either ensuring all entrypoints source config.R before import_paper.R, or adding a local fallback (e.g., defaulting to 0.01 when the constant is not defined) so usage logging works consistently.

[Copilot]

The all(nchar(content) == 0) condition can evaluate to NA if content contains NA values (since nchar(NA_character_) is NA), which would make the if (...) throw “missing value where TRUE/FALSE needed”. Consider making the emptiness check NA-safe (e.g., wrap with isTRUE(...) or treat NA as empty via all(is.na(content) | nchar(content) == 0)).

Suggested change

	if (is.null(content) || (is.character(content) && all(nchar(content) == 0))) {
	if (is.null(content) || (is.character(content) && all(is.na(content) | nchar(content) == 0))) {