feat: unified watch server under org-garden

org-garden/lib/org_garden/transforms/citations.ex

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+defmodule OrgGarden.Transforms.Citations do
+  @moduledoc """
+  Markdown transform: resolves org-citar citation keys to hyperlinks.
+
+  ## Recognised citation syntax (as output by ox-hugo from org-citar)
+
+      [cite:@key]           → org-cite / citar standard (most common)
+      [cite:@key1;@key2]    → multiple citations
+      cite:key              → older roam-style bare cite syntax
+
+  ## Resolution chain (in order)
+
+    1. Zotero (live instance via Better BibTeX JSON-RPC)   — preferred
+    2. BibTeX file (BIBTEX_FILE env var)                   — fallback
+    3. DOI / bare key                                       — always succeeds
+
+  ## Modes (opts.citation_mode)
+
+    :silent  — silently use DOI/bare-key fallback when Zotero+BibTeX fail
+    :warn    — (default) emit a Logger.warning for unresolved keys
+    :strict  — raise on unresolved keys (aborts pipeline)
+
+  ## Format
+
+  Resolved citations are rendered as:
+
+      [Label](url)       when a URL is available
+      [Label]            when no URL could be determined (bare key fallback)
+
+  Multiple semicolon-separated keys become space-separated links:
+
+      [cite:@a;@b]  →  [Author A, 2020](url_a) [Author B, 2019](url_b)
+
+  ## init/1 callback
+
+  Loads the BibTeX file (if configured) once before processing begins,
+  and probes Zotero availability, emitting warnings as appropriate.
+  """
+
+  @behaviour OrgGarden.Transform
+
+  require Logger
+
+  alias OrgGarden.Resolvers.Zotero
+  alias OrgGarden.Resolvers.BibTeX
+  alias OrgGarden.Resolvers.DOI
+
+  # Match [cite:@key] and [cite:@key1;@key2;...] (org-cite / citar style)
+  @cite_bracket_regex ~r/\[cite:(@[^\]]+)\]/
+
+  # Match bare cite:key or cite:@key (older roam style, no brackets, optional @ prefix)
+  @cite_bare_regex ~r/(?<![(\[])cite:@?([a-zA-Z0-9_:-]+)/
+
+  # ------------------------------------------------------------------
+  # OrgGarden callbacks
+  # ------------------------------------------------------------------
+
+  @doc """
+  Called once before processing any files. Loads BibTeX, probes Zotero.
+  Returns a state map passed to every `apply/3` call.
+  """
+  def init(opts) do
+    bibtex_entries = load_bibtex(opts)
+    zotero_available = probe_zotero(opts)
+
+    if not zotero_available and bibtex_entries == %{} do
+      Logger.warning(
+        "Citations: neither Zotero nor a BibTeX file is available. " <>
+          "All citations will fall back to bare-key rendering. " <>
+          "Set BIBTEX_FILE env var or start Zotero with Better BibTeX to resolve citations."
+      )
+    end
+
+    %{
+      bibtex_entries: bibtex_entries,
+      zotero_available: zotero_available,
+      zotero_url: Map.get(opts, :zotero_url, "http://localhost:23119"),
+      citation_mode: Map.get(opts, :citation_mode, :warn)
+    }
+  end
+
+  @doc """
+  Apply citation resolution to a single markdown file's content.
+  """
+  def apply(content, state, _opts) do
+    content
+    |> resolve_bracket_citations(state)
+    |> resolve_bare_citations(state)
+  end
+
+  # ------------------------------------------------------------------
+  # Resolution passes
+  # ------------------------------------------------------------------
+
+  defp resolve_bracket_citations(content, state) do
+    Regex.replace(@cite_bracket_regex, content, fn _full, keys_str ->
+      keys_str
+      |> String.split(";")
+      |> Enum.map(&String.trim/1)
+      |> Enum.map(fn "@" <> key -> key end)
+      |> Enum.map(&resolve_key(&1, state))
+      |> Enum.join(" ")
+    end)
+  end
+
+  defp resolve_bare_citations(content, state) do
+    Regex.replace(@cite_bare_regex, content, fn _full, key ->
+      resolve_key(key, state)
+    end)
+  end
+
+  # ------------------------------------------------------------------
+  # Single-key resolution chain
+  # ------------------------------------------------------------------
+
+  defp resolve_key(key, state) do
+    info =
+      with :error <- try_zotero(key, state),
+           :error <- try_bibtex(key, state) do
+        handle_unresolved(key, state)
+      else
+        {:ok, citation_info} -> citation_info
+      end
+
+    format_result(info)
+  end
+
+  defp try_zotero(_key, %{zotero_available: false}), do: :error
+
+  defp try_zotero(key, %{zotero_url: url}) do
+    Zotero.resolve(key, url)
+  end
+
+  defp try_bibtex(_key, %{bibtex_entries: entries}) when map_size(entries) == 0, do: :error
+
+  defp try_bibtex(key, %{bibtex_entries: entries}) do
+    BibTeX.resolve(key, entries)
+  end
+
+  defp handle_unresolved(key, %{citation_mode: mode}) do
+    case mode do
+      :strict ->
+        raise "Citations: could not resolve citation key '#{key}' and mode is :strict"
+
+      :warn ->
+        Logger.warning("Citations: unresolved citation key '#{key}' — using bare-key fallback")
+        {:ok, result} = DOI.resolve(key)
+        result
+
+      :silent ->
+        {:ok, result} = DOI.resolve(key)
+        result
+    end
+  end
+
+  defp format_result(%{label: label, url: nil}), do: "[#{label}]"
+  defp format_result(%{label: label, url: url}), do: "[#{label}](#{url})"
+
+  # ------------------------------------------------------------------
+  # Init helpers
+  # ------------------------------------------------------------------
+
+  defp load_bibtex(opts) do
+    path = Map.get(opts, :bibtex_file) || System.get_env("BIBTEX_FILE")
+
+    cond do
+      is_nil(path) ->
+        Logger.debug("Citations: BIBTEX_FILE not set — BibTeX resolver disabled")
+        %{}
+
+      not File.exists?(path) ->
+        Logger.warning("Citations: BIBTEX_FILE=#{path} does not exist — BibTeX resolver disabled")
+        %{}
+
+      true ->
+        case BibTeX.load(path) do
+          {:ok, entries} -> entries
+          {:error, reason} ->
+            Logger.warning("Citations: failed to load BibTeX file #{path}: #{inspect(reason)}")
+            %{}
+        end
+    end
+  end
+
+  defp probe_zotero(opts) do
+    url = Map.get(opts, :zotero_url, "http://localhost:23119")
+
+    # Use a no-op JSON-RPC call to probe availability.
+    # /better-bibtex/cayw is intentionally avoided — it blocks waiting for
+    # user interaction and never returns without a pick.
+    payload =
+      Jason.encode!(%{
+        jsonrpc: "2.0",
+        method: "item.search",
+        params: [[[]]],
+        id: 0
+      })
+
+    result =
+      try do
+        Req.post(url <> "/better-bibtex/json-rpc",
+          body: payload,
+          headers: [{"content-type", "application/json"}],
+          receive_timeout: 3_000,
+          finch: OrgGarden.Finch
+        )
+      rescue
+        e -> {:error, e}
+      end
+
+    case result do
+      {:ok, %{status: 200}} ->
+        Logger.info("Citations: Zotero Better BibTeX is available at #{url}")
+        true
+
+      {:ok, %{status: status}} ->
+        Logger.warning(
+          "Citations: Zotero responded HTTP #{status} at #{url} — " <>
+            "is Better BibTeX installed?"
+        )
+        false
+
+      _ ->
+        Logger.warning(
+          "Citations: Zotero not reachable at #{url} — " <>
+            "start Zotero with Better BibTeX or set BIBTEX_FILE as fallback"
+        )
+        false
+    end
+  end
+end