From 4f987cb9841d1bd80d2c71c604103d78685b7acd Mon Sep 17 00:00:00 2001
From: Edmund Miller <20095261+edmundmiller@users.noreply.github.com>
Date: Thu, 7 Nov 2024 19:51:53 -0600
Subject: [PATCH] Add Nextflow Support (#4606)

* feat: Copy lsp-groovy to lsp-nextflow

* chore(nextflow): groovy => nextflow

* chore(nextflow): Run lsp-generate-settings

* fix(nextflow): Rework install logic

* fix(nextflow): Update Nextflow language server installation logic

* Add lsp-nextflow-test

* chore: Try to start over with actionscript as a template

* refactor: Use Nextflow lsp instead of vsix

* fix: Add Nextflow-mode to lsp-clients and lsp-mode

* fix: It's working?

* fix: Reorder client creation and settings

* feat: Add initialization function

* chore: Bump lsp-mode version

* fix: Enable multi-root

Idk what this does, but it makes it work

* chore: Add TODO

* chore: Update formatting

* chore: Update Changelog

* style: Fix docstring wider than 80 characters

* style(nextflow): Fix Summary line
---
 CHANGELOG.org           |   1 +
 clients/lsp-nextflow.el | 139 ++++++++++++++++++++++++++++++++++++++++
 docs/lsp-clients.json   |   8 +++
 lsp-mode.el             |   3 +-
 mkdocs.yml              |   1 +
 5 files changed, 151 insertions(+), 1 deletion(-)
 create mode 100644 clients/lsp-nextflow.el

diff --git a/CHANGELOG.org b/CHANGELOG.org
index 45cf126449..2682f60321 100644
--- a/CHANGELOG.org
+++ b/CHANGELOG.org
@@ -22,6 +22,7 @@
   * Fix zls wrong bin path
   * Add support for buf CLI ([[https://github.com/bufbuild/buf/releases/tag/v1.43.0][beta]])
   * Add fennel support
+  * Add support for [[https://github.com/nextflow-io/language-server][Nextflow]]
 
 ** 9.0.0
   * Add language server config for QML (Qt Modeling Language) using qmlls.
diff --git a/clients/lsp-nextflow.el b/clients/lsp-nextflow.el
new file mode 100644
index 0000000000..917af21543
--- /dev/null
+++ b/clients/lsp-nextflow.el
@@ -0,0 +1,139 @@
+;;; lsp-nextflow.el --- lsp-mode nextflow integration -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2024 Edmund Miller
+
+;; Author: Edmund Miller
+;; Keywords: lsp, nextflow, groovy
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+
+;; LSP Clients for the Nextflow Programming Language.
+
+;;; Code:
+
+(require 'lsp-mode)
+(require 'f)
+
+(defgroup lsp-nextflow nil
+  "LSP support for nextflow, using nextflow-language-server."
+  :group 'lsp-mode
+  :link '(url-link "https://github.com/nextflow-io/language-server"))
+
+(defcustom lsp-nextflow-java-path "java"
+  "Path of the java executable."
+  :group 'lsp-nextflow
+  :type 'string)
+
+(defcustom lsp-nextflow-version "1.0.0"
+  "Version of Nextflow language server."
+  :type 'string
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0"))
+
+(defcustom lsp-nextflow-server-download-url
+  (format "https://github.com/nextflow-io/language-server/releases/download/v%s/language-server-all.jar"
+          lsp-nextflow-version)
+  "Automatic download url for lsp-nextflow."
+  :type 'string
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0"))
+
+(defcustom lsp-nextflow-server-file
+  (f-join lsp-server-install-dir "nextflow-language-server.jar")
+  "The path to the file in which `lsp-nextflow' will be stored."
+  :group 'lsp-nextflow
+  :risky t
+  :type 'file
+  :package-version '(lsp-mode . "9.0.0"))
+
+(defun lsp-nextflow-server-command ()
+  "Startup command for Nextflow language server."
+  `("java" "-jar" ,(expand-file-name lsp-nextflow-server-file)))
+
+(lsp-dependency 'nextflow-lsp
+                '(:system lsp-nextflow-server-file)
+                `(:download :url lsp-nextflow-server-download-url
+                  :store-path lsp-nextflow-server-file))
+
+;;
+;;; Settings
+
+;; (lsp-generate-settings "~/src/nf-core/vscode-language-nextflow/package.json" 'lsp-nextflow)
+
+(lsp-defcustom lsp-nextflow-debug nil
+  "Enable debug logging and debug information in hover hints."
+  :type 'boolean
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0")
+  :lsp-path "nextflow.debug")
+
+(lsp-defcustom lsp-nextflow-files-exclude [".git" ".nf-test" "work"]
+  "Configure glob patterns for excluding folders from being searched for
+Nextflow scripts and configuration files."
+  :type 'lsp-string-vector
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0")
+  :lsp-path "nextflow.files.exclude")
+
+(lsp-defcustom lsp-nextflow-formatting-harshil-alignment nil
+  "Use the [Harshil Alignment™️](https://nf-co.re/docs/contributing/code_editors_and_styling/harshil_alignment) when formatting Nextflow scripts and config files.
+
+*Note: not all rules are supported yet*"
+  :type 'boolean
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0")
+  :lsp-path "nextflow.formatting.harshilAlignment")
+
+(lsp-defcustom lsp-nextflow-java-home nil
+  "Specifies the folder path to the JDK. Use this setting if the extension cannot
+find Java automatically."
+  :type '(choice (const :tag "Auto" nil)
+          (directory :tag "Custom JDK path"))
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0")
+  :lsp-path "nextflow.java.home")
+
+(lsp-defcustom lsp-nextflow-suppress-future-warnings t
+  "Hide warnings for future changes, deprecations, and removals."
+  :type 'boolean
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0")
+  :lsp-path "nextflow.suppressFutureWarnings")
+
+;;
+;;; Client
+
+(lsp-register-client
+ (make-lsp-client
+  ;; FIXME
+  ;; :download-server-fn (lambda (_client callback error-callback _update?)
+  ;;                       (lsp-package-ensure 'nextflow-lsp callback error-callback))
+  :new-connection (lsp-stdio-connection #'lsp-nextflow-server-command)
+  :major-modes '(nextflow-mode)
+  :multi-root t
+  :activation-fn (lsp-activate-on "nextflow")
+  :priority -1
+  :initialized-fn (lambda (workspace)
+                    (with-lsp-workspace workspace
+                      (lsp--set-configuration
+                       (lsp-configuration-section "nextflow"))))
+  ;; TODO Handle preview dag
+  :server-id 'nextflow-lsp))
+
+(lsp-consistency-check lsp-nextflow)
+
+(provide 'lsp-nextflow)
+;;; lsp-nextflow.el ends here
diff --git a/docs/lsp-clients.json b/docs/lsp-clients.json
index b0b17a587d..0b6c2f7f48 100644
--- a/docs/lsp-clients.json
+++ b/docs/lsp-clients.json
@@ -677,6 +677,14 @@
     "installation": "npm install -g @mdx-js/language-server",
     "debugger": "Not available"
   },
+  {
+    "name": "nextflow",
+    "full-name": "Nextflow",
+    "server-name": "nextflow-language-server",
+    "server-url": "https://github.com/nextflow-io/language-server",
+    "installation-url": "https://github.com/nextflow-io/language-server#build",
+    "debugger": "Not available"
+  },
   {
     "name": "nginx",
     "full-name": "Nginx",
diff --git a/lsp-mode.el b/lsp-mode.el
index f5c700dbf3..1dad7b75a0 100644
--- a/lsp-mode.el
+++ b/lsp-mode.el
@@ -182,7 +182,7 @@ As defined by the Language Server Protocol 3.16."
      lsp-graphql lsp-groovy lsp-hack lsp-haskell lsp-haxe lsp-idris lsp-java
      lsp-javascript lsp-jq lsp-json lsp-kotlin lsp-latex lsp-lisp lsp-ltex
      lsp-lua lsp-fennel lsp-magik lsp-markdown lsp-marksman lsp-mdx lsp-meson lsp-metals lsp-mint
-     lsp-mojo lsp-move lsp-mssql lsp-nginx lsp-nim lsp-nix lsp-nushell lsp-ocaml
+     lsp-mojo lsp-move lsp-mssql lsp-nextflow lsp-nginx lsp-nim lsp-nix lsp-nushell lsp-ocaml
      lsp-openscad lsp-pascal lsp-perl lsp-perlnavigator lsp-php lsp-pls
      lsp-purescript lsp-pwsh lsp-pyls lsp-pylsp lsp-pyright lsp-python-ms
      lsp-qml lsp-r lsp-racket lsp-remark lsp-rf lsp-roslyn lsp-rubocop lsp-ruby-lsp
@@ -835,6 +835,7 @@ Changes take effect only when a new session is started."
     (java-ts-mode . "java")
     (jdee-mode . "java")
     (groovy-mode . "groovy")
+    (nextflow-mode . "nextflow")
     (python-mode . "python")
     (python-ts-mode . "python")
     (cython-mode . "python")
diff --git a/mkdocs.yml b/mkdocs.yml
index 2c7912e033..51df17aa94 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -118,6 +118,7 @@ nav:
     - Move: page/lsp-move.md
     - MDX: page/lsp-mdx.md
     - MSSQL: https://emacs-lsp.github.io/lsp-mssql
+    - Nextflow: page/lsp-nextflow.md
     - Nginx: page/lsp-nginx.md
     - Nim: page/lsp-nim.md
     - Nix (nixd-lsp): page/lsp-nix-nixd.md