From 21837d494b604d5c545754edd90cc31e4adc6aef Mon Sep 17 00:00:00 2001
From: Steven Weaver <sweaver@temple.edu>
Date: Sat, 23 Nov 2024 14:41:54 -0500
Subject: [PATCH] bump version and update Node.js requirement to v23 or higher
 in package.json

---
 lib/hpcsocket.js | 56 +++++++++++++++++++++++++++++++-----------------
 package.json     |  5 ++++-
 yarn.lock        | 14 +-----------
 3 files changed, 41 insertions(+), 34 deletions(-)

diff --git a/lib/hpcsocket.js b/lib/hpcsocket.js
index 757fb0c8..1dfad88e 100644
--- a/lib/hpcsocket.js
+++ b/lib/hpcsocket.js
@@ -159,31 +159,47 @@ HPCSocket.prototype.initializeServer = function (url_input, callback) {
 
   // Routine status update
   self.server_socket.on("status update", function (data) {
-    // Update document with status update
-    self.job.analysis.status = data.phase;
-    self.job.analysis.last_status_msg = data.msg;
-    self.job.analysis.creation_time = data.ctime || self.job.analysis.created;
-    self.job.analysis.start_time = data.stime || self.job.analysis.start_time;
-    self.job.analysis.torque_id = data.torque_id;
+      // Update document fields with status update
+      self.job.analysis.status = data.phase;
+      self.job.analysis.last_status_msg = data.msg;
+      self.job.analysis.creation_time = data.ctime || self.job.analysis.created;
+      self.job.analysis.start_time = data.stime || self.job.analysis.start_time;
+      self.job.analysis.torque_id = data.torque_id;
+
+      // Use a flag to ensure save operations do not overlap
+      if (self.job.analysis._isSaving) {
+          winston.info("Save in progress. Skipping this update.");
+          return; // Skip if a save is already in progress
+      }
 
-    //Update the status for the analysis
-    self.job.analysis.save(function (err, result) {
-      if (err) throw err;
+      self.job.analysis._isSaving = true; // Mark as saving
 
-      var redis_packet = {
-        type: "status update",
-        msg: data.msg,
-        phase: data.phase,
-        torque_id: result.torque_id,
-        start_time: result.start_time,
-        creation_time: result.creation_time,
-        percentage: result.percentage_complete,
-      };
+      // Save the document
+      self.job.analysis.save(function (err, result) {
+          self.job.analysis._isSaving = false; // Reset the saving flag
 
-      publisher.publish(self.channel, JSON.stringify(redis_packet));
-    });
+          if (err) {
+              winston.warn("Error saving analysis:", err);
+              return;
+          }
+
+          // Prepare the redis packet
+          const redis_packet = {
+              type: "status update",
+              msg: data.msg,
+              phase: data.phase,
+              torque_id: result.torque_id,
+              start_time: result.start_time,
+              creation_time: result.creation_time,
+              percentage: result.percentage_complete,
+          };
+
+          // Publish the status update to the Redis channel
+          publisher.publish(self.channel, JSON.stringify(redis_packet));
+      });
   });
 
+  
   // Routine status update
   self.server_socket.on("job created", function (data) {
     // Update document with status update
diff --git a/package.json b/package.json
index 3319c916..28f4bb2e 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "datamonkey.js",
-  "version": "1.11.6",
+  "version": "1.12.0",
   "description": "A free public server for comparative analysis of sequence alignments using state-of-the-art statistical models.",
   "private": true,
   "author": {
@@ -15,6 +15,9 @@
     "format": "prettier 'src/**/*.{js,jsx}' 'app/**/*.{js,jsx}' 'lib/**/*.{js,jsx}' 'config/**/*.{js,jsx}' 'test/**/*.{js,jsx}' --write",
     "precommit": "pretty-quick --staged"
   },
+  "engines": {
+    "node": ">=23.0.0"
+  },
   "repository": {
     "type": "git",
     "url": "git://github.com/veg/datamonkey-js.git"
diff --git a/yarn.lock b/yarn.lock
index 3e6cbd1a..386a74cf 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -6774,11 +6774,6 @@ expand-range@^1.8.1:
   dependencies:
     fill-range "^2.1.0"
 
-export-to-csv@^0.2.1:
-  version "0.2.2"
-  resolved "https://registry.yarnpkg.com/export-to-csv/-/export-to-csv-0.2.2.tgz#201ee08453dfb0d07792ee5e01fda48e4ff472ce"
-  integrity sha512-KHExLOjF2yvo8JU8Sv+5RuJAHzP1TpFvUgnWn8ex7zBrv1ZsABJAOpvG1RNRRWr1spYpDJmBBaR5/cV/8aBQSw==
-
 export-to-csv@^1.2.0:
   version "1.4.0"
   resolved "https://registry.yarnpkg.com/export-to-csv/-/export-to-csv-1.4.0.tgz#03fb42a4a4262cd03bde57a7b9bcad115149cf4b"
@@ -9612,12 +9607,6 @@ locate-path@^7.1.0:
   dependencies:
     p-locate "^6.0.0"
 
-lodash-es@^4.17.15:
-  version "4.17.21"
-  resolved "https://registry.yarnpkg.com/lodash-es/-/lodash-es-4.17.21.tgz#43e626c46e6591b7750beb2b50117390c609e3ee"
-  integrity sha512-mKnC+QJ9pWVzv+C4/U3rRsHapFfHvQFoFB92e52xeyGMcX6/OlIl78je1u8vePzYZSkkogMPJ2yjxxsb89cxyw==
-
-
 lodash.camelcase@^4.3.0:
   version "4.3.0"
   resolved "https://registry.yarnpkg.com/lodash.camelcase/-/lodash.camelcase-4.3.0.tgz#b28aa6288a2b9fc651035c7711f65ab6190331a6"
@@ -10208,8 +10197,7 @@ module-deps@^6.2.3:
     through2 "^2.0.0"
     xtend "^4.0.0"
 
-
-moment@^2.30.1:
+moment@^2.29.4, moment@^2.30.1:
   version "2.30.1"
   resolved "https://registry.yarnpkg.com/moment/-/moment-2.30.1.tgz#f8c91c07b7a786e30c59926df530b4eac96974ae"
   integrity sha512-uEmtNhbDOrWPFS+hdjFCBfy9f2YoyzRpwcl+DqpC6taX21FzsTLQVbMV/W7PzNSX6x/bhC1zA3c2UQ5NzH6how==