Get PQR up and running again

Due to lack of maintenance, the codebase has become outdated. I was unable
to build it as is on Ubuntu 22.04. This PR has the minimal changes I needed
to get the server up and running again.

1) Update to Python 2.7.18. Older versions of Python cannot be built.
2) The latest versions of Flask are incompatible with Python 2 and existing
  code. So, Pin dependency versions of Flask and related deps.
3) Remove a secret_config import as the file is not present in the repo.
4) Install lesshat using npm and update lesshat imports.
5) Update gulp and related imports.
6) Fix code in bindevents.js to make gulp build pass.

Author: amCap1712

README.md

@@ -8,7 +8,7 @@ PQR is built upon Flask, a lightweight MVC in Python. PQR also uses MongoDB. We
 
 To run PQR locally, do the following:
 1. Clone this repository
-2. Make sure you have Python 2.7.6 or Python 2.7.9
+2. Make sure you have Python 2.7.18.
 3. Install `virtualenv`. On Debian systems, run `sudo pip install virtualenv`. On Windows, `pip install virtualenv`
 4. Make sure you are in the root of the repo, aka the same level as this README. Then, run `virtualenv venv`. This will create a virtual environment named `venv` in the root of the repo.
 5. On Linux systems, run `. venv/bin/activate` to activate the virtual enviroment. On Windows, run `.\venv\Scripts\activate`.

assets/js/bindevents.js

@@ -176,14 +176,13 @@ module.exports = (function() {
         if ($(selector).length) {
             $(selector).on("click vclick", function(event) {
                 event.preventDefault();
-                if $(this).text()=="Remove Surface"{
+                if ($(this).text()==="Remove Surface") {
                     threeDMole.toggleSurface();
                     $(this).addClass('btn-success');
                     $(this).removeClass('btn-danger');
                     $(this).html('Add Surface');
                     //"feedback", "fa-desktop");
-                }
-                else {
+                } else {
                     threeDMole.toggleSurface2();
                     $(this).addClass('btn-danger');
                     $(this).removeClass('btn-success');

assets/style/main.less

@@ -1,5 +1,5 @@
 //Import bootstrap variables and mixins to use variables
-@import '../../bower_components/lesshat/build/lesshat.less';
+@import "node_modules/lesshat/lesshat.less";
 @import (reference) "bootstrap/bootstrap.less";
 @import "bootstrap/variables.less";
 @import "bootstrap/mixins.less";

gulpfile.js

@@ -1,6 +1,6 @@
 'use strict';
 
-var gulp = require('gulp'),
+const gulp = require('gulp'),
     path = require('path'),
     concat = require('gulp-concat'),
     autoprefixer = require('gulp-autoprefixer'),
@@ -16,9 +16,10 @@ var gulp = require('gulp'),
     uglify = require('gulp-uglify'),
     tape = require('gulp-tape'),
     watch = require('gulp-watch');
-var paths = {
-    source : path.join(__dirname, 'assets/'),
-    dist : path.join(__dirname, 'pqr/static/'),
+
+const paths = {
+    source: path.join(__dirname, 'assets/'),
+    dist: path.join(__dirname, 'pqr/static/'),
     style: 'style/',
     js: 'js/',
     test: 'test/'
@@ -72,11 +73,11 @@ gulp.task('js', function () {
             .pipe(gulp.dest(paths.dist + paths.js));
     });
 });
-gulp.task('compile', ['less', 'js']);
+gulp.task('compile', gulp.series('less', 'js'));
 //test
 gulp.task('test', function() {
   return gulp.src(paths.source + paths.test + 'main.test.js')
     .pipe(tape());
 });
 //default
-gulp.task('default', ['compile']);
+gulp.task('default', gulp.series('compile'));

package.json

@@ -6,28 +6,29 @@
   "dependencies": {
     "bootstrap": "^3.3.6",
     "browsernizr": "^2.1.0",
+    "lesshat": "^4.1.0",
     "qrcode-npm": "0.0.3"
   },
   "devDependencies": {
     "babel-preset-es2015": "^6.5.0",
     "babelify": "^7.2.0",
     "browserify": "^13.0.0",
     "glob": "^6.0.4",
-    "gulp": "^3.9.0",
-    "gulp-autoprefixer": "^3.1.0",
-    "gulp-concat": "^2.6.0",
-    "gulp-cssnano": "^2.1.0",
-    "gulp-jshint": "^2.0.0",
+    "gulp": "4.0.2",
+    "gulp-autoprefixer": "^8.0.0",
+    "gulp-concat": "2.6.1",
+    "gulp-cssnano": "^2.1.3",
+    "gulp-jshint": "^2.1.0",
     "gulp-less": "^3.0.5",
     "gulp-sourcemaps": "^1.6.0",
-    "gulp-tape": "0.0.7",
-    "gulp-uglify": "^1.5.1",
+    "gulp-tape": "1.0.0",
+    "gulp-uglify": "3.0.2",
     "gulp-util": "^3.0.7",
     "gulp-watch": "^4.3.5",
     "jshint": "^2.9.1",
     "tape": "^4.4.0",
-    "vinyl-buffer": "^1.0.0",
-    "vinyl-source-stream": "^1.1.0"
+    "vinyl-buffer": "^1.0.1",
+    "vinyl-source-stream": "^2.0.0"
   },
   "scripts": {
     "postinstall": "bower install",

pqr/static/js/pqr.min.js

@@ -14,7 +14,7 @@
 from pymongo import MongoClient
 
 # PQR specific imports
-from pqr import pqr, secret_config
+from pqr import pqr
 
 from settings import APP_JSON, APP_MOL2, APP_ARTICLES
 
@@ -658,6 +658,7 @@ def get_weekly_molecule_list():
     sunday = today - (today % 7)
     sunday = datetime.date.fromordinal(sunday)
     sunday = datetime.date.isoformat(sunday)
+    last = None
     with open("./pqr/server_start/mol_of_the_week", "r") as molfile:
         for line in molfile:
 
@@ -668,13 +669,15 @@ def get_weekly_molecule_list():
             tokens = line.strip().split(",")
             if len(tokens) < 3:
                 continue
+
+            # inchikey, title, date
+            last = tokens[1] + "," + tokens[2].title() + "," + tokens[0][0:4] + '-' + tokens[0][4:6] + '-' + tokens[0][6:]
             if tokens[0] <= datetime.datetime.isoformat(datetime.datetime.now()).replace('-', ''):
-                return_list.append( # inchikey, title, date
-                    tokens[1] + "," + tokens[2].title() + "," + tokens[0][0:4] + '-' + tokens[0][4:6] + '-' + tokens[0][6:]
-                )
+                return_list.append(last)
+            else:  # We are now past the current date, don't show them yet
+                continue
+    return return_list or [last]
 
-            else: # We are now past the current date, don't show them yet
-                return return_list
 
 def get_json_data_file(key_first_two, key):
     try:

pqr/static/style/pqr.min.css

@@ -1,4 +1,5 @@
-Flask
+Flask==0.11.0
+Werkzeug==0.16.1
 pymongo
 Flask-Cache
 flask-mandrill

pqr/views.py

@@ -1,4 +1,4 @@
-#!./venv/bin/python
+#!/usr/bin/env python
 from pymongo import MongoClient
 import datetime
 import threading