Get PQR up and running again

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/views.py

@@ -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:

requirements.txt

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

server.py

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

unit_test.py

@@ -5,7 +5,7 @@
 
 class PQRTestCase(unittest.TestCase):
 
-    mol = "GNBHRKFJIUUOQI-UHFFFAOYSA-N"
+    mol = "ULGZDMOVFRHVEP-RWJQBGPGSA-N"
 
     def setUp(self):
         pqr.pqr.config['TESTING'] = True