Initial commit

.dockerignore

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+*~
+*__pycache__*

Dockerfile

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+FROM continuumio/miniconda3:4.10.3
+MAINTAINER Mingxun Wang "mwang87@gmail.com"
+
+RUN apt-get update && apt-get install -y build-essential
+
+COPY requirements.txt .
+RUN pip install -r requirements.txt
+
+COPY . /app
+WORKDIR /app

Makefile

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+server-compose-build-nocache:
+	docker-compose --compatibility build --no-cache
+
+server-compose-interactive:
+	docker-compose --compatibility build
+	docker-compose --compatibility up
+
+server-compose:
+	docker-compose --compatibility build
+	docker-compose --compatibility up -d
+
+attach:
+	docker exec -i -t gnpslcms-dash /bin/bash

README.md

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+## Wang Lab Flask Basic Template
+
+This is a minimally viable template for Wang Lab
+
+### Editing Template
+
+1. Replace all references to template to your own name
+1. Change the external port in docker-compose.yml
+1. Make new repo
+1. Bring up the server with ```make server-compose-interactive```
+

app.py

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+# app.py
+import os
+
+from flask import Flask
+from peewee import SqliteDatabase
+
+APP_ROOT = os.path.dirname(os.path.realpath(__file__))
+DATABASE = os.path.join(APP_ROOT, './database/database.db')
+
+class CustomFlask(Flask):
+  jinja_options = Flask.jinja_options.copy()
+  jinja_options.update(dict(
+    block_start_string='(%',
+    block_end_string='%)',
+    variable_start_string='((',
+    variable_end_string='))',
+    comment_start_string='(#',
+    comment_end_string='#)',
+  ))
+
+app = CustomFlask(__name__)
+app.config.from_object(__name__)
+db = SqliteDatabase(app.config['DATABASE'], pragmas=[('journal_mode', 'wal')])
+
+app.config['UPLOAD_FOLDER'] = './tempuploads'
+
+try:
+    os.mkdir(app.config['UPLOAD_FOLDER'])
+except:
+    print("Cannot Create", app.config['UPLOAD_FOLDER'])

docker-compose.yml

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+version: '3'
+services:
+  template-dash:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    container_name: template-dash
+    volumes:
+      - ./logs:/app/logs:rw
+      - ./database:/app/database:rw
+    ports:
+    - "5000:5000"
+    networks:
+      - default
+      - nginx-net
+    restart: unless-stopped
+    command: /app/run_server.sh
+    environment:
+      VIRTUAL_HOST: template.ucsd.edu
+      VIRTUAL_PORT: 5000
+      LETSENCRYPT_HOST: template.ucsd.edu
+      LETSENCRYPT_EMAIL: miw023@ucsd.edu
+
+
+networks:
+  nginx-net:
+    external:
+      name: nginx-net

main.py

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+# main.py
+from app import app
+from models import *
+import views
+
+if __name__ == '__main__':
+    Filename.create_table(True)
+    app.run(host='0.0.0.0', port=5000)

models.py

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+# models.py
+
+from peewee import *
+from app import db
+
+class Filename(Model):
+    filepath = TextField(primary_key=True)
+
+    class Meta:
+        database = db

requirements.txt

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+Flask
+gunicorn
+plotly
+pandas
+requests
+tqdm
+Werkzeug
+Flask-Caching
+peewee

run_server.sh

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+#!/bin/bash
+
+#python ./main.py
+gunicorn -w 6 --threads=12 --worker-class=gthread -b 0.0.0.0:5000 --timeout 120 --max-requests 500 --max-requests-jitter 100 --graceful-timeout 120 main:app --access-logfile /app/logs/access.log

templates/index.html

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+(% extends "layout.html" %)
+
+(% block content %)
+
+<!-- This portion is for drag and drop files -->
+
+<script src="https://rawgit.com/enyo/dropzone/master/dist/dropzone.js"></script>
+<link rel="stylesheet" href="https://rawgit.com/enyo/dropzone/master/dist/dropzone.css">
+
+<style>
+    .dropzone { border: 2px dashed #0087F7; border-radius: 5px; background: white; margin: 20px}
+    .dropzone .dz-message { font-weight: 400; }
+    .dropzone .dz-message .note { font-size: 0.8em; font-weight: 200; display: block; margin-top: 1.4rem; }
+    .container-fluid { min-height: 100%; height: 100%;}
+</style>
+
+<div>
+    <div class="container-fluid">
+        <br>
+        <br>
+        <div class="row">
+          <div class="col-sm"></div>
+          <div class="col-sm text-center">
+              <h2>Upload Files</h2>
+          </div>
+          <div class="col-sm"></div>
+        </div>
+
+        <br>
+        <div class="row">
+            <div class="col-sm-2"></div>
+            <div class="col-sm-8">
+                <p>
+                    Upload Files
+                </p>
+            </div>
+            <div class="col-sm-2"></div>
+        </div>
+
+        <br>
+
+        <div class="row">
+            <div class="col-md-2" id=""></div>
+            <div class="dropzone col-md-8" id="upload">
+                <div class="dz-message">Drop files here!</div>
+            </div>
+            <div class="col-md-2" id=""></div>
+        </div>
+
+        <div id="app-4" class="container-fluid">
+            <br>
+            <h3 class="text-center">Upload Summary</h3>
+            <br>
+            <table class="table table-sm table-striped">
+                <thead>
+                    <tr>
+                        <th>Category</th>
+                        <th>Value</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    <tr v-for="stat in stats">
+                        <td>{{stat.type}}</td>
+                        <td>{{stat.value}}</td>
+                    </tr>
+                </tbody>
+            </table>
+        </div>
+    </div>
+</div>
+
+<script>
+    validatedropzone = new Dropzone("#upload", { url: "upload", maxFilesize: 200, parallelUploads:1});
+    validatedropzone.on("success", function(file, response) {
+        response_json = JSON.parse(response)
+        app4._data.stats = response_json["stats"]
+    });
+    validatedropzone.on("error", function(file) {
+    });
+    var app4 = new Vue({
+        el: '#app-4',
+        methods: {
+        },
+        data: {
+            stats: []
+        }
+    })
+</script>
+
+
+(% endblock %)

templates/layout.html

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+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>Ming Flask Template</title>
+    <script src="https://cdn.jsdelivr.net/npm/vue/dist/vue.js"></script>
+    <script src="https://code.jquery.com/jquery-3.3.1.js" integrity="sha256-2Kok7MbOyxpgUVvAk/HJ2jigOSYS2auK4Pfzbm7uH60=" crossorigin="anonymous"></script>
+    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
+    <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
+    <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.6.1/css/all.css" integrity="sha384-gfdkjb5BdAXd+lj+gudLWI+BXq4IuLW5IT+brZEZsLFm++aCMlF1V92rMkPaX4PP" crossorigin="anonymous">
+
+    <!-- Umami Analytics -->
+    <script async defer data-website-id="ENTER YOUR TOKEN HERE" src="https://analytics.gnps2.org/umami.js"></script>    
+</head>
+
+<body>
+    <!-- A grey horizontal navbar that becomes vertical on small screens -->
+    <nav class="navbar navbar-expand-sm bg-light navbar-light">
+        <a class="navbar-brand" href="https://gnps.ucsd.edu/">
+            <img src="https://ccms-ucsd.github.io/GNPSDocumentation/img/GNPS_logo_original.png" alt="Logo" style="width:120px;">
+        </a>
+
+      <!-- Links -->
+      <ul class="navbar-nav">
+        <li class="nav-item">
+          <a class="nav-link" href="/">Homepage</a>
+        </li>
+      </ul>
+
+    </nav>
+
+
+    <div id="content">
+        (% block content %)(% endblock %)
+    </div>
+
+
+</body>
+
+</html>

views.py

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+# views.py
+from flask import abort, jsonify, render_template, request, redirect, url_for, send_file, make_response
+
+from app import app
+from models import *
+
+import os
+import csv
+import json
+import uuid
+import requests
+
+@app.route('/', methods=['GET'])
+def renderhomepage():
+    return render_template('index.html')
+
+@app.route('/upload', methods=['POST'])
+def validate():
+    request_file = request.files['file']
+
+    local_filename = os.path.join(app.config['UPLOAD_FOLDER'], str(uuid.uuid4()))
+    request_file.save(local_filename)
+
+
+    response_dict = {}
+    response_dict["stats"] = []
+    num_lines = sum(1 for line in open(local_filename))
+    response_dict["stats"].append({"type":"total_rows", "value":num_lines})
+
+    try:
+        os.remove(local_filename)
+    except:
+        print("Cannot Remove File")
+
+    return json.dumps(response_dict)
+
+
+@app.route('/heartbeat', methods=['GET'])
+def testapi():
+    return_obj = {}
+    return_obj["status"] = "success"
+    return json.dumps(return_obj)