Start submit form implementation + add config reader and applications.properties

application.properties

+[global]
+upload_folder = /home/fcabanettes/public_html/tmp
+data_folder = /home/fcabanettes/public_html/test

css/style.css

@@ -213,4 +213,38 @@ input[type=range] {
   Body {
     font-size: 16px;
     }
+}
+
+/* Submit form: */
+table.form td.label {
+    padding-top:5px;
+    padding-right: 10px;
+}
+
+table.form {
+    margin-bottom: 15px;
+    margin-left: 15px;
+}
+
+table.form input[type=text],table.form input[type=email]{
+    width: 250px;
+}
+
+#body {
+    margin-left: 15px;
+    margin-top: 10px;
+}
+
+.errors-submit ul li {
+    background-color: #ff756b;
+    border: solid 2px #7c0000;
+    margin-bottom: 5px;
+    padding: 3px;
+    list-style-type: none;
+    font-weight: bold;
+}
+
+.errors-submit ul {
+    padding: 0;
+    width: 460px;
 }
\ No newline at end of file

js/popper.min.js

+/*
+ Copyright (C) Federico Zivolo 2017
+ Distributed under the MIT License (license terms are at http://opensource.org/licenses/MIT).
+ */(function(e,t){'object'==typeof exports&&'undefined'!=typeof module?module.exports=t():'function'==typeof define&&define.amd?define(t):e.Popper=t()})(this,function(){'use strict';function e(e){return e&&'[object Function]'==={}.toString.call(e)}function t(e,t){if(1!==e.nodeType)return[];var o=window.getComputedStyle(e,null);return t?o[t]:o}function o(e){return'HTML'===e.nodeName?e:e.parentNode||e.host}function n(e){if(!e||-1!==['HTML','BODY','#document'].indexOf(e.nodeName))return window.document.body;var i=t(e),r=i.overflow,p=i.overflowX,s=i.overflowY;return /(auto|scroll)/.test(r+s+p)?e:n(o(e))}function r(e){var o=e&&e.offsetParent,i=o&&o.nodeName;return i&&'BODY'!==i&&'HTML'!==i?-1!==['TD','TABLE'].indexOf(o.nodeName)&&'static'===t(o,'position')?r(o):o:window.document.documentElement}function p(e){var t=e.nodeName;return'BODY'!==t&&('HTML'===t||r(e.firstElementChild)===e)}function s(e){return null===e.parentNode?e:s(e.parentNode)}function 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fe.FLIP:p=[i,n];break;case fe.CLOCKWISE:p=K(i);break;case fe.COUNTERCLOCKWISE:p=K(i,!0);break;default:p=t.behavior;}return p.forEach(function(s,d){if(i!==s||p.length===d+1)return e;i=e.placement.split('-')[0],n=L(i);var a=e.offsets.popper,l=e.offsets.reference,f=_,m='left'===i&&f(a.right)>f(l.left)||'right'===i&&f(a.left)<f(l.right)||'top'===i&&f(a.bottom)>f(l.top)||'bottom'===i&&f(a.top)<f(l.bottom),c=f(a.left)<f(o.left),h=f(a.right)>f(o.right),g=f(a.top)<f(o.top),u=f(a.bottom)>f(o.bottom),b='left'===i&&c||'right'===i&&h||'top'===i&&g||'bottom'===i&&u,y=-1!==['top','bottom'].indexOf(i),w=!!t.flipVariations&&(y&&'start'===r&&c||y&&'end'===r&&h||!y&&'start'===r&&g||!y&&'end'===r&&u);(m||b||w)&&(e.flipped=!0,(m||b)&&(i=p[d+1]),w&&(r=j(r)),e.placement=i+(r?'-'+r:''),e.offsets.popper=de({},e.offsets.popper,S(e.instance.popper,e.offsets.reference,e.placement)),e=N(e.instance.modifiers,e,'flip'))}),e},behavior:'flip',padding:5,boundariesElement:'viewport'},inner:{order:700,enabled:!1,fn:function(e){var t=e.placement,o=t.split('-')[0],i=e.offsets,n=i.popper,r=i.reference,p=-1!==['left','right'].indexOf(o),s=-1===['top','left'].indexOf(o);return n[p?'left':'top']=r[o]-(s?n[p?'width':'height']:0),e.placement=L(t),e.offsets.popper=h(n),e}},hide:{order:800,enabled:!0,fn:function(e){if(!F(e.instance.modifiers,'hide','preventOverflow'))return e;var t=e.offsets.reference,o=T(e.instance.modifiers,function(e){return'preventOverflow'===e.name}).boundaries;if(t.bottom<o.top||t.left>o.right||t.top>o.bottom||t.right<o.left){if(!0===e.hide)return e;e.hide=!0,e.attributes['x-out-of-boundaries']=''}else{if(!1===e.hide)return e;e.hide=!1,e.attributes['x-out-of-boundaries']=!1}return e}},computeStyle:{order:850,enabled:!0,fn:function(e,t){var o=t.x,i=t.y,n=e.offsets.popper,p=T(e.instance.modifiers,function(e){return'applyStyle'===e.name}).gpuAcceleration;void 0!==p&&console.warn('WARNING: `gpuAcceleration` option moved to `computeStyle` modifier and will not be supported in future versions of Popper.js!');var s,d,a=void 0===p?t.gpuAcceleration:p,l=r(e.instance.popper),f=g(l),m={position:n.position},c={left:_(n.left),top:_(n.top),bottom:_(n.bottom),right:_(n.right)},h='bottom'===o?'top':'bottom',u='right'===i?'left':'right',b=B('transform');if(d='bottom'==h?-f.height+c.bottom:c.top,s='right'==u?-f.width+c.right:c.left,a&&b)m[b]='translate3d('+s+'px, '+d+'px, 0)',m[h]=0,m[u]=0,m.willChange='transform';else{var y='bottom'==h?-1:1,w='right'==u?-1:1;m[h]=d*y,m[u]=s*w,m.willChange=h+', '+u}var E={"x-placement":e.placement};return e.attributes=de({},E,e.attributes),e.styles=de({},m,e.styles),e.arrowStyles=de({},e.offsets.arrow,e.arrowStyles),e},gpuAcceleration:!0,x:'bottom',y:'right'},applyStyle:{order:900,enabled:!0,fn:function(e){return U(e.instance.popper,e.styles),Y(e.instance.popper,e.attributes),e.arrowElement&&Object.keys(e.arrowStyles).length&&U(e.arrowElement,e.arrowStyles),e},onLoad:function(e,t,o,i,n){var r=x(n,t,e),p=v(o.placement,r,t,e,o.modifiers.flip.boundariesElement,o.modifiers.flip.padding);return t.setAttribute('x-placement',p),U(t,{position:'absolute'}),o},gpuAcceleration:void 0}}},me});
+//# sourceMappingURL=popper.min.js.map

srv/config_reader.py

+import os
+import inspect
+from configparser import RawConfigParser, NoOptionError
+
+
+class AppConfigReader(object):
+    """
+    """
+
+    CONFIG_FILE_PATH = "../application.properties"
+
+    def __init__(self):
+        """
+        """
+        self.reader = RawConfigParser()
+        self.reader.read(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), self.CONFIG_FILE_PATH))
+
+    def get_upload_folder(self):
+        try:
+            return self.reader.get("global", "upload_folder")
+        except NoOptionError:
+            return None
+
+    def get_app_data(self):
+        try:
+            return self.reader.get("global", "data_folder")
+        except NoOptionError:
+            return None

srv/main.py

@@ -2,32 +2,135 @@
 
 import os
 import json
-from flask import Flask, render_template, request
+import random
+import string
+import time
+import datetime
+from flask import Flask, render_template, request, redirect, flash, session, url_for
+from werkzeug.utils import secure_filename
 from lib.parse_paf import parse_paf
+from config_reader import AppConfigReader
+
+# Init config reader:
+config_reader = AppConfigReader()
+
+UPLOAD_FOLDER = config_reader.get_upload_folder()
+ALLOWED_EXTENSIONS = {'fa', 'fasta', 'fa.gz', "fasta.gz"}
 
 app_title = "ALGECO - A Live GEnome COmparator"
 
-# Init Flash:
+# Init Flask:
 app = Flask(__name__, static_url_path='/static')
+app.config['UPLOAD_FOLDER'] = UPLOAD_FOLDER
+app.config['SECRET_KEY'] = 'dsqdsq-255sdA-fHfg52-25Asd5'
 
 # Folder containing data:
-app_data = "/home/fcabanettes/public_html/test"
+app_data = config_reader.get_app_data()
+
+
+def allowed_file(filename):
+    return '.' in filename and \
+           (filename.rsplit('.', 1)[1].lower() in ALLOWED_EXTENSIONS or ".".join(filename.rsplit('.', 2)[1:]).lower()
+            in ALLOWED_EXTENSIONS)
+
+
+def random_string(s_len):
+    """
+    Generate a random string
+    :param s_len: length of the string to generate
+    :return: the random string
+    """
+    return ''.join([random.choice(string.ascii_letters + string.digits) for n in range(s_len)])
+
+
+def get_valid_uploaded_filename(filename):
+    file_query_s = os.path.join(app.config["UPLOAD_FOLDER"], filename)
+    i = 2
+    filename_orig = filename
+    while os.path.exists(file_query_s):
+        filename = str(i) + "_" + filename_orig
+        file_query_s = os.path.join(app.config["UPLOAD_FOLDER"], filename)
+        i += 1
+    return filename
+
+
+# Main
+@app.route("/", methods=['GET'])
+def main():
+    id_job = random_string(5) + "_" + datetime.datetime.fromtimestamp(time.time()).strftime('%Y%m%d%H%M%S')
+    if "id_job" in request.args:
+        id_job = request.args["id_job"]
+    email = ""
+    if "email" in request.args:
+        email = request.args["email"]
+    return render_template("index.html", title=app_title, id_job=id_job, email=email)
+
+
+# Launch analysis
+@app.route("/launch_analysis", methods=['POST'])
+def launch_analysis():
+    id_job = request.form["id_job"]
+    email = request.form["email"]
+    file_query = request.files["file_query"]
+    file_target = request.files["file_target"]
+
+    # Check form:
+    form_pass = True
+    if id_job == "":
+        flash("Id of job not given")
+        form_pass = False
+
+    if email == "":
+        flash("Email not given")
+        form_pass = False
+    if file_query.filename == "":
+        flash("No query fasta selected")
+        form_pass = False
+    if file_target.filename == "":
+        flash("No target fasta selected")
+        form_pass = False
+
+    # Form pass
+    if form_pass:
+        # Check files are correct:
+        if not allowed_file(file_query.filename):
+            flash("Format of query fasta must be in fasta format (.fa, .fa.gz, .fasta, .fasta.gz)")
+            form_pass = False
+        if not allowed_file(file_target.filename):
+            flash("Format of target fasta must be in fasta format (.fa, .fa.gz, .fasta, .fasta.gz)")
+            form_pass = False
+        if form_pass:
+            # Save files:
+            filename_query = get_valid_uploaded_filename(secure_filename(file_query.filename))
+            file_query.save(os.path.join(app.config["UPLOAD_FOLDER"], filename_query))
+            filename_target = get_valid_uploaded_filename(secure_filename(file_target.filename))
+            file_target.save(os.path.join(app.config["UPLOAD_FOLDER"], filename_target))
+
+            # Get final job id:
+            id_job_orig = id_job
+            while os.path.exists(os.path.join(app_data, id_job)):
+                id_job = id_job_orig + "_2"
+        else:
+            return redirect(url_for(".main", id_job=id_job, email=email))
+    else:
+        return redirect(url_for(".main", id_job=id_job, email=email))
+    return "Ok!"
 
 
 # Results path
 @app.route("/result/<id_res>", methods=['GET'])
 def result(id_res):
     title = app_title
-    return render_template("index.html", title=title, id=id_res)
+    return render_template("results.html", title=title, id=id_res)
 
 
 # Get graph (ajax request)
 @app.route('/get_graph', methods=['POST'])
 def get_graph():
     id_f = request.form["id"]
-    paf = os.path.join(app_data, id_f + ".paf")
-    idx1 = os.path.join(app_data, id_f + "_1.idx")
-    idx2 = os.path.join(app_data, id_f + "_2.idx")
+    paf = os.path.join(app_data, id_f, "map.paf")
+    idx1 = os.path.join(app_data, id_f, "query_1.idx")
+    idx2 = os.path.join(app_data, id_f, "query_2.idx")
 
     success, res = parse_paf(paf, idx1, idx2)
 

srv/templates/header.html

@@ -6,10 +6,13 @@
 
     <script src="{{ url_for('static', filename='js/jquery-3.2.1.min.js') }}" type="text/JavaScript"></script>
 	<script src="{{ url_for('static', filename='js/jquery-ui.min.js') }}" type="text/JavaScript"></script>
+	<script src="{{ url_for('static', filename='js/popper.min.js') }}" type="text/JavaScript"></script>
+	<script src="{{ url_for('static', filename='js/bootstrap.min.js') }}" type="text/JavaScript"></script>
 	<script src="{{ url_for('static', filename='js/d3.min.js') }}" type="text/JavaScript"></script>
 	<script src="{{ url_for('static', filename='js/d3.boxplot.js') }}" type="text/JavaScript"></script>
     <script src="{{ url_for('static', filename='js/d3.boxplot.events.js') }}" type="text/JavaScript"></script>
 	<link rel="stylesheet" href="{{ url_for('static', filename='css/jquery-ui.min.css') }}" type="text/css">
+	<link rel="stylesheet" href="{{ url_for('static', filename='css/bootstrap.min.css') }}" type="text/css">
 	<link rel="stylesheet" href="{{ url_for('static', filename='css/style.css') }}" type="text/css">
 	<link rel="shortcut icon" href="{{ url_for('static', filename='images/favicon.ico') }}">
 </head>
\ No newline at end of file

srv/templates/index.html

+{% include 'header.html' %}
+<body>
+<div id="main-bar-title">
+    <img src="{{ url_for('static', filename='images/logo.png') }}" height="40px" alt=""/><h1>{{ title }}</h1>
+</div>
+<div id="body">
+    <form id="submit_minimap" method=post enctype=multipart/form-data action="/launch_analysis">
+        <h2>Launch map analysis</h2>
+        {% with messages = get_flashed_messages() %}
+        {% if messages %}
+            <div class="errors-submit">
+                <ul class=flashes>
+                {% for message in messages %}
+                    <li>{{ message | safe }}</li>
+                {% endfor %}
+                </ul>
+            </div>
+        {% endif %}
+    {% endwith %}
+        <table class="form">
+            <tr>
+                <td class="label">
+                    <label for="id_job">Name of your job</label>
+                </td>
+                <td>
+                    <input type="text" id="id_job" name="id_job" value="{{ id_job }}" required/>
+                </td>
+            </tr>
+            <tr>
+                <td class="label">
+                    <label for="email">E-mail*</label>
+                </td>
+                <td>
+                    <input type="email" name="email" id="email" value="{{ email }}" required/>
+                </td>
+            </tr>
+            <tr>
+                <td class="label">
+                    <label>Query fasta</label>
+                </td>
+                <td>
+                    <input type="file" name="file_query" id="file_query" required/>
+                </td>
+            </tr>
+            <tr>
+                <td class="label">
+                    <label>Target fasta</label>
+                </td>
+                <td>
+                    <input type="file" name="file_target" id="file_target" required/>
+                </td>
+            </tr>
+        </table>
+        <p>* We will send you results by mail.</p>
+        <button type="submit">Submit</button>
+    </form>
+</div>
+</body>
+</html>
\ No newline at end of file