first commit

Dockerfile

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+ARG pyversion=3.9
+FROM python:${pyversion}-bullseye
+ARG pyversion=3.9
+ENV PYVERSION ${pyversion:-3.9}
+
+# Install packages
+RUN apt-get -yqq update && \
+    apt-get -yqq install apache2 apache2-dev locales libapache2-mod-wsgi-py3 && \
+    apt-get clean
+
+# Install locale
+COPY ./locale.gen /etc/locale.gen
+RUN locale-gen
+
+COPY gerincmet/prog_calc /var/www/html/gerincmet/prog_calc
+
+RUN chown -R www-data:www-data /var/www/
+RUN chmod -R 755 /var/www/
+
+USER www-data
+
+# Prepare virtualenv
+WORKDIR /var/www/html/gerincmet/prog_calc/prog_calc/
+COPY ./requirements.txt .
+RUN python3 -m venv ./venv
+RUN . ./venv/bin/activate
+RUN ./venv/bin/pip install --upgrade pip setuptools
+RUN ./venv/bin/pip install -r ./requirements.txt
+
+# Configure Apache
+USER root
+COPY ./start-apache.sh /
+RUN a2dismod mpm_event && a2enmod mpm_prefork
+COPY ./prog-calc.conf /etc/apache2/sites-available/000-default.conf
+
+# Start Apache
+EXPOSE 80
+CMD ["/bin/sh", "/start-apache.sh"]
+

gerincmet/prog_calc/prog_calc.wsgi

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+#!/var/www/html/gerincmet/prog_calc/prog_calc/venv/bin/python
+import sys
+import logging
+import os
+
+APP_HOME = "/var/www/html/gerincmet/prog_calc/prog_calc/"
+sys.path.insert(0,"/var/www/html/gerincmet/prog_calc/prog_calc/venv/lib/python3.9/site-packages")
+
+logging.basicConfig(stream=sys.stderr)
+sys.path.insert(0,APP_HOME)
+os.chdir(APP_HOME)
+
+from main import app as application

gerincmet/prog_calc/prog_calc/cox.py

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+import pandas as pd
+import numpy as np
+import matplotlib.pyplot as plt
+import lifelines as lf
+import pickle
+import io
+import base64
+
+
+def get_timeline_loc(timeline, val, dur):
+    typestr = f"timedelta64[{dur}]"
+    res = timeline[np.equal(timeline.astype('timedelta64[D]').astype(typestr), np.array(val).astype(typestr))]
+    if len(res) > 0:
+        res = res[0]
+    else:
+        res = np.NaN
+    return res
+
+
+def get_risk(cox, X, val, dur):
+    timeline = cox.predict_survival_function(X).index.to_numpy()
+    l = get_timeline_loc(timeline, val, dur)
+    risk = 1 - cox.predict_survival_function(X)[0][l]
+    return risk
+
+
+def cox_model(primer_tumor_score, age_score, mobility_score, metastasis_score, protein_score):
+    # Predict for this
+    score = primer_tumor_score + age_score + mobility_score + metastasis_score + protein_score
+    if 0 <= score <= 17:
+        nmstpc_category = 1
+    elif 18 <= score <= 24:
+        nmstpc_category = 2
+    elif 25 <= score <= 39:
+        nmstpc_category = 3
+    X = {"primer_tumor": np.array([primer_tumor_score]),
+         "age": np.array([age_score]),
+         "mobility": np.array([mobility_score]),
+         "metastasis": np.array([metastasis_score]),
+         "protein": np.array([protein_score]),
+         "categories": np.array([nmstpc_category])}
+    X = pd.DataFrame(X)
+    # Model is built from this:
+
+    # Get KM-curve for population
+    label = "population"
+    km_in = open("km_model.pickle","rb")
+    km = pickle.load(km_in)
+    km_in.close()
+    fig, ax = plt.subplots()
+    fig.set_figheight(4)
+    fig.set_figwidth(8)
+    ax.plot(1 - km.survival_function_, color='b', label="Populáció")
+    ax.fill_between(km.timeline, 1 - km.confidence_interval_[f"{label}_lower_0.95"],
+                    1 - km.confidence_interval_[f"{label}_upper_0.95"], color='b', alpha=.1)
+
+    # Fit Cox-modell
+    cox_in = open("cox_model.pickle","rb")
+    cox = pickle.load(cox_in)
+    cox_in.close()
+    ax.plot(1 - cox.predict_survival_function(X)[0], color="r", label="Jelenlegi beteg")
+    ax.set_xlabel("Halál ideje (napokban)")
+    ax.set_ylabel("Halál kockázata")
+    ax.legend(loc="lower right")
+    ax.grid()
+    fig.show()
+    buf = io.BytesIO()
+    fig.savefig(buf,format = "png")
+    encoded_img = base64.b64encode(buf.getvalue())
+
+    # Recover risk of death for certain times
+    vals = [1, 3, 6, 1, 2, 4, 8]
+    durs = ["M", "M", "M", "Y", "Y", "Y", "Y"]
+    risks = []
+    for val, dur in zip(vals, durs):
+        risks.append(round(get_risk(cox, X, val, dur) * 100, 1))
+    return risks,encoded_img

gerincmet/prog_calc/prog_calc/form.py

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+from flask_wtf import FlaskForm
+
+from wtforms import SelectField,SubmitField
+from wtforms.validators import DataRequired
+
+class Prognosis_Form(FlaskForm):
+    # Prognostic Factors
+    # Primer tumor
+    primer_tumor_types = [
+        (1, "Hematológiai malginitás"),
+        (2, "Pajzsmirigy carcinoma"),
+        (3, "Emlő daganat"),
+        (4, "Prostata daganat"),
+        (5, "Angiosarcoma"),
+        (6, "Chondrosarcoma"),
+        (7, "Osteosarcoma"),
+        (8, "Ewing-sarcoma"),
+        (9, "Húgyhólyag"),
+        (10, "Colorectalis"),
+        (11, "Garat"),
+        (12, "Vese"),
+        (13, "Máj"),
+        (14, "Melanoma"),
+        (15, "Ovarium"),
+        (16, "Uterus"),
+        (17, "Parotis"),
+        (18, "Gyomor"),
+        (19, "Ismeretlen primer tumor"),
+        (20, "Méhnyak"),
+        (21, "Nyelőcső"),
+        (22, "Gége"),
+        (23, "Tüdő"),
+        (24, "Hasnyálmirigy"),
+        (25, "Orrmelléküreg eredet")]
+    primer_tumor = SelectField(f"Primer tumor típusa", choices = primer_tumor_types, validators = [DataRequired()])
+
+    # Age
+    age_class = [
+        (0,"40 év alatt"),
+        (8,"40 év felett")]
+    age = SelectField(f"Életkor", choices = age_class, validators = [DataRequired()])
+
+    # Status
+    status_calss = [
+        (0, "Járóképes"),
+        (5, "Ágyhoz kötött (járásképtelen)")]
+    status = SelectField(f"Ambulátoros státusz", choices = status_calss, validators = [DataRequired()])
+
+    # Metastasis
+    has_metastasis = [
+        (0, "Nincs"),
+        (4, "Van")]
+    metastasis = SelectField(f"Belszervi áttétek jelenléte", choices = has_metastasis, validators = [DataRequired()])
+
+    # Protein levels
+    protein_class = [
+        (0, "Normál tartomány (>6,5 g/dl)"),
+        (3, "Hypoproteinaemia (<6,5 g/dl)")]
+    protein_levels = SelectField(f"Szérum fehérje szint", choices = protein_class, validators = [DataRequired()])
+
+    #-------------
+    # SINS factors
+    # Localization
+    localization_class = [
+        (3, "Junctionális (occiput-CII, CVII-ThII, ThII-LI, LV-SI)"),
+        (2, "Mobilis gerincszakasz (CIII-VI, LII-IV)"),
+        (1, "Semirigid gerincszakasz (ThIII-X)"),
+        (0, "Rigid (SII-V)")]
+    localization = SelectField(f"Lokalizáció", choices = localization_class, validators = [DataRequired()])
+
+    # Pain
+    has_pain = [
+        (3, "Van"),
+        (2, "Időszakosan"),
+        (0, "Nincs")]
+    pain = SelectField(f"Fájdalom", choices = has_pain, validators = [DataRequired()])
+
+    # Bone lesion
+    bone_lesion_class = [
+        (2, "Osteolyticus"),
+        (1, "Kevert"),
+        (0, "Osteoblasticus")]
+    bone_lesion = SelectField(f"Csontlézió típusa", choices=bone_lesion_class, validators=[DataRequired()])
+
+    # Spinal stability
+    stability_class = [
+        (4, "Subluxatio/luxatio"),
+        (2, "De novo kialakult deformitás (kyphosis, scoliosis)"),
+        (0, "Normál")]
+    stability = SelectField(f"Gerincstabilitás", choices=stability_class, validators=[DataRequired()])
+
+    # Compression
+    compression_class = [
+        (3, ">50% komprimált"),
+        (2, "<50% komprimált"),
+        (1, "Nincs kompresszió a csigolyatest 50%-os involváltság mellett"),
+        (0, "A fentiek közül egyik sem")]
+    compression = SelectField(f"Csigolyatest kompresszió mértéke", choices=compression_class, validators=[DataRequired()])
+
+    # Involvement
+    involvement_class = [
+        (3, "Bilateralis"),
+        (2, "Unilateralis"),
+        (1, "A fentiek közül egyik sem")]
+    involvement = SelectField(f"A spinalis elemek postero-lateralis érintettsége", choices=involvement_class, validators=[DataRequired()])
+
+    #-------
+    # Result
+    submit = SubmitField("Eredmény")

gerincmet/prog_calc/prog_calc/main.py

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+from flask import Flask, render_template
+from form import Prognosis_Form
+from cox import cox_model
+from tumor_type_to_score import type_to_score
+
+app = Flask(__name__)
+app.config["SECRET_KEY"] = "S(JK5Re,7*7Rbm#A"
+
+@app.route("/",methods = ["GET","POST"])
+def index():
+    form = Prognosis_Form()
+    if form.validate_on_submit():
+        tumor_score = type_to_score(int(form.primer_tumor.data))
+        risks,encoded_img = cox_model(tumor_score , int(form.age.data) , int(form.status.data) , int(form.metastasis.data) , int(form.protein_levels.data))
+        nmstpc_score = tumor_score + int(form.age.data) + int(form.status.data) + int(form.metastasis.data) + int(form.protein_levels.data)
+        sins_score = int(form.localization.data) + int(form.pain.data) + int(form.bone_lesion.data) + int(form.stability.data) + int(form.compression.data) + int(form.involvement.data)
+        return render_template("prognosis_block.html",nmstpc_score = nmstpc_score,sins_score=sins_score,m1r=risks[0],m3r=risks[1],m6r=risks[2],y1r=risks[3],y2r=risks[4],y4r=risks[5],y8r=risks[6],form=form, tumor_score=tumor_score,encoded_img = encoded_img.decode('utf-8'))
+    return render_template("form.html",form=form,tumor_score = None)
+@app.route("/contact_us")
+def contact_us():
+    return render_template("contact_us.html")
+
+if __name__ == "__main__":
+    app.run()

gerincmet/prog_calc/prog_calc/static/style.css

@@ -0,0 +1,137 @@
+body {
+  margin: 0;
+  padding: 0;
+  font-family: Calibri, Candara, Segoe, "Segoe UI", Optima, Arial, sans-serif;
+  color: #808080;
+}
+/*
+ * Formatting the header area
+ */
+header {
+  padding: 10px 0px 100px 0px;
+  background-color: #ffffff;
+  height: 35px;
+  width: 1200px;
+  opacity: .9;
+  margin: 0 auto;
+  border-style: hidden hidden hidden hidden;
+  -webkit-border-radius: 6px;
+    -moz-border-radius: 6px;
+        border-radius: 6px;
+}
+header div.container {
+  width: 1200px;
+  margin-top: 10px;
+}
+
+header img.head {
+  position: absolute;
+  z-index: -5;
+}
+
+header h1.logo {
+  margin-top: 65px;
+  margin-left: 175px;
+  font-family: 'neos', Arial, Verdana, Helvetica;
+  font-size: 1.6em;
+  text-transform: uppercase;
+  float: left;
+}
+
+/*
+ * Centering the body content #F0801A
+ */
+.container {
+  width: 1200px;
+  margin: 0 auto;
+}
+div.home {
+  padding: 10px 10px 10px 10px;
+  background-color: #ffffff;
+  -webkit-border-radius: 6px;
+     -moz-border-radius: 6px;
+          border-radius: 6px;
+}
+
+.result_image {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+  width: 70%;
+  -webkit-border-radius: 6px;
+     -moz-border-radius: 6px;
+          border-radius: 6px;
+}
+
+.emk_logo {
+  -webkit-border-radius: 6px;
+     -moz-border-radius: 6px;
+          border-radius: 6px;
+}
+
+hr {
+  border: 1px solid #808080;
+  border-radius: 0px;
+}
+
+div.about {
+  padding: 10px 10px 10px 10px;
+  background-color: #808080;
+  color: white;
+  -webkit-border-radius: 6px;
+     -moz-border-radius: 6px;
+          border-radius: 6px;
+}
+
+h2 {
+  font-size: 1.7em;
+  margin-top: 10px;
+  margin-bottom: 10px;
+  text-align: left;
+  letter-spacing: -2px;
+  color: #F0801A;
+}
+h3 {
+  font-size: 1.5em;
+  font-weight: 100;
+  margin-top: 0px;
+  margin-bottom: 0px;
+  text-align: left;
+  letter-spacing: -1px;
+  color: #3873BA;
+}
+h3.about {
+  color: white;
+}
+
+.menu {
+  float: right;
+  margin-top: -105px;
+  margin-right: 0px;
+}
+.menu li {
+  display: inline;
+}
+.menu li + li {
+  margin-left: 10px;
+}
+.menu li a {
+  color: #3873BA;
+  background-color: transparent;
+  text-decoration: none;
+}
+.menu li a:visited {
+  color: #3873BA;
+  background-color: transparent;
+  text-decoration: none;
+}
+.menu li a:hover {
+  color: #F0801A;
+  background-color: transparent;
+  text-decoration: none;
+}
+.menu li a:active {
+  color: #F0801A;
+  background-color: transparent;
+  text-decoration: none;
+}

gerincmet/prog_calc/prog_calc/templates/contact_us.html

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+{% extends "main.html" %}
+
+{% block content %}
+    <div class="container"><div class="home">
+        <p>A weboldallal kapcsolatos problémákat a <a href="mailto:baskayj@student.elte.hu">baskayj@student.elte.hu</a> címen jelezzék.</p>
+    </div></div>
+{% endblock %}

gerincmet/prog_calc/prog_calc/templates/form.html

@@ -0,0 +1,60 @@
+{% extends "main.html" %}
+
+{% block content %}
+    <div class="container"><div class="home">
+    <form action="" method="post" novalidate>
+
+        {{ form.hidden_tag() }}
+        <p>
+            <h3>Prognosztikai faktorok</h3>
+            {{ form.primer_tumor.label }}{% if not tumor_score == None %}: <b style="color:red">{{ tumor_score }} pont</b>{% endif %}<br>
+            {{ form.primer_tumor() }}
+        </p>
+        <p>
+            {{ form.age.label }}{% if not form.age.data == None %}: <b style="color:red">{{ form.age.data }} pont</b>{% endif %}<br>
+            {{ form.age() }}
+        </p>
+        <p>
+            {{ form.status.label }}{% if not form.status.data == None %}: <b style="color:red">{{ form.status.data }} pont</b>{% endif %}<br>
+            {{ form.status() }}
+        </p>
+        <p>
+            {{ form.metastasis.label }}{% if not form.metastasis.data == None %}: <b style="color:red">{{ form.metastasis.data }} pont</b>{% endif %}<br>
+            {{ form.metastasis() }}
+        </p>
+        <p>
+            {{ form.protein_levels.label }}{% if not form.protein_levels.data == None %}: <b style="color:red">{{ form.protein_levels.data }} pont</b>{% endif %}<br>
+            {{ form.protein_levels() }}
+        </p>
+        <p>
+            <h3>SINS (Spinal Instability Neoplastic Score)<sup>1</sup></h3>
+            {{ form.localization.label }}{% if not form.localization.data == None %}: <b style="color:red">{{ form.localization.data }} pont</b>{% endif %}<br>
+            {{ form.localization() }}
+        </p>
+        <p>
+            {{ form.pain.label }}{% if not form.pain.data == None %}: <b style="color:red">{{ form.pain.data }} pont</b>{% endif %}<br>
+            {{ form.pain() }}
+        </p>
+        <p>
+            {{ form.bone_lesion.label }}{% if not form.bone_lesion.data == None %}: <b style="color:red">{{ form.bone_lesion.data }} pont</b>{% endif %}<br>
+            {{ form.bone_lesion() }}
+        </p>
+        <p>
+            {{ form.stability.label }}{% if not form.stability.data == None %}: <b style="color:red">{{ form.stability.data }} pont</b>{% endif %}<br>
+            {{ form.stability() }}
+        </p>
+        <p>
+            {{ form.compression.label }}{% if not form.compression.data == None %}: <b style="color:red">{{ form.compression.data }} pont</b>{% endif %}<br>
+            {{ form.compression() }}
+        </p>
+        <p>
+            {{ form.involvement.label }}{% if not form.involvement.data == None %}: <b style="color:red">{{ form.involvement.data }} pont</b>{% endif %}<br>
+            {{ form.involvement() }}
+        </p>
+        <p>
+            {{ form.submit() }}
+        </p>
+    </form>
+    </div>
+    {% block results %}{% endblock %}
+{% endblock %}

gerincmet/prog_calc/prog_calc/templates/main.html

@@ -0,0 +1,46 @@
+<!doctpye html>
+<html lang="hu">
+<head>
+    <meta charset="UTF-8">
+    <meta http-equiv="X-Clacks-Overhead" content="GNU Terry Pratchett" />
+    <title>OMIII MGPK</title>
+    <link rel="stylesheet" type="text/css" href="{{url_for('static',filename = 'style.css')}}">
+</head>
+<body>
+    <header>
+        <img src="{{url_for('static',filename='head.jpg')}}" width="1200" height="138" class="head">
+        <div class="container">
+            <h1 class="logo">
+                Országos Mentális, Ideggyógyászati és Idegsebészeti Intézet
+                Metasztatikus Gerincdaganat Prognózis Kalkulátor
+            </h1>
+            <strong><nav><ul class="menu">
+                    <li><a class="link" href="{{ url_for('index') }}">Kalkulátor</a></li>
+                    <li><a class="link" href="{{ url_for('contact_us') }}">Kapcsolat</a></li>
+                    <li><a onclick="window.print()">Nyomtatás</a></li>
+            </ul></nav></strong>
+        </div>
+    </header>
+    {% block content %}{% endblock %}
+    <div class="container"><div class="about">
+        <p>     <img src="{{url_for('static', filename='sote_logo.png')}}" width="150" height="150">
+                <img src="{{url_for('static', filename='sote_phd.png')}}" width="150" height="150">
+                <img src="{{url_for('static', filename='elte_logo.png')}}" width="150" height="150">
+                <img src="{{url_for('static', filename='sote_emk.png')}}" width="150" height="150" class="emk_logo">
+
+        </p>
+        <p>
+            Amennyiben kutatásunkat, pontrendszerünket hasznosnak találta, kérjük hivatkozza kéziratainkat a további fejlődés elősegítése céljából.
+            <ul>
+                <li>Czigléczki G., Mezei T., Pollner P., Horváth A., Banczerowski P. (2018) <i>Prognostic factors of surgical complications and overall survival of patients with metastatic spinal tumor</i> World Neurosurgery, 113:e20-e28. DOI:<a href="https://doi.org/10.1016/j.wneu.2018.01.092">10.1016/j.wneu.2018.01.092</a></li>
+                <li>Pollner P.*, Horváth A.*, Mezei T., Banczerowski P., Czigléczki G. (2018) <i>Analysis of four scoring systems for the prognosis of patients with metastasis of the vertebral column</i> World Neurosurgery, 112:e675-e682. DOI:<a href="https://doi.org/10.1016/j.wneu.2018.01.124">10.1016/j.wneu.2018.01.124</a></li>
+                <li>Mezei T., Horváth A., Pollner P., Czigléczki G., Banczerowski P. (2020) <i>Research on the predicting power of the revised Tokuhashi system: how much time can surgery give to patients with short life expectancy?</i> International Journal of Clinical Oncology, 25 (4):755-764.  DOI:<a href="https://doi.org/10.1007/s10147-019-01612-w">10.1007/s10147-019-01612-w</a></li>
+            </ul>
+        </p>
+        <p>
+            <h3 class="about">Felhasznált Irodalom</h3>
+        [1.] Fisher, C.G. et al. (2010) <i>A novel classification system for spinal instability in neoplastic disease: an evidence-based approach and expert consensus from the Spine Oncology Study Group.</i> Spine (Phila Pa 1976) 35 (22):E1221-1229. DOI:<a href="https://doi.org/10.1097/brs.0b013e3181e16ae2">10.1097/BRS.0b013e3181e16ae2</a>
+        </p>
+    </div></div>
+</body>
+</html>

gerincmet/prog_calc/prog_calc/templates/prognosis_block.html

@@ -0,0 +1,61 @@
+{% extends "form.html" %}
+
+{% block results %}
+    <hr>
+    <h2>Eredmény</h2>
+    <div class="container"><div class="home">
+    <h3>Prognosztikai csoportok</h3>
+    {% if 0 <= nmstpc_score <= 17 %}
+        <div><p><b>Kedvező életkilátású csoport</b> <i>(0-17: <span style="color:red">{{ nmstpc_score }} pont</span>)</i> Műtéti kezelés javasolt. A radiológiai morfológia alapján választandó meg a pontos műtéttechnika, javasoljuk a maximálisan lehetséges radikális eltávolítást („excízionális műtét").</p></div>
+    {% elif 18 <= nmstpc_score <= 24 %}
+        <div><p><b>Közepes életkilátású csoport</b> <i>(18-24: <span style="color:red">{{ nmstpc_score }} pont</span>)</i> Műtéti ellátás javasolt, azonban „kevésbé invazív beavatkozást” preferálandó ebben a csoportban.</p></div>
+    {% elif 25 <= nmstpc_score <= 39 %}
+        <div><p><b>Gyenge életkilátású csoport</b> <i>(24-39: <span style="color:red">{{ nmstpc_score }} pont</span>)</i> Elsősorban palliatív onko-radioterápia javasolt, amennyiben minimal invazív beavatkozással jelentős funkciójavulást, életminőség növekedést, fájdalomcsillapítást érhetünk el, abban az esetben műtéti ellátás is szóba jön.</p></div>
+    {% else %}
+        <div><p>ERROR: nmstpc_score > 39 </p></div>
+    {% endif %}
+    <p>Stabilizáció szükségességének megítéléséhez SINS nyújthat segítséget.</p>
+    <h3>A feltételezett instabilitás mértéke</h3>
+    {% if 0 <= sins_score <= 6 %}
+        <div><p><b>Stabil gerincszakasz.</b> <i>(0-6: <span style="color:red">{{ sins_score }} pont</span>)</i></p></div>
+    {% elif 7 <= sins_score <= 12 %}
+        <div><p><b>Pontenciálisan instabil gerincszakasz.</b> <i>(7-12: <span style="color:red">{{ sins_score }} pont</span>)</i></p></div>
+    {% elif 13 <= sins_score <= 18 %}
+        <div><p><b>Instabil gerincszakasz.</b> <i>(13-18: <span style="color:red">{{ sins_score }} pont</span>)</i></p></div>
+    {% else %}
+        <div><p>ERROR: sins_score > 18 </p></div>
+    {% endif %}
+    <h3> Halál kockázata </h3>
+        <table>
+            <tr>
+                <td>1 hónap:</td>
+                <td><b>{{ m1r }} %</b></td>
+            </tr>
+            <tr>
+                <td>3 hónap:</td>
+                <td><b>{{ m3r }} %</b></td>
+            </tr>
+            <tr>
+                <td>6 hónap:</td>
+                <td><b>{{ m6r }} %</b></td>
+            </tr>
+            <tr>
+                <td>1 év:</td>
+                <td><b>{{ y1r }} %</b></td>
+            </tr>
+            <tr>
+                <td>2 év:</td>
+                <td><b>{{ y2r }} %</b></td>
+            </tr>
+            <tr>
+                <td>4 év:</td>
+                <td><b>{{ y4r }} %</b></td>
+            </tr>
+            <tr>
+                <td>8 év:</td>
+                <td><b>{{ y8r }} %</b></td>
+            </tr>
+        </table>
+    <img src="data:image/png;base64,{{ encoded_img }}" class="result_image">
+    </div></div>
+{% endblock %}

gerincmet/prog_calc/prog_calc/tumor_type_to_score.py

@@ -0,0 +1,33 @@
+primer_tumor_score = [
+        (0, 1),
+        (0, 2),
+        (6, 3),
+        (6, 4),
+        (12, 5),
+        (12, 6),
+        (12, 7),
+        (12, 8),
+        (12, 9),
+        (12, 10),
+        (12, 11),
+        (12, 12),
+        (12, 13),
+        (12, 14),
+        (12, 15),
+        (12, 16),
+        (12, 17),
+        (12, 18),
+        (12, 19),
+        (19, 20),
+        (19, 21),
+        (19, 22),
+        (19, 23),
+        (19, 24),
+        (19, 25)]
+
+def type_to_score(typ):
+        score = 0
+        for i in range(len(primer_tumor_score)):
+                if typ == primer_tumor_score[i][1]:
+                        score = primer_tumor_score[i][0]
+        return int(score)

locale.gen

@@ -0,0 +1 @@
+hu_HU.UTF-8 UTF-8

prog-calc.conf

@@ -0,0 +1,23 @@
+<VirtualHost *:80>
+	ServerAdmin baskayj
+	DocumentRoot /var/www/html/gerincmet
+
+WSGIDaemonProcess prog_calc python-home=/var/www/html/gerincmet/prog_calc/prog_calc/venv python-path=/var/www/html/gerincmet/prog_calc/prog_calc:/var/www/html/gerincmet/prog_calc/prog_calc/venv/local/lib/python3.9/site-packages threads=5
+#    WSGIScriptAlias /omiiimgpk /var/www/html/gerincmet/prog_calc/prog_calc.wsgi
+    WSGIScriptAlias /gerincmet /var/www/html/gerincmet/prog_calc/prog_calc.wsgi
+	WSGIApplicationGroup %{GLOBAL}
+	<Directory /var/www/html/gerincmet/prog_calc/prog_calc/>
+             WSGIProcessGroup prog_calc
+             WSGIApplicationGroup %{GLOBAL}
+             Order deny,allow
+             Allow from all 
+        </Directory>
+	Alias /static /var/www/html/gerincmet/prog_calc/prog_calc/static
+        <Directory /var/www/html/gerincmet/prog_calc/prog_calc/static/>
+                Order allow,deny
+                Allow from all
+        </Directory>
+	ErrorLog ${APACHE_LOG_DIR}/error.log
+	LogLevel warn
+	CustomLog ${APACHE_LOG_DIR}/access.log combined
+</VirtualHost>

requirements.txt

@@ -0,0 +1,36 @@
+Flask==2.0.2
+Flask-WTF==1.0.0
+Jinja2==3.0.3
+MarkupSafe==2.0.1
+Pillow==8.4.0
+WTForms==3.0.0
+Werkzeug==2.0.2
+altgraph==0.17.2
+astor==0.8.1
+autograd==1.3
+autograd-gamma==0.5.0
+click==8.0.3
+cycler==0.11.0
+fonttools==4.28.1
+formulaic==0.2.4
+future==0.18.2
+interface-meta==1.2.4
+itsdangerous==2.0.1
+kiwisolver==1.3.2
+lifelines==0.26.3
+matplotlib==3.5.0
+numpy==1.21.4
+packaging==21.2
+pandas==1.3.4
+pip==20.0.2
+pyinstaller==4.7
+pyinstaller-hooks-contrib==2021.3
+pyparsing==2.4.7
+python-dateutil==2.8.2
+pytz==2021.3
+scipy==1.7.2
+setuptools==44.0.0
+setuptools-scm==6.3.2
+six==1.16.0
+tomli==1.2.2
+wrapt==1.13.3

start-apache.sh

@@ -0,0 +1,9 @@
+#!/bin/sh
+
+set -e
+
+. /etc/apache2/envvars
+ulimit -n 8192
+chown root:www-data /var/lock/apache2
+chown -R www-data:www-data /var/www/html
+exec /usr/sbin/apache2 -k start -DFOREGROUND