added test codes

.gitignore

@@ -19,3 +19,8 @@ dump.rdb
 celery_flower.sh
 .env
 backup.sql
+nginx.conf
+./static/*
+app/static/bclconvert_report_v0.02.html
+app/static/MultiQC_lane1.html
+app/static/MultiQC_lane1.html:Zone.Identifier

app/raw_analysis_view.py

@@ -1,3 +1,4 @@
+import logging, tempfile, os
 from io import BytesIO
 from .models import RawAnalysis, RawMetadataModel
 from flask_appbuilder import ModelView
@@ -6,6 +7,17 @@
 from flask_appbuilder.actions import action
 from flask_appbuilder.models.sqla.interface import SQLAInterface
 from . import db
+from . import celery
+from .raw_analysis.raw_analysis_util import validate_analysis_json
+
+@celery.task(bind=True)
+def async_validate_analysis_yaml(self, id_list):
+    try:
+        pass
+    except Exception as e:
+        logging.error(
+            "Failed to run celery job, error: {0}".\
+                    format(e))
 
 class RawAnalysisView(ModelView):
     datamodel = SQLAInterface(RawAnalysis)
@@ -16,6 +28,7 @@ class RawAnalysisView(ModelView):
     base_filters = [
         ["status", FilterInFunction, lambda: ["UNKNOWN", "FAILED"]]]
     base_order = ("raw_analysis_id", "desc")
+
     @action("validate_and_submit_analysis", "Validate and upload analysis", confirmation="Validate analysis design?", icon="fa-rocket")
     def validate_and_submit_analysis(self, item):
         analysis_list = list()

app/templates/iframe.html

@@ -0,0 +1,6 @@
+{% extends "appbuilder/base.html" %}
+
+{% block content %}
+<h3 align="left"><a href="/sampleindexview/list/">Go Back to run list</a></h3>
+<iframe src="{{url}}" frameborder='0' noresize='noresize' style='position: absolute; background: transparent; width: 100%; height:100%;' title="description" frameborder="0"></iframe> 
+{% endblock %}

docker-compose.yaml

@@ -7,6 +7,8 @@ services:
         image: mysql:5.7
         env_file: env
         restart: always
+        ports:
+          - "3306:3306"
         volumes:
           - /home/vmuser/mysqlappdb:/var/lib/mysql:rw
         container_name: portal_db
@@ -22,7 +24,7 @@ services:
         image: igfportal:v0.0.1
         env_file: env
         ports:
-          - "8080:8080"
+          - 8080:8080
         restart: always
         links:
           - portal_db
@@ -33,8 +35,26 @@ services:
         volumes:
           - /home/vmuser/github/IGFPortal:/github/IGFPortal:ro
           - /home/vmuser/github/ssl:/SSL:ro
+          - ./static:/data/static:rw
         container_name: webserver
-        command: ["flask run -h 0.0.0.0 -p 8080 --cert=/SSL/cert.pem --key=/SSL/key.pem --reload --debugger --without-threads"]
+        command: ["flask run -h 0.0.0.0 -p 8080 --reload --debugger --without-threads"]
+        networks:
+          - portal_network
+    nginx:
+        image: nginx:1.23.3
+        ports:
+          - "80:80"
+          - "443:443"
+        links:
+          - webserver
+        depends_on:
+          - webserver
+        volumes:
+          - /home/vmuser/github/ssl:/SSL:ro
+          - /home/vmuser/github/IGFPortal/nginx.conf:/etc/nginx/nginx.conf:ro
+          - /tmp/nginx:/var/nginx/:rw
+          - ./static:/data/static:rw
+        container_name: nginx
         networks:
           - portal_network
     celery_worker1:
@@ -81,4 +101,4 @@ services:
         restart: always
         container_name: adminer
         networks:
-          - portal_network
+          - portal_network

nginx_template.conf

@@ -0,0 +1,63 @@
+worker_processes 2;
+user nobody nogroup;
+
+error_log  /var/nginx/error.log warn;
+pid /var/nginx/run/nginx.pid;
+
+events {
+  worker_connections 1024; # increase if you have lots of clients
+  accept_mutex off; # set to 'on' if nginx worker_processes > 1
+  # 'use epoll;' to enable for Linux 2.6+
+  # 'use kqueue;' to enable for FreeBSD, OSX
+}
+
+http {
+  include mime.types;
+  # fallback in case we can't determine a type
+  default_type application/octet-stream;
+  access_log /var/nginx/access.log combined;
+  sendfile on;
+
+  ssl_session_cache   shared:SSL:10m;
+  ssl_session_timeout 10m;
+
+  upstream app_server {
+    server webserver:8080 fail_timeout=0;
+  }
+
+  server {
+    # if no Host match, close the connection to prevent host spoofing
+    listen 80 default_server;
+    return 444;
+  }
+
+  server {
+    # Redirect http to https
+    listen 80 default_server;
+    server_name localhost;
+    return 301 https://localhost$request_uri;
+  }
+
+  server {
+    listen              443 ssl;
+    ssl_certificate     /SSL/cert.pem;
+    ssl_certificate_key /SSL/key.pem;
+    keepalive_timeout   70s;
+    server_name localhost;
+    location / {
+      # checks for static file, if not found proxy to app
+      try_files $uri @proxy_to_app;
+    }
+    location @proxy_to_app {
+      proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+      proxy_set_header X-Forwarded-Proto $scheme;
+      proxy_set_header Host $http_host;
+      # we don't want nginx trying to do something clever with
+      # redirects, we set the Host: header above already.
+      proxy_redirect off;
+      proxy_pass http://app_server;
+    }
+
+    error_page 500 502 503 504 /500.html;
+  }
+}

tests/test_app.py

@@ -0,0 +1,36 @@
+import os, unittest, tempfile
+from flask.testing import FlaskClient
+from app import app, db, appbuilder
+from flask import Flask, g, url_for
+
+
+class TestCase1(unittest.TestCase):
+    def setUp(self):
+        app.app_context().push()
+        app.config.from_object("flask_appbuilder.tests.config_api")
+        db.create_all()
+        self.client = app.test_client(use_cookies=True)
+        app.appbuilder.sm.add_user(
+            "admin",
+            "admin",
+            "user",
+            "admin@fab.org",
+            "Admin",
+            "password")
+
+
+    def tearDown(self):
+        self.appbuilder = None
+        db.drop_all()
+
+    def test_access_server(self):
+        uri = "/"
+        rv = self.client.get(uri)
+        #self.assertEqual(rv.status_code, 200)
+        print(rv.status_code)
+
+
+
+
+if __name__ == '__main__':
+  unittest.main()