Merge branch 'release/1.0.9'

app.py

@@ -4,10 +4,11 @@
 
 from flask import Flask, url_for, redirect, \
     render_template, session, request, Response, \
-    flash, get_flashed_messages
+    flash, get_flashed_messages, jsonify
 from flask_sqlalchemy import SQLAlchemy
 from flask_login import LoginManager, login_required, login_user, \
     logout_user, current_user, UserMixin
+from decode_cookie import decodeFlaskCookie
 from elasticsearch import Elasticsearch
 from elasticsearch_dsl import Search
 from models import get_all
@@ -175,7 +176,7 @@ def burndown():
     total_jobs = [int(x.total_jobs) for x in get_all()]
     finished_jobs = [int(x.finished_jobs) for x in get_all()]
     captured_dates = [x.captured_date for x in get_all()]
-    return (total_jobs, finished_jobs, captured_dates)
+    return total_jobs, finished_jobs, captured_dates
 
 
 @app.route('/')
@@ -186,6 +187,54 @@ def index():
     return html_rend('index')
 
 
+def parse_token():
+    """
+    Parses the Authorization token from the request header
+    :return: the bearer and token string
+    """
+    authorization_header = request.headers.get("Authorization", None)
+    assert authorization_header is not None, "No Authorization header in the request"
+    parts = authorization_header.split()
+    # Return the bearer and token string
+    return parts[0], parts[1]
+
+
+@app.route('/check_session/<cookie>')
+def check_session(cookie):
+    if not request.headers.get("Authorization", None):
+        return jsonify({"error": "No Authorization header in the request"})
+    else:
+        # Make sure the auth token is the right one
+        try:
+            bearer, auth_token = parse_token()
+            assert bearer == "Bearer", "Authorization must start with Bearer"
+            assert auth_token == os.getenv("LOG_IN_TOKEN", 'ITS_A_SECRET!')
+        except AssertionError as e:
+            response = {
+                'error': e.message
+            }
+            return jsonify(response)
+        # Now look at the cookie
+        decoded_cookie = decodeFlaskCookie(os.getenv('SECRET_KEY', 'somethingsecret'), cookie)
+        try:
+            assert (decoded_cookie.viewkeys()
+                    >= {'user_id', '_fresh'}), "Cookie not valid; does not have necessary fields"
+            assert (User.query.get(int(decoded_cookie['user_id'])) is not None), "No user with {}".format(
+                decoded_cookie['user_id'])
+            logged_user = User.query.get(int(decoded_cookie['user_id']))
+            response = {
+                'email': logged_user.email,
+                'name': logged_user.name,
+                'avatar': logged_user.avatar,
+                'redwood_token': logged_user.redwood_token
+            }
+        except AssertionError as e:
+            response = {
+                'error': e.message
+            }
+        return jsonify(response)
+
+
 @app.route('/<name>.html')
 def html_rend(name):
     """
@@ -215,6 +264,8 @@ def html_rend(name):
                                total_jobs=total_jobs,
                                finished_jobs=finished_jobs,
                                captured_dates=captured_dates)
+    if name == 'boardwalk':
+        return boardwalk()
     return render_template(name + '.html')
 
 
@@ -247,6 +298,11 @@ def html_rend_file_browser():
     return redirect(url_for('html_rend', name='file_browser'))
 
 
+@app.route('/boardwalk')
+def boardwalk():
+    return redirect(url_for('boardwalk'))
+
+
 @app.route('/token')
 def token():
     """

bdPlots.py

@@ -43,3 +43,7 @@
         "{}:{}".format(x.captured_date.hour,
                        x.captured_date.minute)) for x in get_all()]
 print "Total Jobs: {} Finished Jobs: {}".format(total_jobs, finished_jobs)
+
+session.close_all()
+engine.dispose()
+

decode_cookie.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+from flask.sessions import SecureCookieSessionInterface
+from itsdangerous import URLSafeTimedSerializer
+
+# Adapted from here: https://gist.github.com/aescalana/7e0bc39b95baa334074707f73bc64bfe
+
+
+class SimpleSecureCookieSessionInterface(SecureCookieSessionInterface):
+    # Override method
+    # Take secret_key instead of an instance of a Flask app
+    def get_signing_serializer(self, secret_key):
+        if not secret_key:
+            return None
+        signer_kwargs = dict(
+            key_derivation=self.key_derivation,
+            digest_method=self.digest_method
+        )
+        return URLSafeTimedSerializer(secret_key, salt=self.salt,
+                                      serializer=self.serializer,
+                                      signer_kwargs=signer_kwargs)
+
+
+def decodeFlaskCookie(secret_key, cookieValue):
+    sscsi = SimpleSecureCookieSessionInterface()
+    signingSerializer = sscsi.get_signing_serializer(secret_key)
+    return signingSerializer.loads(cookieValue)
+
+
+# Keep in mind that flask uses unicode strings for the
+# dictionary keys
+def encodeFlaskCookie(secret_key, cookieDict):
+    sscsi = SimpleSecureCookieSessionInterface()
+    signingSerializer = sscsi.get_signing_serializer(secret_key)
+    return signingSerializer.dumps(cookieDict)
+
+

models.py

@@ -6,6 +6,7 @@
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import sessionmaker
 from sqlalchemy import create_engine
+from time import sleep
 
 Base = declarative_base()
 
@@ -28,6 +29,11 @@ def initialize_table():
     session = sessionmaker()
     session.configure(bind=engine)
     Base.metadata.create_all(engine)
+    # We have sleep here because it appears that the call to create call is non-blocking
+    # so we need to wait a little bit for the subprocess to create the table.
+    sleep(5)
+    session.close_all()
+    engine.dispose()
 
 
 def get_all():
@@ -40,5 +46,8 @@ def get_all():
     session = sessionmaker()
     session.configure(bind=engine)
     s = session()
-    q = s.query(Burndown).order_by(Burndown.captured_date.asc()).all()
-    return q
+    query_object = s.query(Burndown).order_by(Burndown.captured_date.asc()).all()
+    query_list = [x for x in query_object]
+    session.close_all()
+    engine.dispose()
+    return query_list

templates/about.html

@@ -41,7 +41,7 @@ <h1 class="md-display-1" style="color:#FF6B6B;">Staff</h1>
 									</div>
 								</div>
 								<div class="flex-75" style="padding:0px">
-									<p class="md-body-1" style="margin-top:0px"> Carlos is a Software Engineer at the Computational Genomics Platform (CGP). He has been heavily involved in DevOps work, focused on integration and deployment using technologies such as Docker and docker-compose. He also worked on the web service that powers the Platform's file browser. Carlos has a B.A. in Computer Science and a B.S. in Molecular, Cell, &amp; Developmental Biology from UCSC.</p>
+									<p class="md-body-1" style="margin-top:0px"> Carlos is a Software Engineer at the Computational Genomics Platform (CGP). He has been heavily involved in DevOps work, focused on integration and deployment using technologies such as Docker and docker-compose. He worked on the web service that powers the Platform's file browser and has been involved in prototyping a file viewer for HCA (Human Cell Atlas). His work uses Python, Flask/Chalice, and Elasticsearch. Carlos has a B.A. in Computer Science and a B.S. in Molecular, Cell, &amp; Developmental Biology from UCSC.</p>
 								</div>
 							</div>
 

templates/base.html

@@ -78,7 +78,7 @@
 								<a href="file_browser.html">Browser</a>
 							</cc-toolbar-nav-item>
 							<cc-toolbar-nav-item {% block page_Boardwalk %}{% endblock  %}>
-								<a href="boardwalk.html">Boardwalk</a>
+								<a href="boardwalk">Boardwalk</a>
 							</cc-toolbar-nav-item>
 							<cc-toolbar-nav-item {% block page_Redwood %}{% endblock  %}>
 								<a href="redwood.html">Redwood</a>