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-rw-r--r--README-wqflask.txt31
-rw-r--r--wqflask/other_config/nginx.conf104
-rw-r--r--wqflask/requirements.txt1
-rw-r--r--wqflask/wqflask/__init__.py3
-rw-r--r--wqflask/wqflask/search_results.py2
5 files changed, 139 insertions, 2 deletions
diff --git a/README-wqflask.txt b/README-wqflask.txt
new file mode 100644
index 00000000..fdade7fa
--- /dev/null
+++ b/README-wqflask.txt
@@ -0,0 +1,31 @@
+This readme concerns the directory wqflask - an officially sanctioned fork of the main GeneNetwork
+code. It's still very early in the process - but we eventually want to port all of the code
+in GeneNetwork to Flask and Jinja2. For more information about the project in general, see
+the file README.md.
+
+For more information about the port to Flask, please keep reading.
+
+*************************
+
+Requirements:
+
+* Python 2.7
+
+* virtualenv 1.7.1.2 or later
+
+* Other python dependencies are listed in the file wqflask/requirements.txt
+
+**************************
+
+Installation:
+
+We highly recommend you create a virtual enviornment called ve27 in your home directory.
+
+> cd ~
+
+> virtualenv ve27
+
+> source ~/ve27/bin/activate
+
+> pip install -r ~/gene/wqflask/requirements.txt
+(Or replace gene with the name of the directory holding your repository)
diff --git a/wqflask/other_config/nginx.conf b/wqflask/other_config/nginx.conf
new file mode 100644
index 00000000..93e6af10
--- /dev/null
+++ b/wqflask/other_config/nginx.conf
@@ -0,0 +1,104 @@
+
+#user nobody;
+worker_processes 1;
+
+#error_log logs/error.log;
+#error_log logs/error.log notice;
+#error_log logs/error.log info;
+
+#pid logs/nginx.pid;
+
+
+events {
+ worker_connections 1024;
+}
+
+
+http {
+ include mime.types;
+ default_type application/octet-stream;
+
+ #log_format main '$remote_addr - $remote_user [$time_local] "$request" '
+ # '$status $body_bytes_sent "$http_referer" '
+ # '"$http_user_agent" "$http_x_forwarded_for"';
+
+ #access_log logs/access.log main;
+
+ sendfile on;
+ #tcp_nopush on;
+
+ #keepalive_timeout 0;
+ keepalive_timeout 65;
+
+ gzip on;
+
+ server {
+ # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
+ listen 80;
+
+ server_name _;
+
+ access_log /var/log/nginx/access.log;
+ error_log /var/log/nginx/error.log;
+
+ location ^~ /css/ {
+ root /home/sam/gene/wqflask/wqflask/static/;
+ }
+
+ location ^~ /javascript/ {
+ root /home/sam/gene/wqflask/wqflask/static/;
+ }
+
+ location ^~ /images/ {
+ root /home/sam/gene/wqflask/wqflask/static/;
+ }
+
+ location / {
+ proxy_pass http://127.0.0.1:5000/;
+ proxy_redirect off;
+
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+ }
+
+ }
+
+
+ # another virtual host using mix of IP-, name-, and port-based configuration
+ #
+ #server {
+ # listen 8000;
+ # listen somename:8080;
+ # server_name somename alias another.alias;
+
+ # location / {
+ # root html;
+ # index index.html index.htm;
+ # }
+ #}
+
+
+ # HTTPS server
+ #
+ #server {
+ # listen 443;
+ # server_name localhost;
+
+ # ssl on;
+ # ssl_certificate cert.pem;
+ # ssl_certificate_key cert.key;
+
+ # ssl_session_timeout 5m;
+
+ # ssl_protocols SSLv2 SSLv3 TLSv1;
+ # ssl_ciphers HIGH:!aNULL:!MD5;
+ # ssl_prefer_server_ciphers on;
+
+ # location / {
+ # root html;
+ # index index.html index.htm;
+ # }
+ #}
+
+}
diff --git a/wqflask/requirements.txt b/wqflask/requirements.txt
index caa5d61e..684722aa 100644
--- a/wqflask/requirements.txt
+++ b/wqflask/requirements.txt
@@ -2,5 +2,4 @@ Flask==0.8
Jinja2==2.6
MySQL-python==1.2.3
Werkzeug==0.8.3
-pyXLWriter==0.4a3
wsgiref==0.1.2
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index d0484c83..a6119dcc 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -1,5 +1,8 @@
from __future__ import absolute_import, division, print_function
+import sys
+print("sys.path is:", sys.path)
+
from flask import Flask
from utility import formatting
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index c100645e..9ec676b8 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -16,7 +16,7 @@ import cPickle
import re
from math import *
import time
-import pyXLWriter as xl
+#import pyXLWriter as xl
#import pp - Note from Sam: is this used?
import math
import datetime