Merge branch 'develop' of github-as-indera:ctsit/redi-dropper-client …

…into develop

CHANGELOG.md

@@ -24,6 +24,7 @@
 
 
 ## [0.0.3a] - 2015-08-27
+
 ### Added
 * Add sample config files for deploying two application instances 
 Paths ==> `/alz` and `/onefl` (Andrei Sura)

app/deploy/fabfile.py

@@ -485,7 +485,9 @@ def restart_wsgi_app():
 def check_app():
     """cURL the target server to check if the app is up"""
     require('environment', provided_by=[production, staging])
-    local('curl -sk https://%(project_url)s | grep "Version " ' % env)
+    local('curl -sk https://%(project_url)s | grep "Version " '
+          ' | grep -oE "[0-9.]{1,2}[0-9.]{1,2}[0-9a-z.]{1,4}" | head -1 ' % env)
+
 
 
 def print_project_repo():

app/redidropper/models/user_entity.py

@@ -67,6 +67,8 @@ def is_active(self):
 
     def is_expired(self):
         """ An user can be blocked by setting expiration date to yesterday"""
+        if self.access_expires_at is None:
+            return False
         return self.access_expires_at < datetime.today()
 
     def is_anonymous(self):

app/redidropper/static/css/parallax.css

@@ -141,3 +141,34 @@ This stylesheet and the associated (x)html may be modified in any way to fit you
 #support button {
   color: #FFFFFF;
 }
+
+/*So that all content and icon is visible on smaller screens*/
+@media all and (max-width: 1000px) {
+  #home {
+    height: 600px;
+  }
+  #about {
+    height: 600px;
+  }
+  #information {
+    height: 600px;
+  }
+  #services {
+    height: 600px;
+  }
+  #gettingstarted {
+    height: 600px;
+  }
+  #faq {
+    height: 600px;
+  }
+  #support {
+    height: 600px;
+  }
+  #image2 {
+    height: 600px;
+  }
+  #image3 {
+    height: 600px;
+  }
+}

app/redidropper/static/js/sidebar.js

@@ -5,8 +5,8 @@ $(document).ready(function() {
         $("#wrapper").toggleClass("toggled");
         var icon = $(this).parent().find(".fa")
         if (icon.hasClass('fa-angle-left'))
-            icon.removeClass('fa-angle-left').addClass("fa-angle-right");
+            icon.removeClass('fa-angle-left').addClass("fa-bars");
         else
-            icon.removeClass('fa-angle-right').addClass("fa-angle-left");
+            icon.removeClass('fa-bars').addClass("fa-angle-left");
     });
 });

docs/functional_specs.md

@@ -0,0 +1,52 @@
+# Functional Specification for the REDI-Dropper Application
+
+## Authors
+
+* Andrei Sura <asura@ufl.edu>
+* Kevin Hanson <kshanson@ufl.edu>
+* Philip Chase <pbc@ufl.edu>
+* Christopher P. Barnes <cpb@ufl.edu>
+
+## Overview
+
+The RED-I Dropper application is a tool where by dynamic data is transferred
+from multiple locations via a modern JavaScript framerwork over encrypted
+channel to storage services for further processing. The application can be
+customized to place datasets into processing environments that provide analysis
+and quanitified data to aggregation points.
+
+
+## Workflow and Use Cases
+
+### Ella gets a MRI scan uploaded with RED-I Dropper for analysis.
+
+Ella is a woman of latin heritage living in Miami, FL. She is a widow living
+with her son-in-law and Daughter. She has undergone a neurocognitive assessment
+with Dr. Miami and now she has been referred to the brain imaging specialists
+at WeCare Hospital to have an MRI brain image performed. A technician conducts
+the MRI image collection process. At the conclusion of which consortium staff
+acquire the images and visit a website that is able to handle image uploads
+potentially 3gb in size per study participant encounter. When the consortium
+staff visits the website they utilize a Shibboleth account to
+authenticate securely to the RED-I Dropper website.  Once logged on, the
+consortium staff see a question asking them which subject goes with the MRI
+scan. They see a list that shows the study participant’s ID.
+
+Once the consortium staff verifies that the subject that was scanned is the
+same as the one in the list they select the study participant. The staff is
+prompted with a <b>file picker</b> where they are able to <b>select
+all images</b> obtained from the MRI process at once and set them to upload.
+Prior to an image upload the RED-I Dropper program <b>checks to see if a folder
+exists</b> on the server for the subjectID and if it doesn't exist
+then the <b>folder is created</b> the moment a file is uploaded. As the image
+begins to upload, a <b>progress bar</b> displays for the upload process and once
+completed they see a message saying “MRI scans for Ella have been uploaded,
+thank you!”
+The RED-I Dropper server then <b>prefixes the file names</b> with a <b>unique
+identifier</b> in the format
+“YYYYMMDD_HHMM_SiteID_SubjectID_5digtSequenceNumber” followed by the
+<b>original file name</b>.
+
+Example:
+original filename: <b>xyz.jpg</b>
+stored filename: 20120101_0123_SiteIDA_SubjectIDB_Sequence123_<b>xyz.jpg</b>

docs/technical_specs.md

@@ -0,0 +1,84 @@
+
+# Work in progress
+
+
+
+Technical Specifications for REDIDropper
+========================================
+
+
+## Software Architecture Considerations
+
+1. **use two repositories**
+
+   One repository is used for the **client** component and the second one for the **server** component
+
+   Advantages:
+      1. develop the UI separately from the server (different language/framework)
+      2. force developers to think about the "Not Breaking the Contract" as defined by the supported API functions
+      3. keep the list of issues related to the UI separate from the Server issues
+
+   Disadvantages:
+      1. can encounter issues with cross-domain requests if the client is deployed on a different server
+      2. forces deployment of two repositories in order to test the application
+      3. forces the need to check two repositories during development in order to keep track of changes
+
+
+2. **use frameworks to allow reusing existing solutions**
+
+   Client Candidates:
+      1. [Angular](https://angularjs.org/)
+      2. [ReactJS](https://github.com/reactjs/react-tutorial) with [Flux](https://github.com/facebook/flux) [comprehensive-guide](http://tylermcginnis.com/reactjs-tutorial-a-comprehensive-guide-to-building-apps-with-react/)
+      3. [Knockout](http://knockoutjs.com/)
+      4. [BackboneJS](http://backbonejs.org/) [blog-posts](https://github.com/jashkenas/backbone/wiki/Tutorials%2C-blog-posts-and-example-sites)
+
+   Server Candidates:
+      1. Python: [Werkzeug](http://werkzeug.pocoo.org/docs/0.9/routing/#), [Flask](http://flask.pocoo.org/docs/0.10/tutorial/), web2py, Tornado, Bottle, CherryPy, Django, Grok, Pylons, Pyjamas, Pyramid
+      2. NodeJS: [Express](http://expressjs.com/starter/basic-routing.html), EmberJS, SailsJS
+      3. PHP: CakePHP, Slim, Laravel, Joomla, Symfony
+      4. Ruby: Sinatra
+
+3. **implement data transfer between the server component and REDCap**
+
+   Candidates:
+      1. [CURL](https://github.com/sburns/advanced-redcap-interfaces/blob/master/slides.md)
+      2. [Pycap](http://pycap.readthedocs.org/en/latest/)
+
+
+4. **use a JS library for implementing the large file upload within the browser**
+
+   Candidates:
+      1. [ng-flow](https://github.com/flowjs/ng-flow) ( [PHP server component](https://github.com/flowjs/flow.js/blob/master/samples/Backend%20on%20PHP.md) )
+      2. [resumable.js](https://github.com/23/resumable.js/blob/master/samples/Backend%20on%20PHP.md)
+      3. [Real ajax uploader](http://www.albanx.com/programing/ajaxupload/?example=2)
+
+
+   @TODO: read http://stackoverflow.com/questions/2502596/python-http-post-a-large-file-with-streaming
+
+
+5. understand shibboleth authorization scheme
+
+![saml2-browser-sso-redirect-post](img/saml.png)
+
+
+6. **choose a server for deployment**
+
+   Candidates:
+      1. [Apache](http://flask.pocoo.org/docs/0.10/deploying/mod_wsgi/)
+      2. [Nginx](https://www.digitalocean.com/community/tutorials/how-to-deploy-python-wsgi-applications-using-uwsgi-web-server-with-nginx) 
+
+         [Servers Comparison](https://www.digitalocean.com/community/tutorials/a-comparison-of-web-servers-for-python-based-web-applications)
+
+
+
+## Flow Charts
+
+![img/flowchart_diagram_redi_dropper_file_upload_process.png](img/flowchart_diagram_redi_dropper_file_upload_process.png)
+
+
+## Creating large test files
+
+<pre>
+   fallocate -l 1G large_file.mri
+   dd if=/dev/zero of=large_file.mri bs=1G count=1
+</pre>