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https://github.com/vsoch/myconnectome-explore

Poral interface for exploration of myconnectome data
https://github.com/vsoch/myconnectome-explore

brain flask flup myconnectome neuro

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Poral interface for exploration of myconnectome data

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README 

        
### myconnectome-explore



This code base provides a flask-driven infrastructure to explore the myconnectome project data, either integrated in the [myconnectome-vm](https://github.com/poldrack/myconnectome-vm) or as a standalone application.



#### myConnectome-vm

If you are interested in reproducing all analyses in your own virtual machine, it is recommended to follow instructions in the [myconnectome-vm repository](https://github.com/poldrack/myconnectome-vm). This vm will use myconnectome-explore to provide interactive exploration for the data that you produce. The installation is automatic and you do not need to do anything beyond following instructions to set up the virtual machine.



If you are looking for a quick (non production) deployment (via a Docker container) of the application, see the [poldracklab/myconnectome-explore](https://hub.docker.com/r/poldracklab/myconnectome-explore/) container served by the [add/dockerfile](https://github.com/vsoch/myconnectome-explore/tree/add/dockerfile) branch of this repository. This is a container that you can run locally to see

a single view of the interface (the interactive logs and progress pages are not relevant). 



```bash

# Bind to port 80 to open at http://127.0.0.1

docker run -p 80:5000 poldracklab/myconnectome-explore  



# Bind to port 5000 to open at http://127.0.0.1:5000

docker run -p 5000:5000 poldracklab/myconnectome-explore 

```



If you want to see how the application is deployed in production,

please see this master branch being cloned in the [myconnectome-vm Vagrantfile](https://github.com/poldrack/myconnectome-vm/blob/master/Vagrantfile#L76).



### standalone application

You should first clone this repository



      git clone https://github.com/vsoch/myconnectome-explore

      cd myconnectome-explore



Install flask and flup



      pip install flask

      pip install flup



And then run the server locally

 

      python databrowser.py



Don't worry about index.py - that is the executable that is integrated into the myconnectome-vm.



### deployment



Your deployment environment will need flask installed to the python that will be running the application. If you are creating a local python environment to run the application, we reccommend using anaconda, as it comes with most of the libraries that you should need. You should also change "debug" "True" to debug "False" in the databrowser.py file. FInally, in the folder you need two files: an .htaccess and a myconnectome.fcgi. The myconnectome.fcgi should look as follows:



      #!/home/youruser/local/anaconda/bin/python

      from flup.server.fcgi import WSGIServer

      from databrowser import app as application

      WSGIServer(application).run()



The first line is the path to your python executable with flup and flask installed. 



Your .htaccess should look like this:



      Options +ExecCGI

      AddHandler fcgid-script .fcgi 

      RewriteEngine On

      RewriteCond %{REQUEST_FILENAME} !=/home/youruser/public_html/myconnectome/myconnectome.fcgi

      RewriteRule ^(.*)$ myconnectome.fcgi/$1 [QSA,L]



The fourth line is the path to the myconnectome.fcgi



Finally, you need to make your myconnectome.fcgi executable



      chmod u+x myconnectome.fcgi



That should be it! Going to the url yourserver/myconnectome should show the databrowser.