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SMDA - Squirrel Monkey Digital Atlas
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SMDA is a web-based volume viewer to be used with MR, DTI, block, histology,
glyph, and label images.

The volumetric data must be made available to the VM under its /smda directory.
This directory can be configured in app/web_server/smda_web_server.cfg. The
required structure of the volumetric data is described in <another document>.

The meta information is set up using the 'meta_updater' script under the
app/web_server directory of this project. It reads information from smda.yaml
to locate the subjects and store access information into a PostgreSQL database.

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Installation
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To install SMDA onto a VM (tested on CentOS 7), source the build script.

$ source build_env.sh <vm_ip> <vm_ssh_port>

This sets up the environment and enables access to the scripts in the tools
folder. Now copy any ssl certificates and keys to the 'certs' folder under the
project root and edit root/etc/nginx.conf, if necessary. Then enter the password
for the ssl certificate into root/etc/keys/fifo.

Now you can execute the smda-install script.

$ ./smda-install.sh 2>&1 | tee install.log

You may be prompted to enter passwords for the root user and the vuiisdev user
several times. At the end of the install process, the VM will be rebooted and
the web server should be available.

The main code lives under app/web_server and app/web_server/js.
Whenever changes are made to the javascript, they must be compiled and minified
by the Google Closure compiler. You can do this with a Makefile target:

$ make package

You can also just copy all of the javascript files in app/web_server/js to the
root/srv/smda/js folder:

$ make

Then you can copy all of the static files (i.e. js, css, html) files as well
as the configuration files under root/srv/smda to the VM

$ copystatic
$ copyconfig

At this point, you may want to update the meta information. From the server
(i.e. ssh login) you can update the web server static content hashes as well:

$ python app/web_server/meta_updater --no-ask-pass
$ python app/web_server/update_hashes

Finally, when changes are made to the server python code, you must copy the
code over and restart the server with the following command:

$ copyweb

To view various logs from your host machine:

$ tailwebserver
$ tailnginx