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A Common Lisp-based web framework supporting custom clinical and patient medical registries. Leverages Weblocks and Elephant to enable a highly dynamic and flexible schemata.
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attic Massive refactoring of LAMsight into registry
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README.md

cl-registry

A patient and clinical registry platform

Copyright (c) 2008-2011 MIT Media Laboratory Portions Copyright (c) 2009-2011 the LAM Treatment Alliance

Upgrade Status as of December 7th, 2011

Known to work with Quicklisp distribution from 2011-11-03

Major Problems:

  • cl-l10n / verify parsing & formatting works properly
  • cl-l10n / fix format to provide hint to UI?

Minor problems:

  • Upgrade to latest cl-twitter
    • Ensure we can use twitter oauth interface?
    • Just don't use twitter for now

SBCL-specific problems:

  • Ensure that Elephant works on SBCL
  • Latest cl-l10n doesn't build on SBCL?

Installation Instructions

  1. Grab the registry from GitHub and ensure that it's accessible via asdf.

  2. Install Berkeley DB v4.7 in /usr/local

If BDB isn't installed on your machine, you can download source from:

http://www.oracle.com/technology/software/products/berkeley-db/

Make sure you compile and link for 64 bits, if you're using a 64-bit CCL:

cd /path/to/db-4.x.y/build_unix
CFLAGS="-m64" LDFLAGS="-arch x86_64" ../dist/configure
make
sudo make install
  1. Get the necessary libraries from quicklisp:

    (ql:quickload '(:weblocks :elephant :montezuma :drakma :cl-markdown :langutils :cl-twitter :cl-smtp :cl-l10n :local-time :parse-number))

  2. Configure quicklisp elephant installation

    a. Add link for ele-bdb.asd

    cat 'dists/quicklisp/software/elephant-20111001-darcs/ele-bdb.asd' > quicklisp/dists/quicklisp/installed/systems/ele-bdb.txt

    b. Add system reference for quicklisp asdf loading

    cat 'elephant ele-bdb ele-bdb uffi bordeaux-threads elephant' >> quicklisp/dists/quicklisp/systems.txt

    c. Modify my-config.sexp to change all occurances of 4.5 to 4.7

    quicklisp/dists/quicklisp/software/elephant-20111001-darcs/my-config.sexp

  3. To start from the REPL

    Start Lisp (ccl or sbcl) (asdf:operate 'asdf:load-op :registry)
    (in-package :registry) (start-registry :debug t :config "lamsight-production")

The start-registry procedure has an optional debug command line and requires a site configuration reference (stored in ./registry/sites). Like CSS, site configurations can be cascaded so you can include a list of configurations with the later files overriding fields in the former. For example, to ensure no production e-mails or twitter messages are sent, you can override those config items using devel.config.

(start-registry :debug t :config '("ilr-production" "devel"))
  1. To load a Registry site from the command line (INCOMPLETE INSTRUCTIONS)

    cd ./registry [port]

If "port" is included, loads Swank (from ../systems/slime/) and starts a server listening on "port" (4005 is the default port for m-x slime-connect in Emacs).

If NOLOAD is set to "true" in the environment, does not load the registry or library code, only registry-loader.lisp:

NOLOAD=true ./registry [port]

In this case, the Slime package will be REGISTRY-LOADER, and you can load the registry code with:

(loadsys :registry)

Otherwise, the Slime package will be REGISTRY.

If REGPORT is an integer, will start up a debugging server on that port. For example, the following will load the registry code, start a server on port 8080, and start a Slime server on port 4005:

REGPORT=8080 ./registry 4005
  1. Alternatively, you can start the server from the REPL with:

    (registry-loader:start-registry 8080)

or:

(start-registry :debug <debug>
              :log-level <log-level>
              :address "localhost"
              :port 8080
              :config <config>)

is NIL to log web site errors, :HTML to display error information in the browser, or anything else to break into the debugger. Default: NIL. You can set ERROR-ACTION to change it.

is :ERROR, :WARNING, :INFO, or :DEBUG. If :ERROR, then only errors will be logged to the log file (/logs/registry.log). If :WARNING, then both errors and warnings will be logged. If :INFO or :DEBUG, then both errors and warnings will be logged, plus explicit calls to LOG-MESSAGE with a LEVEL of :INFO, if is :INFO, or of :INFO or :DEBUG, if is :DEBUG. The default for is :ERROR, if is NIL, or :DEBUG otherwise. You can use SET-LOG-LEVEL to change it.

is a list of paths to configuration files, which are usually stored in the "sites" directory. If it is a string, it will be split on spaces to make a list of strings. Then each element will be merged with "sites/.config" and the directory of "registry-loader.lisp" to get a full (possibly relative) pathname. The default is ("ilr-production" "devel").

If REGCONFIG is set in the environment, it will be passed by REGISTRY-LOADER:START-REGISTRY to REGISTRY:START-REGISTRY as the value for the CONFIG parameter, after being split a list of strings using "+" as a delimiter. Hence REGCONFIG="ilr-production+devel" is equivalent to passing '("ilr-production" "devel") as the CONFIG parameter of REGISTRY:START-REGISTRY.

If REGDEV is set to "true" in the environment, then the build will be done with :REGISTRY-DEVELOPMENT in FEATURES. This builds with (OPTIMIZE (SPEED 1) (SPACE 1) (DEBUG 3) (SAFETY 3)), which is very slow in CCL, but easier to debug.

If REGISTRY_PRODUCTION is set to "true" in the environment, then the build will be done with :REGISTRY-PRODUCTION in FEATURES. This enables Twitter updates.

If ENABLE_EMAILS_TO_USERS is set to "true" in the environment, then the variable enable-email-to-users will be set true after the registry code is loaded, but before the server is started. This enables periodic emails to users who have requested it.

Both Twitter updates and periodic emails can be toggled on the "Admin" page.

Configuration Instructions

This code base supports multiple personalities, user interfaces, module configurations and other features from configuration files stored in sites/. The current configurations support the live sites LAMsight and the International LAM Registry.

More TBD

Loading Data

The first time you start the server, you'll have an empty database, which will cause many of the pages to be blank. To load an initial database, you can do the following on newmed-dev:

(import-model-file "/usr/local/lamsight/anon-db-export-05-27-09.sexp")

Guide to the Code Base

Core Data Models

Application Plugins

Site Events

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