Scientific area explorer

Description

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How to start

The system is written in Common LISP. In order to run it locally, you should setup a working LISP environment and install required system packages.

Setting up Common LISP

There are many Common LISP systems available, both open-source, such as SBCL, ClozureCL, or CLISP, and comercial, e.g. LispWorks, Allegro CL. In short, you need a LISP compiler and quicklisp (quicklisp.org) to be properly configured. Every modern implementation of Common LISP should work. The following commands give a clue how this can be done for ClozureCL under Linux. Note, that you can install ClozureCL in any directory, or move ccl directory later. The procedure is essentially the same for Windows and MacOS operating systems (see https://ccl.clozure.com/ and https://www.quicklisp.org/ for more information).

wget https://github.com/Clozure/ccl/releases/download/v1.11.5/ccl-1.11.5-linuxx86.tar.gz
tar xzf ccl-1.11.5-linuxx86.tar.gz
wget https://beta.quicklisp.org/quicklisp.lisp

Start ClozureCL (64bit version)

./ccl/lx86cl64 --load quicklisp.lisp

and then, when the ClosureCL prompt symbol ? (question) appears, enter the following commands, one by one:

(quicklisp-quickstart:install)
(ql:add-to-init-file)
(quit)

File quicklisp.lisp may be deleted from the current directory.

At this point your HOME directory should contains a ClozureCL initialization file .ccl-init.lisp. In order to simplify SAExplorer loading, add the following line at the end of this file (we assume that the repository was cloned into HOME directory; if it is not the case, replace "~/SAExplorer" by an appropriate value):

(push #p"~/SAExplorer/" asdf:*central-registry*)

Install required packages

SAExplorer depends on SQLite, Redis and ElasticSearch, which are used to store downloaded documents locally. Please, install these systems before running SAExplorer. Redis and ElasticSearch may be installed on separate servers accessable via network.

Running SAExplorer

Once you have successfully installed a Common LISP enviroment of your chioce, you are ready to run SAExplorer!

Load the system by evaluating (ql:quickload "saexplorer")

Then run "the main" function (saexplorer:main)

and open http://localhost:8135/index.html in your favorite browser that supports WebSockets.

Configuration

Configuration file allows to set up local storage (caches and databases), web server parameters, and access credentials for bibliographic databases.

Please, use sample.local.cfg as a template for your local configuration.

Bibliographic databases

The default configuration supports open-access resources only. At the moment, the list of supported open-access resources includes Crossref.org and DBLP.org. If you need an access to databases with restricted access, relevant authentication information must be specified in the configuration file.

Proxy server

Bibliographic databases may be accessed via a proxy server.

Local storage

Webserver

Information for developers

LISP IDE

The most popular development environment for Common LISP is Emacs/SLIME.

apt-get install emacs

While SLIME is available in many Linux distributions by default, it is recommended to download it manually from the official page. https://github.com/slime/slime/archive/v2.20.tar.gz

SLIME archive may be decompressed whenever you like, while the common location is the Emacs packages directory, say ~/.emacs.d/slime-2.0/. The final step is putting some configuraton command into emacs dot-file ~/.emacs.

(add-to-list 'load-path "~/.emacs.d/slime-2.0/")  ; Inform Emacs where SLIME may be found

(require 'slime)

(add-hook 'lisp-mode-hook
          (lambda ()
            (local-set-key (kbd "C-m") 'newline-and-indent)
            (slime-setup '(slime-fancy slime-repl))
            (slime-mode t)
            (add-hook 'lisp-mode-hook
                      (lambda () (add-to-list 'write-file-functions
                                              'delete-trailing-whitespace)))))

(eval-after-load "slime"
  `(progn
     (custom-set-variables
      '(inhibit-splash-screen t)
      '(slime-complete-symbol*-fancy t)
      '(slime-complete-symbol-function 'slime-fuzzy-complete-symbol)
      '(slime-net-coding-system 'utf-8-unix)
      '(slime-startup-animation nil)
      '(slime-lisp-implementations '((sbcl ("/usr/local/bin/sbcl"))
                                     (ccl ("/opt/lisp/ccl-1.11/lx86cl64"))))
      '(inferior-lisp-program "/opt/lisp/ccl-1.11/lx86cl64") ; default Lisp system
      '(slime-default-lisp 'ccl t)
      '(safe-local-variable-values '((Base . 10) (Syntax . ANSI-Common-Lisp) (Encoding . utf-8))))
     (slime-setup '(slime-fancy slime-repl))))

If everythong was configured proprly, you can start Emacs editor and run SLIME by entering Emacs command M-x slime <RET> (Alt+X slime Enter).

The folowing descriptions of basic SLIME/Emacs commands might be useful:

• http://pchristensen.com/wp-content/uploads/2008/02/slimecommands.pdf
• http://dept-info.labri.fr/~idurand/enseignement/lst-info/PFS/Common/slime-refcard.pdf

How to run tests

(ql:quickload "saexplorer-test")
(lift:run-tests :suite 'root :break-on-errors? t)

Or, using the ASDF testing facility

(ql:quickload "saexplorer-test")
(asdf:test-system "saexplorer")
;; or (asdf:operate 'asdf:test-op :saexplorer)