basic working version of get-names

[arxana.git] / latex / arxana-merge.tex

%;; Copyright (C) 2005-2017 Joe Corneli <holtzermann17@gmail.com>
%;; Copyright (C) 2010-2017 Ray Puzio <rsp@novres.org>

%;; This program is free software: you can redistribute it and/or modify
%;; it under the terms of the GNU Affero General Public License as published by
%;; the Free Software Foundation, either version 3 of the License, or
%;; (at your option) any later version.
%;;
%;; This program is distributed in the hope that it will be useful,
%;; but WITHOUT ANY WARRANTY; without even the implied warranty of
%;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%;; GNU Affero General Public License for more details.
%;;
%;; You should have received a copy of the GNU Affero General Public License
%;; along with this program.  If not, see <http://www.gnu.org/licenses/>.

%% (progn
%%   (find-file "~/arxana/latex/arxana-merge.tex")
%%   (save-excursion
%%     (goto-char (point-max))
%%     (let ((beg (progn (search-backward "\\begin{verbatim}")
%%                       (match-end 0)))
%%           (end (progn (search-forward "\\end{verbatim}")
%%                       (match-beginning 0))))
%%       (eval-region beg end)
%%       (lit-eval))))

%%% Commentary:

%% To load: remove %'s above and evaluate with C-x C-e.

%% Alternatively, run this:
% head -n 13 arxana.tex | sed -e "/%/s///" > arxana-loader.el
%% on the command line to produce something you can use
%% to load Arxana when you start Emacs:
% emacs -l arxana-loader.el

%% Or put the expression in your ~/.emacs (perhaps wrapped
%% in function like `eval-arxana').

%% Or search for a similar form below and evaluate there!

%%% Code:

\documentclass{article}

\usepackage[T1]{fontenc}
\usepackage{textcomp}

\usepackage{hyperref}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{verbatim}

\newcommand{\todo}[1]{\footnote{\bf TODO: #1}}
\newcommand{\meta}[1]{$\langle${\it #1}$\rangle$}

\theoremstyle{definition}
\newtheorem{nota}{Note}[section]

\parindent = 1.2em

\newenvironment{notate}[1]
  {\begin{nota}[{\bf {\em #1}}]}%
  {\end{nota}}

\makeatletter
\newenvironment{elisp}
  {\let\ORGverbatim@font\verbatim@font
   \def\verbatim@font{\ttfamily\scshape}%
   \verbatim}
  {\endverbatim
  \let\verbatim@font\ORGverbatim@font}
\makeatother

\makeatletter
\newenvironment{idea}
  {\let\ORGverbatim@font\verbatim@font
   \def\verbatim@font{\ttfamily\slshape}%
   \verbatim}
  {\endverbatim
  \let\verbatim@font\ORGverbatim@font}
\makeatother

\begin{document}

\title{\emph{Arxana 2017}}

\author{Joseph Corneli \& Raymond Puzio\thanks{Copyright (C) 2005-2017
    Joseph Corneli {\tt <holtzermann17@gmail.com>}\newline
   Copyright (C) 2010-2017 Raymond Puzio {\tt <rsp@novres.org>}\newline
    $\longrightarrow$ transferred to the public domain.}}
\date{Last revised: \today}

\maketitle

\abstract{A tool for building hackable semantic hypertext platforms.
  An overview and link to our source code repository is at {\tt
    http://arxana.net}.}

\tableofcontents

\section{Introduction}

\begin{notate}{What is ``Arxana''?} \label{arxana}
\emph{Arxana} is the name of a ``next generation'' hypertext system
that emphasizes annotation.  Every object in this system is
annotatable.  Because of this, our first name for the program ``the
scholium system'', but ``Arxana'' better reflects our aim: to explore
the mysterious world of links, attachments, correspondences, and
side-effects.  This edition of the program relies entirely on Emacs
for storage and display, and integrates a backend storage mechanism
devised by Ray Puzio, and frontend interactions from earlier
prototypes by Joe Corneli, and (in Section \ref{farm-demo}) a new
application to modelling mathematical dialogues jointly developed by
both authors.  Previous versions contain often excessive but
sometimes interesting discussion of ideas for future work.
Such discussion has been kept to a minimum here.
\end{notate}

\begin{notate}{Using the program}
If you are looking at the source version of this document
in Emacs, evaluate the following s-expression (type
\emph{C-x C-e} with the cursor positioned just after its
final parenthesis).  This prepares the Emacs environment
for interactive use.  (The code that achieves this is
in Appendix \ref{appendix-lit}.)

\begin{idea}
(save-excursion
  (let ((beg (search-forward "\\begin{verbatim}"))
        (end (progn (search-forward "\\end{verbatim}")
                    (match-beginning 0))))
    (eval-region beg end)
    (lit-process)))
\end{idea}

If you are looking at this in a PDF or printout, you will see that the
document has a ``literate'' style.  That is, it can be read as text,
not just as code.  In Section \ref{frontend}, we define functions that
allow the user to read and revise the contents of this document as
hypertext.
\end{notate}

\section{Backend}

\begin{notate}{Overview of the backend}
This backend is a Higher Order NEtwork Yarnknotter or HONEY for short.
It stores a \emph{network} of quintuplets of the form {\tt(uid label
  source sink . content)}.  One such quintuplet is called a
\emph{nema}.  The structure of an individual nema is as follows: The
{\tt uid} is a numeric identifier that is unique on a network
basis.  The {\tt label} is an (optional) string that corresponds
uniquely to the uid.  The {\tt source} is the nema (identified by
uid) to the ``left'' of our quintuplet, and the {\tt sink} is the
uid to the ``right'' of our quintuplet.  One or both may be {\tt
  0}, and in case both are, the nema is understood to be a
\emph{node}.  Lastly, the nema's {\tt content} can be any Lisp
object -- including another nema in the same network or another
network.\todo{(Check this last statement...)}
\end{notate}

\subsection{Preliminaries}

\begin{notate}{Some preliminaries}
We define several simple preliminary functions that we use later on.
\end{notate}

\begin{notate}{Required packages}
We use the Common Lisp compatibility functions.
\end{notate}

\begin{elisp}
(require 'cl)
\end{elisp}

\begin{notate}{On `filter'}
This is a useful utility to filter elements of a list satisfying a condition.
Returns the subset of stuff which satisfies the predicate pred.
\end{notate}

\begin{elisp}
(defun filter (pred stuff)
  (let ((ans nil))
    (dolist (item stuff (reverse ans))
      (if (funcall pred item)
            (setq ans (cons item ans))
        nil))))
\end{elisp}

\begin{idea}
(filter '(lambda (x) (= (% x 2) 1)) '(1 2 3 4 5 6 7))
=> (1 3 5 7)
\end{idea}

\begin{notate}{On `intersection'}
Set-theoretic intersection operation.
More general than the version coming from the `cl' package
\end{notate}

\begin{elisp}
(defun intersection (&rest arg)
  (cond ((null arg) nil)
        ((null (cdr arg)) (car arg))
        (t (let ((ans nil))
             (dolist (elmt (car arg) ans)
               (let ((remainder (cdr arg)))
                 (while (and remainder
                             (member elmt (car remainder)))
                   (setq remainder (cdr remainder))
                   (when (null remainder)
                     (setq ans (cons elmt ans))))))))))
\end{elisp}

\begin{idea}
(intersection '(a b c d e f g h j)
              '(a b h j k)
              '(b d g h j k))
=> (j h b)
\end{idea}

\begin{notate}{On `mapply'}
Map and apply rolled into one.
\end{notate}
\begin{elisp}
(defun mapply (f l)
  (if (member nil l) nil
    (cons (apply f (mapcar 'car l))
          (mapply f (mapcar 'cdr l)))))
\end{elisp}

\begin{idea}
(mapply '+ '((1 2) (3 4)))
 => (4 6)
\end{idea}

\begin{notate}{On `sublis'}
Substitute objects in a list.
\end{notate}

\begin{elisp}
(defun sublis (sub lis)
  (cond
   ((null lis) nil)
   ((assoc lis sub) (cadr (assoc lis sub)))
   ((atom lis) lis)
   (t (cons (sublis sub (car lis))
            (sublis sub (cdr lis))))))
\end{elisp}

\subsection{Core definitions}

\begin{notate}{The `add-plexus' function} \label{the-new-net-function}
We use this create a new plexus for storage.  It defines a
counter (beginning at 1), together with several hash tables that allow
efficient access to the plexus' contents: an article table, forward
links, backward links, forward labels, and backward labels.
Additionally, it defines a ``ground'' and
``type'' nodes.\todo{Explain these things in more detail.}\todo{NB. it could be useful
to maintain a registry available networks, by analogy with
Emacs's `buffer-list', which
I think could be done if we use `cl-defstruct' below
instead of `list', and set up the constructor suitably
(info \textquotedbl(cl) Structures\textquotedbl).}
\end{notate}

\begin{elisp}
(defun add-plexus ()
  "Create a new plexus."
  (let ((newbie (list '*plexus*
                      1                               ; nema counter
                      (make-hash-table :test 'equal)  ; nema table
                      (make-hash-table :test 'equal)  ; forward links
                      (make-hash-table :test 'equal)  ; backward links
                      (make-hash-table :test 'equal)  ; forward labels
                      (make-hash-table :test 'equal)  ; backward labels
                      (car plexus-registry))))
    ;; Define ground and type nodes.
    (puthash 0 '(0 0) (nth 2 newbie))
    (puthash 1 '(0 0) (nth 2 newbie))
    (puthash 0 '((0 . 0) (1 . 0)) (nth 3 newbie))
    (puthash 0 '((0 . 0) (1 . 0)) (nth 4 newbie))
    (puthash 0 '"ground" (nth 5 newbie))
    (puthash '"ground" 0 (nth 6 newbie))
    (puthash 1 '"type" (nth 5 newbie))
    (puthash '"type" 1 (nth 6 newbie))
    ;; Register the new object and return it.
    (setq plexus-registry
          (append
           '(,(+ (car plexus-registry) 1)
             (,(car plexus-registry) ,newbie))))
    newbie))
\end{elisp}

\begin{notate}{The ``remove-plexus'' function}
When we're done with our plexus, we should tidy up after ourselves.
\end{notate}

\begin{elisp}
(defun remove-plexus (plex)
  "Remove a plexus."
  ;; Wipe out the hash tables
  (dotimes (i 5)
    (clrhash (nth (+ i 2) plex)))
  ;; Remove the entry from the registry.
  (setq plexus-registry
        (cons
         (car plexus-registry)
         (delete
          (assoc (nth 7 plex)
                 (cdr plexus-registry))
          (cdr plexus-registry)))))
\end{elisp}

\begin{elisp}
(defun show-plexus-registry ()
  plexus-registry)
\end{elisp}

\begin{notate}{HONEY set up}
These variables are needed for a coherent set-up.\todo{Explain
what they will do.}
\end{notate}

\begin{elisp}
(defvar plexus-registry '(0 nil))
(defvar current-plexus nil)
\end{elisp}

\begin{notate}{Network selection}
We can work with several networks, only one of
which is ``current'' at any given time.
\end{notate}

\begin{elisp}
(defun set-current-plexus (plex)
  "Examine a different plexus instead."
  (setq current-plexus plex))

(defmacro with-current-plexus (plex &rest expr)
  (append `(let ((current-plexus ,plex))) ,expr))

(defun show-current-plexus ()
  "Return the plexus currently being examined."
  current-plexus)
\end{elisp}

\begin{notate}{On `next-unique-id'}
Increment the identifier that tells us how many nemas are in our network.
\end{notate}

\begin{elisp}
(defun next-unique-id ()
  "Produce a yet unused unique identifier."
  (1+ (cadr current-plexus)))
\end{elisp}

\begin{notate}{On `reset-plexus'}
Reset article counter and hash tables.  Redefine ``ground'' and
``article-type''.
\end{notate}

\begin{elisp}
(defun reset-plexus ()
  "Reset the database to its initial configuration."
  ; Reset nema counter and hash tables.
  (setcar (cdr current-plexus) 1)
  (dotimes (n 5)
    (clrhash (nth (+ n 2) current-plexus)))
  ;; Define ground and nema-type.
  (puthash 0 '(0 0) (nth 2 current-plexus))
  (puthash 1 '(0 0) (nth 2 current-plexus))
  (puthash 0 '((0 . 0) (1 . 0)) (nth 3 current-plexus))
  (puthash 0 '((0 . 0) (1 . 0)) (nth 4 current-plexus))
  (puthash 0 '"ground" (nth 5 current-plexus))
  (puthash '"ground" 0 (nth 6 current-plexus))
  (puthash 1 '"nema-type" (nth 5 current-plexus))
  (puthash '"nema-type" 1 (nth 6 current-plexus))
  nil)
\end{elisp}

\subsection{Individual Operations}

\begin{notate}{On `add-nema'}
Add record to article table.
Add record to list of forward links of source.
Add record to list of backward links of sink.
Return the id of the new article.\todo{Should we add an alias `add-triple'
for this function, to make it more clear that our middle/frontend
is not implementation specific?}
\end{notate}

\begin{elisp}
(defun add-nema (src txt snk)
  "Enter a new nema to the database."
  (let ((uid (next-unique-id)))
    ;; Add record to nema table.
    (puthash uid
             `(,src ,snk . ,txt)
             (nth 2 current-plexus))
    ;; Add record to list of forward links of source.
    (puthash src
             (cons `(,uid . ,snk)
                   (gethash src (nth 3 current-plexus) nil))
             (nth 3 current-plexus))
    ;; Add record to list of backward links of sink.
    (puthash snk
             (cons
              `(,uid . ,src)
              (gethash snk (nth 4 current-plexus) nil))
             (nth 4 current-plexus))
    ;; Update the counter for long-term storage
    (setcar (cdr current-plexus) uid)
    ;; Return the id of the new nema.
    uid))
\end{elisp}

\begin{notate}{Retrieving elements of a nema}
These functions exist to get the relevant components
of a nema, given its uid.
\end{notate}

\begin{elisp}
(defun get-content (uid)
  "Return the content of the nema."
  (cddr (gethash uid (nth 2 current-plexus))))

(defun get-source (uid)
  "Return the source of the nema."
  (car (gethash uid (nth 2 current-plexus))))

(defun get-sink (uid)
  "Return the sink of the nema."
  (cadr (gethash uid (nth 2 current-plexus))))
\end{elisp}

\begin{notate}{On `update-content'}
old source
old sink
new content
\end{notate}

\begin{elisp}
(defun update-content (uid txt)
  "Replace the content of the nema."
  (puthash uid
              (let ((x (gethash uid (nth 2 current-plexus))))
                     `(,(car x)    ; old source
                              ,(cadr x) . ; old sink
                                     ,txt))      ; new content
                 (nth 2 current-plexus)))
\end{elisp}

\begin{notate}{On `update-source'}
Extract current source.
Extract current sink.
Extract current content.
Update the entry in the article table.
Remove the entry with the old source in the
forward link table.  If that is the only entry
filed under old-src, remove it from table.
Add an entry with the new source in the
forward link table.
Update the entry in the backward link table.
\end{notate}

\begin{elisp}
(defun update-source (uid new-src)
  "Replace the source of the nema."
  (let* ((x (gethash uid (nth 2 current-plexus)))
         (old-src (car x))   ; extract current source
         (old-snk (cadr x))  ; extract current sink
         (old-txt (cddr x))) ; extract current content
    ;; Update the entry in the nema table.
    (puthash uid
             `(,new-src ,old-snk . ,old-txt)
             (nth 2 current-plexus))
    ;; Remove the entry with the old source in the
    ;; forward link table.  If that is the only entry
    ;; filed under old-src, remove it from table.
    (let ((y (delete `(,uid . ,old-snk)
                     (gethash old-src
                              (nth 3 current-plexus)
                              nil))))
      (if y
          (puthash old-src y (nth 3 current-plexus))
        (remhash old-src (nth 3 current-plexus))))
    ;; Add an entry with the new source in the
    ;; forward link table.
    (puthash new-src
             (cons `(,uid . ,old-snk)
                   (gethash old-src (nth 3 current-plexus) nil))
             (nth 3 current-plexus))
    ;; Update the entry in the backward link table.
    (puthash old-snk
             (cons `(,uid . ,new-src)
                   (delete `(,uid . ,old-src)
                           (gethash old-src
                                    (nth 4 current-plexus)
                                    nil)))
             (nth 4 current-plexus))))
\end{elisp}

\begin{notate}{On `update-sink'} \label{update-sink}
Extract current source.
Extract current sink.
Extract current content.
Update the entry in the article table.
Remove the entry with the old sink in the
backward link table.  If that is the only entry
filed under old-src, remove it from table.
Add an entry with the new source in the
backward link table.
Update the entry in the forward link table.
\end{notate}

\begin{elisp}
(defun update-sink (uid new-snk)
  "Change the sink of the nema."
  (let* ((x (gethash uid (nth 2 current-plexus)))
          (old-src (car x))   ; extract current source
           (old-snk (cadr x))  ; extract current sink
            (old-txt (cddr x))) ; extract current content
    ; Update the entry in the nema table.
    (puthash uid
             `(,old-src ,new-snk . ,old-txt)
             (nth 2 current-plexus))
    ;; Remove the entry with the old sink in the
    ;; backward link table.  If that is the only entry
    ;; filed under old-src, remove it from table.
    (let ((y (delete `(,uid . ,old-src)
                     (gethash old-snk
                              (nth 4 current-plexus)
                              nil))))
      (if y
          (puthash old-snk y (nth 4 current-plexus))
        (remhash old-snk (nth 4 current-plexus))))
    ;; Add an entry with the new source in the
    ;; backward link table.
    (puthash new-snk
             (cons `(,uid . ,old-src)
                   (gethash old-snk
                            (nth 4 current-plexus)
                            nil))
             (nth 4 current-plexus))
    ;; Update the entry in the forward link table.
    (puthash old-src
             (cons `(,uid . ,new-snk)
                   (delete `(,uid . ,old-snk)
                           (gethash old-src
                                    (nth 3 current-plexus)
                                    nil)))
             (nth 3 current-plexus))))
\end{elisp}

\begin{notate}{On `remove-nema'}
Remove forward link created by article.
Remove backward link created by article.
Remove record from article table.
\end{notate}

\begin{elisp}
(defun remove-nema (uid)
  "Remove this nema from the database."
  (let ((old-src (car (gethash uid (nth 2 current-plexus))))
        (old-snk (cadr (gethash uid (nth 2 current-plexus)))))
  ;; Remove forward link created by nema.
  (let ((new-fwd (delete `(,uid . ,old-snk)
                          (gethash old-src (nth 3 current-plexus)))))
    (if new-fwd
        (puthash old-src new-fwd (nth 3 current-plexus))
      (remhash old-src (nth 3 current-plexus))))
  ;; Remove backward link created by nema.
  (let ((new-bkw (delete `(,uid . ,old-src)
                          (gethash old-snk (nth 4 current-plexus)))))
    (if new-bkw
        (puthash old-snk new-bkw (nth 4 current-plexus))
      (remhash old-snk (nth 4 current-plexus))))
  ;; Remove record from nema table.
  (remhash uid (nth 2 current-plexus))))
\end{elisp}

\begin{notate}{Functions for gathering links}
Links are stored on triples alongside other
elements.
\end{notate}

\begin{elisp}
(defun get-forward-links (uid)
  "Return all links having given object as source."
  (mapcar 'car (gethash uid (nth 3 current-plexus))))

(defun get-backward-links (uid)
  "Return all links having given object as sink."
  (mapcar 'car (gethash uid (nth 4 current-plexus))))
\end{elisp}

\begin{notate}{On `label-nema'}
Nemas can be given a unique human-readable label in addition
to their numeric uid.
\end{notate}

\begin{elisp}
(defun label-nema (uid label)
  "Assign the label to the given object."
  (puthash uid label (nth 5 current-plexus))
  (puthash label uid (nth 6 current-plexus)))
\end{elisp}

\begin{notate}{Label to uid and uid to label lookup}
These functions allow the exchange of uid and label.
\end{notate}

\begin{elisp}
(defun label2uid (label)
  "Return the unique identifier corresponding to a label."
  (gethash label (nth 6 current-plexus) nil))

(defun uid2label (uid)
  "Return the label associated to a unique identifier."
  (gethash uid (nth 5 current-plexus) nil))
\end{elisp}

\subsection{Bulk Operations}

\begin{notate}{On `download-en-masse'}
Unpack triplets, obtain labels if they exist.
Write data in the network to a list, and return.
\end{notate}

\begin{elisp}
(defun download-en-masse ()
  "Produce a representation of the database as quintuples."
  (let ((plex nil))
    (maphash (lambda (uid tplt)
                                        ; Unpack triplet.
               (let ((src (car tplt))
                     (snk (nth 1 tplt))
                     (txt (nthcdr 2 tplt)))
                                        ; Obtain next label if exists.
                 (setq lbl (gethash uid
                                    (nth 5 current-plexus)
                                    nil))
                                        ; Write data to list.
                 (setq plex (cons `(,uid ,lbl ,src ,snk . ,txt)
                                 plex))))
             (nth 2 current-plexus))
                                        ; Return list of data.
    (reverse plex)))
\end{elisp}

\begin{notate}{On `upload-en-masse'}
Unpack quintuplets.  Plug into tables.
Bump up article counter as needed.
\end{notate}

\begin{elisp}
(defun upload-en-masse (plex)
  "Load a representation of a database as quintuples into memory."
  (dolist (qplt plex t)
    ; unpack quintuplet
    (let ((uid (car qplt))
            (lbl (nth 1 qplt))
              (src (nth 2 qplt))
                (snk (nth 3 qplt))
                  (txt (nthcdr 4 qplt)))
      ; plug into tables
      (puthash uid
                      `(,src ,snk . ,txt)
                             (nth 2 current-plexus))
      (puthash src
                      (cons `(,uid . ,snk)
                                 (gethash src (nth 3 current-plexus) nil))
                             (nth 3 current-plexus))
      (puthash snk
                      (cons
                       `(,uid . ,src)
                       (gethash snk (nth 4 current-plexus) nil))
                             (nth 4 current-plexus))
      (when lbl
          (progn
                (puthash uid lbl (nth 5 current-plexus))
                    (puthash lbl uid (nth 6 current-plexus))))
      ; Bump up nema counter if needed.
      (when (> uid (cadr current-plexus))
             (setcar (cdr current-plexus) uid)))))
\end{elisp}

\begin{notate}{On `add-en-masse'}
Given several articles, add all of them at once.
\end{notate}

\begin{elisp}
(defun add-en-masse (plex)
  "Add multiple nemata given as list of quartuplets."
  (mapcar (lambda (qplt)
            (let ((uid (next-unique-id)))
              (add-nema (nth 1 plex)
                        (nthcar 2 plex)
                        (nth 2 plex))
              (label-nema uid (car qplt))))
          plex))
\end{elisp}

\subsection{Query}

\begin{notate}{Overview of search and query functionality}
We first describe several elementary functions for
accessing elements of the network.  We then describe a
robust search pipeline and show how it is implemented.
\end{notate}

\begin{notate}{Various lookup functions}
These functions allow testing and lookup of various elements
of a net.
\end{notate}

\begin{elisp}
(defun uid-p (uid)
  "Is this a valid uid?"
  (let ((z '(())))
    (not (eq z (gethash uid (nth 2 current-plexus) z)))))

(defun uid-list ()
  "List of all valid uid's."
  (maphash (lambda (key val) key)
           (nth 2 current-plexus)))

(defun ground-p (uid)
  "Is this nema the ground?"
  (= uid 0))

(defun source-p (x y)
  "Is the former nema the sink of the latter?"
  (equal x (get-source y)))

(defun sink-p (x y)
  "Is the former nema the sink of the latter?"
  (equal x (get-sink y)))

(defun links-from (x y)
  "Return all links from nema x to nema y."
  (filter '(lambda (z) (source-p x z))
            (get-backward-links y)))

(defun links-p (x y)
  "Does nema x link to nema y?"
  (when (member x (mapcar
                      'get-source
                      (get-backward-links y)))
    t))

(defun triple-p (x y z)
  "Do the three items form a triplet?"
  (and (source-p y x)
       (sink-p y z)))

(defun plexus-p (x)
  "Is this object a plexus?"
  (let ((ans t))
    (setq ans (and ans
                      (equal (car x) "*plexus*")))
    (setq ans (and ans
                      (integrp (cadr x))))
    (dotimes (n 5)
          (setq ans (and ans (hash-table-p
                                    (nth (+ n 2) x)))))
    ans))
\end{elisp}

\subsection{Iteration}

\begin{notate}{Iterating over a plexus}
  These functions allow users to run loops over a plexus without
  having to delve into its internal structure.\todo{I forget whether the
 use of `apply' here is good form.}
\end{notate}

\begin{elisp}
(defmacro do-plexus (var res body)
  `((maphash (lambda (,var val) ,body)
             (nth 2 current-plexus))
    ,res))

;; This maps over the keys; func should be
;; defined appropriately.
(defun map-plexus (func)
  (let ((ans nil))
    (maphash
     (lambda (key val)
       (push (apply func (list key)) ans))
     (nth 2 current-plexus))
    ans))

(defun filter-plexus (pred)
  (let ((ans nil))
    (maphash
     (lambda (key val)
       (when (apply pred (list val))
         (push key ans)))
       (nth 2 current-plexus))
     ans))
\end{elisp}

\begin{notate}{Filtering convenience functions}
Several convenience functions for filtering the plexus can be
defined.\todo{The code here is just a sketch, but hopefully something similar will actually work!}
\end{notate}

\begin{elisp}
(defun triples-given-beginning (node)
  "Get triples outbound from the given NODE."
  (remove nil (map-plexus
               (lambda (x) (when (equal (get-source x)
                                        node)
                             (list node
                                   (get-content x)
                                   (get-sink x)))))))

(defun triples-given-end (node)
  "Get triples inbound into NODE."
  (remove nil (map-plexus
               (lambda (x) (when (equal (get-sink x)
                                        node)
                             (list (get-source x)
                                   (get-content x)
                                   node))))))

(defun triples-given-middle (edge)
  "Get the triples that run along EDGE."
  (remove nil (map-plexus
               (lambda (x) (when (equal (get-content x)
                                        edge)
                             (list (get-source x)
                                   edge
                                   (get-sink x)))))))

(defun triples-given-middle-and-end (edge node)
  "Get the triples that run along EDGE into NODE."
  (remove nil (map-plexus
               (lambda (x) (when (and
                                  (equal (get-content x)
                                         edge)
                                  (equal (get-sink x)
                                         node))
                             (list (get-source x)
                                   edge
                                   node))))))

(defun triples-given-beginning-and-middle (node edge)
  "Get the triples that run from NODE along EDGE."
  (remove nil (map-plexus
               (lambda (x) (when (and
                                  (equal (get-source x)
                                         node)
                                  (equal (get-content x)
                                         edge))
                             (list node
                                   edge
                                   (get-sink x)))))))

;; Note: `links-from' might sort of works but returns
;; uids rather than triples - to discuss!
(defun triples-given-beginning-and-end (node1 node2)
  "Get the triples that run from NODE1 to NODE2."
  (remove nil (map-plexus
               (lambda (x) (when (and
                                  (equal (get-source x)
                                         node1)
                                  (equal (get-sink x)
                                         node2))
                             (list node1
                                   (get-content x)
                                   node2))))))

;; another concern here: are we meant to return the
;; *triple* or the uid?
(defun triple-exact-match (node1 edge node2)
  "Get the triples that run from NODE1 along EDGE to
NODE2."
  (remove nil (map-plexus
               (lambda (x) (when (and
                                  (equal (get-source x)
                                         node1)
                                  (equal (get-content x)
                                         edge)
                                  (equal (get-sink x)
                                         node2))
                             (list node1
                                   edge
                                   node2))))))
\end{elisp}

\begin{notate}{Additional elementary functions for node access}
These functions give access to the various parts of a node.\todo{Note:
 since `article-list' is not defined, should these functions be deleted?
Or should they be rewritten to access `current-plexus'?}
\end{notate}

\begin{elisp}
(defun get-src (n)
  (car (nth 0 (cdr (assoc n (cdr article-list))))))

(defun get-flk (n)
  (cdr (nth 0 (cdr (assoc n (cdr article-list))))))

(defun get-txt (n)
  (nth 1 (cdr (assoc n (cdr article-list)))))

(defun get-snk (n)
  (car (nth 2 (cdr (assoc n (cdr article-list))))))

(defun get-blk (n)
  (cdr (nth 2 (cdr (assoc n (cdr article-list))))))

(defun get-ids nil
  (mapcar (quote car) (cdr article-list)))

(defun get-gnd nil 0)
\end{elisp}

\begin{notate}{On `search-cond'} \label{search-cond}
Surround the search within dolist loops on free variables.
Wrap no further when finished.\todo{Upgrade this to concatenate the results together.
Also maybe allow options to add headers or to
only loop over unique tuplets.}\todo{Explain; how does this differ from
the function defined at Note \ref{search}?}
\end{notate}

\begin{elisp}
(defmacro search-cond (vars prop)
  "Find all n-tuplets satisfying a condition"
  (let ((foo '(lambda (vars cmnd)
                (if vars
                    Wrap in a loop.
                    `(dolist (,(car vars) uids)
                       ,(funcall foo (cdr vars) cmnd))
                    cmnd))))
    (funcall foo vars prop)))
\end{elisp}

\begin{notate}{Overview of the search pipeline}
We will implement the search as a pipeline which gradually
transforms the query into a series of expressions which produce
the sought-after result, then evaluate those expressions.

A search query designates predicates apply to the nodes
and the network relationships that apply to them.  The network relationships
function as wildcards.

The basic model of the data is triplets that point to other triplets.
The following query asks for a \emph{funny} link from a
\emph{big blue object} to a \emph{small green link} pointing outwards
from the big blue object.
\begin{idea}
(((a blue big) (b funny) (c green small)
  ((b src a) (b snk c) (c src a))
\end{idea}
The first step of processing is to put the quaerenda in some
order so that each item links up with at least one previous item:
\begin{idea}
(scheduler
 '((b funny)
   (c green small))
 '((b src a)
   (b snk c)
   (c src a))
 '((a blue big)))
=>
((c (green small) ((b snk c) (c src a)))
 (b (funny) ((b src a)))
 (a blue big))
\end{idea}
Note that the order is reversed due to technicalities of
implementing `scheduler' --- that is to say, a is first and does
not link to any other variable, b is next and links to only a,
whilst c is last and links to both a and b.
At the same time, we have also rearranged things so that the
links to previous items to which a given object are listed
alongside that object. The next step is to replace the links with the commands which
generate a list of such objects:
\begin{idea}
((c (green small) ((b snk c) (c src a)))
 (b (funny) ((b src a)))
 (a blue big))
=>
((c (green small)
    (intersection (list (get-snk b)) (get-forward-links a)))
 (b (funny)
    (intersection (get-backward-links a)))
 (a blue big))
\end{idea}
This is done using the function `tplts2cmd', e.g.
\begin{idea}
(tplts2cmd 'c  '((b snk c) (c src a)))
=>
(intersection (list (get-snk b)) (get-forward-links a))
\end{idea}
Subsequently, we filter over the predicates:
\begin{idea}
((c (filter '(lambda (c) (and (green c) (small c)))
    (intersection (list (get-snk b))
  (get-forward-links))))
 (b (filter '(lambda (b) (and (funny b)))
    (intersection (get-backward-links a)))))
\end{idea}
This is done with the command `add-filt':
\begin{idea}
(add-filt 'c
  '(green small)
  '((b snk c) (c src a)))
=>
(c (filter (quote (lambda (c) (and (green c) (small c))))
   (intersection (list (get-snk b))
 (get-forward-links a))))
\end{idea}
This routine calls up the previously described routine `tplts2cmd'
to take care of the third argument. The last entry, {\tt (a blue big)}
gets processed a little differently because we don't as yet have
anything to filter over; instead, we generate the initial list by
looping over the current network:
\begin{idea}
(a (let ((ans nil))
     (donet 'node
    (when (and (blue (get-content node))
       (big (get-content node)))
      (setq ans (cons node ans))))
     ans))
\end{idea}
This is done by invoking `first2cmd':
\begin{idea}
(first2cmd '(blue big))
=>
(let ((ans nil))
  (donet (quote node)
 (when (and (blue (get-content node))
    (big (get-content node)))
 (setq ans (cons node ans))))
 ans)
\end{idea}
And putting this all together:
\begin{idea}
(query2cmd
 '((c (green small) ((b snk c) (c src a)))
   (b (funny) ((b src a)))
   (a blue big)))
=>
((c (filter (quote (lambda (c) (and (green c) (small c))))
    (intersection (list (get-snk b))
  (get-forward-links a))))
 (b (filter (quote (lambda (b) (and (funny b))))
    (intersection (get-forward-links a))))
 (a (let ((ans nil))
      (donet (quote node)
     (when (and (blue (get-content node))
(big (get-content node)))
       (setq ans (cons node ans))))
      ans)))
\end{idea}
To carry out these instructions in the correct order and generate
a set of variable assignments, we employ the `matcher' function.
Combining this last layer, we have the complete pipeline:
\begin{idea}
(matcher nil
 (query2cmd
  (scheduler
   '((b funny)
     (c green small))
   '((b src a)
     (b snk c)
     (c src a))
   '((a blue big)))))
\end{idea}
This combination of operations is combined into the `search'
function, which can be called as follows:
\begin{idea}
(search
 '(((a blue big)
    (b funny)
    (c green small))
   ((b src a)
    (b snk c)
    (c src a))))
\end{idea}

Having described what the functions are supposed to do and how
they work together, we now proceed to implement them.
\end{notate}

\begin{notate}{On `scheduler'}
The scheduler function takes a list search query and rearranges it
into an order suitable for computing the answer to that query.
Specifically, a search query is a pair of lists --- the first list
consists of lists whose heads are names of variables and whose
tails are predicates which the values of the variables should
satisfy and the second list consists of triples indicating the
relations between the values of the variables.
Its arguments are:
\begin{itemize}
\item new-nodes, a list of items of the form \verb|(node &rest property)|;
\item \verb|links|, a list of triplets;
\item \verb|sched| is a list whose items consist of triplets of the
form\newline \verb|(node (&rest property) (&rest link))|.
\end{itemize}

A recursive function to find linked nodes.
If done, return answer.
New nodes yet to be examined.
Element of remaining-nodes currently under consideration.
List of links between candidate and old-nodes.
List of nodes already scheduled.
Loop through new nodes until find one linked to an old node.
Look at the next possible node.
Find the old nodes linking to the candidate node and record the answer in ``ties''.
Pick out the triplets whose first element is the node under consideration and whose third element is already on the list or vice-versa.
Recursively add the rest of the nodes.
\end{notate}

\begin{elisp}
(defun scheduler (new-nodes links sched)
  (if (null new-nodes)
      sched
    (let ((remaining-nodes new-nodes)
          (candidate nil)
          (ties nil)
          (old-nodes (mapcar 'car sched)))
      (while (null ties)
        (setq candidate (car remaining-nodes))
        (setq remaining-nodes (cdr remaining-nodes))
        (setq ties
              (filter '(lambda (x)
                         (or
                          (and (eq (first x) (car candidate))
                               (member (third x) old-nodes))
                          (and (member (first x) old-nodes)
                               (eq (third x) (car candidate)))))
                      links)))
      (scheduler (remove candidate new-nodes)
                 links
                 (cons (list (car candidate)
                             (cdr candidate)
                             ties)
                       sched)))))
\end{elisp}

\begin{notate}{On `tplts2cmd'}
\ldots\todo{Explain.}
\end{notate}

\begin{elisp}
(defun tplts2cmd (var tplts)
  (cons 'intersection
        (mapcar
         #'(lambda (tplt)
             (cond ((and (eq (third tplt) var)
                         (eq (second tplt) 'src))
                    `(get-flk ,(first tplt)))
                   ((and (eq (third tplt) var)
                         (eq (second tplt) 'snk))
                    `(get-blk ,(first tplt)))
                   ((and (eq (first tplt) var)
                         (eq (second tplt) 'src))
                    `(list (get-src ,(third tplt))))
                   ((and (eq (first tplt) var)
                         (eq (second tplt) 'snk))
                    `(list (get-snk ,(third tplt))))
                   (t nil)))
         tplts)))
\end{elisp}

\begin{notate}{On `add-filt'}
\ldots\todo{Explain.}
\end{notate}

\begin{elisp}
(defun add-filt (var preds tplts)
  `(,var
    (filter
     #'(lambda (,var)
         ,(cons 'and
                (mapcar
                 #'(lambda (pred)
                     (list pred
                           (list 'get-txt var)))
                 preds)))
     ,(tplts2cmd var tplts))))
\end{elisp}

\begin{notate}{On `first2cmd'}
\ldots\todo{Explain.}
\end{notate}

\begin{elisp}
(defun first2cmd (preds)
  `(let ((ans nil))
     (dolist (node (get-ids) ans)
       (when
           ,(cons 'and
                  (mapcar
                   #'(lambda (pred)
                       (cons pred '((get-txt node))))
                   preds))
         (setq ans (cons node ans))))))
\end{elisp}

\begin{notate}{On `query2cmd'}
\ldots\todo{Explain.}
\end{notate}

\begin{elisp}
(defun query2cmd (query)
  (let ((backwards (reverse query)))
    (reverse
     (cons
      (list (caar backwards)
            (first2cmd (cdar backwards)))
      (mapcar
       #'(lambda (x)
           (add-filt (first x) (second x) (third x)))
       (cdr backwards))))))
\end{elisp}

\begin{notate}{On `matcher'}
\ldots\todo{Explain.}
\end{notate}

\begin{elisp}
(defun matcher (assgmt reqmts)
  (if (null reqmts) (list assgmt)
    (apply 'append
           (mapcar
            #'(lambda (x)
                (matcher (cons (list (caar reqmts) x)
                               assgmt)
                         (cdr reqmts)))
            (apply 'intersection
                   (eval `(let ,assgmt
                            (mapcar 'eval
                                    (cdar reqmts)))))))))
\end{elisp}

\begin{notate}{How matcher works}
Here are some examples unrelated to what comes up in searching
triplets which illustrate how matcher works:
\end{notate}

\begin{idea}
(matcher '((x 1)) '((y (list 1 3))
                    (z (list (+ x y) (- y x)))))
=>
(((z 2) (y 1) (x 1))
 ((z 0) (y 1) (x 1))
 ((z 4) (y 3) (x 1))
 ((z 2) (y 3) (x 1)))

(matcher nil '((x (list 1))
               (y (list 1 3))
               (z (list (+ x y) (- y x)))))
=>
(((z 2) (y 1) (x 1))
 ((z 0) (y 1) (x 1))
 ((z 4) (y 3) (x 1))
 ((z 2) (y 3) (x 1)))
\end{idea}

\begin{notate}{On `search'} \label{search}
\ldots\todo{Explain; how does this differ from
the macro defined at Note \ref{search-cond}?}
\end{notate}

\begin{elisp}
(defun search (query)
  (matcher nil
           (reverse
            (query2cmd
             (scheduler
              (cdar query)
              (cadr query)
              (list (caar query)))))))
\end{elisp}

\subsection{Scholium programming}

\begin{notate}{Scholium programming}
The next several functions allow us to store and retrieve code
from inside of the network.
\end{notate}

\begin{notate}{On `node-fun'}
\ldots\todo{Explain.}
Produce a list of commands to produce temporary bindings.
Produce a list of commands to reset function values.
\end{notate}

\begin{elisp}
(defun node-fun (node get-code get-links)
  (let ((code  (funcall get-code node))
        (links (funcall get-links node)))
    (list
     'lambda
     (car code)
     (cons
      'prog1
      (cons
       (append
        '(progn)
        (mapcar #'(lambda (x)
                    `(fset ',(car x)
                           (node-fun ,(cdr x)
                                     ',get-code
                                     ',get-links)))
                links)
        (cdr code))
       (mapcar #'(lambda (x)
                   (if (fboundp (car x))
                       `(fset ',(car x)
                              ',(symbol-function (car x)))
                     `(fmakunbound ',(car x))))
               links))))))
\end{elisp}

\begin{notate}{On `tangle-module'}
Recursively replace the chunks to recover executable code.\todo{Explain.}
\end{notate}

\begin{elisp}
(defun tangle-module (node get-cont ins-links)
  (insert-chunk
   (funcall get-cont node)
   (mapcar #'(lambda (x)
               (cons (car x)
                     (tangle-module (cdr x)
                                    get-cont
                                    ins-links)))
           (funcall ins-links node))))
\end{elisp}

\begin{notate}{On `insert-chunk'}
Given a node and an association list of replacement texts, insert
the chunks at the appropriate places.
\end{notate}

\begin{elisp}
(defun insert-chunk (body chunks)
  (cond ((null body) nil)
        ((null chunks) body)
        ((equal (car body) '*insert*)
         (cdr (assoc (cadr body) chunks)))
        (t (cons (insert-chunk (car body) chunks)
                 (insert-chunk (cdr body) chunks)))))
\end{elisp}

\begin{notate}{Functions for rewriting nemas}
Several functions for rewriting nemas.\todo{How does this stuff relate to what's
going on in the vicinity of Note \ref{update-sink}?}
\end{notate}

\begin{elisp}
(defun set-src (n x)
  (if (equal n 0)
      0
    (progn (let ((old-backlink
                  (nth 1 (assoc (get-src n)
                                (cdr article-list)))))
             (setcdr old-backlink
                     (delete n (cdr old-backlink))))
           (let ((new-backlink
                  `(nth 1 (assoc x (cdr article-list)))))
             (setcdr new-backlink (cons n (cdr new-backlink))))
           (setcar (nth 1 (assoc n (cdr article-list))) x))))

(defun set-txt (n x)
  (setcar (cdr (cdr (assoc n (cdr article-list)))) x))

(defun set-snk (n x)
  (if (equal n 0)
      0
    (progn (let ((old-backlink
                  (nth 3 (assoc (get-snk n)
                                (cdr article-list)))))
             (setcdr old-backlink
                     (delete n (cdr old-backlink))))
           (let ((new-backlink
                  (nth 3 (assoc x (cdr article-list)))))
             (setcdr new-backlink (cons n (cdr new-backlink))))
           (setcar (nth 3 (assoc n (cdr article-list))) x))))

(defun ins-nod (src txt snk)
  (progn (setcdr article-list
                 (cons (list (car article-list)
                             (list src)
                             txt
                             (list snk))
                       (cdr article-list)))
         (let ((backlink
                (nth 3 (assoc snk (cdr article-list)))))
           (setcdr backlink (cons (car article-list)
                                  (cdr backlink))))
         (let ((backlink
                (nth 1 (assoc src (cdr article-list)))))
           (setcdr backlink (cons (car article-list)
                                  (cdr backlink))))
         (- (setcar article-list (+ 1 (car article-list))) 1)))

(defun del-nod (n)
  (if (or (equal n 0)
          (get-blk n)
          (get-flk n))
      nil
    (progn (let ((old-backlink
                  (nth 3 (assoc (get-snk n)
                                (cdr article-list)))))
             (setcdr old-backlink
                     (delete n (cdr old-backlink))))
           (let ((old-backlink
                  (nth 1 (assoc (get-src n)
                                (cdr article-list)))))
             (setcdr old-backlink
                     (delete n (cdr old-backlink))))
           (setcdr article-list
                   (delete (assoc n (cdr article-list))
                           (cdr article-list)))
            t)))
\end{elisp}

\subsection{Initialization}

\begin{notate}{Initialize with a new network}
For now, we just create one network to import things into.  Additional
networks can be added later (see Section \ref{applications}).
\end{notate}

\begin{elisp}
(set-current-plexus (add-plexus))
\end{elisp}

\section{An example middle\"end} \label{middle-end}

\begin{notate}{A middle\"end for managing collections of articles}
This middle\"end is a set of functions that add triples into the
backend.  At this stage we basically ignore details of storage, and
rely on the convenience functions defined above as the backend's API.
In principle it would be possible to swap out the backend for another
storage mechanism.  We will give an example later on that uses more of
the LISP-specific aspects of the backend implementation.\todo{Let's
  try to be a bit more concrete about this, especially in Section
  \ref{farm-demo}.}  In this example, rather than talking about nemas
and networks, we will talk about \emph{articles} and \emph{scholia}.
These objects are things that user will want to access, create, and
manipulate.  However, we will deal with functions for user interaction
(input, display, and editing) in Section \ref{frontend}, not here.
Like the backend, the middle\"end could also be swapped out in
applications where a different kind of data is modelled.  And in fact,
we come to some examples of other mid-level interfaces in Section
\ref{applications}.
\end{notate}

\subsection{Database interaction} \label{interaction}

\begin{notate}{The `article' function} \label{the-article-function}
You can use this function to create an article with a
given name and contents.  You can optionally put it in a
list by specifying the heading that it is under.  (If this
is used multiple times with the same heading, that just becomes
a cone over the contents.)
\end{notate}

\begin{elisp}
(defun article (name contents &optional heading)
  (let ((coordinates (add-nema name
                               "has content"
                               contents)))
    (when heading (add-nema coordinates "in" heading))
    coordinates))
\end{elisp}

\begin{notate}{The `scholium' function} \label{the-scholium-function}
You can use this function to link annotations to objects.
As with the `article' function, you can optionally
categorize the connection under a given heading (cf. Note
\ref{the-article-function}).
\end{notate}

\begin{elisp}
(defun scholium (beginning link end &optional heading)
  (let ((coordinates (add-nema beginning
                               link
                               end)))
    (when heading (add-nema coordinates "in" heading))
    coordinates))
\end{elisp}

\begin{notate}{Uses of coordinates}
It is convenient to do further immediate processing of the object
we've created while we still have ahold of the coordinates
returned by `add-nema' (e.g., for importing code
that is adjacent to the article, see Note
\ref{import-code-continuations}).
\end{notate}

\begin{notate}{On `get-article'} \label{get-article}
Get the contents of the article named `name'.
We assume that there is only one such article for now.
\end{notate}

\begin{elisp}
 ;; Something like this.
(defun get-article (name)
  (third (triples-given-beginning-and-middle
          name "has content")))
\end{elisp}

\begin{notate}{On `get-names'} \label{get-names}
This function simply gets the names of articles that have
names -- in other words, every triple built around the
``has content'' relation.\todo{This seems to work but
are both map operations needed?}
\end{notate}

\begin{elisp}
(defun get-names (&optional heading)
  (mapcar #'get-source
          (mapcar #'first (triples-given-middle "has content"))))
\end{elisp}

\section{An example frontend} \label{frontend}

\begin{notate}{Overview of the frontend}
The frontend provides a demonstration of Arxana's functionality that
is directly accessible to the user.  Specifically, it is used to
import \LaTeX\ documents into a network structure.  They can then be
edited, remixed, saved, browsed, and exported.\todo{Some of this
  functionality still needs to be merged in or written!}
\end{notate}

\subsection{Importing \LaTeX\ documents} \label{importing}

\begin{notate}{Importing sketch} \label{importing-sketch}
The code in this section imports a document, represented as a
collection of (sub-)sections and notes.  It gathers the sections,
sub-sections, and notes recursively and records their content in a
tree whose nodes are places and whose links express the
``component-of'' relation described in Note \ref{order-of-order}.

This representation lets us see the geometric, hierarchical, structure
of the document we've imported.  It exemplifies a general principle,
that geometric data should be represented by relationships between
places, not direct relationships between strings.  This is because
``the same'' string often appears in ``different'' places in any given
document (e.g. a paper's many sub-sections titled ``Introduction''
will not all have the same content).\todo{Do we need to relax this?}

What goes into the places is in some sense arbitrary.  The key is that
whatever is in or attached to these places must tell us
everything we need to know about the part of the document associated
with that place (e.g., in the case of a note, its title and contents).
That's over and above the structural links which say how the
places relate to one another.  Finally, all of these places and
structural links will be added to a heading that represents the
document as a whole.

A natural convention we'll use is to put the name of any document
component that's associated with a given place into that place, and
add all other information as annotations.\todo{Does this contradict
  what is said above about Introductions?}

Following our usual coding convention, functions are introduced
below ``from the bottom up.''
\end{notate}

\begin{notate}{On `import-code-continuations'} \label{import-code-continuations}
This function will run within the scope of `import-notes'.
In fact, it is meant to run right after a Note itself
has been scanned.  The job of this function is to turn the
series of Lisp chunks or other code snippets that follow a given note
into a scholium attached to that note.  Each separate snippet becomes
its own annotation.  The ``conditional regexps'' form used here only
works with Emacs version 23 or higher.\todo{Note the use of an
edge-pointing-to-an-edge for categorization; is this a good style?}
\end{notate}

\begin{elisp}
;; coords don't exist anymore, now we use uids
(defun import-code-continuations (coords)
  (let ((possible-environments
         "\\(?1:elisp\\|idea\\|common\\)"))
    (while (looking-at
            (concat "\n*?\\\\begin{"
                    possible-environments
                    "}"))
      (let* ((beg (match-end 0))
             (environment (match-string 1))
             (end (progn (search-forward-regexp
                          (concat "\\\\end{"
                                  environment
                                  "}"))
                         (match-beginning 0)))
             (content (buffer-substring-no-properties
                       beg
                       end)))
        (scholium (scholium coords
                            "has attachment"
                            content)
                  "has type"
                  environment)))))
\end{elisp}

\begin{notate}{On `import-notes'} \label{import-notes}
We're going to make the daring assumption that the ``textual''
portions of incoming \LaTeX\ documents are contained in ``Notes''.
That assumption is true, at least, for the current document.  The
function takes a buffer position `end' that denotes the end of the
current section.  The function returns the count of the number of
notes imported, so that `import-within' knows where to start counting
this section's non-note children.\todo{Would this same function work
  to import all notes from a buffer without examining its sectioning
  structure?  Not quite, but close! (Could be a fun exercise to fix
  this.)}
\end{notate}

\begin{elisp}
(defun import-notes (end)
  (let ((index 0))
    (while (re-search-forward (concat "\\\\begin{notate}"
                                      "{\\([^}\n]*\\)}"
                                      "\\( +\\\\label{\\)?"
                                      "\\([^}\n]*\\)?")
                              end t)
      (let* ((name
              (match-string-no-properties 1))
             (tag (match-string-no-properties 3))
             (beg
              (progn (next-line 1)
                     (line-beginning-position)))
             (end
              (progn (search-forward-regexp
                      "\\\\end{notate}")
                     (match-beginning 0)))
             ;; get the uid for our new nema
             (coords (add-nema name "in" buffername)))
        (scholium coords
                  "has content"
                  (buffer-substring-no-properties
                   beg end))
        (setq index (1+ index))
        ;; current-parent is in scope inside import-within
        (scholium current-parent
                  index
                  coords
                  buffername)
        (import-code-continuations coords)))
    index))
\end{elisp}

\begin{notate}{On `import-within'}
Recurse through levels of sectioning in a document to import
\LaTeX\ code.  Children that are notes are attached to the
hierarchical structure by the subroutine `import-notes', called by
this function. Sections are attached directly by `import-within'.  We
observe that a note ``has content'' whereas a section does not.

Incidentally, when looking for the end of an importing level, `nil' is
an OK result: that describes the case when we have reached the
\emph{last} section at this level \emph{and} there is no subsequent
section at a higher level.
\end{notate}

\begin{elisp}
(defun import-within (levels)
  (let ((this-level (car levels))
        (next-level (car (cdr levels))) answer)
    (while (re-search-forward
            (concat
             "^\\\\" this-level "{\\([^}\n]*\\)}"
             "\\( +\\\\label{\\)?"
             "\\([^}\n]*\\)?")
            level-end t)
      (let* ((name (match-string-no-properties 1))
             (at (add-nema name "in" buffername))
             (level-end
              (or (save-excursion
                    (search-forward-regexp
                     (concat "^\\\\" this-level "{.*")
                     level-end t))
                  level-end))
             (notes-end
              (if next-level
                  (or (progn (point)
                             (save-excursion
                               (search-forward-regexp
                                (concat "^\\\\"
                                        next-level "{.*")
                                level-end t)))
                      level-end)
                level-end))
             (index (let ((current-parent at))
                      (import-notes notes-end)))
             (subsections (let ((current-parent at))
                            (import-within (cdr levels)))))
        (while subsections
          (let ((coords (car subsections)))
            (setq index (1+ index))
            (scholium at
                      index
                      coords
                      buffername)
            (setq subsections (cdr subsections))))
        (setq answer (cons at answer))))
    (reverse answer)))
\end{elisp}

\begin{notate}{On `import-buffer'}
This function imports a \LaTeX\ document, taking care of
the high-level, non-recursive, aspects of this operation.
It imports frontmatter (everything up to the first
\texttt{\textbackslash begin\{section\}}), but assumes ``backmatter'' is
trivial, and does not attempt to import it.  The imported
material is classified as a ``document'' with the same
name as the imported buffer.

Links to sections will be made under the ``heading'' of this
document.\todo{The sectioning levels should maybe be scholia attached
  to root-coords, but for some reason that wasn't working so well --
  investigate later -- maybe it just wasn't good to run after running
  `import-within'.}
\end{notate}

\begin{elisp}
(defun import-buffer (&optional buffername)
  (save-excursion
    (set-buffer (get-buffer (or buffername
                                (current-buffer))))
    (goto-char (point-min))
    (search-forward-regexp "\\\\begin{document}")
    (search-forward-regexp "\\\\section")
    (goto-char (match-beginning 0))
    (scholium buffername "is a" "document")
    (scholium buffername
              "has frontmatter"
              (buffer-substring-no-properties
               (point-min)
               (point))
              buffername)
    (let* ((root-coords (add-nema buffername "in" buffername))
           (levels
            '("section" "subsection" "subsubsection"))
           (current-parent buffername)
           (level-end nil)
           (sections (import-within levels))
           (index 0))
      (while sections
        (let ((coords (car sections)))
          (setq index (1+ index))
          (scholium root-coords
                    index
                    coords
                    buffername))
        (setq sections (cdr sections))))))
\end{elisp}

\begin{notate}{On `autoimport-arxana'} \label{autoimport-arxana}
This just calls `import-buffer', and imports this document
into the system.
\end{notate}

\begin{elisp}
(defun autoimport-arxana ()
  (interactive)
  (import-buffer "arxana-merge.tex"))
\end{elisp}

\subsection{Browsing database contents} \label{browsing}

\begin{notate}{Browsing sketch} \label{browsing-sketch}
This section facilitates browsing of documents represented
with structures like those created in Section
\ref{importing}, and sets the ground for browsing other
sorts of contents (e.g. collections of tasks, as in
Section \ref{managing-tasks}).

In order to facilitate general browsing, it is not enough
to simply use `get-article' (Note \ref{get-article}) and
`get-names' (Note \ref{get-names}), although these
functions provide our defaults.  We must provide the means
to find and display different things differently -- for
example, a section's  table of contents will typically
be displayed differently from its actual contents.

Indeed, the ability to display and select elements of
document sections (Note \ref{display-section}) is
basically the core browsing deliverable.  In the process
we develop a re-usable article selector (Note
\ref{selector}; cf. Note \ref{browsing-tasks}).  This in
turn relies on a flexible function for displaying
different kinds of articles (Note \ref{display-article}).
\end{notate}

\begin{notate}{On `display-article'} \label{display-article}
This function takes in the name of the article to display.
Furthermore, it takes optional arguments `retriever' and
`formatter', which tell it how to look up and/or format
the information for display, respectively.

Thus, either we make some statement up front (choosing our
`formatter' based on what we already know about the
article), or we decide what to display after making some
investigation of information attached to the article, some
of which may be retrieved and displayed (this requires
that we specify a suitable `retriever' and a complementary
`formatter').

For example, the major mode in which to display the
article's contents could be stored as a scholium attached
to the article; or we might maintain some information
about ``areas'' of the database that would tell us up
front what which mode is associated with the current area.
(The default is to simply insert the data with no markup
whatsoever.)

Observe that this works when no heading argument is given,
because in that case `get-article' looks for \emph{all}
place pseudonyms.  (But of course that won't work well
when we have multiple theories containing things with the
same names, so we should get used to using the heading
argument.)

(The business about requiring the data to be a sequence
before engaging in further formatting is, of course, just
a matter of expediency for making things work with the
current dataset.)
\end{notate}

\begin{elisp}
(defun display-article
  (name &optional heading retriever formatter)
  (interactive "Mname: ")
  (let* ((data (if retriever
                   (funcall retriever name heading)
                 (get-article name heading))))
    (when (and data (sequencep data))
      (save-excursion
        (if formatter
            (funcall formatter data heading)
          (pop-to-buffer (get-buffer-create
                          "*Arxana Display*"))
          (delete-region (point-min) (point-max))
          (insert "NAME: " name "\n\n")
          (insert data)
          (goto-char (point-min)))))))
\end{elisp}

\begin{notate}{An interactive article selector} \label{selector}
The function `get-names' (Note \ref{get-names}) and
similar functions can give us a collection of articles.
The next few functions provide an interactive
functionality for moving through this collection to find
the article we want to look at.

We define a ``display style'' that the article selector
uses to determine how to display various articles.  These
display styles are specified by text properties attached
to each option the selector provides.  Similarly, when
we're working within a given heading, the relevant heading
is also specified as a text property.

At selection time, these text properties are checked to
determine which information to pass along to
`display-article'.
\end{notate}

\begin{elisp}
(defvar display-style '((nil . (nil nil))))

(defun thing-name-at-point ()
  (buffer-substring-no-properties
   (line-beginning-position)
   (line-end-position)))

(defun get-display-type ()
  (get-text-property (line-beginning-position)
                     'arxana-display-type))

(defun get-relevant-heading ()
  (get-text-property (line-beginning-position)
                     'arxana-relevant-heading))

(defun arxana-list-select ()
  (interactive)
  (apply 'display-article
         (thing-name-at-point)
         (get-relevant-heading)
         (cdr (assoc (get-display-type)
                     display-style))))

(define-derived-mode arxana-list-mode fundamental-mode
  "arxana-list" "Arxana List Mode.

\\{arxana-list-mode-map}")

(define-key arxana-list-mode-map (kbd "RET")
            'arxana-list-select)
\end{elisp}

\begin{notate}{On `pick-a-name'} \label{pick-a-name}
Here `generate' is the name of a function to call to
generate a list of items to display, and `format' is a
function to put these items (including any mark-up) into
the buffer from which individiual items can then be
selected.

One simple way to get a list of names to display would be
to reuse a list that we had already produced (this would
save querying the database each time).  We could, in fact,
store a history list of lists of names that had been
displayed previously (cf. Note \ref{local-storage}).

We'll eventually want versions of `generate' that provide
various useful views into the data, e.g., listing all of
the elements of a given section (Note
\ref{display-section}).

Finding all the elements that match a given search term,
whether that's just normal text search or some kind of
structured search would be worthwhile too.  Upgrading the
display to e.g. color-code listed elements according to
their type would be another nice feature to add.
\end{notate}

\begin{elisp}
(defun pick-a-name (&optional generate format heading)
  (interactive)
  (let ((items (if generate
                   (funcall generate)
                 (get-names heading))))
    (when items
      (set-buffer (get-buffer-create "*Arxana Articles*"))
      (toggle-read-only -1)
      (delete-region (point-min)
                     (point-max))
      (if format
          (funcall format items)
        (mapc (lambda (item) (insert item "\n")) items))
      (toggle-read-only t)
      (arxana-list-mode)
      (goto-char (point-min))
      (pop-to-buffer (get-buffer "*Arxana Articles*")))))
\end{elisp}

\begin{notate}{On `get-section-contents'} \label{get-section-contents}
This function is used by `display-section'
(Note \ref{display-section}) to `pick-a-name' as a generator
for the table of contents of the section with the given
name under the given heading.

This function first finds the triples that begin with the
(placed) name of the section, then checks to see which of
these are in the heading of the document we're examinining
(in other words, which of these links represent structural
information about that document).  It also looks at the
items found at the end of these links to see if they are
sections or notes (``noteness'' is determined by them
having content).  The links are then sorted by their
middles (which show the order in which these components
have in the section we're examining).  After this ordering
information has been used for sorting, it is deleted, and
we're left with just a list of names in the appropriate
order, together with an indication of their noteness.
\end{notate}

\begin{elisp}
(defun get-section-contents (name heading)
  (let (contents)
    (dolist (triple (triples-given-beginning
                     `(1 ,(resolve-ambiguity
                           (get-places name)))))
      (when (triple-exact-match
             `(2 ,(car triple)) "in" heading)
        (let* ((number (print-middle triple))
               (site (isolate-end triple))
               (noteness
                (when (triples-given-beginning-and-middle
                       site "has content")
                  t)))
        (setq contents
              (cons (list number
                          (print-system-object
                           (place-contents site))
                          noteness)
                    contents)))))
    (mapcar 'cdr
            (sort contents
                  (lambda (component1 component2)
                    (< (parse-integer (car component1))
                       (parse-integer (car component2))))))))
\end{elisp}

\begin{notate}{On `format-section-contents'} \label{format-section-contents}
A formatter for document contents, used by
`display-document' (Note \ref{display-document}) as input
for `pick-a-name' (Note \ref{pick-a-name}).

Instead of just printing the items one by one,
like the default formatter in `pick-a-name'  does,
this version adds appropriate text properties, which
we determine based the second component of
of `items' to format.
\end{notate}

\begin{elisp}
(defun format-section-contents (items heading)
  ;; just replicating the default and building on that.
  (mapc (lambda (item)
          (insert (car item))
          (let* ((beg (line-beginning-position))
                 (end (1+ beg)))
            (unless (second item)
              (put-text-property beg end
                                 'arxana-display-type
                                 'section))
            (put-text-property beg end
                               'arxana-relevant-heading
                               heading))
          (insert "\n"))
        items))
\end{elisp}

\begin{notate}{On `display-section'} \label{display-section}
When browsing a document, if you select a section, you
should display a list of that section's constituent
elements, be they notes or subsections.  The question
comes up: when you go to display something, how do you
know whether you're looking at the name of a section, or
the name of an article?

When you get the section's contents out of the database
(Note \ref{get-section-contents})
\end{notate}

\begin{elisp}
(defun display-section (name heading)
  (interactive (list (read-string
                      (concat
                       "name (default "
                       (buffer-name) "): ")
                      nil nil (buffer-name))))
  ;; should this pop to the Articles window?
  (pick-a-name `(lambda ()
                  (get-section-contents
                   ,name ,heading))
               `(lambda (items)
                  (format-section-contents
                   items ,heading))))

(add-to-list 'display-style
             '(section . (display-section
                          nil)))
\end{elisp}

\begin{notate}{On `display-document'} \label{display-document}
When browsing a document, you should first display its
top-level table of contents.  (Most typically, a list of
all of that document's major sections.)  In order to do
this, we must find the triples that are begin at the node
representing this document \emph{and} that are in the
heading of this document.  This boils down to treating the
document's root as if it was a section and using the
function `display-section' (Note \ref{display-section}).
\end{notate}

\begin{elisp}
(defun display-document (name)
  (interactive (list (read-string
                      (concat
                       "name (default "
                       (buffer-name) "): ")
                      nil nil (buffer-name))))
  (display-section name name))
\end{elisp}

\begin{notate}{Work with `heading' argument}
We should make sure that if we know the heading we're
working with (e.g. the name of the document we're
browsing) that this information gets communicated in the
background of the user interaction with the article
selector.
\end{notate}

\begin{notate}{Selecting from a hierarchical display} \label{hierarchical-display}
A fancier ``article selector'' would be able to display
several sections with nice indenting to show their
hierarchical order.
\end{notate}

\begin{notate}{Browser history tricks} \label{history-tricks}
I want to put together (or put back together) something
similar to the multihistoried browser that I had going in
the previous version of Arxana and my Emacs/Lynx-based web
browser, Nero\footnote{{\tt http://metameso.org/~joe/nero.el}}.
The basic features are:
(1) forward, back, and up inside the structure of a given
document; (2) switch between tabs.  More advanced features
might include: (3) forward and back globally across all
tabs; (4) explicit understanding of paths that loop.

These sorts of features are independent of the exact
details of what's printed to the screen each time
something is displayed.  So, for instance, you could flip
between section manifests a la Note \ref{display-section},
or between hierarchical displays a la Note
\ref{hierarchical-display}, or some combination; the key
thing is just to keep track in some sensible way of
whatever's been displayed!
\end{notate}

\begin{notate}{Local storage for browsing purposes} \label{local-storage}
Right now, in order to browse the contents of the
database, you need to query the database every time.  It
might be handy to offer the option to cache names of
things locally, and only sync with the database from time
to time.  Indeed, the same principle could apply in
various places; however, it may also be somewhat
complicated to set up.  Using two systems for storage, one
local and one permanent, is certainly more heavy-duty than
just using one permanent storage system and the local
temporary display.  However, one thing in favor of local
storage systems is that that's what I used in the the
previous prototype of Arxana -- so some code already
exists for local storage!  (Caching the list of
\emph{names} we just made a selection from would be one
simple expedient, see Note \ref{pick-a-name}.)
\end{notate}

\begin{notate}{Hang onto absolute references}
Since `get-article' (Note \ref{get-article}) translates
strings into their ``place pseudonyms'', we may want to
hang onto those pseudonyms, because they are, in fact, the
absolute references to the objects we end up working with.
In particular, they should probably go into the
text-property background of the article selector, so it
will know right away what to select!
\end{notate}

\subsection{Exporting \LaTeX\ documents$^*$}

\begin{notate}{Roundtripping}
The easiest test is: can we import a document into the
system and then export it again, and find it unchanged?
\end{notate}

\begin{notate}{Data format}
We should be able to \emph{stably} import and export a
document, as well as export any modifications to the
document that were generated within Arxana.  This means
that the exporting functions will have to read the data
format that the importing functions use, \emph{and} that
any functions that edit document contents (or structure)
will also have to use the same format.  Furthermore,
\emph{browsing} functions will have to be somewhat aware
of this format.  So, this is a good time to ask -- did we
use a good format?
\end{notate}

\subsection{Editing database contents$^*$} \label{editing}

\begin{notate}{Roundtripping, with changes}
Here, we should import a document into the system and then
make some simple changes, and after exporting, check with
diff to make sure the changes are correct.
\end{notate}

\begin{notate}{Re-importing}
One nice feature would be a function to ``re-import'' a
document that has changed outside of the system, and make
changes in the system's version whereever changes appeared
in the source version.
\end{notate}

\begin{notate}{Editing document structure}
The way we have things set up currently, it is one thing
to make a change to a document's textual components, and
another to change its structure.  Both types of changes
must, of course, be supported.
\end{notate}

\section{Applications} \label{applications}

\subsection{Managing tasks} \label{managing-tasks}

\begin{notate}{What are tasks?}
Each task tends to have a \emph{name}, a
\emph{description}, a collection of \emph{prerequisite
  tasks}, a description of other \emph{material
  dependencies}, a \emph{status}, some \emph{justification
  of that status}, a \emph{creation date}, and an
\emph{estimated time of completion}.  There might actually
be several ``estimated times of completion'', since the
estimate would tend to improve over time.  To really
understand a task, one should keep track of revisions like
this.
\end{notate}

\begin{notate}{On `store-task-data'} \label{store-task-data}
Here, we're just filling in a frame.  Since ``filling in a
frame'' seems like the sort of operation that might happen
over and over again in different contexts, to save space,
it would probably be nice to have a macro (or similar)
that would do a more general version of what this function
does.
\end{notate}

\begin{elisp}
(defun store-task-data
  (name description prereqs materials status
        justification submitted eta)
  (add-nema name "is a" "task")
  (add-nema name "description" description)
  (add-nema name "prereqs" prereqs)
  (add-nema name "materials" materials)
  (add-nema name "status" status)
  (add-nema name "status justification" justification)
  (add-nema name "date submitted" submitted)
  (add-nema name "estimated time of completion" eta))
\end{elisp}

\begin{notate}{On `generate-task-data'} \label{generate-task-data}
This is a simple function to create a new task matching
the description above.
\end{notate}

\begin{elisp}
(defun generate-task-data ()
  (interactive)
  (let ((name (read-string "Name: "))
        (description (read-string "Description: "))
        (prereqs (read-string
                  "Task(s) this task depends on: "))
        (materials (read-string "Material dependencies: "))
        (status (completing-read
                 "Status (tabled, in progress, completed):
                 " '("tabled" "in progress" "completed")))
        (justification (read-string "Why this status? "))
        (submitted
         (read-string
          (concat "Date submitted (default "
                  (substring (current-time-string) 0 10)
                  "): ")
          nil nil (substring (current-time-string) 0 10)))
        (eta
         (read-string "Estimated date of completion:")))
    (store-task-data name description prereqs materials
                     status
                     justification submitted eta)))
\end{elisp}

\begin{notate}{Possible enhancements to `generate-task-data'}
In order to make this function very nice, it would be good
to allow ``completing read'' over known tasks when filling
in the prerequisites.  Indeed, it might be especially nice
to offer a type of completing read that is similar in some
sense to the tab-completion you get when completing a file
name, i.e., quickly completing certain sub-strings of the
final string (in this case, these substrings would
correspond to task areas we are progressively zooming down
into).

As for the task description, rather than forcing the user
to type the description into the minibuffer, it might be
nice to pop up a separate buffer instead (a la the
Emacs/w3m textarea).  If we had a list of all the known
tasks, we could offer completing-read over the names of
existing tasks to generate the list of `prereqs'.  It
might be nice to systematize date data, so we could more
easily e.g. sort and display task info ``by date''.
(Perhaps we should be working with predefined database
types for dates and so on.)

Also, before storing the task, it might be nice to offer
the user the chance to review the data they entered.
\end{notate}

\begin{notate}{On `get-filler'} \label{get-filler}
Just a wrapper for `triples-given-beginning-and-middle'.
(Maybe we should add `heading' as an optional argument here.)
\end{notate}

\begin{elisp}
(defun get-filler (frame slot)
  (third (first
          (print-triples
           (triples-given-beginning-and-middle frame
                                               slot)))))
\end{elisp}

\begin{notate}{On `get-task'} \label{get-task}
Uses `get-filler' (Note \ref{get-filler}) to assemble the
elements of a task's frame.
\end{notate}

\begin{elisp}
(defun get-task (name)
  (when (triple-exact-match name "is a" "task")
    (list (get-filler name "description")
          (get-filler name "prereqs")
          (get-filler name "materials")
          (get-filler name "status")
          (get-filler name "status justification")
          (get-filler name "date submitted")
          (get-filler name
                      "estimated time of completion"))))
\end{elisp}

\begin{notate}{On `review-task'} \label{review-task}
This is a function to review a task by name.
\end{notate}

\begin{elisp}
(defun review-task (name)
  (interactive "MName: ")
  (let ((task-data (get-task name)))
    (if task-data
        (display-task task-data)
      (message "No data."))))

(defun display-task (data)
  (save-excursion
    (pop-to-buffer (get-buffer-create
                    "*Arxana Display*"))
    (delete-region (point-min) (point-max))
    (insert "NAME: " name "\n\n")
    (insert "DESCRIPTION: " (first data) "\n\n")
    (insert "TASKS THIS TASK DEPENDS ON: "
            (second data) "\n\n")
    (insert "MATERIAL DEPENDENCIES: "
            (third data) "\n\n")
    (insert "STATUS: " (fourth data) "\n\n")
    (insert "WHY THIS STATUS?: " (fifth data) "\n\n")
    (insert "DATE SUBMITTED:" (sixth data) "\n\n")
    (insert "ESTIMATED TIME OF COMPLETION: "
            (seventh data) "\n\n")
    (goto-char (point-min))
    (fill-individual-paragraphs (point-min) (point-max))))
\end{elisp}

\begin{notate}{Possible enhancements to `review-task'}
Breaking this down into a function to select the task and
another function to display the task would be nice.  Maybe
we should have a generic function for selecting any object
``by name'', and then special-purpose functions for
displaying objects with different properties.

Using text properties, we could set up a ``field-editing
mode'' that would enable you to select a particular field
and edit it independently of the others.  Another more
complex editing mode would \emph{know} which fields the
user had edited, and would store all edits back to the
database properly.  See Section \ref{editing} for more on
editing.
\end{notate}

\begin{notate}{Browsing tasks} \label{browsing-tasks}
The function `pick-a-name' (Note \ref{pick-a-name}) takes
two functions, one that finds the names to choose from,
and the other that says how to present these names.  We
can therefore build `pick-a-task' on top of `pick-a-name'.
\end{notate}

\begin{elisp}
(defun get-tasks ()
  (mapcar #'first
          (print-triples
           (triples-given-middle-and-end "is a" "task")
           t)))

(defun pick-a-task ()
  (interactive)
  (pick-a-name
   'get-tasks
   (lambda (items)
     (mapc (lambda (item)
             (let ((pos (line-beginning-position)))
               (insert item)
               (put-text-property pos (1+ pos)
                                  'arxana-display-type
                                  'task)
               (insert "\n"))) items))))

(add-to-list 'display-style
             '(task . (get-task display-task)))
\end{elisp}

\begin{notate}{Working with theories}
Presumably, like other related functions, `get-tasks'
should take a heading argument.
\end{notate}

\begin{notate}{Check display style}
Check if this works, and make style consistent between
this usage and earlier usage.
\end{notate}

\begin{notate}{Example tasks}
It might be fun to add some tasks associated with
improving Arxana, just to show that it can be done...
maybe along with a small importer to show how importing
something without a whole lot of structure can be easy.
\end{notate}

\begin{notate}{Org mode integration}
The ``default'' task manager on Emacs is Org mode.  It would be good
to provide integration between Org mode and Arxana.  This is one of
the first things that Emacs people ask about when they hear about
Arxana.
\end{notate}

\subsection{``Modelling mathematics the way it is really done''} \label{farm-demo}

\begin{notate}{A demonstration}
In a paper for the 5th ACM SIGPLAN International Workshop on
Functional Art, Music, Modelling and Design (FARM 2017), we talk about
how Arxana can be applied to model mathematical proofs.  A rather
advanced form of ``mathematical knowledge management'' is proposed,
that integrates dialogue, heuristics, and that ultimately moves in the
direction of an AI system.  In this section, we should walk through
this application.
\end{notate}

\section{Conclusion} \label{conclusion}

\begin{notate}{Ending and beginning again}
This is the end of this Arxana demo system.  Contributions that
support the development of the Arxana project are welcome.
\end{notate}

\appendix

\section{Appendix: A simple literate programming system} \label{appendix-lit}

\begin{notate}{The literate programming system used in this paper}
This code defines functions that grab all the Lisp portions of this
document, and evaluates the Emacs Lisp sections.  It requires that the
\LaTeX\ be written in a certain consistent way.  The function assumes
that this document is the current buffer.

\begin{verbatim}
(defvar lit-code-beginning-regexp
  "^\\\\begin{elisp}")

(defvar lit-code-end-regexp
  "^\\\\end{elisp}")

(defvar lit-count 0)

(defun lit-eval ()
  (interactive)
  (lit-process 'eval))

(defun lit-process (&optional code)
  (interactive)
  (setq lit-count (1+ lit-count))
  (save-excursion
    (let ((to-buffer (concat "*Lit Code " (int-to-string
                                            lit-count)"*"))
          (from-buffer (buffer-name (current-buffer))))
      (set-buffer (get-buffer-create to-buffer))
      (erase-buffer)
      (set-buffer (get-buffer-create from-buffer))
      (goto-char (point-min))
      (while (re-search-forward
              lit-code-beginning-regexp nil t)
        (let* ((beg (match-end 0))
               (end (save-excursion
                      (search-forward-regexp
                       lit-code-end-regexp nil t)
                      (match-beginning 0)))
               (match (buffer-substring beg end)))
          (save-excursion
            (set-buffer to-buffer)
            (insert match))))
      (case code
       ('eval
        (set-buffer to-buffer)
        (eval-buffer)
        ;; (kill-buffer (current-buffer))
        )
       (t
        (switch-to-buffer to-buffer))))))
\end{verbatim}
\end{notate}

\begin{notate}{A literate style}
Ideally, each function will have its own Note to introduce
it, and will not be called before it has been defined.  I
sometimes make an exception to this rule, for example,
functions used to form recursions may appear with no
further introduction, and may be called before they are
defined.
\end{notate}

\end{document}