Using Org-Mode Table Formatting Functions

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Introduction

In large-scale data analysis, one often associates integers with parameter name rather than strings. The performance and storage difference is significant for multi-gigabyte data sets. But integers are not at all convenient or descriptive. Systems like R provide a factor data type that translates the stored integers into user-level strings. Emulating that construct in SQL is handy for data transfer with SQLite or out-of-core analysis in R using a SQL back-end. That leaves the problem of maintaining a registry of integer level codes, string names, and documentation.

Org-mode provide a fast, light-weight table mechanism that can be sent in email, bundled with code, or embedded in documentation. The tables can be transformed and placed elsewhere. It sounds like a perfect registry, generating documentation and code from one data table. Similar techniques could be used in a multi-lingual document to store many translations in one table and send them to sections in specific languages.

We start with a simple table:

Name Level Description
normx 1 norm(x, ∞)
normb 2 norm(b, ∞)
normA 3 norm(A, ∞)

That one source table contains the documentation in the first and third column:

#+BEGIN RECEIVE ORGTBL exdoc

Name Description
normx norm(x, ∞)
normb norm(b, ∞)
normA norm(A, ∞)

#+END RECEIVE ORGTBL exdoc

The first two columns of the source table provide the data we must transfer the SQL. The third column can be used to embed some documentation into the table itself after the string is sanitized for SQL. The remaining necessary information, the SQL destination table name, can be provided as a parameter to #+ORGTBL: SEND, producing the following code chunk:

#+BEGIN RECEIVE ORGTBL exsql

BEGIN TRANSACTION;
INSERT INTO extbl( Name, Level, Description ) VALUES ( 'normx' , 1 , 'norm(x, infty)' );
INSERT INTO extbl( Name, Level, Description ) VALUES ( 'normb' , 2 , 'norm(b, infty)' );
INSERT INTO extbl( Name, Level, Description ) VALUES ( 'normA' , 3 , 'norm(A, infty)' );
COMMIT;

#+END RECEIVE ORGTBL exsql

We will explain the parameters used to produce both outputs. The SQL insertion statements use functions as formatting parameters, some of which are called purely for the side-effect of gathering the header fields. The SQL-generating code is distributed with org-mode in contrib/lisp/orgtbl-sqlinsert.el.

Specifying multiple destinations for a single table

Sending one table to multiple destinations is straight-forward. Add one SEND directive for each destination. For example, the first table has the following two directives prepended, with parameters described later:

#+ORGTBL: SEND exdoc orgtbl-to-orgtbl ...
#+ORGTBL: SEND exsql orgtbl-to-sqlinsert ...

The documentation removes the second column and adds fiddly formatting parameters with

:skipcols (2) :fmt (1 "=%s=") :hfmt (1 "%s")

The SQL-generating line gathers the destination table name and passes integers through unchanged with the parameters

:sqlname "extbl" :fmt (2 "%s")

The SQL table name defaults to the name of the target, exsql in this case. And the default formatting used for other columns is orgtbl-sql-strip-and-quote. That routine only removes potentially non-portable constructs; it is not designed to prevent insertion attacks.

We could apply orgtbl-sql-strip-and-quote to the first column of the documentation table to ensure the strings match exactly, but it easier to use simple, non-mangled strings as names.

By default, a block of insertions is wrapped in BEGIN TRANSACTION and COMMIT statements. These can be supressed by setting :tstart and :tend to nil. The example used in this document uses a "double-embedding" trick to wrap the statement in an org-mode code block:

:tstart "#+BEGIN_EXAMPLE\nBEGIN TRANSACTION;"
:tend "COMMIT;\n#+END_EXAMPLE"

Similar wrapping can embed the SQL statements into literate programs. There is built-in support for Noweb with the :nowebname parameter. Setting :nowebname to a string wraps the insertions in a Noweb code chunk named with the string.

Formatting with functions for side effects and display

The orgtbl-to-sqlinsert routine calls orgtbl-to-generic for all the generic table parsing. The parameters provide an example of using functions for gathering data as well as formatting. Emacs Lisp's dynamic binding allows manipulating any symbols in the current environment, so the formatting functions do not need to pass parameters through the outer functions.

The default :tstart parameter is one example used strictly for formatting. After the :nowebname parameter is decoded and bound to nowebname, it can be checked within a thunk to produce the starting string:

:tstart (lambda () (concat (if nowebname
                               (format "<<%s>>= \n" nowebname)
                             "")
                           "BEGIN TRANSACTION;"))

The functions need not be pure. The header formatting gathers the first header line into the variable hdrlist with

:hfmt (lambda (f) (progn (if firstheader (push f hdrlist)) ""))

Then each line is preceded with a function that uses hdrlist to ensure data values are associated with named columns rather than just positions.

:lstart (lambda () (concat "INSERT INTO "
                           sqlname "( "
                           (mapconcat 'identity (reverse hdrlist)
                                      ", ")
                           " )" (if breakvals "\n" " ")
                                    "VALUES ( "))

Note that orgtbl-to-sqlinsert takes advantage of org-mode's applying the formatting to each cell before checking for a line-formatting function. The header line itself and sectioning line are suppressed with the settings

:hlfmt (lambda (lst) (setq firstheader nil))
:hline nil
:remove-nil-lines t

Similar techniques could be used to generate a table's SQL definition from the second header line.

Current limitations

One current limitation is that all the tables are in the same Emacs buffer and hence the same text file. A literate programming mechanism like Noweb can separate the chunks.

Also, the tables must be sent manually. Writing a function that scans an entire buffer for all SEND and RECEIVE pairs is feasible, as is using overlays to manage automatic updates.

Documentation from the http://orgmode.org/worg/ website (either in its HTML format or in its Org format) is licensed under the GNU Free Documentation License version 1.3 or later. The code examples and css stylesheets are licensed under the GNU General Public License v3 or later.