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[ddlm-group] Proposal to update dREL, ,part I

To: ddlm-group <ddlm-group@iucr.org>
Subject: [ddlm-group] Proposal to update dREL, ,part I
From: James Hester <jamesrhester@gmail.com>
Date: Tue, 28 Aug 2018 12:41:47 +1000
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Dear DDLm group,

As part of working up dREL for Vol G and expanding it for use in validation contexts, I will be presenting a series of small proposals regarding dREL. The first one below simply clears up a few ambiguities in existing documents. Please comment if you see any issues. A marked-up version is available at https://github.com/COMCIFS/dREL/blob/master/drel_changes_1.rst

thanks

James.

=======

Proposed changes to dREL, part I

================================

Introduction

------------

dREL is a machine-actionable language describing data relationships

and designed to be embedded in DDLm dictionaries. The language is

defined both explicitly in the dREL publication [1] and implicitly by

the dREL code appearing in the DDLm core CIF dictionary. Note that

the code in the core CIF dictionary significantly expands the language

presented in the paper, for example, by adding category methods.

The present changes are relatively trivial and intended to simplify

and clarify the syntax. Following proposals will be more substantial.

Proposal 1: underscores

-----------------------

The proposal: A leading underscore in front of a variable is optional,

and has no significance. Its use is deprecated.

Explanation

~~~~~~~~~~~

The dREL paper states that the value of a data name from a Set

category can be accessed by using the form `<category>.<name>` in a

dREL script, for example `cell.volume` (p 1919, "Data References in

dREL"). However, the dREL methods in the current core CIF dictionary

and the dREL paper almost always use a form with a leading underscore,

i.e. `_<category>.<name>`.

Discussion

~~~~~~~~~~

The paper does not explain the appearance of the underscore in the

example methods presented there. It is possible that the underscore is

provided as a way to disambiguate ordinary variables from dictionary

items; however, as a period character must appear in a dictionary

reference, and may not appear in a variable, such disambiguation is

unnecessary. It is also important to note that the period character

is an operator in dREL, so the construction `cell.volume` is formally

referring to the `volume` column in the current packet of the `cell`

category. In this context, the leading underscore is potentially

misleading.

The `with` statement is available to alias category names in any

situation where a category name may collide with a language keyword.

Proposal 2: newline is not significant

--------------------------------------

The proposal: newline should be treated as ordinary whitespace.

Explanation

~~~~~~~~~~~~

If newline is treated as ordinary whitespace it is not significant for

separating expressions. However, the dREL paper Appendix, Section 4,

states that "dREL supports the following expression terminators:

... newline closes a line unless a balancing [bracket] is missing",

which may be construed as allowing newline to terminate an expression.

Discussion

~~~~~~~~~~

The draft dREL grammar at the COMCIFS/drel repository assumes that

newline is whitespace. The example parser based on this grammar does

not identify any problems with the grammar. Nick Spadaccini

has advised me that newline was not meant to be significant in the

dREL grammar.

[1] Spadaccini et. al,

(2012) *J. Chem. Inf. Model.* **52**(8) pp 1917-1925

T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148

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