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Re: [ddlm-group] Relationship asmong CIF2, STAR,CIF1 and Python. . . .

My apologies, it appears Herbert has explained his concerns.   I
discuss them below.

On Sat, Jan 15, 2011 at 7:29 AM, Herbert J. Bernstein
<yaya@bernstein-plus-sons.com> wrote:
> Dear Colleagues,
>
>   I would suggest recalling that this CIF2 exercise began with
> tryin to define a DDLm/dREL-friendly version of CIF.  To the best
> of my knowledge, the current DDLm spec is at what is published
> on the IUCr web site under http://www.iucr.org/resources/cif/ddl/ddlm
> with draft documents from August 2008.  I propose that we all
> take the time to review those documents and make a conscious
> effort to decide if we wish to make use of them as a
> base for CIF2 or not.  They contain many points relevant
> to the current discussion.  For example:
>
> 1.   the top level page contains the bold-faced assurance to
> the community that "No changes are required in existing archival
> data files in order to apply domain dictionaries written in DDLm".
> Do we wish to return to that "minimally distruptive" approach, or
> do we wish to continue on the current "maximally disruptive
> approach" and why.

We have discussed minimal/maximal disruption ad nauseum and COMCIFS
have voted to accept the nuanced approach we took in the CIF2 changes
document.  There is no good reason to reopen this discussion.

> 2.  The DDLm document describes Lists and Arrays as being bracketed
> by [], Tuples as being bracketed by (), and Tables as being
> bracketed by {}.  Do we wish to return to that spec, or to
> use the revised spec which avoids [], and why?

We will update the DDLm document to use the new syntax.  This is a
trivial editorial change, not a fundamental problem.  This change
arose because we realised that Tuples and Lists are not distinct
datatypes in a situation where the concept of mutability is
meaningless (a data file).

> 3.  The dREL document describes rather pythonesque string literals
> with cooked, raw and Unicode strings, treble quotes, C-style elides and
> much more that has been rejected by this group.  Do we wish to
> bring the full dREL data type collection into CIF2 or not, and
> why.  If we reject some portion of the dREL data types, what
> shall we do when a dictionary method using those type generated
> a data item of a type we have rejected?

Just to make it clear to everybody: the presence or absence of
Pythonesque strings in CIF2 syntax has *no relevance* to the use of
Pythonesque strings in dREL.  This comment betrays a lack of
understanding of the relationship between dREL and CIF2.  CIF2
provides a simple container.  In terms of CIF2 syntax, a dREL function
is just another string that the CIF2 parser returns.  While the string
has domain-specific meaning, just as a chemical formula or LaTeX
paragraph has a meaning in the right context, it is just a string in
terms of the CIF2 syntax.  If the string that is returned is known to
be a dREL function, it is processed appropriately. So: whether or not
dREL defines Pythonesque strings is completely irrelevant to our
syntax discussions.

To answer the question above: dREL methods are required to produce
results that accord with the definition of the data name that they
calculate for.  The 'type' of a data name is defined in DDLm and/or
the domain dictionary, not the CIF2 syntax document and not the dREL
document.

> I had been under the mistaken impression that much of what this
> group decided had been donwe to achieve compatability with
> the new STAR and with DDLm and dREL.  It is now clear, that
> instead of achieving compatibility we have made integration
> of CIF2 with CIF1, STAR, DDLm and dREL more difficult.

Rubbish.  None of your above points 1,2 or 3 support this grandiose
statement.  The only result of what we have done is to require
technical editing of DDLm to remove the distinction between Lists and
Tuples.

> The more I look over the original DDLm and and dREL documents,
> the more convinced I am that we either need to revise CIF2 to
> conform with them, or we need to revise them to conform with
> CIF2 or both.

We need to revise the DDLm document to merge lists and tuples. That's all.
>
> It is time to start over.

No, it is time to stop making theatrical statements.
>
> Regards,
>    Herbert
>
> =====================================================
>  Herbert J. Bernstein, Professor of Computer Science
>    Dowling College, Kramer Science Center, KSC 121
>         Idle Hour Blvd, Oakdale, NY, 11769
>
>                  +1-631-244-3035
>                  yaya@dowling.edu
> =====================================================
>
> On Fri, 14 Jan 2011, Bollinger, John C wrote:
>
>> On Friday, January 14, 2011 9:23 AM, Herbert J. Bernstein wrote:
>>> hearing what others think on the current version of CIF2 feature by feature would help.
>>
>> I structure these comments after the changes document, and I comment primarily about the changes and additions in CIF2.  If more is desired then I probably need a list of the CIF features about which comments are solicited.
>>
>> * Feature: Magic Code
>> This, or something like it, is necessary to enable CIF parsers to adapt automatically to CIF1 vs. CIF2 input.  I consider that a worthwhile thing to be able to do, so I am in favor of this feature.
>>
>> * Feature: Unicode support This is my favorite new CIF feature, though I
>> think it could be slightly improved: 1) I think certain Unicode
>> character categories (space and control characters) should be forbidden
>> in data names 2) I think data block and save frame codes should follow
>> the same rules as data names (except for the leading underscore),
>> subject to line length limitations (it's not altogether clear from the
>> changes document whether they do, but I have supposed not)
>>
>> I do not object to limiting recognized whitespace characters and
>> newlines as CIF2 currently does.  However, if (1) above were adopted
>> then it would provide a clearer path to possible future full adoption of
>> Unicode whitespace semantics.
>>
>> I remain satisfied with the compromise we reached on encoding.
>>
>> * Change: treatment of newline I am on record as favoring this sort of
>> treatment as far back as during the preparation of CIF 1.1, and I still
>> favor it.
>>
>> * Change: allowed whitespace-delimited data values I would be happier if
>> it were not necessary to place stronger restrictions on the ASCII
>> content of these values, but if list and table data types are retained
>> then I can live with it. For forward-looking compatibility, it might be
>> better to forbid Unicode whitespace from appearing in these, even though
>> allowing such characters is not a problem for CIF2.
>>
>> * Change: string delimiters ('") cannot be embedded in data values they
>> delimit As unusual as CIF1's rules for quoted data values are, I do not
>> favor changing them in CIF2.  I would find the change more palatable
>> with the addition of some sort of escape or elide by which the delimiter
>> could be embedded, but more than that I would favor backwards
>> compatibility.
>>
>> * Restriction: text blocks cannot contain <newline>; This is not a
>> change from CIF 1.1 as far as I can tell, but our discussions have shown
>> that it differs at least from some older interpretations of CIF.  I am
>> satisfied with it, and I prefer it for compatibility with CIF 1.1.  If
>> there were evidence of a non-trivial body of CIFs relying on a different
>> interpretation, and if the changes to single-quoted string formatting
>> were reversed, then I might be persuaded to change my mind.
>>
>> * Feature: triple-quoted strings I have never been especially hot about
>> these, but I saw the advantage they provided when coupled with the
>> changes to single-quoted string syntax, and their use for quoting text
>> block delimiters.  I also see a compatibility advantage to using
>> exclusively these for new syntax and semantics, such as we have recently
>> been discussing.  I am mildly supportive.
>>
>> * Feature: list data type Inasmuch as this is supposedly needed for ddlm
>> / dREL, I'm OK with it.  I imagine there are other reasonable use cases
>> as well, though none presently come to mind.  I don't object to it, but
>> neither do I particularly favor it.
>>
>> * Feature: table data type My opinion of this is pretty much the same as
>> of the list data type.  I am slightly more negative about it because it
>> requires a restriction of allowable whitespace-delimited data values
>> relative to CIF 1.1, but I still do not object.
>>
>> * Undocumented Change: updated data model I have lately realized that
>> many of the CIF2 syntax changes imply changes to the CIF data model, but
>> that I find no documentation of those data model changes.  Really, the
>> data model updates should have been settled first, for the syntax serves
>> the model, not the other way around.  This would answer questions such
>> as the one I recently injected into the elide discussion, about whether
>> elides should be accepted that represent characters outside the revised
>> CIF character set.
>>
>> I have no problem with extension of the CIF1 data model, but I think we
>> need to better characterize the details of the new model.
>>
>>
>> Regards,
>>
>> John
>>
>> --
>> John C. Bollinger, Ph.D.
>> Department of Structural Biology
>> St. Jude Children's Research Hospital
>>
>>
>> Email Disclaimer:  www.stjude.org/emaildisclaimer
>>
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