Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [Cif2-encoding] Splitting of imgCIF and other sub-topics. .. .

Your step 3 is what we are discussing here.  It is not sufficient to
simply "suggest" reasonable mechanisms, as this leaves developers
bewildered as to which of these potentially vague suggestions they can
and should support, leading to confusion and inability of programs to
communicate with one another.  Far better to *specify* mechanisms,
which is what we are groping towards doing here.

Herbert: you have not reacted to a suggestion that we simply reserve
the first line of a CIF2 file for future expansion, and state that non
UTF8 encodings for CIF2 would be considered by COMCIFS as the need

On Sun, Sep 12, 2010 at 12:33 AM, Herbert J. Bernstein
<yaya@bernstein-plus-sons.com> wrote:
> Dear Colleagues,
>  Let me propose what I think would be a reasonable resolution:
> 1.  We come to a final resolution on what _information_ is in CIF2,
> independent of the representation used.  I think we have that in hand.
> 2.  We present one UTF-8 based _representation_ of that information
> for two essential purposes:
>  2.1.  To have a concrete way in which to present examples of CIF2; and
>  2.2.  To have a default assumed representation in which a CIF2 the
> representation of which is not otherwise identified is most likely
> to have been presented.
> 3.  That we suggest some reasonable mechanisms for helping software
> developers and users to determine which of the very large number of
> possible reprentations has been used for a given file, including,
> but not limited to:
>  BOM
>  Magic number
>  Extended idenfifying comments
>  Encoding tags in the file itself with sufficient detail to allow developers
> to get started, but
> with a final decision deferred on everything other than the BOM
> to allow for broad-based community discussion of what is clearly
> a contentious issue.  The BOM is going to be in _any_ final list
> because is is well-supported by several existing text
> editors, and keeps getting forced into files without any user
> control.
> 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 Sat, 11 Sep 2010, SIMON WESTRIP wrote:
>> Dear all
>> I have found recent exchanges, especially Herbert's contributions
>> regarding
>> the real-world use of imgCIF, very
>> enlightening. Primarily for reasons of flexibility, I now find myself
>> inclined to support a CIF specification
>> that allows a variety of encodings, provided that such are "clearly and
>> unambiguously defined".
>> To me, the clear and unambiguous definition should encompass a clear and
>> unambiguous *declaration*
>>  of the encoding; in the absence of such a declaration in the CIF or in
>> its
>> container, a default encoding
>> should be assummed, either the default CIF encoding (which I think most
>> agree should be UTF8) or inherited
>> from the container?
>> Though CIF1 has been successful without such a declaration (largely
>> because
>> of the ASCII restriction),
>> I beleive it is essential in the case of CIF2.
>> Cheers
>> Simon
>> ____________________________________________________________________________
>> From: "Bollinger, John C" <John.Bollinger@STJUDE.ORG>
>> To: Group for discussing encoding and content validation schemes for CIF2
>> <cif2-encoding@iucr.org>
>> Sent: Friday, 10 September, 2010 19:24:05
>> Subject: Re: [Cif2-encoding] Splitting of imgCIF and other sub-topics. ..
>> .
>> On Friday, September 10, 2010 11:02 AM, Herbert J. Bernstein wrote:
>> >As I have said before, we went through this approach
>> >in 1997 and ended up going the other way -- treating the
>> >text-based CIF and the binary CBF as parts of the _same_
>> >format, not two different formats, not one being a serialization
>> >of the other, but the same format.  This may seem like a
>> >minor distinction, but it actually has strong implications
>> >for software design and implementation, ensuring that
>> >binaries in a CIF context are just a particular type of data
>> >handled with all the same mecnahisms as ASCII data, allowing,
>> >for example, multiple diffraction images and thumbnails in
>> >one file in an order-independent way.
>> >
>> >You may be interested to know that the false dichotomy between
>> >binary and text-based representations is not starting
>> >to imapct HDF5, requiring some significant effort to now
>> >work in database access, an aspect CIF1 supports -- why
>> >throw it away for CIF2?
>> Herb,
>> Perhaps you're reading more into my comments than I intended to put
>> there.
>> In particular, I did not aim to suggest one on-disk/wire format should be
>> a
>> serialization of another, but rather that *all* on-disk/wire formats be
>> characterized in terms of serialization of the Unicode character sequences
>> described by most of the spec.  I meant "text" in that sense -- a sequence
>> of Unicode characters -- not in the sense of a sequence of bytes
>> conforming
>> to some particular set of local conventions for text.  I meant
>> "serialization" in the general sense of any reversible transformation of
>> CIF
>> text into a byte sequence, including those that rely on interpreting the
>> CIF
>> syntax.  That's aimed primarily at recognizing the use case in which CIF2
>> is
>> embedded in or transformed into some other format, such as XML.
>> I postulate, but do not specify, a serialization form defining the CIF2
>> version of what we have conventionally called "a CIF."  The details of
>> that
>> form are exactly what this list was established to discuss, and I did not
>> intend to imply a particular resolution of our ongoing debate.  It was
>> perhaps a mistake to include imgCIF/CBF on the list of possible
>> alternative
>> serialization forms, as it is far from settled whether it will fit under
>> the
>> umbrella of the 'CIF File' serialization form.  I apologize if that caused
>> confusion.
>> [... I wrote:]
>> >> I think this matter would be best addressed by explicitly adopting an
>> idea that we have discussed before: a formal separation between the
>> definition of CIF text (i.e. James's "CIF2-conformant character stream")
>> and
>> the particular kind of packaging that we are accustomed to calling "a CIF"
>> or "a CIF file".  James's suggestion implies such a separation anyway, so
>> let's not do it halfway.  Given such a separation, the explanatory comment
>> could be as simple as:
>> >>
>> >> "This specification's definition of the 'CIF File' serialization form
>> >> for
>> CIF2 text is not intended to preclude definition or use of other
>> serialization forms, such as HDF5-based forms, XML-based forms, or
>> imgCIF/CBF."
>> >>
>> >> I choose the term "serialization form" because it puts primary emphasis
>> on the CIF text (which after all is the subject of the bulk of the
>> specification).  Every correct serialization of CIF text is, by
>> definition,
>> transformable into CIF text form.
>> Regards,
>> John
>> --
>> John C. Bollinger, Ph.D.
>> Department of Structural Biology
>> St. Jude Children's Research Hospital
>> Email Disclaimer:  www.stjude.org/emaildisclaimer
>> _______________________________________________
>> cif2-encoding mailing list
>> cif2-encoding@iucr.org
>> http://scripts.iucr.org/mailman/listinfo/cif2-encoding
> _______________________________________________
> cif2-encoding mailing list
> cif2-encoding@iucr.org
> http://scripts.iucr.org/mailman/listinfo/cif2-encoding

T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148
cif2-encoding mailing list

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Council for Science (admitted 1947). Member of CODATA, the ICSU Committee on Data. Member of ICSTI, the International Council for Scientific and Technical Information. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

ICSU Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.