[Cif2-encoding] How we wrap this up
James Hester
jamesrhester at gmail.com
Tue Sep 28 07:40:40 BST 2010
I happily confess to agreeing with John on this one.
I am beginning to think I might understand Herbert's viewpoint. Correct me
Herbert if I am wrong, but you are suggesting that current CIF1 workflows
are implicitly or explicitly choosing some encoding when they operate with
CIF1 files. If we mandate some other encoding for CIF2, then those
workflows will be adversely affected as they will need to choose a different
encoding.
I'll critique this further if Herbert confirms that this is what he is
getting at.
On Tue, Sep 28, 2010 at 9:14 AM, Herbert J. Bernstein <
yaya at bernstein-plus-sons.com> wrote:
> Now to the substance of John's argument, which he also attributes to
> James:
>
> "I will not support an alternative that fails to make UTF-8 a universally
> supported character encoding for CIF, and it seems clear that James will
> not, either."
>
> To me it seems the key to this position is "universally supported" which
> would seem to imply that there be full documentation and software to allow
> CIF users to work within that context. The practicality of that position
> comes down to the IUCr and the PDB working out workflows and the necessary
> support infrastructure to get the entire small and macromlecular CIF
> community to make the transition. Do the IUCr journal operation and the
> PDB have plans and a realistic timeline to do this? If not, then are CIF2
> and dREL to wait on the sidelines until then? If so, may we please see
> them to get a sense of when the transition could happen?
>
> I suspect we are 90% of the way to where we need to be, but in the same
> sense as 90% is used in the old saw: The first 90% of the effort takes
> the first 90% of the time, and the last 10% of the effort takes the last
> 90% of the time. But I may be wrong. Let's see the plans for the
> proposed transition for the IUCr journal operation and the PDB, dealing
> with both core CIF and mmCIF in a UTF8 CIF2 world.
>
> 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 at dowling.edu
> =====================================================
>
> On Mon, 27 Sep 2010, Herbert J. Bernstein wrote:
>
> > Dear Colleagues,
> >
> > John declines to join in a meeting because ...
> >
> > "Is there anything to gain? The last few days have been more
> illuminating
> > than the last several weeks, but it still seems evident to me that there
> > is a fundamental difference of opinion. I will not support an
> alternative
> > that fails to make UTF-8 a universally supported character encoding for
> > CIF, and it seems clear that James will not, either. You seem adamant
> > that there be no such universal requirement. I think I understand your
> > position better than I used to do, but I don't see where there is any
> > scope for a consensus. My best offer is already on the table in option
> > (5) +- UTF-16."
> >
> > I a very sorry to hear that. I hope the rest of you will have the
> > courtesy to participate in a Skype meeting. Perhaps no new facts
> > or logic will come to light. Perhaps something will come to light
> > that leads to better common understanding and concensus. We'll never
> know
> > unless we try. I for one think that most of us are open minded and
> > willing to try to reach an accomodation that serves the community well.
> >
> > 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 at dowling.edu
> > =====================================================
> >
> > On Mon, 27 Sep 2010, Bollinger, John C wrote:
> >
> >> Dear Herb,
> >>
> >> On Monday, September 27, 2010 8:45 AM, Herbert J. Bernstein wrote:
> >>
> >>> The problem is that options 3,4 and 5 specifically prescribe the use of
> Unicode characters (that is the entire point of those options -- and that is
> the point in dispute -- whether we should be prescribing UTF8 or using is as
> we now use ASCII, as a way to be clear what we are talking about as in CIF1)
> and we simply are not ready to deal such a requirement yet.
> >>
> >> I think I have reached my own epiphany regarding your position. Do
> correct me if I am wrong, but I now think you're saying that you don't want
> to distinguish any particular encoding(s) as universally acceptable (much
> less universally required), correct? If so, would it be fair to describe
> that as just the "local" part of option 5?
> >>
> >> [...]
> >>
> >> On Monday, September 27, 2010 12:07 PM, Herbert J. Bernstein wrote:
> >>
> >>> Ah, now I begin to understand the difference in our view. I view CIF
> for
> >>> journal use and PDB deposition as having a controlled vocabulary, via
> >>> combinations of dictionaries, advice to authors, deposition standards,
> >>> etc. You seem to few CIF as allowing completely arbitrary,
> uncontrolled
> >>> text. [...]
> >>
> >> Yes, I intentionally take an unilluminated view of the problem, but that
> is both purposeful and useful. Text is the foundation on which CIF is
> built. The bulk of the spec is devoted to defining which text conforms and
> which does not. The "F" in "CIF" stands for "file," however, and if the
> spec is to answer the question of which *files* conform, or the related
> question of what a particular file means, then it needs to address the
> mapping between "text" and "file". Options (1) and (2) seem crafted
> specifically to avoid doing so.
> >>
> >> I understand using local convention to fill the gap (ala "local"), but I
> fail to see how any amount of author instructions, deposition standards,
> etc. can adequately do the same. At best that moves a burden that
> rightfully should be borne by the format spec onto application-dependent
> external documents, some outside IUCr's control. I have shown by my
> advocacy for option (5) that I am willing to make the definition of a
> conformant CIF system-dependent. I acknowledge that that various
> applications place different demands on the data content of CIFs they
> consume. I am not, however, willing to make the basic definition of CIF
> conformance application-dependent.
> >>
> >>> Please note that proposals 1 and 2 do _not_ affect "which
> >>> byte-sequence representations of those characters will conform to
> >>> CIF2, under which circumstances" because they are not rigidly
> >>> prescriptive about any
> >>> particular byte sequences.
> >>
> >> Options (1) and (2) certainly DO affect that question, if only by
> leaving it open to later, possibly conflicting, interpretation by COMCIFS,
> individual developers, and others. Option 5 is about as permissive as it
> reasonably can be regarding the binary form a CIF may take, while still
> being definitive enough that general-purpose software can be written to read
> conformant CIFs. If my new understanding of your viewpoint is correct,
> however, then your objection may be that option 5 is *too* permissive on
> account of its explicit allowance for UTF-8 and UTF-16. I would be willing
> to drop the explicit UTF-16 support (though UTF-16 might nevertheless
> squeeze in as "local" in some environments). I will under no circumstances,
> however, support an alternative that allows any file to be found
> non-conformant on account of its being encoded in UTF-8.
> >>
> >> [...]
> >>
> >>> This is really getting out of hand. We need a meeting. If
> >>> everyone will send me their Skype id's, I will volunteer to
> >>> set up a Skype conference call at some time that works for
> >>> everybody (which I suspect will be 4 am EDT). My guess is that
> >>> 1-2 hours of polite discussion will resolve this. What
> >>> do we have to lose?
> >>
> >> Is there anything to gain? The last few days have been more
> illuminating than the last several weeks, but it still seems evident to me
> that there is a fundamental difference of opinion. I will not support an
> alternative that fails to make UTF-8 a universally supported character
> encoding for CIF, and it seems clear that James will not, either. You seem
> adamant that there be no such universal requirement. I think I understand
> your position better than I used to do, but I don't see where there is any
> scope for a consensus. My best offer is already on the table in option (5)
> +- UTF-16.
> >>
> >>
> >> Respectfully,
> >>
> >> 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 at iucr.org
> >> http://scripts.iucr.org/mailman/listinfo/cif2-encoding
> >>
> > _______________________________________________
> > cif2-encoding mailing list
> > cif2-encoding at iucr.org
> > http://scripts.iucr.org/mailman/listinfo/cif2-encoding
> >
> _______________________________________________
> cif2-encoding mailing list
> cif2-encoding at 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://scripts.iucr.org/pipermail/cif2-encoding/attachments/20100928/112127cc/attachment.html
More information about the cif2-encoding
mailing list