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Re: [ddlm-group] Objectives of CIF2 syntax discussion
- To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org>
- Subject: Re: [ddlm-group] Objectives of CIF2 syntax discussion
- From: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
- Date: Wed, 19 Jan 2011 08:36:52 -0500 (EST)
- In-Reply-To: <AANLkTikZoEF_D+5-3+Eg4pbCx0cAu+SJvR-a_XkC3zK2@mail.gmail.com>
- References: <AANLkTikZoEF_D+5-3+Eg4pbCx0cAu+SJvR-a_XkC3zK2@mail.gmail.com>
If the CIF1 interoperability with DDLm is an absolute given, we should be able to work things out. That may or may not require changes in CIF2, but I am fairly sure it will require some new hooks in dREL and DDLm to be able to work fully with CIF1 tags. Perhaps I've missed those hooks. 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 Wed, 19 Jan 2011, James Hester wrote: > Dear all, I've changed the subject line. > > I believe that the objectives of the CIF2 discussion are as follows: > (1) Alter CIF1 syntax to accommodate DDLm and dREL > (2) Take the opportunity to improve CIF1 syntax to provide a net > benefit to the community > > If you like, we can include the constraint from the IUCr website that > "No changes are required in existing archival data files in order to > apply domain dictionaries written in DDLm", although I take this as a > statement of fact arising out of DDLm, not syntax. > > What has to be done for (1) is not contentious. Decisions on what to > do for (2) are, because they involve cost-benefit analyses taking into > account the various communities that Herbert has identified. Because > these assessments of cost/benefit are so dependent on the value that > we place as individuals on various aspects of CIF use, our discussions > have been long and not all decisions are necessarily to everybody's > liking. But those decisions do represent a set of compromises that we > have reached as concerned and involved CIF users. They thus reflect a > collective wisdom, and reopening discussion of them is likely to be > unproductive and time-consuming due to the many imponderables > involved. I would therefore urge anybody with a wishlist of changes > to the current CIF2 standard to stop and ask themselves how successful > they expect to be in convincing a majority of voting members to change > their mind. > > James. > > On Sun, Jan 16, 2011 at 11:26 PM, Herbert J. Bernstein > <yaya@bernstein-plus-sons.com> wrote: >> Dear Simon, >> >> If I read your message correctly, you seem to be saying that the design >> objectives of CIF2 are: >> >> 1. enchance CIF as a data source >> 2. accomodate DDLm >> 3. do 1 and 2 in a way that does not complicate CIF as a data source >> >> I don't understand what you mean by "enhance CIF as a data source". This is >> the first time I recall hearing that objective. Please clarify. >> >> In terms of present practice, I had thought that the major current uses of >> CIF to be: >> >> 1. As a language for publication of papers in IUCr journals; >> 2. As a language for submission of data to CCDC; >> 3. As a language for submission of data to the PDB; >> 4. As a data harvest language for CCP4; and >> 5. As a language for formatting image data from Dectris detectors, >> with some emerging use for data management of synchrotron data >> ( Please fill in uses I have missed ...) > > CIF in general is quite widespread as a format for transfer of > crystallographic data, both for submission to databases and input to a > myriad of niche programs. > >> which would seem to me to represent a large current investment in data >> management software that depends critically on stability and reliability of >> CIF representation of both numeric data and text. As I understand it, DDLm >> and dREL can contribute to these current uses by enhancing the reliabiity of >> validation of data in these contexts, especially in uses 1, 2 and 3, above. >> To me, that would seem to change the objectives to: >> >> 1. Accomodate DDLm and dREL; and >> 2. Do this in a way that keeps required changes to existing >> archives to a minimum; and >> 3. Do this in a way that allows as much existing CIF software >> as possible to continue to operate reliably; and >> 4. To the extent that changes will be needed in archives and >> software, provide a clearly understood mechanism for making >> those changes, with as much support software as possible; and >> 5. Subordinate to the above, add new features to CIF that may >> encourage broader use and more software support > > I agree with 1 and 2. I don't agree with 3 as an objective, because > it is in direct conflict with (1) as no CIF1 software will be able to > read CIF2 list structures. I would drop (3), and simply let objective > (4) carry the weight, that is, make the changes that are necessary to > software and archives as clear and simple as possible. > > I have no objections to 4 or 5. > > I believe that the current CIF2 standard fulfills (1) and (2) > completely as I have explained in other emails today. The changes > needed to current parsers are limited to small, easily understood > additions or changes, so (4) is satisfied. (5) is met by the addition > of Unicode (and I've already had plaudits from a European CIF user for > this change) and the removal of the unusual embedded quotes in > single-quoted strings. >> Please tell me what I have misunderstood in this. >> >> 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 Sun, 16 Jan 2011, SIMON WESTRIP wrote: >> >>> I believe that the CIF2 syntax changes enhance CIF as data source, >>> even with the restriction to the contents of ' and " delimited values, >>> which >>> I suspect will be the main source of incompatability between archived CIFs >>> and CIF2. What we havent acheived is 100% compatability of CIF1 with CIF2, >>> but having agreed that CIF2 is distinct from CIF1 and minimized the >>> incompatability, >>> I do not see the changes as disruptive or retrograde. >>> >>> DDLm methods will not be applicable to a significant percentage of a CIF >>> data source >>> (those 'free text' fields used to report experimental details etc.). I >>> believe other approaches >>> will be needed to enhance their content (referencing other data items from >>> an item etc). >>> Unicode support in CIF2 is beneficial in this area, and the new >>> alternative >>> delimiters may >>> prove convenient. The list and table structures may also be exploited. >>> >>> So from my point of view, though I understood the aim of CIF2 was to >>> accommodate DDLm, >>> it turns out that it does offer a little bit more. I would still like the >>> problem of including all delimiters >>> in a value to be solved, and line-folding to be included. On my 'wish >>> list' >>> are value concatenation >>> and a value-referencing mechanism for use with CIF as a data source. >>> >>> I know this doesnt really answer your question. What we are *not* trying >>> to >>> do is complicate >>> CIF as a data source? >>> >>> Cheers >>> >>> Simon >>> >>> >>> ____________________________________________________________________________ >>> From: Herbert J. Bernstein <yaya@bernstein-plus-sons.com> >>> To: Group finalising DDLm and associated dictionaries >>> <ddlm-group@iucr.org> >>> Sent: Sunday, 16 January, 2011 2:05:59 >>> Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and Python. >>> . >>> >>> Dear Simon, >>> >>> I have reviewed the record on this, and I have trouble finding >>> a strong basis for most of the decisions made other than arguments >>> from the authority of established past practice in STAR and dREL. >>> Now that those arguments have turned out not to have been what they >>> seemed, I have trouble accepting the resulting conclusions without >>> new, clearly stated arguments based in the functionality we are >>> trying to achieve, but it is now not even clear what functionality we >>> are >>> trying to achieve. >>> >>> Perhaps you can help me -- what are we trying to do in defining >>> CIF2? >>> >>> Regards, >>> Herbert >>> >>> >>> At 11:55 PM +0000 1/15/11, SIMON WESTRIP wrote: >>>> That's a question I asked myself when I first joined this discussion >>>> group >>> :-) >>>> >>>> To be honest Herbert, I do not feal qualified to contest anything to do >>> with >>>> dREL, nor DDLm, given that I havent worked on them and respecting the >>>> years of effort that went into development thus far. The same is >>>> true with respect to some of >>>> the changes to CIF syntax that invalidate CIF1: I have accepted that >>>> they are necessary >>>> to facilitate implementation of dREL methods. >>>> >>>> Cheers >>>> >>>> Simon >>>> >>>> >>>> >>>> From: Herbert J. Bernstein <yaya@bernstein-plus-sons.com> >>>> To: Group finalising DDLm and associated dictionaries >>>> <ddlm-group@iucr.org> >>>> Sent: Saturday, 15 January, 2011 23:14:36 >>>> Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and >>>> Python. >>> . >>>> >>>> Why not? It is almost that right now. >>>> >>>> >>>> At 11:08 PM +0000 1/15/11, SIMON WESTRIP wrote: >>>>> True - but I can't see dREL becoming pyREL at this stage? >>>>> >>>>> >>>>> >>>>> From: Herbert J. Bernstein >>>>> <<mailto:yaya@bernstein-plus-sons.com>yaya@bernstein-plus-sons.com> >>>>> To: Group finalising DDLm and associated dictionaries >>>>> <<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org> >>>>> Sent: Saturday, 15 January, 2011 22:57:17 >>>>> Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and >>>>> Python. >>> . >>>>> >>>>> Dear Simon, >>>>> >>>>> But dREL already shares much of Python syntax and data structures, >>>>> but, being significantly mutated, lacks the software support and >>>>> documentation that Python has. Anyone who has to work with the >>>>> methods in a DDLm dictionary would be much better off if we >>>>> simply made Python work with DDLm. We would gain large libraries >>>>> of pre-written utilities, tools to test code fragments interactively, >>>>> and a lot more time to do science or whatever we are actually >>>>> funded to do. >>>>> >>>>> Regards, >>>>> Herbert >>>>> >>>>> >>>>> >>>>> At 10:35 PM +0000 1/15/11, SIMON WESTRIP wrote: >>>>>> As far as I can see, parsing DDLm into an object stucture is fairly >>>>>> uncomplicated; >>>>>> the hurdle is parsing the dREL script as a method of the object. >>>>>> Unless working with python, I'm not sure that adopting python syntax >>>>>> for DDLm/CIF >>>>>> is of any great benefit; likewise for dREL. >>>>>> >>>>>> That said, I have yet to actually do anything with DDLm, let alone >>>>>> dREL, so I may be >>>>>> well off the mark. But even if this is the case, I suspect there >>>>>> will be non-python programmers out >>>>>> there that have cause to work with CIF and similarly will see no >>>>>> obvious benefit in >>>>>> CIF sharing python syntax (especially if it only adopts it for one >>>>>> set of delimiters at the >>>>>> data-source level). >>>>>> >>>>>> Cheers >>>>>> >>>>>> Simon >>>>>> >>>>>> >>>>>> >>>>>> From: Herbert J. Bernstein >>> >>>>>>>>> <<mailto:<mailto:yaya@bernstein-plus-sons.com>yaya@bernstein-plus-sons.c >>> om><mailto:yaya@bernstein-plus-sons.com>yaya@bernstein-plus-sons.com> >>>>>> To: Group finalising DDLm and associated dictionaries >>> >>>>>>>>> <<mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:ddlm-gr >>> oup@iucr.org>ddlm-group@iucr.org> >>>>>> Sent: Saturday, 15 January, 2011 21:16:59 >>>>>> Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and >>> Python. . >>>>>> >>>>>> At 12:43 PM +0000 1/15/11, Brian McMahon wrote: >>>>>>> It might be worth remarking (again) that dREL is being developed as a >>>>>>> canonical methods description language, and not necessarily the >>>>>>> runtime >>>> >>>methods evaluator of choice for future applications. It may be that >>>> in >>>>>>> practice future methods are initially developed and most frequently >>>>>>> executed directly in Python or some other language. As I see it, the >>>>>>> goal of CIF and DDL evolution is not to exclude such a possibility. >>>>>> >>>>>> If we are trying to be Python friendly and much of dREL is derived >>>>>> from a Jython implementation, I don't understand why we are not >>>>>> conforming dREL, DDLm and CIF2 to Python conventions as closely as >>>>>> possible. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> At 12:43 PM +0000 1/15/11, Brian McMahon wrote: >>>>>>> On Thu, Jan 13, 2011 at 05:35:21PM -0600, Bollinger, John C wrote: >>>>>>>> >>>>>>>> (snip) >>>>>>>> >>>>>>>> CIF2 <=> CIF1: >>>>>>>> To the greatest extent feasible, well-formed CIF1 documents should >>>>>>>> be >>>>>>>> well-formed CIF2 documents (modulo a CIF version identification >>>>>>>> signature) having the same meaning. >>>>>>> >>>>>>> Agreed. >>>>>>> >>>>>>>> CIF2 <=> STAR: >>>>>>>> Inasmuch as CIF1 is derived from STAR, I think it appropriate for >>> CIF2 >>>>>>>> to look first to STAR, including its post-CIF1 development, for new >>>>>>>> features it may need. Even if CIF2 is not 100% compatible with >>>>>>>> STAR, >>> it >>>>>>>> is worthwhile to avoid diverging without compelling reason. >>>>>>> >>>>>>> Agreed >>>>>>> >>>>>>>> CIF2 <=> Python: >>>>>>>> I see no particular reason for any formal relationship here beyond >>>>>>>> Python's role as the indirect inspiration for CIF2's new >>>>>>>> triple-quote syntax. I am wary of the idea of tying CIF tightly to >>>>>>>> a particular language. CIF2 documents are not and never will be >>>>>>>> Python programs. I could imagine embedding Python in CIF or vise >>>>> >>> versa, but I have seen no evidence to suggest that greater >>> similarity >>>>>>>> between the two languages' syntax and semantics would benefit >>>>>>>> efforts >>>>>>>> such as those. >>>>>>> >>>>>>> Agreed. As I mention elsewhere, there is a greater influence on the >>>>>>> prototype dREL (arising from the initial Jython implementation), and >>>>>>> the list and table data types doubtless arise from that also. >>>>>>> >>>>>>> It might be worth remarking (again) that dREL is being developed as a >>>>>>> canonical methods description language, and not necessarily the >>>>>>> runtime >>>>>>> methods evaluator of choice for future applications. It may be that in >>>>>> >practice future methods are initially developed and most frequently >>>>>>> executed directly in Python or some other language. As I see it, the >>>>>>> goal of CIF and DDL evolution is not to exclude such a possibility. >>>>>>> >>>>>>> Regards >>>>>>> Brian >>>>>>> _______________________________________________ >>>>>>> ddlm-group mailing list >>> >>>>>>>>>>> <mailto:<mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto >>> >>> :ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:<mailto:ddlm-group@iucr.or >>> g>ddlm-group@iucr.org><mailto:ddlm-group@iucr.org>ddlm-group@iucr.org >>> >>>>>>>>>>> <<<http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.i >>> >>> ucr.org/mailman/listinfo/ddlm-group><http://scripts.iucr.org/mailman/listin >>> >>> fo/ddlm-group>http://scripts.iucr.org/mailman/listinfo/ddlm-group><<http:// >>> >>> scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iucr.org/mailma >>> >>> n/listinfo/ddlm-group><http://scripts.iucr.org/mailman/listinfo/ddlm-group> >>> http://scripts.iucr.org/mailman/listinfo/ddlm-group >>>>>> >>>>>> >>>>>> -- >>>>>> ===================================================== >>>>>> Herbert J. Bernstein, Professor of Computer Science >>>>>> Dowling College, Kramer Science Center, KSC 121 >>>>>> Idle Hour Blvd, Oakdale, NY, 11769 >>>>>> >>>>>> +1-631-244-3035 >>>>>> >>> >>>>>>>>> <mailto:<mailto:<mailto:yaya@dowling.edu>yaya@dowling.edu><mailto:yaya@d >>> >>> owling.edu>yaya@dowling.edu><mailto:<mailto:yaya@dowling.edu>yaya@dowling.e >>> du><mailto:yaya@dowling.edu>yaya@dowling.edu >>>>>> ===================================================== >>>>>> _______________________________________________ >>>>>> ddlm-group mailing list >>> >>>>>>>>> <mailto:<mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto: >>> >>> ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:<mailto:ddlm-group@iucr.org >>>> ddlm-group@iucr.org><mailto:ddlm-group@iucr.org>ddlm-group@iucr.org >>> >>>>>>>>> <<<http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iu >>> >>> cr.org/mailman/listinfo/ddlm-group><http://scripts.iucr.org/mailman/listinf >>> >>> o/ddlm-group>http://scripts.iucr.org/mailman/listinfo/ddlm-group><<http://s >>> >>> cripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iucr.org/mailman >>> >>> /listinfo/ddlm-group><http://scripts.iucr.org/mailman/listinfo/ddlm-group>h >>> ttp://scripts.iucr.org/mailman/listinfo/ddlm-group >>>> >> >>>>>> >>>>>> _______________________________________________ >>>>>> ddlm-group mailing list >>> >>>>>>>>> <mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:ddlm-gro >>> up@iucr.org>ddlm-group@iucr.org >>> >>>>>>>>> <<http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iuc >>> >>> r.org/mailman/listinfo/ddlm-group><http://scripts.iucr.org/mailman/listinfo >>> /ddlm-group>http://scripts.iucr.org/mailman/listinfo/ddlm-group >>>>> >>>>> >>>>> -- >>>>> ===================================================== >>>>> Herbert J. Bernstein, Professor of Computer Science >>>>> Dowling College, Kramer Science Center, KSC 121 >>>>> Idle Hour Blvd, Oakdale, NY, 11769 >>>>> >>>>> +1-631-244-3035 >>>>> >>> >>>>>>> <mailto:<mailto:yaya@dowling.edu>yaya@dowling.edu><mailto:yaya@dowling.ed >>> u>yaya@dowling.edu >>>>> ===================================================== >>>>> _______________________________________________ >>>>> ddlm-group mailing list >>> >>>>>>> <mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:ddlm-grou >>> p@iucr.org>ddlm-group@iucr.org >>> >>>>>>> <<http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iucr >>> >>> .org/mailman/listinfo/ddlm-group><http://scripts.iucr.org/mailman/listinfo/ >>> ddlm-group>http://scripts.iucr.org/mailman/listinfo/ddlm-group >>>>> >>>>> >>>>> _______________________________________________ >>>>> ddlm-group mailing list >>>>> <mailto:ddlm-group@iucr.org>ddlm-group@iucr.org >>> >>>>>>> <http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iucr. >>> org/mailman/listinfo/ddlm-group >>>> >>>> >>>> -- >>>> ===================================================== >>>> Herbert J. Bernstein, Professor of Computer Science >>>> Dowling College, Kramer Science Center, KSC 121 >>>> Idle Hour Blvd, Oakdale, NY, 11769 >>>> >>>> +1-631-244-3035 >>>> <mailto:yaya@dowling.edu>yaya@dowling.edu >>>> ===================================================== >>>> _______________________________________________ >>>> ddlm-group mailing list >>>> <mailto:ddlm-group@iucr.org>ddlm-group@iucr.org >>> >>>>> <http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iucr.o >>> rg/mailman/listinfo/ddlm-group >>>> >>>> >>>> _______________________________________________ >>>> ddlm-group mailing list >>>> ddlm-group@iucr.org >>>> http://scripts.iucr.org/mailman/listinfo/ddlm-group >>> >>> >>> -- >>> ===================================================== >>> 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 >>> ===================================================== >>> _______________________________________________ >>> ddlm-group mailing list >>> ddlm-group@iucr.org >>> http://scripts.iucr.org/mailman/listinfo/ddlm-group >>> >> >> _______________________________________________ >> ddlm-group mailing list >> ddlm-group@iucr.org >> http://scripts.iucr.org/mailman/listinfo/ddlm-group >> >> > > > > -- > T +61 (02) 9717 9907 > F +61 (02) 9717 3145 > M +61 (04) 0249 4148 > _______________________________________________ > ddlm-group mailing list > ddlm-group@iucr.org > http://scripts.iucr.org/mailman/listinfo/ddlm-group >
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