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Re: [ddlm-group] Use of elides in strings
- To: Nick.Spadaccini@uwa.edu.au, Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org>
- Subject: Re: [ddlm-group] Use of elides in strings
- From: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
- Date: Thu, 26 Nov 2009 07:41:46 -0500 (EST)
- In-Reply-To: <C73434A0.1262E%nick@csse.uwa.edu.au>
- References: <C73434A0.1262E%nick@csse.uwa.edu.au>
I am trying to get some CIF-2 related software done, so please advise me on some specific cases: How should the following C-style strings followed by their CIF-1.1 representations be presented in a CIF 2 document? I've only put in CIF 2 cases where I think there is no question, but feel free to correct those. C-style CIF-1.1 style CIF-2 "O'" "O'" or 'O'' "O'" "O\"" "O"" or 'O"' 'O"' "O'\"" "O'"" or 'O'"' ? "''O''" "''O''" or '''O''' "''O''" "'''O'''" "'''O'''" or ''''O'''' ? "\"\"O'\"\"" """O'""" or '""O'""' ? "\"\"\"O'\"\"\"" """"O'"""" or '"""O'"""' ? and for semi-colon delimited string, is the last new-line part of the string or part of the delimiter, i.e. if the string is "abc\n" is the CIF-2 version ;abc ; or ;abc ; ===================================================== 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 Thu, 26 Nov 2009, Nick Spadaccini wrote: > > > > On 25/11/09 10:24 PM, "SIMON WESTRIP" <simonwestrip@btinternet.com> wrote: > >> What Brian has said here - specifically >> >> "if this were dropped as part of the CIF2 specification, >> we would need to think carefully about how else to retain this >> functionality" >> >> is also relevant to how we handle the CIF1.1 markup conventions. >> As I understand it in CIF1.1 these are the default conventions for >> text fields unless the dictionary prohibits them, but in CIF2 all such >> conventions will _not_ be part of the spec, and can only be interpretted at >> the dictionary level. >> >> Is this correct? > > Yes, this is my understanding. There will be many different conventions I > presume, some will be widely accepted and standard, they will be part of the > underlying systems that interpret the files. For instance if something is > declared as a TeX encoding, we know what to do. > >> >> I'm only asking because we (at the IUCr at least) will have to address this >> issue sooner rather than later when adopting CIF2, so I just want to make sure >> I understand base CIF2 correctly >> >> Cheers >> >> Simon >> >> >> >> From: Brian McMahon <bm@iucr.org> >> To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org> >> Sent: Wednesday, 25 November, 2009 13:34:05 >> Subject: Re: [ddlm-group] Use of elides in strings >> >> (I've switched the thread title to deal separately with line folding.) >> >> As Herbert says, line folding is part of the CIF 1.1 spec (pages 34-35 >> of the ITG bible). Currently, it invokes a special meaning for the >> backslash (reverse solidus) character, but only when it is the first >> non-blank after an opening semicolon or comment hash delimiter. We have >> yet to discuss whether to extend it to other string types (specifically >> the triple-quoted strings). >> >> It's quite easy these days to generate single strings that are longer >> than 2048 characters (or any other arbitrary line limit) - e.g. a >> protein or nucleic acid sequence. Many, many chemical names broke the old >> 80-character line length limit. >> >> We're very happy with CIF applications that do not interpret the >> line-folding protocol, so long as they preserve the existing backslashes. >> However, a fully-compliant CIF 1.1 parser should be able to return an >> unfolded string to an application that requests it. >> >> As Herbert says, if this were dropped as part of the CIF2 specification, >> we would need to think carefully about how else to retain this >> functionality. >> >> Regards >> Brian >> >> On Wed, Nov 25, 2009 at 07:54:51AM -0500, Herbert J. Bernstein wrote: >>> The line folding protocol was discussed and adopted by COMCIFS and is >>> posted, aong with other "Common Semantic Features" at >>> >>> http://www.iucr.org/resources/cif/spec/version1.1/semantics >>> >>> but that is neither here nor there. The point is that the IUCr uses CIF >>> to get work done. If we disable something they are using, we should offer >>> some equivalent functionality so they can use CIF 2 to do their work. >>> Otherwise, they will have to do the sensible thing, and continue to use >>> CIF 1, or, worse, create their own dialect of CIF 2. >>> >>> Now, I broke my nose yesterday morning and find myself a bit punchy today, >>> so I will drop out of this discussion for a while. Hopefully, when I >>> return to it, this whole matter will be settled in some way that will >>> allow people to actually use CIF 2, instead of it becoming what it seems >>> on its way to becoming -- something elegant but not terrible useful, a bit >>> like PL/I. >>> >>> Cheers, >>> 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, 25 Nov 2009, Nick Spadaccini wrote: >>> >>>> I am with John. STAR has no line-folding protocol. As far as I can recall >>>> neither did CIF. Somewhere along the way line folding was discussed (or >>>> introduced?), but I am not sure it is formally part of any spec. >>>> >>>> None of my software handles anything about line folding. I can see no reason >>>> for it, since with a 2048 maximum record length, and a free format structure >>>> there is plenty of room to output your data. The only time it would be >>>> necessary is when (dataname + space + datavalue)> 2048 and when is that >>>> ever going to happen? >>>> >>>> May be the desire for it comes from making the data "pretty" and read well >>>> in a text editor. Well that is the task of an application to read the CIF >>>> and present it appropriately. The CIF is strictly about CONTENT and not >>>> FORM. >>>> >>>> Since we have given up on elided characters being part of CIF syntax, and >>>> the belief by others that this not be a lexer issue, I think we should >>>> absolutely consistent. The lexer knows how to identify tokens and reads >>>> everything within them as a raw string. >>>> >>>> If your "encoding" for \n; strings includes characters that break the lexer, >>>> then protect it in some way so that when you pass that string back as raw in >>>> your software, somebody knows how to unprotect it back to the original (as >>>> with ALL string encoding). >>>> >>>> One concession I think we can consider is to change the delimiter from \n; >>>> to \n;\n. I don't see this as causing me any problems, since I handle >>>> >>>> ; stuff >>>> More stuff >>>> ; _newname >>>> >>>> routinely, but others don't. I believe most people do use (and probably >>>> think) the delimiter is \n;\n anyway. >>>> >>>> Two questions >>>> >>>> (1) Do you agree that line folding just another encoding and therefore not a >>>> STAR/CIF issue? Consequently it is the responsibility of the encoding not to >>>> break the lexer. >>>> (2) Do we think \n;\n is a better delimiter? >>>> >>>> On 25/11/09 10:33 AM, "John Westbrook" <jwest@pdb-mail.rutgers.edu> wrote: >>>> >>>>> Hi James, >>>>> >>>>> My preference is avoid the elides in the syntax for the purpose of escaping >>>>> terminators >>>>> in strings deferring interpretation to the application. >>>>> >>>>> I do not understand all of the issues related to line folding, which I >>>>> believe is an issue for Brian and Simon. >>>>> >>>>> John >>>>> >>>>> >>>>> James Hester wrote: >>>>>> Thanks for the quick reply over Thanksgiving, John. I take from your >>>>>> message that the PDB does not need any elide mechanism to be defined >>>>>> in the CIF2 syntax. Would you therefore be prepared to vote in favour >>>>>> of not defining any elides, or would you prefer to abstain? >>>>>> >>>>>> Votes so far: >>>>>> >>>>>> No elides: James, Nick, Herbert if the IUCr + PDB say it is OK >>>>>> Elides:? >>>>>> >>>>>> Unknown: John, Joe, David B., Brian, Simon >>>>>> >>>>>> On Wed, Nov 25, 2009 at 12:03 PM, John Westbrook >>>>>> <jwest@pdb-mail.rutgers.edu> wrote: >>>>>>> I confess that I am having difficulty keeping up with all aspects >>>>>>> of this discussion. Following Herb's suggestion I will try to >>>>>>> summarize the quoting issues from the PDB perspective. >>>>>>> >>>>>>> 1. As there are multiple ways of quoting a string our tools and files >>>>>>> surround embedded quotes with quotes of the opposite sense or with >>>>>>> semicolons in the mixed case. I think that this point has been >>>>>>> covered a number of times now and I believe that Nick has suggested >>>>>>> that all reasonable cases can be handled by using this approach. >>>>>>> >>>>>>> 2. I too was not aware that original definition of terminators >>>>>>> had changed and did not include either a leading or trailing >>>>>>> whitespace. Certainly this must still be the case for single >>>>>>> and double quotes. I cannot recall ever seeing an example >>>>>>> where the terminator \n; was following by a whitespace character, >>>>>>> but about half of the codes that I am familiar with would >>>>>>> fall over on \n;next_token. >>>>>>> >>>>>>> 3. Line folding has never been an issue for PDB nor has line length. >>>>>>> >>>>>>> Regards, >>>>>>> >>>>>>> John >>>>>>> >>>>>>> >>>>>>> Herbert J. Bernstein wrote: >>>>>>>> My major concern about anything we do is to be able to preserve >>>>>>>> the functionality of the practices that the IUCr is following in >>>>>>>> journal publications and the PDB is following. Inasmuch as they seem >>>>>>>> able to cope with no elide in CIF 1.1, the remaining question is whether >>>>>>>> they will be negatively impacted by the change in string termination >>>>>>>> without any elide. If they can use CIF 2 with these changes, my >>>>>>>> objections are purely academic and irrelevant. -- Herberrt >>>>>>>> >>>>>>>> ===================================================== >>>>>>>> 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, 25 Nov 2009, James Hester wrote: >>>>>>>> >>>>>>>>> Herbert: I have the dubious advantage of not having participated in >>>>>>>>> all those CIF1.0/1.1 discussions, so only have the spec as written >>>>>>>>> down to rely on. >>>>>>>>> >>>>>>>>> Anyway, how do you feel about abandoning any specification of elides >>>>>>>>> in CIF2 syntax, as suggested by Nick? >>>>>>>>> >>>>>>>>> On Wed, Nov 25, 2009 at 10:53 AM, Herbert J. Bernstein >>>>>>>>> <yaya@bernstein-plus-sons.com> wrote: >>>>>>>>>> Dear James, >>>>>>>>>> >>>>>>>>>> I started to write: >>>>>>>>>> "No, in CIF 1.1, none of the terminal quote marks, including the \n; >>>>>>>>>> are >>>>>>>>>> effective unless followed by whitespace (\n, space, tab, of end of >>>>>>>>>> file). >>>>>>>>>> This is a well-established, and very tricky part of the CIF spec >>>>>>>>>> going back >>>>>>>>>> to 1990. That is why Nick had to explicitly specify that a terminal >>>>>>>>>> quote >>>>>>>>>> mark would be effective no matter what it was followed by." >>>>>>>>>> >>>>>>>>>> But the grammer currently on the IUCr web site is _not_ the one that >>>>>>>>>> I >>>>>>>>>> recall COMCIFs discussing and approving. It now explcitly removes >>>>>>>>>> the requirement for terminal white space in the special case of >>>>>>>>>> the \n; text field terminator. I don't recall when that change was >>>>>>>>>> adopted, >>>>>>>>>> but it appears that you are right under the current spec >>>>>>>>>> about the example I chose. Inasmuch as there is a lot of working code >>>>>>>>>> that enforces and uses the original whitespace handling and uses it >>>>>>>>>> in line-folding, I will not revise CIFtbx 3, but I will try to do >>>>>>>>>> something to adapt to this change for CIFtbx 4. >>>>>>>>>> >>>>>>>>>> I guess we are just going to have yet another few dialects of CIF. >>>>>>>>>> >>>>>>>>>> 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, 25 Nov 2009, James Hester wrote: >>>>>>>>>> >>>>>>>>>>> To be precise, we are not 'referring all elides to the application' >>>>>>>>>>> because no elides are recognised by the lexer under Nick's latest >>>>>>>>>>> suggestion, so there are no elides to refer to the application. >>>>>>>>>>> >>>>>>>>>>> My understanding of CIF1.1 syntax suggests that the string you >>>>>>>>>>> provide >>>>>>>>>>> would produce a syntax error in CIF1.1, as the semicolon at the start >>>>>>>>>>> of the second line would terminate the string, and so whitespace >>>>>>>>>>> should then appear as the second character on the second line, rather >>>>>>>>>>> than reverse solidus. >>>>>>>>>>> >>>>>>>>>>> On Wed, Nov 25, 2009 at 9:23 AM, Herbert J. Bernstein >>>>>>>>>>> <yaya@bernstein-plus-sons.com> wrote: >>>>>>>>>>>> The only problem with referring all elisdes to the application is >>>>>>>>>>>> that >>>>>>>>>>>> with the removal of the requirement of a blank after a \n; for it >>>>>>>>>>>> to be >>>>>>>>>>>> effective, the line folding protocol develops a slight gap. The >>>>>>>>>>>> case is as follows >>>>>>>>>>>> >>>>>>>>>>>> ;\ >>>>>>>>>>>> ;\ >>>>>>>>>>>> ; >>>>>>>>>>>> >>>>>>>>>>>> Is a valid single text field in CIF 1.1, which when handled with the >>>>>>>>>>>> line folding protocol translates to the equivalent of ';' because >>>>>>>>>>>> the >>>>>>>>>>>> embedded ;\ is not a valid text terminator. If we require that >>>>>>>>>>>> a text field the begins with "\n;\\" must be terminated by "\n; " >>>>>>>>>>>> or "\n;\n" or "\n;\t" that problem would be fixed. >>>>>>>>>>>> >>>>>>>>>>>> ===================================================== >>>>>>>>>>>> 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 > > cheers > > Nick > > -------------------------------- > Associate Professor N. Spadaccini, PhD > School of Computer Science & Software Engineering > > The University of Western Australia t: +61 (0)8 6488 3452 > 35 Stirling Highway f: +61 (0)8 6488 1089 > CRAWLEY, Perth, WA 6009 AUSTRALIA w3: www.csse.uwa.edu.au/~nick > MBDP M002 > > CRICOS Provider Code: 00126G > > e: Nick.Spadaccini@uwa.edu.au > > > > > _______________________________________________ > 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
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