ciftools is not allowing flexibility in case for attributes

[BobHanson]

ciftools-java is requiring exact-case matches to its category and column names. However, http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html:

Data category and data item names are not case sensitive.

corresponding to

https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#case

_Case sensitivity

26. Data names, block and frames codes, and reserved words are case-insensitive. The case of any characters within data values must be respected._

Pull #2 addresses this issue; I thought it would be a separate pull, but I see now that it just attached one push to another. So sorry for that. Included there:

• the original pull request that covered the lazy initialization of categories (See DemoRead)
• additional "...Generic" classes that allow bypassing all generated classes and instead using the actual CIF tags for categories and columns (See DemoReadGeneric)
• code that fixes this capitalization issue -- at least for reading. I didn't implement writing for the generic options and thought perhaps that would be ok anyway, as the point there would be to do the reading specifically generically.

[JonStargaryen]

Good point, @BobHanson. The implementation indeed diverges from the format specification. However, it provides the same behavior as the original JS impl by David. I'll have a look at it and potentially will disentangle that functionality from #2.

[BobHanson]

OK, great. Sorry about the convoluted push. I was not expecting it to join all the commits into one pull request, but I guess that makes sense. As long as we all agree that case-insensitivity is important, I'm sure you can handle it better than I did. One option I didn't try but would of course be a very simple one would be to use .toLowerCase() in the MessagePack map binary reading (probably not map writing). I chose to do it later because I thought perhaps a read/write cycle should preserve the case of the attributes that were read. Totally above my pay grade to think about that.

…

On Mon, Dec 2, 2019 at 5:26 PM Sebastian Bittrich ***@***.***> wrote: Good point, @BobHanson <https://github.com/BobHanson>. The implementation indeed diverges from the format specification. However, it provides the same behavior as the original JS impl <https://github.com/dsehnal/CIFTools.js/blob/34cd913b12af9a0ebb9baca99af79903ab8989d7/src/Text/Parser.ts#L14> by David. I'll have a look at it and potentially will disentangle that functionality from #2 <#2>. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3?email_source=notifications&email_token=AEHNCW3LW5CDNQEESUXLDA3QWWYT7A5CNFSM4JTBSNOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFXYDKY#issuecomment-560955819>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEHNCW34UPW5MYOZGMK4H3TQWWYT7ANCNFSM4JTBSNOA> .

-- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

[JonStargaryen]

Did some reading. A really elegant solution would be to use new TreeMap<String, Object>(String.CASE_INSENSITIVE_ORDER) which keeps the original case of the keys while making get/put/et al case-insensitive. However, that enforces the natural ordering of all map entries.

Handling of category/column names is case insensitive as of a2f798e. CaseSensitivityTest defines the behavior for reading and writing. Thanks again for the input.

[BobHanson]

Great. I would go for the simplest solution possible. (please. ;)

…

On Tue, Dec 3, 2019 at 11:44 AM Sebastian Bittrich ***@***.***> wrote: Did some reading. A really elegant solution would be to use new TreeMap<String, Object>(String.CASE_INSENSITIVE_ORDER) which keeps the keys case sensitive while making get/put/et al case-insensitive. However, that enforces the natural ordering of all map entries. Handling of category/column names is case insensitive as of a2f798e <a2f798e>. CaseSensitivityTest defines the behavior for reading and writing. Thanks again for the input. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3?email_source=notifications&email_token=AEHNCW7SJAKMTN2K44PDYSLQW2ZJZA5CNFSM4JTBSNOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEF2SQLY#issuecomment-561326127>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEHNCW53MOYYP7VMRINBLU3QW2ZJZANCNFSM4JTBSNOA> .

-- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900