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Re: [ddlm-group] Dictionary versioning

  • To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org>
  • Subject: Re: [ddlm-group] Dictionary versioning
  • From: "Bollinger, John C" <John.Bollinger@STJUDE.ORG>
  • Date: Mon, 24 Jul 2017 14:02:10 +0000
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Dear DDLm group,


I completely agree with James’s suggestion to use semantic versioning as the basis for dictionary version numbers.  These principles are probably familiar already to most people on this group, but some may be unaware that there is an actual standard-ish document describing them, published at http://semver.org/.  As presented there, semver is focused on software versioning, but inasmuch as the purpose is determining and managing compatibility between separately-maintained, interdependent software components, I don’t think it’s much of a stretch to apply them to separately-maintained, interdependent data components, such as CIF dictionaries.


As for the behavior of combining dictionaries to form a composite, we now have two procedures for that: the dictionary merging protocol, documented in ITvG, and DDLm’s importing facility.  I suppose James uses the term “import” specifically in reference to DDLm’s import mechanism, but we should not neglect the dictionary merging protocol.  If we don’t want to give it any other consideration then we should at least say that the rest of this discussion, and in particular the principles for assigning version numbers to dictionaries, are specific to DDLm dictionaries.  If that were the direction we went, then I would furthermore recommend deprecating the dictionary merging protocol for use with DDLm dictionaries.


As far as the behavior of DDLm importation when existing and imported attributes collide, we should clarify exactly what situation or situations that would be.  Since the issue is couched in terms of attributes, not whole definitions, I suppose we must be talking about an import defined with


_import_details.mode 'Contents'


, else there is no scope for an attribute-level collision.  Is that correct?  If so, the question seems to assume that the associated value of _import_details.if_dupl is not relevant in that case.  Such an assumption is consistent with the letter of that item’s definition, but seems perhaps contrary to its spirit.  If this is the path we are traversing, then I think we should clarify the meaning and applicability of _import_details.if_dupl as a threshold issue for the rest of this discussion.


For reference, I’m looking at the current version of DDLm as published on the IUCr web site, version 3.11.09.








John C. Bollinger, Ph.D.

Computing and X-Ray Scientist

Department of Structural Biology

St. Jude Children's Research Hospital


(901) 595-3166 [office]




From: ddlm-group [mailto:ddlm-group-bounces@iucr.org] On Behalf Of James Hester
Sent: Monday, July 24, 2017 12:59 AM
To: ddlm-group <ddlm-group@iucr.org>
Subject: [ddlm-group] Dictionary versioning


Dear DDLm group,

The vagueness of dictionary versioning has been raised as an issue (see https://github.com/COMCIFS/cif_core/issues/47). Now that dictionaries can import template dictionaries, it becomes possible that the template dictionary could change in ways that would render the main dictionary incorrect, for example, if a necessary attribute was removed from the template definition.  Such fiddling with template attributes has recently been proposed (see https://github.com/COMCIFS/cif_core/issues/42) as a solution to certain technical issues.

While COMCIFS will obviously endeavour to maintain both template dictionaries and main dictionaries as a compatible whole, we should come up with some principles for versioning to guide authors and editors, as well as authors of dictionary checking software.  I suggest that we use semantic versioning of the form <major>.<minor>.<patch>, where a change in the major version number is required when incompatible changes are introduced.

There are two situations that are important: importing pieces of a definition from a template dictionary, and importing a whole dictionary in order to build on it. 

Versioning in template dictionaries: Firstly, there has been no explicit statement of how importation should treat the presence of the same attribute in both the template and the importing definition - I suggest the simple principle that the value in the importing definition always has precedence over the imported value. Assuming this, a template dictionary will be potentially incompatible with an importing dictionary if attributes are removed from a definition, a definition is itself removed, or the value of an attribute is changed in a way that would change the behaviour of software.  Either of these three changes would require an increase in the major version number of a template dictionary.  Other changes are covered by the rules below for full dictionaries.

Versioning in full dictionaries: we never make any changes in a domain dictionary that would require a change in major version number as this would undermine our goal of stable, universal data names. We are then left with simple rules for changing the non-major version numbers in both full and template dictionaries:

  1. change the patch version for typo correction, rewording and clarification
  2. increment the minor version for all other changes: additions to enumerations, new definitions, moving data names to aliases of new definitions

Feel free to respond either on the github issue or here.



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