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Well, it sounds like there are two types of changes wrapped into one. By two types I mean a set of changes that does not lend itself to code review, and those that do. The overwhelming bulk (by "lines changed") seems to fall into the former category, suggesting that there is a small enough set in the latter category to still enable review. As it is, this PR is unreviewable, so if we keep it we shouldn't pretend it was ever reviewed. It sounds to me though that the changes that don't stand to benefit from review (decrypting files, for example) can be separated out, even if they would necessarily have to be accompanied by some code changes (in the tests) too. But there seem to be additional code changes (items 2, 3, and 6 in your list) that are separable changes of code that seem reviewable and would benefit from having been reviewed. |
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This is the number used by the Gene Ontology, Uberon and other ontologies.
Since the plan is for them to have these terms in the Clade Ontology.
This unencrypts it.
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These are the reviewable changes from PR #89, which are primarily `regnum2phyx.js` changes: - Improvements to how author names are rendered: we now support first-name first, last-name first, or last-name only. - Generate scientific name authorship by using first-name first and combining them with " and ". - Generate specifier authors by using last-name only and combining them with " and ". - Added a CLI option to configure the number of digits in the `CLADO_` name, which now defaults to 7 instead of the previous 6. - Modified the script to produce `CLADO_0000000` filenames instead of `REGNUM_0000000` filenames. Two other minor changes: - Added an optional test to ensure that Phyx files have at least one Newick phylogeny in order to see how many we have. - Removed `phyloref_testcase.owl`, which was previously a copy of the phyloref.owl ontology we used to do reasoning.
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This PR cleans up Regnum phylorefs in several ways:
REGNUM_*toCLADO_*and increased the number of digits to seven.encrypted/directory so that they will no longer be encrypted (closes Unencrypt Phylonym files #82).phyx/phylonymfor two kinds of errors we've been running into:newick-problemsandnewick-recursion-error.phyx2owl.js, a script to convert Phyx files to OWL for testing -- I'll replace this with the phyx.js library later.phyxfix.js, a script to correct errors in curated Phyx files on the fly, and used it to fix specifier authorities that were not loaded correctly (i.e. before PR Improvements to regnum2phyx.js #96).