Fixes to augur export #1218
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Fixes to augur export #1218
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The logic for creating colorings involves many steps, and when adding a coloring we had neglected to check if it had already been added. For instance, colorings explicitly defined in the auspice-config which were provided via node-data files (rather than the metadata tsv) would be added twice. In our current nCoV build there are 7 such duplicates! There were also a few duplicates that were present in our tests. Whoops! These weren't a problem for auspice (the first was used), but added unnecessary complexity and bytes to the JSON. Closes #719
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #1218 +/- ##
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+ Coverage 68.81% 68.88% +0.07%
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Files 64 64
Lines 6936 6939 +3
Branches 1692 1693 +1
==========================================
+ Hits 4773 4780 +7
+ Misses 1856 1854 -2
+ Partials 307 305 -2
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huddlej
reviewed
May 16, 2023
The intention of the coloring logic is that if an auspice-config provides the clade_membership key then it is exported at that position in the colorings list. If clade_membership is not explicitly set in the config (but is present in a node-data file) then we have (for a very long time) added it as the very first entry in the colorings list. PR #728 (augur v22.0.0) erroneously modified the behavior of the second case described above, which has now been restored by this commit.
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huddlej
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May 16, 2023
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I suggest we fast-track review & merge of this PR and then make an augur release to include these changes as well as #1214
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