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| ) | ||
| belongs_to(:publication, optional: true) | ||
| validates(:name, presence: true) | ||
| validates(:parent, presence: true, unless: :incertae_sedis?) |
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This removes the ability to have incertae sedis without a parent. There are almost no cases of that. Wouldn't at least a domain placement always be possible?
| "<i>incertae sedis</i>#{qualifier}".html_safe | ||
| end | ||
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| def incertae_sedis_parent_rank |
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More like minimum_incertae_sedis_parent_rank?
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| def save_batch_placement(name, attributes) |
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I need to see if we can re-use existing paths for this logic.
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@lmrodriguezr Ready for review
We have 7 names with incertae sedis without clarifying if they are bacteria or archaea. I think we will just have to manually go through them.
irb(main):023> Placement.where(incertae_sedis: "Incertae sedis").map(&:name)| incertae_sedis_text: par['description'] | ||
| } | ||
| name = Name.find_by_variants(par['name']) | ||
| placement = name.placements.find_or_initialize_by(parent: parent) |
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Duplication. I wanna tackle this in another PR as previously discussed.
| message: 'can only contain letters, dashes, dots, and apostrophe' | ||
| } | ||
| ) | ||
| validates(:incertae_sedis, inclusion: { in: [true, false] }, allow_nil: true) |
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This is gone when rebased against main.
| # GET /names/autocomplete.json?q=Allo&rank=genus | ||
| # GET /names/autocomplete.json?q=Pseu&minimum_rank=class | ||
| # GET /names/autocomplete.json?q=Allo&ranks=genus | ||
| # GET /names/autocomplete.json?q=Pseu&ranks=domain,phylum,class |
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I've combined these two params into a single param. So you just specify a list of ranks that are allowed. For known placements that list is just ["genus"] if name is a species etc.
| }, | ||
| failure: ->(_w, n) { | ||
| n.class.ranks.index(n.rank) != n.class.ranks.index(n.parent.rank) + 1 | ||
| !n.placement.allowed_parent_ranks.include?(n.placement.parent.rank) |
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In a previous version of this pull req I added a new quality check for the incertae sedis rank. WIth the new Placement#allowed_parent_ranks method they can easily be combined in a single quality check. @lmrodriguezr Please double check that this is OK :)
irb(main):002> Placement.where(incertae_sedis: "Incertae sedis").map(&:name).pluck(:name)
=> ["Adamsella", "Nitrosotaleales", "Endohaliclona", "Syntrophaliphaticia", "Acidifodinimicrobiaceae", "Hakubellales", "Chazhemtonibacteriaceae"] |
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
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@lmrodriguezr Ready to review/merge |
3 participants
Needs #333 to be merged first.
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