feat: make clade_membership node attribute optional
#1457
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Not all trees have `clade_membership` attribute on the nodes. Here I made this attribute optional in Nextclade. If `clade_membership` is not present: - output JSON/NDJSON result entries will not contain `clade` field - `clade` column in output CSV/TSV will be empty - `clade` column in Nextclade Web will be empty it does not affect any other parts of the application. Notably clade-like attributes (from `.meta.extensions.nextclade.clade_node_attrs` are still assigned and being written to the output). Tested on `sars-cov-2` dataset and `clade_membership` node attribute removed using `jq`: ```bash jq 'walk(if (type == "object" and .clade_membership) then del(.clade_membership) else . end )' tree.original.json > tree.json ``` (in real trees you might also need to change metadata, such as colorings) ### Further work: - We might remove empty `clade` column from CSV/TSV and from Web. Thought it might be a bit involved - the results are streamed one at a time and we don't know whether there will be any clades or not until very end. But at that point it is too late - everything has been already written.
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Not all Auspice trees have
clade_membershipattribute on the nodes. Here I make this attribute optional in Nextclade.With this change, if
clade_membershipis not present:output JSON/NDJSON result entries will not contain
cladefieldcladecolumn in output CSV/TSV will be emptycladecolumn in Nextclade Web will be emptyIt does not affect any other parts of the application. Notably, clade-like attributes (from
.meta.extensions.nextclade.clade_node_attrsare still assigned and being written to the output).Tested on
sars-cov-2dataset withclade_membershipnode attribute removed usingjq:(in real trees you might also need to change metadata, such as colorings)
Further work:
cladecolumn from CSV/TSV and from Web. Though it might be a bit involved - the results are streamed one at a time and we don't know whether there will be any clades or not until very end. But at that point it is too late - everything has been already written. And a disappearance of a column is a potential for breakage in users' code.