have ability to add non-taxon node labels to newicks

[josephwb]

Currently only taxon labels are applied to newick nodes.
e.g.

"newick" : "(Gavia_stellata_ott1057044,((Gavia_arctica_ott1085739,Gavia_pacifica_ott651474),(Gavia_immer_ott1057518,Gavia_adamsii_ott90560)))Gavia_ott803675;"

[josephwb]

I guess I should wait for @jar398 to give me the go ahead on this, since people have expressed that they want this, but none of the myriad docs explicitly discusses it.

[jar398]

I think it's a good idea

-- apologies for brevity / using handheld gizmo --

On Feb 16, 2016, at 20:41, "Joseph W. Brown" notifications@github.com
wrote:

I guess I should wait for @jar398 https://github.com/jar398 to give me
the go ahead on this, since people have expressed that they want this, but
none of the myriad docs explicitly discusses it.

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#205 (comment)
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[kcranston]

What methods does this affect?

[josephwb]

"subtree" and "induced_subtree" (only the latter is implemented at the moment; I can turn it off if you like).

[josephwb]

Old:

curl -X POST http://localhost:7474/db/data/ext/tree_of_life_v3/graphdb/induced_subtree -H "content-type:application/json" -d '{"node_ids":["ott501678","ott666104","ott316878"], "ott_ids":[102710,536234,810751,81461,501678]}'
{
  "node_ids_not_in_tree" : [ "ott501678" ],
  "ott_ids_not_in_tree" : [ 501678 ],
  "newick" : "(((Clangula_ott316878,Perdix_ott102710)Galloanserae_ott5839486,((Selasphorus_calliope_ott536234)Trochilidae_ott810751,Setophaga_ott666104))Neognathae_ott241846)Aves_ott81461;",
  "synth_id" : "opentree4.1"
}

New:

curl -X POST http://localhost:7474/db/data/ext/tree_of_life_v3/graphdb/induced_subtree -H "content-type:application/json" -d '{"node_ids":["ott501678","ott666104","ott316878"], "ott_ids":[102710,536234,810751,81461,501678]}'
{
  "node_ids_not_in_tree" : [ "ott501678" ],
  "ott_ids_not_in_tree" : [ 501678 ],
  "newick" : "(((Clangula_ott316878,Perdix_ott102710)Galloanserae_ott5839486,((Selasphorus_calliope_ott536234)Trochilidae_ott810751,Setophaga_ott666104)mrcaott246ott5481)Neognathae_ott241846)Aves_ott81461;",
  "synth_id" : "opentree4.1"
}

[jimallman]

Thanks for the "before" and "after" examples. I was unclear on the consequences of this change. Do I understand correctly that this isn't just a matter of labeling, but of including entirely new nodes (e.g. mrcaott246ott5481 above)?

[jar398]

we could make it an option if there are worries about clutter or space or
compatibility.
{"include_nontaxon_labels" : true , ...}
not sure how to decide this.

On Wed, Feb 17, 2016 at 4:51 PM, Joseph W. Brown notifications@github.com
wrote:

"subtree" and "induced_subtree" (only the latter is implemented at the
moment; I can turn it off if you like).

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#205 (comment)
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[josephwb]

@jimallman the trees are the exact same except for labelling.

[kcranston]

+1 for including them
Ambivalent about option to exclude. Hold off until it becomes a problem? Would be a compatible change.

[josephwb]

"nontaxon" nodes could be part of the query; a reason for them to be returned.

[jimallman]

the trees are the exact same except for labelling

thanks, my Newick-fu is lacking

[josephwb]

Here is subtree. Before:

curl -X POST http://localhost:7474/db/data/ext/tree_of_life_v3/graphdb/subtree -H "content-type:application/json" -d '{"node_id":"ott803675"}'
{
  "newick" : "(Gavia_stellata_ott1057044,((Gavia_arctica_ott1085739,Gavia_pacifica_ott651474),(Gavia_immer_ott1057518,Gavia_adamsii_ott90560)))Gavia_ott803675;",
  "synth_id" : "opentree4.1"
}

After:

curl -X POST http://localhost:7474/db/data/ext/tree_of_life_v3/graphdb/subtree -H "content-type:application/json" -d '{"node_id":"ott803675"}'
{
  "newick" : "(Gavia_stellata_ott1057044,((Gavia_arctica_ott1085739,Gavia_pacifica_ott651474)mrcaott651474ott1085739,(Gavia_immer_ott1057518,Gavia_adamsii_ott90560)mrcaott90560ott1057518)mrcaott90560ott651474)Gavia_ott803675;",
  "synth_id" : "opentree4.1"
}

[josephwb]

Deployed on test for testing. Let me know if you want me to revert things.

[jar398]

It would be compatible in the sense of having a /v3 URL instead of a /v2
URL. But it's easy to imagine clients used to the v2 Newicks barfing on
the v3 Newicks. That's OK with me, just cautioning on "would be a
compatible change"

But I have no strong feelings.

On Wed, Feb 17, 2016 at 5:02 PM, Joseph W. Brown notifications@github.com
wrote:

"nontaxon" nodes could be part of the query; a reason for them to be
returned.

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#205 (comment)
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