No entries in `sourceToMetaMap` for "rootward" nodes

[jimallman]

In calls to getSyntheticTree, it seems we're missing information about non-taxonomy sources for the nodes in the "rootward path" which appears left of the target node. For example, click the "i" (info) icon for Bacteria while on the page for its descendant "aquifer1". The property window fails to display because its supporting source pg_2542_5590_a2c48df995ddc9fd208986c3d4225112550c8452 has no information in sourceToMetaMap.

Note that properties for "cellular organisms" appear as expected, since its only supporting source is taxonomy.

Here's a cURL call that shows the arguson at this location:

curl 'https://api.opentreeoflife.org/cached/treemachine/v1/getSyntheticTree' \
  -H 'Content-Type: application/json' \
  --data-binary '{"treeID":"opentree4.0","format":"arguson","maxDepth":"3","subtreeNodeID":"233952"}'

{
  "name" : "aquifer1",
  "nodeid" : 233952,
  "maxnodedepth" : 0,
  "nTipDescendants" : 0,
  "nleaves" : 0,
  "taxSource" : "silva:JF191423/#2",
  "taxRank" : "no rank - terminal",
  "ottId" : "5246093",
  "pathToRoot" : [ {
    "supporting_sources" : [ "taxonomy", "pg_2542_5590_a2c48df995ddc9fd208986c3d4225112550c8452" ],
    "uniqname" : "Bacteria (domain silva:A16379/#1)",
    "taxSource" : "silva:A16379/#1,ncbi:2,worms:6,gbif:3,irmng:13",
    "name" : "Bacteria",
    "ottId" : "844192",
    "nodeid" : 4,
    "taxRank" : "domain"
  }, {
    "supporting_sources" : [ "taxonomy" ],
    "uniqname" : "cellular organisms",
    "taxSource" : "ncbi:131567",
    "name" : "cellular organisms",
    "ottId" : "93302",
    "nodeid" : 1,
    "taxRank" : "no rank"
  } ],
  "hasChildren" : false,
  "supportedBy" : [ "taxonomy" ],
  "sourceToMetaMap" : {
    "taxonomy" : {
      "version" : "2.9draft12"
    }
  }
}

[josephwb]

Whoops. Thanks for finding this @jimallman. I'll fix it this morning.

[josephwb]

@jimallman Below is how things currently stand on test (no changes made). So I think this was fixed with the tm-lite rewrite?

curl https://test.opentreeoflife.org/treemachine/v1/getSyntheticTree -H 'Content-Type: application/json' --data-binary '{"treeID":"opentree4.0","format":"arguson","maxDepth":"3","node_id":"ott5246093"}'
{
  "name" : "aquifer1",
  "node_id" : "ott5246093",
  "max_node_depth" : 0,
  "n_tip_descendants" : 1,
  "n_leaves" : 0,
  "ott_id" : 5246093,
  "unique_name" : "aquifer1",
  "tax_rank" : "no rank - terminal",
  "tax_sources" : {
    "silva" : "JF191423/#2"
  },
  "path_to_root" : [ {
    "tax_sources" : {
      "irmng" : "13",
      "worms" : "6",
      "silva" : "A16379/#1",
      "gbif" : "3",
      "ncbi" : "2"
    },
    "unique_name" : "Bacteria (domain silva:A16379/#1)",
    "supported_by" : {
      "taxonomy" : "2.9draft12",
      "pg_2542_tree5590" : "node960373"
    },
    "name" : "Bacteria",
    "ott_id" : 844192,
    "tax_rank" : "domain",
    "node_id" : "ott844192"
  }, {
    "tax_sources" : {
      "ncbi" : "131567"
    },
    "unique_name" : "cellular organisms",
    "name" : "cellular organisms",
    "ott_id" : 93302,
    "tax_rank" : "no rank",
    "node_id" : "ott93302"
  } ],
  "has_children" : false,
  "supported_by" : {
    "taxonomy" : "2.9draft12"
  },
  "sourceToMetaMap" : {
    "taxonomy" : {
      "name" : "ott",
      "version" : "2.9draft12"
    },
    "pg_2542_tree5590" : {
      "git_sha" : "c6ce2f9067e9c74ca7b1f770623bde9b6de8bd1f",
      "tree_id" : "tree5590",
      "study_id" : "pg_2542"
    }
  }
}

[jimallman]

Yes, this looks right. Further displayed information is fetched (via AJAX) as needed. You can see this working on ot30: https://test.opentreeoflife.org/opentree/opentree4.1@ott4750919/bacterium-ES1D2

[jar398]

Sounds like this is finished. Closing.