Fix array bindings in knowledge_map and answer viewer?

[frostyfan109]

RTX returns list bindings in knowledge map objects like:

{
    "node_bindings" : {
        "disease": [
            "foo"
        ]
    },
    "edge_bindings": ...
}

It messes up TranQL for some reason.

The answer viewer doesn't work yet again because of this.

[frostyfan109]

Doesn't work on Workflow 5. Robokop error:

TypeError: Cannot read property '0' of undefined
    at n.accessor (MessageAnswersetTable.jsx:117)
    at rtColumnWidth.js:18
    at Array.map (<anonymous>)
    at t.default (rtColumnWidth.js:18)
    at MessageAnswersetTable.jsx:118
    at Array.map (<anonymous>)
    at t.value (MessageAnswersetTable.jsx:80)
    at t.value (MessageAnswersetTable.jsx:72)
    at t.value (MessageAnswersetTable.jsx:44)
    at l.performInitialMount (ReactCompositeComponent.js:348)

[frostyfan109]

links that aren't in knowledge_graph: b2daddd9a793e4edf6b71a99653bffcc VM5787:6 6539f843-9e9f-4a1d-beef-b7af57cc6618 VM5787:6 8d831aa92acf93250b656bec69394233 VM5787:6 67cb45ce0c224efdf84d59514da3665f VM5787:6 67f294d3b850e9f300d56d27c72b8a0c VM5787:6 b3c14e06c6cff74e073a23f65cfe2e14 VM5787:6 c1d966e529ac00180fb10b60d693eeb7 VM5787:6 d1c145dfc10898fcf186a3be0e734176 VM5787:6 3a32e403f71ba08d0f7ec5fd9e5ccb93 VM5787:6 902f9e3dc3edc75acf98c7f36061f40f VM5787:6 57a776fbd2b1f041b43cea45144f2e63 VM5787:6 1c2bd179-658d-4aa3-8d67-ce0f0faf78cd VM5787:6 4a368a641ba993a261132aefc2dae798 VM5787:6 90554cefb511f5c6061a23d6c1b8ac61 VM5787:6 6326f136190faa91ca384182778c0f8b

[frostyfan109]

query:

set chemical = "CHEMBL:CHEMBL1261" -- Citric acid
SELECT chemical_substance->disease->gene
    FROM "/schema"
 WHERE chemical_substance=$chemical

[frostyfan109]

edges not in the knowledge_map: 22d2382a10137ee111c0998c960135dc VM6324:2 43afc98202161f1edce211bfd65fac90 VM6324:2 f7620b0c201e636288473672b5199805 VM6324:2 a1301ff3-7de2-4397-9e32-ce3302efcee4 VM6324:2 96db1847-962f-42d0-8a4d-d9f88943e0f3 VM6324:2 af48c94c60761ff5f4f4c41b425168b3 VM6324:2 e7dd939f07f190ae87ea086b5fa293b3 VM6324:2 949e49e7f817e2f881f72c43137df0b2 VM6324:2 dd008f6b9f3d4b1e47df66f5b009b5d8 VM6324:2 cea68525a4a0a187896d283f934f75bf VM6324:2 a2d258aa7e33bd0598133dde4786360e VM6324:2 e3ca36ff-06d1-40b4-a453-97d72caebee5 VM6324:2 f7b5e814d5e113e7e5ee12b63ceaeef8 VM6324:2 7db15e5ec032e5528f215ee29755b04f VM6324:2 d12a16e4ae641e1e16bb6f5e25d3685d VM6324:2 0b6a64cfc9112f6b0d38fd7316282a2e VM6324:2 8c514b67977f53ae233a092aa495f55a VM6324:2 6cff47549356876bd056482289609e3f VM6324:2 7d6f94fdbbd00741a186491c66b813ba VM6324:2 8f1df3146efadd9ef837615210c83b7e VM6324:2 c8f6538db76a9f408dd54b81e4b99b0d VM6324:2 c20aa2d7f679287c934f6165e8128b5a VM6324:2 8a1bdd9b6bb5b5eba0883a84c1887e6b 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notes:

• all are from robokop
• looks like all target merged nodes

[frostyfan109]

After extensive testing, I've only managed to get this error to occur when the knowledge_map includes a node id that doesn't exist in the knowledge_graph. Therefore, this error shouldn't happen, as this is not the case with these failing queries, so something else must be happening.

[frostyfan109]

Also, when just a single verified-as-valid answer is provided, it will still error.

[frostyfan109]

Could the answers format be wrong? Does every single answer need all the questions in it?

Theoretically invalid (just node_bindings):

chemical_substance: "SCTID:278694008"
population_of_individual_organisms: "COHORT:13"

Theoretically valid (just node_bindings):

biological_process_or_activity: "GO:0007585"
chemical_substance: "MESH:D010126"
gene: "HGNC:10799"
phenotypic_feature: "HP:0005952"

Edit: I just tested this with this knowledge_map and the Workflow 5 default as the rest and it ran successfully:

[
  {
    "node_bindings": {
      "biological_process_or_activity": "GO:0004497",
      "gene": "HGNC:2638",
      "phenotypic_feature": "HP:0005982",
      "chemical_substance": "umlscui:C2341620",
      "population_of_individual_organisms": "COHORT:13"
    },
    "edge_bindings": {
      "e1": [
        "d23b216557ff08aa64c91d5d81546d7d"
      ],
      "e2": [
        "b3747ff2485569b64e308401e646c850"
      ],
      "e3": [
        "80660add35c9440b95c7b1d3c77a3120"
      ],
      "s27": "8b21bb19-0574-4ab9-a8b5-539afd713cf0",
      "e4": [
        "COHORT:13_Mometasone_umlscui:C2341620"
      ]
    },
    "score": 0.10530346936255496
  }
]

It is the answer at index 8605. It has an artificially inserted "population_of_individual_organisms" node_binding and an artificially inserted "e4" edge_binding. It could be that all answers are missing the population_of_individual_organisms binding which causes it not to work normally?

[frostyfan109]

Pretty confident that this is fixed.