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Pathfinder dryrun mode: showing what queries are created from the "template-generation" #862

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colleenXu opened this issue Sep 4, 2024 · 1 comment
Open

Pathfinder dryrun mode: showing what queries are created from the "template-generation" #862

colleenXu opened this issue Sep 4, 2024 · 1 comment
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I think it'd be helpful to have a feature similar to the dryrun parameter (ref, issue) for Pathfinder.

I imagine:

  • preferably a parameter we can set in the POST query parameters (dryrun or caching both work this way). That's better than an environ variable set at startup (INSTANCE_ENV).
  • Won't fully execute pathfinder mode
  • Instead, once the categories of the starting nodes are known...BTE constructs the 3 templates/queries it's going to run for pathfinder. Return info on what those 3 queries are in a TRAPI response (in logs) AND console logs
  • Ideally, give this info in a nicer format. Current format of execution plan in console logs looks like this:
Click here 

  bte:biothings-explorer-trapi:qedge2btedge KG Filters: {
  bte:biothings-explorer-trapi:qedge2btedge   "input_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "SmallMolecule",
  bte:biothings-explorer-trapi:qedge2btedge     "MolecularEntity",
  bte:biothings-explorer-trapi:qedge2btedge     "NucleicAcidEntity",
  bte:biothings-explorer-trapi:qedge2btedge     "ChemicalMixture",
  bte:biothings-explorer-trapi:qedge2btedge     "MolecularMixture",
  bte:biothings-explorer-trapi:qedge2btedge     "Drug",
  bte:biothings-explorer-trapi:qedge2btedge     "ComplexMolecularMixture",
  bte:biothings-explorer-trapi:qedge2btedge     "ProcessedMaterial",
  bte:biothings-explorer-trapi:qedge2btedge     "Food",
  bte:biothings-explorer-trapi:qedge2btedge     "EnvironmentalFoodContaminant",
  bte:biothings-explorer-trapi:qedge2btedge     "FoodAdditive",
  bte:biothings-explorer-trapi:qedge2btedge     "ChemicalEntity"
  bte:biothings-explorer-trapi:qedge2btedge   ],
  bte:biothings-explorer-trapi:qedge2btedge   "output_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "Gene"
  bte:biothings-explorer-trapi:qedge2btedge   ],
  bte:biothings-explorer-trapi:qedge2btedge   "predicate": [
  bte:biothings-explorer-trapi:qedge2btedge     "regulates",
  bte:biothings-explorer-trapi:qedge2btedge     "regulated_by",
  bte:biothings-explorer-trapi:qedge2btedge     "affects_response_to",
  bte:biothings-explorer-trapi:qedge2btedge     "increases_response_to",
  bte:biothings-explorer-trapi:qedge2btedge     "decreases_response_to",
  bte:biothings-explorer-trapi:qedge2btedge     "disrupts",
  bte:biothings-explorer-trapi:qedge2btedge     "ameliorates_condition",
  bte:biothings-explorer-trapi:qedge2btedge     "exacerbates_condition",
  bte:biothings-explorer-trapi:qedge2btedge     "has_adverse_event",
  bte:biothings-explorer-trapi:qedge2btedge     "has_side_effect",
  bte:biothings-explorer-trapi:qedge2btedge     "affects",
  bte:biothings-explorer-trapi:qedge2btedge     "response_affected_by",
  bte:biothings-explorer-trapi:qedge2btedge     "response_increased_by",
  bte:biothings-explorer-trapi:qedge2btedge     "response_decreased_by",
  bte:biothings-explorer-trapi:qedge2btedge     "disrupted_by",
  bte:biothings-explorer-trapi:qedge2btedge     "condition_ameliorated_by",
  bte:biothings-explorer-trapi:qedge2btedge     "condition_prevented_by",
  bte:biothings-explorer-trapi:qedge2btedge     "condition_exacerbated_by",
  bte:biothings-explorer-trapi:qedge2btedge     "adverse_event_of",
  bte:biothings-explorer-trapi:qedge2btedge     "is_side_effect_of",
  bte:biothings-explorer-trapi:qedge2btedge     "affected_by",
  bte:biothings-explorer-trapi:qedge2btedge     "physically_interacts_with",
  bte:biothings-explorer-trapi:qedge2btedge     "directly_physically_interacts_with",
  bte:biothings-explorer-trapi:qedge2btedge     "binds",
  bte:biothings-explorer-trapi:qedge2btedge     "indirectly_physically_interacts_with",
  bte:biothings-explorer-trapi:qedge2btedge     "genetically_interacts_with",
  bte:biothings-explorer-trapi:qedge2btedge     "gene_fusion_with",
  bte:biothings-explorer-trapi:qedge2btedge     "genetic_neighborhood_of",
  bte:biothings-explorer-trapi:qedge2btedge     "interacts_with",
  bte:biothings-explorer-trapi:qedge2btedge     "associated_with_likelihood_of",
  bte:biothings-explorer-trapi:qedge2btedge     "associated_with_increased_likelihood_of",
  bte:biothings-explorer-trapi:qedge2btedge     "associated_with_decreased_likelihood_of",
  bte:biothings-explorer-trapi:qedge2btedge     "likelihood_associated_with",
  bte:biothings-explorer-trapi:qedge2btedge     "increased_likelihood_associated_with",
  bte:biothings-explorer-trapi:qedge2btedge     "decreased_likelihood_associated_with",
  bte:biothings-explorer-trapi:qedge2btedge     "associated_with_sensitivity_to",
  bte:biothings-explorer-trapi:qedge2btedge     "sensitivity_associated_with",
  bte:biothings-explorer-trapi:qedge2btedge     "associated_with_resistance_to",
  bte:biothings-explorer-trapi:qedge2btedge     "resistance_associated_with",
  bte:biothings-explorer-trapi:qedge2btedge     "genetic_association",
  bte:biothings-explorer-trapi:qedge2btedge     "genetically_associated_with",
  bte:biothings-explorer-trapi:qedge2btedge     "gene_associated_with_condition",
  bte:biothings-explorer-trapi:qedge2btedge     "condition_associated_with_gene",
  bte:biothings-explorer-trapi:qedge2btedge     "correlated_with",
  bte:biothings-explorer-trapi:qedge2btedge     "positively_correlated_with",
  bte:biothings-explorer-trapi:qedge2btedge     "negatively_correlated_with",
  bte:biothings-explorer-trapi:qedge2btedge     "occurs_together_in_literature_with",
  bte:biothings-explorer-trapi:qedge2btedge     "coexpressed_with",
  bte:biothings-explorer-trapi:qedge2btedge     "has_biomarker",
  bte:biothings-explorer-trapi:qedge2btedge     "biomarker_for",
  bte:biothings-explorer-trapi:qedge2btedge     "associated_with"
  bte:biothings-explorer-trapi:qedge2btedge   ]
  bte:biothings-explorer-trapi:qedge2btedge } +0ms
  bte:biothings-explorer-trapi:edge-manager (4) Edges not yet executed = 1 +140ms
  bte:biothings-explorer-trapi:edge-manager (5) Sending next edge 'un_obj' WITH entity count...(134) +0ms
  bte:biothings-explorer-trapi:edge-manager Checking entity max : (20)--(0) +0ms
  bte:biothings-explorer-trapi:QEdge (8) Choosing lower entity count in edge... +139ms
  bte:biothings-explorer-trapi:QNode (8) Node "un" holding undefined aside. +142ms
  bte:biothings-explorer-trapi:QEdge (8) Chose lower entity value in object (20) +0ms
  bte:biothings-explorer-trapi:edge-manager 'sub_un' : (1) --> (134) +0ms
  bte:biothings-explorer-trapi:edge-manager 'un_obj' : (134) <-- (20) +0ms
  bte:biothings-explorer-trapi:qedge2btedge Input node is creativeQueryObject +139ms
  bte:biothings-explorer-trapi:qedge2btedge Output node is un +0ms
  bte:biothings-explorer-trapi:QEdge Expanded edges: gene_associated_with_condition,biomarker_for,affects_response_to,increases_response_to,decreases_response_to,regulates,disrupts,ameliorates_condition,exacerbates_condition,has_adverse_event,has_side_effect,affects,causes,contributes_to +0ms
  bte:biothings-explorer-trapi:QEdge Expanded edges: gene_associated_with_condition,biomarker_for,affects_response_to,increases_response_to,decreases_response_to,regulates,disrupts,ameliorates_condition,exacerbates_condition,has_adverse_event,has_side_effect,affects,causes,contributes_to +1ms
  bte:biothings-explorer-trapi:qedge2btedge KG Filters: {
  bte:biothings-explorer-trapi:qedge2btedge   "input_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "Disease"
  bte:biothings-explorer-trapi:qedge2btedge   ],
  bte:biothings-explorer-trapi:qedge2btedge   "output_type": [
  bte:biothings-explorer-trapi:qedge2btedge     "Gene"
  bte:biothings-explorer-trapi:qedge2btedge   ],
  bte:biothings-explorer-trapi:qedge2btedge   "predicate": [
  bte:biothings-explorer-trapi:qedge2btedge     "condition_associated_with_gene",
  bte:biothings-explorer-trapi:qedge2btedge     "has_biomarker",
  bte:biothings-explorer-trapi:qedge2btedge     "response_affected_by",
  bte:biothings-explorer-trapi:qedge2btedge     "response_increased_by",
  bte:biothings-explorer-trapi:qedge2btedge     "response_decreased_by",
  bte:biothings-explorer-trapi:qedge2btedge     "regulated_by",
  bte:biothings-explorer-trapi:qedge2btedge     "disrupted_by",
  bte:biothings-explorer-trapi:qedge2btedge     "condition_ameliorated_by",
  bte:biothings-explorer-trapi:qedge2btedge     "condition_exacerbated_by",
  bte:biothings-explorer-trapi:qedge2btedge     "adverse_event_of",
  bte:biothings-explorer-trapi:qedge2btedge     "is_side_effect_of",
  bte:biothings-explorer-trapi:qedge2btedge     "affected_by",
  bte:biothings-explorer-trapi:qedge2btedge     "caused_by",
  bte:biothings-explorer-trapi:qedge2btedge     "contribution_from"
  bte:biothings-explorer-trapi:qedge2btedge   ]
  bte:biothings-explorer-trapi:qedge2btedge } +1ms
  bte:biothings-explorer-trapi:edge-manager (3) Edge manager is managing 2 qEdges. +128ms
  bte:biothings-explorer-trapi:edge-manager (4) Edges not yet executed = 2 +0ms
  bte:biothings-explorer-trapi:edge-manager (5) Sending next edge 'sub_un' WITH entity count...(1) +1ms
  bte:biothings-explorer-trapi:edge-manager Checking entity max : (0)--(1) +0ms
  bte:biothings-explorer-trapi:edge-manager 'sub_un' : (1) --> (0) +0ms
  bte:biothings-explorer-trapi:edge-manager 'un_obj' : (0) <-- (20) +0ms
  bte:biothings-explorer-trapi:edge-manager (5) Executing current edge >> "sub_un" +1ms

@tokebe Anything to add? Particularly on urgency? I think this would be useful right now (aka do ASAP) but it's also fine to have this later...

@rjawesome @NeuralFlux Jackson mentioned that one of you two could pick this issue and self-assign.
@colleenXu colleenXu changed the title Pathfinder dry-run mode: showing what queries are created from the "template-generation" Pathfinder dryrun mode: showing what queries are created from the "template-generation" Sep 4, 2024
@rjawesome rjawesome self-assigned this Sep 6, 2024
@rjawesome rjawesome mentioned this issue Sep 9, 2024
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@tokebe tokebe added the On Dev Related changes are deployed to Dev server label Sep 17, 2024
@colleenXu colleenXu mentioned this issue Sep 17, 2024
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@tokebe tokebe added On CI Related changes are deployed to CI server and removed On Dev Related changes are deployed to Dev server labels Sep 26, 2024
@tokebe tokebe mentioned this issue Sep 26, 2024
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colleenXu referenced this issue in biothings/bte-server Sep 28, 2024
@colleenXu
feat: enable dryrun_pathfinder parameter for ARA endpoints
5790cb4
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colleenXu commented Sep 28, 2024 •
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biothings/bte-server@5790cb4 this commit also required.

Deployed on CI Mon 9/30.

@colleenXu colleenXu added On CI -> Test and removed On CI Related changes are deployed to CI server labels Oct 24, 2024
@colleenXu colleenXu mentioned this issue Oct 24, 2024
Open
@tokebe tokebe added On Test Related changes are deployed to Test server and removed On CI -> Test labels Oct 28, 2024
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