biothings / biothings_explorer

TRAPI service for BioThings Explorer
https://explorer.biothings.io
Apache License 2.0
10 stars 11 forks source link

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

Open colleenXu opened 3 weeks ago

colleenXu commented 3 weeks ago

I think it'd be helpful to have a feature similar to the dryrun parameter (ref, issue) for Pathfinder.

I imagine:

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 commented 4 days ago

https://github.com/biothings/bte-server/commit/5790cb40b80782df14cb6bae4c0ead5d88b1e3bc this commit also required.

Deployed on CI Mon 9/30.