diff --git a/mixer b/mixer index d7cac6597a..8a5d4ee1a4 160000 --- a/mixer +++ b/mixer @@ -1 +1 @@ -Subproject commit d7cac6597a2dc2871eb7585a9ade5254d0b63f4f +Subproject commit 8a5d4ee1a4cbe4b3a757aaf37040082f31a4e1e7 diff --git a/server/integration_tests/test_data/detection_api_multivar/comparemalepopulationwithfemalepopulation/debug_info.json b/server/integration_tests/test_data/detection_api_multivar/comparemalepopulationwithfemalepopulation/debug_info.json index 2d0e12d09d..4243c66dd7 100644 --- a/server/integration_tests/test_data/detection_api_multivar/comparemalepopulationwithfemalepopulation/debug_info.json +++ b/server/integration_tests/test_data/detection_api_multivar/comparemalepopulationwithfemalepopulation/debug_info.json @@ -54,7 +54,7 @@ "Parts": [ { "CosineScore": [ - 0.925786018371582 + 0.9257858991622925 ], "QueryPart": "male population", "SV": [ @@ -63,8 +63,8 @@ }, { "CosineScore": [ - 0.9296978712081909, - 0.884743332862854 + 0.9296979904174805, + 0.8847434520721436 ], "QueryPart": "female population", "SV": [ @@ -89,8 +89,8 @@ }, { "CosineScore": [ - 0.8982377648353577, - 0.8723466396331787 + 0.8982378244400024, + 0.8723468780517578 ], "QueryPart": "population", "SV": [ @@ -106,10 +106,10 @@ "Parts": [ { "CosineScore": [ - 0.8088871240615845, - 0.8034241795539856, - 0.8017653822898865, - 0.7751558423042297 + 0.808887243270874, + 0.8034241199493408, + 0.8017654418945312, + 0.775155782699585 ], "QueryPart": "male", "SV": [ @@ -121,7 +121,7 @@ }, { "CosineScore": [ - 0.9170327186584473, + 0.9170328378677368, 0.873018741607666 ], "QueryPart": "population female population", diff --git a/server/integration_tests/test_data/detection_api_multivar/howarefactorslikeobesity,bloodpressureandasthmaimpactedbyclimatechange/debug_info.json b/server/integration_tests/test_data/detection_api_multivar/howarefactorslikeobesity,bloodpressureandasthmaimpactedbyclimatechange/debug_info.json index bef680e6ec..f30c230689 100644 --- a/server/integration_tests/test_data/detection_api_multivar/howarefactorslikeobesity,bloodpressureandasthmaimpactedbyclimatechange/debug_info.json +++ b/server/integration_tests/test_data/detection_api_multivar/howarefactorslikeobesity,bloodpressureandasthmaimpactedbyclimatechange/debug_info.json @@ -86,7 +86,7 @@ }, { "CosineScore": [ - 0.9999995827674866 + 0.9999996423721313 ], "QueryPart": "blood pressure", "SV": [ diff --git a/server/integration_tests/test_data/detection_api_multivar/showmetheimpactofclimatechangeondrought/debug_info.json b/server/integration_tests/test_data/detection_api_multivar/showmetheimpactofclimatechangeondrought/debug_info.json index 9687559ff7..6a55c79242 100644 --- a/server/integration_tests/test_data/detection_api_multivar/showmetheimpactofclimatechangeondrought/debug_info.json +++ b/server/integration_tests/test_data/detection_api_multivar/showmetheimpactofclimatechangeondrought/debug_info.json @@ -41,7 +41,7 @@ "Parts": [ { "CosineScore": [ - 0.8787485361099243 + 0.8787486553192139 ], "QueryPart": "show climate change", "SV": [ @@ -65,8 +65,8 @@ "Parts": [ { "CosineScore": [ - 0.794236958026886, - 0.7929013967514038 + 0.7942368984222412, + 0.7929012775421143 ], "QueryPart": "show climate", "SV": [ diff --git a/server/integration_tests/test_data/detection_api_undata_idx/chart_config.json b/server/integration_tests/test_data/detection_api_undata_idx/chart_config.json index 217eacd4cf..4c380e6dc3 100644 --- a/server/integration_tests/test_data/detection_api_undata_idx/chart_config.json +++ b/server/integration_tests/test_data/detection_api_undata_idx/chart_config.json @@ -1,10 +1,6 @@ { "childEntityType": "", - "classifications": [ - { - "type": 100 - } - ], + "classifications": [], "client": "test_detect", "comparisonEntities": [], "comparisonVariables": [], diff --git a/server/integration_tests/test_data/e2e_triple/tellmeaboutheartdisease/chart_config.json b/server/integration_tests/test_data/e2e_triple/tellmeaboutheartdisease/chart_config.json index 396db083db..6b8e25c35b 100644 --- a/server/integration_tests/test_data/e2e_triple/tellmeaboutheartdisease/chart_config.json +++ b/server/integration_tests/test_data/e2e_triple/tellmeaboutheartdisease/chart_config.json @@ -9,10 +9,102 @@ { "tiles": [ { + "answerTableTileSpec": { + "columns": [ + { + "header": "Date Created", + "propertyExpr": "->dateCreated" + }, + { + "header": "Date Established", + "propertyExpr": "->dateEstablished" + }, + { + "header": "Date Revised", + "propertyExpr": "->dateRevised" + }, + { + "header": "Description", + "propertyExpr": "->description" + }, + { + "header": "Disease Ontology ID", + "propertyExpr": "->diseaseOntologyID" + }, + { + "header": "Has MeSH Qualifier", + "propertyExpr": "->hasMeSHQualifier" + }, + { + "header": "Identifier", + "propertyExpr": "->identifier" + }, + { + "header": "Medical Dictionary For Regulatory Activities Id", + "propertyExpr": "->medicalDictionaryForRegulatoryActivitiesId" + }, + { + "header": "Medical Subject Heading ID", + "propertyExpr": "->medicalSubjectHeadingID" + }, + { + "header": "Medical Subject Heading Tree Number", + "propertyExpr": "->medicalSubjectHeadingTreeNumber" + }, + { + "header": "Name", + "propertyExpr": "->name" + }, + { + "header": "National Drug File Reference Terminology Code", + "propertyExpr": "->nationalDrugFileReferenceTerminologyCode" + }, + { + "header": "National Library Of Medicine Classification Number", + "propertyExpr": "->nationalLibraryOfMedicineClassificationNumber" + }, + { + "header": "Pharm GKBID", + "propertyExpr": "->pharmGKBID" + }, + { + "header": "Provenance", + "propertyExpr": "->provenance" + }, + { + "header": "Snomed CT", + "propertyExpr": "->snomedCT" + }, + { + "header": "Specialization Of", + "propertyExpr": "->specializationOf" + }, + { + "header": "Synonym", + "propertyExpr": "->synonym" + }, + { + "header": "Type Of", + "propertyExpr": "->typeOf" + }, + { + "header": "Umls Concept Unique ID", + "propertyExpr": "->umlsConceptUniqueID" + } + ] + }, "entities": [ + "bio/D002275", + "bio/D003327", + "bio/D006331", + "bio/D006349", + "bio/D011660", + "bio/D012214", + "bio/D017202", "bio/DOID_114" ], - "type": "ENTITY_OVERVIEW" + "title": "Here are all the properties for Carcinoid Heart Disease, Coronary Disease and 6 more others", + "type": "ANSWER_TABLE" } ] } @@ -25,6 +117,41 @@ "context": {}, "debug": {}, "entities": [ + { + "dcid": "bio/D002275", + "name": "Carcinoid Heart Disease", + "type": "" + }, + { + "dcid": "bio/D003327", + "name": "Coronary Disease", + "type": "" + }, + { + "dcid": "bio/D006331", + "name": "Heart Diseases", + "type": "" + }, + { + "dcid": "bio/D006349", + "name": "Heart Valve Diseases", + "type": "" + }, + { + "dcid": "bio/D011660", + "name": "Pulmonary Heart Disease", + "type": "" + }, + { + "dcid": "bio/D012214", + "name": "Rheumatic Heart Disease", + "type": "" + }, + { + "dcid": "bio/D017202", + "name": "Myocardial Ischemia", + "type": "" + }, { "dcid": "bio/DOID_114", "name": "heart disease", diff --git a/server/integration_tests/test_data/e2e_triple/whatgenesareassociatedwiththegeneticvariantrs13317/chart_config.json b/server/integration_tests/test_data/e2e_triple/whatgenesareassociatedwiththegeneticvariantrs13317/chart_config.json index 1393dbd784..011e017b1a 100644 --- a/server/integration_tests/test_data/e2e_triple/whatgenesareassociatedwiththegeneticvariantrs13317/chart_config.json +++ b/server/integration_tests/test_data/e2e_triple/whatgenesareassociatedwiththegeneticvariantrs13317/chart_config.json @@ -9,28 +9,25 @@ { "tiles": [ { - "answerMessageTileSpec": { - "propertyExpr": "<-referenceSNPClusterID{typeOf:GeneticVariantGeneAssociation}->geneSymbol" + "answerTableTileSpec": { + "columns": [ + { + "header": "associated gene", + "propertyExpr": "<-referenceSNPClusterID{typeOf:GeneticVariantGeneAssociation}->geneSymbol" + } + ] }, "entities": [ + "bio/D012873", + "bio/D014178", + "bio/D020022", + "bio/D020132", + "bio/D007562", + "bio/D020326", "bio/rs13317" ], - "title": "The associated genes for rs13317 are", - "type": "ANSWER_MESSAGE" - } - ] - } - ] - }, - { - "columns": [ - { - "tiles": [ - { - "entities": [ - "bio/rs13317" - ], - "type": "ENTITY_OVERVIEW" + "title": "The associated genes for Genetic, Genetic Predisposition to Disease and 4 more others are", + "type": "ANSWER_TABLE" } ] } @@ -43,6 +40,36 @@ "context": {}, "debug": {}, "entities": [ + { + "dcid": "bio/D012873", + "name": "Genetic", + "type": "" + }, + { + "dcid": "bio/D014178", + "name": "Genetic", + "type": "" + }, + { + "dcid": "bio/D020022", + "name": "Genetic Predisposition to Disease", + "type": "" + }, + { + "dcid": "bio/D020132", + "name": "Anticipation", + "type": "" + }, + { + "dcid": "bio/D007562", + "name": "Creutzfeldt-Jakob Syndrome", + "type": "" + }, + { + "dcid": "bio/D020326", + "name": "Migraine without Aura", + "type": "" + }, { "dcid": "bio/rs13317", "name": "rs13317", diff --git a/server/integration_tests/test_data/e2e_triple/whatgenesareassociatedwiththegeneticvariantrs13317andrs7903146/chart_config.json b/server/integration_tests/test_data/e2e_triple/whatgenesareassociatedwiththegeneticvariantrs13317andrs7903146/chart_config.json index f2fc4a5360..4640217bf3 100644 --- a/server/integration_tests/test_data/e2e_triple/whatgenesareassociatedwiththegeneticvariantrs13317andrs7903146/chart_config.json +++ b/server/integration_tests/test_data/e2e_triple/whatgenesareassociatedwiththegeneticvariantrs13317andrs7903146/chart_config.json @@ -18,10 +18,16 @@ ] }, "entities": [ + "bio/D012873", + "bio/D014178", + "bio/D020022", + "bio/D020132", + "bio/D007562", + "bio/D020326", "bio/rs13317", "bio/rs7903146" ], - "title": "The associated genes for rs13317 and rs7903146 are", + "title": "The associated genes for Genetic, Genetic Predisposition to Disease and 5 more others are", "type": "ANSWER_TABLE" } ] @@ -35,6 +41,36 @@ "context": {}, "debug": {}, "entities": [ + { + "dcid": "bio/D012873", + "name": "Genetic", + "type": "" + }, + { + "dcid": "bio/D014178", + "name": "Genetic", + "type": "" + }, + { + "dcid": "bio/D020022", + "name": "Genetic Predisposition to Disease", + "type": "" + }, + { + "dcid": "bio/D020132", + "name": "Anticipation", + "type": "" + }, + { + "dcid": "bio/D007562", + "name": "Creutzfeldt-Jakob Syndrome", + "type": "" + }, + { + "dcid": "bio/D020326", + "name": "Migraine without Aura", + "type": "" + }, { "dcid": "bio/rs13317", "name": "rs13317", diff --git a/server/integration_tests/test_data/e2e_triple/whatistheprevalenceofheartdiseaseincalifornia/chart_config.json b/server/integration_tests/test_data/e2e_triple/whatistheprevalenceofheartdiseaseincalifornia/chart_config.json index a94723cab5..108f094835 100644 --- a/server/integration_tests/test_data/e2e_triple/whatistheprevalenceofheartdiseaseincalifornia/chart_config.json +++ b/server/integration_tests/test_data/e2e_triple/whatistheprevalenceofheartdiseaseincalifornia/chart_config.json @@ -469,6 +469,41 @@ "context": {}, "debug": {}, "entities": [ + { + "dcid": "bio/D002275", + "name": "Carcinoid Heart Disease", + "type": "" + }, + { + "dcid": "bio/D003327", + "name": "Coronary Disease", + "type": "" + }, + { + "dcid": "bio/D006331", + "name": "Heart Diseases", + "type": "" + }, + { + "dcid": "bio/D006349", + "name": "Heart Valve Diseases", + "type": "" + }, + { + "dcid": "bio/D011660", + "name": "Pulmonary Heart Disease", + "type": "" + }, + { + "dcid": "bio/D012214", + "name": "Rheumatic Heart Disease", + "type": "" + }, + { + "dcid": "bio/D017202", + "name": "Myocardial Ischemia", + "type": "" + }, { "dcid": "bio/DOID_114", "name": "heart disease", diff --git a/server/integration_tests/test_data/e2e_triple/whatvirusspeciesarers13317andrs7903146/chart_config.json b/server/integration_tests/test_data/e2e_triple/whatvirusspeciesarers13317andrs7903146/chart_config.json index edf220d27e..6715bf39dc 100644 --- a/server/integration_tests/test_data/e2e_triple/whatvirusspeciesarers13317andrs7903146/chart_config.json +++ b/server/integration_tests/test_data/e2e_triple/whatvirusspeciesarers13317andrs7903146/chart_config.json @@ -43,6 +43,18 @@ "header": "Clin Var Variation ID", "propertyExpr": "->clinVarVariationID" }, + { + "header": "Clinical Annotation Count", + "propertyExpr": "->clinicalAnnotationCount" + }, + { + "header": "Clinical Annotation Count Level1_2", + "propertyExpr": "->clinicalAnnotationCountLevel1_2" + }, + { + "header": "Clinical Guideline Annotation Count", + "propertyExpr": "->clinicalGuidelineAnnotationCount" + }, { "header": "Clinical Significance", "propertyExpr": "->clinicalSignificance" @@ -51,10 +63,30 @@ "header": "Clinical Source", "propertyExpr": "->clinicalSource" }, + { + "header": "Date Created", + "propertyExpr": "->dateCreated" + }, + { + "header": "Date Established", + "propertyExpr": "->dateEstablished" + }, + { + "header": "Date Revised", + "propertyExpr": "->dateRevised" + }, + { + "header": "Description", + "propertyExpr": "->description" + }, { "header": "Disease Name", "propertyExpr": "->diseaseName" }, + { + "header": "Drug Label Annotation Count", + "propertyExpr": "->drugLabelAnnotationCount" + }, { "header": "Exceptions", "propertyExpr": "->exceptions" @@ -71,6 +103,10 @@ "header": "Gene Symbol", "propertyExpr": "->geneSymbol" }, + { + "header": "Genetic Variant Annotation Count", + "propertyExpr": "->geneticVariantAnnotationCount" + }, { "header": "Genetic Variant Attribute", "propertyExpr": "->geneticVariantAttribute" @@ -87,6 +123,10 @@ "header": "Genetic Variant Molecular Type", "propertyExpr": "->geneticVariantMolecularType" }, + { + "header": "Has MeSH Qualifier", + "propertyExpr": "->hasMeSHQualifier" + }, { "header": "Hg19 Genomic Location", "propertyExpr": "->hg19GenomicLocation" @@ -111,6 +151,10 @@ "header": "Human Phenotype Ontology ID", "propertyExpr": "->humanPhenotypeOntologyID" }, + { + "header": "Identifier", + "propertyExpr": "->identifier" + }, { "header": "In Chromosome", "propertyExpr": "->inChromosome" @@ -123,6 +167,18 @@ "header": "Med Gen ID", "propertyExpr": "->medGenID" }, + { + "header": "Medical Dictionary For Regulatory Activities Id", + "propertyExpr": "->medicalDictionaryForRegulatoryActivitiesId" + }, + { + "header": "Medical Subject Heading ID", + "propertyExpr": "->medicalSubjectHeadingID" + }, + { + "header": "Medical Subject Heading Tree Number", + "propertyExpr": "->medicalSubjectHeadingTreeNumber" + }, { "header": "Mondo ID", "propertyExpr": "->mondoID" @@ -135,6 +191,10 @@ "header": "Name", "propertyExpr": "->name" }, + { + "header": "National Drug File Reference Terminology Code", + "propertyExpr": "->nationalDrugFileReferenceTerminologyCode" + }, { "header": "Ncbi Gene ID", "propertyExpr": "->ncbiGeneID" @@ -187,6 +247,10 @@ "header": "Snomed CT", "propertyExpr": "->snomedCT" }, + { + "header": "Specialization Of", + "propertyExpr": "->specializationOf" + }, { "header": "Strand Orientation", "propertyExpr": "->strandOrientation" @@ -199,10 +263,18 @@ "header": "Submitter Count", "propertyExpr": "->submitterCount" }, + { + "header": "Synonym", + "propertyExpr": "->synonym" + }, { "header": "Type Of", "propertyExpr": "->typeOf" }, + { + "header": "Umls Concept Unique ID", + "propertyExpr": "->umlsConceptUniqueID" + }, { "header": "Validation Status", "propertyExpr": "->validationStatus" @@ -210,10 +282,11 @@ ] }, "entities": [ + "bio/D014777", "bio/rs13317", "bio/rs7903146" ], - "title": "Here are all the properties for rs13317 and rs7903146", + "title": "Here are all the properties for Virus Diseases, rs13317 and rs7903146", "type": "ANSWER_TABLE" } ] @@ -227,6 +300,11 @@ "context": {}, "debug": {}, "entities": [ + { + "dcid": "bio/D014777", + "name": "Virus Diseases", + "type": "" + }, { "dcid": "bio/rs13317", "name": "rs13317", @@ -253,7 +331,7 @@ "peerPlaces": [], "peerTopics": [] }, - "svSource": "UNKNOWN", + "svSource": "CURRENT_QUERY", "userMessage": "", "userMessages": [] } \ No newline at end of file