Merge branch 'pf-dryrun' of https://github.com/biothings/bte_trapi_qu…

…ery_graph_handler into dev
biothings · Sep 17, 2024 · affe4d5 · affe4d5
2 parents df33afb + 07ed2de
commit affe4d5
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Showing 3 changed files with 67 additions and 16 deletions.
diff --git a/__test__/unittest/pf_template_generator.test.ts b/__test__/unittest/pf_template_generator.test.ts
@@ -3,13 +3,15 @@ import generateTemplates from '../../src/inferred_mode/pf_template_generator';
 describe('Test Pathfinder Template Generator', () => {
   test('Should generate correct templates', async () => {
     const sub = {
-      categories: ['biolink:Drug']
+      categories: ['biolink:Drug'],
+      ids: ['subject']
     };
     const un = {
       categories: ['biolink:Gene']
     };
     const obj = {
-      categories: ['biolink:Disease']
+      categories: ['biolink:Disease'],
+      ids: ['object']
     };
 
     const templatesWithUnCat = await generateTemplates(sub, un, obj);
@@ -21,12 +23,14 @@ describe('Test Pathfinder Template Generator', () => {
         "creativeQuerySubject": {
           "categories": [
             "biolink:Drug"
-          ]
+          ],
+          "ids": ["subject"]
         },
         "creativeQueryObject": {
           "categories": [
             "biolink:Disease"
-          ]
+          ],
+          "ids": ["object"]
         },
         "un": {
           "categories": [
@@ -57,7 +61,8 @@ describe('Test Pathfinder Template Generator', () => {
             "biolink:contributes_to"
           ]
         }
-      }
+      },
+      "log": "(subject) -(regulates,regulated_by,affects,affected_by,interacts_with,associated_with)-> (Gene) -(gene_associated_with_condition,biomarker_for,affects,contributes_to)-> (object)",
     });
     expect(templatesWithoutUnCat[0]).toEqual(templatesWithUnCat[0]);
 
@@ -67,12 +72,14 @@ describe('Test Pathfinder Template Generator', () => {
         "creativeQuerySubject": {
           "categories": [
             "biolink:Drug"
-          ]
+          ],
+          "ids": ["subject"]
         },
         "creativeQueryObject": {
           "categories": [
             "biolink:Disease"
-          ]
+          ],
+          "ids": ["object"]
         },
         "un": {
           "categories": [
@@ -125,7 +132,8 @@ describe('Test Pathfinder Template Generator', () => {
             "biolink:occurs_in"
           ]
         }
-      }
+      },
+      "log": "(subject) -(regulates,regulated_by,affects,affected_by,interacts_with,associated_with)-> (Gene) -(related_to_at_instance_level,affects,contributes_to,participates_in,regulates,regulated_by,affected_by,interacts_with,correlated_with)-> (AnatomicalEntity,BiologicalProcessOrActivity,ChemicalEntity) -(related_to_at_instance_level,affects,affected_by,occurs_in)-> (object)"
     });
     expect(templatesWithoutUnCat[1]).toEqual(templatesWithUnCat[1]);
 
@@ -135,12 +143,14 @@ describe('Test Pathfinder Template Generator', () => {
         "creativeQuerySubject": {
           "categories": [
             "biolink:Drug"
-          ]
+          ],
+          "ids": ["subject"]
         },
         "creativeQueryObject": {
           "categories": [
             "biolink:Disease"
-          ]
+          ],
+          "ids": ["object"]
         },
         "un": {
           "categories": [
@@ -187,20 +197,23 @@ describe('Test Pathfinder Template Generator', () => {
             "biolink:contributes_to"
           ]
         }
-      }
+      },
+      "log": "(subject) -(regulates,regulated_by,affects,affected_by,interacts_with,associated_with)-> (Gene) -(regulates,regulated_by,affects,affected_by,interacts_with)-> (Gene) -(gene_associated_with_condition,biomarker_for,affects,contributes_to)-> (object)"
     });
     expect(templatesWithoutUnCat[2]).toEqual(templatesWithUnCat[2]);
   });
 
   test('template with no predicates should not have predicate property', async () => {
     const sub = {
-      categories: ['biolink:Drug']
+      categories: ['biolink:Drug'],
+      ids: ['subject']
     };
     const un = {
       categories: ['biolink:Dummy']
     };
     const obj = {
-      categories: ['biolink:Drug']
+      categories: ['biolink:Drug'],
+      ids: ['object']
     };
 
     const templates = await generateTemplates(sub, un, obj);

diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts
@@ -89,6 +89,31 @@ export default class PathfinderQueryHandler {
     debug(logMessage);
     this.logs.push(new LogEntry('INFO', null, logMessage).getLog());
 
+    // log all the templates
+    const templateNames = ['A', 'B', 'C'];
+    for (let i = 0; i < 3; i++) {
+      let logMessage = `Pathfinder Template ${templateNames[i]}: ${templates[i].log}`;
+      debug(logMessage);
+      this.logs.push(new LogEntry('INFO', null, logMessage).getLog());
+    }
+
+    // handle dry run scenario
+    if (this.options.dryrun_pathfinder) {
+      return {
+        description: `Pathfinder Dry Run completed successfully. No results received. ${templates.length} templates generated.`,
+        schema_version: global.SCHEMA_VERSION,
+        biolink_version: global.BIOLINK_VERSION,
+        workflow: [{ id: this.options.smartAPIID || this.options.teamName ? 'lookup' : 'lookup_and_score' }],
+        message: {
+          query_graph: this.parent.originalQueryGraph,
+          knowledge_graph: this.parent.knowledgeGraph.kg,
+          auxiliary_graphs: {},
+          results: [],
+        },
+        logs: this.logs.map((log) => log.toJSON()),
+      };
+    }
+
     // remove unpinned node & all edges involving unpinned node for now
     delete this.queryGraph.nodes[this.unpinnedNodeId];
 

diff --git a/src/inferred_mode/pf_template_generator.ts b/src/inferred_mode/pf_template_generator.ts
@@ -12,6 +12,10 @@ interface PredicateTable {
   [category1: string]: { [category2: string]: { predicate: string }[] };
 }
 
+interface AnnotatedQueryGraph extends TrapiQueryGraph {
+  log: string;
+}
+
 let categoryTable: CategoryTable;
 let predicateTable: PredicateTable;
 let loadTablesPromise: Promise<void>;
@@ -44,7 +48,7 @@ async function loadTables() {
   tablesLoaded = true;
 }
 
-export default async function generateTemplates(sub: TrapiQNode, un: TrapiQNode, obj: TrapiQNode): Promise<TrapiQueryGraph[]> {
+export default async function generateTemplates(sub: TrapiQNode, un: TrapiQNode, obj: TrapiQNode): Promise<(AnnotatedQueryGraph & {log: string})[]> {
   // load tables
   if (!tablesLoaded) {
     if (!loadTablesPromise) {
@@ -70,6 +74,9 @@ export default async function generateTemplates(sub: TrapiQNode, un: TrapiQNode,
         object: 'creativeQueryObject',
         predicates: new Set<string>(),
       }
+    },
+    generateLog: function() {
+      return `(${sub.ids.join(',')}) -(${[...this.edges.sub_un.predicates].join(',')})-> (${Array.from(this.nodes.un.categories).join(',')}) -(${[...this.edges.un_obj.predicates].join(',')})-> (${obj.ids.join(',')})`.replace(/biolink:/g, '');
     }
   };
   const templateB = {
@@ -95,6 +102,9 @@ export default async function generateTemplates(sub: TrapiQNode, un: TrapiQNode,
         object: 'creativeQueryObject',
         predicates: new Set<string>()
       }
+    },
+    generateLog: function() {
+      return `(${sub.ids.join(',')}) -(${[...this.edges.sub_un.predicates].join(',')})-> (${Array.from(this.nodes.un.categories).join(',')}) -(${[...this.edges.un_b.predicates].join(',')})-> (${Array.from(this.nodes.nb.categories).join(',')}) -(${[...this.edges.b_obj.predicates].join(',')})-> (${obj.ids.join(',')})`.replace(/biolink:/g, '');
     }
   };
   const templateC = {
@@ -120,6 +130,9 @@ export default async function generateTemplates(sub: TrapiQNode, un: TrapiQNode,
         object: 'creativeQueryObject',
         predicates: new Set<string>()
       }
+    },
+    generateLog: function() {
+      return `(${sub.ids.join(',')}) -(${[...this.edges.sub_c.predicates].join(',')})-> (${Array.from(this.nodes.nc.categories).join(',')}) -(${[...this.edges.c_un.predicates].join(',')})-> (${Array.from(this.nodes.un.categories).join(',')}) -(${[...this.edges.un_obj.predicates].join(',')})-> (${obj.ids.join(',')})`.replace(/biolink:/g, '');
     }
   };
   for (const subCat of sub.categories) {
@@ -154,9 +167,9 @@ export default async function generateTemplates(sub: TrapiQNode, un: TrapiQNode,
     }
   }
 
-  const queryGraphs: TrapiQueryGraph[] = [];
+  const queryGraphs: AnnotatedQueryGraph[] = [];
   for (const template of [templateA, templateB, templateC]) {
-    const queryGraph: TrapiQueryGraph = { nodes: {}, edges: {} };
+    const queryGraph: AnnotatedQueryGraph = { nodes: {}, edges: {}, log: template.generateLog()};
     for (const node in template.nodes) {
       queryGraph.nodes[node] = {
         ...template.nodes[node],