feat: federate WorkflowsAggregate endpoint (#108)

Co-authored-by: Nina Bernick <nbernick@CZIMACOS4338.local>
Co-authored-by: Nina Bernick <nbernick@chanzuckerberg.com>

.meshrc.yaml

@@ -173,6 +173,13 @@ sources:
             method: POST
             requestSchema: ./json-schemas/workflowRunsRequest.json
             responseSchema: ./json-schemas/workflowRunsResponse.json
+          - type: Query
+            field: workflowRunsAggregate
+            path: /projects.json
+            method: GET
+            requestSchema: ./json-schemas/workflowRunsAggregateRequest.json
+            responseSchema: ./json-schemas/workflowRunsAggregateResponse.json
+            responseTypeName: workflowRunsAggregate
           - type: Query
             field: ZipLink
             path: /workflow_runs/{args.workflowRunId}/zip_link.json

example-queries/workflows-aggregate-query.graphql

@@ -0,0 +1,23 @@
+query workflowRunsAggregateQuery {
+  workflowRunsAggregate(
+    input: {
+      where: {
+        id: {
+          _in: ["1", "2", "3"]
+        } 
+      },
+      todoRemove: { 
+        domain: "my_data",
+        offset: 0,
+        visibility: "public",
+        search: "abc",
+        time: ["20240214", "20240222"]
+      }
+    }
+  ) {
+    collectionId
+    amrRunsCount
+    cgRunsCount
+    mngsRunsCount
+  }
+}

json-schemas/workflowRunsAggregateRequest.json

@@ -0,0 +1,105 @@
+{
+    "type": "object",
+    "properties": {
+        "where": {
+            "type": "object",
+            "properties": {
+                "id": {
+                    "type": "object",
+                    "properties": {
+                        "_in": {
+                            "type": "array",
+                            "items": {
+                                "type": "string"
+                            }
+                        }
+                    }
+                }
+            }
+        },
+        "todoRemove": {
+            "type": "object",
+            "properties": {
+                "projectId": {
+                    "type": "string"
+                },
+                "domain": {
+                    "type": "string"
+                },
+                "host": {
+                    "type": "array",
+                    "items": {
+                        "type": "integer"
+                    }
+                },
+                "locationV2": {
+                    "type": "array",
+                    "items": {
+                        "type": "string"
+                    }
+                },
+                "taxonThresholds": {
+                    "type": "array",
+                    "items": {
+                        "type": "object",
+                        "properties": {
+                            "metric": {
+                                "type": "string"
+                            },
+                            "count_type": {
+                                "type": "string"
+                            },
+                            "operator": {
+                                "type": "string"
+                            },
+                            "value": {
+                                "type": "string"
+                            }
+                        }
+                    }
+                },
+                "annotations": {
+                    "type": "array",
+                    "items": {
+                        "type": "object",
+                        "properties": {
+                            "name": {
+                                "type": "string"
+                            }
+                        }
+                    }
+                },
+                "tissue": {
+                    "type": "array",
+                    "items": {
+                        "type": "string"
+                    }
+                },
+                "visibility": {
+                    "type": "string"
+                },
+                "time": {
+                    "type": "array",
+                    "items": {
+                        "type": "string"
+                    }
+                },
+                "taxaLevels": {
+                    "type": "array",
+                    "items": {
+                        "type": "string"
+                    }
+                },
+                "taxon": {
+                    "type": "array",
+                    "items": {
+                        "type": "integer"
+                    }
+                },
+                "search": {
+                    "type": "string"
+                }
+            }
+        }
+    }
+}

json-schemas/workflowRunsAggregateResponse.json

@@ -0,0 +1,26 @@
+{
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "collectionId": {
+                "type": "string"
+            },
+            "mngsRunsCount": {
+                "type": "integer"
+            },
+            "cgRunsCount": {
+                "type": "integer"
+            },
+            "amrRunsCount": {
+                "type": "integer"
+            }
+        },
+        "required": [
+            "collectionId",
+            "mngsRunsCount",
+            "cgRunsCount",
+            "amrRunsCount"
+        ]
+    }
+}

resolvers.ts

@@ -4,6 +4,7 @@ import {
   query_consensusGenomes_items,
   query_samples_items,
   query_sequencingReads_items,
+  query_workflowRunsAggregate_items,
   query_workflowRuns_items,
 } from "./.mesh";
 import {
@@ -787,6 +788,43 @@ export const resolvers: Resolvers = {
         })
       );
     },
+    workflowRunsAggregate: async (root, args, context, info) => {
+      const input = args.input;
+
+      const { projects } = await get("/projects.json" + 
+        formatUrlParams({
+          projectId: input?.todoRemove?.projectId,
+          domain: input?.todoRemove?.domain,
+          limit: TEN_MILLION,
+          listAllIds: false,
+          offset: 0,
+          host: input?.todoRemove?.host,
+          locationV2: input?.todoRemove?.locationV2,
+          taxonThresholds: input?.todoRemove?.taxonThresholds,
+          annotations: input?.todoRemove?.annotations,
+          search: input?.todoRemove?.search,
+          tissue: input?.todoRemove?.tissue,
+          visibility: input?.todoRemove?.visibility,
+          time: input?.todoRemove?.time,
+          taxaLevels: input?.todoRemove?.taxaLevels,
+          taxon: input?.todoRemove?.taxon,
+        }), args, context);
+
+      if (!projects?.length) {
+        return [];
+      }
+      return projects.map((project): query_workflowRunsAggregate_items => {
+        return {
+          collectionId: project.id.toString(),
+          mngsRunsCount: project.sample_counts.mngs_runs_count,
+          cgRunsCount:
+            project.sample_counts.cg_runs_count,
+          amrRunsCount: project.sample_counts.amr_runs_count,
+        };
+      });
+
+      // TODO (nina): call nextgen in addition to rails to get CG count
+    },
     ZipLink: async (root, args, context, info) => {
       const res = await getFullResponse(
         `/workflow_runs/${args.workflowRunId}/zip_link.json`,

sample-requests/workflowRunsAggregate.json

@@ -0,0 +1,50 @@
+{
+  "where": {
+    "id": {
+      "_in": {
+        "items": [
+          "1234"
+        ]
+      }
+    }
+  },
+  "todoRemove": {
+    "projectId": "1056",
+    "domain": "my_data",
+    "host": [
+      1,
+      11
+    ],
+    "locationV2": [
+      "California, USA"
+    ],
+    "taxonThresholds": [
+      {
+        "metric": "rpm",
+        "count_type": "NT",
+        "operator": ">=",
+        "value": "1"
+      }
+    ],
+    "annotations": [
+      {
+        "name": "Hit"
+      }
+    ],
+    "tissue": [
+      "CSF"
+    ],
+    "visibility": "public",
+    "time": [
+      "20240205",
+      "20240213"
+    ],
+    "taxaLevels": [
+      "species"
+    ],
+    "taxon": [
+      244366
+    ],
+    "search": "abc"
+  }
+}

sample-responses/workflowRunsAggregate.json

@@ -0,0 +1,8 @@
+[
+  {
+    "collectionId": "123",
+    "mngsRunsCount": 0,
+    "cgRunsCount": 5,
+    "amrRunsCount": 0
+  }
+]

tests/WorkflowRunsAggregateQuery.test.ts

@@ -0,0 +1,49 @@
+import { ExecuteMeshFn } from "@graphql-mesh/runtime";
+import { getMeshInstance } from "./utils/MeshInstance";
+
+import * as httpUtils from "../utils/httpUtils";
+import { getExampleQuery } from "./utils/ExampleQueryFiles";
+jest.spyOn(httpUtils, "get");
+
+beforeEach(() => {
+  (httpUtils.get as jest.Mock).mockClear();
+});
+
+describe("workflows aggregate query:", () => {
+  let execute: ExecuteMeshFn;
+
+  beforeEach(async () => {
+    const mesh$ = await getMeshInstance();
+    ({ execute } = mesh$);
+  });
+
+  it("Returns aggregate counts for each workflow", async () => {
+    (httpUtils.get as jest.Mock).mockImplementation(() => ({
+      projects: [
+        {
+          id: 1,
+          sample_counts: {
+            cg_runs_count: 1,
+            amr_runs_count: 2,
+            mngs_runs_count: 3
+          }
+        }
+      ],
+    }));
+
+    const query = getExampleQuery("workflows-aggregate-query");
+
+    const response = await execute(query, {});
+    expect(httpUtils.get).toHaveBeenCalledWith(
+      "/projects.json?&domain=my_data&limit=10000000&listAllIds=false&offset=0&search=abc&visibility=public&time[]=20240214&time[]=20240222",
+      expect.anything(),
+      expect.anything()
+    );
+
+    expect(response.data.workflowRunsAggregate).toHaveLength(1);
+    expect(response.data.workflowRunsAggregate[0].collectionId).toBe("1");
+    expect(response.data.workflowRunsAggregate[0].amrRunsCount).toBe(2);
+    expect(response.data.workflowRunsAggregate[0].cgRunsCount).toBe(1);
+    expect(response.data.workflowRunsAggregate[0].mngsRunsCount).toBe(3);
+  });
+});

tests/__snapshots__/UnifiedSchema.test.ts.snap

@@ -75,6 +75,7 @@ type Query @globalOptions(sourceName: "CZIDREST", endpoint: "http://web:3001/")
   UserBlastAnnotations(sampleId: String, workflowVersionId: String): [query_UserBlastAnnotations_items] @httpOperation(path: "/samples/{args.sampleId}/report_v2?&id={args.sampleId}&pipeline_version={args.workflowVersionId}&merge_nt_nr=false", httpMethod: GET)
   ValidateUserCanDeleteObjects(input: queryInput_ValidateUserCanDeleteObjects_input_Input): ValidateUserCanDeleteObjects @httpOperation(path: "/samples/validate_user_can_delete_objects.json", httpMethod: POST)
   workflowRuns(input: queryInput_workflowRuns_input_Input): [query_workflowRuns_items] @httpOperation(path: "/workflow_runs.json", httpMethod: POST)
+  workflowRunsAggregate(input: queryInput_workflowRunsAggregate_input_Input): [query_workflowRunsAggregate_items] @httpOperation(path: "/projects.json", httpMethod: GET)
   ZipLink(workflowRunId: String): ZipLink @httpOperation(path: "/workflow_runs/{args.workflowRunId}/zip_link.json", httpMethod: GET)
   GraphQLFederationVersion: GraphQLFederationVersion
 }
@@ -3316,6 +3317,52 @@ input queryInput_workflowRuns_input_entityInputsInput_where_fieldName_Input {
   _eq: String
 }
 
+type query_workflowRunsAggregate_items {
+  collectionId: String!
+  mngsRunsCount: Int!
+  cgRunsCount: Int!
+  amrRunsCount: Int!
+}
+
+input queryInput_workflowRunsAggregate_input_Input {
+  where: queryInput_workflowRunsAggregate_input_where_Input
+  todoRemove: queryInput_workflowRunsAggregate_input_todoRemove_Input
+}
+
+input queryInput_workflowRunsAggregate_input_where_Input {
+  id: queryInput_workflowRunsAggregate_input_where_id_Input
+}
+
+input queryInput_workflowRunsAggregate_input_where_id_Input {
+  _in: [String]
+}
+
+input queryInput_workflowRunsAggregate_input_todoRemove_Input {
+  projectId: String
+  domain: String
+  host: [Int]
+  locationV2: [String]
+  taxonThresholds: [queryInput_workflowRunsAggregate_input_todoRemove_taxonThresholds_items_Input]
+  annotations: [queryInput_workflowRunsAggregate_input_todoRemove_annotations_items_Input]
+  tissue: [String]
+  visibility: String
+  time: [String]
+  taxaLevels: [String]
+  taxon: [Int]
+  search: String
+}
+
+input queryInput_workflowRunsAggregate_input_todoRemove_taxonThresholds_items_Input {
+  metric: String
+  count_type: String
+  operator: String
+  value: String
+}
+
+input queryInput_workflowRunsAggregate_input_todoRemove_annotations_items_Input {
+  name: String
+}
+
 type ZipLink {
   url: String
   error: String