Merge branch 'main' into agora/migration-gene-search

Sage-Bionetworks · Oct 24, 2024 · 73104ff · 73104ff
2 parents 0c106a7 + 4bd0277
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -29,6 +29,7 @@
         "alefragnani.Bookmarks",
         "Angular.ng-template",
         "dbaeumer.vscode-eslint",
+        "donjayamanne.python-environment-manager",
         "dorzey.vscode-sqlfluff",
         "eamodio.gitlens",
         "emeraldwalk.RunOnSave",

diff --git a/.eslintrc.json b/.eslintrc.json
@@ -3,6 +3,11 @@
   "ignorePatterns": ["**/*"],
   "plugins": ["@nx"],
   "overrides": [
+    {
+      "files": "*.json",
+      "parser": "jsonc-eslint-parser",
+      "rules": {}
+    },
     {
       "files": ["*.ts", "*.tsx", "*.js", "*.jsx"],
       "rules": {}

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -7,15 +7,15 @@
 /.yarn @tschaffter
 
 # OpenChallenges
-/apps/openchallenges/ @rrchai @tschaffter @vpchung
-/libs/openchallenges/ @rrchai @tschaffter @vpchung
+/apps/openchallenges/ @rrchai @tschaffter
+/libs/openchallenges/ @rrchai @tschaffter
 
 ## DB content
-/apps/openchallenges/challenge-service/src/main/resources/db/     @tschaffter @vpchung @gaiaandreoletti
-/apps/openchallenges/organization-service/src/main/resources/db/  @tschaffter @vpchung @gaiaandreoletti
+/apps/openchallenges/challenge-service/src/main/resources/db/     @tschaffter @gaiaandreoletti
+/apps/openchallenges/organization-service/src/main/resources/db/  @tschaffter @gaiaandreoletti
 
 ## EDAM ETL
-/apps/openchallenges/edam-etl/  @mdsage1
+/apps/openchallenges/edam-etl/ @rrchai
 
 # Schematic
 /apps/schematic/ @andrewelamb @GiaJordan @linglp @milen-sage
@@ -27,7 +27,7 @@
 
 /libs/shared/ @tschaffter
 
-/apps/model-ad/ @hallieswan @sagely1
-/docker/model-ad/ @hallieswan @sagely1
-/libs/model-ad/ @hallieswan @sagely1
-/libs/results-visualization-framework/ @hallieswan @sagely1
+/apps/model-ad/ @sagely1
+/docker/model-ad/ @sagely1
+/libs/model-ad/ @sagely1
+/libs/results-visualization-framework/ @sagely1
diff --git a/.github/actions/setup-dev-container/action.yml b/.github/actions/setup-dev-container/action.yml
@@ -3,13 +3,13 @@ description: 'Installs the dev container CLI, fetches caches (if exist), and sta
 runs:
   using: 'composite'
   steps:
-    - name: Set up pnpm cache
-      uses: actions/cache@v3
-      with:
-        path: '/tmp/.pnpm-store'
-        key: ${{ runner.os }}-pnpm-store-${{ hashFiles('**/pnpm-lock.yaml') }}
-        restore-keys: |
-          ${{ runner.os }}-pnpm-store-
+    # - name: Set up pnpm cache
+    #   uses: actions/cache@v3
+    #   with:
+    #     path: '/tmp/.pnpm-store'
+    #     key: ${{ runner.os }}-pnpm-store-${{ hashFiles('**/pnpm-lock.yaml') }}
+    #     restore-keys: |
+    #       ${{ runner.os }}-pnpm-store-
 
     - name: Set up Renv cache
       uses: actions/cache@v3

diff --git a/.github/workflows/locust-load-test.yml b/.github/workflows/locust-load-test.yml
@@ -0,0 +1,53 @@
+name: Locust Load Test
+
+on:
+  workflow_dispatch:
+    inputs:
+      product:
+        type: choice
+        description: 'Name of the product to test'
+        required: true
+        options:
+          - agora
+          - openchallenges
+      # user_count:
+      #   description: 'Number of users to simulate in Locust'
+      #   required: true
+      #   default: '50'
+      # spawn_rate:
+      #   description: 'Rate at which users are spawned (users per second)'
+      #   required: true
+      #   default: '10'
+
+jobs:
+  deploy:
+    runs-on: ubuntu-22.04-4core-16GBRAM-150GBSSD
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Derive appropriate SHAs for base and head for `nx affected` commands
+        uses: nrwl/nx-set-shas@v4
+
+      - name: Set up the dev container
+        uses: ./.github/actions/setup-dev-container
+
+      # - name: Build the specified product, serve it, and perform a load test
+      #   run: |
+      #     devcontainer exec --workspace-folder ../sage-monorepo bash -c ". ./dev-env.sh \
+      #       && nx run-many --target=build-image --projects=${{ inputs.product }}-*" \
+      #       && nx serve-detach ${{ inputs.product }}-apex \
+      #       && nx serve sandbox-locust --configuration=${{ inputs.product }}
+
+      - name: Perform a load test
+        run: |
+          devcontainer exec --workspace-folder ../sage-monorepo bash -c ". ./dev-env.sh \
+            && nx run sandbox-locust:serve:${{ inputs.product }} --headless
+
+      - name: Upload Locust reports as artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: locust-reports
+          path: apps/sandbox/locust/locust_*.csv
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -22,10 +22,14 @@
   "editor.inlayHints.enabled": "off",
   "eslint.enable": true,
   "eslint.workingDirectories": ["."],
-  "eslint.validate": ["javascript", "javascriptreact", "typescript", "typescriptreact", "html"],
-  // We need to explicitly set Prettier as the format for JSON formats, otherwise the formatter
-  // provided with VS Code will set itself as the default one, despite us specifying that Prettier
-  // is the default formatter (editor.defaultFormatter).
+  "eslint.validate": [
+    "javascript",
+    "javascriptreact",
+    "typescript",
+    "typescriptreact",
+    "html",
+    "json"
+  ],
   "[json]": {
     "editor.defaultFormatter": "esbenp.prettier-vscode"
   },
@@ -42,16 +46,13 @@
     "editor.defaultFormatter": "esbenp.prettier-vscode"
   },
   "typescript.tsdk": "node_modules/typescript/lib",
-  // Python settings
   "python.analysis.autoImportCompletions": true,
   "python.analysis.typeCheckingMode": "basic",
-  // "python.terminal.activateEnvironment": false,
   "python.terminal.activateEnvInCurrentTerminal": false,
   "[python]": {
     "editor.defaultFormatter": "ms-python.black-formatter",
     "editor.tabSize": 4
   },
-  // SQL settings
   "sqltools.autoOpenSessionFiles": false,
   "sqltools.connections": [
     {

diff --git a/apps/agora/apex/project.json b/apps/agora/apex/project.json
@@ -16,17 +16,6 @@
         "command": "docker/agora/serve-detach.sh agora-apex"
       }
     },
-    "build-image": {
-      "executor": "@nx-tools/nx-container:build",
-      "options": {
-        "context": "apps/agora/apex",
-        "metadata": {
-          "images": ["ghcr.io/sage-bionetworks/agora-apex"],
-          "tags": ["type=edge,branch=main", "type=raw,value=local", "type=sha"]
-        },
-        "push": false
-      }
-    },
     "publish-image": {
       "executor": "@nx-tools/nx-container:build",
       "options": {

diff --git a/apps/agora/api-docs/project.json b/apps/agora/api-docs/project.json
@@ -30,18 +30,6 @@
         "command": "docker/agora/serve-detach.sh agora-api-docs"
       }
     },
-    "build-image": {
-      "executor": "@nx-tools/nx-container:build",
-      "options": {
-        "context": "apps/agora/api-docs",
-        "metadata": {
-          "images": ["ghcr.io/sage-bionetworks/agora-api-docs"],
-          "tags": ["type=edge,branch=main", "type=raw,value=local", "type=sha"]
-        },
-        "push": false
-      },
-      "dependsOn": ["build"]
-    },
     "publish-image": {
       "executor": "@nx-tools/nx-container:build",
       "options": {

diff --git a/apps/agora/api/project.json b/apps/agora/api/project.json
@@ -60,18 +60,6 @@
         "fix": true
       }
     },
-    "build-image": {
-      "executor": "@nx-tools/nx-container:build",
-      "options": {
-        "context": ".",
-        "metadata": {
-          "images": ["ghcr.io/sage-bionetworks/agora-api"],
-          "tags": ["type=edge,branch=main", "type=raw,value=local", "type=sha"]
-        },
-        "push": false
-      },
-      "dependsOn": ["build"]
-    },
     "publish-image": {
       "executor": "@nx-tools/nx-container:build",
       "options": {

diff --git a/apps/agora/app/project.json b/apps/agora/app/project.json
@@ -156,18 +156,6 @@
       },
       "defaultConfiguration": "development"
     },
-    "build-image": {
-      "executor": "@nx-tools/nx-container:build",
-      "options": {
-        "context": ".",
-        "metadata": {
-          "images": ["ghcr.io/sage-bionetworks/agora-app"],
-          "tags": ["type=edge,branch=main", "type=raw,value=local", "type=sha"]
-        },
-        "push": false
-      },
-      "dependsOn": ["server"]
-    },
     "publish-image": {
       "executor": "@nx-tools/nx-container:build",
       "options": {

diff --git a/apps/agora/data/project.json b/apps/agora/data/project.json
@@ -31,22 +31,6 @@
         "command": "docker/agora/serve-detach.sh {projectName}"
       }
     },
-    "build-image": {
-      "executor": "@nx-tools/nx-container:build",
-      "options": {
-        "context": "{projectRoot}",
-        "metadata": {
-          "images": ["ghcr.io/sage-bionetworks/{projectName}"],
-          "tags": [
-            "type=edge,branch=main",
-            "type=raw,value=local",
-            "type=sha",
-            "type=raw,value=$DATA_FILE.$DATA_VERSION"
-          ]
-        },
-        "push": false
-      }
-    },
     "publish-image": {
       "executor": "@nx-tools/nx-container:build",
       "options": {

diff --git a/apps/agora/mongo/project.json b/apps/agora/mongo/project.json
@@ -18,17 +18,6 @@
         "command": "docker/agora/serve-detach.sh {projectName}"
       }
     },
-    "build-image": {
-      "executor": "@nx-tools/nx-container:build",
-      "options": {
-        "context": "apps/agora/mongo",
-        "metadata": {
-          "images": ["ghcr.io/sage-bionetworks/{projectName}"],
-          "tags": ["type=edge,branch=main", "type=raw,value=local", "type=sha"]
-        },
-        "push": false
-      }
-    },
     "publish-image": {
       "executor": "@nx-tools/nx-container:build",
       "options": {

diff --git a/apps/openchallenges/apex/project.json b/apps/openchallenges/apex/project.json
@@ -17,28 +17,6 @@
         "command": "docker/openchallenges/serve-detach.sh openchallenges-apex"
       }
     },
-    "build-image": {
-      "executor": "@nx-tools/nx-container:build",
-      "options": {
-        "context": "{projectRoot}"
-      },
-      "configurations": {
-        "local": {
-          "metadata": {
-            "images": ["ghcr.io/sage-bionetworks/{projectName}"],
-            "tags": ["type=edge,branch=main", "type=raw,value=local", "type=sha"]
-          }
-        },
-        "ci": {
-          "metadata": {
-            "images": ["ghcr.io/sage-bionetworks/{projectName}"],
-            "tags": ["type=semver,pattern={{version}},value=${VERSION}", "type=sha"]
-          },
-          "push": true
-        }
-      },
-      "defaultConfiguration": "local"
-    },
     "publish-image": {
       "executor": "@nx-tools/nx-container:build",
       "options": {

diff --git a/apps/openchallenges/api-docs/project.json b/apps/openchallenges/api-docs/project.json
@@ -31,18 +31,6 @@
         "command": "docker/openchallenges/serve-detach.sh openchallenges-api-docs"
       }
     },
-    "build-image": {
-      "executor": "@nx-tools/nx-container:build",
-      "options": {
-        "context": "apps/openchallenges/api-docs",
-        "metadata": {
-          "images": ["ghcr.io/sage-bionetworks/openchallenges-api-docs"],
-          "tags": ["type=edge,branch=main", "type=raw,value=local", "type=sha"]
-        },
-        "push": false
-      },
-      "dependsOn": ["build"]
-    },
     "publish-image": {
       "executor": "@nx-tools/nx-container:build",
       "options": {

diff --git a/apps/openchallenges/api-gateway/project.json b/apps/openchallenges/api-gateway/project.json
@@ -67,18 +67,6 @@
       },
       "dependsOn": ["^install"]
     },
-    "build-image": {
-      "executor": "@nx-tools/nx-container:build",
-      "options": {
-        "context": "apps/openchallenges/api-gateway",
-        "metadata": {
-          "images": ["ghcr.io/sage-bionetworks/openchallenges-api-gateway"],
-          "tags": ["type=edge,branch=main", "type=raw,value=local", "type=sha"]
-        },
-        "push": false
-      },
-      "dependsOn": ["build-image-base"]
-    },
     "publish-image": {
       "executor": "@nx-tools/nx-container:build",
       "options": {

diff --git a/apps/openchallenges/app/project.json b/apps/openchallenges/app/project.json
@@ -132,18 +132,6 @@
         "jestConfig": "apps/openchallenges/app/jest.config.ts"
       }
     },
-    "build-image": {
-      "executor": "@nx-tools/nx-container:build",
-      "options": {
-        "context": ".",
-        "metadata": {
-          "images": ["ghcr.io/sage-bionetworks/openchallenges-app"],
-          "tags": ["type=edge,branch=main", "type=raw,value=local", "type=sha"]
-        },
-        "push": false
-      },
-      "dependsOn": ["server"]
-    },
     "publish-image": {
       "executor": "@nx-tools/nx-container:build",
       "options": {

diff --git a/apps/openchallenges/challenge-service/project.json b/apps/openchallenges/challenge-service/project.json
@@ -75,18 +75,6 @@
       },
       "dependsOn": ["^install"]
     },
-    "build-image": {
-      "executor": "@nx-tools/nx-container:build",
-      "options": {
-        "context": "apps/openchallenges/challenge-service",
-        "metadata": {
-          "images": ["ghcr.io/sage-bionetworks/{projectName}"],
-          "tags": ["type=edge,branch=main", "type=raw,value=local", "type=sha"]
-        },
-        "push": false
-      },
-      "dependsOn": ["build-image-base"]
-    },
     "publish-image": {
       "executor": "@nx-tools/nx-container:build",
       "context": "apps/openchallenges/challenge-service",