Merge pull request #3603 from kbase/develop

Merge to main for 5.4.0 release

.github/codeql.yml

@@ -12,7 +12,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@master
       with:
         # We must fetch at least the immediate parents so that if this is
         # a pull request then we can checkout the head.
@@ -25,15 +25,15 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@master
       # Override language selection by uncommenting this and choosing your languages
       # with:
       #   languages: go, javascript, csharp, python, cpp, java
 
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v3
+      uses: github/codeql-action/autobuild@master
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -47,4 +47,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@master

.github/workflows/build_and_push_image.yml

@@ -18,7 +18,7 @@ jobs:
       name: Check out GitHub Repo
       with:
         ref: "${{ github.event.pull_request.head.sha }}"
-      uses: actions/checkout@v4
+      uses: actions/checkout@main
     -
       name: Set up environment
       run: |
@@ -42,17 +42,17 @@ jobs:
       run: echo "date=$(date -u +'%Y-%m-%dT%H:%M:%SZ')" >> $GITHUB_OUTPUT
     -
       name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v3
+      uses: docker/setup-buildx-action@master
     -
       name: Log in to the Container registry
-      uses: docker/login-action@v3
+      uses: docker/login-action@master
       with:
         registry: ghcr.io
         username: ${{ secrets.GHCR_USERNAME }}
         password: ${{ secrets.GHCR_TOKEN }}
     -
       name: Build narrative image
-      uses: docker/build-push-action@v5
+      uses: docker/build-push-action@master
       with:
         context: .
         file: ./Dockerfile
@@ -67,7 +67,7 @@ jobs:
           TAG='${{ github.ref }}'
     -
       name: Build version image
-      uses: docker/build-push-action@v5
+      uses: docker/build-push-action@master
       if: ${{ github.base_ref }} == 'main' || ${{ github.base_ref }} == 'develop'
       with:
         context: .

.github/workflows/integration_test.yml

@@ -16,14 +16,14 @@ jobs:
     steps:
     -
       name: Log in to the Container registry
-      uses: docker/login-action@v3
+      uses: docker/login-action@master
       with:
         registry: ghcr.io
         username: ${{ secrets.GHCR_USERNAME }}
         password: ${{ secrets.GHCR_TOKEN }}
     -
       name: Repo checkout
-      uses: actions/checkout@v4
+      uses: actions/checkout@master
     -
       name: Set up environment
       run: |
@@ -48,7 +48,7 @@ jobs:
       run: docker pull ${{ env.APP_IMAGE_TAG }}
     -
       name: Use Node JS 20
-      uses: actions/setup-node@v4
+      uses: actions/setup-node@master
       with:
         node-version: 20
     -

.github/workflows/tag_latest_image.yaml

@@ -16,10 +16,10 @@ jobs:
     - name: Check out GitHub Repo
       with:
         ref: "${{ github.event.pull_request.head.sha }}"
-      uses: actions/checkout@v4
+      uses: actions/checkout@master
     -
       name: Log in to the Container registry
-      uses: docker/login-action@v3
+      uses: docker/login-action@master
       with:
         registry: ghcr.io
         username: ${{ secrets.GHCR_USERNAME }}

.github/workflows/unit_test.yml

@@ -16,14 +16,14 @@ jobs:
     steps:
     -
       name: Log in to the Container registry
-      uses: docker/login-action@v3
+      uses: docker/login-action@master
       with:
         registry: ghcr.io
         username: ${{ secrets.GHCR_USERNAME }}
         password: ${{ secrets.GHCR_TOKEN }}
     -
       name: Repo checkout
-      uses: actions/checkout@v4
+      uses: actions/checkout@master
     -
       name: Set up environment
       run: |
@@ -58,7 +58,7 @@ jobs:
       continue-on-error: true
     -
       name: Use Node JS 20
-      uses: actions/setup-node@v4
+      uses: actions/setup-node@main
       with:
         node-version: 20
     -
@@ -76,7 +76,7 @@ jobs:
     -
       name: Send to Codecov
       id: send_to_codecov
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@main
       continue-on-error: true
       with:
         token: ${{ secrets.CODECOV_TOKEN }}

RELEASE_NOTES.md

@@ -4,6 +4,15 @@ The Narrative Interface allows users to craft KBase Narratives using a combinati
 
 This is built on the Jupyter Notebook v6.5.6 and IPython 8.25.0 (more notes will follow).
 
+## Version 5.4.0
+-   UIP-43
+    -   Change Narrative JSON downloads to use a download-to-staging app.
+    -   Add an optional "wildcard" field to app cells that can be used to allow any data object as an app input.
+    -   Add a text-only output field for app cells to optionally use.
+-   UIP-44 - Convert data object transform-and-download URLs to use the Blobstore endpoint instead of the Data Import Export service
+-   UIP-45 - Convert the report object viewer to use the Blobstore endpoint instead of the Data Import Export service
+-   Remove last references to the Data Import Export service so we can lay it to rest in KBase.
+
 ## Version 5.3.0
 
 -   PTV-1845 - kbaseTabs now shows another tab after a closable tab is closed;

docs/developer/widget_helper_modules.md

@@ -21,7 +21,6 @@ This replies with the currently configured service (or other) url endpoints. Sup
 ```
 awe
 catalog
-data_import_export
 fba
 feature_values
 gene_families

eslint.config.mjs

@@ -0,0 +1,66 @@
+import globals from "globals";
+import path from "node:path";
+import { fileURLToPath } from "node:url";
+import js from "@eslint/js";
+import { FlatCompat } from "@eslint/eslintrc";
+
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = path.dirname(__filename);
+const compat = new FlatCompat({
+    baseDirectory: __dirname,
+    recommendedConfig: js.configs.recommended,
+    allConfig: js.configs.all
+});
+
+export default [{
+    ignores: [
+        "**/.git",
+        "**/.github",
+        "**/.husky",
+        "**/cover",
+        "**/docs",
+        "**/js-coverage",
+        "kbase-extension/static/ext_components",
+        "kbase-extension/static/ext_modules",
+        "kbase-extension/static/ext_packages",
+        "**/node_modules",
+        "**/python-coverage",
+        "**/venv",
+    ],
+}, ...compat.extends("eslint:recommended", "prettier"), {
+    languageOptions: {
+        globals: {
+            ...globals.amd,
+            ...globals.browser,
+            ...globals.node,
+            ...globals.jasmine,
+            ...globals.mocha,
+        },
+
+        ecmaVersion: 2018,
+    },
+
+    rules: {
+        strict: ["error", "function"],
+
+        "no-console": ["error", {
+            allow: ["warn", "error"],
+        }],
+
+        "require-await": ["error"],
+        "no-confusing-arrow": ["error"],
+        "no-const-assign": ["error"],
+        "no-duplicate-imports": ["error"],
+        "no-useless-computed-key": ["error"],
+        "no-useless-rename": ["error"],
+        "no-var": ["error"],
+        "prefer-arrow-callback": ["warn"],
+        "prefer-const": ["error"],
+        "prefer-rest-params": ["warn"],
+        "prefer-spread": ["warn"],
+
+        indent: ["error", 4, {
+            SwitchCase: 1,
+        }],
+    },
+}];

kbase-extension/scss/all_concat.scss

@@ -37,6 +37,7 @@
 @import "partials/bulkImportCell";
 @import "partials/cellToolbar";
 @import "partials/dataStaging";
+@import "partials/downloadPanel";
 @import "partials/dropzoneDz";
 @import "partials/errorDisplay";
 @import "partials/errorMessage";

kbase-extension/scss/partials/_downloadPanel.scss

@@ -0,0 +1,27 @@
+.kb-download-panel {
+    display: flex;
+
+    // .kb-download-panel__label
+    &__label {
+        white-space: nowrap;
+        padding: 1px;
+        align-self: center;
+    }
+
+    // .kb-download-panel__buttons
+    &__buttons {
+        text-align: left;
+        padding: 1px;
+    }
+
+    // .kb-download-panel__status
+    &__status {
+        margin: 15px;
+        word-wrap: wrap-word;
+        overflow: none;
+
+        &__error {
+            color: use-color('error');
+        }
+    }
+}

kbase-extension/static/kbase/config/cdn-service-config.json

@@ -8,10 +8,6 @@
             "url": "https://kbase.us/services/cdmi_api",
             "name": "CDMI"
         },
-        "data_import_export": {
-            "url": "https://ci.kbase.us/services/data_import_export",
-            "name": "Data Import Export"
-        },
         "fba": {
             "url": "https://ci.kbase.us/services/KBaseFBAModeling",
             "name": "FBA"
@@ -147,4 +143,4 @@
         "icon": "flask",
         "name": "Continuous Integration"
     }
-}
+}

kbase-extension/static/kbase/config/services-appdev.json

@@ -8,10 +8,6 @@
             "url": "https://kbase.us/services/cdmi_api",
             "name": "CDMI"
         },
-        "data_import_export": {
-            "url": "https://kbase.us/services/data_import_export",
-            "name": "Data Import Export"
-        },
         "fba": {
             "url": "https://kbase.us/services/KBaseFBAModeling",
             "name": "FBA"
@@ -151,4 +147,4 @@
         "icon": "wrench",
         "name": "App Dev"
     }
-}
+}

kbase-extension/static/kbase/config/services-ci.json

@@ -8,10 +8,6 @@
             "url": "https://kbase.us/services/cdmi_api",
             "name": "CDMI"
         },
-        "data_import_export": {
-            "url": "https://ci.kbase.us/services/data_import_export",
-            "name": "Data Import Export"
-        },
         "fba": {
             "url": "https://ci.kbase.us/services/KBaseFBAModeling",
             "name": "FBA"
@@ -151,4 +147,4 @@
         "icon": "flask",
         "name": "Continuous Integration"
     }
-}
+}