Merge pull request #3009 from kbase/develop-to-main

DATAUP-697 Merge to main for 5.1.0 release

Author: briehl

.flake8

@@ -3,7 +3,8 @@ max-line-length = 88
 # E203: whitespace before ‘,’, ‘;’, or ‘:’
 # E501: line length
 # W503: line break after binary operator
-ignore = E203, E501, W503
+ignore = E203, E501, W503, D, DAR
+extend-select = B902, B903, B904
 extend-exclude =
 *.pyc,
 .github,

.github/workflows/build_and_push_image.yml

@@ -24,7 +24,7 @@ jobs:
         if [ ${{ github.base_ref }} == 'main' ]; then
             branch=''
         else
-            branch="-""${{ github.base_ref }}"
+            branch=`"-""${{ github.base_ref }}" | awk '{print tolower($0)}'`
         fi
         narrative_version=`grep '\"version\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g'`
         narrative_git_hash=`grep '\"git_commit_hash\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g' | sed 's/,//'`

.github/workflows/build_test_pr.yaml

@@ -2,8 +2,8 @@
 name: Build Dev Image
 on:
   pull_request:
-    branches:
-    - develop
+    branches-ignore:
+    - main
     types:
     - opened
     - synchronize

.github/workflows/build_truss_pr.yaml

@@ -30,7 +30,7 @@ jobs:
         if [ ${{ github.base_ref }} == 'main' ]; then
             branch=''
         else
-            branch="-""${{ github.base_ref }}"
+            branch=`"-""${{ github.base_ref }}" | awk '{print tolower($0)}'`
         fi
         narrative_version=`grep '\"version\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g'`
         narrative_git_hash=`grep '\"git_commit_hash\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g' | sed 's/,//'`

.github/workflows/build_truss_push.yaml

@@ -0,0 +1,23 @@
+name: Build and Tag Latest Image
+
+# Controls when the workflow will run
+on:
+  # Manually triggers the workflow on the develop branch 
+  workflow_dispatch:
+    inputs:
+      branch: 
+        description: 'Branch to build the new image from'     
+        required: true
+        default: 'develop' 
+        type: choice
+        options:
+        - develop
+        - main
+    
+jobs:
+  run_build_and_push:
+    runs-on: ubuntu-latest
+    steps:
+    - 
+      name: say hello
+      run: echo "hello world"

.github/workflows/integration_test.yml

@@ -28,7 +28,7 @@ jobs:
         if [ ${{ github.base_ref }} == 'main' ]; then
             branch=''
         else
-            branch="-""${{ github.base_ref }}"
+            branch=`"-""${{ github.base_ref }}" | awk '{print tolower($0)}'`
         fi
         narrative_version=`grep '\"version\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g'`
         narrative_git_hash=`grep '\"git_commit_hash\":' src/config.json.templ | awk '{print $2}' | sed 's/"//g' | sed 's/,//'`

.github/workflows/manual_build.yml

@@ -4,8 +4,74 @@ The Narrative Interface allows users to craft KBase Narratives using a combinati
 
 This is built on the Jupyter Notebook v6.0.2 (more notes will follow).
 
+### Version 5.1.0
+- PTV-1783 - fixed issue where the previous object revert option was unavailable
+- DATAUP-639 - fix problems with dynamic dropdown app cell input
+  - selected value wasn't being displayed properly after a page reload or cell refresh
+  - selected value wasn't being displayed in view-only version
+  - "Loading..." message wasn't displayed while fetching data from a service.
+  - Update the dynamic dropdown to support the `exact_match_on` field in app specs.
+  - Add a copy button to the dynamic dropdown - this will copy the most relevant text from the dropdown to the clipboard.
+    - For dropdowns with an `exact_match_on` field, this will copy the contents of that field (e.g. for those that present taxonomy ids for a species, this copies just the scientific name)
+    - For dropdowns that go against the FTP staging area, this copies the file name and path.
+    - For other dropdowns, this copies the formatted text
+- DATAUP-751 - add link to staging area docs in the upload tour
+- DATAUP-753 - alter the error text for Select input boxes in app cells to be a bit more generalized.
+- DATAUP-756 - add a copy button for other, non-dynamic dropdowns. This copies the displayed text to the clipboard.
+
+Dependency Changes
+- Javascript dependency updates
+  - @wdio/browserstack-service: 7.16.16 -> 7.19.7
+  - @wdio/cli: 7.16.16 -> 7.19.6
+  - @wdio/local-runner: 7.16.6 -> 7.19.3
+  - @wdio/mocha-framework: 7.16.15 -> 7.20.0
+  - @wdio/selenium-standalone-service: 7.16.16 -> 7.19.1
+  - @wdio/spec-reporter: 7.16.14 -> 7.19.1
+  - autoprefixer: 10.2.6 -> 10.4.5
+  - commander: 9.0.0 -> 9.3.0
+  - chromedriver: 100.0.0 -> 101.0.0
+  - corejs-typeahead: 1.6.1 -> 1.3.1
+  - datatables.net: 1.11.3 -> 1.12.1
+  - datatables.net-bs 1.11.5 -> 1.12.1
+  - datatables.net-buttons-bs: 1.4.2 -> 2.2.3
+  - ejs: 3.1.6 -> 3.1.7
+  - eslint: 8.14.0 -> 8.16.0
+  - grunt: 1.4.1 -> 1.5.3
+  - grunt-contrib-concat: 1.0.1 -> 2.1.0
+  - handlebars: 4.0.5 -> 4.7.7
+  - jasmine-core: 4.0.0 -> 4.1.0
+  - jquery-nearest: 1.3.1 -> 1.4.0
+  - jquery-ui: 1.12.1 -> 1.13.1
+  - js-yaml: 3.3.1 -> 3.14.1
+  - karma-jasmine: 4.0.1 -> 5.0.1
+  - karma-jasmine-matchers: 4.0.2 -> 5.0.0
+  - postcss-remove-comments: 5.0.1 -> 5.1.2
+  - postcss-cli: 8.3.1 -> 9.1.0
+  - postcss-scss: 3.0.5 -> 4.0.4
+  - pure-uuid: 1.4.2 -> 1.6.2
+  - sass: 1.34.1 -> 1.51.0
+  - selenium-standalone: 8.0.9 -> 8.0.10
+  - selenium-webdriver: 4.1.1 -> 4.1.2
+  - spark-md5: 3.0.0 -> 3.0.2
+  - underscore: 1.8.3 -> 1.13.3
+  - webdriverio: 7.16.16 -> 7.19.7
+
+- Python dependency updates
+  - beautifulsoup4: 4.8.1 -> 4.11.1
+  - cryptography: 3.3.2 -> 36.0.2
+  - html5lib: 1.0.1 -> 1.1
+  - idna: 2.8 -> 3.3
+  - jinja2: 3.1.1 -> 3.0.3
+  - plotly: 5.6.0 -> 5.7.0
+  - pygments: 2.11.2 -> 2.12.0
+  - jupyter-console: 6.0.0 -> 6.4.3
+  - jsonschema: 4.4.0 -> 3.2.0
+  - pymongo: 4.1.0 -> 4.1.1
+  - pyopenssl: 19.0.0 -> 22.0.0
+  - setuptools: 62.0.0 -> 62.1.0
+
 ### Version 5.0.3
-- DATAUP-641 
+- DATAUP-641
   - Adds custom error messages when app cell dropdown menu inputs are incorrect in various different ways.
   - Adds custom error messages when app cell checkboxes are initialized with non binary data (should only happen with a bulk import cell from a spreadsheet file)
   - Adds custom error messages when app cell numeric inputs are initialized with non-numeric data.

.github/workflows/unit_test.yml

@@ -79,7 +79,7 @@ The [next](https://next.kbase.us), [appdev](https://appdev.kbase.us), and [produ
 
 ### Deploying Narrative-Refactor
 
-The [narrative-refactor](https://narrative-refactor.kbase.us) image is automatically built against the "truss" branch of the repo and is called narrative-truss:pr### when still in a PR state or narrative-truss:latest after merge. The images can be found here: https://github.com/orgs/kbase/packages
+The [narrative-refactor](https://narrative-refactor.kbase.us) image is automatically built against the "develop" branch of the repo and is called narrative-develop:pr### when still in a PR state or narrative-develop:latest after merge. The images can be found here: https://github.com/orgs/kbase/packages
 
 ### Deploying Narrative-Dev
 The [narrative-dev](https://narrative-dev.kbase.us) environment is meant for pre-release and iterative testing of new UI features and changes. As such, this isn't always tied to any particular branch, although it is most often set to deploy the production image. Contact a DevOps team member if there are any questions.
@@ -117,7 +117,7 @@ Once a pull request is merged from `develop` to `main` a new _production_ image
 | Environment | Image URL                                                      |
 | ----------- | -------------------------------------------------------------- |
 | CI          | ghcr.io/kbase/narrative-develop:latest |
-| Narrative-refactor| ghcr.io/kbase/narrative-truss:latest |
+| Narrative-refactor| ghcr.io/kbase/narrative-develop:latest |
 | Appdev      | ghcr.io/kbase/narrative:appdev         |
 | Next        | ghcr.io/kbase/narrative:next           |
 | Production  | ghcr.io/kbase/narrative:prod           |