Merge pull request #2425 from kbase/develop

Staging release of version 4.5.0

Author: briehl

Diff for: .coveragerc

@@ -1,3 +1,10 @@
 [run]
 omit =
-    src/biokbase/narrative/tests/*
+    */biokbase/narrative/tests/*
+    */biokbase/narrative/sphinxext/*
+
+[html]
+directory = ./python-coverage
+
+[xml]
+output = ./python-coverage/coverage.xml

Diff for: .eslintrc.yml

@@ -4,10 +4,10 @@ env:
   es6: true
   node: true
 extends:
-  - 'eslint:recommended'
+  - "eslint:recommended"
   - prettier
 parserOptions:
-    ecmaVersion: 2018
+  ecmaVersion: 2018
 root: true
 rules:
   strict:
@@ -16,8 +16,8 @@ rules:
   no-console:
     - error
     - allow:
-      - warn
-      - error
+        - warn
+        - error
   require-await:
     - error
   no-confusing-arrow:
@@ -40,3 +40,7 @@ rules:
     - warn
   prefer-spread:
     - warn
+  indent:
+    - error
+    - 4
+    - SwitchCase: 1

Diff for: .github/workflows/integration_test.yml

@@ -0,0 +1,44 @@
+name: CI-integration-testing
+
+on:
+  [push, pull_request]
+
+jobs:
+  build-and-test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/[email protected]
+      with:
+        miniconda-version: 'latest'
+        activate-environment: test-environment
+        python-version: 3.6.10
+        auto-activate-base: false
+        auto-update-conda: true
+        condarc-file: test/condarc.yml
+
+    - name: Use Node JS 14.x
+      uses: actions/setup-node@v1
+      with:
+        node-version: 14.x
+
+    - name: Install JS dependencies
+      run: |
+        npm ci
+        npm install bower
+        ./node_modules/bower/bin/bower install
+
+    - name: Install Narrative Application
+      shell: bash -l {0}
+      run: |
+          bash ./scripts/install_narrative.sh
+          npm run minify
+          sed <src/config.json.templ >src/config.json "s/{{ .Env.CONFIG_ENV }}/dev/"
+          sed -i 's/{{ if ne .Env.CONFIG_ENV "prod" }} true {{- else }} false {{- end }}/true/' src/config.json
+          jupyter notebook --version
+
+    - name: Run Narrative Frontend Integration Tests
+      shell: bash -l {0}
+      env:
+        KBASE_TEST_TOKEN: ${{ secrets.NARRATIVE_TEST_TOKEN }}
+      run: make test-integration

Diff for: .github/workflows/test.yml renamed to .github/workflows/unit_test.yml

@@ -1,4 +1,4 @@
-name: CI-testing
+name: CI-unit-testing
 
 on:
   [push, pull_request]
@@ -45,23 +45,17 @@ jobs:
       shell: bash -l {0}
       run: make test-frontend-unit
 
-    - name: make test output available as artefact in case of failure
+    - name: make test output available as artifact in case of failure
       if: ${{ failure() }}
       uses: actions/upload-artifact@v2
       with:
         name: karma-result.json
         path: karma-result.json
 
-    - name: Run Narrative Frontend Integration Tests
-      shell: bash -l {0}
-      env:
-        KBASE_TEST_TOKEN: ${{ secrets.NARRATIVE_TEST_TOKEN }}
-      run: make test-integration
-
     - name: Send to Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v1.5.2
       with:
         file: |
-          ./coverage.xml
+          ./python-coverage/coverage.xml
           ./js-coverage/lcov/lcov.info
         fail_ci_if_error: true

Diff for: .gitignore

@@ -11,6 +11,7 @@ kbase-extension/log/
 kbase-extension/kbase_templates/old/
 kbase-extension/static/components/
 kbase-extension/static/ext_components/
+kbase-extension/static/ext_modules/
 node_modules/
 install.log
 /src/build/
@@ -24,6 +25,7 @@ narrative_venv/
 new_narrative_env_2/
 js-coverage
 cover
+_attic
 
 # From https://github.com/github/gitignore/blob/master/Python.gitignore
 
@@ -65,6 +67,7 @@ pip-delete-this-directory.txt
 
 # Unit test / coverage reports
 /coverage/
+/python-coverage/
 htmlcov/
 .tox/
 .coverage
@@ -99,3 +102,6 @@ target/
 .vscode
 /tags
 .idea
+
+# For yarn users
+yarn.lock

Diff for: .husky/pre-push

@@ -1,4 +1,5 @@
 #!/bin/sh
 . "$(dirname "$0")/_/husky.sh"
 
-npm run husky_msg && npm run prettier_check
+#npm run husky_msg && npm run prettier_check
+npx lint-staged

Diff for: .prettierignore

@@ -2,8 +2,11 @@
 .github
 docs
 js-coverage
+python-coverage
 kbase-extension/static/ext_components
 kbase-extension/static/ext_packages
+kbase-extension/static/ext_modules
 kbase-extension/static/kbase/js/patched-components
-venv
+node_modules
 cover
+venv

Diff for: Makefile

@@ -38,7 +38,7 @@ build-travis-narrative:
 test: test-backend test-frontend
 	@echo "done running backend and frontend test scripts"
 
-# test-backend should use nose, or the like, to test our
+# test-backend uses pytest to test our
 # Python extensions to the IPython notebook.
 #
 # Testing the IPython notebook itself is out of the scope

Diff for: RELEASE_NOTES.md

@@ -4,6 +4,39 @@ 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 4.5.0
+- PTV-1561 - SampleSet viewer fixes to allow AMA features; not complete support for AMA features as GenomeSearchUtil does not yet support AMA.
+- SCT-3100 - Improve SampleSet viewer; add improved JSON-RPC 1.1 client and associatedKBase service client; add msw (Mock Service Worker) support;
+- SCT-3084 - Fixed broken (non-functional) search in the data panel
+- SCT-3602 - refseq public data tool now searches by lineage as well; for all public data tools: automatically focus the search input; fix paging bug.
+- No ticket - migrate from `nosetests` to `pytest` for testing the Python stack.
+- Python dependency updates
+  - bokeh 2.3.2 -> 2.3.3
+  - pillow 8.2.0 -> 8.3.1
+  - plotly 4.14.3 -> 5.1.0
+  - pymongo 3.11.4 -> 3.12.0
+  - pytest 6.2.3. -> 6.2.4
+  - pytest-cov 2.11.1 -> 2.12.1
+  - requests 2.25.1 -> 2.26.0
+  - setuptools 57.0.0 -> 57.4.0
+- Javascript dependency updates
+  - @types/puppeteer 5.0.0 -> 5.4.4
+  - @wdio/browserstack-service 7.7.3 -> 7.9.0
+  - @wdio/cli 7.7.3 -> 7.9.0
+  - @wdio/local-runner 7.7.3 -> 7.9.0
+  - @wdio/mocha-framework 7.7.3 -> 7.9.0
+  - @wdio/selenium-standalone-service 7.7.3 -> 7.7.4
+  - @wdio/spec-reporter 7.7.7 -> 7.9.0
+  - chromedriver 91.0.0 -> 91.0.1
+  - eslint 7.28.0 -> 7.32.0
+  - husky 6.0.0 -> 7.0.1
+  - karma 6.3.3. -> 6.3.4
+  - puppeteer 10.0.0 -> 10.1.0
+  - selenium-standalone 6.23.0 -> 7.1.0
+  - terser 5.7.0 -> 5.7.1
+  - wdio-chromedriver-service 7.1.0 -> 7.1.1
+  - webdriverio 7.7.3 -> 7.9.1
+
 ### Version 4.4.0
 -   No ticket: boatloads of code cleanup and fixes to the unit and internal testing
 -   PTV-1635: fix bug in data slideout tab selection

Diff for: bower.json

@@ -1,6 +1,6 @@
 {
   "name": "kbase-narrative",
-  "version": "4.4.0",
+  "version": "4.5.0",
   "homepage": "https://kbase.us",
   "dependencies": {
     "bluebird": "3.7.2",

Diff for: docs/developer/local-docker.md

@@ -24,10 +24,10 @@ The following changes are required:
       - `ENV` sets the `CONFIG_ENV` environment variable for the Docker container; ci is the environment in which you are working (needs to be same as the ui is running on.)
       - `PORT` sets the host port that can be used. E.g. if you use PORT=12345, then http://localhost:12345 will start the Narrative. Default is 8888.
         - Note that the logging on the console will always show 8888 since that will be used internal to the container.
-      - uses the config set $env; makes it easy to test different environments alongside ui
-      - uses kbase-dev network; allows interoperation with the kbase-ui proxier
-      - uses name "narrative"; same
-      - mounts kbase static directory inside container; allows editing files on host and having changes reflected with a Narrative reload
+      - uses the config set in `$ENV`; makes it easy to test different environments alongside ui
+      - uses `kbase-dev` network; allows interoperation with the kbase-ui proxier to access local services
+      - uses container host name "narrative"
+      - mounts `kbase-extension/static/kbase` directory inside container; allows editing files on host and having changes reflected with a Narrative reload
       - removes container when done; easy cleanup
       - uses "dev" tagged container; matches the docker build task above
 

Diff for: docs/testing/integration-testing.md

@@ -31,7 +31,8 @@
         - `source ./venv/bin/activate`
     - build the narrative locally
         - `make install`
-- obtain a kbase login (or dev) CI token
+- obtain a KBase login (or dev) CI token
+  - it must be either for the "narrativetest" account, or account which has view access to the same narratives as narrativetest (e.g. kbaseuitest).
   - log into `https://ci.kbase.us`
   - in the browser console issue
     - `document.cookie`

Diff for: docs/testing/testing.md

@@ -2,15 +2,24 @@
 
 ***Table of Contents***
 
-- [Installation](#installation)
-- [Short Version](#short-version)
-- [Long Version](#long-version)
-  - [About](#about)
-  - [How to Run Tests](#how-to-run-tests)
-  - [Add Credentials for Tests](#add-credentials-for-tests)
-  - [Testing with Travis-CI and Coveralls](#testing-with-travis-ci-and-coveralls)
-  - [Adding Your Own Tests](#adding-your-own-tests)
-  - [Manual Testing and Debugging](#manual-testing-and-debugging)
+- [Narrative Unit Testing](#narrative-unit-testing)
+  - [Installation](#installation)
+  - [Short version](#short-version)
+  - [Long version](#long-version)
+    - [About](#about)
+    - [How to Run Tests](#how-to-run-tests)
+    - [Add Credentials for Tests](#add-credentials-for-tests)
+      - [***Python***](#python)
+      - [***JavaScript***](#javascript)
+      - [***Frontend Integration Tests***](#frontend-integration-tests)
+    - [Testing with Github Actions and Codecov](#testing-with-github-actions-and-codecov)
+    - [Adding Your Own Tests](#adding-your-own-tests)
+      - [***Python***](#python-1)
+      - [***JavaScript***](#javascript-1)
+      - [***Frontend Integration Tests***](#frontend-integration-tests-1)
+    - [Manual Testing and Debugging](#manual-testing-and-debugging)
+      - [***Python***](#python-2)
+      - [***JavaScript***](#javascript-2)
 
 ## Installation
 
@@ -31,7 +40,7 @@ npm install -g grunt-cli
 
 ### About
 
-Because the Narrative Interface is built on both the front and back ends of the Jupyter Notebook, there's two sides to Narrative testing. The front end tests are in JavaScript, and make use of [Karma](http://karma-runner.github.io/1.0/index.html) as a test runner, and [Jasmine](https://jasmine.github.io/2.0/introduction.html) as a testing language. The back end tests are written in Python using the unittest framework, and run with [nose](http://nose.readthedocs.io/en/latest/).
+Because the Narrative Interface is built on both the front and back ends of the Jupyter Notebook, there's two sides to Narrative testing. The front end tests are in JavaScript, and make use of [Karma](http://karma-runner.github.io/1.0/index.html) as a test runner, and [Jasmine](https://jasmine.github.io/2.0/introduction.html) as a testing language. The back end tests are written in Python using the unittest framework, and run with [pytest](https://docs.pytest.org/en/6.2.x/).
 
 ### How to Run Tests