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Merge pull request #3665 from kbase/develop
Merge to main for 5.4.2. release
2 parents 419a1d7 + 22db152 commit 26d3fc0

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‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: pip
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- package-ecosystem: "pip"
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directory: "/src"
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schedule:
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interval: monthly
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time: '11:00'
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interval: "monthly"
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groups:
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python-dependencies:
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pip:
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patterns:
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- "*"
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open-pull-requests-limit: 20
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ignore:
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- dependency-name: "notebook"
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versions: '>= 7.0.0'
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- package-ecosystem: npm
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versions: ">= 7.0.0"
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- package-ecosystem: "npm"
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directory: "/"
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schedule:
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interval: monthly
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time: '11:00'
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interval: "monthly"
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groups:
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npm-dependencies:
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npm:
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patterns:
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"*"
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- "*"
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open-pull-requests-limit: 20
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- package-ecosystem: docker
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- package-ecosystem: "docker"
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directory: "/"
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schedule:
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interval: monthly
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time: '11:00'
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interval: "monthly"
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open-pull-requests-limit: 20
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- package-ecosystem: github-actions
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- package-ecosystem: "github-actions"
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directory: "/.github"
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schedule:
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interval: monthly
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time: '11:00'
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interval: "monthly"
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open-pull-requests-limit: 20

‎RELEASE_NOTES.md‎

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@@ -4,6 +4,86 @@ The Narrative Interface allows users to craft KBase Narratives using a combinati
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This is built on the Jupyter Notebook v6.5.6 and IPython 8.26.0 (more notes will follow).
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## Version 5.4.2
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- UIP-52 - repair integration tests, get WebDriverIO up to date
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- PTV-1913 - fix potential authentication issues affecting report viewing and downloads in narratives
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### Dependency Changes
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- Python dependency updates
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- coverage 7.5.3 -> 7.6.1
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- pytest 8.2.2 -> 8.3.2
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- pytest-recording 0.13.1 -> 0.13.2
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- ruff 0.5.5 -> 0.6.3
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- certifi 2027.7.4 -> 2024.8.30
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- cryptography 42.0.8 -> 43.0.0
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- idna 3.7 -> 3.8
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- jsonschema 4.16.0 -> 4.23.0
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- markdown 3.4.1 -> 3.7
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- markupsafe 2.1.4 -> 2.1.5
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- pycurl 7.45.1 -> 7.45.3
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- pyopenssl 24.1.0 -> 24.2.1
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- setuptools 71.1.0 -> 74.0.0
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- terminado 0.18.0 -> 0.18.1
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- bokeh 3.5.1 -> 3.5.2
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- ete3 3.1.2 -> 3.1.3
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- numpy 2.0.1 -> 2.1.0
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- plotly 5.23.0 -> 5.24.0
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- scipy 1.14.0 -> 1.14.1
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- sympy 1.13.1 -> 1.13.2
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- ipython 8.26.0 -> 8.27.0
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- ipywidgets 7.7.1 -> 8.1.5
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- notebook 6.5.6 -> 6.5.7
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- pymongo 4.7.3 -> 4.8.0
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- pyyaml 6.0.1 -> 6.0.2
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- scikit-learn 1.5.0 -> 1.5.1
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- Javascript Dependency Changes
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- wdio-chromedriver-service -- Deprecated and removed, functionality is now built-in to WebdriverIO
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- @babel/traverse 7.24.7 -> 7.25.6
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- @eslint/js 9.6.0 -> 9.9.1
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- @wdio/browserstack-service 8.38.2 -> 9.0.9
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- @wdio/cli 8.38.2 -> 9.0.9
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- @wdio/local-runner 8.38.2 -> 9.0.9
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- @wdio/mocha-framwork 8.39.0 -> 9.0.8
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- @wdio/spec-reporter 8.38.2 -> 9.0.8
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- autoprefixer 10.4.19 -> 10.4.20
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- axios 1.7.2 -> 1.7.7
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- chromedriver 128.0.0 -> 128.0.1
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- cssnano 7.0.2 -> 7.0.6
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- eslint 9.4.0 -> 9.9.1
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- expect-webdriverio 3.6.0 -> 5.0.2
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- glob 10.4.1 -> 11.0.0
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- globals 15.6.0 -> 15.9.0
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- grunt-cli 1.4.3 -> 1.5.0
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- grunt-stylelint 0.20.0 -> 0.20.1
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- husky 9.0.11 -> 9.1.5
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- jasmine-core 5.1.2 -> 5.2.0
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- jquery-migrate 1.4.1 -> 3.5.2
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- karma 6.4.3 -> 6.4.4
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- lint-staged 15.2.6 -> 15.2.10
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- postcss 8.4.39 -> 8.4.45
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- prettier 3.3.2 -> 3.3.3
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- puppeteer 23.2.1 -> 23.3.0
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- requirejs 2.3.6 -> 2.3.7
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- sass 1.77.5 -> 1.78.0
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- selenium-standalone 9.5.0 -> 10.0.0
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- selenium-webdriver 4.22.0 -> 4.24.0
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- stylelint 16.6.1 -> 16.9.0
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- stylelint-config-recommended 14.0.0 -> 14.0.1
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- stylelint-config-sass-guidelines 11.1.0 -> 12.0.0
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- stylelint-config-standard 36.0.0 -> 36.0.1
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- terser 5.31.1 -> 5.31.6
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- webdriverio 8.38.2 -> 9.0.9
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- dompurify 2.5.5 -> 3.1.6
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- follow-redirects 1.15.6 -> 1.15.9
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- jquery-ui 1.13.2 -> 1.14.0
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- plotly.js-dist-min 2.33.0 -> 2.35.0
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- underscore 1.13.6 -> 1.13.7
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## Version 5.4.1
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- UIP-51 fix issue where JSON and STAGING download apps aren't getting properly instantiated with object inputs.
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‎eslint.config.mjs‎

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},
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rules: {
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strict: ["error", "function"],
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"no-console": ["error", {
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allow: ["warn", "error"],
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}],

‎kbase-extension/static/kbase/custom/custom.js‎

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NarrativeRuntime,
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html
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) => {
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'use strict';
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// Handlebars global configuration. Since these changes affect all usage of handlebars
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// in this app, they should be performed just once.
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Handlebars.registerHelper('numeral', (value, format, defaultValue, options) => {
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options = defaultValue;
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defaultValue = undefined;
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}
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let missing = false;
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if (typeof value === 'string') {
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if (value.trim().length === 0) {
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missing = true;
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}
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} else if (typeof value !== 'number') {
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missing = true;
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}
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const numeralValue = numeral(value);
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if (isNaN(numeralValue)) {
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missing = true;
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}
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if (missing) {
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if (numeralValue.value() === null) {
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return defaultValue || 'n/a';
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}
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try {

‎kbase-extension/static/kbase/js/api/auth.js‎

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},
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};
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const TOKEN_AGE = 14; // days
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const DEFAULT_TOKEN_LIFE = 14 * 24 * 60 * 60 * 1000; // millis
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/**
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* Meant for managing auth or session cookies (mainly auth cookies as set by
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* If it's missing name or value, does nothing.
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* Default expiration time is 14 days.
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* domain, expires, and max-age are optional
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* expires is expected to be in days
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* auto set fields are:
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* expires is expected to be the timestamp (ms since epoch) it will expire
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* default fields are:
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* - path = '/'
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* - expires = TOKEN_AGE (default 14) days
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* - expires = now + 14 days
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* @param {object} cookie
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* - has the cookie keys: name, value, path, expires, max-age, domain
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* - adds secure=true, samesite=Lax for KBase use.
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const name = encodeURIComponent(cookie.name);
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const value = encodeURIComponent(cookie.value || '');
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const props = {
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expires: TOKEN_AGE, // gets translated to GMT string
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expires: Date.now() + DEFAULT_TOKEN_LIFE, // gets translated to GMT string
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path: '/',
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};
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if (cookie.domain) {
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props.domain = cookie.domain;
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props['max-age'] = 86400 * props.expires;
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if (props.expires === 0) {
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props.expires = new Date(0).toUTCString();
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} else {
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props.expires = new Date(
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new Date().getTime() + 86400000 * props.expires
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).toUTCString();
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}
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props['max-age'] = parseInt((props.expires - Date.now()) / 1000);
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props.expires = new Date(props.expires).toUTCString();
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const fields = Object.keys(props).map((key) => {
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return `${key}=${props[key]}`;
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const newCookie = `${name}=${value}; ${propStr}`;
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const newCookie = `${name}=${value};${propStr}`;
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document.cookie = newCookie;
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}
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return getCookie(cookieConfig.auth.name);
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}
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/* Sets the given auth token into the browser's cookie.
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* Does nothing if the token is null.
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/**
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* Returns a Promise that ets the given auth token into the
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* browser's cookie, as configured. The cookie has the
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* same lifespan as the token.
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* If the token is null or expired, this does nothing.
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* If there's an error in looking up the token, this throws
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* an error.
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* @param {string} token
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* @returns
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function setAuthToken(token) {
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async function setAuthToken(token) {
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const tokenInfo = await getTokenInfo(token);
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// if it's expired, don't set (actually should've thrown
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// here, and get caught by the caller, but check anyway)
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if (tokenInfo.expires - Date.now() <= 0) {
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return;
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}
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if (config.enableIn && !config.enableIn.includes(deployEnv)) {
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return;
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const cookieField = {
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‎kbase-extension/static/kbase/js/narrativeLogin.js‎

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'util/bootstrapDialog',
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const baseUrl = JupyterUtils.get_body_data('baseUrl');
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const authClient = Auth.make({ url: Config.url('auth') });
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function showNotLoggedInDialog() {
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<p>You will be redirected to the sign in page after closing this, or ${
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} seconds,
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whichever comes first.</p>
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<p>You will be redirected to the sign in page after closing this, or
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${AUTO_LOGOUT_DELAY / 1000} seconds, whichever comes first.</p>
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clearTokenCheckTimers();
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return Promise.all([
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authClient.getUserProfile(sessionToken),
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return authClient
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.setAuthToken(sessionToken)
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.then(() =>
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Promise.all([
310+
authClient.getTokenInfo(sessionToken),
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authClient.getUserProfile(sessionToken),
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])
313+
)
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.then(([tokenInfo, accountInfo]) => {
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sessionInfo = tokenInfo;
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this.sessionInfo = tokenInfo;

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