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Merge pull request #263 from smaht-dac/utk_react_18
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React bootstrap v2, React 18, Redux and Misc. Npm Packages Upgrade
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@Onurcankaratay
Onurcankaratay authored Oct 18, 2024
2 parents 0e56cdf + 1fa8951 commit c478613
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19 changes: 18 additions & 1 deletion CHANGELOG.rst
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Expand Up @@ -7,11 +7,28 @@ smaht-portal
Change Log
----------

`PR 266: Node v20 Upgrade <https://github.com/smaht-dac/smaht-portal/pull/266>`_

0.106.0
=======

`PR 263: React bootstrap v2, React 18, Redux and Misc. Npm Packages Upgrade <https://github.com/smaht-dac/smaht-portal/pull/263>`_

* Upgrade: React v17 to v18
* Upgrade: Redux v4 to v5 (there are breaking changes in store and dispatchers. SPC is updated to support both new and legacy usage)
* Upgrade: auth0-Lock v11 to v12
* Upgrade: gulp.js v4 to v5
* Upgrade: react-workflow-viz (animation updates to eliminate findDOMNode errors)
* Fix: User Content updates to fix markdown, jsx, and HTML static section rendering
* Upgrade: Bootstrap v5
* Upgrade: React-Bootstrap v2
* Upgrade: FontAwesome v6


0.105.0
=====

`PR 266: Node v20 Upgrade <https://github.com/smaht-dac/smaht-portal/pull/266>`_

* Node 18 to 20 upgrade including GitHub actions


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32 changes: 10 additions & 22 deletions deploy/post_deploy_testing/cypress/e2e/01_homepage.cy.js
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Expand Up @@ -22,29 +22,17 @@ describe('Home Page', function () {

it('Timeline dropdowns work as expected', () => {
/* ==== Generated with Cypress Studio ==== */
cy.get(
':nth-child(1) > .timeline-content > .accordion > :nth-child(1) > .card-header > .d-flex > .border-0 > div > .icon'
).click();
cy.get(
':nth-child(1) > .timeline-content > .accordion > :nth-child(1) > .card-header > .d-flex > .border-0 > div > .icon'
).click();
cy.get(
':nth-child(1) > .timeline-content > .accordion > :nth-child(1) > .collapse > .card-body'
).click();
cy.get(
':nth-child(3) > .card-header > .d-flex > .border-0 > div > .icon'
).click();
cy.get(
':nth-child(4) > .card-header > .d-flex > .border-0 > div > .icon'
).click();
cy.get(
':nth-child(2) > .timeline-content > .accordion > .card > .card-header > .d-flex > .border-0 > div > .icon'
).click();
cy.get(
':nth-child(3) > .timeline-content > .accordion > .card > .card-header > .d-flex > .border-0 > div > .icon'
).click();
cy.get('#timeline .timeline-item .accordion .card-header-button').first().click({ force: true });
cy.get('#timeline .timeline-item .accordion .card-header-button').first().click({ force: true });

cy.get('#timeline .timeline-item .accordion .accordion-collapse.show .card-body').should('be.visible');

cy.get('#timeline .timeline-item:nth-child(3) .card-header-button').click({ force: true });
cy.get('#timeline .timeline-item:nth-child(4) .card-header-button').click({ force: true });

cy.get('#timeline .timeline-item:nth-child(2) .accordion .card-header-button').first().click({ force: true });
cy.get('#timeline .timeline-item:nth-child(3) .card-header-button').click({ force: true });
/* ==== End Cypress Studio ==== */
cy.end();
});

it('Navbar dropdowns work as expected when logged in', () => {
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14 changes: 14 additions & 0 deletions deploy/post_deploy_testing/cypress/support/e2e.js
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Expand Up @@ -18,3 +18,17 @@ import './commands';

// Alternatively you can use CommonJS syntax:
// require('./commands')

Cypress.on("uncaught:exception", (err) => {
// TODO: Investigate hydration errors occurring during SSR in Cypress tests.
// It appears that Cypress injects a prop into the div on the client side, which doesn't exist on the server side, leading to hydration issues.
// This suppression is temporary and should be removed once the issue is resolved.
// https://github.com/cypress-io/cypress/issues/27204
if (
/hydrat/i.test(err.message) ||
/Minified React error #418/.test(err.message) ||
/Minified React error #423/.test(err.message)
) {
return false;
}
});
18 changes: 9 additions & 9 deletions docs/public/colo829_snv_indel_detection.jsx
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Expand Up @@ -17,21 +17,21 @@
<h3>Release History</h3>

<div class="table-responsive">
<table class="table table-borderless table-sm text-left">
<table class="table table-borderless table-sm text-start">
<thead class="thead-smaht-purple">
<tr>
<th className="pl-1">Release Version</th>
<th className="pl-1">Description</th>
<th className="pl-1">Release date</th>
<th className="pl-1">Document</th>
<th className="ps-1">Release Version</th>
<th className="ps-1">Description</th>
<th className="ps-1">Release date</th>
<th className="ps-1">Document</th>
</tr>
</thead>
<tbody class="table-border-inner">
<tr>
<td className="pl-1">V1.0 [Latest]</td>
<td className="pl-1">COLO829 SNV/indel detection challenge - SNV truth set and related datasets</td>
<td className="pl-1">August 29, 2024</td>
<td className="pl-1">
<td className="ps-1">V1.0 [Latest]</td>
<td className="ps-1">COLO829 SNV/indel detection challenge - SNV truth set and related datasets</td>
<td className="ps-1">August 29, 2024</td>
<td className="ps-1">
<a href="/static/files/SMaHT_Benchmark_SNVIndel_Challenge-DataRelease_V1_Aug12-2024.pdf" download>
<i className="icon fas icon-file-pdf text-danger icon-lg"></i>
</a>
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28 changes: 14 additions & 14 deletions docs/public/smaht_nomenclature.rst
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Expand Up @@ -72,7 +72,7 @@ Table 1A. Protocol IDs for SMaHT benchmarking tissues.
.. raw:: html

<div class="table-responsive">
<table class="table table-striped table-sm text-left">
<table class="table table-striped table-sm text-start">
<thead class="thead-smaht table-borderless">
<tr>
<th style="min-width:95px">Protocol ID</th>
Expand Down Expand Up @@ -142,7 +142,7 @@ Table 1B. Protocol IDs for SMaHT production tissues.
.. raw:: html

<div class="table-responsive">
<table class="table table-striped table-sm text-left">
<table class="table table-striped table-sm text-start">
<thead class="thead-smaht table-borderless">
<tr>
<th style="min-width:95px">Protocol ID</th>
Expand Down Expand Up @@ -358,45 +358,45 @@ Table 3A. Sequencing platform codes.
<thead class="thead-smaht table-borderless">
<tr>
<th class="text-center" width="25%">SMaHT code</th>
<th class="text-left">Sequencing platform</th>
<th class="text-start">Sequencing platform</th>
</tr>
</thead>
<tbody class="table-border-inner">
<tr>
<td class="text-center">A</td>
<td class="text-left">Illumina NovaSeq X</td>
<td class="text-start">Illumina NovaSeq X</td>
</tr>
<tr>
<td class="text-center">B</td>
<td class="text-left">PacBio Revio HiFi</td>
<td class="text-start">PacBio Revio HiFi</td>
</tr>
<tr>
<td class="text-center">C</td>
<td class="text-left">Illumina NovaSeq 6000</td>
<td class="text-start">Illumina NovaSeq 6000</td>
</tr>
<tr>
<td class="text-center">D</td>
<td class="text-left">ONT PromethION 24</td>
<td class="text-start">ONT PromethION 24</td>
</tr>
<tr>
<td class="text-center">E</td>
<td class="text-left">ONT PromethION 2 Solo</td>
<td class="text-start">ONT PromethION 2 Solo</td>
</tr>
<tr>
<td class="text-center">F</td>
<td class="text-left">ONT MinION Mk1B</td>
<td class="text-start">ONT MinION Mk1B</td>
</tr>
<tr>
<td class="text-center">G</td>
<td class="text-left">Illumina HiSeq X</td>
<td class="text-start">Illumina HiSeq X</td>
</tr>
<tr>
<td class="text-center">H</td>
<td class="text-left">Illumina NovaSeq X Plus</td>
<td class="text-start">Illumina NovaSeq X Plus</td>
</tr>
<tr>
<td class="cell-small-text text-left">(set the codes as data are generated on different sequencing platforms and submitted to DAC)</td>
<td class="text-left">ONT MinION, Ultima Genomics, PacBio Onso, Element Aviti, PacBio Sequel</td>
<td class="cell-small-text text-start">(set the codes as data are generated on different sequencing platforms and submitted to DAC)</td>
<td class="text-start">ONT MinION, Ultima Genomics, PacBio Onso, Element Aviti, PacBio Sequel</td>
</tr>
</tbody>
</table>
Expand All @@ -410,7 +410,7 @@ Table 3B. Experimental Assay Codes.
.. raw:: html

<div class="table-responsive">
<table class="table table-sm text-left">
<table class="table table-sm text-start">
<thead class="thead-smaht table-borderless">
<tr>
<th>Code</th>
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16 changes: 8 additions & 8 deletions docs/source/genome_reference_and_related_data.rst
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Expand Up @@ -14,13 +14,13 @@ Genome Alignment & Variant Calling

<hr />
<div class="table-responsive">
<table class="table table-borderless table-sm text-left" style="min-width: 1200px;">
<table class="table table-borderless table-sm text-start" style="min-width: 1200px;">
<thead class="thead-smaht">
<tr class="sticky-first-column">
<th class="px-2"><i class="icon fas icon-download"></i></th>
<th class="px-2">File</th>
<th class="px-2">Description</th>
<th class="px-2 text-right">Date Created</th>
<th class="px-2 text-end">Date Created</th>
<th class="px-2 text-center" style="width: 80px;">Size</th>
</tr>
</thead>
Expand All @@ -45,8 +45,8 @@ Genome Alignment & Variant Calling
(View Source)
</a>
</td>
<td class="px-2 text-right">12-13-2023</td>
<td class="px-2 text-right">2.89 GB</td>
<td class="px-2 text-end">12-13-2023</td>
<td class="px-2 text-end">2.89 GB</td>
</tr>
<tr class="sticky-first-column">
<td class="px-2">
Expand All @@ -68,8 +68,8 @@ Genome Alignment & Variant Calling
(View Source)
</a>
</td>
<td class="px-2 text-right">12-13-2023</td>
<td class="px-2 text-right">2.93 GB</td>
<td class="px-2 text-end">12-13-2023</td>
<td class="px-2 text-end">2.93 GB</td>
</tr>
<tr class="sticky-first-column">
<td class="px-2">
Expand All @@ -91,8 +91,8 @@ Genome Alignment & Variant Calling
(View Source)
</a>
</td>
<td class="px-2 text-right">12-13-2023</td>
<td class="px-2 text-right">2.89 GB</td>
<td class="px-2 text-end">12-13-2023</td>
<td class="px-2 text-end">2.89 GB</td>
</tr>
</tbody>
</table>
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