Init cassia

[alexvpickering]

Description

adds CASSIA cell type annotation

Details

N/A

Link to staging deployment URL (or set N/A)

N/A

Links to any PRs or resources related to this PR

Integration test branch

master

Merge checklist

Your changes will be ready for merging after all of the steps below have been completed.

Code updates

Have best practices and ongoing refactors being observed in this PR

• Migrated any selector / reducer used to the new format.
• All new dependency licenses have been checked for compatibility.

Manual/unit testing

• Tested changes using InfraMock locally or no tests required for change, e.g. Kubernetes chart updates.
• Validated that current unit tests for code work as expected and are sufficient for code coverage or no unit tests required for change, e.g. documentation update.
• Unit tests written or no unit tests required for change, e.g. documentation update.

Integration testing

You must check the box below to run integration tests on the latest commit on your PR branch.
Integration tests have to pass before the PR can be merged. Without checking the box, your PR
will not pass the required status checks for merging.

• Started end-to-end tests on the latest commit.

Documentation updates

• Relevant Github READMEs updated or no GitHub README updates required.
• Relevant Wiki pages created/updated or no Wiki updates required.

Optional

• Staging environment is unstaged before merging.
• Photo of a cute animal attached to this PR.

[github-actions]

📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page	Size (compressed)
global	686.82 KB (🟡 +303 B)

Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Sixteen Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page	Size (compressed)	First Load
/data-management	202.54 KB (🟡 +67 B)	889.36 KB
/experiments/[experimentId]/data-exploration	1.51 MB (🟡 +1.45 KB)	2.18 MB
/experiments/[experimentId]/data-processing	515.44 KB (🟡 +65 B)	1.17 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression	64.52 KB (🟡 +59 B)	751.34 KB
/experiments/[experimentId]/plots-and-tables/dot-plot	448.23 KB (🟡 +46 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/embedding-categorical	446.84 KB (🟡 +66 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/embedding-continuous	469.71 KB (🟡 +64 B)	1.13 MB
/experiments/[experimentId]/plots-and-tables/frequency	448.33 KB (🟡 +67 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap	537.51 KB (🟡 +61 B)	1.2 MB
/experiments/[experimentId]/plots-and-tables/normalized-matrix	140.83 KB (🟡 +66 B)	827.65 KB
/experiments/[experimentId]/plots-and-tables/spatial-categorical	485.78 KB (🟡 +68 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/spatial-feature	491.66 KB (🟡 +63 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/spatial-molecules	644.04 KB (🟡 +66 B)	1.3 MB
/experiments/[experimentId]/plots-and-tables/trajectory-analysis	450.12 KB (🟡 +67 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/violin	470.89 KB (🟡 +54 B)	1.13 MB
/experiments/[experimentId]/plots-and-tables/volcano	452.68 KB (🟡 +58 B)	1.11 MB

Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

[dbmi-svc-checkmarx]

Checkmarx One – Scan Summary & Details – 93483a8b-0f3b-4a4e-ab1a-f0e13f701c77

---

New Issues (10)

Checkmarx found the following issues in this Pull Request

#	Severity	Issue	Source File / Package	Checkmarx Insight
1		CVE-2026-14257	Npm-brace-expansion-1.1.11	details Description: brace-expansion through 5.0.7 is vulnerable to denial of service via memory exhaustion. The expand() function limits the number of results with a m... Attack Vector: NETWORK Attack Complexity: LOW Vulnerable Package
2		CVE-2026-64641	Npm-next-15.5.18	details Recommended version: 15.5.21 Description: Crafted requests targeting Next.js applications using App Router with at least one Server Action can lead to excessive CPU usage blocking processin... Attack Vector: NETWORK Attack Complexity: LOW Vulnerable Package
3		CVE-2026-64645	Npm-next-15.5.18	details Recommended version: 15.5.21 Description: A `rewrites()` or `redirects()` rule that builds its external destination hostname from request-controlled input can be pointed at an arbitrary hos... Attack Vector: NETWORK Attack Complexity: LOW Vulnerable Package
4		CVE-2026-64649	Npm-next-15.5.18	details Recommended version: 15.5.21 Description: When a Server Action forwards or redirects a request, an attacker can cause the server to send that outbound request to a malicious host (Server-Si... Attack Vector: NETWORK Attack Complexity: LOW Vulnerable Package
5		Cx5d6ad42a-3b42	Npm-sharp-0.34.5	details Recommended version: 0.35.0 Description: A number of vulnerabilities, two rated as "High" severity using CVSSv4, have been discovered and fixed in the upstream libvips dependency. All vers... Attack Vector: LOCAL Attack Complexity: LOW Vulnerable Package
6		Unpinned Actions Full Length Commit SHA	/ci.yaml: 306	details Pinning an action to a full length commit SHA is currently the only way to use an action as an immutable release. Pinning to a particular SHA help...
7		Unpinned Actions Full Length Commit SHA	/ci.yaml: 447	details Pinning an action to a full length commit SHA is currently the only way to use an action as an immutable release. Pinning to a particular SHA help...
8		Unpinned Actions Full Length Commit SHA	/ci.yaml: 428	details Pinning an action to a full length commit SHA is currently the only way to use an action as an immutable release. Pinning to a particular SHA help...
9		Unpinned Actions Full Length Commit SHA	/ci.yaml: 313	details Pinning an action to a full length commit SHA is currently the only way to use an action as an immutable release. Pinning to a particular SHA help...
10		Unpinned Actions Full Length Commit SHA	/ci.yaml: 477	details Pinning an action to a full length commit SHA is currently the only way to use an action as an immutable release. Pinning to a particular SHA help...

---

Fixed Issues (5)

Great job! The following issues were fixed in this Pull Request

Severity	Issue	Source File / Package
	Unpinned Actions Full Length Commit SHA	/ci.yaml: 445
	Unpinned Actions Full Length Commit SHA	/ci.yaml: 304
	Unpinned Actions Full Length Commit SHA	/ci.yaml: 426
	Unpinned Actions Full Length Commit SHA	/ci.yaml: 311
	Unpinned Actions Full Length Commit SHA	/ci.yaml: 475

---

Use @Checkmarx to interact with Checkmarx PR Assistant.
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[github-actions]

📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page	Size (compressed)
global	686.82 KB (🟡 +303 B)

Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Sixteen Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page	Size (compressed)	First Load
/data-management	202.54 KB (🟡 +67 B)	889.36 KB
/experiments/[experimentId]/data-exploration	1.51 MB (🟡 +1.45 KB)	2.18 MB
/experiments/[experimentId]/data-processing	515.44 KB (🟡 +65 B)	1.17 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression	64.52 KB (🟡 +59 B)	751.34 KB
/experiments/[experimentId]/plots-and-tables/dot-plot	448.23 KB (🟡 +46 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/embedding-categorical	446.84 KB (🟡 +66 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/embedding-continuous	469.71 KB (🟡 +64 B)	1.13 MB
/experiments/[experimentId]/plots-and-tables/frequency	448.33 KB (🟡 +67 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap	537.51 KB (🟡 +61 B)	1.2 MB
/experiments/[experimentId]/plots-and-tables/normalized-matrix	140.83 KB (🟡 +66 B)	827.65 KB
/experiments/[experimentId]/plots-and-tables/spatial-categorical	485.78 KB (🟡 +68 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/spatial-feature	491.66 KB (🟡 +63 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/spatial-molecules	644.04 KB (🟡 +66 B)	1.3 MB
/experiments/[experimentId]/plots-and-tables/trajectory-analysis	450.12 KB (🟡 +67 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/violin	470.89 KB (🟡 +54 B)	1.13 MB
/experiments/[experimentId]/plots-and-tables/volcano	452.68 KB (🟡 +58 B)	1.11 MB

Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

[github-actions]

📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page	Size (compressed)
global	686.82 KB (🟡 +303 B)

Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Sixteen Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page	Size (compressed)	First Load
/data-management	202.54 KB (🟡 +67 B)	889.36 KB
/experiments/[experimentId]/data-exploration	1.51 MB (🟡 +1.45 KB)	2.18 MB
/experiments/[experimentId]/data-processing	515.44 KB (🟡 +65 B)	1.17 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression	64.52 KB (🟡 +59 B)	751.34 KB
/experiments/[experimentId]/plots-and-tables/dot-plot	448.23 KB (🟡 +46 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/embedding-categorical	446.84 KB (🟡 +66 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/embedding-continuous	469.71 KB (🟡 +64 B)	1.13 MB
/experiments/[experimentId]/plots-and-tables/frequency	448.33 KB (🟡 +67 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap	537.51 KB (🟡 +61 B)	1.2 MB
/experiments/[experimentId]/plots-and-tables/normalized-matrix	140.83 KB (🟡 +66 B)	827.65 KB
/experiments/[experimentId]/plots-and-tables/spatial-categorical	485.78 KB (🟡 +68 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/spatial-feature	491.66 KB (🟡 +63 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/spatial-molecules	644.04 KB (🟡 +66 B)	1.3 MB
/experiments/[experimentId]/plots-and-tables/trajectory-analysis	450.12 KB (🟡 +67 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/violin	470.89 KB (🟡 +54 B)	1.13 MB
/experiments/[experimentId]/plots-and-tables/volcano	452.68 KB (🟡 +58 B)	1.11 MB

Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

[codecov]

Codecov Report

❌ Patch coverage is 83.83838% with 16 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.11%. Comparing base (41e674c) to head (eadde08).
⚠️ Report is 3 commits behind head on master.

Files with missing lines	Patch %	Lines
...ponents/data-exploration/spatial/SpatialViewer.jsx	50.00%	4 Missing ⚠️
src/components/Loader.jsx	40.00%	2 Missing and 1 partial ⚠️
src/redux/actions/cellSets/runCassiaAnnotation.js	76.92%	3 Missing ⚠️
...xploration/cell-sets-tool/AnnotateClustersTool.jsx	97.61%	1 Missing ⚠️
src/redux/actions/cellSets/deleteCellClass.js	50.00%	1 Missing ⚠️
src/redux/actions/cellSets/deleteCellSet.js	50.00%	1 Missing ⚠️
...rc/redux/actions/cellSets/updateCellSetProperty.js	50.00%	1 Missing ⚠️
src/redux/store.js	90.90%	1 Missing ⚠️
src/utils/work/waitForWorkRequest.js	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1068      +/-   ##
==========================================
+ Coverage   77.02%   77.11%   +0.09%     
==========================================
  Files         608      610       +2     
  Lines       14763    14876     +113     
  Branches     3710     3753      +43     
==========================================
+ Hits        11371    11472     +101     
- Misses       3173     3184      +11     
- Partials      219      220       +1     

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📢 Have feedback on the report? Share it here.

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[github-actions]

📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page	Size (compressed)
global	686.82 KB (🟡 +303 B)

Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Sixteen Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page	Size (compressed)	First Load
/data-management	202.54 KB (🟡 +67 B)	889.36 KB
/experiments/[experimentId]/data-exploration	1.51 MB (🟡 +1.45 KB)	2.18 MB
/experiments/[experimentId]/data-processing	515.44 KB (🟡 +65 B)	1.17 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression	64.52 KB (🟡 +59 B)	751.34 KB
/experiments/[experimentId]/plots-and-tables/dot-plot	448.23 KB (🟡 +46 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/embedding-categorical	446.84 KB (🟡 +66 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/embedding-continuous	469.71 KB (🟡 +64 B)	1.13 MB
/experiments/[experimentId]/plots-and-tables/frequency	448.33 KB (🟡 +67 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap	537.51 KB (🟡 +61 B)	1.2 MB
/experiments/[experimentId]/plots-and-tables/normalized-matrix	140.83 KB (🟡 +66 B)	827.65 KB
/experiments/[experimentId]/plots-and-tables/spatial-categorical	485.78 KB (🟡 +68 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/spatial-feature	491.66 KB (🟡 +63 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/spatial-molecules	644.04 KB (🟡 +66 B)	1.3 MB
/experiments/[experimentId]/plots-and-tables/trajectory-analysis	450.12 KB (🟡 +67 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/violin	470.89 KB (🟡 +54 B)	1.13 MB
/experiments/[experimentId]/plots-and-tables/volcano	452.68 KB (🟡 +58 B)	1.11 MB

Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.

[github-actions]

📦 Next.js Bundle Analysis for ui

This analysis was generated by the Next.js Bundle Analysis action. 🤖

⚠️ Global Bundle Size Increased

Page	Size (compressed)
global	686.82 KB (🟡 +303 B)

Details

The global bundle is the javascript bundle that loads alongside every page. It is in its own category because its impact is much higher - an increase to its size means that every page on your website loads slower, and a decrease means every page loads faster.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

If you want further insight into what is behind the changes, give @next/bundle-analyzer a try!

Sixteen Pages Changed Size

The following pages changed size from the code in this PR compared to its base branch:

Page	Size (compressed)	First Load
/data-management	202.54 KB (🟡 +67 B)	889.36 KB
/experiments/[experimentId]/data-exploration	1.51 MB (🟡 +1.45 KB)	2.18 MB
/experiments/[experimentId]/data-processing	515.44 KB (🟡 +65 B)	1.17 MB
/experiments/[experimentId]/plots-and-tables/batch-differential-expression	64.52 KB (🟡 +59 B)	751.34 KB
/experiments/[experimentId]/plots-and-tables/dot-plot	448.23 KB (🟡 +46 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/embedding-categorical	446.84 KB (🟡 +66 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/embedding-continuous	469.71 KB (🟡 +64 B)	1.13 MB
/experiments/[experimentId]/plots-and-tables/frequency	448.33 KB (🟡 +67 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/marker-heatmap	537.51 KB (🟡 +61 B)	1.2 MB
/experiments/[experimentId]/plots-and-tables/normalized-matrix	140.83 KB (🟡 +66 B)	827.65 KB
/experiments/[experimentId]/plots-and-tables/spatial-categorical	485.78 KB (🟡 +68 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/spatial-feature	491.66 KB (🟡 +63 B)	1.15 MB
/experiments/[experimentId]/plots-and-tables/spatial-molecules	644.04 KB (🟡 +66 B)	1.3 MB
/experiments/[experimentId]/plots-and-tables/trajectory-analysis	450.12 KB (🟡 +67 B)	1.11 MB
/experiments/[experimentId]/plots-and-tables/violin	470.89 KB (🟡 +54 B)	1.13 MB
/experiments/[experimentId]/plots-and-tables/volcano	452.68 KB (🟡 +58 B)	1.11 MB

Details

Only the gzipped size is provided here based on an expert tip.

First Load is the size of the global bundle plus the bundle for the individual page. If a user were to show up to your website and land on a given page, the first load size represents the amount of javascript that user would need to download. If next/link is used, subsequent page loads would only need to download that page's bundle (the number in the "Size" column), since the global bundle has already been downloaded.

Any third party scripts you have added directly to your app using the <script> tag are not accounted for in this analysis

Next to the size is how much the size has increased or decreased compared with the base branch of this PR. If this percentage has increased by 20% or more, there will be a red status indicator applied, indicating that special attention should be given to this.