Feature: Zarr Conversion by BrianWhitneyAI · Pull Request #858 · AllenInstitute/biofile-finder

BrianWhitneyAI · 2026-06-30T22:29:49Z

Summary

Adds in zarr-conversion to the pipelines option. In order to accomodate some of the new params, we have to update the pipeline-param display and typing logic.

Try it out on https://staging.bff.allencell.org/ select a CZI or ND2, -> process files -> conversion ->submit

🤖 Generated with Claude Code

Support string and select (dropdown) pipeline parameters in addition to numbers, and add the zarr-conversion pipeline mock data. Render the appropriate control per parameter type, validate string params against an optional regex pattern, and URL-encode file paths before submitting since FSS curls them directly. Restore environment-based load balancer URL selection (removing the temporary staging pin). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

BrianWhitneyAI · 2026-06-30T22:32:15Z

            validation: { min: 0 },
        },
    ],
+    "zarr-conversion": [


mock data to be dropped when discovery is live

Is there an anticipated date for that?

SeanDuHare · 2026-07-02T21:49:45Z

-                                                        selectedKey={
-                                                            optionalSelectorKey ?? undefined
-                                                        }
+                                                        // null (not undefined) so the dropdown


A bit verbose of a comment IMO - the type is defined elsewhere for this variable so perhaps it would belong there

SeanDuHare · 2026-07-02T21:51:04Z

+                    <BaseComboBox
+                        label=""
+                        selectedKey={
+                            value !== null && value !== undefined && value !== ""


FWIW I feel like using isNil and isEmpty from lodash are handy for making things like this more readable - just an opinion though

Suggested change

value !== null && value !== undefined && value !== ""

(!isNil(value) && !isEmpty(value)) ? String(value) : null

SeanDuHare · 2026-07-02T21:51:55Z

+                return (
+                    <TextField
+                        type="text"
+                        value={value !== null && value !== undefined ? String(value) : ""}


Same comment here for isNil usage but (again) just an opinion

SeanDuHare · 2026-07-02T21:53:12Z

+                        className={styles.textField}
+                    />
+                );
+            case "number":


Does this mean the default would also catch the file_paths type?

No file paths are already filtered out

Yes, I think an explicit catch of file_paths here would be good to avoid relying on an upstream type guard

SeanDuHare · 2026-07-02T21:54:27Z

-        const body: Record<string, unknown> = { files: file_paths };
+        const files = Array.isArray(file_paths)
+            ? file_paths.map((p) => PipelineService.encodeFilePath(p))
+            : file_paths;


Why do they not need to be encoded when not in an array?

@BrianWhitneyAI ?

SeanDuHare · 2026-07-02T21:54:58Z

+        const files = Array.isArray(file_paths)
+            ? file_paths.map((p) => PipelineService.encodeFilePath(p))
+            : file_paths;
+        const body: Record<string, unknown> = { files };


Can the type narrow down from unknown? I assume the values that get added below must be of some constrained typing like string | number | boolean etc

moved away from the unknown typing in 0d86855

SeanDuHare · 2026-07-02T21:57:36Z

            validation: { min: 0 },
        },
    ],
+    "zarr-conversion": [


Is there an anticipated date for that?

SeanDuHare · 2026-07-02T21:58:00Z

 interface Props {
    className?: string;
-    selectedKey?: string;
+    selectedKey?: string | null;


Should undefined be removed in favor of null?

null is the clear value so I think having both undefined and null here is ok/

we also still need undefined because it's currently an optional param, so if it were removed ExistingAnnotationPathway and MetadataDetails would need to be refactored slightly

BrianWhitneyAI · 2026-07-02T22:20:58Z

Is there an anticipated date for that?

3 of the 4 parts of it are out for review now

- Use lodash isNil/isEmpty in PipelineParameterInput (isEmpty only for select case, since it treats numbers as empty) - Narrow encodeFilePath to string -> string and only encode string entries - Trim verbose selectedKey comment in ComputePipelineModal Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

aswallace

+1 on Sean's comments, otherwise lgtm

aswallace · 2026-07-02T23:07:00Z

 interface Props {
    className?: string;
-    selectedKey?: string;
+    selectedKey?: string | null;


we also still need undefined because it's currently an optional param, so if it were removed ExistingAnnotationPathway and MetadataDetails would need to be refactored slightly

Form-state values only ever come from text/select inputs, so type them as string. validateParam/onBlur take string | undefined to still flag untouched required fields. Defaults are String()-ified on load. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

- Hoist filePaths to its own string[] field on ComputeTaskRequest, removing the Array.isArray/typeof guards in submitComputeTask - Type parameters as Record<string, string> (all form values are strings), collapsing the null/undefined guard in the submit loop - Drop redundant `default !== undefined` checks (default is never undefined) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

BrianWhitneyAI commented Jun 30, 2026

View reviewed changes

BrianWhitneyAI changed the title ~~Add string & select parameter types for compute pipelines~~ Feature: Zarr Conversion Jun 30, 2026

Merge branch 'main' into zarr-conversion-pipeline-params

f62a002

BrianWhitneyAI marked this pull request as ready for review July 2, 2026 17:13

BrianWhitneyAI requested review from SeanDuHare and aswallace as code owners July 2, 2026 17:13

BrianWhitneyAI temporarily deployed to staging July 2, 2026 17:15 — with GitHub Actions Inactive

SeanDuHare reviewed Jul 2, 2026

View reviewed changes

aswallace approved these changes Jul 2, 2026

View reviewed changes

BrianWhitneyAI and others added 2 commits July 2, 2026 16:18

SeanDuHare approved these changes Jul 7, 2026

View reviewed changes

BrianWhitneyAI and others added 3 commits July 7, 2026 11:09

add file_path guard

d81d10c

add restriction note

e2fb46a

Merge branch 'main' into zarr-conversion-pipeline-params

f74f29a

BrianWhitneyAI temporarily deployed to staging July 7, 2026 18:14 — with GitHub Actions Inactive

BrianWhitneyAI temporarily deployed to staging July 7, 2026 18:30 — with GitHub Actions Inactive

BrianWhitneyAI merged commit a873e96 into main Jul 7, 2026
11 checks passed

BrianWhitneyAI deleted the zarr-conversion-pipeline-params branch July 7, 2026 18:32

	value !== null && value !== undefined && value !== ""
	(!isNil(value) && !isEmpty(value)) ? String(value) : null

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BrianWhitneyAI commented Jul 2, 2026

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BrianWhitneyAI commented Jun 30, 2026 •

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