migrate resource (resource migration 3/3) by interim17 · Pull Request #72 · AllenCell/idea-board

interim17 · 2026-03-11T06:42:52Z

Problem

Closes #40

We love a negative code line PR.

Final PR in this series.

Solution

Mostly we are removing the old code and markdown from how we used to handle resources.

Change summary:

removal of markdown and data for software, datasets, etc in the old system
removal of schema typing, resolvers, etc for `MaterialsAndMethods
updated Materials and Methods component that consumes the new data
updated draft resource index page (proof of concept)

…ions

…/idea-board into migrate-resources

interim17 · 2026-03-11T06:45:18Z

src/components/IdeaRoll.tsx

        concerns: post.frontmatter.concerns || "",
        dataset: {
-            ...post.frontmatter.materialsAndMethods?.dataset?.frontmatter,
+            ...post.frontmatter.resources.find((r) => r.type === "dataset"),


This file has an outdated approach to typing and querying, but it's not essential to do more than patch in this PR.

interim17 · 2026-03-11T06:45:49Z

src/components/IdeaRoll.tsx

+                                    resources {
+                                        ...ResourceFields


Using fragments defined in src/graphql/fragments

interim17 · 2026-03-11T14:59:12Z

src/constants/resourceTypes.ts

+export const RESOURCE_TYPES = {
+    SOFTWARE_TOOL: "softwareTool",
+    DATASET: "dataset",
+    PROTOCOL_LINK: "protocolLink",
+    PROTOCOL_FILE: "protocolFile",
+    CELL_LINE: "cellLine",
+} as const;
+
+export type ResourceType = (typeof RESOURCE_TYPES)[keyof typeof RESOURCE_TYPES];


There are places in both gatsby and decap where the frameworks limit our ability to use constants (in query filters for example) but trying to use them everywhere else that we can to keep things aligned.

interim17 · 2026-03-11T15:00:57Z

src/pages/resource/index.tsx

+                {!!softwareResources?.nodes.length && (
+                    <>
+                        <h2>Software</h2>
+                        <ul>
+                            {softwareResources.nodes.map((node) => (
+                                <li key={node.slug}>
+                                    <Link to={node.slug}>{node.name}</Link>
+                                    {node.description && (
+                                        <p>{node.description}</p>
+                                    )}
+                                </li>
+                            ))}
+                        </ul>
+                    </>
+                )}


Bucketed resources using filtered queries + fragmentes below with a basic render here. A demonstration/proof of concept, not styled.

…/idea-board into migrate-resources

Copilot

Pull request overview

Migrates “Materials and Methods” content from legacy dataset/software collections into the unified resources collection, updating CMS config, Gatsby schema/resolvers, GraphQL fragments, and UI consumers.

Changes:

Remove legacy materialsAndMethods, dataset, and software content/types/templates; add new resource markdown entries.
Update Gatsby schema/custom resolvers and GraphQL fragments/constants to query typed resources.
Refactor idea templates/components (IdeaPost, IdeaRoll, MaterialsAndMethods) to consume resources.

Reviewed changes

Copilot reviewed 37 out of 37 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
static/admin/config.yml	Removes legacy Materials & Methods / dataset / software CMS fields and collections; keeps `resources` relation fields.
src/utils/formattingUtils.tsx	Adds `NameWithLink` helper for consistent name/link rendering.
src/types/index.ts	Removes legacy MaterialsAndMethods-derived types; adjusts `Figure` type derivation.
src/templates/idea-post.tsx	Stops querying legacy `materialsAndMethods`; passes `resources` into MaterialsAndMethods UI.
src/templates/dataset.tsx	Removes legacy dataset template page.
src/pages/software/timelapse-feature-explorer.md	Removes legacy software markdown entry.
src/pages/software/simularium.md	Removes legacy software markdown entry.
src/pages/resource/timelapse-feature-explorer.md	Adds resource entry (software tool) in new location/format.
src/pages/resource/simularium.md	Adds resource entry (software tool) in new location/format.
src/pages/resource/released-nucmorph-data-included-pre-calculated-pcs.md	Adds resource entry (dataset) in new location/format.
src/pages/resource/released-emt-dataset.md	Adds resource entry (dataset) in new location/format.
src/pages/resource/index.tsx	Refactors resources index into type-grouped sections with filtered queries.
src/pages/resource/emc.md	Adds resource entry (dataset) in new location/format.
src/pages/resource/aics-67.md	Adds resource entry (cell line) in new location/format.
src/pages/resource/aics-42.md	Adds resource entry (cell line) in new location/format.
src/pages/resource/actin-compression-simulation-dataset.md	Adds resource entry (dataset) with detailed description content.
src/pages/resource/60x-timelapse-images-of-tagged-lines-after-emt-sandwich-dataset.md	Adds resource entry (dataset) in new location/format.
src/pages/ideas/dev-example.md	Updates idea frontmatter to reference `resources` instead of legacy Materials & Methods block.
src/pages/ideas/2026-02-06-compare-actin-filament-compression-between-different-fiber-scale-simulators.md	Updates idea frontmatter to reference `resources`.
src/pages/ideas/2025-10-29-relate-cell-cell-junction-remodeling-to-migration-onset.md	Updates idea frontmatter to reference `resources`.
src/pages/ideas/2025-10-24-how-do-the-number-and-size-of-holes-in-the-basement-membrane-change-with-time-during-emt-induction.md	Updates idea frontmatter to reference `resources`.
src/pages/dataset/released-nucmorph-data-included-pre-calculated-pcs.md	Removes legacy dataset markdown entry.
src/pages/dataset/released-emt-dataset.md	Removes legacy dataset markdown entry.
src/pages/dataset/emc.md	Removes legacy dataset markdown entry.
src/pages/dataset/actin-compression-simulation-dataset.md	Removes legacy dataset markdown entry (migrated into resources).
src/graphql/fragments.ts	Splits resource fragments by resource type and composes a `ResourceFields` fragment.
src/constants/resourceTypes.ts	Adds centralized `RESOURCE_TYPES` constants + `ResourceType` union type.
src/components/ResourcesComponent.tsx	Removes placeholder component now that MaterialsAndMethods consumes resources.
src/components/MaterialsAndMethods.tsx	Refactors to derive datasets/software/protocols/cell lines from `resources` list.
src/components/IdeaRoll.tsx	Updates list item dataset display to read from `resources` instead of legacy Materials & Methods.
src/cms/widgets/VariableResourceWidget/constants.ts	Switches resource type values to use centralized `RESOURCE_TYPES`.
gatsby/utils/test/gatsby-resolver-utils.test.js	Updates tests to use `RESOURCES_TEMPLATE_KEY` constant.
gatsby/utils/gatsby-resolver-utils.js	Removes legacy software-tool resolver; keeps slug + resource query helpers.
gatsby/schema/base.gql	Removes `materialsAndMethods` from schema; adds `file` to `Resource`.
gatsby/constants.js	Removes dataset/software path constants; adds template-key constants for data-only pages.
gatsby-node.js	Removes legacy Materials & Methods schema/resolvers; ensures `resources` resolver links to Resource nodes.

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Copilot · 2026-03-11T15:29:30Z

src/pages/resource/index.tsx

+    if (!site) {
+        return (
+            <Layout>
+                <p>Data not found.</p>
+            </Layout>
+        );


Layout is referenced in the !site guard but isn’t imported in this module, which will cause a compile/runtime error. Import Layout (likely from ../../components/Layout) or remove the wrapper and render the fallback without it (and ideally keep the wrapper consistent with the normal render path).

Copilot · 2026-03-11T15:29:31Z

src/components/MaterialsAndMethods.tsx

                <ul>
                    {protocols.map((item, index) => (
                        <li key={index}>
-                            <a
-                                href={item.protocol}
-                                target="_blank"
-                                rel="noreferrer"
-                            >
-                                {item.protocol.split("/").pop()}
-                            </a>
+                            <NameWithLink name={item.name} link={item.link} />
                        </li>


Protocol resources of type protocolFile store the file path in the file field (see schema and CMS widget), but this renderer only links using item.link. As a result, protocol-file resources will render as plain text with no usable link. Consider using item.link ?? item.file (and optionally display the filename) when rendering protocol items.

This is being left as TODO

src/utils/formattingUtils.tsx

+            <a href={link} target="_blank" rel="noreferrer">
+                {name}


…ea-board into migrate-resources

Copilot

Pull request overview

Copilot reviewed 24 out of 24 changed files in this pull request and generated 6 comments.

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Copilot · 2026-03-11T18:56:06Z

src/templates/idea-post.tsx

                    </div>
                )}
-                {!!resources?.length && (
-                    <ResourcesComponent resources={[...resources]} />
-                )}
-                <MaterialsAndMethodsComponent {...materialsAndMethods} />
+                <MaterialsAndMethodsComponent resources={[...resources]} />
                {tags && tags.length ? <div>{getTagList(tags)}</div> : null}


IdeaPostTemplate spreads resources ([...resources]) before passing to MaterialsAndMethodsComponent. This will throw at runtime if resources is ever undefined (e.g., the Decap CMS preview (IdeaPostPreview) calls IdeaPostTemplate without providing resources). Consider defaulting resources to an empty array in the template/component props, or passing resources ?? [] without spreading.

Copilot · 2026-03-11T18:56:06Z

src/components/MaterialsAndMethods.tsx

+                    {datasets.map((dataset, index) => (
+                        <div key={index}>


Using the array index as the React key (key={index}) can cause incorrect UI updates when the list order changes. Since resources have stable identifiers (e.g., slug), prefer a stable unique key like dataset.slug.

Suggested change

{datasets.map((dataset, index) => (

<div key={index}>

{datasets.map((dataset) => (

<div key={dataset.slug}>

Copilot · 2026-03-11T18:56:07Z

src/components/MaterialsAndMethods.tsx

                    {protocols.map((item, index) => (
                        <li key={index}>
-                            <a
-                                href={item.protocol}
-                                target="_blank"
-                                rel="noreferrer"
-                            >
-                                {item.protocol.split("/").pop()}
-                            </a>
+                            <NameWithLink name={item.name} link={item.link} />
                        </li>


Using the array index as the React key (key={index}) can cause incorrect UI updates when the list order changes. Since resources have stable identifiers (e.g., slug), prefer a stable unique key like item.slug.

Copilot · 2026-03-11T18:56:07Z

src/components/MaterialsAndMethods.tsx

                    {cellLines.map((item, index) => (
-                        <li key={index}>{getCellLineRender(item)}</li>
+                        <li key={index}>
+                            <NameWithLink name={item.name} link={item.link} />
+                        </li>
                    ))}


Using the array index as the React key (key={index}) can cause incorrect UI updates when the list order changes. Since resources have stable identifiers (e.g., slug), prefer a stable unique key like item.slug.

Copilot · 2026-03-11T18:56:07Z

src/components/MaterialsAndMethods.tsx

+                    {softwareTools.map((tool, index) => (
+                        <div key={index}>
+                            <p>
+                                <strong>Name: </strong>


Using the array index as the React key (key={index}) can cause incorrect UI updates when the list order changes. Since resources have stable identifiers (e.g., slug), prefer a stable unique key like tool.slug.

Copilot · 2026-03-11T18:56:07Z

src/components/IdeaRoll.tsx

        dataset: {
-            ...post.frontmatter.materialsAndMethods?.dataset?.frontmatter,
+            ...post.frontmatter.resources.find((r) => r.type === "dataset"),
        },


resources.find((r) => r.type === "dataset") hard-codes the resource type string. Since the codebase already defines RESOURCE_TYPES.DATASET, using the constant here will prevent drift if the underlying type values ever change.

rugeli

LGTM!

rugeli · 2026-03-16T19:59:02Z

static/admin/config.yml

Love the cleanup here! moving them to their designate collection simplifies things a lot

…ea-board into migrate-resources

interim17 added 5 commits March 10, 2026 18:40

use resources collection data in MaterialsAndMethods component

2e00e4c

remove materials and methods from markdown, schema and gatsby node api

10bdf7a

remove data and utilities associated with old multi resourece collect…

a23a49f

…ions

patch idea roll component to use resources

2c3bf14

Merge branch 'feature/resource-query' of https://github.com/AllenCell…

1ff999e

…/idea-board into migrate-resources

interim17 commented Mar 11, 2026

View reviewed changes

interim17 changed the title ~~Migrate resources~~ migrate resource (resource migration 2/3) Mar 11, 2026

interim17 commented Mar 11, 2026

View reviewed changes

Merge branch 'feature/resource-query' of https://github.com/AllenCell…

3febfd8

…/idea-board into migrate-resources

interim17 mentioned this pull request Mar 11, 2026

resource query (resource migration 1/3) #71

Merged

interim17 requested a review from Copilot March 11, 2026 15:23

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interim17 changed the title ~~migrate resource (resource migration 2/3)~~ migrate resource (resource migration 2/2) Mar 11, 2026

add noopener to NameWithLink util

5965024

interim17 marked this pull request as ready for review March 11, 2026 18:14

interim17 requested review from jessicasyu, meganrm and rugeli March 11, 2026 18:19

interim17 marked this pull request as draft March 11, 2026 18:37

interim17 mentioned this pull request Mar 11, 2026

make new resource markdown (resource migration 2/3) #73

Open

interim17 changed the base branch from feature/resource-query to migrate-resources-1 March 11, 2026 18:44

interim17 changed the title ~~migrate resource (resource migration 2/2)~~ migrate resource (resource migration 3/3) Mar 11, 2026

interim17 added 2 commits March 11, 2026 11:46

Merge branch 'migrate-resources-1' of https://github.com/AllenCell/id…

432db80

…ea-board into migrate-resources

don't use constant in resolver tests

7b2f553

interim17 requested a review from Copilot March 11, 2026 18:50

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interim17 marked this pull request as ready for review March 11, 2026 18:51

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rugeli approved these changes Mar 16, 2026

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static/admin/config.yml

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Love the cleanup here! moving them to their designate collection simplifies things a lot

Merge branch 'migrate-resources-1' of https://github.com/AllenCell/id…

5dfb1cd

…ea-board into migrate-resources

meganrm approved these changes Mar 19, 2026

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interim17 commented Mar 11, 2026 •

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