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use local file or url for protocols #39

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3007636
use local file or url for protocols
interim17 Feb 6, 2026
950eb8b
remove console log
interim17 Feb 6, 2026
2d362b2
Update gatsby-node.js
interim17 Feb 6, 2026
46b40d3
add missing noopener attributes
interim17 Feb 6, 2026
41f6a46
Merge branch 'feature/protocols' of https://github.com/AllenCell/idea…
interim17 Feb 6, 2026
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14 changes: 11 additions & 3 deletions gatsby-node.js
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Expand Up @@ -48,13 +48,21 @@ exports.createSchemaCustomization = ({ actions, schema }) => {
"""
type MaterialsAndMethods {
dataset: MarkdownRemark @link(by: "frontmatter.name")
protocols: [ProtocolItem!]!
protocols: [Protocol!]!
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Copilot AI Feb 6, 2026

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In the CMS config, protocols is marked required: false, but the schema declares protocols: [Protocol!]! (non-null). If a markdown entry omits materialsAndMethods.protocols, Gatsby schema/query resolution can fail at build time. Consider making this field nullable (e.g., [Protocol!]) or making the CMS field required so the data always exists.

Suggested change
protocols: [Protocol!]!
protocols: [Protocol!]

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@interim17 interim17 Feb 6, 2026

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We have a resolver to handle this case and provide an empty array in that case.

cellLines: [CellLineItem!]!
software: [SoftwareTool!]!
}

type ProtocolItem {
protocol: String!
"""
The front end and CMS assume that you enter EITHER a url OR a file which
this type doesn't strictly enforce. Directly entering data into markdown
with both fields populated may lead to unexpected behavior.
"""
type Protocol @dontInfer {
type: String!
name: String!
url: String
file: File @fileByRelativePath
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@interim17 interim17 Feb 6, 2026

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This and the query are where I think we could get a little more into the weeds with graphql especially if we had more complex varied types, but this is fine for now IMHO.

}

type CellLineItem {
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34 changes: 20 additions & 14 deletions src/components/MaterialsAndMethods.tsx
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Expand Up @@ -20,7 +20,7 @@ export const MaterialsAndMethodsComponent: React.FC<MaterialsAndMethods> = ({
return cellLine.name;
}
return (
<a href={cellLine.link} target="_blank" rel="noreferrer">
<a href={cellLine.link} target="_blank" rel="noreferrer noopener">
{cellLine.name}
</a>
);
Expand All @@ -34,7 +34,7 @@ export const MaterialsAndMethodsComponent: React.FC<MaterialsAndMethods> = ({
const title = link ? (
<p>
<strong>{`Name: `}</strong>
<a href={link} target="_blank" rel="noreferrer">
<a href={link} target="_blank" rel="noreferrer noopener">
{name}
</a>
</p>
Expand Down Expand Up @@ -72,7 +72,7 @@ export const MaterialsAndMethodsComponent: React.FC<MaterialsAndMethods> = ({
<a
href={datasetFm.link}
target="_blank"
rel="noreferrer"
rel="noreferrer noopener"
>
{datasetFm.name}
</a>
Expand All @@ -98,17 +98,23 @@ export const MaterialsAndMethodsComponent: React.FC<MaterialsAndMethods> = ({
label: "Protocols",
children: (
<ul>
{protocols.map((item, index) => (
<li key={index}>
<a
href={item.protocol}
target="_blank"
rel="noreferrer"
>
{item.protocol.split("/").pop()}
</a>
</li>
))}
{protocols.map((item, index) => {
const href =
item.type === "protocolLink"
? item.url
: item.file?.publicURL;
return (
<li key={index}>
<a
href={href ?? "#"}
target="_blank"
rel="noreferrer noopener"
>
{item.name}
</a>
</li>
);
})}
</ul>
),
});
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8 changes: 6 additions & 2 deletions src/pages/ideas/dev-example.md
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Expand Up @@ -27,8 +27,12 @@ preliminaryFindings:
materialsAndMethods:
dataset: Released EMT dataset
protocols:
# - protocol: /protocols/emt_junction_segmentation.pdf
# - protocol: /protocols/emt_tracking_qc.pdf
- type: protocolLink
name: Culture And Freezing Methods
url: https://cell-catalog.allencell.org/pdf/AICS_WTC_cell_culture_protocol.pdf
- type: protocolFile
name: Cell culture protocol
file: /img/cell_culture_protocol.pdf
Comment on lines +30 to +35
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@interim17 interim17 Feb 6, 2026

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The type field is created by Decap when you use a variable type widget.

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Copilot AI Feb 6, 2026

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The schema uses file: File @fileByRelativePath, which typically expects a relative path like img/cell_culture_protocol.pdf (no leading slash). Using /img/... may prevent Gatsby from resolving the File node, resulting in file being null and the UI falling back to #. Align the stored value with what @fileByRelativePath expects (or adjust the CMS public_folder/value format accordingly).

Suggested change
file: /img/cell_culture_protocol.pdf
file: img/cell_culture_protocol.pdf

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@interim17 interim17 Feb 6, 2026

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Not sure about this, it's working as is, and its the same way the img file path for the banner was written.

cellLines:
- name: AICS-42
link: https://allencell.org/cell-catalog
Expand Down
7 changes: 6 additions & 1 deletion src/templates/idea-post.tsx
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Expand Up @@ -144,7 +144,12 @@ export const pageQuery = graphql`
}
}
protocols {
protocol
type
name
url
file {
publicURL
}
}
cellLines {
name
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54 changes: 46 additions & 8 deletions static/admin/config.yml
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Expand Up @@ -127,12 +127,45 @@ collections:
widget: "list",
required: false,
hint: "List any relevant protocols used in this analysis.",
field:
{
label: "Protocol",
name: "protocol",
widget: "file",
},
types:
[
{
label: "Protocol link",
name: "protocolLink",
widget: "object",
fields:
[
{
label: "Name",
name: "name",
widget: "string",
},
{
label: "URL",
name: "url",
widget: "string",
},
],
},
{
label: "Protocol file",
name: "protocolFile",
widget: "object",
fields:
[
{
label: "Name",
name: "name",
widget: "string",
},
{
label: "File",
name: "file",
widget: "file",
},
],
},
],
},
{
label: "Cell lines used",
Expand Down Expand Up @@ -173,7 +206,7 @@ collections:
hint: "Optionally provide a custom or supplementary description for how this tool was used in this specific analysis. Leave blank to use the default description.",
},
],
}
},
],
}
- {
Expand Down Expand Up @@ -330,7 +363,12 @@ collections:
options: ["Public", "In development", "Internal use only"],
required: false,
}
- { label: "Publish Date", name: "date", widget: "datetime", required: false }
- {
label: "Publish Date",
name: "date",
widget: "datetime",
required: false,
}

- name: "pages"
label: "Pages"
Expand Down
Binary file added static/img/cell_culture_protocol.pdf
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