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A followup description fix and reference count fix #979

Merged
merged 8 commits into from
Feb 15, 2025
Merged

A followup description fix and reference count fix #979

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de0f27f
figureReferences and figureNumbering
isTravis Feb 13, 2025
8fe7ecb
Format fix
isTravis Feb 13, 2025
afeb881
Fix descriptions and support vertical tables
isTravis Feb 14, 2025
23ab244
Merge branch 'main' into tr/25-02-14-updatedGoogleProcessing
isTravis Feb 14, 2025
5756414
Remove console.logs
isTravis Feb 14, 2025
268ffde
Second description fix
isTravis Feb 15, 2025
3103b5a
merge fix
isTravis Feb 15, 2025
18a0ec2
Fix reference count bug
isTravis Feb 15, 2025
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8 changes: 4 additions & 4 deletions core/actions/googleDriveImport/gdocPlugins.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -841,7 +841,7 @@ test("Structure References", async () => {
<html>
<head></head>
<body>
<div><p>Here is some text {ref2}, {ref1}, {ref38}</p></div>
<div><p>Here is some text {ref2}{ref1}, {ref38}</p></div>
<table>
<tbody>
<tr>
Expand Down Expand Up @@ -889,7 +889,7 @@ test("Structure References", async () => {
Here is some text <a
data-type="reference" data-value="https://doi.org/10.1038/s41586-020-2983-4" data-unstructured-value="">
[1]
</a>, <a
</a><a
data-type="reference" data-value="https://doi.org/10.57844/arcadia-0zvp-xz86" data-unstructured-value="">
[2]
</a>, {ref38}
Expand Down Expand Up @@ -1225,14 +1225,14 @@ test("getDescription", async () => {
</tr>
<tr>
<td>Description</td>
<td>Seeing how <i>microbes</i> are organized ...</td>
<td><p style="padding:0;margin:0;color:#000000;font-size:11pt;font-family:&#x22;Arial&#x22;;line-height:1.0;text-align:left"><span>We previously released a draft genome assembly for the lone star tick, <span style="font-style:italic">A. americanum. </span><span style="color:#000000;font-weight:400;text-decoration:none;vertical-align:baseline;font-size:11pt;font-family:&#x22;Arial&#x22;;font-style:normal">We've now predicted genes from this assembly to use for downstream functional characterization and comparative genomics efforts.</span></p></span></td>
</tr>
</table><p>Hello</p>
</body>
</html>

`;
const expectedOutputHtml = `Seeing how <i>microbes</i> are organized ...`;
const expectedOutputHtml = `We previously released a draft genome assembly for the lone star tick, <i>A. americanum. </i>We've now predicted genes from this assembly to use for downstream functional characterization and comparative genomics efforts.`;

const result = getDescription(inputHtml);

Expand Down
15 changes: 10 additions & 5 deletions core/actions/googleDriveImport/gdocPlugins.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -153,6 +153,9 @@ export const tableToObjectArray = (node: any) => {
export const getDescription = (htmlString: string): string => {
let description = "";
rehype()
.use(structureFormatting)
.use(removeVerboseFormatting)
.use(removeGoogleLinkForwards)
.use(() => (tree: Root) => {
visit(tree, "element", (node: any) => {
if (node.tagName === "table") {
Expand All @@ -165,9 +168,10 @@ export const getDescription = (htmlString: string): string => {
properties: {},
children: tableData[0].value,
};
description = rehypeFragmentToHtmlString(valueFragment)
.replace("<span>", "")
.replace("</span>", "");
description = rehypeFragmentToHtmlString(valueFragment).replace(
/<\/?(span|p)>/g,
""
);
return false;
}
}
Expand Down Expand Up @@ -707,6 +711,7 @@ export const structureAnchors = () => (tree: Root) => {
};
export const structureReferences = () => (tree: Root) => {
const allReference: any[] = [];

const doiReferenceCounts: { [key: string]: number } = {};
visit(tree, (node: any, index: any, parent: any) => {
if (node.tagName === "table") {
Expand Down Expand Up @@ -767,12 +772,12 @@ export const structureReferences = () => (tree: Root) => {
}
}
});

const referenceIds = allReference.map((ref) => ref.id);
const referenceVarOrder: string[] = [];

visit(tree, "text", (textNode: any, index: any, parent: any) => {
if (typeof textNode.value === "string") {
const regex = new RegExp(/\{([^\s\]]+)\}/g);
const regex = new RegExp(/\{([^\{\}]+?)\}/g);
let match;

while ((match = regex.exec(textNode.value)) !== null) {
Expand Down
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