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Fetch CIF files from the PDB preferentially #99

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merged 2 commits into from
Jun 5, 2024
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Merged

Fetch CIF files from the PDB preferentially #99

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c9a50b2
Add "rel=noreferrer" to external links
Dialpuri Jun 5, 2024
c011fdc
Add function to fetch PDB file if CIF file fails
Dialpuri Jun 5, 2024
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11 changes: 10 additions & 1 deletion webapp/src/layouts/Footer.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,16 @@ export default function Footer(): ReactElement {
<footer className="bg-gray w-full mt-auto">
<div className="w-full mx-auto max-w-screen-xl p-4 flex items-center justify-center">
<span className="text-sm text-primary text-center justify-center dark:text-gray-400">
<p>Spotted an issue? Please email us or <a href="https://github.com/glycojones/privateer/issues/new/choose" target='_blank' > submit a GitHub issue </a>
<p>
Spotted an issue? Please email us or{' '}
<a
href="https://github.com/glycojones/privateer/issues/new/choose"
target="_blank"
rel="noreferrer"
>
{' '}
submit a GitHub issue{' '}
</a>
</p>
York Structural Biology Laboratory
<br />
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7 changes: 6 additions & 1 deletion webapp/src/layouts/NavBar.tsx
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Expand Up @@ -92,7 +92,12 @@ export default function NavBar(): ReactElement {
</a>
</div>
<div className="h-12 w-12 mx-auto my-4 sm:w-12 sm:mt-12 sm:mr-12 flex items-center ">
<a id="github" href={GITHUB_REPO} target="_blank">
<a
id="github"
href={GITHUB_REPO}
target="_blank"
rel="noreferrer"
>
<img
className="w-full hover:scale-125 transition-all hidden dark:block"
src="/github-mark.png"
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37 changes: 31 additions & 6 deletions webapp/src/modals/Citations/Citations.tsx
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Expand Up @@ -72,17 +72,42 @@ export default function CitationModal(props: {
McNicholas, S. J. & Agirre, J. (2024). Online
carbohydrate 3D structure validation with the Privateer
web app. Acta Cryst. F80.
<p><a href="https://doi.org/10.1107/S2053230X24000359" target="_blank">https://doi.org/10.1107/S2053230X24000359</a></p>
<p>
<a
href="https://doi.org/10.1107/S2053230X24000359"
target="_blank"
rel="noreferrer"
>
https://doi.org/10.1107/S2053230X24000359
</a>
</p>
</strong>
</div>

<div className="mt-4 flex flex-col space-y-2">
<h3>If you have used the <b><i>Privateer Database</i></b>, please cite: </h3>
<div className="mt-4 flex flex-col space-y-2">
<h3>
If you have used the{' '}
<b>
<i>Privateer Database</i>
</b>
, please cite:{' '}
</h3>

<strong>Dialpuri, J. S.; Bagdonas, H.; Schofield, L. C.; Pham, P. T.; Holland, L.; Agirre, J. Beilstein J. Org. Chem. 2024, 20, 931–939.
<p><a href="https://doi.org/10.3762/bjoc.20.83" target="_blank">https://doi.org/10.3762/bjoc.20.83</a></p>
<strong>
Dialpuri, J. S.; Bagdonas, H.; Schofield, L. C.; Pham,
P. T.; Holland, L.; Agirre, J. Beilstein J. Org. Chem.
2024, 20, 931–939.
<p>
<a
href="https://doi.org/10.3762/bjoc.20.83"
target="_blank"
rel="noreferrer"
>
https://doi.org/10.3762/bjoc.20.83
</a>
</p>
</strong>
</div>
</div>

<div className="mt-4 flex flex-col space-y-2 font text-sm sm:text-base">
<h3>
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12 changes: 10 additions & 2 deletions webapp/src/shared/Information/Information.tsx
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Expand Up @@ -89,7 +89,11 @@ export function Information() {
<div className="flex flex-col gap-6 justify-center">
<span className="text-xl font-body">
<b>Glycomics-Powered Validation</b>
<a href={GLYCOMICS_CITATION} target="_blank">
<a
href={GLYCOMICS_CITATION}
target="_blank"
rel="noreferrer"
>
<svg
className="inline pl-2 h-4 transition-all hover:h-5 fill-secondary"
xmlns="http://www.w3.org/2000/svg"
Expand Down Expand Up @@ -119,7 +123,11 @@ export function Information() {
<div className="flex flex-col gap-6 justify-center">
<span className="text-xl font-body">
<b>Linkage Torsion Validation</b>
<a href={TORSIONS_CITATION} target="_blank">
<a
href={TORSIONS_CITATION}
target="_blank"
rel="noreferrer"
>
<svg
className="inline pl-2 h-4 transition-all hover:h-5 fill-secondary"
xmlns="http://www.w3.org/2000/svg"
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34 changes: 31 additions & 3 deletions webapp/src/utils/fetch_from_pdb.ts
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Original file line number Diff line number Diff line change
@@ -1,9 +1,32 @@
async function fetchPDBFile(PDBCode: string): Promise<string | void> {
console.warn(
'The CIF file for this PDB could not be found, trying for the PDB'
);
const pdbURL = `https://files.rcsb.org/download/${PDBCode.toUpperCase()}.pdb`;

const file = fetch(pdbURL)
.then(async (response) => {
if (!response.ok) {
throw new Error('Network error');
}
return await response.text();
})
.then(async (file) => {
return file;
})
.catch(async (error) => {
return await Promise.reject(error);
});
return await file;
}

export async function fetchPDB(PDBCode: string): Promise<string | void> {
if (PDBCode == null) {
return;
}
// first try fetching the cif
console.log('Fetching PDB ', PDBCode);
const pdbURL = `https://files.rcsb.org/download/${PDBCode.toUpperCase()}.pdb`;
const pdbURL = `https://files.rcsb.org/download/${PDBCode.toUpperCase()}.cif`;

const file = fetch(pdbURL)
.then(async (response) => {
Expand All @@ -15,8 +38,13 @@ export async function fetchPDB(PDBCode: string): Promise<string | void> {
.then(async (file) => {
return file;
})
.catch(() => {
throw new Error('PDB Not Found');
.catch(async () => {
// if we can't find the cif, try the PDB, if that fails, then report the failure.
try {
return await fetchPDBFile(PDBCode);
} catch (e) {
return await Promise.reject(e);
}
});
return await file;
}
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