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Include support for neuroglancer url for umembargoed zarr and nifti #2063

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Include support for neuroglancer url for umembargoed zarr and nifti #2063

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Draft: Include support for neuroglancer url for umembargoed zarr and …
Oct 30, 2024
af09af6
include asset service interface appropriately
Oct 30, 2024
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39 changes: 35 additions & 4 deletions web/src/views/FileBrowserView/FileBrowser.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -230,7 +230,8 @@
<v-list-item
v-for="el in item.services"
:key="el.name"
:href="el.url"
@click="el.isPublicNeuroglancer ? redirectNeuroglancerUrl(item) : null"
:href="!el.isPublicNeuroglancer ? el.url : null"
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as for embargoed -- we are providing URLs unconditionally ATM but they would not even work for embargoed. Filed more generic:

target="_blank"
rel="noreferrer"
>
Expand Down Expand Up @@ -288,6 +289,7 @@ const FILES_PER_PAGE = 15;
interface AssetService {
name: string,
url: string,
isPublicNeuroglancer: boolean,
}

interface ExtendedAssetPath extends AssetPath {
Expand Down Expand Up @@ -330,7 +332,6 @@ const EXTERNAL_SERVICES = [
maxsize: 1e9,
endpoint: 'http://nwbexplorer.opensourcebrain.org/nwbfile=$asset_url$',
},

{
name: 'VTK/ITK Viewer',
regex: /\.ome\.zarr$/,
Expand All @@ -351,19 +352,23 @@ const EXTERNAL_SERVICES = [
maxsize: Infinity,
endpoint: 'https://neurosift.app?p=/nwb&url=$asset_dandi_url$&dandisetId=$dandiset_id$&dandisetVersion=$dandiset_version$', // eslint-disable-line max-len
},

{
name: 'Neurosift',
regex: /\.nwb\.lindi\.(json|tar)$/,
maxsize: Infinity,
endpoint: 'https://neurosift.app?p=/nwb&url=$asset_dandi_url$&st=lindi&dandisetId=$dandiset_id$&dandisetVersion=$dandiset_version$', // eslint-disable-line max-len
},

{
name: 'Neurosift',
regex: /\.avi$/,
maxsize: Infinity,
endpoint: 'https://neurosift.app?p=/avi&url=$asset_dandi_url$&dandisetId=$dandiset_id$&dandisetVersion=$dandiset_version$', // eslint-disable-line max-len
},
{
name: 'Neuroglancer',
regex: /\.nii(\.gz)?$|\.zarr$/,
maxsize: Infinity,
endpoint: '', // defaults to redirectNeuroglancerUrl logic
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I think we should aim for adjusting the "schema" here to reflect this new need -- that we need

Suggested change
endpoint: '', // defaults to redirectNeuroglancerUrl logic
item_handler: 'redirectNeuroglancerUrl',

and then use that in the service code?

}
];
type Service = typeof EXTERNAL_SERVICES[0];
Expand Down Expand Up @@ -453,6 +458,7 @@ function getExternalServices(path: AssetPath, info: {dandisetId: string, dandise
assetDandiUrl,
assetS3Url,
}),
isPublicNeuroglancer: service.name === 'Neuroglancer' && !embargoed.value,
}));
}

Expand Down Expand Up @@ -557,6 +563,31 @@ async function deleteAsset() {
itemToDelete.value = null;
}

function redirectNeuroglancerUrl(item: any) {
const assetS3Url = trimEnd((item.asset as AssetFile).url, '/');
const baseUrl = `https://neuroglancer-demo.appspot.com/#!`; // Public neuroglancer instance
const jsonObject = {
layers: [
{
type: "new",
source: assetS3Url.includes("zarr") ? `zarr://${assetS3Url}`
: `nifti://${assetS3Url}`,
tab: "source",
name: item.asset.asset_id
}
],
selectedLayer: {
visible: true,
layer: item.asset.asset_id
},
layout: "4panel"
};

const jsonStr = JSON.stringify(jsonObject);
const encodedJson = encodeURIComponent(jsonStr);
window.open(`${baseUrl}${encodedJson}`);
}

// Update URL if location changes
watch(location, () => {
const { location: existingLocation } = route.query;
Expand Down