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Merge pull request #104 from EyeSeeTea/development
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Release 3.10.1
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@adrianq
adrianq authored Feb 19, 2024
2 parents 6f964e9 + a81ae77 commit b5fda70
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Showing 7 changed files with 109 additions and 49 deletions.
2 changes: 1 addition & 1 deletion README.md
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@@ -1,4 +1,4 @@
# 3DBIONOTES-WS v3.10.0
# 3DBIONOTES-WS v3.10.1

## Integrating molecular biology

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2 changes: 1 addition & 1 deletion app/assets/javascripts/3dbio_viewer/package.json
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@@ -1,6 +1,6 @@
{
"name": "3dbio-viewer",
"version": "3.10.0",
"version": "3.10.1",
"private": true,
"dependencies": {
"@3dbionotes/pdbe-molstar": "3.1.0-est-2",
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4 changes: 2 additions & 2 deletions app/assets/javascripts/3dbio_viewer/public/index.html
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Expand Up @@ -17,8 +17,8 @@
type="text/css"
/>

<script src="/protvista-pdb/protvista-pdb-2.0.1-est-1-beta.1.js"></script>
<script src="/pdbe-molstar/pdbe-molstar-plugin-3.1.0-est-2-beta.3.js"></script>
<script src="/protvista-pdb/protvista-pdb-2.0.1-est-2.js"></script>
<script src="/pdbe-molstar/pdbe-molstar-plugin-3.1.0-est-2.js"></script>

<title>3dbio Viewer</title>
</head>
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117 changes: 76 additions & 41 deletions ...assets/javascripts/3dbio_viewer/src/webapp/components/molecular-structure/usePdbPlugin.ts
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Expand Up @@ -52,6 +52,7 @@ export const loaderErrors = {
unexpectedUploadError: (url: string) =>
i18n.t(`Unkown error while loading the model URL: ${url}`),
modelNotFound: (pdbId: string) => i18n.t(`${pdbId} was not found`),
serviceUnavailable: (pdbId: string) => i18n.t(`Unable to load ${pdbId}. Service unavailable`),
pdbRequest: (url: string, status: number) =>
i18n.t(`Error loading PDB model: url=${url} - ${status}`),
request: (url: string, status: number) => i18n.t(`Error loading model: url=${url} - ${status}`),
Expand Down Expand Up @@ -136,18 +137,20 @@ export function usePdbePlugin(options: MolecularStructureProps) {
newSelection.type === "free"
? Promise.all(
newSelection.refinedModels.map(
async m =>
await checkModelUrl(getRefinedModelId(m), m.type).then(loaded => {
if (loaded) return m;
else {
pdbePlugin.canvas.showToast({
title: i18n.t("Error"),
message: loaderErrors.modelNotFound(m.id),
key: errorsKeys.modelNotFound,
});
return undefined;
async model =>
await checkModelUrl(getRefinedModelId(model), model.type).then(
res => {
if (res.loaded) return model;
else {
pdbePlugin.canvas.showToast({
title: i18n.t("Error"),
message: getErrorByStatus(model.id, res.status),
key: errorKeyByStatus(res.status),
});
return undefined;
}
}
})
)
)
).then(models => _.compact(models))
: Promise.resolve([]);
Expand Down Expand Up @@ -241,8 +244,8 @@ export function usePdbePlugin(options: MolecularStructureProps) {
loaderKeys.uploadedModel,
new Promise<void>((resolve, reject) => {
checkUploadedModelUrl(uploadUrl)
.then(result => {
if (result) {
.then(res => {
if (res.loaded) {
pdbePlugin.events.loadComplete.subscribe({
next: loaded => {
console.debug("molstar.events.loadComplete", loaded);
Expand Down Expand Up @@ -353,8 +356,8 @@ export async function applySelectionChangesToPlugin(
const item = items[i];
if (item) {
const id: string = getRefinedModelId(item);
await checkModelUrl(id, item.type).then(async loaded => {
if (loaded) {
await checkModelUrl(id, item.type).then(async res => {
if (res.loaded) {
const url = urls[item.type](id);
const loadParams: LoadParams = {
url,
Expand All @@ -373,8 +376,8 @@ export async function applySelectionChangesToPlugin(
} else
plugin.canvas.showToast({
title: i18n.t("Error"),
message: loaderErrors.modelNotFound(id),
key: errorsKeys.modelNotFound,
message: getErrorByStatus(id, res.status),
key: errorKeyByStatus(res.status),
});
});
}
Expand Down Expand Up @@ -425,8 +428,8 @@ export async function applySelectionChangesToPlugin(
const item = pdbs[i];
if (item) {
const pdbId = item.id;
await checkModelUrl(pdbId, "pdb").then(async loaded => {
if (loaded) {
await checkModelUrl(pdbId, "pdb").then(async res => {
if (res.loaded) {
const url = urls.pdb(pdbId);
const loadParams: LoadParams = {
url,
Expand All @@ -445,12 +448,12 @@ export async function applySelectionChangesToPlugin(
setVisibility(plugin, item);
updateItems(item);
} else if (getMainItem(newSelection, "pdb") === pdbId)
updateLoader("loadModel", Promise.reject(loaderErrors.modelNotFound(pdbId)));
if (!loaded)
updateLoader("loadModel", Promise.reject(getErrorByStatus(pdbId, res.status)));
if (!res.loaded)
plugin.canvas.showToast({
title: i18n.t("Error"),
message: loaderErrors.modelNotFound(pdbId),
key: errorsKeys.modelNotFound,
message: getErrorByStatus(pdbId, res.status),
key: errorKeyByStatus(res.status),
});
});
}
Expand All @@ -460,8 +463,8 @@ export async function applySelectionChangesToPlugin(
const item = emdbs[i];
if (item) {
const emdbId = item.id;
await checkModelUrl(emdbId, "emdb").then(async loaded => {
if (loaded) {
await checkModelUrl(emdbId, "emdb").then(async res => {
if (res.loaded) {
await updateLoader(
"loadModel",
loadEmdb(plugin, urls.emdb(item.id)),
Expand All @@ -475,8 +478,8 @@ export async function applySelectionChangesToPlugin(
} else
plugin.canvas.showToast({
title: i18n.t("Error"),
message: loaderErrors.modelNotFound(emdbId),
key: errorsKeys.modelNotFound,
message: getErrorByStatus(emdbId, res.status),
key: errorKeyByStatus(res.status),
});
});
}
Expand Down Expand Up @@ -545,29 +548,61 @@ function getId<T extends { id: string }>(obj: T): string {
return obj.id;
}

export async function checkModelUrl(id: Maybe<string>, modelType: Type): Promise<boolean> {
if (!id) return false;
export async function checkModelUrl(id: Maybe<string>, modelType: Type): Promise<Response> {
if (!id) return { loaded: true, status: 404 };

const url = urls[modelType](id);
//method HEAD makes 404 be 200 anyways
const res = await fetch(url, { method: "GET", cache: "force-cache" }); //we are only caching if url exist

if (res.ok && res.status != 404 && res.status != 500) {
return true;
} else {
const msg = loaderErrors.pdbRequest(url, res.status);
console.error(msg);
return false;
}
return await fetch(url, { method: "GET", cache: "force-cache" })
.then(res => {
console.debug("Checking model: " + id, res.status);
return res.ok
? { loaded: true, status: res.status }
: { loaded: false, status: res.status };
})
.catch(res => {
const msg = loaderErrors.pdbRequest(url, res.status);
console.error(msg);
return { loaded: false, status: res.status };
}); //we are only caching if url exist
}

export async function checkUploadedModelUrl(url: string): Promise<boolean> {
export async function checkUploadedModelUrl(url: string): Promise<Response> {
return fetch(url, { method: "HEAD", cache: "force-cache" }).then(res => {
if (res.ok && res.status != 404 && res.status != 500) return true;
if (res.ok && res.status != 404 && res.status != 500 && res.status != 503)
return { loaded: true, status: res.status };
else {
const msg = loaderErrors.request(url, res.status);
console.error(msg);
return false;
return { loaded: false, status: res.status };
}
});
}

export function getErrorByStatus(id: string, status: number) {
switch (status) {
case 404:
return loaderErrors.modelNotFound(id);
case 500:
return loaderErrors.serviceUnavailable(id);
case 503:
return loaderErrors.serviceUnavailable(id);
default:
return loaderErrors.modelNotFound(id);
}
}

function errorKeyByStatus(status: number) {
switch (status) {
case 404:
return errorsKeys.modelNotFound;
case 500:
return errorsKeys.serviceUnavailable;
case 503:
return errorsKeys.serviceUnavailable;
default:
return errorsKeys.modelNotFound;
}
}

type Response = { loaded: boolean; status: number };
7 changes: 4 additions & 3 deletions ...assets/javascripts/3dbio_viewer/src/webapp/components/molecular-structure/usePluginRef.ts
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Expand Up @@ -7,6 +7,7 @@ import {
applySelectionChangesToPlugin,
checkModelUrl,
checkUploadedModelUrl,
getErrorByStatus,
getLigandView,
loaderErrors,
} from "./usePdbPlugin";
Expand Down Expand Up @@ -164,14 +165,14 @@ export function usePluginRef(options: Options) {

function loadFromPdb(pdbId: string, element: HTMLDivElement) {
checkModelUrl(pdbId, "pdb")
.then(loaded => {
if (loaded) {
.then(res => {
if (res.loaded) {
plugin.render(element, initParams);
molstarState.current = MolstarStateActions.fromInitParams(
initParams,
newSelection
);
} else loadVoidMolstar(loaderErrors.modelNotFound(pdbId));
} else loadVoidMolstar(getErrorByStatus(pdbId, res.status));
})
.catch(err => loadVoidMolstar(err));
}
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24 changes: 24 additions & 0 deletions app/assets/javascripts/3dbio_viewer/src/webapp/pages/app/App.css
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Expand Up @@ -165,3 +165,27 @@ header {
font-size: 2rem;
color: #123546;
}

.msp-plugin .msp-toast-container .msp-toast-entry {
font-size: 1.2em;
background: #f6d6d6;
border: 1px solid #f15151;
}

.msp-plugin .msp-toast-container .msp-toast-entry .msp-toast-title {
background: #ffa7a7;
padding: 0.25em 0.75em;
}

.msp-plugin .msp-toast-container .msp-toast-entry .msp-toast-message {
padding: 0.25em 2.5em 0.25em 0.75em;
}

.msp-plugin .msp-toast-container .msp-toast-entry .msp-material-icon svg {
color: #913131;
margin-bottom: 0;
}

.rangeForm .inputs input {
width: 70px;
}
2 changes: 1 addition & 1 deletion app/assets/javascripts/covid19/package.json
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@@ -1,7 +1,7 @@
{
"name": "covid19",
"description": "3dbionotes COVID-19",
"version": "3.10.0",
"version": "3.10.1",
"homepage": ".",
"dependencies": {
"@dhis2/d2-i18n": "1.0.6",
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