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TASK-5864 - Variant link route does not work #894

Merged
merged 16 commits into from
Apr 17, 2024
Merged

TASK-5864 - Variant link route does not work #894

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f68692c
Rename #broser tool to #variant-browser
imedina Mar 14, 2024
ce8b95e
Many improvements and clean-ups in hashFragmentListener
imedina Mar 18, 2024
6a274df
First funcitonal implementation
imedina Mar 19, 2024
1e42aef
Merge branch 'release-2.12.x' into TASK-5864
jmjuanes Mar 28, 2024
07a3d6c
wc: fix listening for changed properties in variant-browser TASK-5864
jmjuanes Mar 28, 2024
99d2825
Merge branch 'TASK-5674' into TASK-5864
imedina Mar 29, 2024
80578bf
Code cleanups
imedina Mar 30, 2024
7288c16
Merge branch 'release-2.12.x' into TASK-5864
jmjuanes Apr 2, 2024
c2c6efe
Several fixes in the Variant link routing
imedina Apr 12, 2024
434e77e
Merge branch 'release-2.12.x' into TASK-5864
imedina Apr 12, 2024
4f2c347
Fix change study
imedina Apr 12, 2024
0f0a140
iva: fix bug when changing app or tool from navbar or sidebar #TASK-5864
jmjuanes Apr 12, 2024
fe3c775
iva: remove useless requestUpdate after changing app #TASK-5864
jmjuanes Apr 12, 2024
5d85521
iva: added minor checks in hashFragmentListener #TASK-5864
jmjuanes Apr 12, 2024
a4f70f0
Merge branch 'release-2.12.x' into TASK-5864
imedina Apr 14, 2024
88025cd
Merge branch 'release-2.12.x' into TASK-5864
jmjuanes Apr 17, 2024
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33 changes: 8 additions & 25 deletions src/core/clients/opencga/opencga-client.js
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Original file line number Diff line number Diff line change
Expand Up @@ -357,7 +357,8 @@ export class OpenCGAClient {
// check that a session exists
// TODO should we check the session has not expired?
if (_this._config.token) {
_this.users().info(_this._config.userId)
_this.users()
.info(_this._config.userId)
.then(async response => {
console.log("Creating session");
const session = {
Expand All @@ -370,7 +371,6 @@ export class OpenCGAClient {
session.server = {
host: _this._config.host,
version: _this._config.version,
// serverVersion: _this._config.serverVersion,
};
session.opencgaClient = _this;
const userConfig = await this.updateUserConfig("IVA", {
Expand All @@ -392,7 +392,6 @@ export class OpenCGAClient {
.search({limit: 100})
.then(async function (response) {
try {
// session.projects = response.responses[0].results;
for (const project of response.responses[0].results) {
const projectIndex = session.projects.findIndex(proj => proj.fqn === project.fqn);
if (projectIndex < 0) {
Expand Down Expand Up @@ -425,29 +424,12 @@ export class OpenCGAClient {
// FIXME line above should check cohort.internal instead
// .filter(cohort => cohort.internal.index?.status === "READY");

// Check if lastStudy form User Configuration matches
if (session.user?.configs?.IVA?.lastStudy === study.fqn) {
session.project = project;
session.study = study;
}

// Keep track of the studies to fetch Disease Panels
studies.push(study.fqn);
}
}
}

// If the user doesn't have his own default study then we select the first project and study as default
if (!session.project && !session.study) {
for (const project of session.projects) {
if (project.studies?.length > 0) {
session.project = project;
session.study = project.studies[0];
break;
}
}
}

// Fetch the CellBase sources for each Project
const cellbaseSourcesPromises = [];
const indexesMap = [];
Expand Down Expand Up @@ -482,11 +464,12 @@ export class OpenCGAClient {
console.log("Fetching disease panels");
const panelPromises = [];
for (const study of studies) {
const promise = _this.panels().search({
study: study,
limit: 2000,
include: "id,name,stats,source,genes.id,genes.name,genes.modeOfInheritance,genes.confidence,regions.id"
});
const promise = _this.panels()
.search({
study: study,
limit: 1000,
include: "id,name,stats,source,genes.id,genes.name,genes.modeOfInheritance,genes.confidence,regions.id"
});
panelPromises.push(promise);
}
const panelResponses = await Promise.all(panelPromises);
Expand Down
6 changes: 3 additions & 3 deletions src/sites/iva/conf/config.js
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Original file line number Diff line number Diff line change
Expand Up @@ -32,10 +32,10 @@ const hosts = [
];

const opencga = {
host: hosts[2].url,
host: hosts[1].url,
version: "v2",
cookie: {
prefix: "iva-" + hosts[2].id,
prefix: "iva-" + hosts[1].id,
secure: true,
},
sso: {
Expand Down Expand Up @@ -316,7 +316,7 @@ const SUITE = {
},
menu: [
{
id: "browser",
id: "variant-browser",
name: "Variant Browser",
icon: "img/tools/icons/variant_browser.svg",
visibility: "public",
Expand Down
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