diff --git a/.gitignore b/.gitignore index 7c7c31c39..689a566d8 100644 --- a/.gitignore +++ b/.gitignore @@ -1,8 +1,11 @@ build +dist bower_components node_modules +web_modules private +web_modules # General *.jar diff --git a/Jenkinsfile b/Jenkinsfile index f473aa974..1ea7dc578 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -1,7 +1,7 @@ pipeline { agent any stages { - stage ('Build source code') { + stage ('Build source code') { options { timeout(time: 5, unit: 'MINUTES') } @@ -9,7 +9,7 @@ pipeline { sh 'npm install --unsafe-perm && npm run build' } } - stage ('Docker Build and Push') { + stage ('Build and Push Stable Docker') { options { timeout(time: 25, unit: 'MINUTES') } @@ -18,14 +18,31 @@ pipeline { } steps { script { - def tag = sh(returnStdout: true, script: "git tag --sort version:refname | tail -1").trim() + def tag = sh(returnStdout: true, script: "node -p \"require('./package.json').version\"").trim() sh "docker build -t opencb/iva:'${tag}' -f docker/Dockerfile ." withDockerRegistry([ credentialsId: "wasim-docker-hub", url: "" ]) { sh "docker push opencb/iva:'${tag}'" } } } - } + } + stage ('Build and Push Development Docker') { + options { + timeout(time: 25, unit: 'MINUTES') + } + when { + branch "develop" + } + steps { + script { + def tag = sh(returnStdout: true, script: "node -p \"require('./package.json').version\"").trim() + sh "docker build -t opencb/iva:'${tag}' -f docker/Dockerfile ." + withDockerRegistry([ credentialsId: "wasim-docker-hub", url: "" ]) { + sh "docker push opencb/iva:'${tag}'" + } + } + } + } } } diff --git a/bs-config.js b/bs-config.js new file mode 100644 index 000000000..eee77d81c --- /dev/null +++ b/bs-config.js @@ -0,0 +1,29 @@ +const path = require("path"); + +/* + |-------------------------------------------------------------------------- + | IVA Browser-sync config file + |-------------------------------------------------------------------------- + */ +module.exports = { + files: [ + "src", + "lib/jsorolla/src", + "lib/jsorolla/styles" + ], + server: { + //baseDir: path.resolve(__dirname), + //directory: true + }, + startPath: "src", + open: true, + timestamps: true, + excludedFileTypes: [], + notify: { + styles: { + top: 'auto', + bottom: '0' + } + } + +}; diff --git a/credentials.sh b/credentials.sh new file mode 100755 index 000000000..09266cf89 --- /dev/null +++ b/credentials.sh @@ -0,0 +1,10 @@ +#!/bin/bash + +echo -n "Enter your Opencga Username [ENTER]: " +read username +stty -echo +printf "Enter your Opencga password [ENTER]: " +read password +stty echo + +CYPRESS_username=$username CYPRESS_password=$password "$@" diff --git a/cypress.json b/cypress.json new file mode 100644 index 000000000..36c445610 --- /dev/null +++ b/cypress.json @@ -0,0 +1,6 @@ +{ + "baseUrl": "http://localhost:3000/src/", + "chromeWebSecurity": false, + "viewportWidth": 1600, + "viewportHeight": 660 +} diff --git a/cypress/integration/login.js b/cypress/integration/login.js new file mode 100644 index 000000000..a66f41a88 --- /dev/null +++ b/cypress/integration/login.js @@ -0,0 +1,31 @@ +context("Login", () => { + beforeEach(() => { + cy.visit("http://localhost:3000/src/#login") + }) + + it("login unsuccessful", () => { + cy.get("#opencgaUser").type("demo") + cy.get("#opencgaPassword").type("demo") + cy.get("form#formLogin").submit() + + cy.get("#error").contains( "Incorrect user or password.") + }) + + it("login uccessful", () => { + + const username = Cypress.env("username") + const password = Cypress.env("password") + + //console.log("username", username) + //console.log("password", password) + + expect(username, "username was set").to.be.a("string").and.not.be.empty + expect(password, "password was set").to.be.a("string").and.not.be.empty + cy.get("#opencgaUser").type(username) + cy.get("#opencgaPassword").type(password) + cy.get("form#formLogin").submit() + + cy.url().should("include", "#home") + cy.get(".subtitle").contains( "Interactive Variant Analysis") + }) +}) diff --git a/cypress/integration/opencga-clinical-portal.spec.js b/cypress/integration/opencga-clinical-portal.spec.js new file mode 100644 index 000000000..4a74456da --- /dev/null +++ b/cypress/integration/opencga-clinical-portal.spec.js @@ -0,0 +1,34 @@ +import {login} from "../plugins/utils.js"; +import "cypress-wait-until"; + +context("Case Portal", () => { + before(() => { + login(); + }) + + it("query", () => { + /*cy.waitUntil(() => cy.getCookie("iva_sid").then(cookie => { + console.log("cookie", cookie) + return Boolean(cookie && cookie.value) + }));*/ + + cy.get("a[data-id=clinicalAnalysisPortal]").click({force: true}) + + //long timeout to make sure you are logged in + cy.get("div.page-title h2", {timeout: 60000}).should("be.visible").and("contain", "Case Portal") + + //cy.get(".lhs button").should("have.length", 2) + cy.get(".clearfix > .pull-left > .pagination-info", {timeout: 10000}) + .should("be.visible") + //.should('contain', /Showing \d+ to \d+ of \d+ records/) + //.and("contain", "Showing 1 to 10 of 18 records") + + + cy.get("opencga-clinical-analysis-grid .success > :nth-child(1)").then(elem => { + // elem is the underlying Javascript object targeted by the .get() command. + const firstCase = Cypress.$(elem).text().trim(); + //opencga-clinical-analysis-view > data-form div:nth-child(1) > div.col-md-9 + }); + + }) +}) diff --git a/cypress/integration/opencga-file-browser.spec.js b/cypress/integration/opencga-file-browser.spec.js new file mode 100644 index 000000000..e21da461a --- /dev/null +++ b/cypress/integration/opencga-file-browser.spec.js @@ -0,0 +1,34 @@ +import {login} from "../plugins/utils.js"; + +context("File Browser", () => { + before(() => { + login(); + }) + + it("query", () => { + cy.get("a[data-id=files]").click({force: true}) + cy.get("div.page-title h2", {timeout: 60000}).should("be.visible").and("contain", "File Browser") + + cy.get("#format + .subsection-content a").contains( "VCF").click({force: true}) + cy.get("#bioformat + .subsection-content a").contains( "VARIANT").click({force: true}) + + cy.get(".lhs button[data-filter-name]").should("have.length", 2) + + //cy.get('.fixed-table-toolbar').find(".pagination-info", {log:true}) + cy.get("div.search-button-wrapper button").click() + }) + + it("aggregated query", () => { + cy.get("a[data-id=files]").click({force: true}) + cy.get("a[href='#facet_tab']").click({force: true}) + //cy.get("div.search-button-wrapper button").click() + + //cy.wait(2000); + + cy.get("#bs-select-4-2").click({force: true}) // creation year field + cy.get(`a[data-collapse="#creationYear_nested"]`).click({force: true}) // creation y field + cy.get("#bs-select-7-3").click({force: true}) // creation month nested in year field + cy.get("div.search-button-wrapper button").click() + + }) +}) diff --git a/cypress/integration/opencga-individual-browser.spec.js b/cypress/integration/opencga-individual-browser.spec.js new file mode 100644 index 000000000..a746f077a --- /dev/null +++ b/cypress/integration/opencga-individual-browser.spec.js @@ -0,0 +1,39 @@ +import {login} from "../plugins/utils.js"; + +context("Individual Browser", () => { + before(() => { + login(); + }) + + it("query", () => { + cy.get("a[data-id=individuals]").click({force: true}) + cy.get("div.page-title h2", {timeout: 60000}).should("be.visible").and("contain", "Individual Browser") + + cy.get("#sex + .subsection-content a").contains( "MALE").click({force: true}) + cy.get("#sex + .subsection-content a").contains( "FEMALE").click({force: true}) + + cy.get("#date + .subsection-content input[data-tab=recent] + label").click(); //creationDate recent + + cy.get(".lhs button[data-filter-name]").should("have.length", 2); + cy.get("div.search-button-wrapper button").click(); + + }) + + it("aggregated query", () => { + cy.get("a[data-id=individuals]").click({force: true}) + + cy.get("a[href='#facet_tab']").click({force: true}) + cy.get("button.default-facets-button").click(); + + cy.get(".lhs button[data-filter-name]:nth-child(3)").click(); //remove creationDate + + cy.get("button.default-facets-button").click(); + + //cy.get("div.search-button-wrapper button").click() + + //cy.get(".facet-wrapper .button-list button").should("have.length", 4); + + //cy.get("opencb-facet-results opencga-facet-result-view").should("have.length", 4); + + }) +}) diff --git a/cypress/integration/opencga-sample-browser.spec.js b/cypress/integration/opencga-sample-browser.spec.js new file mode 100644 index 000000000..90455f4c2 --- /dev/null +++ b/cypress/integration/opencga-sample-browser.spec.js @@ -0,0 +1,34 @@ +import {login} from "../plugins/utils.js"; + +context("File Browser", () => { + before(() => { + login(); + }) + + it("query", () => { + cy.get("a[data-id=samples]").click({force: true}) + cy.get("div.page-title h2", {timeout: 60000}).should("be.visible").and("contain", "Sample Browser") + + cy.get("#somatic + .subsection-content label").contains( "True").click({force: true}) + + cy.get(".lhs button[data-filter-name]").should("have.length", 1); + cy.get("div.search-button-wrapper button").click(); + + cy.get(".lhs .somaticActiveFilter").click(); + cy.get(".lhs button[data-filter-name]").should("have.length", 0); + + }) + + it("aggregated query", () => { + cy.get("a[data-id=samples]").click({force: true}) + + cy.get("a[href='#facet_tab']").click({force: true}) + cy.get("button.default-facets-button").click() + cy.get("div.search-button-wrapper button").click() + + cy.get(".facet-wrapper .button-list button").should("have.length", 4); + + cy.get("opencb-facet-results opencga-facet-result-view").should("have.length", 4); + + }) +}) diff --git a/cypress/integration/opencga-variant-browser.spec.js b/cypress/integration/opencga-variant-browser.spec.js new file mode 100644 index 000000000..d31387b11 --- /dev/null +++ b/cypress/integration/opencga-variant-browser.spec.js @@ -0,0 +1,31 @@ +import {login} from "../plugins/utils.js"; + +context("Variant Browser", () => { + before(() => { + login(); + }) + + it("query", () => { + cy.get("a[data-id=browser]").click({force: true}) + cy.get("div.page-title h2", {timeout: 60000}).should("be.visible").and("contain", "Variant Browser") + + + cy.get("input#lof").click({force: true}); + cy.get("opencga-active-filters").contains("Consequence Types 10") + cy.get("button.ctActiveFilter").click() + }) + + it("aggregated query", () => { + cy.get("a[data-id=browser]").click({force: true}) + cy.get("a[href='#facet_tab']").click({force: true}) + cy.get("button.default-facets-button").click() + cy.get("div.search-button-wrapper button").click() + + cy.wait(2000); + + cy.get("#bs-select-1-4").click({force: true}) // gene aggregation field + cy.get("#type_Select a").contains( "INSERTION").click({force: true}) + cy.get("div.search-button-wrapper button").click() + + }) +}) diff --git a/cypress/integration/playground/scripts.js b/cypress/integration/playground/scripts.js new file mode 100644 index 000000000..696bb2865 --- /dev/null +++ b/cypress/integration/playground/scripts.js @@ -0,0 +1,111 @@ +//import "cypress-wait-until"; + +function preventFormSubmitDefault(selector) { + cy.get(selector).then(form$ => { + form$.on("submit", e => { + e.preventDefault(); + }); + }); +} + +let i = 0 + +context("Variant Browser", () => { + beforeEach(() => { + //cy.visit("http://localhost:3000/src/#login") + }) + + it("login", () => { + + /* + cy.server( { + onRequest: () => { + i++; + }, + onResponse: () => { + i--; + } + });*/ + + /*cy.on('url:changed', url => { + //cy.visit(url); + console.log("URL CHANGED", url) + });*/ + + const username = Cypress.env("username") + + const password = Cypress.env("password") + + console.log("username", username) + console.log("password", password) + + expect(username, "username was set").to.be.a("string").and.not.be.empty + expect(password, "password was set").to.be.a("string").and.not.be.empty + + + cy.visit("http://localhost:3000/src/#login") + cy.get("#opencgaUser").type(username).should("have.value", "///") + cy.get("#opencgaPassword").type(password).should("have.value", "///") + + //cy.clock() + + cy.get("form#formLogin").submit() + + cy.wait(1000); + + //cy.visit("http://localhost:3000/src/#home"); + + cy.get("#home-nav").click() + + + //cy.reload(); + cy.url().should("include", "#home") + + //cy.window().then(win => win["alert"]("HELLO!!")) + + cy.get(".subtitle").contains( "Interactive Variant Analysis") + //cy.get(".version").contains( "v2.0.0-beta") + + cy.get("a[data-id=browser]").click({force:true}) + + //cy.wait(5000); + //cy.visit("http://localhost:3000/src/#browser"); + //cy.reload(); + //cy.url().should("include", "#browser"); + + //cy.get(".page-title").contains( "Variant Browser") + + /*cy.waitUntil(() => i > 0) + cy.waitUntil(() => i === 0)*/ + + + //cy.wait(["@POST", "@GET"]) + + //cy.tick(10000) + + //cy.get("@POST.all").should("have.length", 1) + //cy.get("@GET.all").should("have.length", 1) + + //cy.reload(); + + + + //preventFormSubmitDefault("form"); + //cy.get("button[type=submit]").click() + //cy.visit("http://localhost:3000/src/#browser") + + + //cy.visit("http://localhost:3000/src/#browser")//.should("eq", "#home") + //cy.get(".subtitle").should("have.value", "Interactive Variant Analysis") + //cy.get("a[data-id=browser]").click({force: true}) + //cy.url().should("include", "#home") + + /* + cy.get("a[data-id=browser]").click({force: true}) + cy.waitUntil(() => i > 0) + cy.waitUntil(() => i === 0) + cy.reload();*/ + + //cy.get("button[type=submit]").click() + }) +}) diff --git a/cypress/integration/playground/test-routing.js b/cypress/integration/playground/test-routing.js new file mode 100644 index 000000000..5d1f7cce8 --- /dev/null +++ b/cypress/integration/playground/test-routing.js @@ -0,0 +1,16 @@ +context("Variant Browser", () => { + beforeEach(() => { + // cy.visit("http://localhost:3000/src/#login") + }) + + it("login", () => { + + /*cy.get("#loginButton").within(() => { + // ends the current chain and yields null + cy.contains("Login").click().end() + })*/ + cy.visit("http://localhost:3000/src/test-routing.html") + cy.get("#about-menu").click() + + }) +}) diff --git a/cypress/plugins/index.js b/cypress/plugins/index.js new file mode 100644 index 000000000..aa9918d21 --- /dev/null +++ b/cypress/plugins/index.js @@ -0,0 +1,21 @@ +/// +// *********************************************************** +// This example plugins/index.js can be used to load plugins +// +// You can change the location of this file or turn off loading +// the plugins file with the 'pluginsFile' configuration option. +// +// You can read more here: +// https://on.cypress.io/plugins-guide +// *********************************************************** + +// This function is called when a project is opened or re-opened (e.g. due to +// the project's config changing) + +/** + * @type {Cypress.PluginConfig} + */ +module.exports = (on, config) => { + // `on` is used to hook into various events Cypress emits + // `config` is the resolved Cypress config +} diff --git a/cypress/plugins/utils.js b/cypress/plugins/utils.js new file mode 100644 index 000000000..24b0f4486 --- /dev/null +++ b/cypress/plugins/utils.js @@ -0,0 +1,8 @@ +export const login = () => { + cy.visit("http://localhost:3000/src/#login") + const username = Cypress.env("username"); + const password = Cypress.env("password"); + cy.get("#opencgaUser").type(username) + cy.get("#opencgaPassword").type(password, {log: false}) + cy.get("form#formLogin").submit() +} diff --git a/docker/Dockerfile b/docker/Dockerfile deleted file mode 100644 index 502910d4f..000000000 --- a/docker/Dockerfile +++ /dev/null @@ -1,20 +0,0 @@ -FROM httpd - -# Minimum compatible git commit, please only use later commits. - -# Install dependencies -RUN apt-get update && \ - apt-get upgrade -y && \ - apt-get install -y curl gnupg2 && \ - curl -sL https://deb.nodesource.com/setup_8.x | bash && \ - apt-get install -y git nodejs npm - -RUN echo '{ "allow_root": true }' > /root/.bowerrc && \ - npm install -g grunt-cli - -COPY ./build /usr/local/apache2/htdocs - -EXPOSE 80 - -VOLUME /usr/local/apache2/htdocs/conf - diff --git a/docker/docker-build.py b/docker/docker-build.py new file mode 100755 index 000000000..1e6f33a34 --- /dev/null +++ b/docker/docker-build.py @@ -0,0 +1,151 @@ +#!/usr/bin/env python3 + +import argparse +import os +import requests +import sys +import json +import pathlib +from pathlib import Path + +## Configure command-line options +parser = argparse.ArgumentParser() +parser.add_argument('action', help="Action to execute", choices=["build", "push", "delete"], default="build") +parser.add_argument('--images', help="comma separated list of images to be made, e.g. app", default="app") +parser.add_argument('--tag', help="the tag for this code, e.g. v2.0.0") +parser.add_argument('--build-folder', help="the location of the build folder, if not default location") +parser.add_argument('--username', help="credentials for dockerhub (REQUIRED if deleting from DockerHub)") +parser.add_argument('--password', help="credentials for dockerhub (REQUIRED if deleting from DockerHub)") + +## Some ANSI colors to print shell output +shell_colors = { + 'red': '\033[91m', + 'green': '\033[92m', + 'blue': '\033[94m', + 'magenta': '\033[95m', + 'bold': '\033[1m', + 'reset': '\033[0m' +} + +def error(message): + sys.stderr.write(shell_colors['red'] + 'ERROR: %s\n' % message + shell_colors['reset']) + sys.exit(2) + +def run(command): + print(shell_colors['bold'] + command + shell_colors['reset']) + code = os.system(command) + if code != 0: + error("Error executing: " + command) + +def print_header(str): + print(shell_colors['magenta'] + "*************************************************" + shell_colors['reset']) + print(shell_colors['magenta'] + str + shell_colors['reset']) + print(shell_colors['magenta'] + "*************************************************" + shell_colors['reset']) + +def package_json(): + basedir = str(Path(__file__).resolve().parents[1]) + p = Path(basedir + "/package.json") + with open(p, "r") as package_json: + data=package_json.read() + return json.loads(data) + +# def login(loginRequired=False): +# if args.username is None or args.password is None: +# if loginRequired: +# error("Username and password are required") +# else: +# return +# +# code = os.system("docker login -u " + args.username + " --password " + args.password) +# if code != 0: +# error("Error executing: docker login") + + +def build(): + print_header('Building docker images: ' + ', '.join(images)) + for image in images: + print(shell_colors['blue'] + "Building opencb/iva-" + image + ":" + tag + " ..." + shell_colors['reset']) + run("docker build -t opencb/iva-" + image + ":" + tag + " -f " + build_folder + "/docker/iva-" + image + "/Dockerfile " + build_folder) + +def tag_latest(image): + latest_tag = os.popen(("curl -s https://registry.hub.docker.com/v1/repositories/opencb/iva-" + image + "/tags" + + " | jq -r .[].name" + + " | grep -v latest" + + " | sort -h" + + " | head")) + if tag >= latest_tag.read(): + print(shell_colors['blue'] + "Pushing opencb/iva-" + image + ":latest" + shell_colors['reset']) + run("docker tag opencb/iva-" + image + ":" + tag + " opencb/iva-" + image + ":latest") + run("docker push opencb/iva-" + image + ":latest") + + +def push(): + print_header('Pushing to DockerHub: ' + ', '.join(images)) + for i in images: + print() + print(shell_colors['blue'] + "Pushing opencb/iva-" + i + ":" + tag + " ..." + shell_colors['reset']) + run("docker push opencb/iva-" + i + ":" + tag) + tag_latest(i) + + +def delete(): + print_header('Deleting from DockerHub: ' + ', '.join(images)) + if args.username is None or args.password is None: + error("Username and password are required") + headers = { + 'Content-Type': 'application/json', + } + data = '{"username": "' + args.username + '", "password": "' + args.password + '"}' + response = requests.post('https://hub.docker.com/v2/users/login/', headers=headers, data=data) + json_response = json.loads(response.content) + if response.status_code != 200: + error("dockerhub login failed") + for i in images: + print() + print(shell_colors['blue'] + 'Deleting image on Docker hub for opencb/iva-' + i + ':' + tag + shell_colors['reset']) + headers = { + 'Authorization': 'JWT ' + json_response["token"] + } + requests.delete('https://hub.docker.com/v2/repositories/opencb/iva-' + i + '/tags/' + tag + '/', headers=headers) + + +## Parse command-line parameters and init basedir, tag and build_folder +args = parser.parse_args() + +# 1. init basedir: root of the iva repo +basedir = str(Path(__file__).resolve().parents[1]) + +# 2. init tag: set tag to default value if not set +if args.tag is not None: + tag = args.tag +else: + tag = package_json()["version"] + +# 3. init build_folder: set build folder to default value if not set +if args.build_folder is not None: + build_folder = args.build_folder +else: + build_folder = basedir + +if not os.path.isdir(build_folder): + error("Build folder does not exist: " + build_folder) + +# 4. init images: get a list with all images +if args.images is None: + images = ["app"] +else: + images = args.images.split(",") + + +## Execute the action +if args.action == "build": + # login(loginRequired=False) + build() +elif args.action == "push": + # login(loginRequired=False) + build() + push() +elif args.action == "delete": + delete() +else: + error("Unknown action: " + args.action) diff --git a/docker/iva-app/Dockerfile b/docker/iva-app/Dockerfile new file mode 100644 index 000000000..e084441fa --- /dev/null +++ b/docker/iva-app/Dockerfile @@ -0,0 +1,25 @@ +FROM httpd:2.4-alpine + +## To run the docker use: +## docker build -f ./docker/Dockerfile -t iva-httpd . +## docker run -dit --name iva -p 81:80 -v [ABS_PATH]/iva/build/conf/:/usr/local/apache2/htdocs/iva/conf opencb/iva-app +## Then open: http://localhost:81/iva + +LABEL org.label-schema.vendor="OpenCB" \ + org.label-schema.name="iva" \ + org.label-schema.url="http://docs.opencb.org/display/iva" \ + org.label-schema.description="An open-source web app for interactive variant analysis" \ + maintainer="Antonio Altamura " \ + org.label-schema.schema-version="1.0" + +## Create and change user +#RUN addgroup -S iva && adduser -S iva -G iva +#USER iva + +## Copy files +COPY ./docker/iva-app/entrypoint.sh /usr/local/bin +COPY ./build/ /usr/local/apache2/htdocs/iva/ + +EXPOSE 80 + +CMD ["httpd-foreground"] diff --git a/docker/iva-app/entrypoint.sh b/docker/iva-app/entrypoint.sh new file mode 100755 index 000000000..2228d582c --- /dev/null +++ b/docker/iva-app/entrypoint.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +echo "total args:" $# +echo "first:" $1 +echo "second:" $2 +#sed -i 's/host:".*"/host: "val" /g' /usr/local/apache2/htdocs/iva/conf/conf.js diff --git a/favicon.ico b/favicon.ico new file mode 100644 index 000000000..97e6fc47d Binary files /dev/null and b/favicon.ico differ diff --git a/lib/jsorolla b/lib/jsorolla index 131698b8b..333668a64 160000 --- a/lib/jsorolla +++ b/lib/jsorolla @@ -1 +1 @@ -Subproject commit 131698b8b0a9c0d2b4c3830143ac30f16368707b +Subproject commit 333668a64645a8e1833058b5d5b006f7b963238f diff --git a/nightwatch.conf.js b/nightwatch.conf.js index c061fd4e3..29498c1f0 100644 --- a/nightwatch.conf.js +++ b/nightwatch.conf.js @@ -13,7 +13,7 @@ const config = { "selenium": { "start_process": true, - "server_path": BIN_PATH + "selenium-server-standalone-3.7.0.jar", + "server_path": BIN_PATH + "selenium-server-standalone-3.141.59.jar", "log_path": "", "port": 4444, "cli_args": { diff --git a/package-lock.json b/package-lock.json new file mode 100644 index 000000000..a98946d06 --- /dev/null +++ b/package-lock.json @@ -0,0 +1,18969 @@ +{ + "name": "iva", + "version": "2.0.0", + "lockfileVersion": 1, + "requires": true, + "dependencies": { + "@babel/code-frame": { + 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"sha512-oVAVsHz6uFrg3XQheFII8ESO2ssAf9luWuAd6Wexsu4F3OtIW0o8IribPXYrD4WC24LWtPrJlGy87y5udK+dxQ==", + "dev": true, + "requires": { + "camelcase": "^5.0.0", + "decamelize": "^1.2.0" + } + }, + "yauzl": { + "version": "2.4.1", + "resolved": "https://registry.npmjs.org/yauzl/-/yauzl-2.4.1.tgz", + "integrity": "sha1-lSj0QtqxsihOWLQ3m7GU4i4MQAU=", + "requires": { + "fd-slicer": "~1.0.1" + } + }, + "yeast": { + "version": "0.1.2", + "resolved": "https://registry.npmjs.org/yeast/-/yeast-0.1.2.tgz", + "integrity": "sha1-AI4G2AlDIMNy28L47XagymyKxBk=", + "dev": true + } + } +} diff --git a/package.json b/package.json index e4d5d868b..20ae6fed6 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "iva", - "version": "1.0.2", + "version": "2.0.0-rc", "description": "IVA description", "repository": { "type": "git", @@ -14,12 +14,20 @@ "copy": "mkdir -p build/vendors && cp -r src/*.html src/conf src/img LICENSE README.md build && cp src/prod/index.html build && ./build-vendors.js", "copy-jsorolla": "mkdir -p build/jsorolla && cd lib/jsorolla && npm run dist && cd ../.. && cp -r lib/jsorolla/dist build/jsorolla", "vulcanize": "node_modules/vulcanize/bin/vulcanize build/iva-app.html > build/iva-app-vulcanize.html && mv build/iva-app-vulcanize.html build/iva-app.html", - "build-iva-app": "./post-replace-iva.js", - "build": "npm run clean && npm run copy && npm run copy-jsorolla && npm run vulcanize && npm run build-iva-app", - "test-e2e": "./node_modules/.bin/nightwatch" + "build-iva-app_old": "./post-replace-iva.js", + "build_old": "npm run clean && npm run copy && npm run copy-jsorolla && npm run vulcanize && npm run build-iva-app", + "test-e2e_old": "./node_modules/.bin/nightwatch", + "serve": "browser-sync start --config bs-config.js", + "prepare": "npx snowpack", + "browser-support": "npx browserslist", + "build": "npx webpack", + "deploy": "npx webpack && ./docker/docker-build.py push", + "e2e": "./credentials.sh npx cypress open" }, "dependencies": { + "@fortawesome/fontawesome-free": "^5.11.2", "@polymer/polymer": "2.6.1", + "@svgdotjs/svg.js": "^3.0.16", "@webcomponents/shadycss": "^1.1.0", "@webcomponents/webcomponentsjs": "^1.1.0", "animate.css": "^3.5.2", @@ -28,37 +36,92 @@ "bootstrap-3-typeahead": "^4.0.2", "bootstrap-colorpicker": "2.3.6", "bootstrap-notify": "git://github.com/mouse0270/bootstrap-notify#master", - "bootstrap-select": "1.12.4", - "bootstrap-table": "1.11.1", + "bootstrap-select": "^1.13.12", + "bootstrap-table": "^1.16.0", "bootstrap-treeview": "1.2.0", "bootstrap-validator": "~0.11.9", "cookies-js": "~1.2.3", + "countup.js": "^2.0.4", "crypto-js": "~3.1.9-1", "eonasdan-bootstrap-datetimepicker": "~4.17.43", "file-saver": "~1.3.2", - "@fortawesome/fontawesome-free": "^5.6.0", - "highcharts": "~4.2.7", + "highcharts": "^8.0.4", "jquery": "~2.2.4", - "jquery.json-viewer": "^1.1.0", + "jquery.json-viewer": "^1.4.0", "jwt-decode": "^2.2.0", + "lit-element": "^2.3.1", + "lodash": "^4.17.19", "moment": "^2.15.1", "qtip2": "~3.0.3", + "sweetalert2": "^9.13.1", + "tokenize2": "^1.3.1", "underscore": "~1.8.3", "urijs": "~1.18.10" }, "devDependencies": { - "eslint": "~4.11.0", - "eslint-plugin-jsx-a11y": "^5.1.1", - "eslint-plugin-import": "^2.7.0", - "eslint-plugin-react": "^7.1.0", + "@babel/core": "^7.9.6", + "@babel/plugin-proposal-class-properties": "^7.8.3", + "@babel/plugin-proposal-export-default-from": "^7.8.3", + "@babel/plugin-transform-runtime": "^7.9.6", + "@babel/preset-env": "^7.9.6", + "@purtuga/esm-webpack-plugin": "^1.2.1", + "@rollup/plugin-alias": "^3.0.1", + "@rollup/plugin-replace": "^2.3.1", + "babel-eslint": "^10.0.3", + "babel-loader": "^8.1.0", + "bower": "*", + "browser-sync": "^2.26.7", + "clean-webpack-plugin": "^3.0.0", + "copy-webpack-plugin": "^5.1.1", "crisper": "~2.1.1", + "css-loader": "^3.4.2", + "cypress": "^4.12.1", + "cypress-wait-until": "^1.7.0", + "eslint": "^6.5.1", + "eslint-config-google": "^0.14.0", + "eslint-plugin-cypress": "^2.10.3", + "eslint-plugin-import": "^2.18.2", + "file-loader": "^5.0.2", + "html-loader": "^0.5.5", + "html-replace-webpack-plugin": "^2.5.6", + "html-webpack-plugin": "^3.2.0", + "jest": "^25.1.0", "js-beautify": "~1.6.4", - "uglify-js": "^2.7.3", - "vulcanize": "~1.16.0", - "xmldom": "0.1.27", - "shelljs": "0.7.8", - "bower": "*", "nightwatch": "^0.9.16", - "selenium-download": "^2.0.10" - } + "null-loader": "^4.0.0", + "rollup-plugin-babel": "^4.3.3", + "rollup-plugin-cleaner": "^1.0.0", + "rollup-plugin-copy": "^3.3.0", + "rollup-plugin-eslint": "^7.0.0", + "rollup-plugin-fill-html": "^1.1.0", + "selenium-download": "^2.0.10", + "shelljs": "0.7.8", + "snowpack": "^1.7.1", + "string-replace-loader": "^2.2.0", + "string-replace-webpack-plugin": "^0.1.3", + "uglify-js": "^3.8.0", + "uglifycss": "0.0.29", + "vulcanize": "~1.16.0", + "webpack": "^4.43.0", + "webpack-cli": "^3.3.11", + "webpack-merge-and-include-globally": "^2.1.24", + "xmldom": "0.1.27" + }, + "snowpack": { + "webDependencies": [ + "lit-element", + "lit-html", + "lit-html/directives/class-map.js", + "lit-html/directives/if-defined.js" + ] + }, + "browserslist": [ + ">1%", + "not dead", + "not ie 11" + ], + "_browserslist": [ + "chrome > 79", + "firefox > 75" + ] } diff --git a/src/about.html b/src/about.html deleted file mode 100644 index ef3b8b2d8..000000000 --- a/src/about.html +++ /dev/null @@ -1,66 +0,0 @@ - - - - - - - diff --git a/src/about.js b/src/about.js new file mode 100644 index 000000000..e7456f5d5 --- /dev/null +++ b/src/about.js @@ -0,0 +1,47 @@ +/** + * Copyright 2015-2019 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +import {LitElement, html} from "/web_modules/lit-element.js"; +import "../lib/jsorolla/src/core/webcomponents/tool-header.js"; + + +export default class AboutWeb extends LitElement { + + constructor() { + super(); + } + + createRenderRoot() { + return this; + } + + render() { + return html` +
+ +
+
+
+
+
+
+
+ `; + } + +} + +customElements.define("about-web", AboutWeb); diff --git a/src/assets.js b/src/assets.js new file mode 100644 index 000000000..01ba8602e --- /dev/null +++ b/src/assets.js @@ -0,0 +1 @@ +console.log("assets entry point"); diff --git a/src/category-page.js b/src/category-page.js new file mode 100644 index 000000000..b0e7f2136 --- /dev/null +++ b/src/category-page.js @@ -0,0 +1,171 @@ +/** + * Copyright 2015-2019 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +import {LitElement, html} from "/web_modules/lit-element.js"; +import Utils from "../lib/jsorolla/src/core/utils.js"; +import UtilsNew from "../lib/jsorolla/src/core/utilsNew.js"; +import "../lib/jsorolla/src/core/webcomponents/tool-header.js"; +import "../lib/jsorolla/src/core/webcomponents/text-icon.js"; + +// TODO the property "disabled" in config have to be renamed in active (boolean for an user or an usergroup) + +export default class CategoryPage extends LitElement { + + constructor() { + super(); + this._init(); + } + + createRenderRoot() { + return this; + } + + static get properties() { + return { + opencgaSession: { + type: Object + }, + config: { + type: Object + } + }; + } + + _init() { + this._prefix = "sf-" + Utils.randomString(6) + "_"; + this._config = {...this.getDefaultConfig(), ...this.config}; + + } + + updated(changedProperties) { + if (changedProperties.has("property")) { + this.propertyObserver(); + } + } + + isVisible(item) { + switch (item.visibility) { + case "public": + return true; + case "private": + return UtilsNew.isNotUndefinedOrNull(this.opencgaSession) && UtilsNew.isNotEmpty(this.opencgaSession.token); + case "none": + default: + return false; + } + } + + renderHTML(html) { + return document.createRange().createContextualFragment(`${html}`); + } + + getDefaultConfig() { + + } + + render() { + return html` + + + + +
+ ${this.config.submenu && this.config.submenu.length ? this.config.submenu.map( (item, i) => item.category ? html` +
${item.title}
+ ` : item.separator ? null : html` + + + ${item.disabled ? html` +
+ +
+ ` : null} + +
+ + +
+
+
${item.title}
+
${this.renderHTML(item.description || "")}
+
+ + ` ) : null} +
+ `; + } + +} + +customElements.define("category-page", CategoryPage); diff --git a/src/client_test.html b/src/client_test.html new file mode 100644 index 000000000..3da60010c --- /dev/null +++ b/src/client_test.html @@ -0,0 +1,60 @@ + + + + + Opencga Client test + + + + + + + + +
+ + +
+ +
+ + +
+
+
+ + + + + + diff --git a/src/conf/config.js b/src/conf/config.js index 4cc29da70..087940615 100644 --- a/src/conf/config.js +++ b/src/conf/config.js @@ -15,15 +15,13 @@ */ const cellbase = { - hosts: [""], - version: "v4", + host: "http://bioinfo.hpc.cam.ac.uk/cellbase", + version: "v4" }; const opencga = { - host: "", - // host: "http://bioinfodev.hpc.cam.ac.uk/opencga-test", - // host: "http://bioinfo.hpc.cam.ac.uk/hgva", - version: "v1", + host: "http://bioinfo.hpc.cam.ac.uk/opencga-prod", + version: "v2", serverVersion: "1.4", // This forces the following projects to be used instead of the user's project @@ -69,697 +67,599 @@ const opencga = { // } // ] // }, - summary: true, + // summary: true, cookie: { - prefix: "iva", - }, + prefix: "iva" + } }; const application = { title: "IVA", - version: "v1.0.2", - logo: "img/opencb-logo.png", + version: "v2.0.0-rc", + logo: "img/iva.svg", + mode: "development", + appConfig: "opencb", + // defaultStudy: "serena@cancer37:test", + // defaultStudy: "emee-glh@cancer:myeloid", // The order, title and nested submenus are respected menu: [ { id: "browser", title: "Variant Browser", + description: "", + icon: "variant_browser.svg", visibility: "public", - }, - { - id: "clinicalAnalysisPortal", - title: "Interpretation Portal", - visibility: "public", - }, - { - id: "beacon", - title: "Beacon", - visibility: "public", - }, - { - id: "facet", - title: "Aggregation Stats", - visibility: "public", - }, - { - id: "case", - title: "Clinical", - visibility: "none", submenu: [ { - id: "clinical", - title: "Clinical (Old)", + id: "browser", + title: "Variant Browser", + acronym: "VB", + description: ` +

Explore all variants identified by the 100,000 Genomes Project

+
    +
  • Rich annotation and links to leading reference databases
    • +
  • Filter by gene, consequence, frequency and much more
    • +
`, visibility: "public", + fa_icon: "fa fa-list", + icon: "variant_browser.svg" }, + // { + // id: "genomeBrowser", + // title: "Genome Browser", + // acronym: "GB", + // description: `
    + //
  • Based on Genome Maps (http://genomemaps.org)
    • + //
  • Smooth, interactive variant visualisation
    • + //
`, + // visibility: "private", + // thumbnail: "screenshot3.png", + // fa_icon: "fa fa-globe-europe", + // icon: "genome_browser.svg" + // + // }, ] }, - { - id: "genomeBrowser", - title: "Genome Browser", - visibility: "private" - }, { id: "analysis", - title: "Analysis (Pending)", - visibility: "private", + title: "Variant Analysis", + description: "", + icon: "aggregation.svg", + visibility: "public", submenu: [ { title: "Summary Stats", category: true, - visibility: "public", + id: "cat-analysis", + visibility: "public" }, { - id: "stats", - title: "Cohort Variant Stats", - visibility: "public", + id: "sample-variant-stats", + title: "Sample Variant Stats", + acronym: "SVS", + description: "", + icon: "", + visibility: "public" }, { - id: "ibs", - title: "IBS/IBD", - visibility: "public", - }, - { - id: "h-w", - title: "Hardy-Weinberg", - visibility: "public", - }, - { - id: "mendel", - title: "Mendel Errors", + id: "cohort-variant-stats", + title: "Cohort Variant Stats", + acronym: "CS", + description: "", + icon: "", visibility: "public", }, + // { + // id: "hw", title: "Hardy-Weinberg", acronym: "HW", + // description: "", + // icon: "", + // visibility: "public" + // }, { separator: true, - visibility: "public", + visibility: "public" }, { - title: "GWAS", + title: "Association Analysis", category: true, - visibility: "public", + id: "cat-analysis", + visibility: "public" }, { - id: "assoc", - title: "Association", - visibility: "public", - }, - { - id: "tdt", - title: "Family-based Association (TDT)", - visibility: "public", + id: "gwas", + title: "Genome-Wide Association Study (GWAS)", + acronym: "GWAS", + description: "Study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait", + icon: "", + visibility: "public" }, + // { + // id: "tdt", + // title: "Family-Based Association (TDT)", + // acronym: "TDT", + // description: "", + // icon: "", + // visibility: "public" + // }, { separator: true, - visibility: "public", + visibility: "public" }, { - title: "Clinical Interpretation Analysis", + title: "Sample Analysis", category: true, - visibility: "public", + id: "cat-analysis", + visibility: "public" }, { - id: "interpretation", - title: "Variant Interpreter", - visibility: "public", + id: "knockout", + title: "Knockout Analysis", + acronym: "KO", + description: "", + icon: "", + visibility: "public" }, { - id: "tiering", - title: "OpenCGA Tiering (Based on GEL Tiering)", - visibility: "public", - }, - { - id: "team", - title: "TEAM", - visibility: "public", + id: "sample-eligibility", + title: "Eligibility Analysis", + description: "", + icon: "", + visibility: "public" }, + { separator: true, - visibility: "public", + visibility: "public" }, { - title: "Other", + title: "Individual Analysis", category: true, - visibility: "public", + id: "cat-analysis", + visibility: "public" }, { - id: "compound", - title: "Compound Heterozygous", - visibility: "public", + id: "inferred-sex", + title: "Sex Inference", + acronym: "SI", + description: "", + icon: "", + visibility: "public" }, { - id: "sampleFacet", - title: "Aggregation Stats", - visibility: "public", + id: "individual-relatedness", + title: "Relatedness", + acronym: "RL", + description: "", + icon: "", + visibility: "public" }, { - id: "exporter", - title: "Exporter", - visibility: "public", - } - ] - }, - { - id: "catalog", - title: "Catalog Metadata", - visibility: "public", - submenu: [ - { - id: "projects", - title: "Projects", - visibility: "public", - }, - { - id: "sample", - title: "Sample View", - visibility: "public", + id: "mendelian-errors", + title: "Mendelian Errors", + acronym: "ME", + description: "", + icon: "", + visibility: "public" }, { separator: true, - visibility: "public", + visibility: "public" }, { - title: "Browsers", + title: "Cancer Analysis", category: true, - visibility: "public", + id: "cat-analysis", + visibility: "public" }, { - id: "files", - title: "File Browser", - visibility: "public", + id: "mutational-signature", + title: "Mutational Signature", + acronym: "SG", + description: "", + icon: "aggregation.svg", + visibility: "public" }, { - id: "samples", - title: "Sample Browser", - visibility: "public", + separator: true, + visibility: "public" }, { - id: "individuals", - title: "Individual Browser", - visibility: "public", + title: "Clinical Interpretation", + category: true, + id: "cat-analysis", + visibility: "public" }, { - id: "families", - title: "Family Browser", - visibility: "public", + id: "rd-tiering", + title: "RD Tiering", + acronym: "RDT", + description: "", + icon: "", + visibility: "public" }, + // { + // id: "team", + // title: "TEAM", + // description: "", + // icon: "", + // visibility: "public" + // }, + // { + // id: "zetta", + // title: "Zetta", + // description: "", + // icon: "", + // visibility: "public" + // }, + // { + // id: "cancer-tiering", + // title: "OpenCGA Cancer Tiering (Based on GEL algorithm)", + // description: "", + // icon: "", + // visibility: "public" + // }, { - id: "cohorts", - title: "Cohort Browser", - visibility: "public", + separator: true, + visibility: "public" }, { - id: "clinicalAnalysis", - title: "Clinical Analysis Browser", - visibility: "public", - } - ], - }, - ], - search: { - placeholder: "Search", - visible: true, - }, - settings: { - visible: false, - }, - about: { - dropdown: true, - links: [ - {id: "code", name: "Source code", url: "https://github.com/opencb/iva", icon: "fa fa-github"}, - {id: "documentation", name: "Documentation", url: "http://docs.opencb.org/display/iva", icon: "fa fa-book"}, - {id: "tutorial", name: "Tutorial", url: "http://docs.opencb.org/display/iva/Tutorials", icon: ""}, - {id: "releases", name: "Releases", url: "https://github.com/opencb/iva/releases", icon: ""}, - {id: "about", name: "About", url: "http://docs.opencb.org/display/iva/About", icon: "fa fa-envelope"}, - {id: "terms", name: "Terms", url: "http://docs.opencb.org/display/iva/About", icon: "fa fa-envelope"}, - {id: "contact", name: "Contact", url: "http://docs.opencb.org/display/iva/About", icon: "fa fa-envelope"}, - {id: "faq", name: "FAQ", url: "http://docs.opencb.org/display/iva/About", icon: "fa fa-envelope"}, - ] - }, - login: { - visible: true, - }, - breadcrumb: { - title: "Projects", - visible: true, - }, - notifyEventMessage: "notifymessage", - session: { - // 60000 ms = 1 min - checkTime: 60000, - // 60000 ms = 1 min - minRemainingTime: 60000, - // 600000 ms = 10 min = 1000(1sec) * 60(60 sec = 1min) * 10(10 min) - maxRemainingTime: 600000 - } -}; - -const sampleBrowser = { - title: "Sample Browser", - showTitle: true, - filter: { - - }, - grid: { - showSelect: true, - } -}; - -const fileBrowser = { - title: "File Browser", - showTitle: true, - filter: { - - }, - grid: { - showSelect: true, - } -}; - - -const cohortBrowser = { - title: "Cohort Browser", - showTitle: true, - filter: { - - }, - grid: { - showSelect: true, - } -}; - -const beacon = { - hosts: [ - "brca-exchange", "cell_lines", "cosmic", "wtsi", "wgs", "ncbi", "ebi", "ega", "broad", "gigascience", - "ucsc", "lovd", "hgmd", "icgc", "sahgp" - ] -}; - -const populationFrequencies = { - // This is based on this figure: - // http://www.dialogues-cns.com/wp-content/uploads/2015/03/DialoguesClinNeurosci-17-69-g001.jpg - color: { - veryRare: "#ff0000", - rare: "#ff8080", - average: "#8080ff", - common: "#0000ff", - unobserved: "black" - }, - tooltip: `1000 Genomes Only considers variants whose observed allelic frequency in the 1000 genomes phase 3 database - is below (or above) the defined value. Genome-wide allelic frequencies were obtained from more than 2.500 genomes.

- gnomAD Genomes Only considers variants whose observed allelic frequency in the gnomAD Genomes database is - below (or above) the defined value. Frequencies were calculated from about 15,000 unrelated individuals`, - studies: [ - { - id: "1kG_phase3", - title: "1000 Genomes", - // tooltip: "Only considers variants whose observed allelic frequency in the 1000 genomes phase 3 database is below (or above) " + - // "the defined value. Genome-wide allelic frequencies were obtained from more than 2.500 genomes.", - populations: [ - { - id: "ALL", title: "All populations [ALL]", + title: "Quality Control", + category: true, + id: "cat-analysis", + visibility: "public" }, { - id: "AFR", title: "African [AFR]", + id: "sample-qc", + title: "Sample Quality Control", + description: "Calculate different genetic checks and metrics and store data in Sample Catalog", + icon: "", + visibility: "public" }, { - id: "AMR", title: "American [AMR]", + id: "individual-qc", + title: "Individual Quality Control", + description: "Calculate different genetic checks and metrics and store data in Individual Catalog", + icon: "", + visibility: "public" }, { - id: "EAS", title: "East Asian [EAS]", + id: "family-qc", + title: "Family Quality Control", + description: "Calculate different genetic checks and metrics and store data in Family Catalog", + icon: "", + visibility: "public" }, { - id: "EUR", title: "European [EUR]", + separator: true, + visibility: "public" }, { - id: "SAS", title: "South Asian [SAS]", - } - ], - }, - { - id: "GNOMAD_GENOMES", - title: "gnomAD Genomes", - // tooltip: "Only considers variants whose observed allelic frequency in the gnomAD Genomes database is below (or above) the " + - // "defined value. Frequencies were calculated from about 15,000 unrelated individuals.", - populations: [ - { - id: "ALL", title: "gnomAD [ALL]", + title: "External Tools", + category: true, + id: "cat-analysis", + visibility: "public" }, { - id: "AFR", title: "African/African American [AFR]", + id: "plink", + title: "Plink", + acronym: "Pl", + description: "", + icon: "", + visibility: "public" }, { - id: "AMR", title: "American [AMR]", + id: "gatk", + title: "GATK", + acronym: "GT", + description: "", + icon: "", + visibility: "public" }, { - id: "EAS", title: "East Asian [EAS]", + separator: true, + visibility: "public" }, { - id: "FIN", title: "Finnish[FIN]", + title: "Other", + category: true, + id: "cat-analysis", + visibility: "public" }, { - id: "NFE", title: "Non-Finnish European [NFE]", + id: "variant-exporter", + title: "Variant Exporter", + acronym: "EX", + description: "", + icon: "", + visibility: "public" }, { - id: "SAS", title: "South Asian [SAS]", + id: "variant-stats-exporter", + title: "Variant Stats Exporter", + acronym: "VSE", + description: "Export variant stats for different cohorts", + icon: "", + visibility: "public", }, - ], + { + id: "beacon", + title: "GA4GH Beacon", + description: "", + icon: "beacon.svg", + visibility: "public" + } + ] }, - ], -}; - -const proteinSubstitutionScores = { - // This is to show the predictions in respective colors - sift: { - deleterious: "red", - tolerated: "green", - }, - polyphen: { - probablyDamaging: "red", - possiblyDamaging: "darkorange", - benign: "green", - unknown: "black", - }, -}; - -const consequenceTypes = { - // This is the impact color. It allows to customise both the impact categories and desired colors - color: { - high: "red", - moderate: "darkorange", - low: "blue", - modifier: "green", - }, - - // Loss-of-function SO terms - lof: ["transcript_ablation", "splice_acceptor_variant", "splice_donor_variant", "stop_gained", "frameshift_variant", - "stop_lost", "start_lost", "transcript_amplification", "inframe_insertion", "inframe_deletion"], - - // 'Title' is optional. if there is not title provided then 'name' will be used. - // There are two more optional properties - 'checked' and 'impact'. They can be set to display them default in web application. - // Similarly 'description' is optional as well. - categories: [ { - title: "Intergenic", - terms: [ + id: "clinical", + title: "Case Interpretation", + description: "", + icon: "interpretation_portal.svg", + visibility: "public", + submenu: [ { - id: "SO:0001631", - name: "upstream_gene_variant", - description: "A sequence variant located 5' of a gene", - impact: "modifier", + title: "Clinical Management", + category: true, + id: "cat-clinical", + visibility: "public" }, { - id: "SO:0001636", - name: "2KB_upstream_variant", - description: "A sequence variant located within 2KB 5' of a gene", - impact: "modifier", + id: "clinicalAnalysisPortal", + title: "Case Portal", + acronym: "", + icon: "", + description: "", + visibility: "public" }, { - id: "SO:0001632", - name: "downstream_gene_variant", - description: "A sequence variant located 3' of a gene", - impact: "modifier", + id: "clinical-analysis-writer", + title: "Create Case", + acronym: "", + icon: "", + description: "", + visibility: "public" }, { - id: "SO:0002083", - name: "2KB_downstream_variant", - description: "A sequence variant located within 2KB 3' of a gene", - impact: "modifier", + separator: true, + visibility: "public" }, { - id: "SO:0001628", - name: "intergenic_variant", - description: "A sequence variant located in the intergenic region, between genes", - impact: "modifier", + title: "Case Interpretation", + category: true, + id: "cat-clinical", + visibility: "public" }, - ], - }, - { - title: "Regulatory", - terms: [ { - id: "SO:0001620", - name: "mature_miRNA_variant", - description: "A transcript variant located with the sequence of the mature miRNA", - impact: "modifier", + id: "interpreter", + title: "Case Interpreter", + acronym: "", + icon: "", + description: "", + visibility: "public" }, // { - // id: "SO:0001894", - // name: "regulatory_region_ablation", - // description: "A feature ablation whereby the deleted region includes a regulatory region", - // impact: "moderate", - // }, - // { - // id: "SO:0001891", - // name: "regulatory_region_amplification", - // description: "A feature amplification of a region containing a regulatory region", - // impact: "modifier", + // separator: true, + // visibility: "public" // }, - { - id: "SO:0001566", - name: "regulatory_region_variant", - description: "A sequence variant located within a regulatory region", - impact: "modifier", - }, - { - id: "SO:0001782", - name: "TF_binding_site_variant", - description: "A sequence variant located within a transcription factor binding site", - impact: "modifier", - }, // { - // id: "SO:0001895", - // name: "TFBS_ablation", - // description: "A feature ablation whereby the deleted region includes a transcription factor binding site", - // impact: "modifier", + // title: "Reported Variants", + // category: true, + // id: "cat-clinical", + // visibility: "public" // }, // { - // id: "SO:0001892", - // name: "TFBS_amplification", - // description: "A feature amplification of a region containing a transcription factor binding site", - // impact: "modifier", - // }, - ], + // id: "cva", + // title: "Clinical Variant Browser", + // acronym: "CVB", + // description: "", + // icon: "", + // visibility: "public" + // } + ] }, { - title: "Coding", - terms: [ + id: "alignment", + title: "Alignment", + description: "", + icon: "alignment.svg", + visibility: "public", + submenu: [ { - id: "SO:0001580", - name: "coding_sequence_variant", - description: "A sequence variant that changes the coding sequence", - impact: "modifier", + title: "Data Management", + category: true, + id: "cat-alignment", + visibility: "public" }, - // { - // id: "SO:0001907", - // name: "feature_elongation", - // description: "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence", - // impact: "modifier", - // }, { - id: "SO:0001906", - name: "feature_truncation", - description: "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence", - impact: "modifier", + id: "alignment-index", + title: "Alignment Index", + description: "Create a .bai index file.", + icon: "", + visibility: "public" }, { - id: "SO:0001589", - name: "frameshift_variant", - description: "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three", - impact: "high", + id: "coverage-index", + title: "Coverage Index", + description: "Precompute coverage in a BigWig file", + icon: "", + visibility: "public" }, { - id: "SO:0001626", - name: "incomplete_terminal_codon_variant", - description: "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed", - impact: "low", + separator: true, + visibility: "public" }, { - id: "SO:0001822", - name: "inframe_deletion", - description: "An inframe non synonymous variant that deletes bases from the coding sequence", - impact: "high", + title: "Summary Stats", + category: true, + id: "cat-alignment", + visibility: "public" }, { - id: "SO:0001821", - name: "inframe_insertion", - description: "An inframe non synonymous variant that inserts bases into in the coding sequence", - impact: "high", + id: "alignment-stats", + title: "Alignment Stats", + description: "Compute BAM stats using samtools", + icon: "", + visibility: "public" }, + ] + }, + { + id: "catalog", + title: "Catalog", + visibility: "public", + icon: "aggregation2.svg", + submenu: [ { - id: "SO:0001650", - name: "inframe_variant", - description: "A sequence variant which does not cause a disruption of the translational reading frame", - impact: "low", + id: "projects", + title: "Projects", + visibility: "public" }, { - id: "SO:0001582", - name: "initiator_codon_variant", - description: "A codon variant that changes at least one base of the first codon of a transcript", - impact: "moderate", + separator: true, + visibility: "public" }, { - id: "SO:0001583", - name: "missense_variant", - description: "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved", - impact: "moderate", + title: "Browsers", + category: true, + id: "cat-catalog", + visibility: "public" }, { - id: "SO:0001621", - name: "NMD_transcript_variant", - description: "A variant in a transcript that is the target of NMD", - impact: "modifier", + id: "files", + title: "File Browser", + visibility: "public" }, - // { - // id: "SO:0001818", - // name: "protein_altering_variant", - // description: "A sequence_variant which is predicted to change the protein encoded in the coding sequence", - // impact: "moderate", - // }, { - id: "SO:0001819", - name: "synonymous_variant", - description: "A sequence variant where there is no resulting change to the encoded amino acid", - impact: "low", + id: "samples", + title: "Sample Browser", + visibility: "public" }, { - id: "SO:0002012", - name: "start_lost", - description: "A codon variant that changes at least one base of the canonical start codon", - impact: "high", + id: "individuals", + title: "Individual Browser", + visibility: "public" }, { - id: "SO:0001587", - name: "stop_gained", - description: "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript", - impact: "high", + id: "families", + title: "Family Browser", + visibility: "public" }, { - id: "SO:0001578", - name: "stop_lost", - description: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript", - impact: "high", + id: "cohorts", + title: "Cohort Browser", + visibility: "public" }, { - id: "SO:0001567", - name: "stop_retained_variant", - description: "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains", - impact: "low", + id: "clinicalAnalysis", + title: "Clinical Analysis Browser", + visibility: "public" }, { - id: "SO:0001590", - name: "terminator_codon_variant", - description: "A sequence variant whereby at least one of the bases in the terminator codon is changed", - impact: "low", - }, - ], + id: "jobs", + title: "Job Browser", + visibility: "public" + } + ] }, + ], + search: { + placeholder: "Search", + visible: false + }, + about: { + dropdown: true, + links: [ + {id: "code", name: "Source code", url: "https://github.com/opencb/iva", icon: "fa fa-code"}, + {id: "documentation", name: "Documentation", url: "http://docs.opencb.org/display/iva", icon: "fa fa-book"}, + {id: "tutorial", name: "Tutorial", url: "http://docs.opencb.org/display/iva/Tutorials", icon: "fa fa-question-circle"}, + {id: "releases", name: "Releases", url: "https://github.com/opencb/iva/releases", icon: "fa fa-archive"}, + {id: "about", name: "About", url: "#about", icon: "fa fa-info-circle"}, + {id: "terms", name: "Terms", url: "#terms", icon: "fa fa-file-alt"}, + {id: "contact", name: "Contact", url: "#contact", icon: "fa fa-envelope"}, + {id: "faq", name: "FAQ", url: "#faq", icon: "fa fa-question"} + ] + }, + login: { + visible: true + }, + breadcrumb: { + title: "Projects", + visible: true + }, + notifyEventMessage: "notifymessage", + session: { + // 60000 ms = 1 min + checkTime: 60000, + // 60000 ms = 1 min + minRemainingTime: 60000, + // 600000 ms = 10 min = 1000(1sec) * 60(60 sec = 1min) * 10(10 min) + maxRemainingTime: 600000 + }, + // Components in the welcome page + welcomePageContent: `

+ Welcome to the IVA tool for whole genome variant analysis.
+ This interactive tool allows finding genes affected by deleterious variants
that segregate along family + pedigrees, case-controls or sporadic samples. +

+
`, + welcomePageFooter: `

`, + components: [ { - title: "Non-coding", - terms: [ - { - id: "SO:0001624", - name: "3_prime_UTR_variant", - description: "A UTR variant of the 3' UTR", - impact: "modifier", - }, - { - id: "SO:0001623", - name: "5_prime_UTR_variant", - description: "A UTR variant of the 5' UTR", - impact: "modifier", - }, - { - id: "SO:0001627", - name: "intron_variant", - description: "A transcript variant occurring within an intron", - impact: "modifier", - }, - { - id: "SO:0001792", - name: "non_coding_transcript_exon_variant", - description: "A sequence variant that changes non-coding exon sequence in a non-coding transcript", - impact: "modifier", - }, - { - id: "SO:0001619", - name: "non_coding_transcript_variant", - description: "A transcript variant of a non coding RNA gene", - impact: "modifier", - }, - ], + id: "browser", + title: "Variant Browser", + visibility: "public", + thumbnail: "variant-browser.png", + fa_icon: "fa fa-list", + icon: "variant_browser.svg", + description: ` +

Explore all variants identified by the 100,000 Genomes Project

+
    +
  • Rich annotation and links to leading reference databases
    • +
  • Filter by gene, consequence, frequency and much more
    • +
` }, { - title: "Splice", - terms: [ - { - id: "SO:0001574", - name: "splice_acceptor_variant", - description: "A splice variant that changes the 2 base region at the 3' end of an intron", - impact: "high", - }, - { - id: "SO:0001575", - name: "splice_donor_variant", - description: "A splice variant that changes the 2 base pair region at the 5' end of an intron", - impact: "high", - }, - { - id: "SO:0001630", - name: "splice_region_variant", - description: "A sequence variant in which a change has occurred within the region of the splice site, either " + - "within 1-3 bases of the exon or 3-8 bases of the intron", - impact: "low", - }, - ], + id: "facet", + title: "Aggregation Stats", + visibility: "public", + thumbnail: "variant-browser_aggregation.png", + fa_icon: "fa fa-chart-bar", + icon: "aggregation2.svg", + description: ` +
    +
  • Filter by gene, consequence, frequency and much more
    • +
  • Add nested facets to generate aggregate statistics
    • +
+

` }, { - id: "SO:0001893", - name: "transcript_ablation", - description: "A feature ablation whereby the deleted region includes a transcript feature", - impact: "high", + id: "clinicalAnalysisPortal", + title: "Interpretation portal", + visibility: "public", + thumbnail: "interpretation_portal.png", + fa_icon: "fa fa-user-md", + icon: "interpretation_portal.svg", + description: ` +
    +
  • Analyse the genomes of participants in the 100,000 Genomes Project
    • +
  • Filter by gene, consequence, frequency and much more
    • +
+ ` }, { - id: "SO:0001889", - name: "transcript_amplification", - description: "A feature amplification of a region containing a transcript", - impact: "high", - }, - ], + id: "beacon", + title: "GA4GH Beacon", + visibility: "public", + thumbnail: "beacon.png", + fa_icon: "fa fa-globe-europe", + icon: "beacon.svg", + description: ` +
    +
  • Federated search from the Global Alliance for Genomics and Health
    • +
  • Find databases that have information about specific variants
    • +
` + } + ] }; -// const DEFAULT_SPECIES = { -// vertebrates: [ -// { -// -// id: "hsapiens", -// scientificName: "Homo sapiens", -// assembly: { -// -// name: "GRCh37", -// ensemblVersion: "75_37", -// -// }, -// assemblies: [ -// { -// -// name: "GRCh37", -// ensemblVersion: "75_37", -// -// }, -// { -// name: "GRCh38", -// ensemblVersion: "79_38", -// }, -// ], -// data: [ -// "genome", -// "gene", -// "variation", -// "regulation", -// "protein", -// "conservation", -// "clinical", -// "gene2disease", -// ], -// }, -// ], -// }; +//export {application, beacon, cellbase, consequenceTypes, opencga, populationFrequencies, proteinSubstitutionScores} diff --git a/src/conf/opencga-clinical-analysis-browser.config.js b/src/conf/opencga-clinical-analysis-browser.config.js new file mode 100644 index 000000000..7873e3d01 --- /dev/null +++ b/src/conf/opencga-clinical-analysis-browser.config.js @@ -0,0 +1,3 @@ +const OpencgaClinicalAnalysisBrowserConfig = { + +}; diff --git a/src/conf/opencga-clinical-analysis-view.settings.js b/src/conf/opencga-clinical-analysis-view.settings.js new file mode 100644 index 000000000..0209fcc41 --- /dev/null +++ b/src/conf/opencga-clinical-analysis-view.settings.js @@ -0,0 +1,3 @@ +const OpencgaClinicalAnalysisViewSettings = { + hiddenFields: [] +} diff --git a/src/conf/opencga-clinical-portal.config.js b/src/conf/opencga-clinical-portal.config.js new file mode 100644 index 000000000..935eaec18 --- /dev/null +++ b/src/conf/opencga-clinical-portal.config.js @@ -0,0 +1,3 @@ +const OpencgaClinicalPortalConfig = { + showCreate: true +}; diff --git a/src/conf/opencga-cohort-browser.config.js b/src/conf/opencga-cohort-browser.config.js new file mode 100644 index 000000000..209b72552 --- /dev/null +++ b/src/conf/opencga-cohort-browser.config.js @@ -0,0 +1,3 @@ +const OpencgaCohortBrowserConfig = { + +}; diff --git a/src/conf/opencga-family-browser.config.js b/src/conf/opencga-family-browser.config.js new file mode 100644 index 000000000..e265ddb8a --- /dev/null +++ b/src/conf/opencga-family-browser.config.js @@ -0,0 +1,3 @@ +const OpencgaFamilyBrowserConfig = { + +}; diff --git a/src/conf/opencga-file-browser.config.js b/src/conf/opencga-file-browser.config.js new file mode 100644 index 000000000..5bc8bfc98 --- /dev/null +++ b/src/conf/opencga-file-browser.config.js @@ -0,0 +1,3 @@ +const OpencgaFileBrowserConfig = { + +}; diff --git a/src/conf/opencga-individual-browser.config.js b/src/conf/opencga-individual-browser.config.js new file mode 100644 index 000000000..2e778cbb5 --- /dev/null +++ b/src/conf/opencga-individual-browser.config.js @@ -0,0 +1,3 @@ +const OpencgaIndividualBrowserConfig = { + +}; diff --git a/src/conf/opencga-jobs-browser.config.js b/src/conf/opencga-jobs-browser.config.js new file mode 100644 index 000000000..a370240d6 --- /dev/null +++ b/src/conf/opencga-jobs-browser.config.js @@ -0,0 +1,3 @@ +const OpencgaJobsBrowserConfig = { + +}; diff --git a/src/conf/opencga-sample-browser.config.js b/src/conf/opencga-sample-browser.config.js new file mode 100644 index 000000000..9ed1a7e20 --- /dev/null +++ b/src/conf/opencga-sample-browser.config.js @@ -0,0 +1,3 @@ +const OpencgaSampleBrowserConfig = { + +}; diff --git a/src/conf/opencga-variant-browser.config.js b/src/conf/opencga-variant-browser.config.js new file mode 100644 index 000000000..f71e460e4 --- /dev/null +++ b/src/conf/opencga-variant-browser.config.js @@ -0,0 +1,3 @@ +const OpencgaVariantBrowserConfig = { + +}; diff --git a/src/conf/opencga-variant-browser.settings.js b/src/conf/opencga-variant-browser.settings.js new file mode 100644 index 000000000..9d90789cc --- /dev/null +++ b/src/conf/opencga-variant-browser.settings.js @@ -0,0 +1,3 @@ +const OpencgaVariantBrowserSettings = { + +}; diff --git a/src/conf/opencga-variant-constants.js b/src/conf/opencga-variant-constants.js new file mode 100644 index 000000000..63ef10176 --- /dev/null +++ b/src/conf/opencga-variant-constants.js @@ -0,0 +1,446 @@ +/** + * Copyright 2015-2019 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + + +// export const biotypes = VARIANT_CONSTANTS.biotypes; + +const biotypes = [ + "3prime_overlapping_ncrna", "IG_C_gene", "IG_C_pseudogene", "IG_D_gene", "IG_J_gene", "IG_J_pseudogene", + "IG_V_gene", "IG_V_pseudogene", "Mt_rRNA", "Mt_tRNA", "TR_C_gene", "TR_D_gene", "TR_J_gene", "TR_J_pseudogene", + "TR_V_gene", "TR_V_pseudogene", "antisense", "lincRNA", "miRNA", "misc_RNA", "non_stop_decay", + "nonsense_mediated_decay", "polymorphic_pseudogene", "processed_pseudogene", "processed_transcript", + "protein_coding", "pseudogene", "rRNA", "retained_intron", "sense_intronic", "sense_overlapping", "snRNA", + "snoRNA", "transcribed_processed_pseudogene", "transcribed_unprocessed_pseudogene", + "translated_processed_pseudogene", "unitary_pseudogene", "unprocessed_pseudogene" +]; + +const types = ["SNV", "INDEL", "CNV", "INSERTION", "DELETION", "MNV"]; + +const consequenceTypes = { + style: { + // This is the impact color. It allows to customise both the impact categories and desired colors + high: "red", + moderate: "darkorange", + low: "blue", + modifier: "green" + }, + + // Loss-of-function SO terms + lof: ["transcript_ablation", "splice_acceptor_variant", "splice_donor_variant", "stop_gained", "frameshift_variant", + "stop_lost", "start_lost", "transcript_amplification", "inframe_insertion", "inframe_deletion"], + + // 'Title' is optional. if there is not title provided then 'name' will be used. + // There are two more optional properties - 'checked' and 'impact'. They can be set to display them default in web application. + // Similarly 'description' is optional as well. + categories: [ + { + title: "Intergenic", + terms: [ + { + id: "SO:0001631", + name: "upstream_gene_variant", + description: "A sequence variant located 5' of a gene", + impact: "modifier" + }, + { + id: "SO:0001636", + name: "2KB_upstream_variant", + description: "A sequence variant located within 2KB 5' of a gene", + impact: "modifier" + }, + { + id: "SO:0001632", + name: "downstream_gene_variant", + description: "A sequence variant located 3' of a gene", + impact: "modifier" + }, + { + id: "SO:0002083", + name: "2KB_downstream_variant", + description: "A sequence variant located within 2KB 3' of a gene", + impact: "modifier" + }, + { + id: "SO:0001628", + name: "intergenic_variant", + description: "A sequence variant located in the intergenic region, between genes", + impact: "modifier" + } + ] + }, + { + title: "Regulatory", + terms: [ + { + id: "SO:0001620", + name: "mature_miRNA_variant", + description: "A transcript variant located with the sequence of the mature miRNA", + impact: "modifier" + }, + // { + // id: "SO:0001894", + // name: "regulatory_region_ablation", + // description: "A feature ablation whereby the deleted region includes a regulatory region", + // impact: "moderate", + // }, + // { + // id: "SO:0001891", + // name: "regulatory_region_amplification", + // description: "A feature amplification of a region containing a regulatory region", + // impact: "modifier", + // }, + { + id: "SO:0001566", + name: "regulatory_region_variant", + description: "A sequence variant located within a regulatory region", + impact: "modifier" + }, + { + id: "SO:0001782", + name: "TF_binding_site_variant", + description: "A sequence variant located within a transcription factor binding site", + impact: "modifier" + } + // { + // id: "SO:0001895", + // name: "TFBS_ablation", + // description: "A feature ablation whereby the deleted region includes a transcription factor binding site", + // impact: "modifier", + // }, + // { + // id: "SO:0001892", + // name: "TFBS_amplification", + // description: "A feature amplification of a region containing a transcription factor binding site", + // impact: "modifier", + // }, + ] + }, + { + title: "Coding", + terms: [ + { + id: "SO:0001580", + name: "coding_sequence_variant", + description: "A sequence variant that changes the coding sequence", + impact: "modifier" + }, + // { + // id: "SO:0001907", + // name: "feature_elongation", + // description: "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence", + // impact: "modifier", + // }, + { + id: "SO:0001906", + name: "feature_truncation", + description: "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence", + impact: "modifier" + }, + { + id: "SO:0001589", + name: "frameshift_variant", + description: "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three", + impact: "high" + }, + { + id: "SO:0001626", + name: "incomplete_terminal_codon_variant", + description: "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed", + impact: "low" + }, + { + id: "SO:0001822", + name: "inframe_deletion", + description: "An inframe non synonymous variant that deletes bases from the coding sequence", + impact: "high" + }, + { + id: "SO:0001821", + name: "inframe_insertion", + description: "An inframe non synonymous variant that inserts bases into in the coding sequence", + impact: "high" + }, + { + id: "SO:0001650", + name: "inframe_variant", + description: "A sequence variant which does not cause a disruption of the translational reading frame", + impact: "low" + }, + { + id: "SO:0001582", + name: "initiator_codon_variant", + description: "A codon variant that changes at least one base of the first codon of a transcript", + impact: "moderate" + }, + { + id: "SO:0001583", + name: "missense_variant", + description: "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved", + impact: "moderate" + }, + { + id: "SO:0001621", + name: "NMD_transcript_variant", + description: "A variant in a transcript that is the target of NMD", + impact: "modifier" + }, + // { + // id: "SO:0001818", + // name: "protein_altering_variant", + // description: "A sequence_variant which is predicted to change the protein encoded in the coding sequence", + // impact: "moderate", + // }, + { + id: "SO:0001819", + name: "synonymous_variant", + description: "A sequence variant where there is no resulting change to the encoded amino acid", + impact: "low" + }, + { + id: "SO:0002012", + name: "start_lost", + description: "A codon variant that changes at least one base of the canonical start codon", + impact: "high" + }, + { + id: "SO:0001587", + name: "stop_gained", + description: "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript", + impact: "high" + }, + { + id: "SO:0001578", + name: "stop_lost", + description: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript", + impact: "high" + }, + { + id: "SO:0001567", + name: "stop_retained_variant", + description: "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains", + impact: "low" + }, + { + id: "SO:0001590", + name: "terminator_codon_variant", + description: "A sequence variant whereby at least one of the bases in the terminator codon is changed", + impact: "low" + } + ] + }, + { + title: "Non-coding", + terms: [ + { + id: "SO:0001624", + name: "3_prime_UTR_variant", + description: "A UTR variant of the 3' UTR", + impact: "modifier" + }, + { + id: "SO:0001623", + name: "5_prime_UTR_variant", + description: "A UTR variant of the 5' UTR", + impact: "modifier" + }, + { + id: "SO:0001627", + name: "intron_variant", + description: "A transcript variant occurring within an intron", + impact: "modifier" + }, + { + id: "SO:0001792", + name: "non_coding_transcript_exon_variant", + description: "A sequence variant that changes non-coding exon sequence in a non-coding transcript", + impact: "modifier" + }, + { + id: "SO:0001619", + name: "non_coding_transcript_variant", + description: "A transcript variant of a non coding RNA gene", + impact: "modifier" + } + ] + }, + { + title: "Splice", + terms: [ + { + id: "SO:0001574", + name: "splice_acceptor_variant", + description: "A splice variant that changes the 2 base region at the 3' end of an intron", + impact: "high" + }, + { + id: "SO:0001575", + name: "splice_donor_variant", + description: "A splice variant that changes the 2 base pair region at the 5' end of an intron", + impact: "high" + }, + { + id: "SO:0001630", + name: "splice_region_variant", + description: "A sequence variant in which a change has occurred within the region of the splice site, either " + + "within 1-3 bases of the exon or 3-8 bases of the intron", + impact: "low" + } + ] + }, + { + id: "SO:0001893", + name: "transcript_ablation", + description: "A feature ablation whereby the deleted region includes a transcript feature", + impact: "high" + }, + { + id: "SO:0001889", + name: "transcript_amplification", + description: "A feature amplification of a region containing a transcript", + impact: "high" + } + ] +}; + +const populationFrequencies = { + style: { + // This is based on this figure: + // http://www.dialogues-cns.com/wp-content/uploads/2015/03/DialoguesClinNeurosci-17-69-g001.jpg + veryRare: "#ff0000", + rare: "#ff8080", + average: "#8080ff", + common: "#0000ff", + unobserved: "black" + }, + studies: [ + { + id: "1kG_phase3", + title: "1000 Genomes", + // tooltip: "Only considers variants whose observed allelic frequency in the 1000 genomes phase 3 database is below (or above) " + + // "the defined value. Genome-wide allelic frequencies were obtained from more than 2.500 genomes.", + populations: [ + { + id: "ALL", title: "All populations [ALL]" + }, + { + id: "AFR", title: "African [AFR]" + }, + { + id: "AMR", title: "American [AMR]" + }, + { + id: "EAS", title: "East Asian [EAS]" + }, + { + id: "EUR", title: "European [EUR]" + }, + { + id: "SAS", title: "South Asian [SAS]" + } + ] + }, + { + id: "GNOMAD_GENOMES", + title: "gnomAD Genomes", + // tooltip: "Only considers variants whose observed allelic frequency in the gnomAD Genomes database is below (or above) the " + + // "defined value. Frequencies were calculated from about 15,000 unrelated individuals.", + populations: [ + { + id: "ALL", title: "gnomAD [ALL]" + }, + { + id: "AFR", title: "African/African American [AFR]" + }, + { + id: "AMR", title: "American [AMR]" + }, + { + id: "EAS", title: "East Asian [EAS]" + }, + { + id: "FIN", title: "Finnish[FIN]" + }, + { + id: "NFE", title: "Non-Finnish European [NFE]" + }, + // { + // id: "SAS", title: "South Asian [SAS]" + // } + ] + } + ] +}; + +const tooltips = { + conservation: "PhyloP scores measure evolutionary conservation at individual alignment sites. The scores " + + "are interpreted as follows compared to the evolution expected under neutral drift: positive scores (max 3.0) mean " + + "conserved positions and negative scores (min -14.0) indicate positive selection. PhyloP scores are useful to " + + "evaluate signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, " + + "or first positions of miRNA target sites).
" + + "PhastCons estimates the probability that each nucleotide belongs to a conserved element, based on " + + "the multiple alignment. The phastCons scores represent probabilities of negative selection and range between 0 " + + "(non-conserved) and 1 (highly conserved).
" + + "Genomic Evolutionary Rate Profiling (GERP) score estimate the level of conservation of positions." + + " Scores ≥ 2 indicate evolutionary constraint to and ≥ 3 indicate purifying selection.", + populationFrequencies: `1000 Genomes Only considers variants whose observed allelic frequency in the 1000 genomes phase 3 database + is below (or above) the defined value. Genome-wide allelic frequencies were obtained from more than 2.500 genomes.

+ gnomAD Genomes Only considers variants whose observed allelic frequency in the gnomAD Genomes database is + below (or above) the defined value. Frequencies were calculated from about 15,000 unrelated individuals`, + proteinSubstitutionScore: "SIFT score: Choose either a Tolerated/Deleterious qualitative score or provide below a " + + "quantitative impact value. SIFT scores <0.05 are considered deleterious. " + + "Polyphen: Choose, either a Benign/probably damaging qualitative score or provide below a " + + "quantitative impact value. Polyphen scores can be Benign (<0.15), Possibly damaging (0.15-0.85) or Damaging (>0.85)", + study: "Only considers variants from the selected studies", + region: "Filter out variants falling outside the genomic interval(s) defined", + feature: "Filter out variants falling outside the genomic features (gene, transcript, SNP, etc.) defined", + diseasePanels: "Filter out variants falling outside the genomic intervals (typically genes) defined by the panel(s) chosen", + biotype: "Filter out variants falling outside the genomic features (gene, transcript, SNP, etc.) defined", + type: "Only considers variants of the selected type", + consequenceTypeSelect: "Filter out variants falling outside the genomic features (gene, transcript, SNP, etc.) defined", + go: "Filter out variants falling outside the genomic features (gene, transcript, SNP, etc.) defined", + hpo: "Filter out variants falling outside the genomic features (gene, transcript, SNP, etc.) defined", + clinvar: "Filter out variants falling outside the genomic features (gene, transcript, SNP, etc.) defined", + fullTextSearch: "Filter out variants falling outside the genomic features (gene, transcript, SNP, etc.) defined", + cadd: "Raw values have relative meaning, with higher values indicating that a variant is more likely to be " + + "simulated (or not observed) and therefore more likely to have deleterious effects. If discovering causal variants " + + "within an individual, or small groups, of exomes or genomes te use of the scaled CADD score is recommended", + cohort: "Filter variants by the cohort alternate allele frequency", + sample: "Filter variants by sample genotypes or mode of inheritance (Compounf Het., de Novo, ...)" +}; + +const beacon = { + hosts: [ + "brca-exchange", "cell_lines", "cosmic", "wtsi", "wgs", "ncbi", "ebi", "ega", "broad", "gigascience", + "ucsc", "lovd", "hgmd", "icgc", "sahgp" + ] +}; + +const proteinSubstitutionScore = { + style: { + // This is to show the predictions in respective colors + sift: { + deleterious: "red", + tolerated: "green" + }, + polyphen: { + "probably damaging": "red", + "possibly damaging": "darkorange", + "benign": "green", + "unknown": "black" + } + } +}; + diff --git a/src/conf/panels.js b/src/conf/panels.js deleted file mode 100644 index bdec7adc2..000000000 --- a/src/conf/panels.js +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/src/conf/tools.js b/src/conf/tools.js index 4cf937eaa..aad4e73c8 100644 --- a/src/conf/tools.js +++ b/src/conf/tools.js @@ -21,12 +21,12 @@ const cohortFileMenu = { id: "cohort", title: "Cohort Alternate Allele Stats", - cohorts: { // organised in projects and studies + cohorts: { // organised in projects and studies reference_grch37: { "1kG_phase3": [ {id: "ALL", name: "All"}, {id: "MXL", name: "Mexican"} ], - EXAC: [ + "EXAC": [ {id: "ALL", name: "All"} ] }, @@ -35,22 +35,28 @@ const cohortFileMenu = { {id: "ALL", name: "ALL"} ] }, - tooltip: "Filter variants by cohort Alternate allele frequency" - } + exomes_grch37: { + corpasome: [ + {id: "ALL", name: "ALL"} + ] + } + }, + tooltip: "Filter variants by cohort Alternate allele frequency" }; +/* MOVED in variant-browser config (TODO copy in interpretation portal) */ const filterMenu = { searchButtonText: "Search", tooltip: { - classes: "qtip-rounded qtip-shadow qtip-custom-class", + classes: "qtip-rounded qtip-shadow qtip-custom-class" // classes: "qtip-dark qtip-rounded qtip-shadow" }, - skipSubsections: [], // controls which subsections are disabled and should not be displayed - sections: [ // sections and subsections, structure and order is respected + skipSubsections: [], // controls which subsections are disabled and should not be displayed + sections: [ // sections and subsections, structure and order is respected { title: "Study and Cohorts", collapsed: false, - subsections: [ + fields: [ { id: "study", title: "Studies Filter", @@ -62,9 +68,9 @@ const filterMenu = { { title: "Genomic", collapsed: true, - subsections: [ + fields: [ { - id: "location", + id: "region", title: "Chromosomal Location", tooltip: "Filter out variants falling outside the genomic interval(s) defined" }, @@ -103,7 +109,7 @@ const filterMenu = { { title: "Population Frequency", collapsed: true, - subsections: [ + fields: [ { id: "populationFrequency", title: "Select Population Frequency", @@ -115,7 +121,7 @@ const filterMenu = { { title: "Consequence Type", collapsed: true, - subsections: [ + fields: [ { id: "consequenceType", title: "Select SO terms", @@ -126,51 +132,51 @@ const filterMenu = { { title: "Deleteriousness", collapsed: true, - subsections: [ + fields: [ { id: "proteinSubstitutionScore", title: "Protein Substitution Score", tooltip: "SIFT score: Choose either a Tolerated/Deleterious qualitative score or provide below a " + - "quantitative impact value. SIFT scores <0.05 are considered deleterious. " + - "Polyphen: Choose, either a Benign/probably damaging qualitative score or provide below a " + - "quantitative impact value. Polyphen scores can be Benign (<0.15), Possibly damaging (0.15-0.85) or Damaging (>0.85)" + "quantitative impact value. SIFT scores <0.05 are considered deleterious. " + + "Polyphen: Choose, either a Benign/probably damaging qualitative score or provide below a " + + "quantitative impact value. Polyphen scores can be Benign (<0.15), Possibly damaging (0.15-0.85) or Damaging (>0.85)" }, { id: "cadd", title: "CADD", tooltip: "Raw values have relative meaning, with higher values indicating that a variant is more likely to be " + - "simulated (or not observed) and therefore more likely to have deleterious effects. If discovering causal variants " + - "within an individual, or small groups, of exomes or genomes te use of the scaled CADD score is recommended" + "simulated (or not observed) and therefore more likely to have deleterious effects. If discovering causal variants " + + "within an individual, or small groups, of exomes or genomes te use of the scaled CADD score is recommended" } ] }, { title: "Conservation", collapsed: true, - subsections: [ + fields: [ { id: "conservation", title: "Conservation Score", tooltip: "PhyloP scores measure evolutionary conservation at individual alignment sites. The scores " + - "are interpreted as follows compared to the evolution expected under neutral drift: positive scores (max 3.0) mean " + - "conserved positions and negative scores (min -14.0) indicate positive selection. PhyloP scores are useful to " + - "evaluate signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, " + - "or first positions of miRNA target sites).
" + - "PhastCons estimates the probability that each nucleotide belongs to a conserved element, based on " + - "the multiple alignment. The phastCons scores represent probabilities of negative selection and range between 0 " + - "(non-conserved) and 1 (highly conserved).
" + - "Genomic Evolutionary Rate Profiling (GERP) score estimate the level of conservation of positions." + - " Scores ≥ 2 indicate evolutionary constraint to and ≥ 3 indicate purifying selection." + "are interpreted as follows compared to the evolution expected under neutral drift: positive scores (max 3.0) mean " + + "conserved positions and negative scores (min -14.0) indicate positive selection. PhyloP scores are useful to " + + "evaluate signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, " + + "or first positions of miRNA target sites).
" + + "PhastCons estimates the probability that each nucleotide belongs to a conserved element, based on " + + "the multiple alignment. The phastCons scores represent probabilities of negative selection and range between 0 " + + "(non-conserved) and 1 (highly conserved).
" + + "Genomic Evolutionary Rate Profiling (GERP) score estimate the level of conservation of positions." + + " Scores ≥ 2 indicate evolutionary constraint to and ≥ 3 indicate purifying selection." } ] }, { title: "Gene Ontology", collapsed: true, - subsections: [ + fields: [ { id: "go", - title: "GO Accessions", + title: "GO Accessions (max. 100 terms)", tooltip: "Filter out variants falling outside the genomic features (gene, transcript, SNP, etc.) defined" } ] @@ -178,7 +184,7 @@ const filterMenu = { { title: "Phenotype-Disease", collapsed: true, - subsections: [ + fields: [ { id: "hpo", title: "HPO Accessions", @@ -201,10 +207,10 @@ const filterMenu = { // Clone menu for interpretation and add clinical section -let clinical = { +/*const clinical = { title: "Sample and File", collapsed: false, - subsections: [ + fields: [ { id: "sample", title: "Sample Genotype", @@ -220,22 +226,27 @@ let clinical = { tooltip: "Filter by sample genotype and mode of inheritance" }, { - id: "file", - title: "File Attributes", - tooltip: "Filter by file attributes such as QUAL and FILTER" + id: "file-qual", + title: "File QUAL Attribute", + tooltip: "Filter by file attribute QUAL" + }, + { + id: "file-pass", + title: "File PASS Attribute", + tooltip: "Filter by file attribute PASS" } ] }; -let interpreterMenu = JSON.parse(JSON.stringify(filterMenu)); -let interpreterSections = interpreterMenu.sections.slice(1); // remove first section "Study and Cohorts" -interpreterSections.unshift(clinical); // insert "Clinical" section +const interpreterMenu = JSON.parse(JSON.stringify(filterMenu)); +const interpreterSections = interpreterMenu.sections.slice(1); // remove first section "Study and Cohorts" +interpreterSections.unshift(clinical); // insert "Clinical" section // interpreterSections[1].subsections.splice(2,1); // remove "Disease Panels" subsection from "Genomic" section -interpreterMenu.sections = interpreterSections; +interpreterMenu.sections = interpreterSections;*/ const tools = { - browser: { + /*browser: { title: "Variant Browser", active: false, showSummary: true, @@ -249,15 +260,31 @@ const tools = { query: { gene: "BRCA2", conservation: "phylop<0.001" - }, + } }, { name: "Example OR11", query: { gene: "OR11H1", conservation: "phylop<=0.001" - }, + } }, + { + name: "Full Example", + query: { + "studies": "exomes_grch37:corpasome;opencga@exomes_grch37:ceph_trio", + "region": "3:444-555", + "xref": "BRCA1,DDEF", + "panel": "Albinism_or_congenital_nystagmus-PanelAppId-511,Amyloidosis-PanelAppId-502", + "biotype": "IG_C_gene,IG_C_pseudogene", + "type": "INDEL", + "ct": "frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,3_prime_UTR_variant,5_prime_UTR_variant,intron_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant", + "populationFrequencyAlt": "1kG_phase3:ALL<1;1kG_phase3:AFR<1;1kG_phase3:AMR<1;1kG_phase3:EAS<1;1kG_phase3:EUR<1;1kG_phase3:SAS<1;GNOMAD_GENOMES:ALL<1;GNOMAD_GENOMES:AFR<1;GNOMAD_GENOMES:AMR<1;GNOMAD_GENOMES:EAS<1;GNOMAD_GENOMES:FIN<1;GNOMAD_GENOMES:NFE<1;GNOMAD_GENOMES:SAS<1", + "protein_substitution": "sift>5,polyphen>4", + "annot-functional-score": "cadd_raw>2,cadd_scaled<4", + "conservation": "phylop>1;phastCons>2;gerp<=3" + } + } ] }, grid: { @@ -275,24 +302,24 @@ const tools = { detail: [ { id: "annotation", - component: "cellbase-variantannotation-view", + // component: "cellbase-variantannotation-view", title: "Advanced Annotation", active: true }, { id: "cohortStats", - component: "opencga-variant-cohort-stats", + // component: "opencga-variant-cohort-stats", title: "Cohort Stats" }, { - id: "samples", - component: "opencga-variant-samples", + id: "sample", + // component: "opencga-variant-sample", title: "Samples" }, { id: "beacon", - component: "variant-beacon-network", - title: "Beacon", + // component: "variant-beacon-network", + title: "Beacon" // Uncomment and edit Beacon hosts to change default hosts // hosts: [ // "brca-exchange", "cell_lines", "cosmic", "wtsi", "wgs", "ncbi", "ebi", "ega", "broad", "gigascience", "ucsc", @@ -301,23 +328,23 @@ const tools = { }, { id: "network", - component: "reactome-variant-network", + // component: "reactome-variant-network", title: "Reactome Pathways" - }, + } // { // id: "template", // component: "opencga-variant-detail-template", // title: "Template" // } ] - }, - interpretation: { - title: "Variant Interpreter", + },*/ + /*"rd-interpreter": { + title: "Variant RD Interpreter", disableSaveInterpretation: false, active: false, showOtherTools: true, filter: { - menu: interpreterMenu, + ...interpreterMenu, lof: ["transcript_ablation", "splice_acceptor_variant", "splice_donor_variant", "stop_gained", "frameshift_variant", "stop_lost", "start_lost", "transcript_amplification", "inframe_insertion", "inframe_deletion"], examples: [ @@ -330,7 +357,7 @@ const tools = { // alternate_frequency: "1kG_phase3:ALL<0.001;GNOMAD_GENOMES:ALL<0.001", ct: "transcript_ablation,splice_acceptor_variant,splice_donor_variant,stop_gained," + "frameshift_variant,stop_lost,start_lost,transcript_amplification,inframe_insertion,inframe_deletion," + - "missense_variant", + "missense_variant" } }, { @@ -380,9 +407,9 @@ const tools = { // }, queryParams: { useSearchIndex: "yes", - skipCount: true, + skipCount: false, approximateCount: true, - approximateCountSamplingSize: 1000, + approximateCountSamplingSize: 500, timeout: 30000 } }, @@ -401,79 +428,30 @@ const tools = { { id: "beacon", component: "variant-beacon-network", - title: "Beacon", + title: "Beacon" // Uncomment and edit Beacon hosts to change default hosts // hosts: [ // "brca-exchange", "cell_lines", "cosmic", "wtsi", "wgs", "ncbi", "ebi", "ega", "broad", "gigascience", "ucsc", // "lovd", "hgmd", "icgc", "sahgp" // ] - }, + } ], css: { style: "font-size: 12px" } - }, - clinicalPortal: { - title: "Clinical Interpretation Portal", + },*/ +/* clinicalPortal: { + title: "Case Portal", reviewCases: { grid: { columns: { - hidden: ["dueDate"] + hidden: [] } } } - }, - facet: { - // title: "Facet Analysis", - active: false, - // fields: [ - // { - // name: "Chromosome", value: "chromosome" - // }, - // { - // name: "Studies", value: "studies" - // }, - // { - // name: "Variant Type", value: "type" - // }, - // { - // name: "Genes", value: "genes" - // }, - // { - // name: "Biotypes", value: "biotypes" - // }, - // { - // name: "Consequence Type", value: "soAcc" - // } - // ], - // ranges: [ - // { - // name: "PhastCons", value: "phastCons" - // }, - // { - // name: "PhyloP", value: "phylop" - // }, - // { - // name: "Gerp", value: "gerp" - // }, - // { - // name: "CADD Raw", value: "caddRaw" - // }, - // { - // name: "CADD Scaled", value: "caddScaled" - // }, - // { - // name: "Sift", value: "sift" - // }, - // { - // name: "Polyphen", value: "polyphen" - // } - // ], - filter: { - menu: Object.assign({}, filterMenu, {skipSubsections: ["sample"]}), - } - }, - panel: { + },*/ + + /*panel: { active: false }, individual: { @@ -481,7 +459,7 @@ const tools = { }, family: { active: false - }, + },*/ gene: { protein: { color: { @@ -492,30 +470,30 @@ const tools = { start_lost: "red", stop_gained: "red", stop_lost: "red", - stop_retained_variant: "red", - }, + stop_retained_variant: "red" + } }, - active: false, + active: false }, - beacon: { + /*beacon: { active: false, hosts: [ "brca-exchange", "cell_lines", "cosmic", "wtsi", "wgs", "ncbi", "ebi", "ega", "broad", "gigascience", "ucsc", "lovd", "hgmd", "icgc", "sahgp" ] - }, - clinical: { + },*/ + /*clinical: { icd10: ICD_10, upload: { - visible: true, + visible: true }, analysis: { - visible: true, + visible: true }, interpretation: { visible: true, algorithms: [ {id: "interactive", title: "Interactive (based on TEAM paper)"}, - {id: "automatic", title: "Automatic", checked: true}, + {id: "automatic", title: "Automatic", checked: true} ], // Interpretation standard config @@ -534,12 +512,12 @@ const tools = { approximateCount: true, skipCount: false, approximateCountSamplingSize: 5000, - timeout: 30000, + timeout: 30000 } } }, report: { - visible: true, + visible: true }, @@ -553,8 +531,8 @@ const tools = { name: "clinical_vs", exclude: [ { - webComponent: "variant-samples-filter", - variables: ["HPO", "diagnosis"], + webComponent: "variant-sample-filter", + variables: ["HPO", "diagnosis"] } ] }, @@ -672,13 +650,13 @@ const tools = { { id: "germline", title: "constitutive (germline)", - checked: true, + checked: true }, { id: "somatic", title: "somatic", - checked: false, - }, + checked: false + } ], active: false, filter: filterMenu, @@ -687,8 +665,8 @@ const tools = { nucleotideGenotype: true, downloadQcSample: false } - }, - genomeBrowser: { - active: false, - } + },*/ + /*genomeBrowser: { + active: false + }*/ }; diff --git a/src/conf/variant-interpreter.config.js b/src/conf/variant-interpreter.config.js new file mode 100644 index 000000000..b6e72c253 --- /dev/null +++ b/src/conf/variant-interpreter.config.js @@ -0,0 +1,51 @@ +const VariantInterpreterConfig = { + title: "Case Interpreter", + icon: "fas fa-user-md", + clinicalAnalysisSelector: true, + tools: [ + { + id: "select", + title: "Case Info", + acronym: "VB", + description: "", + icon: "fa fa-folder-open" + }, + { + id: "qc", + title: "Quality Control", + acronym: "VB", + description: "", + icon: "fa fa-chart-bar" + }, + { + id: "interpretation", + title: "Interpretation Methods", + acronym: "VB", + description: "", + icon: "fa fa-sync", + hidden: true + }, + { + id: "variant-browser", + title: "Sample Variant Browser", + acronym: "VB", + description: "", + icon: "fa fa-search" + }, + { + id: "review", + title: "Interpretation Review", + acronym: "VB", + description: "", + icon: "fa fa-edit" + }, + { + id: "report", + title: "Report", + acronym: "VB", + description: "", + disabled: true, + icon: "fa fa-file-alt" + } + ] +}; diff --git a/src/contact.html b/src/contact.html deleted file mode 100644 index c90a4f539..000000000 --- a/src/contact.html +++ /dev/null @@ -1,66 +0,0 @@ - - - - - - - diff --git a/src/contact.js b/src/contact.js new file mode 100644 index 000000000..f7edb2a4c --- /dev/null +++ b/src/contact.js @@ -0,0 +1,47 @@ +/** + * Copyright 2015-2019 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +import {LitElement, html} from "/web_modules/lit-element.js"; +import "../lib/jsorolla/src/core/webcomponents/tool-header.js"; + + +export default class ContactWeb extends LitElement { + + constructor() { + super(); + } + + createRenderRoot() { + return this; + } + + render() { + return html` +
+ +
+
+
+
+
+
+
+ `; + } + +} + +customElements.define("contact-web", ContactWeb); diff --git a/src/faq.html b/src/faq.html deleted file mode 100644 index 069883184..000000000 --- a/src/faq.html +++ /dev/null @@ -1,66 +0,0 @@ - - - - - - - diff --git a/src/faq.js b/src/faq.js new file mode 100644 index 000000000..f247ea29f --- /dev/null +++ b/src/faq.js @@ -0,0 +1,47 @@ +/** + * Copyright 2015-2019 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +import {LitElement, html} from "/web_modules/lit-element.js"; +import "../lib/jsorolla/src/core/webcomponents/tool-header.js"; + + +export default class FaqWeb extends LitElement { + + constructor() { + super() + } + + createRenderRoot() { + return this; + } + + render() { + return html` +
+ +
+
+
+
+
+
+
+ `; + } + +} + +customElements.define("faq-web",FaqWeb); diff --git a/src/favicon.ico b/src/favicon.ico new file mode 100644 index 000000000..97e6fc47d Binary files /dev/null and b/src/favicon.ico differ diff --git a/src/getting-started.js b/src/getting-started.js new file mode 100644 index 000000000..46bdfe5bb --- /dev/null +++ b/src/getting-started.js @@ -0,0 +1,151 @@ +/** + * Copyright 2015-2019 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +import {LitElement, html} from "/web_modules/lit-element.js"; +import UtilsNew from "../lib/jsorolla/src/core/utilsNew.js"; + +// TODO Video-Tutorial here? + +export default class GettingStarted extends LitElement { + + constructor() { + super(); + this._init(); + } + + createRenderRoot() { + return this; + } + + static get properties() { + return { + version: { + type: String + }, + opencgaSession: { + type: Object + }, + config: { + type: Object + } + }; + } + + _init() { + this._prefix = "gs-" + UtilsNew.randomString(6) + "_"; + } + + openModal(e) { + $("#thumbnail_modal img", this).attr("src", e.target.src); + $("#thumbnail_modal", this).modal("show"); + } + + isVisible(item) { + switch (item.visibility) { + case "public": + return true; + case "private": + return UtilsNew.isNotUndefinedOrNull(this.opencgaSession) && UtilsNew.isNotEmpty(this.opencgaSession.token); + case "none": + default: + return false; + } + } + + renderHTML(html) { + return document.createRange().createContextualFragment(`${html}`); + } + + render() { + return html` + +
+
+
+

Getting started with IVA

+
+
+
+ ${this.config.components.filter(this.isVisible).map( (tool, i) => html` +
+
+
+ +
+
+

${tool.title}

+
${this.renderHTML(tool.description)}
+
+
+
+ `)} +
+
+ + + `; + } + +} + +customElements.define("getting-started", GettingStarted); diff --git a/src/img/Genomics-England-logo-2015-white.png b/src/img/Genomics-England-logo-2015-white.png new file mode 100644 index 000000000..dc8af2160 Binary files /dev/null and b/src/img/Genomics-England-logo-2015-white.png differ diff --git a/src/img/Genomics-England-logo-2015.png b/src/img/Genomics-England-logo-2015.png new file mode 100644 index 000000000..14211e4a4 Binary files /dev/null and b/src/img/Genomics-England-logo-2015.png differ diff --git a/src/img/iva-white.svg b/src/img/iva-white.svg new file mode 100644 index 000000000..9ac146189 --- /dev/null +++ b/src/img/iva-white.svg @@ -0,0 +1,20 @@ + + + + + + + + + + + + + + + diff --git a/src/img/iva.svg b/src/img/iva.svg new file mode 100644 index 000000000..a2ff4d79e --- /dev/null +++ b/src/img/iva.svg @@ -0,0 +1 @@ +IVA diff --git a/src/img/iva2.svg b/src/img/iva2.svg new file mode 100644 index 000000000..3850b0efb --- /dev/null +++ b/src/img/iva2.svg @@ -0,0 +1 @@ +IVA2 diff --git a/src/img/tools/icons/aggregation.svg b/src/img/tools/icons/aggregation.svg new file mode 100644 index 000000000..6c0b3cd41 --- /dev/null +++ b/src/img/tools/icons/aggregation.svg @@ -0,0 +1,25 @@ + + + + + + + + + + + diff --git a/src/img/tools/icons/aggregation2.svg b/src/img/tools/icons/aggregation2.svg new file mode 100644 index 000000000..460c9156d --- /dev/null +++ b/src/img/tools/icons/aggregation2.svg @@ -0,0 +1,16 @@ + + + + + + + + + diff --git a/src/img/tools/icons/alignment.svg b/src/img/tools/icons/alignment.svg new file mode 100644 index 000000000..8efbb5f3b --- /dev/null +++ b/src/img/tools/icons/alignment.svg @@ -0,0 +1,15 @@ + + + + + + + + + + + diff --git a/src/img/tools/icons/beacon.svg b/src/img/tools/icons/beacon.svg new file mode 100644 index 000000000..8c6d7f6bd --- /dev/null +++ b/src/img/tools/icons/beacon.svg @@ -0,0 +1,317 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/img/tools/icons/file-explorer.svg b/src/img/tools/icons/file-explorer.svg new file mode 100644 index 000000000..3ee0b1491 --- /dev/null +++ b/src/img/tools/icons/file-explorer.svg @@ -0,0 +1,28 @@ + + + + + + + + + + + + + diff --git a/src/img/tools/icons/gene-view.svg b/src/img/tools/icons/gene-view.svg new file mode 100644 index 000000000..04b3429a0 --- /dev/null +++ b/src/img/tools/icons/gene-view.svg @@ -0,0 +1,19 @@ + + + + + + + + + + diff --git a/src/img/tools/icons/genome_browser.svg b/src/img/tools/icons/genome_browser.svg new file mode 100644 index 000000000..3f6ec006d --- /dev/null +++ b/src/img/tools/icons/genome_browser.svg @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + + + diff --git a/src/img/tools/icons/interpretation_portal.svg b/src/img/tools/icons/interpretation_portal.svg new file mode 100644 index 000000000..04fe5a6b9 --- /dev/null +++ b/src/img/tools/icons/interpretation_portal.svg @@ -0,0 +1,21 @@ + + + + + + + diff --git a/src/img/tools/icons/variant_browser.svg b/src/img/tools/icons/variant_browser.svg new file mode 100644 index 000000000..2dc14f755 --- /dev/null +++ b/src/img/tools/icons/variant_browser.svg @@ -0,0 +1,26 @@ + + + + + + + + + + + + + diff --git a/src/img/tools/thumbnails/beacon.png b/src/img/tools/thumbnails/beacon.png new file mode 100644 index 000000000..450d33218 Binary files /dev/null and b/src/img/tools/thumbnails/beacon.png differ diff --git a/src/img/tools/thumbnails/interpretation_portal.png b/src/img/tools/thumbnails/interpretation_portal.png new file mode 100644 index 000000000..b7b073f21 Binary files /dev/null and b/src/img/tools/thumbnails/interpretation_portal.png differ diff --git a/src/img/tools/thumbnails/variant-browser.png b/src/img/tools/thumbnails/variant-browser.png new file mode 100644 index 000000000..7361f1235 Binary files /dev/null and b/src/img/tools/thumbnails/variant-browser.png differ diff --git a/src/img/tools/thumbnails/variant-browser_aggregation.png b/src/img/tools/thumbnails/variant-browser_aggregation.png new file mode 100644 index 000000000..49073baad Binary files /dev/null and b/src/img/tools/thumbnails/variant-browser_aggregation.png differ diff --git a/src/index.html b/src/index.html index 07ffc1f39..a7955ebd2 100644 --- a/src/index.html +++ b/src/index.html @@ -1,4 +1,3 @@ - - + @@ -27,7 +26,7 @@ - + @@ -49,60 +48,33 @@ - - + + + + + + + + + + + + + - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + + @@ -112,10 +84,9 @@ - - + @@ -123,50 +94,45 @@ + + + + + + + + + + + + + + + + + + - - + + - - - @@ -174,41 +140,38 @@ - - - - - - - - - - - - - - - + + --> + + + + + + + + + + + + + + - - - + - + diff --git a/src/iva-app.html b/src/iva-app.html deleted file mode 100644 index df4280523..000000000 --- a/src/iva-app.html +++ /dev/null @@ -1,1317 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/iva-app.js b/src/iva-app.js new file mode 100644 index 000000000..894e16036 --- /dev/null +++ b/src/iva-app.js @@ -0,0 +1,1894 @@ +/** + * Copyright 2015-2019 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +// import { LitElement, html } from 'lit-element'; // bare import by name doesn't work yet in browser, +// see: https://www.polymer-project.org/blog/2018-02-26-3.0-preview-paths-and-names +import {LitElement, html} from "/web_modules/lit-element.js"; +import "./welcome.js"; +import "./about.js"; +import "./contact.js"; +import "./faq.js"; +import "./terms.js"; +import "./getting-started.js"; +import "./opencga-breadcrumb.js"; +import "./category-page.js"; +import "./iva-profile.js"; +import "./iva-settings.js"; + +// @dev[jsorolla] +import {OpenCGAClient} from "../lib/jsorolla/src/core/clients/opencga/opencga-client.js"; +import {CellBaseClient} from "../lib/jsorolla/src/core/clients/cellbase/cellbase-client.js"; +import {ReactomeClient} from "../lib/jsorolla/src/core/clients/reactome/reactome-client.js"; + +import UtilsNew from "../lib/jsorolla/src/core/utilsNew.js"; +import NotificationUtils from "../lib/jsorolla/src/core/NotificationUtils.js"; +import "../lib/jsorolla/src/core/webcomponents/clinical/opencga-clinical-analysis-browser.js"; +import {NotificationQueue} from "../lib/jsorolla/src/core/webcomponents/Notification.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/opencga-variant-browser.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/variant-beacon.js"; +import "../lib/jsorolla/src/core/webcomponents/opencga/opencga-gene-view.js"; +import "../lib/jsorolla/src/core/webcomponents/opencga/opencga-transcript-view.js"; +import "../lib/jsorolla/src/core/webcomponents/opencga/opencga-protein-view.js"; +import "../lib/jsorolla/src/core/webcomponents/user/opencga-projects.js"; +import "../lib/jsorolla/src/core/webcomponents/samples/opencga-sample-browser.js"; +import "../lib/jsorolla/src/core/webcomponents/samples/opencga-sample-view.js"; +import "../lib/jsorolla/src/core/webcomponents/samples/sample-variant-stats-browser.js"; +import "../lib/jsorolla/src/core/webcomponents/samples/sample-cancer-variant-stats-browser.js"; +import "../lib/jsorolla/src/core/webcomponents/files/opencga-file-browser.js"; +import "../lib/jsorolla/src/core/webcomponents/family/opencga-family-browser.js"; +import "../lib/jsorolla/src/core/webcomponents/user/opencga-login.js"; +import "../lib/jsorolla/src/core/webcomponents/individual/opencga-individual-browser.js"; +import "../lib/jsorolla/src/core/webcomponents/cohorts/opencga-cohort-browser.js"; +import "../lib/jsorolla/src/core/webcomponents/jobs/opencga-jobs-browser.js"; +import "../lib/jsorolla/src/core/webcomponents/jobs/opencga-jobs-view.js"; +import "../lib/jsorolla/src/core/webcomponents/clinical/opencga-clinical-portal.js"; +import "../lib/jsorolla/src/core/webcomponents/clinical/opencga-clinical-analysis-browser.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-gwas-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-sample-variant-stats-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-cohort-variant-stats-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-mutational-signature-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-sample-elegibility-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-knockout-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-inferred-sex-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-individual-relatedness-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-individual-mendelian-error-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-sample-qc-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-individual-qc-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-family-qc-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-plink-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-gatk-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-variant-exporter-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/analysis/opencga-variant-stats-exporter-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/interpretation/variant-interpreter-browser-rd.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/interpretation/variant-interpreter-browser-cancer.js"; +import "../lib/jsorolla/src/core/webcomponents/variant/interpretation/variant-interpreter.js"; +import "../lib/jsorolla/src/core/webcomponents/clinical/analysis/opencga-rd-tiering-analysis.js"; +import "../lib/jsorolla/src/core/webcomponents/clinical/opencga-clinical-analysis-writer.js"; +import "../lib/jsorolla/src/core/webcomponents/files/opencga-file-manager.js"; +import "../lib/jsorolla/src/core/webcomponents/job-monitor.js"; +//import "../lib/jsorolla/src/core/webcomponents/alignment/analysis/opencga-alignment-stats-analysis.js"; +// /@dev + + +class IvaApp extends LitElement { + + constructor() { + super(); + this._init(); + } + + createRenderRoot() { + return this; + } + + static get properties() { + return { + opencgaSession: { + type: Object + }, + // sample: { + // type: Array + // }, + // studySummaries: { + // type: Array + // }, + // tool: { + // type: String + // }, + // cellbaseClient: { + // type: Object + // }, + config: { + type: Object + } + }; + } + + /** + * This function creates all the initial configuration + * @private + */ + _init() { + + // Create the 'config' , this objects contains all the different configuration + const _config = application; + _config.menu.counter = 0; + _config.cellbase = cellbase; + _config.tools = tools; + _config.opencga = opencga; + // _config.species = DEFAULT_SPECIES; + _config.enabledComponents = {}; + // _config.panelExamples = diseasePanels; + _config.populationFrequencies = populationFrequencies; + _config.proteinSubstitutionScores = proteinSubstitutionScore.style; + _config.consequenceTypes = consequenceTypes; + + // We can customise which components are active by default, this improves the first loading time. + _config.enabledComponents.home = true; + + // Enable tools reading the configuration + for (const tool in _config.tools) { + if (UtilsNew.isNotUndefinedOrNull(_config.tools[tool].active)) { + _config.enabledComponents[tool] = _config.tools[tool].active; + } + } + + // console.log("this.config.enabledComponents",_config.enabledComponents) + const components = [ + "home", + "about", + "contact", + "terms", + "faq", + "gettingstarted", + "login", + "settings", + "account", + "projects", + "file-manager", + //"beacon", + "project", + "sample", + "files", + "samples", + "individuals", + "families", + "cohorts", + "clinicalAnalysis", + "clinicalAnalysisPortal", + "clinicalAnalysisCreator", + "settings", + "gene", + "transcript", + "protein", + "sample-grid", + "browser", + "family", + "cohorts", + "jobs", + "cat-browser", + "cat-analysis", + "cat-clinical", + "cat-catalog", + "cat-alignment", + "cat-ga4gh", + // Sample + "sampleVariantStatsBrowser", + "sampleCancerVariantStatsBrowser", + // Variant + "eligibility", + "gwas", + "sample-variant-stats", + "cohort-variant-stats", + "sample-eligibility", + "knockout", + "inferred-sex", + "mutational-signature", + "individual-relatedness", + "mendelian-errors", + "plink", + "gatk", + "variant-exporter", + "variant-stats-exporter", + // Quality Control + "sample-qc", + "individual-qc", + "family-qc", + // Clinical + "clinical-analysis-writer", + "interpreter", + "rd-tiering", + // Alignment + "alignment-index", + "alignment-stats", + "coverage-index", + "job-view"]; + + for (const component of components) { + _config.enabledComponents[component] = false; + } + + // We set the global Polymer variable, this produces one single event + this.config = _config; + + + // TODO do we need this? + // We deep clone some config sections for having a default initial copy, this allows us to reset config. + /*this.defaultConfig = {}; + if (UtilsNew.isNotUndefined(populationFrequencies)) { + this.defaultConfig.populationFrequencies = JSON.parse(JSON.stringify(populationFrequencies)); + } + if (UtilsNew.isNotUndefined(proteinSubstitutionScore.style)) { + this.defaultConfig.proteinSubstitutionScores = JSON.parse(JSON.stringify(proteinSubstitutionScore.style)); + } + if (UtilsNew.isNotUndefined(consequenceTypes)) { + this.defaultConfig.consequenceTypes = JSON.parse(JSON.stringify(consequenceTypes)); + }*/ + + + // We need to listen to hash fragment changes to update the display and breadcrumb + const _this = this; + window.onhashchange = function(e) { + //e.preventDefault(); + _this.hashFragmentListener(_this); + }; + + // Remember the tool that was previously set + this.tool = window.location.hash.split("/")[0]; + if (UtilsNew.isEmpty(this.tool)) { + this.tool = "#home"; + } + + // Go to the page that tool has + if (window.location.hash !== this.tool) { + window.location.hash = this.tool; + } + + + // Other initialisations + this.icd10 = ICD_10; + this._isBreadcrumbVisible = false; + // This manages the sample selected in each tool for updating the breadcrumb + this.samples = []; + this._samplesPerTool = {}; + + + // TODO remove browserSearchQuery + this.browserSearchQuery = {}; + // keeps track of the executedQueries transitioning from browser tool to facet tool + this.queries = []; + + this.remoteCall = {completed: 0, total: 0}; + globalThis.addEventListener("request", () => { + this.remoteCall.total++; + //console.log("REMOTE CALL!", this.remoteCall.total) + this.requestUpdate(); + }, false); + globalThis.addEventListener("response", () => { + //this.remoteCall.total--; + this.remoteCall.completed++; + if (this.remoteCall.completed >= this.remoteCall.total) { + this.remoteCall.total = 0; + this.remoteCall.completed = 0; + } + //console.log("REMOTE CALL DONE! total", this.remoteCall.total, "completed", this.remoteCall.completed) + this.requestUpdate(); + }, false); + } + + connectedCallback() { + super.connectedCallback(); + new NotificationQueue().setContext(this); + + // Initialise clients and create the session + // this.opencgaClientConfig = new OpenCGAClientConfig(this.config.opencga.host, this.config.opencga.version, true, this.config.opencga.cookie.prefix); + // this.opencgaClientConfig.serverVersion = this.config.opencga.serverVersion; + const sid = Cookies.get(this.config.opencga.cookie.prefix + "_sid"); + const userId = Cookies.get(this.config.opencga.cookie.prefix + "_userId"); + this.opencgaClient = new OpenCGAClient({ + host: this.config.opencga.host, + version: this.config.opencga.version, + token: sid, + userId: userId, + cookies: {active: true, prefix: this.config.opencga.cookie.prefix}, + // TODO remove this soon! + serverVersion: this.config.opencga.serverVersion + }); + + // this.cellBaseClientConfig = new CellBaseClientConfig(this.config.cellbase.hosts, this.config.cellbase.version, "hsapiens"); + this.cellbaseClient = new CellBaseClient({ + hosts: this.config.cellbase.hosts, + version: this.config.cellbase.version, + species: "hsapiens" + }); + + console.log("cellbaseClient iva-app", this.cellbaseClient); + + this.reactomeClient = new ReactomeClient(); + + if (UtilsNew.isNotEmpty(sid)) { // && !this._publicMode + // this.opencgaClient._config.token = sid; + this._createOpenCGASession(); + // This must happen after creating the OpencgaClient + this.checkSessionActive(); + this.intervalCheckSession = setInterval(this.checkSessionActive.bind(this), this.config.session.checkTime); + } else { + this._createOpencgaSessionFromConfig(); + } + } + + updated(changedProperties) { + if (changedProperties.has("opencgaSession")) { + this.opencgaSessionObserver(); + } + } + + + opencgaSessionObserver() { + this.renderHashFragments(); + this.queries = {}; + this.requestUpdate(); + } + + _createOpenCGASession() { + const _this = this; + const opencgaSession = this.opencgaClient.createSession() + .then(function(response) { + console.log("_createOpenCGASession", response); + // check if project array has been defined in the config.js + if (UtilsNew.isNotEmptyArray(_this.config.opencga.projects)) { + // We store the project and study ids the user needs to visualise (defined in the config.js) + const configProjects = {}; + for (let i = 0; i < _this.config.opencga.projects.length; i++) { + configProjects[_this.config.opencga.projects[i].id] = []; + + for (let j = 0; j < _this.config.opencga.projects[i].studies.length; j++) { + configProjects[_this.config.opencga.projects[i].id].push( + _this.config.opencga.projects[i].studies[j].id + ); + } + } + + // We must keep only the projects defined in the configuration file + const activeProjects = []; + for (let i = 0; i < response.projects.length; i++) { + if (response.projects[i].id in configProjects) { + const project = response.projects[i]; + const activeStudies = []; + for (let j = 0; j < project.studies.length; j++) { + const study = project.studies[j]; + if (configProjects[project.id].indexOf(study.id) > -1) { + activeStudies.push(study); + } + } + + // We replace the studies obtained with the ones from the configuration file + project.studies = activeStudies; + activeProjects.push(project); + } + } + + // TODO we must query projects/info URL to get the whole object + response.projects = activeProjects || []; + if (UtilsNew.isNotEmptyArray(response.projects[0].studies)) { + response.project = response.projects[0]; + response.study = response.projects[0].studies[0]; + } + } + + // this forces the observer to be executed. + _this.opencgaSession = Object.assign({}, response); + _this.opencgaSession.mode = _this.config.mode; + // _this.set('config.menu', application.menu.slice()); // Do not remove: this is for refreshing the menu + // TODO check if render works + _this.config.menu = application.menu.slice(); + _this.config = {..._this.config}; + }) + .catch( e => { + console.log("An error occurred creating the OpenCGA session:"); + const restResponse = e.value; + console.error(restResponse); + if(restResponse.getEvents?.("ERROR")?.length) { + const msg = restResponse.getEvents("ERROR").map(error => error.message).join("
"); + new NotificationQueue().push(e.message, msg, "error"); + } else { + new NotificationQueue().push("Server error!", null, "error"); + } + }); + } + + // TODO turn this into a Promise + _createOpencgaSessionFromConfig() { + // Create a private opencga-session to avoid calling to the Observer + const opencgaSession = this.opencgaClient.createAnonymousSession(); + + // If 'config.opencga.anonymous' exists and contains either 'user' or 'projects' + if (UtilsNew.isNotUndefinedOrNull(this.config.opencga.anonymous) && Object.keys(this.config.opencga.anonymous).length > 0) { + // If 'projects' is defined we only load those projects + if (UtilsNew.isNotUndefinedOrNull(this.config.opencga.anonymous.projects)) { + if (this.config.opencga.anonymous.projects.length > 0) { + // TODO we must query projects/info URL to get the whole object + opencgaSession.projects = this.config.opencga.anonymous.projects; + if (UtilsNew.isNotEmptyArray(opencgaSession.projects[0].studies)) { + opencgaSession.project = opencgaSession.projects[0]; + opencgaSession.study = opencgaSession.projects[0].studies[0]; + } + } + + // This triggers the event and call to opencgaSessionObserver + this.opencgaSession = opencgaSession; + } else { + // When no 'projects' is defined we fetch all public projects + if (UtilsNew.isNotUndefinedOrNull(this.config.opencga.anonymous.user)) { + const _this = this; + this.opencgaClient.users().projects(this.config.opencga.anonymous.user, {}) + .then(function(response) { + // _this._setup(_projects); + + opencgaSession.projects = response.response[0].result; + if (UtilsNew.isNotEmptyArray(opencgaSession.projects) && UtilsNew.isNotEmptyArray(opencgaSession.projects[0].studies)) { + // this sets the current active project and study + opencgaSession.project = opencgaSession.projects[0]; + opencgaSession.study = opencgaSession.projects[0].studies[0]; + } + + // This triggers the event and call to opencgaSessionObserver + _this.opencgaSession = opencgaSession; + }) + .catch(function(response) { + console.log("An error when getting projects"); + console.log(response); + }); + } + } + } else { + // This triggers the event and call to opencgaSessionObserver + this.opencgaSession = opencgaSession; + } + } + + onLogin(credentials) { + // This creates a new authenticated opencga-session object + + console.log("iva-app: roger I'm in", credentials); + this.opencgaClient._config.token = credentials.detail.token; + this._createOpenCGASession(); + + if (this.tool === "#login") { + this.tool = "#home"; + } + + // 60000 ms = 1 min. Every 1 min we check if session is close to expire. + this.intervalCheckSession = setInterval(this.checkSessionActive.bind(this), this.config.session.checkTime); + } + + refresh() { + this.opencgaClient.refresh(); + } + + async logout() { + // this delete token in the client and removes the Cookies + this.opencgaClient.logout(); + this._createOpencgaSessionFromConfig(); + + // TODO check if render works + this.config.menu = application.menu.slice(); // Do not remove: this is for refreshing the menu + + this.tool = "#home"; + window.location.hash = "home"; + + window.clearInterval(this.intervalCheckSession); + } + + onUrlChange(e) { + let hashFrag = e.detail.id; + if (UtilsNew.isNotUndefined(this.opencgaSession.project) && UtilsNew.isNotEmpty(this.opencgaSession.project.alias)) { + + hashFrag += "/" + this.opencgaSession.project.alias; + if (UtilsNew.isNotUndefined(this.opencgaSession.study) && UtilsNew.isNotEmpty(this.opencgaSession.study.alias)) { + hashFrag += "/" + this.opencgaSession.study.alias; + } + } + + const myQueryParams = []; + for (const key in e.detail.query) { + myQueryParams.push(key + "=" + e.detail.query[key]); + } + if (myQueryParams.length > 0) { + hashFrag += `?${myQueryParams.join("&")}`; + } + + window.location.hash = hashFrag; + } + + checkSessionActive() { + let _message = ""; + // We check if refresh token has updated session id cookie + // let sid = Cookies.get(this.config.opencga.cookie.prefix + "_sid"); + + if (UtilsNew.isNotUndefinedOrNull(this.opencgaClient._config.token)) { // UtilsNew.isNotEmpty(this.opencgaSession.token) && + // this.token = sid; + const decoded = jwt_decode(this.opencgaClient._config.token); + const currentTime = new Date().getTime(); + const remainingTime = ((decoded.exp * 1000) - currentTime); + // 600000 ms = 10 min = 1000(1sec) * 60(60 sec = 1min) * 10(10 min) + if (remainingTime <= this.config.session.maxRemainingTime && remainingTime >= this.config.session.minRemainingTime) { + const remainingMinutes = Math.floor(remainingTime / this.config.session.minRemainingTime); + + //_message = html`Your session is close to expire. ${remainingMinutes} minutes remaining Click here to refresh ` + new NotificationQueue().pushRemainingTime(remainingMinutes, this.opencgaClient); + + } else { + // TODO remove NotificationUtils + if (remainingTime < this.config.session.minRemainingTime) { + _message = "Your session has expired."; + this.logout(); + window.clearInterval(this.intervalCheckSession); + } else { + if (UtilsNew.isNotUndefinedOrNull(this.notifySession)) { + NotificationUtils.closeNotify(this.notifySession); + } + return; + } + } + } else { + // _message = "Your session has expired."; + // window.clearInterval(this.intervalCheckSession); + } + // delay = 0 to fix the notify until user closes it. + if (UtilsNew.isNotEmpty(_message)) { + this.notifySession = NotificationUtils.showNotify(_message, UtilsNew.MESSAGE_INFO, + {}, { + delay: 0, + onClosed: this.onCloseRefreshNotify.bind(this) + }, this.opencgaClient, this.notifySession); + } + } + + onCloseRefreshNotify() { + delete this.notifySession; + } + + changeTool(e) { + e.preventDefault() + const target = e.currentTarget; + $(".navbar-inverse ul > li", this).removeClass("active"); + $(target).parent("li").addClass("active"); + if ($(target).closest("ul").hasClass("dropdown-menu")) { + $(target).closest("ul").closest("li").addClass("active"); + } + + if (UtilsNew.isNotUndefined(e)) { + e.preventDefault(); // prevents the hash change to "#" and allows to manipulate the hash fragment as needed + } + + if (UtilsNew.isNotUndefined(target) && UtilsNew.isNotUndefined(target.attributes.href)) { + // $(e.target.attributes.href.value).show(); // get the href and use it find which div to show + this.tool = target.attributes.href.value; + if (UtilsNew.isNotUndefinedOrNull(this._samplesPerTool)) { + if (this._samplesPerTool.hasOwnProperty(this.tool.replace("#", ""))) { + this.samples = this._samplesPerTool[this.tool.replace("#", "")]; + } else { + this.samples = []; + } + } + // this.renderBreadcrumb() + } else { + this.tool = "#home"; + } + + this.renderHashFragments(); + } + + renderHashFragments() { + console.log("renderHashFragments - DEBUG", this.tool); + let hashFrag = this.tool; + if (this.opencgaSession?.project?.alias) { + + hashFrag += "/" + this.opencgaSession.project.id; + if (UtilsNew.isNotUndefined(this.opencgaSession.study) && UtilsNew.isNotEmpty(this.opencgaSession.study.alias)) { + hashFrag += "/" + this.opencgaSession.study.id; + } + } + + if (window.location.hash === hashFrag) { + //debugger + this.hashFragmentListener(this); + } else { + //debugger + window.location.hash = hashFrag; + } + + } + + hashFragmentListener(ctx) { + console.log("hashFragmentListener - DEBUG", this.tool); + // Hide all elements + for (const element in this.config.enabledComponents) { + if (UtilsNew.isNotUndefined(this.config.enabledComponents[element])) { + this.config.enabledComponents[element] = false; + } + } + + let arr = window.location.hash.split("/"); + + // TODO evaluate refactor + const [hashTool, hashProject, hashStudy, feature] = arr; + + // Stopping the recursive call + if (hashTool !== this.tool || (this.opencgaSession?.project && hashProject !== this.opencgaSession.project.alias) || + (UtilsNew.isNotUndefined(this.study) && hashStudy !== this.opencgaSession.study.alias)) { + if (arr.length > 1) { + // Field 'project' is being observed, just in case Polymer triggers + // an unnecessary event we can check they are really different + if (ctx.opencgaSession?.project?.alias && ctx.opencgaSession.project.alias !== hashProject) { + ctx.opencgaSession.project.alias = hashProject; + } + if (ctx.opencgaSession?.study && arr.length > 2 && ctx.opencgaSession.study !== hashStudy) { + for (let i = 0; i < ctx.opencgaSession.projects.length; i++) { + if (ctx.opencgaSession.projects[i].name === ctx.opencgaSession.project.name || + ctx.opencgaSession.projects[i].alias === ctx.opencgaSession.project.alias) { + for (let j = 0; j < ctx.opencgaSession.projects[i].studies.length; j++) { + if (ctx.opencgaSession.projects[i].studies[j].name === hashStudy || ctx.opencgaSession.projects[i].studies[j].alias === hashStudy) { + ctx.opencgaSession.study = ctx.opencgaSession.projects[i].studies[j]; + break; + } + } + break; + } + } + } + } + + switch (hashTool) { + case "#browser": + this.browserSearchQuery = Object.assign({}, this.browserSearchQuery); + break; + case "#protein": + break; + case "#interpreter": + this.clinicalAnalysisId = feature; + break; + case "#sampleVariantStatsBrowser": + case "#sampleCancerVariantStatsBrowser": + this.sampleId = feature; + break; + } + + + if (UtilsNew.isNotEmpty(feature)) { + if (hashTool === "#protein") { + ctx.protein = feature; + } else if (feature.startsWith("ENST")) { + ctx.transcript = feature; + } else { + ctx.gene = feature; + } + } + ctx.tool = hashTool; + } + + const searchArr = window.location.hash.split("?"); + if (searchArr.length > 1) { + const search = searchArr[1]; + arr = search.split("&"); + const query = {}; + for (let i = 0; i < arr.length; i++) { + const split = arr[i].split("="); + query[split[0]] = split[1]; + } + this.query = query; + } + + if (UtilsNew.isNotUndefined(this.config.enabledComponents[this.tool.replace("#", "")])) { + //debugger + this.config.enabledComponents[this.tool.replace("#", "")] = true; + } + + //debugger + this.config = {...this.config}; + // TODO quickfix to avoid hash browser scroll + $('body,html').animate({ + scrollTop: 0 + }, 1); + } + + // TODO recheck what's the use for this + refreshConfig(e) { + const colorConfig = e.detail.config; + const _this = this; + for (const key in colorConfig) { + switch (key) { + case "consequenceTypes": + const ctColor = colorConfig[key].color; + for (const impact in ctColor) { + _this.consequenceTypes.color[impact] = ctColor[impact]; + } + const ctModified = Object.assign({}, _this.consequenceTypes); + _this.consequenceTypes = ctModified; + break; + case "proteinSubstitutionScores": + for (const source in colorConfig[key]) { + if (source === "sift") { + const sift = colorConfig[key].sift; + for (const prediction in sift) { + _this.proteinSubstitutionScores.sift[prediction] = sift[prediction]; + } + } else if (source === "polyphen") { + const polyphen = colorConfig[key].polyphen; + for (const pred in polyphen) { + _this.proteinSubstitutionScores.polyphen[pred] = polyphen[pred]; + } + } + } + const pssModified = Object.assign({}, _this.proteinSubstitutionScores); + _this.proteinSubstitutionScores = pssModified; + break; + case "populationFrequencies": + const pfColor = colorConfig[key].color; + for (const i in pfColor) { + _this.populationFrequencies.color[i] = pfColor[i]; + } + const pfModified = Object.assign({}, _this.populationFrequencies); + _this.populationFrequencies = pfModified; + break; + } + } + } + + onStudySelect(e) { + e.preventDefault(); // prevents the hash change to "#" and allows to manipulate the hash fragment as needed + + const [_studyId, _projectId] = [e.target.getAttribute("data-study"), e.target.getAttribute("data-project")]; + let _project, _study; + for (let i = 0; i < this.opencgaSession.projects.length; i++) { + if (this.opencgaSession.projects[i].id === _projectId) { + _project = this.opencgaSession.projects[i]; + for (let j = 0; j < this.opencgaSession.projects[i].studies.length; j++) { + if (this.opencgaSession.projects[i].studies[j].id === _studyId) { + _study = this.opencgaSession.projects[i].studies[j]; + break; + } + } + break; + } + } + this.opencgaSession = {...this.opencgaSession, project: _project, study: _study}; + } + + updateProject(e) { + for (let i = 0; i < this.projects.length; i++) { + if (this.projects[i].name === e.detail.project.name) { // getting the selected project from projects array + this.project = this.projects[i]; + } + } + this.tool = "#project"; + this.renderHashFragments(); + // this.renderBreadcrumb(); + } + + updateStudy(e) { + if (UtilsNew.isNotUndefined(e.detail.project) && UtilsNew.isNotEmpty(e.detail.project.name)) { + this.project = e.detail.project; + } + for (let i = 0; i < this.project.studies.length; i++) { + if (this.project.studies[i].name === e.detail.study.name || this.project.studies[i].alias === e.detail.study.alias) { + this.study = this.project.studies[i]; + } + } + + // TODO: Opencga study will be shown later. For now variant browser is shown when the study changes + // this.tool = "studyInformation"; + this.tool = "#browser"; + this.renderHashFragments(); + // this.renderBreadcrumb(); + } + + onSampleChange(e) { + if (UtilsNew.isNotUndefinedOrNull(this.samples) && UtilsNew.isNotUndefinedOrNull(e.detail)) { + this.samples = e.detail.samples; + this._samplesPerTool[this.tool.replace("#", "")] = this.samples; + // this.renderBreadcrumb(); + } + } + + buildQuery(e) { + const query = {}; + let value = ""; + // TODO searchTextBox is not used anymore. Remove related code + if (UtilsNew.isNotUndefined(e) && UtilsNew.isNotUndefined(e.detail.value)) { + value = e.detail.value; // It takes care of the fired event from welcome.html + } else if (UtilsNew.isNotUndefined(e) && e.keyCode === "13" || UtilsNew.isNotUndefined(e) && e.type === "click") { + value = this.querySelector("#" + searchTextBox).value; // When enter key is pressed or search icon is clicked, it takes the value entered and assign it + } + + if (value !== "") { + if (value.startsWith("rs") || value.split(":").length > 2) { + query.ids = value; + } else if (value.indexOf(":") > -1 && value.indexOf("-") > -1) { + query.region = value; + } else if (value.startsWith("GO:")) { + query["annot-go"] = value; + } else if (value.startsWith("HP:")) { + query["annot-hpo"] = value; + } else if (value.startsWith("ENST")) { + this.transcript = value; + this.tool = "#transcript"; + } else { + this.gene = value.toUpperCase(); + this.tool = "#gene"; + } + + // This query object is built for variant browser. Only when the queries to browser are made, we are setting the tool to browser + if (Object.keys(query).length > 0) { + this._query = query; + this.tool = "#browser"; + } + + this.renderHashFragments(); + // TODO convert in LitElement compliant + this.$.searchTextBox.value = ""; // Empty the value of search text box when search is complete and respective view is loaded + } + } + + onQuickSearch(e) { + const gene = PolymerUtils.getValue("searchTextBox"); + if (UtilsNew.isNotUndefinedOrNull(this.tool)) { + const _query = { + xref: gene + }; + switch (this.tool) { + case "#browser": + window.location.hash = "browser/" + this.opencgaSession.project.id + "/" + this.opencgaSession.study.id; + this.browserSearchQuery = _query; + break; + case "#interpretation": + window.location.hash = "interpretation/" + this.opencgaSession.project.id + "/" + this.opencgaSession.study.id; + this.interpretationSearchQuery = _query; + break; + default: + this.tool = "#browser"; + window.location.hash = "browser/" + this.opencgaSession.project.id + "/" + this.opencgaSession.study.id; + this.browserSearchQuery = _query; + break; + } + } + // debugger + } + + quickSearch(e) { + // debugger + this.tool = "#browser"; + window.location.hash = "browser/" + this.opencgaSession.project.id + "/" + this.opencgaSession.study.id; + // this.browserQuery = {xref: e.detail.value}; + + this.browserSearchQuery = e.detail; + } + + quickFacetSearch(e) { + console.log("IVA-APP quickfacetsearch"); + this.tool = "#facet"; + window.location.hash = "facet/" + this.opencgaSession.project.id + "/" + this.opencgaSession.study.id; + // this.browserQuery = {xref: e.detail.value}; + this.browserSearchQuery = e.detail; + } + + onJobSelected(e) { + console.log("JOB", e.detail) + this.jobSelected = e.detail.jobId; + this.requestUpdate(); + + } + + _isMenuItemVisible(item) { + switch (item.visibility) { + case "public": + return true; + case "private": + return UtilsNew.isNotUndefinedOrNull(this.opencgaSession) && UtilsNew.isNotEmpty(this.opencgaSession.token); + case "none": + default: + return false; + } + } + + //TODO remove + onNotifyMessage(e) { + //NotificationUtils.closeNotify(this.notifySession); + //NotificationUtils.showNotify(e.detail.message, e.detail.type, e.detail.options, e.detail.settings); + new NotificationQueue().push(e.detail.title, e.detail.message, e.detail.type); + } + + // TODO geneSelected() is called by several components but it doesn't exists + + // TODO this should keep in sync the query object between variant-browser and variant-facet + onQueryChange(e) { + console.log("onQueryChange", e); + this.browserSearchQuery = {...e.detail.query}; + } + + + onQueryFilterSearch(e, source) { + // FIXME filters component emits a event containing {detail:{query:Object}} while active-filter emits {detail:{Object}} + // TODO fix active-filters + const q = e.detail.query ? {...e.detail.query} : {...e.detail}; + this.queries[source] = {...q}; + this.queries = {...this.queries}; + //console.log("this.queries",this.queries); + this.requestUpdate(); + } + + onSelectClinicalAnalysis(e) { + this.clinicalAnalysis = e.detail.clinicalAnalysis; + } + + /* Set the width of the side navigation to 250px */ + openNav() { + this.querySelector("#side-nav").style.width = "250px"; + console.log("open"); + } + + /* Set the width of the side navigation to 0 */ + closeNav() { + this.querySelector("#side-nav").style.width = "0"; + } + + toggleSideNav(e) { + e.preventDefault(); + const sidenav = this.querySelector("#side-nav"); + $("#side-nav").toggleClass("active"); + $("#overlay").toggleClass("active"); + } + + isVisible(item) { + switch (item.visibility) { + case "public": + return true; + case "private": + return !!this?.opencgaSession?.token; + case "none": + default: + return false; + } + } + + isLoggedIn() { + return !!this?.opencgaSession?.token; + } + + render() { + return html` + + + + +
+
+ × + +
+ + + + + + + +
+ ${this.config.enabledComponents.home ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents.about ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents.terms ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents.contact ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents.faq ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents.gettingstarted ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents.login ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents.browser ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents.clinicalAnalysisPortal ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents["rd-interpreter"] ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents["cancer-interpreter"] ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents.beacon ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents.genomeBrowser ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents.projects ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents["samples"] ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents.panel ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents.files ? html` +
+ + +
+ ` : null} + + + ${this.config.enabledComponents.gene ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents.sample ? html` +
+ + +
+ ` : null} + + + ${this.config.enabledComponents.transcript ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents.protein ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents.individuals ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents.families ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents.cohorts ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents.clinicalAnalysis ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents["jobs"] ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents["cat-browser"] ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents["cat-analysis"] ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents["cat-clinical"] ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents["cat-catalog"] ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents["cat-alignment"] ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents["cat-ga4gh"] ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents["sampleVariantStatsBrowser"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["sampleCancerVariantStatsBrowser"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["sample-variant-stats"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["cohort-variant-stats"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["eligibility"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["sample-eligibility"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["knockout"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["inferred-sex"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["individual-relatedness"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["mendelian-errors"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["sample-qc"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["individual-qc"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["family-qc"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["plink"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["gatk"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["variant-exporter"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["variant-stats-exporter"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["mutational-signature"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents.gwas ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["rd-tiering"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["clinical-analysis-writer"] ? html` + +
+ + +
+ ` : null} + + ${this.config.enabledComponents.account ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents["file-manager"] ? html` +
+ + +
+ ` : null} + + ${this.config.enabledComponents.settings ? html` +
+ + +
+ ` : null} + + + ${this.config.enabledComponents["interpreter"] ? html` +
+ + +
+ ` : null} + + + ${this.config.enabledComponents["alignment-index"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["coverage-index"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["alignment-stats"] ? html` +
+ +
+ ` : null} + + ${this.config.enabledComponents["job-view"] ? html` + +
+ +
+ ` : null} + +
+ +
+ +`; + + } + +} + +customElements.define("iva-app", IvaApp); diff --git a/src/iva-profile.js b/src/iva-profile.js new file mode 100644 index 000000000..00f9a153e --- /dev/null +++ b/src/iva-profile.js @@ -0,0 +1,224 @@ +/** + * Copyright 2015-2019 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +import {LitElement, html} from "/web_modules/lit-element.js"; +import UtilsNew from "../lib/jsorolla/src/core/utilsNew.js"; +import "../lib/jsorolla/src/core/webcomponents/commons/view/data-form.js"; +import "../lib/jsorolla/src/core/webcomponents/tool-header.js"; + +export default class IvaProfile extends LitElement { + + constructor() { + super(); + this._init(); + } + + createRenderRoot() { + return this; + } + + static get properties() { + return { + opencgaSession: { + type: Object + }, + config: { + type: Object + } + }; + } + + _init() { + + } + + connectedCallback() { + super.connectedCallback(); + this._config = {...this.getDefaultConfig(), ...this.config}; + + } + + updated(changedProperties) { + if (changedProperties.has("property")) { + this.propertyObserver(); + } + if (changedProperties.has("opencgaSession")) { + this.opencgaSessionObserver(); + } + } + + opencgaSessionObserver() { + this.requestUpdate(); + + } + + onFilterChange(field, value) { + console.log("field, value", field, value) + + } + + getDefaultConfig() { + return { + title: "Your profile", + icon: "", + display: { + collapsable: true, + showTitle: false, + labelWidth: 2, + defaultValue: "-" + }, + sections: [ + { + title: "General", + collapsed: false, + elements: [ + { + name: "id", + field: "user.id" + }, + { + name: "Name", + field: "user.name" + }, + { + name: "Organization", + field: "user.organization" + }, + { + name: "Account type", + field: "user.account.type" + }, + { + name: "Status", + field: "user.internal.status", + type: "custom", + display: { + render: field => `${field?.name} (${UtilsNew.dateFormatter(field?.date)})` + } + }, + { + name: "Project and studies", + field: "projects", + type: "table", + display: { + columns: [ + { + name: "Id", + field: "id" + }, + { + name: "Name", + field: "name" + }, + { + name: "Studies", + field: "studies", + type: "custom", + display: { + render: studies => { + return studies.map( study => study.name).join(", ") + } + } + } + ] + } + }, + /*{ + name: "Quota", + field: "quota", + type: "custom", + display: { + render: field => html`${Object.entries(field).map( ([k, v]) => html`${k}:${v}
`)}` + } + }*/ + ] + }, + /*{ + title: "Administration", + collapsed: false, + elements: [ + { + name: "User", + field: "user.id", + type: "custom", + display: { + render: data => { + const config = { + addButton: false, + fields: item => ({ + name: item.id + }), + dataSource: (query, process) => { + this.opencgaSession.opencgaClient.studies().acl(this.opencgaSession.study.fqn).then(restResponse => { + const results = restResponse.getResults(); + process(results.map(config.fields)); + }); + } + }; + return html`` + } + } + }, + { + name: "Permissions", + type: "select", + multiple: true, + defaultValue: ["WRITE_FILES"], + allowedValues: ["CONFIDENTIAL_VARIABLE_SET_ACCESS", "EXECUTION", + {name: "Files", fields: ["WRITE_FILES", "VIEW_FILE_HEADERS", "VIEW_FILE_CONTENTS", "VIEW_FILES", "DELETE_FILES", "DOWNLOAD_FILES", "UPLOAD_FILES", "WRITE_FILE_ANNOTATIONS", "VIEW_FILE_ANNOTATIONS", "DELETE_FILE_ANNOTATIONS"]}, + {name: "Jobs", fields: ["VIEW_JOBS", "WRITE_JOBS", "DELETE_JOBS"]}, + {name: "Sample", fields: ["VIEW_SAMPLES", "WRITE_SAMPLES", "DELETE_SAMPLES", "WRITE_SAMPLE_ANNOTATIONS", "VIEW_SAMPLE_ANNOTATIONS", "DELETE_SAMPLE_ANNOTATIONS"]}, + {name: "Individual", fields: ["VIEW_INDIVIDUALS", "WRITE_INDIVIDUALS", "DELETE_INDIVIDUALS", "WRITE_INDIVIDUAL_ANNOTATIONS", "VIEW_INDIVIDUAL_ANNOTATIONS", "DELETE_INDIVIDUAL_ANNOTATIONS"]}, + {name: "Family", fields: ["VIEW_FAMILIES", "WRITE_FAMILIES", "DELETE_FAMILIES", "WRITE_FAMILY_ANNOTATIONS", "VIEW_FAMILY_ANNOTATIONS", "DELETE_FAMILY_ANNOTATIONS"]}, + {name: "Cohort", fields: ["VIEW_COHORTS", "WRITE_COHORTS", "DELETE_COHORTS", "WRITE_COHORT_ANNOTATIONS", "VIEW_COHORT_ANNOTATIONS", "DELETE_COHORT_ANNOTATIONS"]}, + {name: "Disease Panels", fields: ["VIEW_PANELS", "WRITE_PANELS", "DELETE_PANELS"]}, + {name: "Clinical Analysis", fields: ["VIEW_CLINICAL_ANALYSIS", "WRITE_CLINICAL_ANALYSIS", "DELETE_CLINICAL_ANALYSIS"]}] + }, + { + name: "Study", + field: "study", + type: "select", + allowedValues: ["study1"], + defaultValue: ["study1"], + errorMessage: "No found...", + display: { + width: 9 + } + } + ] + },*/ + + ] + }; + } + + render() { + return html` +
+ +
+
+
+ +
+
+
+
+ `; + } +} + +customElements.define("iva-profile", IvaProfile); diff --git a/src/iva-settings.js b/src/iva-settings.js new file mode 100644 index 000000000..2e75eeb32 --- /dev/null +++ b/src/iva-settings.js @@ -0,0 +1,63 @@ +/** + * Copyright 2015-2019 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +import {LitElement, html} from "/web_modules/lit-element.js"; + +export default class IvaSettings extends LitElement { + + constructor() { + super(); + this._init(); + } + + createRenderRoot() { + return this; + } + + static get properties() { + return { + cellbaseClient: { + type: Object + }, + query: { + type: Object + }, + config: { + type: Object + } + } + } + + _init(){ + this._prefix = "s-"; + } + + updated(changedProperties) { + if(changedProperties.has("property")) { + this.propertyObserver(); + } + } + + render() { + return html` +
+

Settings

+
+ `; + } +} + +customElements.define("iva-settings", IvaSettings); diff --git a/src/jso-styles.html b/src/jso-styles.html deleted file mode 100644 index 1aa30cb59..000000000 --- a/src/jso-styles.html +++ /dev/null @@ -1,99 +0,0 @@ - - - - - diff --git a/src/opencga-breadcrumb.js b/src/opencga-breadcrumb.js new file mode 100644 index 000000000..a686153cd --- /dev/null +++ b/src/opencga-breadcrumb.js @@ -0,0 +1,84 @@ +/** + * Copyright 2015-2019 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +import {LitElement, html} from "/web_modules/lit-element.js"; + +export default class OpencgaBreadcrumb extends LitElement { + + constructor() { + super(); + this._init(); + } + + createRenderRoot() { + return this; + } + + static get properties() { + return { + opencgaSession: { + type: Object + }, + config: { + type: Object + } + }; + } + + _init() { + this._prefix = "bc-"; + } + + render() { + let breadcrumHtml, projectAndStudy; + if (this.opencgaSession.project && this.opencgaSession.project.id) { + let studyId = this.opencgaSession.study ? this.opencgaSession.study.id : "null"; + projectAndStudy = this.opencgaSession.project.id + "/" + studyId; + breadcrumHtml = html` +
  • + ${this.opencgaSession.project.id} +
    • +
  • + ${studyId} +
    • `; + } else { + projectAndStudy = "null"; + breadcrumHtml = html` +
  • + null +
    • `; + } + + return html` + +
    +
      +
    1. + ${this.config.breadcrumb.title}
      2. + + ${breadcrumHtml} +
    +
    + `; + } +} + +customElements.define("opencga-breadcrumb", OpencgaBreadcrumb); diff --git a/src/prod/index.html b/src/prod/index.html deleted file mode 100644 index 467bf67b0..000000000 --- a/src/prod/index.html +++ /dev/null @@ -1,145 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/rollup.html b/src/rollup.html new file mode 100644 index 000000000..7475b69d9 --- /dev/null +++ b/src/rollup.html @@ -0,0 +1,94 @@ + + + + + Title + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/styles/global.css b/src/styles/global.css new file mode 100644 index 000000000..b91c885dd --- /dev/null +++ b/src/styles/global.css @@ -0,0 +1,2063 @@ +:root { + --main-bg-color: #0c2f4c; + --main-bg-color-darker: #09243a; +} + +body, * { + font-family: "Lato", Helvetica, Arial, sans-serif; +} + +p { + margin: 0; +} + +a:link, a:visited { + color: #286090; +} + +a:focus, a:hover { + /*color: #333;*/ + text-decoration: none; +} + +a.disabled, a.disabled:hover { + cursor: not-allowed; + text-decoration: none; +} + +.uppercase { + font-size: 15px; + text-transform: uppercase; + letter-spacing: 2px; +} + +.inline-block { + display: inline-block; +} + +.pad5 { + padding: 5px; +} + +.pad15 { + padding: 15px; +} + +.mag5 { + margin: 5px; +} + +input[type="text"] { + width: 100%; +} + +.v-space { + height: 100px; +} + +.badge {; + margin: 0 1px; + background: #337ab7; +} + +.badge .close-icon { + cursor: pointer; +} + +/* badge style from bootstrap 4 */ +.badge-info { + color: #fff; + background-color: #17a2b8; +} + +.badge-success { + color: #fff; + background-color: #28a745; +} + +.badge-secondary { + color: #fff; + background-color: #6c757d; +} + +.badge-warning { + color: #212529; + background-color: #ffc107; +} + +.badge-danger { + color: #fff; + background-color: #dc3545; +} + +.badge-light { + color: #ffffff; + background-color: #a5a5a5; +} + +.badge-dark { + color: #fff; + background-color: #343a40; +} + +.align-middle { + vertical-align: middle; +} + +.break-word { + word-break: break-all; +} + +.multi-line { + white-space: normal; +} + +.one-line { + white-space: nowrap !important; +} + +.force-text-left { + text-align: left !important; +} + +.bg-white { + background: white !important; +} +/* TODO input material effect continue*/ +.input { + border: 0; + transition: 0.5s; + border-bottom: 1px solid #ccc; + box-shadow: 0px 0px 4px rgba(0, 0, 0, .1); +} + +.input:focus { + transition: 0.5s; + border-radius: 0; + border-bottom: 1px solid rgba(12, 47, 76); + box-shadow: 0px 0px 4px rgba(0, 0, 0, .3); +} + +#welcome-page-title { + font-size: 10px; + text-align: center; + letter-spacing: -20px; + position: relative; + margin-top: 40px; +} + +#welcome-page-title .iva-logo{ + +} + +.company-logo { + padding: 1px; +} +.company-logo img{ + height: 45px; +} + +.iva-logo img { + width: 35em; +} + +.iva-logo span.subtitle { + font-size: 2em; + display: block; + font-variant: all-small-caps; + letter-spacing: .3em; + font-weight: bold; +} + +.iva-logo .version { + font-size: 2.5em; + font-variant: all-small-caps; + display: inline-block; + vertical-align: top; + letter-spacing: 0px; + margin: 0px 0 0 10px; + position: absolute; +} + +.iva-logo .bracket { + font-size: 1em; + color: black; + font-weight: bold; + margin: 0 4px; +} + +.iva-logo-white { + padding: 10px; +} + +.iva-logo-white img{ + width: 70px; + display: inline-block; +} + +.iva-logo-white sup{ + font-variant: all-small-caps; + top: -1em; + text-transform: uppercase; + font-size: .6em; +} + +/* plain text in form-group (instead of input text) */ +.form-group .text { + padding-top: 7px; + margin-bottom: 0; +} + +/* bringing bootstrap dropdown (opencga-active-filters) above bootstraptable */ +.dropdown-menu { + z-index: 1001; +} + +.main-navbar { + margin: 0; + border-radius: 0px; +} + +.main-navbar .nav-item-category{ + font-weight: bold; +} + +.main-navbar .separator { + background: rgba(255, 255, 255, 0.3); + width: 1px; + height: 32px; + margin: 9px; +} + +/*********** bootstrap override *****************/ +@media (min-width: 576px) { + .modal-lg { + width: 100%; + } +} + +@media (min-width: 768px) { + .modal-lg { + width: 60%; + } +} + +.nav-tabs > li.active > a { + border-top: 1px solid var(--main-bg-color) !important; +} + +.study-switcher { + display: flex !important; + justify-content: center; + align-items: center; + padding: 0; + height: 50px; +} + +.study-switcher p{ + padding: 0; + line-height: 1.1em; +} + +.study-switcher p.project-name { + color: #afafaf; +} + +.study-switcher p.study-id{ + font-size: 1.2em; + font-weight: bold; +} + +.study-switcher .caret { + /*align-self: flex-end;*/ +} + +/*********** bootstrap tabs customisation *****************/ +.table>tbody>tr.success>td { + /*background-color: #d0e9c6 !important;*/ +} + +/* Bootstrap panel and button overrides */ +h3.page-title { + margin: 10px 10px 10px 15px; + font-size: 2em; +} + +.panel-title { + font-size: 1.2em; + text-transform: uppercase; + letter-spacing: 2px; +} + +.panel-default > .panel-heading { + background: none; +} + +.panel-default > .panel-heading + .panel-collapse > .panel-body { + border: none; +} + +.btn-primary.ripple { + color: white; +} + +.btn-group .ripple { + margin: 0; +} +.btn-group>.btn+.dropdown-toggle { + padding-bottom: 9px; +} + +/*.btn-group .btn:first-child { + clip-path: inset(-17px 0px -17px -17px); +} + +.btn-group .btn:last-child { + clip-path: inset(-17px -17px -17px 0px); +}*/ + +.shadow { + -webkit-box-shadow: 0 2px 5px 0 rgba(0, 0, 0, 0.16), 0 2px 10px 0 rgba(0, 0, 0, 0.12); + box-shadow: 0 2px 5px 0 rgba(0, 0, 0, 0.16), 0 2px 10px 0 rgba(0, 0, 0, 0.12); + -webkit-transition: color 0.15s ease-in-out, background-color 0.15s ease-in-out, border-color 0.15s ease-in-out, -webkit-box-shadow 0.15s ease-in-out; + transition: color 0.15s ease-in-out, background-color 0.15s ease-in-out, border-color 0.15s ease-in-out, box-shadow 0.15s ease-in-out, -webkit-box-shadow 0.15s ease-in-out; +} + +.shadow-lg { + -webkit-box-shadow: 0 0 16px rgba(0, 0, 0, .28); + box-shadow: 0 0 16px rgba(0, 0, 0, .28); +} + +.shadow-sm { + -webkit-box-shadow: 0 2px 2px 0 rgba(0, 0, 0, .16), 0 0 2px 0 rgba(0, 0, 0, .12); + box-shadow: 0 2px 2px 0 rgba(0, 0, 0, .16), 0 0 2px 0 rgba(0, 0, 0, .12); +} + +.no-shadow { + box-shadow: none !important; +} + +.ripple { + margin: 0 .375rem; /* visual issues with toggle-switch*/ + margin: 0; + text-transform: uppercase; + word-wrap: break-word; + white-space: normal; + cursor: pointer; + border: 0; + border-radius: 0px; + -webkit-box-shadow: 0 2px 5px 0 rgba(0, 0, 0, 0.16), 0 2px 10px 0 rgba(0, 0, 0, 0.12); + box-shadow: 0 2px 5px 0 rgba(0, 0, 0, 0.16), 0 2px 10px 0 rgba(0, 0, 0, 0.12); + -webkit-transition: color 0.15s ease-in-out, background-color 0.15s ease-in-out, border-color 0.15s ease-in-out, -webkit-box-shadow 0.15s ease-in-out; + transition: color 0.15s ease-in-out, background-color 0.15s ease-in-out, border-color 0.15s ease-in-out, box-shadow 0.15s ease-in-out, -webkit-box-shadow 0.15s ease-in-out; + padding: 0.8rem 2.2rem; + position: relative; + overflow: hidden; + transform: translate3d(0, 0, 0); +} + +.ripple:hover { + outline: 0; + -webkit-box-shadow: 0 4px 8px 0 rgba(0, 0, 0, 0.18), 0 3px 10px 0 rgba(0, 0, 0, 0.15); + box-shadow: 0 4px 8px 0 rgba(0, 0, 0, 0.18), 0 3px 10px 0 rgba(0, 0, 0, 0.15); + +} + +.ripple:active, .ripple:focus { + -webkit-box-shadow: 0 5px 11px 0 rgba(0, 0, 0, 0.18), 0 4px 15px 0 rgba(0, 0, 0, 0.15); + box-shadow: 0 5px 11px 0 rgba(0, 0, 0, 0.18), 0 4px 15px 0 rgba(0, 0, 0, 0.15); +} + +.ripple:after { + content: ""; + display: block; + position: absolute; + width: 100%; + height: 100%; + top: 0; + left: 0; + pointer-events: none; + background-image: radial-gradient(circle, #000 10%, transparent 10.01%); + background-repeat: no-repeat; + background-position: 50%; + transform: scale(10, 10); + opacity: 0; + transition: transform .4s, opacity .6s; +} + +.ripple:active:after { + transform: scale(0, 0); + opacity: .2; + transition: 0s; +} +/* TODO evaluate remove .ripple-disabled */ +.ripple-disabled:after { + display: none; +} + +.ripple-disabled, +.ripple-disabled:active, +.ripple-disabled:hover, +.ripple-disabled:focus, +.btn-primary.ripple-disabled:active:hover, +.ripple[disabled] { + -webkit-box-shadow: none; + box-shadow: none; + cursor: default; + outline: 0; +} + +.ripple[disabled] { + cursor: not-allowed; +} + +.btn-primary.ripple-disabled:hover, +.btn-primary.ripple-disabled:active:hover { + background: #337ab7; +} + +.ripple.no-transform { + text-transform: none; +} + +.ripple.btn-small { + padding: 0.8rem 1.3rem; + font-size: .8em; +} + +.button-wrapper { + padding: 15px 0; +} + +/*********** bootstrap tabs customisation *****************/ +.nav-tabs.nav-center { + text-align: center; +} + +.nav-tabs.nav-center > li { + float: none; + display: inline-block; +} + +.content-tab-wrapper > .content-tab:not(.active) { + display: none; +} + +/*********** main view tabs *****************/ +.main-view .content-tab { + display: none; +} + +.main-view .content-tab.active { + display: block; +} + +/********** browser components *************/ +.page-title { + background-color: #f5f5f5; + margin: 0 -15px 20px -15px; + padding: 10px 30px 10px 10px; +} + +.page-title.no-background { + background: none; +} + +.page-title h2 { + text-transform: uppercase; + letter-spacing: .2em; + margin: 0; + padding: 8px; + text-decoration: none; + color: var(--main-bg-color);; + display: block; + transition: 0.3s; + font-size: 2em; +} + +.page-title h2 .inverse, +.detail-tabs h3 .inverse { + background: var(--main-bg-color); + color: white; + display: inline-block; + padding: 4px 10px; + margin: 0 0 0 10px; +} + +.page-title img, +.page-title i { + width: 40px; + font-size: 40px; + vertical-align: middle; +} + +.variant-interpreter-interpretation > tool-header > .page-title { + height: 5em; +} + +.variant-interpreter-interpretation > tool-header > .page-title h2 { + float: left; +} + +.variant-interpreter-interpretation > tool-header > .page-title .page-title-right i{ + font-size: 14px; +} +.variant-interpreter-interpretation .page-title-right { + padding: 7px; +} +.variant-interpreter-interpretation .page-title-right a, +.variant-interpreter-interpretation .page-title-right button{ + background: var(--main-bg-color); +} + +.page-title-right { + float: right; +} + +.search-button-wrapper { + text-align: center; + margin: 0 0 20px 0; +} + +.search-button-wrapper i { + padding: 0 5px; +} + +.full-width { + width: 100%; +} + +.content-pills { + margin: 0 0 20px 0; +} + +/********** active-filters *************/ +.active-filter-button:hover { + text-decoration: line-through; +} + +.active-filter-button[disabled]:hover { + text-decoration: none; +} + +.facet-wrapper { + margin: 10px 0 0 0; +} + +.double-arrow { + transform: rotate(90deg); + width: 60px; + display: block; + margin: 0 auto; + height: 60px; +} + +.double-arrow-wrapper { + display: flex; + margin: 5px 0; +} + +.button-list{ + padding-left: 20px; + display: inline-block; +} + +.active-filter-label{ + display: inline-block; + font-size: 15px; + text-transform: uppercase; + letter-spacing: 2px; + height: 34px; + line-height: 34px; + margin: 0; + padding-right: 10px; +} + +.lhs { + display: inline-block; + padding: 5px 0; +} + +.lhs .btn-group { + padding: 2px 0; +} + +.rhs { + float: right; + padding:5px +} + +.rhs .dropdown { + display: inline-block; +} + +.filter-warning { + padding: 10px; + margin-bottom: 10px; + display: none; +} + +.left-menu-tabs { + font-size: 1.2em; + font-weight: bold; + margin-bottom: 20px; +} + +.left-menu-tabs li { + width: 50%; +} + +.facet-selector { + margin-top: 15px; +} + +.facet-list-container { + margin-top: 15px; + padding-top: 15px; + border-top: 1px solid rgba(221, 221, 221, 1); +} + +.facet-box:not(:first-child) { + border-top: 1px solid rgba(221, 221, 221, 1); +} + +.facet-row { + margin: 0; +} + +.facet-row > div { + padding: 3px; + margin: 0; +} + +.facet-row .nested { + /*padding: 15px;*/ +} + +.panel-title p { + margin: 0; +} + +.facetResultsDiv { + padding-top: 20px; +} + +.content-pills { + margin: 0 0 20px 0; +} + +.icon-padding { + padding-right: 5px; +} + +.or-text { + text-align: center; +} + +.facet-list .alert-info small { + display: block; +} + +/********** toggle-switch plugin override ************/ +.switch-toggle-wrapper { + margin: 10px 0; +} + +.switch-toggle { + background: #f3f3f3; +} + +.switch-toggle.text-white input[disabled] + label { + color: #bfbfbf; +} + +.switch-toggle.text-white input + label { + color: #c7c7c7; +} + +.switch-toggle input[disabled] ~ a.btn { + background: #e4e4e4; + -webkit-box-shadow: none; + box-shadow: none; +} + +/* switch-toggle BUG trying to style the :checked input only. A checked disabled radio input remains grey after you enable it (e.g.Study-filter). Same problem in somatic-filter too on "None" value */ +.switch-toggle input:checked + label { + color: white +} + +/********** waffle icon ************/ +a#waffle-icon-wrapper { + padding: 10px; +} + +#waffle-icon { + background-image: url("data:image/svg+xml;base64, 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"); + background-size: cover; + width: 30px; + height: 30px; +} + +/********** sidenav ************/ +.ms-sidenav { + position: absolute; + z-index: 1000000; + background-color: #fff; + width: 320px; + min-width: 320px; + max-width: 320px; + box-sizing: border-box; + outline: none; + overflow-y: auto; + visibility: visible; + pointer-events: auto; + top: 0; + left: 0; + right: auto; + height: 100vh; + -webkit-transform-origin: top left; + -ms-transform-origin: top left; + transform-origin: top left; + -webkit-animation-duration: .18s; + animation-duration: .18s; + -webkit-animation-timing-function: ease; + animation-timing-function: ease; + -webkit-animation-name: slideOutFrames; + animation-name: slideOutFrames + +} + +.ms-sidenav.active { + -webkit-animation-name: slideInFrames; + animation-name: slideInFrames +} + +@-webkit-keyframes slideInFrames { + 0% { + opacity: 0; + -webkit-transform: scale(.95); + -ms-transform: scale(.95); + transform: scale(.95) + } + to { + opacity: 1; + -webkit-transform: scale(1); + -ms-transform: scale(1); + transform: scale(1) + } +} + +@keyframes slideInFrames { + 0% { + opacity: 0; + -webkit-transform: scale(.95); + -ms-transform: scale(.95); + transform: scale(.95) + } + to { + opacity: 1; + -webkit-transform: scale(1); + -ms-transform: scale(1); + transform: scale(1) + } +} + +@-webkit-keyframes slideOutFrames { + 0% { + visibility: visible; + opacity: 1; + -webkit-transform: scale(1); + -ms-transform: scale(1); + transform: scale(1) + } + to { + visibility: hidden; + opacity: 0; + -webkit-transform: scale(.95); + -ms-transform: scale(.95); + transform: scale(.95) + } +} + +@keyframes slideOutFrames { + 0% { + visibility: visible; + opacity: 1; + -webkit-transform: scale(1); + -ms-transform: scale(1); + transform: scale(1) + } + to { + visibility: hidden; + opacity: 0; + -webkit-transform: scale(.95); + -ms-transform: scale(.95); + transform: scale(.95) + } +} + +/********** cards ************/ +.card { + background: #fff; + display: inline-block; + border: 1px solid #ddd; +} + +.card .image { + float: left; + background: #000; + width: 25%; + height: 150px +} + +.card .content { + float: left; + height: 140px; + width: 73%; + overflow: hidden; + padding: 5px; +} + +.card .content h4 { + margin: 5px 0; +} + +/********** text-only icons in category pages ************/ +.text-icon-wrapper { + float: left; + height: 100px; + width: 100px; + margin: 0 15px 0 0; +} + +.text-icon { + border: 5px solid var(--main-bg-color); + color: var(--main-bg-color); + font-size: 32px; + text-align: center; + border-radius: 50%; + line-height: 85px; + font-weight: 500; + letter-spacing: -2px; + font-family: "Lato", serif; + overflow: hidden; + /* + -webkit-box-shadow: 5px 5px 5px -2px rgba(0, 0, 0, 0.75); + -moz-box-shadow: 5px 5px 5px -2px rgba(0, 0, 0, 0.75); + box-shadow: 5px 5px 5px -2px rgba(0, 0, 0, 0.75); + */ + background: linear-gradient(135deg, #c4d3e0 0%, #c4d3e0 50%, #c4d3e0 100%); + background: #c6ddf3; + text-shadow: 2px 2px 0px rgba(12, 47, 76, 0.3), + 4px 4px 3px rgba(163, 191, 216, 1), + 6px 6px 3px rgba(163, 191, 216, 1), + 8px 8px 3px rgba(163, 191, 216, 1), + 10px 10px 3px rgba(163, 191, 216, 1), + 12px 12px 3px rgba(163, 191, 216, 1), + 14px 14px 3px rgba(163, 191, 216, 1), + 16px 16px 3px rgba(163, 191, 216, 1), + 18px 18px 3px rgba(163, 191, 216, 1), + 20px 20px 3px rgba(163, 191, 216, 1), + 22px 22px 3px rgba(163, 191, 216, 1), + 24px 24px 3px rgba(163, 191, 216, 1), + 26px 26px 3px rgba(163, 191, 216, 1), + 28px 28px 3px rgba(163, 191, 216, 1), + 30px 30px 3px rgba(163, 191, 216, 1), + 32px 32px 3px rgba(163, 191, 216, 1), + 34px 34px 3px rgba(163, 191, 216, 1), + 36px 36px 3px rgba(163, 191, 216, 1), + 38px 38px 3px rgba(163, 191, 216, 1), + 40px 40px 3px rgba(163, 191, 216, 1), + 42px 42px 3px rgba(163, 191, 216, 1), + 44px 44px 3px rgba(163, 191, 216, 1) +} + +.text-icon.grey { + border: 5px solid var(--main-bg-color); + color: var(--main-bg-color); + background: linear-gradient(135deg, #c4d3e0 0%, #c4d3e0 50%, #c4d3e0 100%); + background: #ffffff; + text-shadow: 2px 2px 0px rgba(12, 47, 76, 0.3), + 4px 4px 3px rgb(236, 236, 236), + 6px 6px 3px rgb(236, 236, 236), + 8px 8px 3px rgb(236, 236, 236), + 10px 10px 3px rgb(236, 236, 236), + 12px 12px 3px rgb(236, 236, 236), + 14px 14px 3px rgb(236, 236, 236), + 16px 16px 3px rgb(236, 236, 236), + 18px 18px 3px rgb(236, 236, 236), + 20px 20px 3px rgb(236, 236, 236), + 22px 22px 3px rgb(236, 236, 236), + 24px 24px 3px rgb(236, 236, 236), + 26px 26px 3px rgb(236, 236, 236), + 28px 28px 3px rgb(236, 236, 236), + 30px 30px 3px rgb(236, 236, 236), + 32px 32px 3px rgb(236, 236, 236), + 34px 34px 3px rgb(236, 236, 236), + 36px 36px 3px rgb(236, 236, 236), + 38px 38px 3px rgb(236, 236, 236), + 40px 40px 3px rgb(236, 236, 236), + 42px 42px 3px rgb(236, 236, 236), + 44px 44px 3px rgb(236, 236, 236) +} + +.text-icon.green { + border: 5px solid green; + color: green; + background: #d2ffd2; + text-shadow: 2px 2px 0px rgba(12, 47, 76, 0.3), + 4px 4px 3px rgba(171, 211, 174, 1), + 6px 6px 3px rgba(171, 211, 174, 1), + 8px 8px 3px rgba(171, 211, 174, 1), + 10px 10px 3px rgba(171, 211, 174, 1), + 12px 12px 3px rgba(171, 211, 174, 1), + 14px 14px 3px rgba(171, 211, 174, 1), + 16px 16px 3px rgba(171, 211, 174, 1), + 18px 18px 3px rgba(171, 211, 174, 1), + 20px 20px 3px rgba(171, 211, 174, 1), + 22px 22px 3px rgba(171, 211, 174, 1), + 24px 24px 3px rgba(171, 211, 174, 1), + 26px 26px 3px rgba(171, 211, 174, 1), + 28px 28px 3px rgba(171, 211, 174, 1), + 30px 30px 3px rgba(171, 211, 174, 1), + 32px 32px 3px rgba(171, 211, 174, 1), + 34px 34px 3px rgba(171, 211, 174, 1), + 36px 36px 3px rgba(171, 211, 174, 1), + 38px 38px 3px rgba(171, 211, 174, 1), + 40px 40px 3px rgba(171, 211, 174, 1), + 42px 42px 3px rgba(171, 211, 174, 1), + 44px 44px 3px rgba(171, 211, 174, 1) +} + +.text-icon.red { + background: #e4c5c5; + border: 5px solid #bb0000; + color: #bb0000; + text-shadow: 2px 2px 0px rgba(12, 47, 76, 0.3), + 4px 4px 3px rgba(218, 166, 166, 1), + 6px 6px 3px rgba(218, 166, 166, 1), + 8px 8px 3px rgba(218, 166, 166, 1), + 10px 10px 3px rgba(218, 166, 166, 1), + 12px 12px 3px rgba(218, 166, 166, 1), + 14px 14px 3px rgba(218, 166, 166, 1), + 16px 16px 3px rgba(218, 166, 166, 1), + 18px 18px 3px rgba(218, 166, 166, 1), + 20px 20px 3px rgba(218, 166, 166, 1), + 22px 22px 3px rgba(218, 166, 166, 1), + 24px 24px 3px rgba(218, 166, 166, 1), + 26px 26px 3px rgba(218, 166, 166, 1), + 28px 28px 3px rgba(218, 166, 166, 1), + 30px 30px 3px rgba(218, 166, 166, 1), + 32px 32px 3px rgba(218, 166, 166, 1), + 34px 34px 3px rgba(218, 166, 166, 1), + 36px 36px 3px rgba(218, 166, 166, 1), + 38px 38px 3px rgba(218, 166, 166, 1), + 40px 40px 3px rgba(218, 166, 166, 1), + 42px 42px 3px rgba(218, 166, 166, 1), + 44px 44px 3px rgba(218, 166, 166, 1) +} + +/* TODO move in jsorolla */ +.bootstrap-table { + font-size: 13px; +} + +.bootstrap-table thead { + background-color: #f5f5f5; +} + +.bootstrap-table .fixed-table-body { + /* min-height: 170px; /* making space for the loading spinner */ +} + +.bootstrap-table .fixed-table-body{ + min-height: 20vh; +} + +/* hide the default loading animation */ +.bootstrap-table .animation-wrap { + display: none !important; +} + +.bootstrap-table .fixed-table-loading { + min-height: 90px; +} + +.bootstrap-table > .fixed-table-pagination .pagination{ + +} + +.bootstrap-table .detail-view:hover { + background-color: white; +} + +.bootstrap-table .detail-view-row:hover { + background-color: #f5f5f5; +} + +/* fix the dropdown hidden in a bootstrap table */ +.force-overflow .fixed-table-body { + overflow: visible !important; +} + +/* Custom pagination-detail on top of the boostrap-table grids. + This removes the pager buttons on top pf the grids leaving only the counter of records. + nth-child(2) is the top pager while nth-child(4) would the bottom pager. +*/ +.bootstrap-table.bootstrap3 .fixed-table-pagination:nth-child(2) .pagination-info { + line-height: 1; +} +.bootstrap-table.bootstrap3 .fixed-table-pagination:nth-child(2) .pagination-detail { + margin: 0 0 3px 0; +} +.bootstrap-table.bootstrap3 .fixed-table-pagination:nth-child(2) .page-list, +.bootstrap-table.bootstrap3 .fixed-table-pagination:nth-child(2) .pagination { + display: none; +} + +.bootstrap-table .pagination-info { + font-size: 12px; +} + +/* qtip tooltip style */ +.qtip-content > p { + padding: 5px 0; +} + +/* browsers style */ +.browser-subsection { + font-size: 1.5rem; + font-weight: bold; + padding: 7px 0px 5px 0px; + color: #444444; + border: none +} + +opencga-facet .panel-body > .form-group:not(:first-child) { + border-top: 1px solid rgba(221, 221, 221, 0.8); +} + +.subsection-content { + margin: 5px 5px; +} + +.panel.filter-section { + margin-bottom: 10px; + font-size: 13px; +} + +/********** annotation-filter-modal ************/ +.map-field-input { + +} +.map-field-wrapper { + margin-: 10px 0; +} +.map-field-inputs { + margin-top: 10px; + margin-bottom: 15px; +} + +/********** checkbox widget TODO remove ************/ +/* +.checkbox-container { + margin:0; + padding:0; +} +.checkbox-container li{ + display: block; + position: relative; + cursor: pointer; + -webkit-user-select: none; + -moz-user-select: none; + -ms-user-select: none; + user-select: none; +} +.checkbox-container > li > a { + padding: 3px 10px 3px 0; + display: block; +} +.checkbox-container span + span { + margin: 0 5px; +} +.checkbox-container .checkmark-label { + padding:0 0 0 30px; + color: #333; +} +.checkbox-container input[type=checkbox] { + position: absolute; + opacity: 0; + cursor: pointer; + height: 0; + width: 0; +} +.checkbox-container .checkmark { + position: absolute; + top: 3px; + left: 0; + height: 20px; + width: 20px; + background-color: #f5f5f5; +} +.checkbox-container input:checked ~ .checkmark { + background-color: #337ab7; +} +.checkbox-container .checkmark:after { + content: ""; + position: absolute; + display: none; +} +.checkbox-container input:checked ~ .checkmark:after { + display: block; +} +.checkbox-container .checkmark:after { + left: 8px; + top: 4px; + width: 5px; + height: 10px; + border: solid white; + border-width: 0 3px 3px 0; + -webkit-transform: rotate(45deg); + -ms-transform: rotate(45deg); + transform: rotate(45deg); +} + +.checkbox-container a:focus .checkmark-label, +.checkbox-container a:hover .checkmark-label { + color: #337ab7; +} + +.checkbox-container li a:focus, +.checkbox-container li a:hover { + text-decoration: none; +}*/ + +/********** checkbox container 2 ************/ +ul.checkbox-container { + list-style: none; + margin: 0; + padding: 0; +} + +.checkbox-container input[type=checkbox] { + display: none; +} + +/* Draw our custom check box */ +.checkbox-container { + line-height: 20px; +} + +.checkbox-container label { + cursor: pointer; + transition: all 1s; +} + +.checkbox-container label:before { + display: inline-block; + width: 20px; + margin-right: 5px; + content: "\00a0"; + text-align: center; + background: #eee; +} + +.checkbox-container label:hover::before { + background: #d2d2d2; +} + +.checkbox-container input:checked ~ label:before { + content: "\02714"; + background: #337ab7; + color: #fff; +} + +/********** switch widget ************/ +.switch-container { + position: relative; + width: 180px; + padding-top: 10px; +} + +.switch-container .flex-center { + display: flex; + align-items: center; + justify-content: center; +} + +.switch-container .rating-label { + position: relative; + text-align: center; + flex: 0.5; + z-index: 3; + font-weight: bold; + cursor: pointer; + color: #bbbbbb; + transition: 500ms; +} + +.switch-container .rating-label:hover, +.switch-container .rating-label:active { + color: #bbbbbb; +} + +.switch-container .rating-label-and { + left: -27px; + text-align: right; +} + +.switch-container .rating-label-or { + left: 33px; + text-align: left; + color: #222; +} + +.switch-container input { + display: none; +} + +.switch-container .toggle-rating-pill { + position: relative; + height: 30px; + width: 60px; + background: #347ab7; + border-radius: 50px; + transition: all 500ms; +} + +.switch-container .rating-toggle { + position: absolute; + width: 26px; + height: 26px; + background-color: white; + left: 62px; + border-radius: 50%; + transition: all 300ms; + z-index: 4; +} + +.switch-container input[disabled].radio-or ~ .rating-label-or, +.switch-container input[disabled].radio-and ~ .rating-label-and { + color: #e4e4e4; +} + +.switch-container input[disabled] ~ .toggle-rating-pill { + background: #e4e4e4; +} + +/* +Toggle Changes +*/ +.switch-container .radio-or:checked ~ .rating-label-or { + color: #555e63; +} + +.switch-container .radio-and:checked ~ .rating-label-or { + color: #bbbbbb; +} + +.switch-container .radio-and:checked ~ .rating-label-and { + color: #555e63; +} + +.switch-container .radio-and:checked ~ .rating-toggle { + left: 92px; +} + +.switch-container .radio-and:checked ~ .toggle-rating-pill { + /*background-color: #00b9ee;*/ +} + +/* Notification */ + +#notifications-queue { + position: fixed; + top: 10px; + z-index: 9999; + left: 33%; +} + +#notifications-queue .alert { + display: flex; + align-items: center; + margin: 5px auto; + position: relative; + transition: all 0.5s ease-in-out 0s; + z-index: 2020; + box-shadow: 0 1px 3px 0 rgba(60, 64, 67, 0.302), 0 4px 8px 3px rgba(60, 64, 67, 0.149); + font-size: .9em; + letter-spacing: .2px; + background-color: #373743; + border: none; + -webkit-border-radius: 4px; + border-radius: 4px; + bottom: 0; + -webkit-box-sizing: border-box; + box-sizing: border-box; + color: #fff; + left: 0; + padding: 10px 24px 11px 24px; + white-space: normal; +} + +#notifications-queue .alert p.title { + font-size: 1.2em; +} + +#notifications-queue .alert p.title i { + vertical-align: sub; +} + +#notifications-queue .alert p.details { + color: #b6c1c9; + word-break: break-all; +} + +#notifications-queue .alert a { + color: #c9c9c9; +} + +#notifications-queue .alert .close { + position: absolute; + top: 5px; + right: 0px; + font-size: 1em; + opacity: .4; +} + +#notifications-queue .alert .close i { + color: #fff; +} + +#notifications-queue .alert .fa { + margin-right: .3em; +} + +#notifications-queue .alert-success i { + color: #91f096; +} + +#notifications-queue .alert-info i { + color: #d2e6f7; +} + +#notifications-queue .alert-warning i { + color: #f5e513; +} + +#notifications-queue .alert-danger i { + color: #f28c8b; +} + +.guard-page { + display: flex; + justify-content: center; + align-items: center; + flex-direction: column; + padding-top: 50px; +} + +.guard-page i { + color: grey; +} + +/* custom animations */ +.anim-rotate { + animation: rotate 1.5s linear infinite; +} + +@keyframes rotate { + to { + transform: rotate(360deg); + } +} + +/********** range slider ************/ +.slide-container { + height: 20px; +} + +.slider { + -webkit-appearance: none; /* Override default CSS styles */ + appearance: none; + width: 100%; + height: 5px; + background: #d3d3d3; + outline: none; + opacity: 0.7; + -webkit-transition: .2s; + transition: opacity .2s; +} + +.slider:hover { + opacity: 1; +} + +/* The slider handle (use -webkit- (Chrome, Opera, Safari, Edge) and -moz- (Firefox) to override default look) */ +.slider::-webkit-slider-thumb { + -webkit-appearance: none; /* Override default look */ + appearance: none; + width: 15px; + height: 15px; + background: #337ab7; + cursor: pointer; + border-radius: 50%; +} + +.slider::-moz-range-thumb { + width: 10px; + height: 10px; + background: #337ab7; + cursor: pointer; + border-radius: 50%; + +} + +/********** center page box ************/ +.flex-center { + +} + +/********** interpreter ************/ +.save-button { + padding: 20px 0px 10px 10px; +} + +/********** interpreter side-nav & opencga-project side-nav ************/ +.side-tabs.side-nav button{ + padding: 15px; +} + +.side-tabs.side-nav button.active { + padding: 15px; + font-weight: bold; + background-color: #EEEEEE; + color: #555; + border-color: #ddd #ddd #ddd var(--main-bg-color); +} + +.side-tabs.side-nav button:focus { + border-color: #ddd; + outline: 0; +} + + +/********** welcome page / interpreter icons ************/ +.hi-icon-wrap { + text-align: center; + margin: 0 auto; + padding: 2em 0 3em; + padding-top: 10px; + padding-top: 10px; + padding-bottom: 20px; +} + +.hi-icon { + display: inline-block; + margin: 10px 20px; + width: 80px; + height: 80px; + border-radius: 50%; + text-align: center; + position: relative; + z-index: 1; +} + +.hi-icon a p { + text-decoration: none; + color: #000966; +} + +.hi-icon a:hover p { + text-decoration: none; +} + +.hi-icon:after { + pointer-events: none; + position: absolute; + width: 100%; + height: 100%; + border-radius: 50%; + content: ''; + -webkit-box-sizing: content-box; + -moz-box-sizing: content-box; + box-sizing: content-box; +} + +.hi-icon:before { + /*font-family: 'ecoicon';*/ + speak: none; + font-size: 32px; + line-height: 80px; + font-style: normal; + font-variant: normal; + text-transform: none; + display: block; + -webkit-font-smoothing: antialiased; + color: var(--main-bg-color); +} + +.hi-icon-mobile:before { + content: "\e009"; +} + +.hi-icon-animation .hi-icon { + background: #fff; + -webkit-transition: box-shadow 0.2s; + -moz-transition: box-shadow 0.2s; + transition: box-shadow 0.2s; +} + +.hi-icon-animation p { + -webkit-transition: all 0.3s; + -moz-transition: all 0.3s; + transition: all 0.3s; + color: #797979; +} + +.hi-icon-animation .hi-icon svg { + -webkit-transition: -webkit-transform 0.2s, all 0.2s; + -moz-transition: -moz-transform 0.2s, all 0.2s; + transition: transform 0.2s, all 0.2s; + fill: var(--main-bg-color); + height: 90px; + width: 90px; +} + +.hi-icon-animation .hi-icon.fa, +.hi-icon-animation .icon-wrapper:hover .hi-icon img { + -webkit-transition: -webkit-transform 0.2s, all 0.2s; + -moz-transition: -moz-transform 0.2s, all 0.2s; + transition: transform 0.2s, all 0.2s; +} + +.hi-icon-animation .hi-icon svg image { + height: 90px; + width: 90px; +} + +.hi-icon-animation .hi-icon:after { + top: 0; + left: 0; + padding: 0; + box-shadow: 0 0 0 4px var(--main-bg-color); + -webkit-transition: -webkit-transform 0.2s, opacity 0.2s; + -moz-transition: -moz-transform 0.2s, opacity 0.2s; + transition: transform 0.2s, opacity 0.2s; +} + +.hi-icon-animation .icon-wrapper:not(.disabled):hover .hi-icon:after, +.hi-icon-animation .icon-wrapper:not(.disabled).active .hi-icon:after { + -webkit-transform: scale(0.85); + -moz-transform: scale(0.85); + -ms-transform: scale(0.85); + transform: scale(0.85); + opacity: 0.5; +} + +/* in case of svg or image[src=svg] icon */ +.hi-icon-animation .icon-wrapper:hover .hi-icon svg, +.hi-icon-animation .icon-wrapper:hover .hi-icon img, +.hi-icon-animation .icon-wrapper.active .hi-icon svg, +.hi-icon-animation .icon-wrapper.active .hi-icon img { + transform: scale(0.85); +} + +/* in case of fa icon*/ +.hi-icon-animation .icon-wrapper:not(.disabled):hover .hi-icon.fa, +.hi-icon-animation .icon-wrapper.active:not(.disabled) .hi-icon.fa { + transform: scale(0.85); +} + +.hi-icon-animation .icon-wrapper:hover .hi-icon, +.hi-icon-animation .icon-wrapper.active .hi-icon { + box-shadow: 0 0 0 10px var(--main-bg-color); + color: #fff; +} + +.hi-icon-animation .icon-wrapper:not(.disabled):hover p, +.hi-icon-animation .icon-wrapper:not(.disabled).active p { + color: var(--main-bg-color); +} + +.hi-icon-animation .icon-wrapper.disabled .hi-icon:after, +.hi-icon-animation .icon-wrapper.active.disabled .hi-icon.fa, +.hi-icon-animation .icon-wrapper.disabled:hover .hi-icon.fa, +.hi-icon-animation .icon-wrapper.disabled:hover .hi-icon:after { + transform: none; + opacity: 1; + box-shadow: 0 0 0 4px #8e8e8e; +} + +.hi-icon-animation .icon-wrapper.disabled { + cursor: not-allowed; +} + +.hi-icon-animation .icon-wrapper.disabled .hi-icon.fa:before { + color: #8e8e8e; +} + +.hi-icon-animation .icon-wrapper.active:not(.disabled) .hi-icon:before { + transition: all .2s; + font-size: 36px; +} + +.hi-icon-wrap { + display: flex; + justify-content: space-evenly; +} + +/* valid for the wizard only (interpreter page) */ +.hi-icon-wrap.wizard a.icon-wrapper { + position: relative; +} + +.hi-icon-wrap.wizard a.icon-wrapper:before { + content: ""; + position: absolute; + width: 270px; + height: 3px; + top: 50px; + background: var(--main-bg-color); + left: 60px; +} + +.hi-icon-wrap.wizard a.icon-wrapper.disabled:before { + background: #8e8e8e; +} + +.hi-icon-wrap.wizard a.icon-wrapper:last-child:before { + content: none; +} + +/****** magic checkbox / radio ********/ +.magic-radio + .magic-horizontal-label { + display: inline-block; + margin-right: 15px; +} + +.magic-checkbox:checked + label:before { + border: #337ab7; + background: #337ab7; +} + +/****** detail-tabs ********/ +.detail-tabs h3, +data-form h3, +.cellbase-variant-annotation-summary h3 /* TODO refactor this component in detail-tabs*/, +.interpreter-content-tab h3, +.modal-header, +opencga-gene-view h3.section-title /* TODO refactor */{ + text-transform: uppercase; + letter-spacing: .2em; + margin: 0; + padding: 10px 0 10px 0; + color: var(--main-bg-color); + display: block; + font-size: 1.6em; +} + +.cellbase-variant-annotation-summary h3 { + +} + +.modal-header { + padding: 15px; +} + +.detail-tabs .nav-tabs li a{ + font-weight: bold; + font-size: 1.1em; +} + +.detail-tabs .tab-content, +.cellbase-variant-annotation-summary /* TODO refactor this component in detail-tabs*/{ + padding: 10px 30px +} +/****** data-view ********/ +.detail-row { + padding: 5px 0; +} + +/****** sweetalert2 fix ********/ +.swal2-popup { + font-size: 1em; +} + +.list-item-arrow { + margin-left: 1em; + position: relative; + color: #2b388f; + font-weight: bold; +} + +.list-item-arrow:before { + content: ""; + position: absolute; + width: .9em; + height: 1.1em; + left: -1.1em; + background: transparent url('data:image/svg+xml;base64, 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') no-repeat center center; +} + +/****** job logs ********/ +.cmd { + background: black; + font-family: "Courier New", monospace; + padding: 15px; + color: #a5a5a5; + font-size: .9em; +} + +/****** file manager ********/ +.file-manager { + padding: 0; +} + +.file-manager > li { + border-radius: 3px; + background-color: #373743; + width: 307px; + height: 118px; + list-style-type: none; + margin: 10px; + display: inline-block; + position: relative; + overflow: hidden; + padding: 0.3em; + z-index: 1; + cursor: pointer; + box-sizing: border-box; + transition: 0.3s background-color; +} + +.file-manager-breadcrumbs { + padding: 10px; +} + +.file-manager-breadcrumbs a, +.file-manager-breadcrumbs .path-separator { + font-size: 1.5em; + cursor: pointer; +} + +.file-manager li a { + position: absolute; + top: 0; + left: 0; + width: 100%; + height: 100%; + display: flex; + align-items: center; +} + +.file-manager li:hover { + background-color: #42424E; +} + +.file-manager li:hover .icon { + color: #286090; +} + +.file-manager .icon { + margin: 1em; + background-color: transparent; + overflow: hidden; +} +.file-manager .content { + width: 210px; +} + +.file-manager .name { + color: #ffffff; + font-size: 15px; + font-weight: 700; + line-height: 20px; + word-break: break-all; +} + +.file-manager .name .max-lines-2 { + display: -webkit-box; + -webkit-line-clamp: 2; + -webkit-box-orient: vertical; + overflow: hidden; +} + +.file-manager .details { + color: #b6c1c9; + font-size: 13px; + font-weight: 400; + width: 55px; + height: 10px; + white-space: nowrap; + display: block; +} +.file-manager .format { + display: block; + color: #fff; + text-align: center; + margin-top: 3px; + width: 45px; + text-overflow: ellipsis; + overflow: hidden; +} +.file-manager .file.active { + background-color: #626269; + outline: thick solid #d0d0d0; +} + +.file-manager-tree { + border-right: 1px solid gainsboro; +} + +.file-manager-tree ul { + font-size: 14px; + margin-top: 30px; +} + +.file-manager-tree ul { + margin: 0; + padding: 0; + list-style-type: none; +} + +.file-manager-tree .folder { + padding: 10px 0 0 15px; +} + +.file-manager-tree .folder-name { + font-weight: bold; + word-break: break-all; + white-space: nowrap; + overflow: hidden; + text-overflow: ellipsis; +} + +.file-manager-tree .folder-name, +.file-manager-tree .home{ + cursor: pointer; +} + +.file-manager-tree .folder-name + ul { + display: none; +} + +.file-manager-tree .folder-name.exploded + ul { + display: block; +} + +.file-manager-tree .file { + word-break: break-all; + padding: 5px 0 0px 12px; + cursor: pointer; + color: #337ab7; +} + +.file-manager-tree .file i{ + margin-right: 10px; + color: #747474; +} + +.file-manager-tree .file.active { + color: black; +} + +.opencga-file-manager .opencga-file-view { + margin-left: 5px; +} + +.opencga-file-manager .file-manager-full-height, +.opencga-file-manager .file-manager-tree{ + min-height: calc(100vh - 160px); +} + +/* temp fix for long filenames in opencga-file-manager */ +.opencga-file-manager .file-manager-tree .file { + display: flex; +} +.file-manager-tree .file { + word-break: normal; +} +.file-manager-tree .folder { + overflow: auto; +} + +/* jobs-monitor*/ +.notification-nav li.notification, +.notification-nav li.notification > a { + height: 50px; + min-width: 40px; +} + +.notification-nav .dropdown-menu { + width: 340px; +} + +.notification-nav .info { + padding: 3px 20px; + font-weight: bold; +} + +.notification-nav .dropdown-menu a { + border-top: 1px solid #dedede; +} +.notification-nav .dropdown-menu li:first-child a { + border: 0; +} + +.notification-nav .media-body .media-heading { + font-size: 14px; + margin: 3px 0 0px 0; +} +.notification-nav .media-body small { + color: #5d5d5d; +} + +.notification-nav .media-left { + font-size: 20px; + color: #5d5d5d; + vertical-align: middle; +} + +.media-heading { + width: 270px; + overflow: hidden; + text-overflow: ellipsis; +} + +.notification-nav .media-body p { + width: 270px; + overflow: hidden; + text-overflow: ellipsis; + white-space: nowrap; + color: grey; +} + +.notification-nav .updated.status-ERROR { + background: rgba(255, 0, 0, 0.05); +} + +.notification-nav .updated.status-DONE { + background: rgba(72, 255, 0, 0.05); +} + +#job-monitor .job-monitor-item { +} + +.rocket-RUNNING { + animation: spaceOutUp 2s infinite; +} + +.rocket-PENDING, +.rocket-QUEUED, +.rocket-REGISTERING { + animation: float-rocket .5s infinite; +} + +/****** animation ********/ +.anim-float { + animation: float .5s infinite; +} +.anim-spaceOutUp { + animation: spaceOutUp .5s infinite; +} + +@keyframes float { + 0% { + -webkit-transform: translateY(0); + transform: translateY(0); + } + 50% { + -webkit-transform: translateY(-6px); + transform: translateY(-6px); + } + 100% { + -webkit-transform: translateY(0); + transform: translateY(0); + } +} + +@keyframes float-rocket { + 0% { + -webkit-transform: translateY(0); + transform: translateY(-2px) translateX(0px) rotate(-45deg); + } + 50% { + -webkit-transform: translateY(-6px); + transform: translateY(0px) translateX(0px) rotate(-45deg); + } + 100% { + -webkit-transform: translateY(0) translateX(10px); + transform: translateY(-2px) translateX(0px) rotate(-45deg); + } +} + +@keyframes spaceOutUp { + 0% { + opacity: 1; + -webkit-transform-origin: 50% 0%; + transform-origin: 50% 0%; + -webkit-transform: scale(1) translate(-200%, 200%); + transform: scale(1) translate(-200%, 200%); + } + 50% { + opacity: 1; + -webkit-transform-origin: 50% 0%; + transform-origin: 50% 0%; + -webkit-transform: scale(1) translate(0%, 0%); + transform: scale(1) translate(0%, 0%); + } + 100% { + opacity: 0; + -webkit-transform-origin: 50% 0%; + transform-origin: 50% 0%; + -webkit-transform: scale(.2) translate(200%, -200%); + transform: scale(.2) translate(200%, -200%); + } +} + +/********** opencga-projects *************/ +#projects .project-tab .project-name { + padding: 15px 0 20px 0; +} + +#projects .panel-container { + display: flex; + justify-content: center; +} + +#projects .panel-container .panel{ + flex-basis: 250px; + margin: 1em; + background: #f1f1f1; +} + +#projects .panel-container .panel .counter { + font-size: 4em; + color: #204d74; +} + +#projects .panel-container .panel .counter-title { + margin: -20px 0 0 0; + font-size: 15px; + text-transform: uppercase; + letter-spacing: 2px; +} + +#projects .study-title { + font-size: 15px; + text-transform: uppercase; + letter-spacing: 2px; +} + +/********** TODO refactor. variant-interpreter tooltip quickfix *************/ +.zygosity-formatter, +.predictionTooltip-inner { + width: 250px; +} +.zygosity-formatter .col-md-5, +.predictionTooltip-inner .col-md-5, +.zygosity-formatter .col-md-7 +.predictionTooltip-inner .col-md-7{ + padding: 0; +} diff --git a/src/styles/magic-check.css b/src/styles/magic-check.css new file mode 100644 index 000000000..824506728 --- /dev/null +++ b/src/styles/magic-check.css @@ -0,0 +1,141 @@ +@keyframes hover-color { + from { + border-color: #c0c0c0; + } + to { + border-color: #3e97eb; + } +} + +.magic-radio, +.magic-checkbox { + position: absolute; + display: none; +} + +.magic-radio[disabled], +.magic-checkbox[disabled] { + cursor: not-allowed; +} + +.magic-radio + label, +.magic-checkbox + label { + position: relative; + display: block; + padding-left: 30px; + cursor: pointer; + vertical-align: middle; +} + +.magic-radio + label:hover:before, +.magic-checkbox + label:hover:before { + animation-duration: 0.4s; + animation-fill-mode: both; + animation-name: hover-color; +} + +.magic-radio + label:before, +.magic-checkbox + label:before { + position: absolute; + top: 0; + left: 0; + display: inline-block; + width: 20px; + height: 20px; + content: ''; + border: 1px solid #c0c0c0; +} + +.magic-radio + label:after, +.magic-checkbox + label:after { + position: absolute; + display: none; + content: ''; +} + +.magic-radio[disabled] + label, +.magic-checkbox[disabled] + label { + cursor: not-allowed; + color: #e4e4e4; +} + +.magic-radio[disabled] + label:hover, .magic-radio[disabled] + label:before, .magic-radio[disabled] + label:after, +.magic-checkbox[disabled] + label:hover, +.magic-checkbox[disabled] + label:before, +.magic-checkbox[disabled] + label:after { + cursor: not-allowed; +} + +.magic-radio[disabled] + label:hover:before, +.magic-checkbox[disabled] + label:hover:before { + border: 1px solid #e4e4e4; + animation-name: none; +} + +.magic-radio[disabled] + label:before, +.magic-checkbox[disabled] + label:before { + border-color: #e4e4e4; +} + +.magic-radio:checked + label:before, +.magic-checkbox:checked + label:before { + animation-name: none; +} + +.magic-radio:checked + label:after, +.magic-checkbox:checked + label:after { + display: block; +} + +.magic-radio + label:before { + border-radius: 50%; +} + +.magic-radio + label:after { + top: 6px; + left: 6px; + width: 8px; + height: 8px; + border-radius: 50%; + background: #3e97eb; +} + +.magic-radio:checked + label:before { + border: 1px solid #3e97eb; +} + +.magic-radio:checked[disabled] + label:before { + border: 1px solid #c9e2f9; +} + +.magic-radio:checked[disabled] + label:after { + background: #c9e2f9; +} + +.magic-checkbox + label:before { + border-radius: 3px; +} + +.magic-checkbox + label:after { + top: 2px; + left: 7px; + box-sizing: border-box; + width: 6px; + height: 12px; + transform: rotate(45deg); + border-width: 2px; + border-style: solid; + border-color: #fff; + border-top: 0; + border-left: 0; +} + +.magic-checkbox:checked + label:before { + border: #3e97eb; + background: #3e97eb; +} + +.magic-checkbox:checked[disabled] + label:before { + border: #c9e2f9; + background: #c9e2f9; +} diff --git a/src/styles/toggle-switch.css b/src/styles/toggle-switch.css new file mode 100644 index 000000000..d04fc89db --- /dev/null +++ b/src/styles/toggle-switch.css @@ -0,0 +1,493 @@ +@charset "UTF-8"; +/* +* CSS TOGGLE SWITCH +* +* IonuČ› Colceriu - ghinda.net +* https://github.com/ghinda/css-toggle-switch +* +*/ +/* supported values are px, rem-calc, em-calc + */ +/* imports + */ +/* Functions + */ +/* Shared + */ +/* Hide by default + */ +.switch-toggle a, +.switch-light span span { + display: none; } + +/* We can't test for a specific feature, + * so we only target browsers with support for media queries. + */ +@media only screen { + /* Checkbox + */ + .switch-light { + position: relative; + display: block; + /* simulate default browser focus outlines on the switch, + * when the inputs are focused. + */ } + .switch-light::after { + clear: both; + content: ''; + display: table; } + .switch-light *, + .switch-light *:before, + .switch-light *:after { + box-sizing: border-box; } + .switch-light a { + display: block; + transition: all 0.2s ease-out; } + .switch-light label, + .switch-light > span { + /* breathing room for bootstrap/foundation classes. + */ + line-height: 2em; } + .switch-light input:focus ~ span a, + .switch-light input:focus + label { + outline-width: 2px; + outline-style: solid; + outline-color: Highlight; + /* Chrome/Opera gets its native focus styles. + */ } } + @media only screen and (-webkit-min-device-pixel-ratio: 0) { + .switch-light input:focus ~ span a, + .switch-light input:focus + label { + outline-color: -webkit-focus-ring-color; + outline-style: auto; } } + +@media only screen { + /* don't hide the input from screen-readers and keyboard access + */ + .switch-light input { + position: absolute; + opacity: 0; + z-index: 3; } + .switch-light input:checked ~ span a { + right: 0%; } + /* inherit from label + */ + .switch-light strong { + font-weight: inherit; } + .switch-light > span { + position: relative; + overflow: hidden; + display: block; + min-height: 2em; + /* overwrite 3rd party classes padding + * eg. bootstrap .alert + */ + padding: 0; + text-align: left; } + .switch-light span span { + position: relative; + z-index: 2; + display: block; + float: left; + width: 50%; + text-align: center; + user-select: none; } + .switch-light a { + position: absolute; + right: 50%; + top: 0; + z-index: 1; + display: block; + width: 50%; + height: 100%; + padding: 0; } + /* bootstrap 4 tweaks +*/ + .switch-light.row { + display: flex; } + .switch-light .alert-light { + color: #333; } + /* Radio Switch + */ + .switch-toggle { + position: relative; + display: block; + /* simulate default browser focus outlines on the switch, + * when the inputs are focused. + */ + /* For callout panels in foundation + */ + padding: 0 !important; + /* 2 items + */ + /* 3 items + */ + /* 4 items + */ + /* 5 items + */ + /* 6 items + */ } + .switch-toggle::after { + clear: both; + content: ''; + display: table; } + .switch-toggle *, + .switch-toggle *:before, + .switch-toggle *:after { + box-sizing: border-box; } + .switch-toggle a { + display: block; + transition: all 0.2s ease-out; } + .switch-toggle label, + .switch-toggle > span { + /* breathing room for bootstrap/foundation classes. + */ + line-height: 2em; } + .switch-toggle input:focus ~ span a, + .switch-toggle input:focus + label { + outline-width: 2px; + outline-style: solid; + outline-color: Highlight; + /* Chrome/Opera gets its native focus styles. + */ } } + @media only screen and (-webkit-min-device-pixel-ratio: 0) { + .switch-toggle input:focus ~ span a, + .switch-toggle input:focus + label { + outline-color: -webkit-focus-ring-color; + outline-style: auto; } } + +@media only screen { + .switch-toggle input { + position: absolute; + left: 0; + opacity: 0; } + .switch-toggle input + label { + position: relative; + z-index: 2; + display: block; + float: left; + padding: 0 0.5em; + margin: 0; + text-align: center; } + .switch-toggle a { + position: absolute; + top: 0; + left: 0; + padding: 0; + z-index: 1; + width: 10px; + height: 100%; } + .switch-toggle label:nth-child(2):nth-last-child(4), + .switch-toggle label:nth-child(2):nth-last-child(4) ~ label, + .switch-toggle label:nth-child(2):nth-last-child(4) ~ a { + width: 50%; } + .switch-toggle label:nth-child(2):nth-last-child(4) ~ input:checked:nth-child(3) + label ~ a { + left: 50%; } + .switch-toggle label:nth-child(2):nth-last-child(6), + .switch-toggle label:nth-child(2):nth-last-child(6) ~ label, + .switch-toggle label:nth-child(2):nth-last-child(6) ~ a { + width: 33.33%; } + .switch-toggle label:nth-child(2):nth-last-child(6) ~ input:checked:nth-child(3) + label ~ a { + left: 33.33%; } + .switch-toggle label:nth-child(2):nth-last-child(6) ~ input:checked:nth-child(5) + label ~ a { + left: 66.66%; } + .switch-toggle label:nth-child(2):nth-last-child(8), + .switch-toggle label:nth-child(2):nth-last-child(8) ~ label, + .switch-toggle label:nth-child(2):nth-last-child(8) ~ a { + width: 25%; } + .switch-toggle label:nth-child(2):nth-last-child(8) ~ input:checked:nth-child(3) + label ~ a { + left: 25%; } + .switch-toggle label:nth-child(2):nth-last-child(8) ~ input:checked:nth-child(5) + label ~ a { + left: 50%; } + .switch-toggle label:nth-child(2):nth-last-child(8) ~ input:checked:nth-child(7) + label ~ a { + left: 75%; } + .switch-toggle label:nth-child(2):nth-last-child(10), + .switch-toggle label:nth-child(2):nth-last-child(10) ~ label, + .switch-toggle label:nth-child(2):nth-last-child(10) ~ a { + width: 20%; } + .switch-toggle label:nth-child(2):nth-last-child(10) ~ input:checked:nth-child(3) + label ~ a { + left: 20%; } + .switch-toggle label:nth-child(2):nth-last-child(10) ~ input:checked:nth-child(5) + label ~ a { + left: 40%; } + .switch-toggle label:nth-child(2):nth-last-child(10) ~ input:checked:nth-child(7) + label ~ a { + left: 60%; } + .switch-toggle label:nth-child(2):nth-last-child(10) ~ input:checked:nth-child(9) + label ~ a { + left: 80%; } + .switch-toggle label:nth-child(2):nth-last-child(12), + .switch-toggle label:nth-child(2):nth-last-child(12) ~ label, + .switch-toggle label:nth-child(2):nth-last-child(12) ~ a { + width: 16.6%; } + .switch-toggle label:nth-child(2):nth-last-child(12) ~ input:checked:nth-child(3) + label ~ a { + left: 16.6%; } + .switch-toggle label:nth-child(2):nth-last-child(12) ~ input:checked:nth-child(5) + label ~ a { + left: 33.2%; } + .switch-toggle label:nth-child(2):nth-last-child(12) ~ input:checked:nth-child(7) + label ~ a { + left: 49.8%; } + .switch-toggle label:nth-child(2):nth-last-child(12) ~ input:checked:nth-child(9) + label ~ a { + left: 66.4%; } + .switch-toggle label:nth-child(2):nth-last-child(12) ~ input:checked:nth-child(11) + label ~ a { + left: 83%; } + /* Candy Theme + * Based on the "Sort Switches / Toggles (PSD)" by Ormal Clarck + * http://www.premiumpixels.com/freebies/sort-switches-toggles-psd/ + */ + .switch-toggle.switch-candy, + .switch-light.switch-candy > span { + background-color: #2d3035; + border-radius: 3px; + box-shadow: inset 0 2px 6px rgba(0, 0, 0, 0.3), 0 1px 0 rgba(255, 255, 255, 0.2); } + .switch-light.switch-candy span span, + .switch-light.switch-candy input:checked ~ span span:first-child, + .switch-toggle.switch-candy label { + color: #fff; + font-weight: bold; + text-align: center; + text-shadow: 1px 1px 1px #191b1e; } + .switch-light.switch-candy input ~ span span:first-child, + .switch-light.switch-candy input:checked ~ span span:nth-child(2), + .switch-candy input:checked + label { + color: #333; + text-shadow: 0 1px 0 rgba(255, 255, 255, 0.5); } + .switch-candy a { + border: 1px solid #333; + border-radius: 3px; + box-shadow: 0 1px 1px rgba(0, 0, 0, 0.2), inset 0 1px 1px rgba(255, 255, 255, 0.45); + background-color: #70c66b; + background-image: linear-gradient(rgba(255, 255, 255, 0.2), transparent); } + .switch-candy-blue a { + background-color: #38a3d4; } + .switch-candy-yellow a { + background-color: #f5e560; } + /* iOS Theme +*/ + .switch-ios.switch-light span span { + color: #888b92; } + .switch-ios.switch-light a { + left: 0; + top: 0; + width: 2em; + height: 2em; + background-color: #fff; + border-radius: 100%; + border: 0.25em solid #D8D9DB; + transition: all .2s ease-out; } + .switch-ios.switch-light > span { + display: block; + width: 100%; + height: 2em; + background-color: #D8D9DB; + border-radius: 1.75em; + transition: all .4s ease-out; } + .switch-ios.switch-light > span span { + position: absolute; + top: 0; + left: 0; + width: 100%; + opacity: 0; + line-height: 1.875em; + vertical-align: middle; + transition: all .2s ease-out; } + .switch-ios.switch-light > span span:first-of-type { + opacity: 1; + padding-left: 1.875em; } + .switch-ios.switch-light > span span:last-of-type { + padding-right: 1.875em; } + .switch-ios.switch-light input:checked ~ span a { + left: 100%; + border-color: #4BD865; + margin-left: -2em; } + .switch-ios.switch-light input:checked ~ span { + border-color: #4BD865; + box-shadow: inset 0 0 0 30px #4BD865; } + .switch-ios.switch-light input:checked ~ span span:first-of-type { + opacity: 0; } + .switch-ios.switch-light input:checked ~ span span:last-of-type { + opacity: 1; + color: #fff; } + .switch-ios.switch-toggle { + background-color: #D8D9DB; + border-radius: 30px; + box-shadow: inset rgba(0, 0, 0, 0.1) 0 1px 0; } + .switch-ios.switch-toggle a { + background-color: #4BD865; + border: 0.125em solid #D8D9DB; + border-radius: 1.75em; + transition: all 0.12s ease-out; } + .switch-ios.switch-toggle label { + height: 2.4em; + color: #888b92; + line-height: 2.4em; + vertical-align: middle; } + .switch-ios input:checked + label { + color: #3e4043; } + /* Holo Theme + */ + .switch-toggle.switch-holo, + .switch-light.switch-holo > span { + background-color: #464747; + border-radius: 1px; + box-shadow: inset rgba(0, 0, 0, 0.1) 0 1px 0; + color: #fff; + text-transform: uppercase; } + .switch-holo label { + color: #fff; } + .switch-holo > span span { + opacity: 0; + transition: all 0.1s; } + .switch-holo > span span:first-of-type { + opacity: 1; } + .switch-holo > span span, + .switch-holo label { + font-size: 85%; + line-height: 2.15625em; } + .switch-holo a { + background-color: #666; + border-radius: 1px; + box-shadow: inset rgba(255, 255, 255, 0.2) 0 1px 0, inset rgba(0, 0, 0, 0.3) 0 -1px 0; } + /* Selected ON switch-light +*/ + .switch-holo.switch-light input:checked ~ span a { + background-color: #0E88B1; } + .switch-holo.switch-light input:checked ~ span span:first-of-type { + opacity: 0; } + .switch-holo.switch-light input:checked ~ span span:last-of-type { + opacity: 1; } + /* Material Theme + */ + /* switch-light + */ + .switch-light.switch-material a { + top: -0.1875em; + width: 1.75em; + height: 1.75em; + border-radius: 50%; + background: #fafafa; + box-shadow: 0 0.125em 0.125em 0 rgba(0, 0, 0, 0.14), 0 0.1875em 0.125em -0.125em rgba(0, 0, 0, 0.2), 0 0.125em 0.25em 0 rgba(0, 0, 0, 0.12); + transition: right 0.28s cubic-bezier(0.4, 0, 0.2, 1); } + .switch-material.switch-light { + overflow: visible; } + .switch-material.switch-light::after { + clear: both; + content: ''; + display: table; } + .switch-material.switch-light > span { + overflow: visible; + position: relative; + top: 0.1875em; + width: 3.25em; + height: 1.5em; + min-height: auto; + border-radius: 1em; + background: rgba(0, 0, 0, 0.26); } + .switch-material.switch-light span span { + position: absolute; + clip: rect(0 0 0 0); } + .switch-material.switch-light input:checked ~ span a { + right: 0; + background: #3f51b5; + box-shadow: 0 0.1875em 0.25em 0 rgba(0, 0, 0, 0.14), 0 0.1875em 0.1875em -0.125em rgba(0, 0, 0, 0.2), 0 0.0625em 0.375em 0 rgba(0, 0, 0, 0.12); } + .switch-material.switch-light input:checked ~ span { + background: rgba(63, 81, 181, 0.5); } + /* switch-toggle + */ + .switch-toggle.switch-material { + overflow: visible; } + .switch-toggle.switch-material::after { + clear: both; + content: ''; + display: table; } + .switch-toggle.switch-material a { + top: 48%; + width: 0.375em !important; + height: 0.375em; + margin-left: 0.25em; + background: #3f51b5; + border-radius: 100%; + transform: translateY(-50%); + transition: transform .4s ease-in; } + .switch-toggle.switch-material label { + color: rgba(0, 0, 0, 0.54); + font-size: 1em; } + .switch-toggle.switch-material label:before { + content: ''; + position: absolute; + top: 48%; + left: 0; + display: block; + width: 0.875em; + height: 0.875em; + border-radius: 100%; + border: 0.125em solid rgba(0, 0, 0, 0.54); + transform: translateY(-50%); } + .switch-toggle.switch-material input:checked + label:before { + border-color: #3f51b5; } + /* ripple + */ + .switch-light.switch-material > span:before, + .switch-light.switch-material > span:after, + .switch-toggle.switch-material label:after { + content: ''; + position: absolute; + top: 0; + left: 0; + z-index: 3; + display: block; + width: 4em; + height: 4em; + border-radius: 100%; + background: #3f51b5; + opacity: .4; + margin-left: -1.25em; + margin-top: -1.25em; + transform: scale(0); + transition: opacity .4s ease-in; } + .switch-light.switch-material > span:after { + left: auto; + right: 0; + margin-left: 0; + margin-right: -1.25em; } + .switch-toggle.switch-material label:after { + width: 3.25em; + height: 3.25em; + margin-top: -0.75em; } + @keyframes materialRipple { + 0% { + transform: scale(0); } + 20% { + transform: scale(1); } + 100% { + opacity: 0; + transform: scale(1); } } + .switch-material.switch-light input:not(:checked) ~ span:after, + .switch-material.switch-light input:checked ~ span:before, + .switch-toggle.switch-material input:checked + label:after { + animation: materialRipple .4s ease-in; } + /* trick to prevent the default checked ripple animation from showing + * when the page loads. + * the ripples are hidden by default, and shown only when the input is focused. + */ + .switch-light.switch-material.switch-light input ~ span:before, + .switch-light.switch-material.switch-light input ~ span:after, + .switch-material.switch-toggle input + label:after { + visibility: hidden; } + .switch-light.switch-material.switch-light input:focus:checked ~ span:before, + .switch-light.switch-material.switch-light input:focus:not(:checked) ~ span:after, + .switch-material.switch-toggle input:focus:checked + label:after { + visibility: visible; } } + +/* Bugfix for older Webkit, including mobile Webkit. Adapted from + * http://css-tricks.com/webkit-sibling-bug/ + */ +@media only screen and (-webkit-max-device-pixel-ratio: 2) and (max-device-width: 80em) { + .switch-light, + .switch-toggle { + -webkit-animation: webkitSiblingBugfix infinite 1s; } } + +@-webkit-keyframes webkitSiblingBugfix { + from { + -webkit-transform: translate3d(0, 0, 0); } + to { + -webkit-transform: translate3d(0, 0, 0); } } + +/*# sourceMappingURL=toggle-switch.css.map */ \ No newline at end of file diff --git a/src/terms.html b/src/terms.html deleted file mode 100644 index b60c657bc..000000000 --- a/src/terms.html +++ /dev/null @@ -1,66 +0,0 @@ - - - - - - - diff --git a/src/terms.js b/src/terms.js new file mode 100644 index 000000000..3886d97d9 --- /dev/null +++ b/src/terms.js @@ -0,0 +1,47 @@ +/** + * Copyright 2015-2019 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +import {LitElement, html} from "/web_modules/lit-element.js"; +import "../lib/jsorolla/src/core/webcomponents/tool-header.js"; + + +export default class TermsWeb extends LitElement { + + constructor() { + super(); + } + + createRenderRoot() { + return this; + } + + render() { + return html` +
    + +
    +
    +
    +
    +
    +
    +
    + `; + } + +} + +customElements.define("terms-web", TermsWeb); diff --git a/src/welcome.html b/src/welcome.html deleted file mode 100644 index b2a3fc113..000000000 --- a/src/welcome.html +++ /dev/null @@ -1,194 +0,0 @@ - - - - - - - diff --git a/src/welcome.js b/src/welcome.js new file mode 100644 index 000000000..ef9a590a2 --- /dev/null +++ b/src/welcome.js @@ -0,0 +1,292 @@ +/** + * Copyright 2015-2019 OpenCB + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +import {LitElement, html} from "/web_modules/lit-element.js"; +import UtilsNew from "./../lib/jsorolla/src/core/utilsNew.js"; +import PolymerUtils from "../lib/jsorolla/src/core/webcomponents/PolymerUtils.js"; + +export default class WelcomeWeb extends LitElement { + + constructor() { + super(); + this.checkProjects = false; + } + + createRenderRoot() { + return this; + } + + static get properties() { + return { + opencgaSession: { + type: Object + }, + version: { + type: String + }, + cellbaseClient: { + type: Object + }, + checkProjects: { + type: Boolean + }, + config: { + type: Object + } + }; + } + + updated(changedProperties) { + if (changedProperties.has("opencgaSession")) { + this.opencgaSessionObserver(); + } + } + + opencgaSessionObserver() { + //console.log("opencgaSessionObserver") + //console.log(this.opencgaSession) + this._checkProjects(); + } + + _checkProjects() { + return !!(UtilsNew.isNotUndefinedOrNull(this.opencgaSession) && UtilsNew.isNotUndefinedOrNull(this.opencgaSession.project)); + + } + + onExampleClick(e) { + const query = {study: this.opencgaSession.study.fqn}; + switch (e.currentTarget.dataset.type) { + case "gene": + query.gene = e.currentTarget.text; + break; + case "region": + query.region = e.currentTarget.text; + break; + case "snp": + query.xref = e.currentTarget.text; + break; + case "variant": + query.xref = e.currentTarget.text; + break; + } + this.notify(query); + } + + notify(query) { + this.dispatchEvent(new CustomEvent("search", { + detail: { + ...query, + study: this.opencgaSession.study.fqn + }, + bubbles: true, + composed: true + })); + } + + callAutocomplete(e) { + // Only gene symbols are going to be searched and not Ensembl IDs + const featureId = this.querySelector("#welcomeSearchTextBox").value; + if (UtilsNew.isNotEmpty(featureId)) { + const query = {}; + if (featureId.startsWith("chr") || featureId.startsWith("X") || featureId.startsWith("Y") || featureId.startsWith("MT") || featureId.match(/^\d/)) { + if (featureId.split(":").length < 3) { + // It's a region, contains only one ':' character + query.region = featureId; + } else { + query.xref = featureId; + } + } else if (featureId.startsWith("rs")) { + query.xref = featureId; + } else { + // The ID written seems to be a gene name + query.gene = featureId; + if (featureId.length >= 3 && !featureId.startsWith("ENS")) { + const _this = this; + _this.cellbaseClient.get("feature", "id", featureId.toUpperCase(), "starts_with", {}, {}) + .then(function(response) { + let options = ""; + for (const id of response.response[0].result) { + options += `