Merge branch 'develop'

.gitignore

@@ -1,8 +1,11 @@
 
 build
+dist
 bower_components
 node_modules
+web_modules
 private
+web_modules
 
 # General
 *.jar

Jenkinsfile

@@ -1,15 +1,15 @@
 pipeline {
     agent any
     stages {
-         stage ('Build source code') {
+        stage ('Build source code') {
             options {
                 timeout(time: 5, unit: 'MINUTES')
             }
             steps {
                 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}'"
+       			    }
+       		    }
+            }
+        }
     }
 }
 

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'
+        }
+    }
+
+};

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 "$@"

cypress.json

@@ -0,0 +1,6 @@
+{
+  "baseUrl": "http://localhost:3000/src/",
+  "chromeWebSecurity": false,
+  "viewportWidth": 1600,
+  "viewportHeight": 660
+}

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")
+    })
+})

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
+        });
+
+    })
+})

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()
+
+    })
+})

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);
+
+    })
+})

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);
+
+    })
+})

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()
+
+    })
+})