Merge branch 'develop' into TASK-6559

README.md

@@ -1,19 +1,11 @@
 # Overview
 JSorolla is a JavaScript library for biological and genomic data visualization.
 
-### Documentation
-You can find JSorolla documentation and tutorials at: http://docs.opencb.org/display/jsorolla/JSorolla+Home.
-
 ### Issue Tracking
-You can report bugs or request new features at [GitHub issue tracking](https://github.com/opencb/jsorolla/issues).
+Found a bug or have an idea for a new feature? Let us know at https://zettagenomics.com/academic/
 
 ### Release Notes and Roadmap
-Releases notes are available at [GitHub releases](https://github.com/opencb/jsorolla/releases).
-
-Roadmap is available at [GitHub milestones](https://github.com/opencb/jsorolla/milestones). You can report bugs or request new features at [GitHub issue tracking](https://github.com/opencb/jsorolla/issues).
-
-### Versioning
-JSorolla is versioned following the rules from [Semantic versioning](http://semver.org/).
+Releases notes are available at [[GitHub releases](https://github.com/opencb/jsorolla/releases).](https://zettagenomics.com/release-notes/)
 
 ### Maintainers
 The main developers and maintainers are:

cypress/e2e/iva/genome-browser.cy.js

@@ -97,7 +97,7 @@ context("GenomeBrowser", () => {
 
             cy.get("@karyotype")
                 .find(`div[data-cy="gb-karyotype-toggle"]`)
-                .trigger("click");
+                .trigger("click", {force: true});
 
             cy.get("@karyotypeContent")
                 .invoke("css", "display")
@@ -763,6 +763,17 @@ context("GenomeBrowser", () => {
                         .find("polyline")
                         .should("exist");
                 });
+
+                it("should display a tooltip when hovering the coverage", () => {
+                    // eslint-disable-next-line cypress/no-force
+                    cy.get("@coverage")
+                        .find(`rect[data-cy="gb-coverage-tooltip-mask"]`)
+                        .trigger("mouseenter", {force: true});
+
+                    cy.get("@coverage")
+                        .find(`text[data-cy="gb-coverage-tooltip-text"]`)
+                        .should("not.have.css", "display", "none");
+                });
             });
 
             context("alignments", () => {

cypress/e2e/iva/variant-browser-grid.cy.js

@@ -271,6 +271,38 @@ context("Variant Browser Grid", () => {
         });
     });
 
+    context("clinical info", () => {
+        context("cosmic column", () => {
+            const columnIndex = 18;
+            it("should display an 'x' icon if no cosmic information is available", () => {
+                cy.get("@variantBrowser")
+                    .find(`tbody > tr[data-uniqueid="14:91649938:A:G"] > td`)
+                    .eq(columnIndex)
+                    .find("i")
+                    .should("have.class", "fa-times");
+            });
+
+            it("should display the number of entries and total trait associations", () => {
+                cy.get("@variantBrowser")
+                    .find("tbody tr:first > td")
+                    .eq(columnIndex)
+                    .should("contain.text", "1 entry (1)");
+            });
+
+            it("should display a tooltip with a link to cosmic", () => {
+                cy.get("@variantBrowser")
+                    .find("tbody tr:first > td")
+                    .eq(columnIndex)
+                    .find("a")
+                    .trigger("mouseover");
+
+                cy.get(`div[class="qtip-content"]`)
+                    .find(`a[href^="https://cancer.sanger.ac.uk/cosmic/search?q="]`)
+                    .should("exist");
+            });
+        });
+    });
+
     context("actions", () => {
         const variant = "14:91649858:C:T";
         beforeEach(() => {

cypress/e2e/iva/variant-interpreter-grid-cancer-cnv.cy.js

@@ -168,11 +168,9 @@ context("Variant Interpreter Grid Cancer CNV", () => {
 
         it("should display Cohort Stats (Population Frequencies) tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(10)
-                .within(() => {
-                    cy.get("a")
-                        .trigger("mouseover");
-                });
+                .eq(13)
+                .find("a")
+                .trigger("mouseover");
             cy.get(".qtip-content")
                 .should("be.visible");
         });

cypress/e2e/iva/variant-interpreter-grid-cancer.cy.js

@@ -208,23 +208,20 @@ context("Variant Interpreter Grid Cancer", () => {
             });
         });
 
-        it("should display cohort stats (population frequencies) tooltip", () => {
+        it("should display cohort stats tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(10)
-                .within(() => {
-                    cy.get("a").trigger("mouseover");
-                });
+                .eq(13)
+                .find("a")
+                .trigger("mouseover");
             cy.get(".qtip-content")
                 .should("be.visible");
         });
 
-        it("should reference population frequencies tooltip", () => {
+        it("should display reference population frequencies tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(11)
-                .within(() => {
-                    cy.get("a")
-                        .trigger("mouseover");
-                });
+                .eq(14)
+                .find("a")
+                .trigger("mouseover");
             cy.get(".qtip-content")
                 .should("be.visible");
         });

cypress/e2e/iva/variant-interpreter-grid-germline.cy.js

@@ -168,51 +168,23 @@ context("Variant Interpreter Grid Germiline", () => {
             });
         });
 
-        it("should display cohort stats (Population Frequencies) tooltip", () => {
+        it("should display cohort stats tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(9)
-                .within(() => {
-                    cy.get("a")
-                        .trigger("mouseover");
-                });
+                .eq(12)
+                .find("a")
+                .trigger("mouseover");
             cy.get(".qtip-content")
                 .should("be.visible");
         });
 
         it("should display reference population frequencies tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(10)
-                .within(() => {
-                    cy.get("a")
-                        .trigger("mouseover");
-                });
-            cy.get(".qtip-content")
-                .should("be.visible");
-        });
-
-        it("should display ACMG Prediction (Classification) tooltip", () => {
-            cy.get("tbody tr:first > td")
-                .eq(16)
-                .within(() => {
-                    cy.get("a")
-                        .trigger("mouseover");
-                });
-            cy.get(".qtip-content")
-                .should("be.visible");
-        });
-
-        it("should display OMIM Prediction (Classification) tooltip", () => {
-            UtilsTest.changePage(browserInterpreterGrid,2);
-
-            cy.get("tbody tr:nth-child(6) > td:nth-child(15)")
-                .within(() => {
-                    cy.get("a")
-                        .trigger("mouseover");
-                });
+                .eq(13)
+                .find("a")
+                .trigger("mouseover");
             cy.get(".qtip-content")
                 .should("be.visible");
         });
-
     });
 
     context("Helpers", () => {

cypress/support/utils-test.js

@@ -14,24 +14,11 @@
  * limitations under the License.
  */
 
-import UtilsNew from "../../src/core/utils-new.js";
-import JSZip from "jszip";
 import {TIMEOUT} from "./constants.js";
 
 
 export default class UtilsTest {
 
-
-    static getFileJson = async (path, filename ) => {
-        try {
-            const zipFiles = await JSZip.loadAsync(UtilsNew.importBinaryFile(path));
-            const content = await zipFiles.file(filename).async("string");
-            return JSON.parse(content);
-        } catch (err) {
-            console.error("File not exist", err);
-        }
-    }
-
     static getByDataTest = (selector, tag, ...args) => cy.get(`div[data-testid='${selector}'] ${tag ?? ""}`, ...args);
 
     static setInput = (selectors, val) => {

docker/iva-app/Dockerfile

@@ -1,10 +1,8 @@
 FROM httpd:2.4-bullseye
-## Custom httpd.conf file to update exposed port from 80 to 8080
-COPY ./docker/iva-app/custom-httpd.conf /usr/local/apache2/conf/httpd.conf
 
 ## To run the docker use:
 ## docker build -f ./docker/iva-app/Dockerfile -t iva-httpd .
-## docker run --name jsorolla -p 8888:8080 opencb/iva-app
+## docker run --name jsorolla -p 8888:80 opencb/iva-app
 ## Then open:  http://localhost:8888/iva o http://localhost:8888/api
 
 LABEL org.label-schema.vendor="OpenCB" \
@@ -17,27 +15,23 @@ LABEL org.label-schema.vendor="OpenCB" \
 ## Update and create iva user
 RUN apt-get update && apt-get -y upgrade && \
     apt-get install -y vim jq && \
-    rm -rf /var/lib/apt/lists/* && \
-    chown -R www-data /usr/local/apache2/logs/
+    rm -rf /var/lib/apt/lists/*
 
 ## Allow to build different images by passing the path to the SITE
 ARG     SITE=src/sites
 
 ## Copy files
 ## IVA
-COPY --chown=www-data   ./build/iva              /usr/local/apache2/htdocs/iva
-COPY --chown=www-data   ./${SITE}/iva/conf       /usr/local/apache2/htdocs/iva/conf/
-COPY --chown=www-data   ./${SITE}/iva/img        /usr/local/apache2/htdocs/iva/img/
+COPY    ./build/iva                 /usr/local/apache2/htdocs/iva
+COPY    ./${SITE}/iva/conf          /usr/local/apache2/htdocs/iva/conf/
+COPY    ./${SITE}/iva/img           /usr/local/apache2/htdocs/iva/img/
 
 RUN true
 
 ## API
-COPY --chown=www-data    ./build/api             /usr/local/apache2/htdocs/api
-COPY --chown=www-data    ./${SITE}/api/conf      /usr/local/apache2/htdocs/api/conf/
-COPY --chown=www-data    ./${SITE}/api/img       /usr/local/apache2/htdocs/api/img/
-
-## Run Docker images as non root
-USER www-data
+COPY    ./build/api                 /usr/local/apache2/htdocs/api
+COPY    ./${SITE}/api/conf          /usr/local/apache2/htdocs/api/conf/
+COPY    ./${SITE}/api/img           /usr/local/apache2/htdocs/api/img/
 
 ## Genome Maps (Coming soon  :-) )
 #COPY    ./build/genome-maps                 /usr/local/apache2/htdocs/genome-maps