Merge remote-tracking branch 'cbio/master' into fix-10375

.gitignore

@@ -65,3 +65,4 @@ e2e-localdb-workspace/
 junit.xml
 .nvim.lua
 .luarc.json
+.vs/

OPEN-SOURCE-DOCUMENTATION

@@ -49,3 +49,20 @@ Available under license:
     5. Products derived from this software may not be called
     "ColorBrewer", nor may "ColorBrewer" appear in their name, without
     prior written permission of Cynthia Brewer.
+
+* JavaScript/CSS Font Detector
+
+JavaScript/CSS Font Detector
+----------------------------
+Available under license:
+
+    JavaScript code to detect available availability of a
+    particular font in a browser using JavaScript and CSS.
+
+    Author : Lalit Patel
+    Website: http://www.lalit.org/lab/javascript-css-font-detect/
+    License: Apache Software License 2.0
+             http://www.apache.org/licenses/LICENSE-2.0
+
+
+

README.md

@@ -17,7 +17,9 @@ Note: you can check the frontend version of the live instance by checking `windo
 Make sure you have installed the node version and yarn version specified in
 [package.json](https://github.com/cBioPortal/cbioportal-frontend/blob/master/package.json).
 
-> **Tip:**  We recommend that you use [nvm:  Node Version Manager](https://github.com/nvm-sh/nvm) and [yvm:  Yarn Version Manager](https://yvm.js.org/docs/overview) to switch between versions more easily.
+> **Tip:**  For node, we recommend that you use [nvm:  Node Version Manager](https://github.com/nvm-sh/nvm) to switch between versions easily.
+
+> **Tip:** For yarn, you can use [yarn set version](https://yarnpkg.com/cli/set/version) or `npm install yarn@(version)`.
 
 > **Windows Tip:** If you are developing on Windows, we recommend that you use [Ubuntu / Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install-win10).
 
@@ -52,6 +54,8 @@ export BRANCH_ENV=master # or rc if branching from rc
 yarn run start
 ```
 
+> **Tip:** BRANCH_ENV should be set to `master` or `rc`, and not to your local branch name. You can set this in your ~/.bashrc if you don't intend to change it often.
+
 Example pages:
  - http://localhost:3000/
  - http://localhost:3000/patient?studyId=lgg_ucsf_2014&caseId=P04
@@ -71,8 +75,6 @@ GREP=example.spec.js yarn run testModules
 
 ```
 
-> **Windows Tip:** There is a known solved hiccup running the tests on Ubuntu via Windows Subsystem for Linux (WSL): [#7096](https://github.com/cBioPortal/cbioportal/issues/7096)
-
 To run unit/integration tests in watch mode
 ```
 yarn run test:watch
@@ -139,6 +141,12 @@ or clear entire local storage
 ```
 localStorage.clear()
 ```
+You can also add a bookmarklet to quickly switch to your local frontend server. Set the URL to the following:
+
+```
+javascript:(function()%7BlocalStorage.setItem%28%60localdev%60,true%29%3Bwindow.location.reload()%3B %7D)()
+```
+
 You can also use a netlify deployed cbioportal-frontend pull request for serving the JS:
 1. Create the following bookmarklet: 
 ```
@@ -147,6 +155,8 @@ javascript:(function()%7Bvar pr %3D prompt("Please enter PR%23")%3Bif (pr %26%26
 2. Navigate to the cBioPortal installation that you want to test.
 3. Click the bookmarklet and enter your pull request number.
 
+
+
 ## Run e2e-tests
 
 End-to-end tests can be run against public cbioportal instances or against a local dockerized backend. These two e2e-tests types are referred to as `remote` and `local` types of e2e-tests.
@@ -161,6 +171,7 @@ cd end-to-end-test
 // install deps
 yarn --ignore-engines
 
+cd ..
 ```
 
 ```
@@ -349,3 +360,16 @@ Please make sure to not introduce any dependencies from `cbioportal-frontend` wo
 ### react-mutation-mapper
 
 [react-mutation-mapper](https://www.npmjs.com/package/react-mutation-mapper/) is a separate public npm library that contains the Mutation Mapper and related components.
+
+## WSL Tips
+
+When running on a Windows environment, use [WSL: Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install-win10). You will be able to run a linux shell, which is necessary for many of the scripts used. You will also be able to use it concurrently with Windows applications.
+
+Make sure the git repo is cloned under the WSL file system (under your home directory).  If you instead clone it to the Windows file system (e.g. `/mnt/c/...` from WSL), then all scripts will be extremely slow.
+
+If you may be working with the git repo via the Windows system, then make sure your line returns are set to `lf` as opposed to the Windows default `crlf`. 
+
+```
+# from the repo folder
+git config core.autocrlf false
+```

end-to-end-test/local/runtime-config/portal.properties

@@ -181,6 +181,8 @@ session.service.url=
 # session.service.user=user
 # session.service.password=pass
 
+session.endpoint.publisher-api-key=SECRETKEY
+
 # disabled tabs, | delimited
 # possible values: cancer_types_summary, mutual_exclusivity, plots, mutations, co_expression, enrichments, survival, network, download, bookmark, IGV
 disabled_tabs=

end-to-end-test/local/specs/virtual-study.spec.js

@@ -0,0 +1,171 @@
+var assert = require('assert');
+var goToUrlAndSetLocalStorage = require('../../shared/specUtils')
+    .goToUrlAndSetLocalStorage;
+
+const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, '');
+const studyEs0Summary = CBIOPORTAL_URL + '/study/summary?id=study_es_0';
+
+describe('Virtual Study life cycle', function() {
+    const vsTitle = 'Test VS ' + Date.now();
+    let link;
+    let vsId;
+    const X_PUBLISHER_API_KEY = 'SECRETKEY';
+
+    it('Login and navigate to the study_es_0 study summary page', function() {
+        goToUrlAndSetLocalStorage(studyEs0Summary, true);
+    });
+    it('Click Share Virtual Study button', function() {
+        const studyView = $('.studyView');
+        const shareVSBtn = studyView.$(
+            'button[data-tour="action-button-bookmark"]'
+        );
+        shareVSBtn.waitForClickable();
+        shareVSBtn.click();
+    });
+    it('Provide the title and save', function() {
+        const modalDialog = $('.modal-dialog');
+        modalDialog.waitForDisplayed();
+        const titleInput = modalDialog.$('input#sniglet');
+        titleInput.setValue(vsTitle);
+        const saveBtn = modalDialog.$(
+            '[data-tour="virtual-study-summary-save-btn"]'
+        );
+        saveBtn.click();
+        modalDialog.$('.text-success').waitForDisplayed();
+        const linkInput = modalDialog.$('input[type="text"]');
+        link = linkInput.getValue();
+        assert.ok(
+            link.startsWith('http'),
+            'The value should be link, but was ' + link
+        );
+        vsId = link
+            .split('?')[1]
+            .split('&')
+            .map(paramEqValue => paramEqValue.split('='))
+            .find(([key, value]) => key === 'id')[1];
+        assert.ok(vsId, 'Virtual Study ID has not to be empty');
+    });
+    it('See the VS in My Virtual Studies section on the landing page', function() {
+        goToUrlAndSetLocalStorage(CBIOPORTAL_URL, true);
+        const vsSection = $(`//*[text()="${vsTitle}"]/ancestor::ul[1]`);
+        vsSection.waitForDisplayed();
+        const sectionTitle = vsSection.$('li label span');
+        assert.equal(sectionTitle.getText(), 'My Virtual Studies');
+    });
+    it('Publish the VS', function() {
+        const result = browser.executeAsync(
+            function(cbioUrl, vsId, key, done) {
+                const url = cbioUrl + '/api/public_virtual_studies/' + vsId;
+                const headers = new Headers();
+                headers.append('X-PUBLISHER-API-KEY', key);
+                fetch(url, {
+                    method: 'POST',
+                    headers: headers,
+                })
+                    .then(response => {
+                        done({
+                            success: response.ok,
+                            message: 'HTTP Status: ' + response.status,
+                        });
+                    })
+                    .catch(error => {
+                        done({ success: false, message: error.message });
+                    });
+            },
+            CBIOPORTAL_URL,
+            vsId,
+            X_PUBLISHER_API_KEY
+        );
+        assert.ok(result.success, result.message);
+    });
+    it('See the VS in Public Virtual Studies section on the landing page', function() {
+        goToUrlAndSetLocalStorage(CBIOPORTAL_URL, true);
+        const vsSection = $(`//*[text()="${vsTitle}"]/ancestor::ul[1]`);
+        vsSection.waitForDisplayed();
+        const sectionTitle = vsSection.$('li label span');
+        assert.equal(sectionTitle.getText(), 'Public Virtual Studies');
+    });
+    it('Re-publish the VS specifying PubMed ID and type of cancer', function() {
+        const result = browser.executeAsync(
+            function(cbioUrl, vsId, key, done) {
+                const headers = new Headers();
+                headers.append('X-PUBLISHER-API-KEY', key);
+                fetch(
+                    cbioUrl +
+                        '/api/public_virtual_studies/' +
+                        vsId +
+                        '?pmid=28783718&typeOfCancerId=aca',
+                    {
+                        method: 'POST',
+                        headers: headers,
+                    }
+                )
+                    .then(response => {
+                        done({
+                            success: response.ok,
+                            message: 'HTTP Status: ' + response.status,
+                        });
+                    })
+                    .catch(error => {
+                        done({ success: false, message: error.message });
+                    });
+            },
+            CBIOPORTAL_URL,
+            vsId,
+            X_PUBLISHER_API_KEY
+        );
+        assert.ok(result.success, result.message);
+    });
+    it('See the VS in the Adrenocortical Adenoma section with PubMed link', function() {
+        goToUrlAndSetLocalStorage(CBIOPORTAL_URL, true);
+        const vsRow = $(`//*[text()="${vsTitle}"]/ancestor::li[1]`);
+        const vsSection = vsRow.parentElement();
+        vsSection.waitForDisplayed();
+        const sectionTitle = vsSection.$('li label span');
+        assert.equal(sectionTitle.getText(), 'Adrenocortical Adenoma');
+        //has PubMed link
+        assert.ok(vsRow.$('.fa-book').isExisting());
+    });
+    it('Un-publish the VS', function() {
+        const result = browser.executeAsync(
+            function(cbioUrl, vsId, key, done) {
+                const headers = new Headers();
+                headers.append('X-PUBLISHER-API-KEY', key);
+                fetch(cbioUrl + '/api/public_virtual_studies/' + vsId, {
+                    method: 'DELETE',
+                    headers: headers,
+                })
+                    .then(response => {
+                        done({
+                            success: response.ok,
+                            message: 'HTTP Status: ' + response.status,
+                        });
+                    })
+                    .catch(error => {
+                        done({ success: false, message: error.message });
+                    });
+            },
+            CBIOPORTAL_URL,
+            vsId,
+            X_PUBLISHER_API_KEY
+        );
+        assert.ok(result.success, result.message);
+    });
+
+    it('Removing the VS', function() {
+        goToUrlAndSetLocalStorage(CBIOPORTAL_URL, true);
+        const vsRow = $(`//*[text()="${vsTitle}"]/ancestor::li[1]`);
+        vsRow.waitForDisplayed();
+
+        const removeBtn = vsRow.$('.fa-trash');
+        removeBtn.click();
+    });
+
+    it('The VS disappears from the landing page', function() {
+        goToUrlAndSetLocalStorage(CBIOPORTAL_URL, true);
+        $('[data-test="cancerTypeListContainer"]').waitForDisplayed();
+        const vsRowTitle = $(`//*[text()="${vsTitle}"]`);
+        browser.pause(100);
+        assert.ok(!vsRowTitle.isExisting());
+    });
+});