Release 13.0.0 (#201)

* Pass drug screen when multiple data types are selected

* Clean up code

* Add additional depletion screen scores

Caleydo/tdp_bi_bioinfodb#1364

* orphan import

* Linting and other fixes

* Linting

* prepare next development version 12.0.1-SNAPSHOT

* Replace `gene_map_ensgs` with idtype mapping

Closes Caleydo/tdp_bi_bioinfodb#419

* Replace `gene_map_ensgs` request with native idtype mapping
* Remove python DB view
* Remove `_id` from typing, as it was not returned by the API and was not used previously

* Remove orphan import

* Fix typo in depletion screen score name

* Allow for the domain of the scores to be auto-inferred (#175)

Co-authored-by: Holger Stitz <[email protected]>

* Fix Typescript compile errors in `selectionChanged` and `parameterCanged` of ranking views (#191)

* Fix TS errors ranking views

The return value of `selectionChanged` and `parameterCanged` has been typed/changed in datavisyn/tdp_core#725

* Fix data type select in welcome tour (#192)

* Fix outdated dist folder (#194)

* Prepare github changes

* Remove circleci

* prepare next dev version

* Update fontawesome

* refactor: Improve Cypress setup and use Cypress commands.js (#169)

Co-authored-by: Florian Engertsberger <[email protected]>
Co-authored-by: Holger Stitz <[email protected]>

* Merge visyn_scripts

* prepare release 13.0.0

Co-authored-by: oltionchampari <[email protected]>
Co-authored-by: Holger Stitz <[email protected]>
Co-authored-by: Champari Oltion <[email protected]>
Co-authored-by: anita-steiner <>
Co-authored-by: Florian Engertsberger <[email protected]>

.eslintrc.js

@@ -1,71 +1 @@
-module.exports = {
-  root: true,
-  extends: [
-    "airbnb",
-    "airbnb-typescript",
-    "airbnb/hooks",
-    "eslint:recommended",
-    "plugin:import/recommended",
-    "plugin:react/recommended",
-    "plugin:@typescript-eslint/recommended",
-    "plugin:jest/recommended",
-    "plugin:prettier/recommended"
-  ],
-  plugins: ["react", "@typescript-eslint", "jest"],
-  ignorePatterns: ["*.js"],
-  env: {
-    browser: true,
-    es6: true,
-    jest: true
-  },
-  globals: {
-    Atomics: "readonly",
-    SharedArrayBuffer: "readonly",
-  },
-  parser: "@typescript-eslint/parser",
-  parserOptions: {
-    // Make sure eslint and VS Code use the same path for the tsconfig.json:
-    // https://github.com/typescript-eslint/typescript-eslint/issues/251
-    tsconfigRootDir: __dirname,
-    project: "./tsconfig.eslint.json"
-  },
-  rules: {
-    // Disables jsx-a11y https://github.com/import-js/eslint-plugin-import/blob/v2.25.4/docs/rules/no-webpack-loader-syntax.md
-    ...Object.keys(require('eslint-plugin-jsx-a11y').rules).reduce((acc, rule) => { acc[`jsx-a11y/${rule}`] = 'off'; return acc }, {}),
-    "class-methods-use-this":"off",
-    "linebreak-style": "off",
-    "no-continue": "off",
-    "no-multi-assign": "warn",
-    "no-nested-ternary": "off",
-    "no-param-reassign": ["error", { "props": false }],
-    "no-return-assign": "warn", 
-    "no-restricted-syntax": "off",
-    "no-plusplus": "off",
-    "no-prototype-builtins": "warn",
-    "no-minusminus": "off",
-    "no-underscore-dangle": "off",
-    "max-classes-per-file": "off",
-    "no-param-reassign": "warn",
-    "import/no-extraneous-dependencies": "off",
-    // Disable the following 2 lines because to allow webpack file-loaders syntax
-    "import/no-webpack-loader-syntax": "off",
-    "import/no-unresolved": "off",
-    "import/prefer-default-export": "off",
-    "import/order": "error",
-    "prefer-destructuring": ["warn", {"object": true, "array": false}],
-    "prefer-promise-reject-errors": "warn",
-    "prefer-spread": "warn",
-    "@typescript-eslint/ban-ts-comment": "warn",
-    "react/destructuring-assignment": "warn",
-    "react/jsx-props-no-spreading": "off",
-    "react/no-unused-class-component-methods": "warn",
-    "react/prop-types": "off",
-    "react/require-default-props": "off",
-    "react/static-property-placement": ["warn", "property assignment", {
-      childContextTypes: "static getter",
-      contextTypes: "static public field",
-      contextType: "static public field",
-      displayName: "static public field",
-    }]
-  }
-};
+module.exports = require('visyn_scripts/config/eslintrc.template')({ tsconfigRootDir: __dirname });

.gitignore

@@ -4,7 +4,6 @@
 /.idea
 /lib/
 /build/
-/dist/tsBuildInfoFile
 /dist_python/
 *.egg-info/
 *.egg
@@ -27,3 +26,12 @@ node_modules/
 /tests/**/*.map
 *.css
 package-lock.json
+/yarn.lock
+# yarn
+.pnp.*
+.yarn/*
+!.yarn/patches
+!.yarn/plugins
+!.yarn/releases
+!.yarn/sdks
+!.yarn/versions

.prettierrc.js

@@ -1,6 +1 @@
-module.exports = {
-  "endOfLine": "auto",
-  "singleQuote": true,
-  "trailingComma": "all",
-  "printWidth": 160
-};
+module.exports = require('visyn_scripts/config/prettierrc.template')

.yarnrc.yml

@@ -0,0 +1,2 @@
+yarnPath: .yarn/releases/yarn-3.2.2.cjs
+nodeLinker: node-modules

.yo-rc.json

@@ -44,9 +44,6 @@
     "today": "Sun, 06 Nov 2016 23:21:43 GMT",
     "app": "",
     "clientOnly": false,
-    "entries": {
-      "app": "./src/index.ts"
-    },
     "libraryAliases": {
       "d3": "d3/d3",
       "scrollTo": "jquery.scrollto/jquery.scrollTo.js"

README.md

@@ -2,7 +2,7 @@ tdp_publicdb
 =====================
 [![Phovea][phovea-image-client]][phovea-url] [![Phovea][phovea-image-server]][phovea-url] [![NPM version][npm-image]][npm-url] [![Build Status][circleci-image]][circleci-url]
 
-This repository contains the database connector to the bioinfoDB.hg38 database and the respective SQL queries to drive the [tdp_gene](https://github.com/Caleydo/tdp_gene/) views and visualizations.
+This repository contains the database connector to the bioinfoDB.hg38 database and the respective SQL queries to show the views and visualizations.
 
 Installation
 ------------

cypress/integration/index.js

@@ -0,0 +1,6 @@
+export * from './long-running-score.spec';
+export * from './session_all_genes.spec';
+export * from './session_all_celllines.spec';
+export * from './session_all_tissues.spec';
+
+export * from './ordino-video-test.spec';

cypress/integration/long-running-score.spec.js

@@ -0,0 +1,43 @@
+// https://www.youtube.com/watch?v=JZIIf-k852g&t=1s
+it('Long Running Score', function() {
+    cy.visit(Cypress.env('host'));
+    // Login
+    cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click();
+
+    cy.login(); // use Cypress command registerd in Ordino app
+
+    // Show you can select single genes if you wanted
+    cy.scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+    cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+    // wait intentionally a few seconds
+    cy.wait(2000)
+    cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-link]').click();
+
+    // Open Lineup ranking
+    // Define api calls to wait:
+    cy.intercept('/api/tdp/db/publicdb/gene/desc').as('gene_desc');
+    cy.intercept('/api/tdp/db/publicdb/gene/filter?filter_species=human&filter_panel=normal+chromosome+protein+coding+human+genes').as('human_genes');
+    cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click();
+    cy.wait('@gene_desc');
+    cy.wait('@human_genes');
+    cy.waitLineupReadyOrdino(0)
+
+    // Add column
+    cy.get('[data-testid=add-column-button]').click();
+    cy.wait(2000);
+    cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click();
+    cy.select2SingleSelect("data-type", "Relative Copy Number")
+    cy.formSelect("aggregation", "Boxplot")
+    cy.get('[data-testid=primary-dialog-button]').click();
+    cy.checkScoreColLoadedOrdino(0, ['Relative Copy Number', 'Boxplot'], 9)
+
+    // Add column
+    cy.get('[data-testid=add-column-button]').click();
+    cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click();
+    cy.formSelect("aggregation", "Frequency")
+    cy.formSelect("comparison-operator", "> greater than")
+    cy.get(':nth-child(5) > .form-control').clear();
+    cy.get(':nth-child(5) > .form-control').type('4');
+    cy.get('[data-testid=primary-dialog-button]').click();
+    cy.checkScoreColLoadedOrdino(0, ['Frequency > 4'], 10)
+})

cypress/integration/ordino-video-test.spec.js

@@ -0,0 +1,151 @@
+import { cy, it, Cypress } from 'local-cypress';
+
+// https://www.youtube.com/watch?v=JZIIf-k852g&t=1s
+it('ordino video', function() {
+    cy.visit(Cypress.env('host'));
+
+    cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click();
+
+    cy.login(); // use Cypress command registerd in Ordino app
+
+    // Show you can select single genes if you wanted
+    cy.scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+    cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+    // wait intentionally a few seconds
+    cy.wait(2000)
+    cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-link]').click();
+
+    // Open Lineup ranking
+    // Define api calls to wait:
+    cy.intercept('/api/tdp/db/publicdb/gene/desc').as('gene_desc');
+    cy.intercept('/api/tdp/db/publicdb/gene/filter?filter_species=human&filter_panel=normal+chromosome+protein+coding+human+genes').as('human_genes');
+    cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click();
+    cy.wait('@gene_desc');
+    cy.wait('@human_genes');
+    cy.waitLineupReadyOrdino(0)
+
+    // Add column
+    cy.get('[data-testid=add-column-button]').click();
+    cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click();
+    cy.select2MultiSelect("cell-line", "HCC1954")
+    cy.select2MultiSelect("data-type", "Relative Copy Number")
+    cy.get('[data-testid=primary-dialog-button]').click();
+    cy.checkScoreColLoadedOrdino(0, ['HCC1954', 'Relative Copy Number'], 9);
+
+    // Sort by column
+    cy.get('[data-testid=viewWrapper-0] > .view > .inner > .tdp-view > :nth-child(1) > .le > .le-header > .le-thead > section:nth-last-child(-n+1) > .lu-toolbar > .lu-action-sort').click();
+
+    // Show some information
+    cy.get('[data-testid="(un)collapse-button"] > .fas').click();
+    // intentionally wait 1 second
+    cy.wait(1000)
+    // filter with histogram not possible
+    cy.get('[data-testid="(un)collapse-button"] > .fas').click();
+
+    // Add column
+    cy.get('[data-testid=add-column-button]').click();
+    cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click();
+    cy.select2MultiSelect("cell-line", "HCC1954")
+    cy.select2MultiSelect("data-type", "Normalized Gene Expression (TPM Values)")
+    cy.get('[data-testid=primary-dialog-button]').click();
+    cy.checkScoreColLoadedOrdino(0, ['HCC1954', 'Normalized Gene Expression (TPM Values)'], 10)
+
+    // Add column
+    cy.get('[data-testid=add-column-button]').click();
+    cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span').click();
+    cy.select2MultiSelect("cell-line", "HCC1954")
+    cy.select2MultiSelect("data-type", "DRIVE RSA (ER McDonald III et al., Cell, 2017)")
+    cy.get('[data-testid=primary-dialog-button]').click();
+    cy.checkScoreColLoadedOrdino(0, ['HCC1954', 'DRIVE RSA (ER McDonald III et al., Cell, 2017)'], 11)
+
+    // Invert column
+    // Here the title should be used. For some reason cypress has problmes, because there is a " character in the title. For now I use the data-id
+    cy.get('[data-id="col10"] > .lu-toolbar > .lu-action-more').click();
+    cy.get('.lu-action-data-mapping > span').click();
+    cy.get('.browser-default').select('linear_invert');
+    cy.get('.lu-dialog-buttons > [type="submit"]').click();
+
+    // Add column
+    cy.get('[data-testid=add-column-button]').click();
+    cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click();
+    cy.formSelect("row-1", "Tumor Type")
+    cy.select2MultiSelect("row-1", "breast carcinoma")
+    cy.select2SingleSelect("data-type", "Normalized Gene Expression (TPM Values)")
+    cy.get('[data-testid=primary-dialog-button]').click();
+    cy.checkScoreColLoadedOrdino(0, ['Tumor Type', 'breast carcinoma', 'Normalized Gene Expression (TPM Values)'], 12)
+
+    // Add column
+    cy.get('[data-testid=add-column-button]').click();
+    cy.wait(2000);
+    cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click();
+    cy.select2SingleSelect("data-type", "Relative Copy Number")
+    cy.formSelect("aggregation", "Boxplot")
+    cy.get('[data-testid=primary-dialog-button]').click();
+    cy.checkScoreColLoadedOrdino(0, ['Relative Copy Number', 'Boxplot'], 13)
+
+    // Add column
+    cy.get('[data-testid=add-column-button]').click();
+    cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click();
+    cy.formSelect("aggregation", "Frequency")
+    cy.formSelect("comparison-operator", "> greater than")
+    cy.get(':nth-child(5) > .form-control').clear();
+    cy.get(':nth-child(5) > .form-control').type('4');
+    cy.get('[data-testid=primary-dialog-button]').click();
+    cy.checkScoreColLoadedOrdino(0, ['Frequency > 4'], 14)
+
+    // Select elements and click on detail views
+    cy.waitLineupReadyOrdino(0)
+    cy.get('[data-index="0"] > .lu-renderer-selection').click();
+    cy.get('[data-testid=celllinedb_expression_vs_copynumber]').click();
+    cy.waitTdpNotBusy()
+    cy.waitLineupReadyOrdino(0)
+    cy.wait(2000)
+    // cy.get('[data-index="6"] > .lu-renderer-selection').click();
+    // cy.waitTdpNotBusy()
+    // cy.waitLineupReadyOrdino(0)
+    // cy.wait(2000)
+    cy.get('[data-testid=targetvalidation]').click();
+    cy.waitTdpNotBusy()
+    cy.wait(2000)
+    cy.get('[data-testid=ensembl_org]').click();
+    cy.waitTdpNotBusy()
+    cy.wait(2000)
+    cy.get('[data-testid=copynumbertable]').click();
+    cy.waitTdpNotBusy()
+    cy.wait(2000)
+
+    // Sort and filter columns
+    cy.get('[data-testid=viewWrapper-1] > .view > .inner > .tdp-view > :nth-child(1) > .le > .le-header > .le-thead > section:nth-last-child(-n+1) > .lu-toolbar > .lu-action-sort').click();
+    cy.get('[title="Tumor Type"] > .lu-toolbar > .lu-action-filter').click();
+    cy.get('.lu-dialog-table > :nth-child(1) > :nth-child(2) > div').click();
+    cy.get('.lu-dialog-table > :nth-child(1) > input').uncheck();
+    cy.get(':nth-child(6) > :nth-child(2) > .lu-dialog-filter-table-entry-label').click();
+    cy.get('.lu-dialog-table > :nth-child(6) > input').check();
+    cy.get('.lu-dialog-buttons > [type="submit"]').click();
+
+    // Add column
+    cy.get('[data-testid=viewWrapper-1] [data-testid=side-panel-wrapper] [data-testid=lu-adder-div] [data-testid=add-column-button]').click();
+    cy.get('[data-testid=viewWrapper-1] > .view > .inner > .tdp-view > [data-testid=side-panel-wrapper] > .panel-header > :nth-child(2) > [data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click();
+    cy.select2MultiSelect("gene-symbol", ["BRCA1", "BRCA2"])
+    cy.select2MultiSelect("data-type", "AA Mutated")
+    cy.get('[data-testid=primary-dialog-button]').click();
+    cy.checkScoreColLoadedOrdino(1, ['BRCA1', 'AA Mutated'], 10)
+    cy.checkScoreColLoadedOrdino(1, ['BRCA2', 'AA Mutated'], 10)
+
+    cy.waitLineupReadyOrdino(1)
+    cy.get('[data-testid=viewWrapper-1] [data-index="0"] > .lu-renderer-selection').click();
+    cy.get('[data-testid=viewWrapper-1] [data-index="12"] > .lu-renderer-selection').click();
+    cy.get('[data-testid=cosmic]').click();
+    // Intentionally wait 2 seconds
+    cy.waitTdpNotBusy()
+    cy.wait(2000)
+    cy.get('[data-testid=show] [data-testid=form-select]').select('687455');
+    // Intentionally wait 2 seconds
+    cy.waitTdpNotBusy()
+    cy.wait(2000)
+    cy.get('[data-testid=ordino_sessions_shortcut-link]').click();
+    cy.get('[data-testid=current-session-sessionscard] [data-testid=ordino0] [data-testid=save-button]').click();
+    cy.get('[data-testid=agree-input]').check();
+    cy.get('[data-testid=primary-dialog-button]').click();
+    cy.get('[data-testid=ordino_sessions_tab] [data-testid=close-button]').click();
+})

cypress/integration/session_all_celllines.spec.js

@@ -0,0 +1,24 @@
+it('Load all Celllines', function() {
+    cy.visit(Cypress.env('host'));
+
+    // Login
+    cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click();
+
+    cy.login(); // use Cypress command registerd in Ordino app
+
+    // Show you can select single genes if you wanted
+    cy.scrollElementIntoCenter('[data-testid=dataset-card-cellline-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+    cy.get('[data-testid=dataset-card-cellline-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+    // wait intentionally a few seconds
+    cy.wait(2000)
+    cy.get('[data-testid=dataset-card-cellline-dataset] [data-testid=human-link]').click();
+
+    // Open Lineup ranking
+    // Define api calls to wait:
+    cy.intercept('/api/tdp/db/publicdb/cellline/desc').as('cellline_desc');
+    cy.intercept('/api/tdp/db/publicdb/cellline/filter?filter_species=human&filter_panel=CCLE').as('human_cellline');
+    cy.get('[data-testid=ccle-button]').click();
+    cy.wait('@cellline_desc');
+    cy.wait('@human_cellline');
+    cy.waitLineupReadyOrdino(0)
+});

cypress/integration/session_all_genes.spec.js

@@ -0,0 +1,24 @@
+it('Load all Genes', function() {
+    cy.visit(Cypress.env('host'));
+
+    // Login
+    cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click();
+
+    cy.login(); // use Cypress command registerd in Ordino app
+
+    // Show you can select single genes if you wanted
+    cy.scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+    cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+    // wait intentionally a few seconds
+    cy.wait(2000)
+    cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-link]').click();
+
+    // Open Lineup ranking
+    // Define api calls to wait:
+    cy.intercept('/api/tdp/db/publicdb/gene/desc').as('gene_desc');
+    cy.intercept('/api/tdp/db/publicdb/gene/filter?filter_species=human&filter_panel=normal+chromosome+protein+coding+human+genes').as('human_genes');
+    cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click();
+    cy.wait('@gene_desc');
+    cy.wait('@human_genes');
+    cy.waitLineupReadyOrdino(0)
+});