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Please file issues for this repository and Web site at the dockstore/dockstore repository!

Table of Contents

Dockstore UI2

This project was generated with Angular CLI version 1.0.0-rc.4.

Set Up Angular CLI

Prerequisites

  • Java 17+
  • Node and its included NPM (see .nvmrc for the correct version of node to install)
  • wget

Install NPM and Node using nvm:

wget -qO- https://raw.githubusercontent.com/creationix/nvm/v0.34.0/install.sh | bash

Close current terminal and open a new one or source ~/.bashrc

nvm install $(cat .nvmrc)

Optionally, install a global Angular CLI in order to execute ng commands without prepending npx.
Otherwise, prepend npx to every command in this README if a global @angular/cli was not installed. Before installing, follow https://docs.npmjs.com/getting-started/fixing-npm-permissions#option-two-change-npms-default-directory to fix permissions if needed.

$npm i -g @angular/cli@14.2.8

NPM

After cloning the repo from GitHub, you can install the npm packages.

git clone https://github.com/dockstore/dockstore-ui2.git
cd dockstore-ui2
git checkout develop
git pull

npm ci

npm ci will install all npm dependencies including Prettier and the Husky Git hook. Ensure CI=true is not set when using npm ci or else the Git hook will not work. Prettier + Husky will automatically format changed files before each commit:

$ git commit -m "Test"
ghusky > pre-commit (node v10.13.0)
  ↓ Stashing changes... [skipped]
    → No partially staged files found...
  ✔ Running linters...
[feature/2130/prettier b6da3e7c] Test

Check to make sure Angular CLI has been properly set up

 ng v

     _                      _                 ____ _     ___
    / \   _ __   __ _ _   _| | __ _ _ __     / ___| |   |_ _|
   / △ \ | '_ \ / _` | | | | |/ _` | '__|   | |   | |    | |
  / ___ \| | | | (_| | |_| | | (_| | |      | |___| |___ | |
 /_/   \_\_| |_|\__, |\__,_|_|\__,_|_|       \____|_____|___|
                |___/
    

Angular CLI: 14.2.7
Node: 16.18.1
Package Manager: npm 8.19.2 
OS: darwin arm64

Angular: 14.2.8
... animations, common, compiler, compiler-cli, core, forms
... language-service, platform-browser, platform-browser-dynamic
... router

Package                         Version
---------------------------------------------------------
@angular-devkit/architect       0.1402.7
@angular-devkit/build-angular   14.2.7
@angular-devkit/core            14.2.7
@angular-devkit/schematics      14.2.7
@angular/cdk                    14.2.6
@angular/cli                    14.2.7
@angular/flex-layout            14.0.0-beta.41
@angular/material               14.2.6
@schematics/angular             14.2.7
rxjs                            6.6.7
typescript                      4.8.4

If you wish to serve the dist folder in a VM, make sure you have nginx and security rules set up properly. Nginx

Project Set Up

The Dockstore class in src/app/shared/dockstore.model.ts is for integrating supported services.

In dockstore-webservice, the dockstore.yml being served must be edited to include the client IDs.

Development server

Run npm run start -- --host=<host> for a dev server. Navigate to http://<host>:4200/. The app will automatically reload if you change any of the source files.

Updating dependencies

Run npm update. This will automatically update package.json and package-lock.json.

When you update a dependency in the package.json, make sure to update the third party licenses file THIRD-PARTY-LICENSES.csv. To update this file, run npm run license. Unfortunately, there is not a way to permanently say a certain dependency should be x license using this package. So, once we manually update a dependency's license info and we continue to use it, running the above command will always result in it being unknown in the updated file. Be sure to review the updated file (i.e. revert changes as needed and update any new unknown or unlicensed dependencies).

For more documentation on license-checker, visit here

Code scaffolding

Run ng g component component-name to generate a new component. You can also use ng generate directive/pipe/service/class/module. See https://github.com/datorama/akita-schematics#create-a-new-feature for how to generate Akita-related components.

Build

When building against artifactory, the build should use the latest SNAPSHOT. In this scenario, the package.json will look like

 "config": {
    "webservice_version_prefix": "1.16.0",
    "webservice_version": "1.16.0-alpha.10",
    "use_snapshot": true

Optionally override the webservice version using npm config set dockstore-ui2:webservice_version ${WEBSERVICE_VERSION}

For example, to build against a specific branch, edit the package.json with

  "config": {
    "webservice_version_prefix": "1.16.0",
    "webservice_version": "feature/seab-6420/modify-endpoint-description-for-new-health-checks",
    "use_snapshot": false
  },

For example, to build against a specific commit, edit the package.json with

  "config": {
    "webservice_version_prefix": "1.16.0",
    "webservice_version": "1550b549c45b2f4ba7f205e2f64502d523417dcd",
    "use_snapshot": false
  },

Run npm run build to build the project. The build artifacts will be stored in the dist/ directory.

Angular Production Build

For an Angular Production Build, you will need to install Nginx. Replace your nginx.conf file (location depends on your installation) with this template, filling in the two paths:

events {
}
http {
  include       /usr/local/etc/nginx/mime.types;
  server {
    listen 4200;
      location = /swagger.json {
        proxy_pass  http://localhost:8080/swagger.json;
      }
    location /api/ {
          rewrite ^ $request_uri;
          rewrite ^/api/(.*) $1 break;
          return 400;
          proxy_pass     http://localhost:8080/$uri;
    }
    location / {
        root  /<path to>/dockstore-ui2/dist; # FILL IN
        index  index.html index.htm;
        try_files $uri $uri/ /index.html =404;
    }
  }
  server {
    listen 5200;
    location / {
        root  /<path to>/dockstore-ui2/dist; # FILL IN
        index  index.html index.htm;
        try_files $uri $uri/ /index.html =404;
        if ($request_method = 'OPTIONS') {
            add_header 'Access-Control-Allow-Origin' '*';
            add_header 'Access-Control-Allow-Methods' 'GET, POST, OPTIONS';
            #
            # Custom headers and headers various browsers *should* be OK with but aren't
            #
            add_header 'Access-Control-Allow-Headers' 'DNT,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range';
            #
            # Tell client that this pre-flight info is valid for 20 days
            #
            add_header 'Access-Control-Max-Age' 1728000;
            add_header 'Content-Type' 'text/plain; charset=utf-8';
            add_header 'Content-Length' 0;
            return 204;
         }
         if ($request_method = 'POST') {
            add_header 'Access-Control-Allow-Origin' '*';
            add_header 'Access-Control-Allow-Methods' 'GET, POST, OPTIONS';
            add_header 'Access-Control-Allow-Headers' 'DNT,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range';
            add_header 'Access-Control-Expose-Headers' 'Content-Length,Content-Range';
         }
         if ($request_method = 'GET') {
            add_header 'Access-Control-Allow-Origin' '*';
            add_header 'Access-Control-Allow-Methods' 'GET, POST, OPTIONS';
            add_header 'Access-Control-Allow-Headers' 'DNT,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range';
            add_header 'Access-Control-Expose-Headers' 'Content-Length,Content-Range';
         }
      }
    }
}

Use npm run build.prod for an Angular Production Build and start it with nginx. localhost:4200 should be available immediately.

Running unit tests

Run ng test to execute the unit tests via Karma.

Running end-to-end tests

Cypress is no longer specified in the package.json, check the .circleci/config.yml for the version and how to install it.

Run npx cypress open or npx cypress run to execute the end-to-end tests via Cypress.io. Before running the tests make sure you:

  • have a postgresql database
  • serve the app via ng serve or similar.
  • have the Dockstore webservice jar in the root directory and run it (see scripts/run-webservice-script.sh for guideline)

Running smoke tests

Smoke tests are part of the end-to-end testing suite and are located under cypress/integration/smokeTests/. The smoke tests can be executed alongside other integration tests when running npx cypress open or npx cypress run.

Various sets of smoke tests are runnable from scripts in package.json. To run smoke tests against your local service, run npm run test-local-no-auth. Before running the tests make sure you have Dockstore set up locally, as described in the above section.

npm run test-local-no-auth is also executed in CircleCI when a branch is pushed, or a pull request is made. When run on CircleCI, the smoke tests leverage a dummy database stored in test/smoke_test_db.sql. If a smoke test fails on CircleCI, there are two main scenarios to consider:

  1. The smoke tests are failing due to a change in the UI. This can be fixed by modifying the tests in cypress/integration/smokeTests/.
  2. The dummy smoke test database does not have the proper data for the tested version of the UI. This can be fixed by modifying the data in test/smoke_test_db.sql.

Modifying the smoke test database

Note: Do not link any real accounts in the smoke test database as that will add tokens to the database dump, which is publicly visible. This means you cannot register an account in the normal fashion, as that will add either a GitHub or Google token to the database.

To modify the smoke test database, test/smoke_test_db.sql:

  1. Load test/smoke_test_db.sql into your postgres database.
  2. Run Dockstore locally.
  3. Login to one of the test users already in the database by setting the browser ng2-ui-auth_token to fake-admin-token, fake-curator-token or fake-basic-1-token. Then, refresh the page. (To locate ng2-ui-auth_token in chrome, go to developer tools -> application -> storage (on the left snackbar) -> local storage -> http://localhost:4200)
  4. Make any desired changes to the database, preferably via the UI. It's not recommended to manually change the smoke test database with SQL commands, as this can cause constraint issues, but in some cases it is required.
  5. Create a new database dump for the content in postgres, for example if postgres is running in a Docker container, execute: docker exec -t postgres1 pg_dump -U postgres --column-inserts webservice_test > smoke_test_db.sql
  6. Verify the database dump doesn't have any live tokens in the tokens table (Search for Data for Name: token; Type: TABLE DATA; Schema: public; Owner: dockstore), then commit the new database dump.

Further help

To get more help on the Angular CLI use ng help or go check out the Angular CLI README.