Feature/preinstall (#601)

* Preinstall script

* Manually install global @angular/cli

* Optimize Travis

* Change timeout to more sane levels

* Move configuration to config

* Move openapi code generation to scripts

* Silent install

* Update README.md [skip ci]

* nvm version file

* Try using nvm version

* Update README.md [skip ci]

* What happens when you lint with broken imports

* Rename config variable

* Fix

* Use variable

* Comment [skip ci]

* Just removing it to avoid confusion

.nvmrc

@@ -0,0 +1 @@
+v10.13.0

.travis.yml

@@ -1,8 +1,6 @@
 sudo: required
 dist: trusty
 language: node_js
-node_js:
-  - '10.13.0'
 services:
   - postgresql
 jdk:
@@ -12,41 +10,41 @@ cache:
   directories:
     # we also need to cache folder with Cypress binary
     - ~/.cache
-env:
-  global:
-    - WEBSERVICE_VERSION="1.6.0-beta.4"
 addons:
   firefox: "latest"
   postgresql: "9.6"
   chrome: stable
 
 install:
-  - ./scripts/install-travis-script.sh
+  - npm ci
 
 jobs:
   include:
     - stage: unit test
       name: "Lint, Unit Test, and Prod Test"
       script:
-        - ng lint
-        - ng test --watch=false --code-coverage --browsers ChromeHeadless
-        - ng version
+        - npx ng lint
         - npm run build.prod
+        - npx ng test --watch=false --code-coverage --browsers ChromeHeadless
+        - npm install --no-save codecov
     - stage: integration test
       name: "Cypress Group 1"
       env:
         - TEST='cypress/integration/group1/**/*'
-      script: ./scripts/run-travis-script.sh
+      script:
+        - ./scripts/run-travis-script.sh
     - stage: integration test
       name: "Cypress Group 2"
       env:
         - TEST='cypress/integration/group2/**/*'
-      script: ./scripts/run-travis-script.sh
+      script:
+        - ./scripts/run-travis-script.sh
     - stage: integration test
       name: "Cypress Group 3"
       env:
         - TEST='cypress/integration/group3/**/*'
-      script: ./scripts/run-travis-script.sh
+      script:
+        - ./scripts/run-travis-script.sh
 
 script: echo "overriding test"
 

README.md

@@ -28,19 +28,21 @@ This project was generated with [Angular CLI](https://github.com/angular/angular
 
 ### Prerequisites
 
-Angular CLI requires Node and NPM.  See [.travis.yml](.travis.yml) for the correct versions of Node, NPM and Angular CLI.
-Then make sure Angular CLI has been properly set up.
+- Java 8+ 
+- Node and its included NPM (see [.nvmrc](.nvmrc) for the correct version of node to install)
+- wget 
 
-[Install NPM and Node](https://nodejs.org/en/download/package-manager/)
+Install NPM and Node using nvm:
 ```
-$curl -sL https://deb.nodesource.com/setup_7.x | sudo -E bash -
-$sudo apt-get install -y nodejs
-$nodejs -v
-v7.10.0
-$npm -v
-4.2.0
+wget -qO- https://raw.githubusercontent.com/creationix/nvm/v0.34.0/install.sh | bash
 ```
-Follow https://docs.npmjs.com/getting-started/fixing-npm-permissions#option-two-change-npms-default-directory to fix permissions and then...
+Close current terminal and open a new one or `source ~/.bashrc`
+```
+nvm install 10.13.0
+```
+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/[email protected]		
@@ -55,7 +57,7 @@ cd dockstore-ui2
 git checkout develop
 git pull
 
-npm ci
+CI=true npm ci
 ```
 
 Check to make sure Angular CLI has been properly set up
@@ -94,18 +96,6 @@ The Dockstore class in [src/app/shared/dockstore.model.ts](src/app/shared/dockst
 
 In `dockstore-webservice`, the `dockstore.yml` being served <b>must be edited to include the client IDs</b>.
 
-## Pre-build/serve
-<!-- 
-  Possible bash command
-  export WEBSERVICE_VERSION=`grep -oP 'WEBSERVICE_VERSION="\K[0-9].[0-9].[0-9]' .travis.yml`
--->
-Run `export WEBSERVICE_VERSION=`[dockstore release version](https://github.com/dockstore/dockstore-ui2/blob/develop/.travis.yml#L12), for example `export WEBSERVICE_VERSION=1.5.3`.
-
-Run `npm run prebuild` before running or building the project. This command will:
-- generate a file which contains the UI tag version 
-- download the openapi codegen
-- generate code from the swagger.yaml
-
 ## Development server
 
 Run `ng serve` for a dev server. Navigate to `http://localhost:4200/`. The app will automatically reload if you change any of the source files. Run `ng serve --host 0.0.0.0` in order to serve your site to other computers on the same network. 
@@ -121,7 +111,8 @@ Run `ng g component component-name` to generate a new component. You can also us
 
 ## Build
 
-Run `ng build` to build the project. The build artifacts will be stored in the `dist/` directory. Use the `-prod` flag for a production build.
+Optionally override the webservice version using `npm config set dockstore-ui2:webservice_version ${WEBSERVICE_VERSION}
+Run `npm run build` to build the project. The build artifacts will be stored in the `dist/` directory. Use the `npm run build.prod` for a production build.
 
 ## Running unit tests
 
@@ -131,9 +122,9 @@ Run `ng test` to execute the unit tests via [Karma](https://karma-runner.github.
 
 Run `$(npm bin)/cypress open` or `$(npm bin)/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`.
-- run the Dockstore webservice
-- have a webservice jar in the root directory
+- have the Dockstore webservice jar in the root directory and run it (see scripts/run-webservice-script.sh for guideline)
 
 ## Documentation Generation
 
@@ -143,7 +134,7 @@ To manually run it:
 npm install -g @compodoc/compodoc
 npm run compodoc
 ```
-Then go to `docs/index.html`
+Then open `docs/index.html` with browser
 
 ## Further help
 

cypress/support/commands.ts

@@ -34,7 +34,7 @@ export function resetDB() {
   before(() => {
     cy.exec('PGPASSWORD=dockstore psql -h localhost -f scripts/resetDb.sql -U dockstore -d webservice_test');
     cy.exec('PGPASSWORD=dockstore psql -h localhost -f travisci/db_dump.sql webservice_test -U dockstore');
-    cy.exec('java -jar dockstore-webservice-*.jar db migrate -i 1.5.0,1.6.0 travisci/web.yml');
+    cy.exec('java -jar dockstore-webservice.jar db migrate -i 1.5.0,1.6.0 travisci/web.yml');
   });
 }
 export function setTokenUserViewPort() {

git.version.ts

@@ -28,11 +28,11 @@ const tag$ = new Observable<string>(s => {
 });
 
 observableCombineLatest(revision$, tag$)
-  .subscribe(([revision, tag]) => {
-    console.log(`tag: '${tag}', version: '${process.env.WEBSERVICE_VERSION}', revision: '${revision}'`);
+.subscribe(([revision, tag]) => {
+    console.log(`tag: '${tag}', version: '${process.env.npm_package_config_webservice_version}', revision: '${revision}'`);
 
     const content = '// this file is automatically generated by git.version.ts script\n' +
-      `export const versions = {tag: '${tag}', version: '${process.env.WEBSERVICE_VERSION}', revision: '${revision}'};\n`;
+      `export const versions = {tag: '${tag}', version: '${process.env.npm_package_config_webservice_version}', revision: '${revision}'};\n`;
 
     fs.writeFileSync(
       'src/app/footer/versions.ts',

package.json

@@ -2,20 +2,21 @@
   "name": "dockstore-ui2",
   "version": "2.3.0",
   "license": "Apache License 2.0",
+  "config": {
+    "webservice_version": "1.6.0"
+  },
   "scripts": {
-    "ng": "ng",
-    "start": "ng serve",
-    "prebuild:tsnode": "ts-node git.version.ts",
-    "prebuild:downloadcodegen": "wget --no-verbose http://central.maven.org/maven2/org/openapitools/openapi-generator-cli/3.3.4/openapi-generator-cli-3.3.4.jar -O openapi-generator-cli-3.3.4.jar",
-    "prebuild:generatecode": "rm -Rf src/app/shared/swagger && java -jar openapi-generator-cli-3.3.4.jar generate -i https://raw.githubusercontent.com/ga4gh/dockstore/${WEBSERVICE_VERSION}/dockstore-webservice/src/main/resources/swagger.yaml -l typescript-angular -o src/app/shared/swagger -c swagger-config.json",
-    "prebuild": "npm run prebuild:tsnode && npm run prebuild:downloadcodegen && npm run prebuild:generatecode",
-    "prebuild.prod": "npm run prebuild:tsnode && npm run prebuild:downloadcodegen && npm run prebuild:generatecode",
-    "build.prod": "ng build --progress false --prod",
-    "build": "ng build --progress false",
+    "ng": "npx ng",
+    "start": "npx ng serve --progress=false",
+    "webservice": "./scripts/run-webservice-script.sh",
+    "prebuild": "ts-node git.version.ts && ./scripts/generate-openapi-script.sh",
+    "prebuild.prod": "npm run prebuild",
+    "build.prod": "npx ng build --progress false --prod",
+    "build": "npx ng build --progress false",
     "compodoc": "npx compodoc -p src/tsconfig.compodoc.json --output docs",
-    "test": "ng test",
-    "lint": "ng lint",
-    "e2e": "ng e2e"
+    "test": "npx ng test",
+    "lint": "npx ng lint",
+    "e2e": "npx ng e2e"
   },
   "private": true,
   "dependencies": {

scripts/generate-openapi-script.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+set -o errexit
+set -o pipefail
+set -o nounset
+set -o xtrace
+
+GENERATOR_VERSION="3.3.4"
+wget --no-verbose http://central.maven.org/maven2/org/openapitools/openapi-generator-cli/${GENERATOR_VERSION}/openapi-generator-cli-${GENERATOR_VERSION}.jar -O openapi-generator-cli.jar
+rm -Rf src/app/shared/swagger
+java -jar openapi-generator-cli.jar generate -i https://raw.githubusercontent.com/ga4gh/dockstore/$npm_package_config_webservice_version/dockstore-webservice/src/main/resources/swagger.yaml -l typescript-angular -o src/app/shared/swagger -c swagger-config.json

scripts/run-travis-script.sh

@@ -4,14 +4,8 @@ set -o pipefail
 set -o nounset
 set -o xtrace
 
-psql -c "create user dockstore with password 'dockstore' createdb;" -U postgres
-psql -c "ALTER USER dockstore WITH superuser;" -U postgres
-psql -c 'create database webservice_test with owner = dockstore;' -U postgres
-psql -f travisci/db_dump.sql webservice_test
-java -jar dockstore-webservice-${WEBSERVICE_VERSION}.jar db migrate -i 1.5.0,1.6.0 travisci/web.yml
-java -jar dockstore-webservice-${WEBSERVICE_VERSION}.jar server travisci/web.yml 1>/dev/null &
-
+npm run webservice
 npm run build
-ng serve --progress=false &
+npm run start &
 ./scripts/wait-for.sh
 cypress run --record --config defaultCommandTimeout=10000 --spec ${TEST}

scripts/run-webservice-script.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+set -o errexit
+set -o pipefail
+set -o nounset
+set -o xtrace
+
+wget -O dockstore-webservice.jar --no-verbose --tries=10 https://artifacts.oicr.on.ca/artifactory/collab-release/io/dockstore/dockstore-webservice/${npm_package_config_webservice_version}/dockstore-webservice-${npm_package_config_webservice_version}.jar
+chmod u+x dockstore-webservice.jar
+psql -c "create user dockstore with password 'dockstore' createdb;" -U postgres
+psql -c "ALTER USER dockstore WITH superuser;" -U postgres
+psql -c 'create database webservice_test with owner = dockstore;' -U postgres
+psql -f travisci/db_dump.sql webservice_test
+java -jar dockstore-webservice.jar db migrate -i 1.5.0,1.6.0 travisci/web.yml
+java -jar dockstore-webservice.jar server travisci/web.yml 1>/dev/null &
+