Merge branch 'develop' into 'master'

Develop

See merge request !29

.gitignore

+# See http://help.github.com/ignore-files/ for more about ignoring files.
+
+# compiled output
+/dist
+/tmp
+/out-tsc
+# Only exists if Bazel was run
+/bazel-out
+
+# dependencies
+/node_modules
+
+# profiling files
+chrome-profiler-events*.json
+
+# IDEs and editors
+/.idea
+.project
+.classpath
+.c9/
+*.launch
+.settings/
+*.sublime-workspace
+
+# IDE - VSCode
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+.history/*
+
+# misc
+/.sass-cache
+/connect.lock
+/coverage
+/libpeerconnection.log
+npm-debug.log
+yarn-error.log
+testem.log
+/typings
+
+# System Files
+.DS_Store
+Thumbs.db

.gitlab-ci.yml

+stages: 
+    - trigger-child-pipelines
+
+anis-client:
+    stage: trigger-child-pipelines
+    trigger:
+        include: client/.gitlab-ci.yml
+        strategy: depend
+    only:
+        changes:
+            - client/**/*
+        refs:
+            - develop
+
+anis-server:
+    stage: trigger-child-pipelines
+    trigger:
+        include: server/.gitlab-ci.yml
+        strategy: depend
+    only:
+        changes:
+            - server/**/*
+        refs:
+            - develop
+
+anis-services:
+    stage: trigger-child-pipelines
+    trigger:
+        include: services/.gitlab-ci.yml
+        strategy: depend
+    only:
+        changes:
+            - services/**/*
+        refs:
+            - develop
\ No newline at end of file

LICENSE

-AstroNomical Information System
+AstroNomical Information System - ANIS
   
+  website: https://anis.lam.fr
   Copyright: CNRS - 2021
-  Address:  Centre de donneeS Astrophysique de Marseille (CeSAM)              
+  Address:  Centre de donnéeS Astrophysique de Marseille (CeSAM)              
             Laboratoire d'Astrophysique de Marseille                          
-            Ple de l'Etoile, site de Chteau-Gombert                         
-            38, rue Frdric Joliot-Curie                                     
+            Pôle de l'Etoile, site de Château-Gombert                         
+            38, rue Frédéric Joliot-Curie                                     
             13388 Marseille cedex 13 France                                   
             CNRS U.M.R 7326
 
-Anis Server is governed by the CeCILL license under French law and
+ANIS is governed by the CeCILL license under French law and
 abiding by the rules of distribution of free software.  You can  use, 
 modify and/ or redistribute the software under the terms of the CeCILL
 license as circulated by CEA, CNRS and INRIA at the following URL

Makefile

@@ -5,23 +5,25 @@ list:
 	@echo ""
 	@echo "Useful targets:"
 	@echo ""
-	@echo "  rebuild          > rebuild all images and start containers for dev only"
-	@echo "  start            > start containers"
-	@echo "  restart          > restart containers"
-	@echo "  stop             > stop and kill running containers"
-	@echo "  status           > display stack containers status"
-	@echo "  logs             > display containers logs"
-	@echo "  install_client   > install client dependencies"
-	@echo "  shell_client     > shell into angular client container"
-	@echo "  build_client     > generate the angular client dist application (html, css, js)"
-	@echo "  test_client      > Starts the angular client unit tests"
-	@echo "  install_server   > install server dependencies"
-	@echo "  shell_server     > shell into php server container"
+	@echo "  rebuild          > Rebuild all images and start containers for dev only"
+	@echo "  start            > Start containers"
+	@echo "  restart          > Restart containers"
+	@echo "  stop             > Stop and kill running containers"
+	@echo "  status           > Display stack containers status"
+	@echo "  logs             > Display containers logs"
+	@echo "  install_client   > Install client dependencies"
+	@echo "  shell_client     > Shell into angular client container"
+	@echo "  build_client     > Generate the angular client dist application (html, css, js)"
+	@echo "  test_client      > Run the angular client unit tests and generate code coverage report"
+	@echo "  test_client-live > Run the angular client unit tests on every file change"
+	@echo "  open-coverage    > Open the client code coverage report in a browser (only available for Linux)"
+	@echo "  install_server   > Install server dependencies"
+	@echo "  shell_server     > Shell into php server container"
 	@echo "  test_server      > Starts the server php unit tests"
-	@echo "  phpcs            > run php code sniffer test suite"
-	@echo "  shell_services   > shell into python services"
-	@echo "  create-db        > create a database for dev only (need token_enabled=0)"
-	@echo "  remove-pgdata    > remove the anis-next database"
+	@echo "  phpcs            > Run php code sniffer test suite"
+	@echo "  shell_services   > Shell into python services"
+	@echo "  create-db        > Create a database for dev only (need token_enabled=0)"
+	@echo "  remove-pgdata    > Remove the anis-next database"
 	@echo ""
 
 rebuild:
@@ -54,7 +56,13 @@ build_client:
 	@docker-compose exec client ng build
 
 test_client:
-	@docker-compose exec client ng test --no-watch --code-coverage
+	@docker-compose exec client npx jest --coverage --collectCoverageFrom='src/**/*.ts'
+
+test_client_live:
+	@docker-compose exec client npx jest --watchAll --coverage
+
+open_coverage_report:
+	xdg-open client/coverage/anis-client/index.html
 
 install_server:
 	@docker run --init -it --rm --user $(UID):$(GID) \

README.md

+# AstroNomical Information System - ANIS 
+
+## Introduction
+
+AstroNomical Information System is a generic web tool that aims to facilitate
+the provision of data (Astrophysics), accessible from a database, for the scientific 
+community.
+
+This software allows you to control one or more databases related to astronomical 
+projects and allows access to datasets via a web interface or URLs.
+
+Anis is protected by the CeCILL licence (see LICENCE file at the software root).
+
+## Authors
+
+Here is the list of people involved in the development:
+
+* `François Agneray` : Laboratoire d'Astrophysique de Marseille (CNRS)
+* `Chrystel Moreau` : Laboratoire d'Astrophysique de Marseille (CNRS)
+* `Tifenn Guillas` : Laboratoire d'Astrophysique de Marseille (CNRS)
+
+## More resources:
+
+* [Website](https://anis.lam.fr)
+* [Documentation](https://anis.lam.fr/doc/)
+
+## Installing and starting the application
+
+Anis Server contains a Makefile that helps the developer to install and start the application.
+
+To list all operations availables just type `make` in your terminal at the root of this application.
+
+- To install client dependancies: `make install_client`
+- To install server dependancies: `make install_server`
+- To build or rebuild all docker images and start containers: `make rebuild`
+- To start/stop/restart/status all services: `make start|stop|restart|status`
+- To display logs for all services: `make logs`
+- To open a shell command into client container: `make shell_client`
+- To open a shell command into server container: `make shell_server`
+- To execute server tests suite: `make test_server`
+- To execute php code sniffer: `make phpcs`
+- To create the metamodel database: `make create-db`
+- TO remove the metadata database: `make remove-pgdata`
+
+## Web interface
+
+In development mode the web interface can be accessed at the following url : http://localhost:4200

client/.editorconfig

@@ -4,7 +4,7 @@ root = true
 [*]
 charset = utf-8
 indent_style = space
-indent_size = 2
+indent_size = 4
 insert_final_newline = true
 trim_trailing_whitespace = true
 

client/.gitlab-ci.yml

+stages:
+    - install_dependencies
+    - test
+    - sonar
+    - build
+    - dockerize
+    - deploy
+
+variables:
+    VERSION: "3.7.0"
+    SONARQUBE_URL: https://sonarqube.lam.fr
+
+install_dependencies:
+    image: node:16-slim
+    stage: install_dependencies
+    cache: 
+        key: ${CI_COMMIT_REF_SLUG}_client
+        paths:
+            - client/node_modules
+        policy: pull-push
+    script:
+        - cd client
+        - yarn install
+
+test:
+    image: node:16-slim
+    stage: test
+    cache: 
+        key: ${CI_COMMIT_REF_SLUG}_client
+        paths:
+            - node_modules
+        policy: pull
+    script:
+        - cd client
+        - npx jest --coverage --coverageReporters lcov 
+    artifacts:
+        paths:
+            - client/coverage
+
+sonar_scanner:
+    image: sonarsource/sonar-scanner-cli:latest
+    stage: sonar
+    cache: 
+        key: ${CI_COMMIT_REF_SLUG}_client
+        paths:
+            - client/node_modules
+        policy: pull
+    script:
+        - cd client
+        - sonar-scanner
+            -Dsonar.projectKey=anis-client
+            -Dsonar.sources=src
+            -Dsonar.projectVersion=$VERSION 
+            -Dsonar.host.url=$SONARQUBE_URL 
+            -Dsonar.login=$SONAR_TOKEN_CLIENT
+            -Dsonar.exclusions=**.spec.ts
+            -Dsonar.typescript.lcov.reportPaths=./coverage/anis-client/lcov.info
+
+build:
+    image: node:16-slim
+    stage: build
+    cache: 
+        key: ${CI_COMMIT_REF_SLUG}_client
+        paths:
+            - client/node_modules
+        policy: pull
+    script:
+        - cd client
+        - yarn global add @angular/cli@latest
+        - ng build
+    artifacts:
+        paths:
+            - client/dist
+
+dockerize:
+    image: docker:stable
+    stage: dockerize
+    cache: {}
+    script:
+        - cd client
+        - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+        - docker pull $CI_REGISTRY/anis/anis-next/client:latest || true
+        - docker build --cache-from $CI_REGISTRY/anis/anis-next/client:latest -t $CI_REGISTRY/anis/anis-next/client:latest .
+        - docker push $CI_REGISTRY/anis/anis-next/client:latest
+
+deploy:
+    image: alpine
+    stage: deploy
+    variables:
+        GIT_STRATEGY: none
+    cache: {}
+    dependencies: []
+    script:
+        - apk add --update curl
+        - curl -XPOST $DEV_WEBHOOK_CLIENT
+    only:
+        refs:
+            - develop
\ No newline at end of file

client/90-update-base-href.sh

+#!/bin/bash
+
+if [[ -v ANIS_BASE_HREF ]]; then
+  sed -i 's@<base href="/">@<base href="'$ANIS_BASE_HREF'">@' /usr/share/nginx/html/index.html
+fi
+
+exit 0

client/Dockerfile

 FROM nginx
 
+COPY ./90-update-base-href.sh /docker-entrypoint.d/
 COPY dist/client /usr/share/nginx/html
 COPY nginx.conf /etc/nginx/conf.d/default.conf

client/angular.json

@@ -37,7 +37,10 @@
             "scripts": [
               "node_modules/@fortawesome/fontawesome-free/js/all.js",
               "src/assets/samp.js"
-            ]
+            ],
+            "allowedCommonJsDependencies": [
+              "keycloak-js"
+           ]
           },
           "configurations": {
             "production": {
@@ -89,24 +92,6 @@
           "options": {
             "browserTarget": "client:build"
           }
-        },
-        "test": {
-          "builder": "@angular-devkit/build-angular:karma",
-          "options": {
-            "main": "src/test.ts",
-            "polyfills": "src/polyfills.ts",
-            "tsConfig": "tsconfig.spec.json",
-            "karmaConfig": "karma.conf.js",
-            "inlineStyleLanguage": "scss",
-            "assets": [
-              "src/favicon.ico",
-              "src/assets"
-            ],
-            "styles": [
-              "src/styles.scss"
-            ],
-            "scripts": []
-          }
         }
       }
     }

client/jest.config.js

+const { pathsToModuleNameMapper } = require('ts-jest/utils');
+const { compilerOptions } = require('./tsconfig');
+
+module.exports = {
+    preset: 'jest-preset-angular',
+    testMatch: ['**/+(*.)+(spec).+(ts|js)'],
+    setupFilesAfterEnv: ['<rootDir>/src/test.ts'],
+    coverageReporters: ['html'],
+    coverageDirectory: 'coverage/anis-client',
+    moduleDirectories: ["node_modules", "./"],
+    moduleNameMapper: pathsToModuleNameMapper(compilerOptions.paths || {}, {
+        prefix: '<rootDir>/',
+    }),
+};

client/karma.conf.js

-// Karma configuration file, see link for more information
-// https://karma-runner.github.io/1.0/config/configuration-file.html
-
-module.exports = function (config) {
-  config.set({
-    basePath: '',
-    frameworks: ['jasmine', '@angular-devkit/build-angular'],
-    plugins: [
-      require('karma-jasmine'),
-      require('karma-chrome-launcher'),
-      require('karma-jasmine-html-reporter'),
-      require('karma-coverage'),
-      require('@angular-devkit/build-angular/plugins/karma')
-    ],
-    client: {
-      jasmine: {
-        // you can add configuration options for Jasmine here
-        // the possible options are listed at https://jasmine.github.io/api/edge/Configuration.html
-        // for example, you can disable the random execution with `random: false`
-        // or set a specific seed with `seed: 4321`
-      },
-      clearContext: false // leave Jasmine Spec Runner output visible in browser
-    },
-    jasmineHtmlReporter: {
-      suppressAll: true // removes the duplicated traces
-    },
-    coverageReporter: {
-      dir: require('path').join(__dirname, './coverage/client'),
-      subdir: '.',
-      reporters: [
-        { type: 'html' },
-        { type: 'text-summary' }
-      ]
-    },
-    reporters: ['progress', 'kjhtml'],
-    port: 9876,
-    colors: true,
-    logLevel: config.LOG_INFO,
-    autoWatch: true,
-    browsers: ['Chrome'],
-    singleRun: false,
-    restartOnFileChange: true
-  });
-};

client/package.json

@@ -5,8 +5,7 @@
     "ng": "ng",
     "start": "ng serve",
     "build": "ng build",
-    "watch": "ng build --watch --configuration development",
-    "test": "ng test"
+    "watch": "ng build --watch --configuration development"
   },
   "private": true,
   "dependencies": {
@@ -26,6 +25,7 @@
     "@ngrx/store": "12.1.0",
     "@ngrx/store-devtools": "12.1.0",
     "bootstrap": "4.6",
+    "d3": "^5.15.1",
     "keycloak-angular": "^8.2.0",
     "keycloak-js": "^14.0.0",
     "ngx-bootstrap": "^7.0.0-rc.1",
@@ -39,14 +39,14 @@
     "@angular-devkit/build-angular": "~12.0.4",
     "@angular/cli": "~12.0.4",
     "@angular/compiler-cli": "~12.0.4",
+    "@types/d3": "^5.7.2",
     "@types/jasmine": "~3.6.0",
+    "@types/jest": "^26.0.24",
     "@types/node": "^12.11.1",
     "jasmine-core": "~3.7.0",
-    "karma": "~6.3.0",
-    "karma-chrome-launcher": "~3.1.0",
-    "karma-coverage": "~2.0.3",
-    "karma-jasmine": "~4.0.0",
-    "karma-jasmine-html-reporter": "^1.5.0",
+    "jasmine-marbles": "^0.8.3",
+    "jest": "^27.0.6",
+    "jest-preset-angular": "^9.0.5",
     "typescript": "~4.2.3"
   }
 }

client/src/app/admin/admin-auth.guard.ts

+/**
+ * This file is part of Anis Client.
+ *
+ * @copyright Laboratoire d'Astrophysique de Marseille / CNRS
+ *
+ * For the full copyright and license information, please view the LICENSE
+ * file that was distributed with this source code.
+ */
+
+import { Injectable } from '@angular/core';
+import { CanActivate, Router } from '@angular/router';
+
+import { Store, select } from '@ngrx/store';
+import { combineLatest, Observable } from 'rxjs';
+import { map } from 'rxjs/operators';
+
+import * as authActions from 'src/app/auth/auth.actions';
+import * as authSelector from 'src/app/auth/auth.selector';
+import { AppConfigService } from 'src/app/app-config.service';
+
+@Injectable({
+    providedIn: 'root',
+})
+export class AdminAuthGuard implements CanActivate {
+    constructor(
+        protected readonly router: Router,
+        private store: Store<{ }>,
+        private config: AppConfigService
+    ) { }
+
+    canActivate(): Observable<boolean> {
+        return combineLatest([
+            this.store.pipe(select(authSelector.selectUserRoles)),
+            this.store.pipe(select(authSelector.selectIsAuthenticated))
+        ]).pipe(
+            map(([userRoles, isAuthenticated]) => {
+                // Auth disabled
+                if (!this.config.authenticationEnabled) {
+                    return true;
+                }
+
+                // Force the user to log in if currently unauthenticated.
+                if (!isAuthenticated) {
+                    this.store.dispatch(authActions.login());
+                    return false;
+                }
+
+                // If authenticated but not admin go to unauthorized page.
+                if (!userRoles.includes(this.config.adminRole)) {
+                    this.router.navigateByUrl('/unauthorized');
+                    return false;
+                }
+
+                // Let "Router" allow user entering the page
+                return true;
+            })
+        );
+    }
+}

client/src/app/admin/admin-routing.module.ts

@@ -11,73 +11,26 @@ import { NgModule } from '@angular/core';
 import { RouterModule, Routes } from '@angular/router';
 
 import { AdminComponent } from './admin.component';
-import { InstanceListComponent } from './containers/instance/instance-list.component';
-import { NewInstanceComponent } from './containers/instance/new-instance.component';
-import { EditInstanceComponent } from './containers/instance/edit-instance.component';
-import { ConfigureInstanceComponent } from './containers/instance/configure-instance.component';
-import { GroupListComponent } from './containers/group/group-list.component';
-import { NewGroupComponent } from './containers/group/new-group.component';
-import { EditGroupComponent } from './containers/group/edit-group.component';
-import { NewDatasetComponent } from './containers/dataset/new-dataset.component';
-import { EditDatasetComponent } from './containers/dataset/edit-dataset.component';
-import { AttributeListComponent } from './containers/attribute/attribute-list.component';
-import { SurveyListComponent } from './containers/survey/survey-list.component';
-import { NewSurveyComponent } from './containers/survey/new-survey.component';
-import { EditSurveyComponent } from './containers/survey/edit-survey.component';
-import { DatabaseListComponent } from './containers/database/database-list.component';
-import { NewDatabaseComponent } from './containers/database/new-database.component';
-import { EditDatabaseComponent } from './containers/database/edit-database.component';
-import { SettingsComponent } from './containers/settings/settings.component';
+import { AdminAuthGuard } from './admin-auth.guard';
 
 const routes: Routes = [
     { 
-        path: 'admin', component: AdminComponent, children: [
-            { path: '', redirectTo: 'instance-list', pathMatch: 'full' },
-            { path: 'instance-list', component: InstanceListComponent },
-            { path: 'new-instance', component: NewInstanceComponent },
-            { path: 'edit-instance/:iname', component: EditInstanceComponent },
-            { path: 'configure-instance/:iname', component: ConfigureInstanceComponent },
-            { path: 'configure-instance/:iname/group', component: GroupListComponent },
-            { path: 'configure-instance/:iname/new-group', component: NewGroupComponent },
-            { path: 'configure-instance/:iname/edit-group/:id', component: EditGroupComponent },
-            { path: 'configure-instance/:iname/new-dataset', component: NewDatasetComponent },
-            { path: 'configure-instance/:iname/edit-dataset/:dname', component: EditDatasetComponent },
-            { path: 'configure-instance/:iname/configure-dataset/:dname', component: AttributeListComponent },
-            { path: 'survey-list', component: SurveyListComponent },
-            { path: 'new-survey', component: NewSurveyComponent },
-            { path: 'edit-survey/:name', component: EditSurveyComponent },
-            { path: 'database-list', component: DatabaseListComponent },
-            { path: 'new-database', component: NewDatabaseComponent },
-            { path: 'edit-database/:id', component: EditDatabaseComponent },
-            { path: 'settings', component: SettingsComponent },
-            { path: 'settings/:select', component: SettingsComponent }
+        path: '', component: AdminComponent, canActivate: [AdminAuthGuard], children: [
+            { path: '', redirectTo: 'instance/instance-list', pathMatch: 'full' },
+            { path: 'instance', loadChildren: () => import('./instance/instance.module').then(m => m.InstanceModule) },
+            { path: 'survey', loadChildren: () => import('./survey/survey.module').then(m => m.SurveyModule) },
+            { path: 'database', loadChildren: () => import('./database/database.module').then(m => m.DatabaseModule) },
+            { path: 'settings', loadChildren: () => import('./settings/settings.module').then(m => m.SettingsModule) }
         ]
     }
 ];
 
 @NgModule({
-    imports: [RouterModule.forRoot(routes)],
+    imports: [RouterModule.forChild(routes)],
     exports: [RouterModule]
 })
 export class AdminRoutingModule { }
 
 export const routedComponents = [
-    AdminComponent,
-    InstanceListComponent,
-    NewInstanceComponent,
-    EditInstanceComponent,
-    ConfigureInstanceComponent,
-    GroupListComponent,
-    NewGroupComponent,
-    EditGroupComponent,
-    NewDatasetComponent,
-    EditDatasetComponent,
-    AttributeListComponent,
-    SurveyListComponent,
-    NewSurveyComponent,
-    EditSurveyComponent,
-    DatabaseListComponent,
-    NewDatabaseComponent,
-    EditDatabaseComponent,
-    SettingsComponent
+    AdminComponent
 ];

client/src/app/instance/detail/detail.module.ts → client/src/app/admin/admin-shared/admin-shared.module.ts

@@ -10,13 +10,24 @@
 import { NgModule } from '@angular/core';
 
 import { SharedModule } from 'src/app/shared/shared.module';
-import { DetailRoutingModule, routedComponents } from './detail-routing.module';