🔀 Merge pull request #26 from cnr-ibba/devel

🔖 release v0.3.0

package.json

@@ -1,6 +1,6 @@
 {
   "name": "smarter-frontend",
-  "version": "0.2.2",
+  "version": "0.3.0-0",
   "scripts": {
     "ng": "ng",
     "start": "ng serve",
@@ -28,7 +28,7 @@
     "zone.js": "^0.11.8"
   },
   "devDependencies": {
-    "@angular-devkit/build-angular": "^14.2.10",
+    "@angular-devkit/build-angular": "^14.2.13",
     "@angular/cli": "~14.2.4",
     "@angular/compiler-cli": "^14.2.12",
     "@types/jasmine": "~4.0.0",

src/app/about/about.component.html

@@ -1,35 +1,37 @@
-<h1 class="free-text">About the SMARTER database</h1>
 
 <div flex fxLayout="row" fxLayoutAlign="center center">
   <div fxFlex="90">
 
+    <h1>About the SMARTER Database</h1>
+
     <p>
       The SMARTER project site is a place where WP4 partners of the
-      <a href="https://www.smarterproject.eu/">Smarter project</a>
-      can browse and access their data.
+      <a href="https://www.smarterproject.eu/">SMARTER project</a>
+      can browse and access their data. This dataset is now open and available
+      to the community.
     </p>
 
-    <h2>The SMARTER project</h2>
+    <h2>The SMARTER Project</h2>
 
     <p>
-      Small ruminant populations play a fundamental role for the livelihood and
+      Small ruminant populations play a fundamental role in the livelihood and
       socio-economic well-being of human settlements, especially in marginal areas
       of Europe. Under-utilized sheep and goat breeds may be highly valuable in
-      increasing the profitability of small ruminant farming in such marginal areas.
-      These breeds are valuable because they have peculiar and often atypical
-      genetic make-up which make them a potentially extraordinary resource to
-      be exploited for adaptation to (harsh) environments, resilience to farming
+      increasing the profitability of small ruminant farming in these marginal areas.
+      These breeds are valuable because they have unique and often atypical
+      genetic make-ups, making them potentially extraordinary resources for
+      adaptation to harsh environments, resilience to farming
       conditions, resistance to biotic and abiotic stressors, and the production
-      of quality of products of animal origin.
+      of high-quality animal products.
     </p>
 
     <p>
-      In this particular context, WP4 aims to address knowledge gaps concerning
+      In this context, WP4 aims to address knowledge gaps concerning
       genetic diversity in goats and sheep. Its objective is to identify genetic
       factors that contribute to their ability to adapt to climate conditions and,
       more broadly, to withstand environmental disturbances.
-      Available datasets relevant to the genomic characterization
-      were identified and furthermore comprehensive data on hardy and under-utilized
+      Available datasets relevant to genomic characterization
+      were identified, and comprehensive data on hardy and under-utilized
       breeds were collected, including genotypes, phenotypes, and environmental
       measurements associated with rearing conditions.
       To ensure consistency, the recording of this data was standardized: genotypes
@@ -40,78 +42,89 @@ <h2>The SMARTER project</h2>
     </p>
 
     <p>
-      Data are made available to the community using three different instruments:
+      Data are made available to the community using four different instruments:
     </p>
 
-      <ul>
-        <li>
-          The <a href="https://github.com/cnr-ibba/SMARTER-database">SMARTER-database</a>,
-          which is a collection of tools and scripts to collect, standardize and provide
-          to the community a collection of genotype data and metadata information
-          in hardy goat and sheep populations by combining new with already existing datasets.
-          This project is better explained and documented in its
-          <a href="https://smarter-database.readthedocs.io/en/latest/index.html">manual pages</a>.
-        </li>
-        <li>
-          The <a href="https://github.com/cnr-ibba/SMARTER-backend">SMARTER-backend</a>,
-          which is a REST API service developed on top of the <em>SMARTER-database</em>
-          which provide methods to interact and access with SMARTER data using web resources.
-          By using <em>SMARTER-backend</em>, you can develop softwares or scripts which get
-          access to SMARTER data through web, without have a local instance
-          of the <em>SMARTER-database</em>. An example of this is the
-          <a href="https://github.com/cnr-ibba/r-smarter-api">smarterapi R package</a>,
-          which allow to collect SMARTER data using the <em>SMARTER-backend</em>. More
-          information can be found in the
-          <a href="https://smarter-backend.readthedocs.io/en/latest/index.html">SMARTER-backend documentation</a>
-          and <a href="https://cnr-ibba.github.io/r-smarter-api/index.html">smarterapi manual pages</a>.
-        </li>
-        <li>
-          The <a href="https://github.com/cnr-ibba/SMARTER-frontend">SMARTER-frontend</a>
-          (<a routerLink="/">this site</a>), which is a web interface to browse <em>SMARTER-database</em>
-          data relying on <em>SMARTER-backend</em>.
-        </li>
-      </ul>
+    <ul>
+      <li>
+        The <a href="https://github.com/cnr-ibba/SMARTER-database">SMARTER database</a>,
+        which is a collection of tools and scripts to collect, standardize, and provide
+        a collection of genotype data and metadata information
+        on hardy goat and sheep populations by combining new and existing datasets.
+        This project is better explained and documented in its
+        <a href="https://smarter-database.readthedocs.io/en/latest/index.html">manual pages</a>.
+      </li>
+      <li>
+        The <a href="https://webserver.ibba.cnr.it/smarter-api/docs/">SMARTER backend</a>,
+        which is a REST API service developed on top of the <em>SMARTER database</em>
+        providing methods to interact with and access SMARTER data using web resources.
+        By using the <em>SMARTER backend</em>, you can develop software or scripts that access
+        SMARTER data via the web without needing a local instance
+        of the <em>SMARTER database</em>. An example of this is the
+        <a href="https://github.com/cnr-ibba/r-smarter-api">smarterapi R package</a>,
+        which allows the collection of SMARTER data using the <em>SMARTER backend</em>. More
+        information can be found in the
+        <a href="https://smarter-backend.readthedocs.io/en/latest/index.html">SMARTER backend documentation</a>
+        and <a href="https://cnr-ibba.github.io/r-smarter-api/index.html">smarterapi manual pages</a>.
+      </li>
+      <li>
+        The <a href="https://github.com/cnr-ibba/SMARTER-frontend">SMARTER frontend</a>
+        (<a routerLink="/">this site</a>), which is a web interface to browse <em>SMARTER database</em>
+        data relying on the <em>SMARTER backend</em>.
+      </li>
+      <li>
+        The SMARTER <a href="ftp://webserver.ibba.cnr.it/smarter/">FTP site</a>, which collects
+        the genotype files of the animals described in the <em>SMARTER database</em>.
+      </li>
+    </ul>
 
-      <p>
-        Those instrument can be used to collect metadata and other samples information: genotypes
-        are available for both <em>Goat and Sheep species</em> as a whole PLINK binary file for each
-        of the supported assemblies. Users are required to identify their samples of interest and then
-        subset the genotype files according their needs. Additional filtering steps
-        on the selected genotypes can be done to get rid of missing samples or variants.
-      </p>
+    <p>
+      These instruments can be used to collect metadata and other sample information. Genotypes
+      are available for both <em>Goat and Sheep species</em> as whole PLINK binary files for each
+      of the supported assemblies. You can download the genotype files from the
+      <a href="ftp://webserver.ibba.cnr.it/smarter/">FTP site</a> for the available assemblies.
+      Users are required to identify their samples of interest using the
+      <a href="https://github.com/cnr-ibba/SMARTER-frontend">SMARTER frontend</a>,
+      the <a href="https://webserver.ibba.cnr.it/smarter-api/docs/">SMARTER backend</a>, or the
+      <a href="https://github.com/cnr-ibba/r-smarter-api">smarterapi R package</a>.
+      These are three different ways to access the same data: the first one is a web interface,
+      the second one is a REST API service, and the third one is an R package to interact with the API service.
+      Users can then subset the genotype files according to their needs. Additional filtering steps
+      on the selected genotypes can be done to remove missing samples or variants.
+    </p>
 
-    <h2>About this site</h2>
+    <h2>About This Site</h2>
 
     <p>
-      You can browse WP4 SMARTER using the different tabs. Data like samples, variants
-      and breed can be browsed by <em>species</em> (Goat, Sheep): you will find
-      a button on the top of the page which will select the data you can browse.
-      Data like datasets are available in the same page for both species. Here's
+      You can browse WP4 SMARTER data using the different tabs. Data like samples, variants,
+      and breeds can be browsed by <em>species</em> (Goat, Sheep). You will find
+      a button on the top of the page to select the data you want to browse.
+      Data like datasets are available on the same page for both species. Here's
       a list of the site sections:
     </p>
 
     <ul>
       <li>
-        <a routerLink="/breeds">Breeds</a>: navigate data by breeds, you can
+        <a routerLink="/breeds">Breeds</a>: navigate data by breeds. You can
         search for a specific breed or get general information about how many samples
         belong to the same breed. You can follow the links to retrieve all samples
         of a particular breed.
       </li>
       <li>
-        <a routerLink="/datasets">Datasets</a>: navigate data by datasets, browse
+        <a routerLink="/datasets">Datasets</a>: navigate data by datasets. Browse
         data relying on the files submitted by the partners or by file content. For
-        a <em>genotypes</em> dataset you can follow the links a retrieve all samples
+        a <em>genotypes</em> dataset, you can follow the links to retrieve all samples
         belonging to the same dataset.
       </li>
       <li>
         <a routerLink="/samples">Samples</a>: navigate samples by species.
-        You can filter out samples by filling the form fields.
+        You can filter samples by filling out the form fields.
       </li>
       <li>
         <a routerLink="/variants">Variants</a>: navigate the variants used
         to normalize the genotype files and collect information about their positions
         and genotype codings. You can browse variants by species and
-        by assembly versions, and filter out variants by filling the form fields.
+        by assembly versions, and filter variants by filling out the form fields.
       </li>
     </ul>
 

src/app/app-routing.module.ts

@@ -1,10 +1,8 @@
-import { Component, NgModule } from '@angular/core';
+import { NgModule } from '@angular/core';
 import { RouterModule, Routes } from '@angular/router';
 
-import { AuthGuard } from './auth/auth.guard';
 import { HomeComponent } from './home/home.component';
 import { AboutComponent } from './about/about.component';
-import { LoginComponent } from './auth/login/login.component';
 import { DatasetsComponent } from './datasets/datasets.component';
 import { DatasetDetailComponent } from './datasets/dataset-detail/dataset-detail.component';
 import { DatasetResolver } from './datasets/dataset-detail/dataset-resolver.service';
@@ -21,43 +19,35 @@ import { VariantResolver } from './variants/variant-detail/variant-resolver.serv
 const routes: Routes = [
   { path: '', component: HomeComponent },
   { path: 'about', component: AboutComponent },
-  { path: 'login', component: LoginComponent },
   {
     path: 'breeds',
-    component: BreedsComponent,
-    canActivate: [ AuthGuard ]
+    component: BreedsComponent
   },
   {
     path: 'datasets',
-    component: DatasetsComponent,
-    canActivate: [ AuthGuard ]
+    component: DatasetsComponent
   },
   {
     path: 'datasets/:_id',
     component: DatasetDetailComponent,
-    canActivate: [ AuthGuard ],
     resolve: { dataset: DatasetResolver }
   },
   {
     path: 'samples',
     component: SamplesComponent,
-    canActivate: [ AuthGuard ]
   },
   {
     path: 'samples/:species/:_id',
     component: SampleDetailComponent,
-    canActivate: [ AuthGuard ],
     resolve: { sample: SampleResolver }
   },
   {
     path: 'variants',
     component: VariantsComponent,
-    canActivate: [ AuthGuard ],
   },
   {
     path: 'variants/:species/:_id',
     component: VariantDetailComponent,
-    canActivate: [ AuthGuard ],
     resolve: { variant: VariantResolver }
   },
   {

src/app/app.component.ts

@@ -1,19 +1,11 @@
-import { Component, OnInit } from '@angular/core';
-
-import { AuthService } from './auth/auth.service';
+import { Component } from '@angular/core';
 
 @Component({
   selector: 'app-root',
   templateUrl: './app.component.html',
   styleUrls: ['./app.component.scss']
 })
-export class AppComponent implements OnInit {
+export class AppComponent {
   title = 'SMARTER-frontend';
 
-  constructor(private authService: AuthService) { }
-
-  ngOnInit(): void {
-    // try authologin when starting application
-    this.authService.autoLogin();
-  }
 }

src/app/app.module.ts

@@ -9,11 +9,9 @@ import { AppRoutingModule } from './app-routing.module';
 import { AppComponent } from './app.component';
 import { MaterialModule } from './material/material.module';
 import { HomeComponent } from './home/home.component';
-import { LoginComponent } from './auth/login/login.component';
 import { HeaderComponent } from './navigation/header/header.component';
 import { SidenavListComponent } from './navigation/sidenav-list/sidenav-list.component';
 import { DatasetsComponent } from './datasets/datasets.component';
-import { AuthInterceptorService } from './auth/auth-interceptor.service';
 import { NotFoundComponent } from './not-found/not-found.component';
 import { ShortenPipe } from './shared/shorten.pipe';
 import { BreedsComponent } from './breeds/breeds.component';
@@ -33,7 +31,6 @@ import { AboutComponent } from './about/about.component';
   declarations: [
     AppComponent,
     HomeComponent,
-    LoginComponent,
     HeaderComponent,
     SidenavListComponent,
     DatasetsComponent,
@@ -62,12 +59,7 @@ import { AboutComponent } from './about/about.component';
     MaterialModule
   ],
   providers: [
-    {
-      provide: HTTP_INTERCEPTORS,
-      useClass: AuthInterceptorService,
-      // required, even if it is the only interceptor defined
-      multi: true
-    }
+
   ],
   bootstrap: [AppComponent]
 })