Merge pull request #205 from EGA-archive/develop

updating master branch
EGA-archive · Sep 18, 2023 · 328b84c · 328b84c
2 parents f77373a + d982d98
commit 328b84c
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Showing 19 changed files with 1,674 additions and 1,113 deletions.
diff --git a/beacon/conf.py b/beacon/conf.py
@@ -12,7 +12,7 @@
 beacon_id = 'org.ega-archive.ga4gh-approval-beacon-test'  # ID of the Beacon
 beacon_name = 'GA4GH Approval Beacon Test'  # Name of the Beacon service
 api_version = 'v2.0.0'  # Version of the Beacon implementation
-uri = 'https://ega-archive.org/test-beacon-apis/cineca/'
+uri = 'https://beacon-apis-test.ega-archive.org/api/'
 
 #
 # Beacon granularity

diff --git a/beacon/request/routes.py b/beacon/request/routes.py
@@ -136,5 +136,4 @@
     web.post('/api/runs/{id}/g_variants', generic_handler(db_fn=runs.get_variants_of_run)),
     web.post('/api/runs/{id}/analyses', generic_handler(db_fn=runs.get_analyses_of_run)),
 
-    web.post('/api/verifier', verifier_handler),
 ]
diff --git a/beacon/response/build_response.py b/beacon/response/build_response.py
@@ -1,5 +1,5 @@
 from typing import Optional
-
+import subprocess
 from beacon import conf
 from beacon.db.schemas import DefaultSchemas
 from beacon.request import RequestParams
@@ -334,3 +334,4 @@ def build_filtering_terms_response(data,
         'beaconHandovers': conf.beacon_handovers,
     }
     return beacon_response
+
diff --git a/beacon/response/info.py b/beacon/response/info.py
@@ -10,7 +10,7 @@
 * ``/service-info`` GA4GH
 
 """
-
+import subprocess
 import logging
 import json
 from aiohttp.web_request import Request

diff --git a/beacon/response/verifier.py b/beacon/response/verifier.py
diff --git a/deploy/conf.py b/deploy/conf.py
@@ -6,7 +6,7 @@
 beacon_id = 'org.ega-archive.ga4gh-approval-beacon-test'  # ID of the Beacon
 beacon_name = 'GA4GH Approval Beacon Test'  # Name of the Beacon service
 api_version = 'v2.0.0'  # Version of the Beacon implementation
-uri = 'https://ega-archive.org/test-beacon-apis/cineca/'
+uri = 'https://beacon-apis-test.ega-archive.org/api/'
 
 #
 # Beacon granularity

diff --git a/deploy/docker-compose.yml b/deploy/docker-compose.yml
@@ -172,8 +172,6 @@ services:
     #command: ["yarn", "node", "/opt/yarn-v1.22.19/bin/yarn.js", "start" ]
     command: ["node", "/opt/yarn-v1.22.19/bin/yarn.js", "start" ]
     container_name: react
-    depends_on:
-      - beacon
     ports:
       - 3000:3000
     volumes:

diff --git a/frontend/src/App.css b/frontend/src/App.css
@@ -514,6 +514,13 @@ html {
   margin-bottom: 40px;
 }
 
+.NavlinkVerifier{
+  color: #3fa18e;
+}
+.NavlinkVerifier:hover{
+  margin: 0px !important;
+}
+
 .alphanumContainer {
   display: flex;
   width: 50vw;
@@ -560,7 +567,8 @@ html {
   display: flex;
   align-content: center;
   justify-content: center;
-  margin-right: 20px;
+  width: 100%;
+  text-underline-offset: 2px;
 }
 
 .elixirLogo {
@@ -592,7 +600,6 @@ select {
 }
 
 
-
 .alphaIdModule {
   display: flex;
   flex-direction: column;
@@ -687,7 +694,6 @@ hr {
 .helpButton {
   display: flex;
   align-items: center;
-  width: 188px;
   margin-left: 20px;
 }
 

diff --git a/frontend/src/App.js b/frontend/src/App.js
@@ -1,24 +1,25 @@
-import 'devextreme/dist/css/dx.light.css';
+import 'devextreme/dist/css/dx.light.css'
 
-import './App.css';
-import { Route, Routes } from 'react-router-dom';
+import './App.css'
+import { Route, Routes } from 'react-router-dom'
 
-import Individuals from './components/Individuals/Individuals';
-import GenomicVariations from './components/GenomicVariations/GenomicVariations';
-import Biosamples from './components/Biosamples/Biosamples';
-import Runs from './components/Runs/Runs';
-import Analyses from './components/Analyses/Analyses';
-import Cohorts from './components/Cohorts/Cohorts';
-import ErrorPage from './pages/ErrorPage';
-import Navbar from './components/NavBar/Navbar';
-import SignInForm from './components/SignIn/SignInForm';
-import ResultsDatasets from './components/Datasets/ResultsDatasets';
-import CrossQueries from './components/CrossQueries/CrossQueries';
-import LoggedIn from './components/SignIn/LoggedIn';
+import Individuals from './components/Individuals/Individuals'
+import GenomicVariations from './components/GenomicVariations/GenomicVariations'
+import Biosamples from './components/Biosamples/Biosamples'
+import Runs from './components/Runs/Runs'
+import Analyses from './components/Analyses/Analyses'
+import Cohorts from './components/Cohorts/Cohorts'
+import ErrorPage from './pages/ErrorPage'
+import Navbar from './components/NavBar/Navbar'
+import SignInForm from './components/SignIn/SignInForm'
+import ResultsDatasets from './components/Datasets/ResultsDatasets'
+import CrossQueries from './components/CrossQueries/CrossQueries'
+import LoggedIn from './components/SignIn/LoggedIn'
+import Verifier from './components/Verifier/Verifier'
 
-function App() {
+function App () {
   return (
-    <div className="App">
+    <div className='App'>
       <Navbar />
       <Routes>
         <Route path='/' element={<Individuals />} />
@@ -29,15 +30,14 @@ function App() {
         <Route path='/analyses' element={<Analyses />} />
         <Route path='/cohorts' element={<Cohorts />} />
         <Route path='/members' element={<ResultsDatasets />} />
-        <Route path="/sign-in" element={<SignInForm />} />
-        <Route path="/loggedOut" element={<LoggedIn />} />
-        <Route path="/cross-queries" element={<CrossQueries />} />
-        <Route path="*" element={<ErrorPage />} />
+        <Route path='/sign-in' element={<SignInForm />} />
+        <Route path='/loggedOut' element={<LoggedIn />} />
+        <Route path='/cross-queries' element={<CrossQueries />} />
+        <Route path='/verifier' element={<Verifier />} />
+        <Route path='*' element={<ErrorPage />} />
       </Routes>
     </div>
-  );
+  )
 }
 
-
-
-export default App;
+export default App
diff --git a/frontend/src/components/CrossQueries/CrossQueries.css b/frontend/src/components/CrossQueries/CrossQueries.css
@@ -1,89 +1,89 @@
-.crossQueriesForm{
-    display: flex;
-    flex-direction: column;
-    /* justify-content: center; */
-    margin-top: 40px; 
-    margin-right: 30px;
-    align-content: center;
-    align-items: flex-start;
+.crossQueriesForm {
+  display: flex;
+  flex-direction: column;
+  /* justify-content: center; */
+  margin-top: 40px;
+  margin-right: 30px;
+  align-content: center;
+  align-items: flex-start;
 }
 
-
-select{
-    background: white;
-    border: 2px solid #010a7d;
-    font-size: medium;
-    border-radius: 5px;
-    width: 150px;
-    margin-left: 10px;
-    height: 29px;
-    box-shadow: 1px 2px 2px #cecece;
-    cursor: pointer;
+select {
+  background: white;
+  border: 2px solid #010a7d;
+  font-size: medium;
+  border-radius: 5px;
+  width: 150px;
+  margin-left: 10px;
+  height: 29px;
+  box-shadow: 1px 2px 2px #cecece;
+  cursor: pointer;
 }
 
-.inputId{
-    background: white;
-    border: 2px solid #010a7d;
-    font-size: medium;
-    border-radius: 5px;
-    width: 150px;
-    margin-left: 10px;
-    height: 19px;
-    box-shadow: 1px 2px 2px #cecece;
-    cursor: pointer;
+.inputId {
+  background: white;
+  border: 2px solid #010a7d;
+  font-size: medium;
+  border-radius: 5px;
+  width: 150px;
+  margin-left: 10px;
+  height: 19px;
+  box-shadow: 1px 2px 2px #cecece;
+  cursor: pointer;
 }
 
-.divCrossQueries{
-    display: flex;
-    justify-content: center;
+.divCrossQueries {
+  display: flex;
+  justify-content: center;
 }
 
-.crossQueriesForm label{
-    margin-top: 20px;
-    margin-bottom: 20px;
+.crossQueriesForm label {
+  margin-top: 20px;
+  margin-bottom: 20px;
 }
 
-.formButton{
-    cursor: pointer;
-    background: rgb(214, 207, 207);
-    border: 2px 2px 2px 0px solid #010a7d;
-    font-size: medium;
-    border-radius: 5px;
-    width: 100px;
-    height: 35px;
-    box-shadow: 1px 2px 2px #cecece;
-    margin-top: 30px;
+.formButton {
+  cursor: pointer;
+  background: rgb(214, 207, 207);
+  border: 2px 2px 2px 0px solid #010a7d;
+  font-size: medium;
+  border-radius: 5px;
+  width: 100px;
+  height: 35px;
+  box-shadow: 1px 2px 2px #cecece;
+  margin-top: 30px;
 }
 
-.formButton:hover{
-    background: rgb(237, 142, 40);
+.formButton:hover {
+  background: rgb(237, 142, 40);
 }
 
-h5{
-    color: rgb(209, 66, 66);
-    font-weight: bold;
-    width: 100%;
-    display: flex;
-    align-items: center;
-    justify-content: center;
+h5 {
+  color: rgb(209, 66, 66);
+  font-weight: bold;
+  width: 150%;
+  display: flex;
+  /* align-items: center; */
+  justify-content: flex-start;
+  font-size: 14px;
 }
 
-h5:hover{
-    color: rgb(118, 151, 228);
-    font-weight: bold;
-    width: 100%;
-    display: flex;
-    align-items: center;
-    justify-content: center;
+h5:hover {
+  color: rgb(118, 151, 228);
+  font-weight: bold;
+  width: 100%;
+  display: flex;
+  align-items: center;
+  justify-content: center;
 }
 
-.preCrossQueries{
-    margin-left: 30px;
+.preCrossQueries {
+  margin-left: 30px;
 }
 
-.preCrossQueries p{
-    font-size: 11px;
-    background: #e5e5e5;
-    color: black;
-    padding: 20px;
-}
+.preCrossQueries p {
+  font-size: 11px;
+  background: #e5e5e5;
+  color: black;
+  padding: 20px;
+}
diff --git a/frontend/src/components/Datasets/ResultsDatasets.js b/frontend/src/components/Datasets/ResultsDatasets.js
@@ -54,7 +54,7 @@ function ResultsDatasets(props) {
                         {result.meta.beaconId !== 'org.ega-archive.ga4gh-approval-beacon-test' && <p>{result.response.description}</p>}
                         <div className="linksBeacons">
                             {result.meta.beaconId === 'org.ega-archive.ga4gh-approval-beacon-test' &&
-                                <a href="https://ega-archive.org/test-beacon-apis/cineca" target="_blank">Beacon API</a>}
+                                <a href="https://beacon-apis-test.ega-archive.org/api" target="_blank">Beacon API</a>}
                             {result.meta.beaconId === 'es.elixir.bsc.beacon' &&
                                 <a href="https://beacons.bsc.es/beacon/v2.0.0/" target="_blank">Beacon API</a>}
                             {result.meta.beaconId === 'org.progenetix' &&