Merge pull request #628 from SynBioHub/checkbackend

Checkbackend

backend/src/main/java/com/synbiohub/sbh3/controllers/AdminController.java

@@ -130,8 +130,14 @@ public String deletePlugin(@RequestParam Map<String,String> allParams, HttpServl
     @GetMapping(value = "/admin/registries")
     @ResponseBody
     public JsonNode getRegistries() throws IOException {
-        return ConfigUtil.get("webOfRegistries");
-
+        try {
+            JsonNode result = ConfigUtil.get("webOfRegistries");
+            return result;
+        } catch (IOException e) {
+            e.printStackTrace();
+            // Optionally, handle the exception or log more details here.
+            throw e; // rethrow the exception if you want to maintain the current method signature
+        }
     }
 
     @PostMapping(value = "/admin/saveRegistry")

backend/src/main/java/com/synbiohub/sbh3/controllers/DownloadController.java

@@ -1,6 +1,5 @@
 package com.synbiohub.sbh3.controllers;
 
-import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.synbiohub.sbh3.services.DownloadService;
 import com.synbiohub.sbh3.utils.ConfigUtil;
@@ -13,7 +12,6 @@
 import org.springframework.util.AntPathMatcher;
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.ResponseBody;
 import org.springframework.web.bind.annotation.RestController;
 
 import java.io.ByteArrayInputStream;
@@ -30,9 +28,16 @@ public class DownloadController extends AntPathMatcher {
     private final ObjectMapper mapper;
 
     @GetMapping(value = "/public/{db}/{id}/{ver}/sbol") // Separate mapping for private components /user/{username}/{db}/{id}/{ver}
+    public ResponseEntity<?> getSBOLRecursiveRDFDownload(@PathVariable String db, @PathVariable String id, @PathVariable String ver) throws IOException {
+        return getInputStreamResourceResponseEntity(db, id, ver);
+    }
+
+    @GetMapping(value = "/public/{db}/{id}/{ver}") // Separate mapping for private components /user/{username}/{db}/{id}/{ver}
     public ResponseEntity<?> getSBOLRecursiveRDF(@PathVariable String db, @PathVariable String id, @PathVariable String ver) throws IOException {
-//        var uri = request.getRequestURL().toString();
-//        String splitUri = uri.split("/sbol")[0]; //TODO replace http://localhost:6789 with https://synbiohub.org
+        return getInputStreamResourceResponseEntity(db, id, ver);
+    }
+
+    private ResponseEntity<InputStreamResource> getInputStreamResourceResponseEntity(String db, String id, String ver) throws IOException {
         String splitUri = ConfigUtil.get("defaultGraph").toString().replace("\"","") + "/" + db + "/" + id + "/" + ver;
         String uri = splitUri + "/sbol";
 
@@ -50,7 +55,7 @@ public ResponseEntity<?> getSBOLRecursiveRDF(@PathVariable String db, @PathVaria
                 //.contentLength(results.length)
                 .contentType(
                         MediaType.parseMediaType("application/xml"))
-                .header("Content-Disposition", "attachment; filename=\"" + uriArr[uriArr.length-3] + ".xml\"")
+                .header("Content-Disposition", "attachment; filename=\"" + uriArr[uriArr.length - 3] + ".xml\"")
                 .body(new InputStreamResource(new ByteArrayInputStream(byteOutput.toByteArray())));
     }
 

backend/src/main/java/com/synbiohub/sbh3/controllers/SearchController.java

@@ -8,9 +8,7 @@
 import org.json.JSONObject;
 import org.springframework.web.bind.annotation.*;
 
-import javax.json.Json;
 import java.io.IOException;
-import java.io.UnsupportedEncodingException;
 import java.util.Map;
 
 @RestController
@@ -199,8 +197,9 @@ public String getTypeCount(@PathVariable("type") String type, HttpServletRequest
      */
     @RequestMapping(value = "/sparql", headers = "Accept=application/json")
     @ResponseBody
-    public String getSPARQL(@RequestParam String query) throws IOException {
-        return searchService.SPARQLQuery(query);
+    public String getSPARQL(@RequestParam Map<String, String> params) throws IOException {
+        System.out.println(params);
+        return searchService.SPARQLQuery(params.get("query"));
     }
 
 //    @GetMapping(value = "/search/**")

backend/src/main/java/com/synbiohub/sbh3/security/config/SecurityConfig.java

@@ -53,7 +53,7 @@ public SecurityFilterChain securityFilterChain(HttpSecurity http) throws Excepti
                 .cors()
                 .and()
                 .authorizeHttpRequests()
-                .requestMatchers("/setup", "/login", "/register", "/search", "/search/**", "/searchCount", "/searchCount/**", "/twins", "/uses", "/similar", "/sbol", "/sbolnr", "/metadata", "/gb", "/fasta", "/gff", "/download", "/public/**", "/sparql", "/ComponentDefinition/**", "/**/count", "/count", "/admin/theme").permitAll()
+                .requestMatchers("/setup", "/login", "/register", "/search", "/search/**", "/searchCount", "/searchCount/**", "/twins", "/uses", "/similar", "/sbol", "/sbolnr", "/metadata", "/gb", "/fasta", "/gff", "/download", "/public/**", "/sparql", "/ComponentDefinition/**", "/**/count", "/count", "/admin/theme", "/admin/registries", "admin/plugins").permitAll()
                 .anyRequest().authenticated()
                 .and()
                 .csrf().disable()

backend/src/main/java/com/synbiohub/sbh3/services/SearchService.java

@@ -350,7 +350,7 @@ public String SPARQLQuery(String query) throws IOException {
         HashMap<String, String> params = new HashMap<>();
         params.put("default-graph-uri", ConfigUtil.get("defaultGraph").asText());
         params.put("query", query);
-
+        System.out.println(query.getClass().getName());
         url = ConfigUtil.get("sparqlEndpoint").asText() + "?default-graph-uri={default-graph-uri}&query={query}&format=json&";
 //        url = ConfigUtil.get("sparqlEndpoint").asText() + "?default-graph-uri={default-graph-uri}&query={query}";
         // has to be the first one. without format json, getting root collections fails
@@ -369,7 +369,7 @@ public byte[] SPARQLRDFXMLQuery(String query) throws IOException {
         httpHeaders.add("Accept", "application/rdf+xml");
         HttpEntity entity = new HttpEntity(httpHeaders);
 
-        url = ConfigUtil.get("sparqlEndpoint").asText() + "?default-graph-uri={default-graph-uri}&query={query}";
+        url = ConfigUtil.get("sparqlEndpoint").asText();
 
         var rest = restTemplate.exchange(url, HttpMethod.GET, entity, byte[].class, params);
         return rest.getBody();
@@ -385,12 +385,12 @@ public byte[] queryOldSBHSparqlEndpoint(String WOREndpoint, String query) throws
         String url;
         HashMap<String, String> params = new HashMap<>();
 //        params.put("default-graph-uri", ConfigUtil.get("defaultGraph").asText());
-        params.put("query", query);
-        params.put("format", "application/rdf+xml");
+//        params.put("query", query);
+//        params.put("format", "application/rdf+xml");
         HttpHeaders httpHeaders = new HttpHeaders();
 //        httpHeaders.add("Accept", "application/json");
-        httpHeaders.add("Accept", "application/rdf+xml");
-        HttpEntity entity = new HttpEntity<>("body", httpHeaders);
+        httpHeaders.add("Accept", "text/plain");
+        HttpEntity entity = new HttpEntity<>(httpHeaders);
 
 //        url = WOREndpoint + "/sparql?query="+query;
 //        var result = restTemplate.getForObject(url, String.class);

frontend/.env.development

@@ -1,2 +1,2 @@
-backend="http://localhost:6789"
-backendSS="http://localhost:6789"
+backend="http://localhost:7777"
+backendSS="http://localhost:7777"

frontend/components/Admin/Registries.js

@@ -324,7 +324,7 @@ const sortMethods = {
 
 const useRegistries = (token, dispatch) => {
   const { data, error } = useSWR(
-    [`${publicRuntimeConfig.backend}/admin/registries`, token, dispatch],
+    [`${publicRuntimeConfig.backend}/admin/registries`, dispatch],
     fetcher
   );
   return {
@@ -334,13 +334,12 @@ const useRegistries = (token, dispatch) => {
   };
 };
 
-const fetcher = (url, token, dispatch) =>
+const fetcher = (url, dispatch) =>
   axios
     .get(url, {
       headers: {
         'Content-Type': 'application/json',
-        Accept: 'application/json',
-        'X-authorization': token
+        Accept: 'application/json'
       }
     })
     .then(response => response.data)
@@ -352,14 +351,24 @@ const fetcher = (url, token, dispatch) =>
 
 export async function processUrl(inputUrl, token, dispatch) {
 
-  const data = await fetcher(`${publicRuntimeConfig.backend}/admin/registries`, token, dispatch);
+  const data = await fetcher(`${publicRuntimeConfig.backend}/admin/registries`, dispatch);
 
-  if (data) {
-    const registries = data.registries;
+
+
+  if (data && data.registries) {
+    let registries;
+    // Check if data.registries is an array
+    if (data.registries && Array.isArray(data.registries)) {
+      registries = data.registries;
+    } else if (data && typeof data === 'object') {
+      registries = [data]; // This is an example, adjust based on your needs
+    } else {
+      registries = [];
+    }
 
     for (const registry of registries) {
       if (inputUrl.startsWith(registry.uri)) {
-        const urlRemovedForLink = inputUrl.replace(registry.uri, "");
+        const urlRemovedForLink = inputUrl.replace(registry.uri, ""); // TODO: Should only strip for only "you"
         const urlReplacedForBackend = inputUrl.replace(registry.uri, registry.url);
         return { urlRemovedForLink, urlReplacedForBackend };
       }
@@ -371,9 +380,9 @@ export async function processUrl(inputUrl, token, dispatch) {
 
 export async function processUrlReverse(inputUrl, token, dispatch) {
 
-  const data = await fetcher(`${publicRuntimeConfig.backend}/admin/registries`, token, dispatch);
+  const data = await fetcher(`${publicRuntimeConfig.backend}/admin/registries`, dispatch);
 
-  if (data) {
+  if (data && data.registries) {
     const registries = data.registries;
 
     for (const registry of registries) {

frontend/components/Viewing/Collection/Members.js

@@ -25,6 +25,7 @@ import { FontAwesomeIcon } from '@fortawesome/react-fontawesome';
 import { faTrash, faUnlink } from '@fortawesome/free-solid-svg-icons';
 import { getAfterThirdSlash } from '../ViewHeader';
 import Status, { useStatus } from '../../Admin/Status';
+import { useTheme } from '../../Admin/Theme';
 
 /* eslint sonarjs/cognitive-complexity: "off" */
 
@@ -51,6 +52,7 @@ export default function Members(properties) {
   const [typeFilter, setTypeFilter] = useState('Show Only Root Objects');
   const dispatch = useDispatch();
   const [processedUri, setProcessedUri] = useState(publicRuntimeConfig.backend);
+  const { theme } = useTheme();
 
   let preparedSearch =
     search !== ''
@@ -74,7 +76,7 @@ export default function Members(properties) {
 
   const parameters = {
     from: '',
-    graphPrefix: 'https://synbiohub.org/', // TODO: Maybe get this from somewhere? 
+    graphPrefix: `${theme.uriPrefix}`, // TODO: Maybe get this from somewhere? 
     collection: properties.uri,
     sort: sort,
     search: preparedSearch,

frontend/components/Viewing/PageJSON/Fetching/executeQueryFromTableJSON.js

@@ -10,15 +10,17 @@ export default function executeQueryFromTableJSON(
 ) {
   if (typeof uri === "undefined") {
     uri = "URI is undefined";
-}
+  }
+
+  console.log(uri);
 
-
   return getQueryResponse(
     dispatch,
     prefixes + '\n' + buildQuery(uri, table),
-    {},
+    { uri },
     '',
     false,
-    urlOverride
+    urlOverride, 
+    uri
   );
 }

frontend/components/Viewing/PageJSON/Rendering/TableBuilder.js

@@ -48,8 +48,12 @@ function TableRenderer({ uri, prefixes, table, metadata, owner }) {
   const token = useSelector(state => state.user.token);
   const [content, setContent] = useState(null);
   const dispatch = useDispatch();
+  console.log(uri);
+  console.log(prefixes);
+  console.log(table);
   useEffect(() => {
     executeQueryFromTableJSON(dispatch, uri, prefixes, table).then(response => {
+      console.log(response);
       setContent(parseQueryResult(table, response, prefixes));
     });
   }, [uri, prefixes, table]);

frontend/components/Viewing/Sections/Details/Details.js

@@ -29,7 +29,7 @@ export default function Details(properties) {
     if (details == undefined) {
       getQueryResponse(dispatch, getDetails, { uri: properties.uri }).then(
         details => {
-          if (details.length > 0) setDetails(details[0]);
+          if (details && details.length > 0) setDetails(details[0]);
         }
       );
 

frontend/pages/[...view].js

@@ -13,6 +13,7 @@ import getQueryResponse from '../sparql/tools/getQueryResponse';
 import { addError } from '../redux/actions';
 import styles from '../styles/view.module.css';
 import LinkedSearch from '../components/Search/StandardSearch/LinkedSearch';
+import { useTheme } from '../components/Admin/Theme'; 
 
 export default function View({ data, error }) {
   const dispatch = useDispatch();
@@ -24,7 +25,7 @@ export default function View({ data, error }) {
   const token = useSelector(state => state.user.token);
   const url = view ? view.join('/') : '';
   const [metadata, setMetadata] = useState();
-  const uri = `https://synbiohub.org/${url}`;
+  const { theme } = useTheme();
   const [urlExists, setUrlExists] = useState(true); // New state for URL existence
   const backenduri = `${publicRuntimeConfig.backend}/${url}`;
 
@@ -65,13 +66,20 @@ export default function View({ data, error }) {
     marginTop: '-10vh',
   };
 
+  let uri;
+  // let uri = `https://dan.org/${url}`;
+  if (theme) {
+    uri = `${theme.uriPrefix}${url}`;
+  }
+
+
   useEffect(() => {
     // Check if URL exists
     axios.get(backenduri)
       .then(response => {
         // URL exists
         setUrlExists(true);
-        if (!metadata)
+        if (!metadata && uri)
           getQueryResponse(dispatch, getMetadata, { uri: uri }, token).then(
             metadata => setMetadata(metadata)
           );

frontend/public/commitHash.txt

@@ -1 +1 @@
-9dae7d40f1fe6b8ebf1ba96d0e4b585927c0a95b
+f6f9da07901a90dad77c15690464facfc1fa8e67

frontend/sparql/tools/getQueryResponse.js

@@ -13,6 +13,8 @@ export default async function getQueryResponse(
   admin,
   urlOverride
 ) {
+console.log(options);
+
   query = loadTemplate(query, options);
 
   const currentURL = window.location.href;
@@ -23,7 +25,9 @@ export default async function getQueryResponse(
     const result = regex.exec(currentURL)[0];
     const lastSlash = result.lastIndexOf('/');
     const graphURL = result.substring(0, lastSlash);
-    graphEx = `&default-graph-uri=https://synbiohub.org${graphURL}`;
+    const uriPrefix = getUrlBeforeThirdSlash(options.uri);
+    console.log(`${uriPrefix}${graphURL}`);
+    graphEx = `&default-graph-uri=${uriPrefix}${graphURL}`;
   }
 
   const params = admin ? '/admin/sparql?query=' : '/sparql?query=';
@@ -32,6 +36,9 @@ export default async function getQueryResponse(
     urlOverride || publicRuntimeConfig.backend
   }${params}${encodeURIComponent(query)}${graph}`;
 
+  console.log(options);
+  console.log(url);
+
   const headers = {
     'Content-Type': 'application/json',
     Accept: 'application/json',
@@ -66,3 +73,14 @@ const processResults = results => {
     return resultObject;
   });
 };
+
+function getUrlBeforeThirdSlash(url) {
+  if (typeof url !== 'string') return '';
+  let slashCount = 0, result = '';
+  for (let i = 0; i < url.length; i++) {
+    if (url[i] === '/') slashCount++;
+    if (slashCount === 3) break;
+    result += url[i];
+  }
+  return result;
+}