search implementation/fixes

EBISPOT · Jun 14, 2024 · d11dbe0 · d11dbe0
1 parent 4baf710
commit d11dbe0
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Showing 19 changed files with 171 additions and 117 deletions.
diff --git a/.gitignore b/.gitignore
@@ -18,4 +18,5 @@ graph.db
 *.txt
 *.swp
 .nextflow*
+work
 
diff --git a/grebi_api/src/main/java/uk/ac/ebi/grebi/GrebiApi.java b/grebi_api/src/main/java/uk/ac/ebi/grebi/GrebiApi.java
@@ -47,7 +47,7 @@ public static void main(String[] args) throws ParseException, org.apache.commons
                     ctx.result("{}");
 
                     var q = new GrebiSolrQuery();
-                    q.addFilter("grebi__nodeId", List.of(ctx.pathParam("nodeId")), SearchType.WHOLE_FIELD);
+                    q.addFilter("grebi:nodeId", List.of(ctx.pathParam("nodeId")), SearchType.WHOLE_FIELD, false);
 
                     var res = solr.getFirstNode(q);
 
@@ -71,12 +71,15 @@ public static void main(String[] args) throws ParseException, org.apache.commons
                     q.setSearchText(ctx.queryParam("q"));
                     q.setExactMatch(false);
                     q.addSearchField("id", 1000, SearchType.WHOLE_FIELD);
-                    q.addSearchField("grebi__synonym", 900, SearchType.WHOLE_FIELD);
+                    q.addSearchField("grebi:name", 900, SearchType.WHOLE_FIELD);
+                    q.addSearchField("grebi:synonym", 800, SearchType.WHOLE_FIELD);
                     q.addSearchField("id", 500, SearchType.CASE_INSENSITIVE_TOKENS);
-                    q.addSearchField("grebi__synonym", 450, SearchType.CASE_INSENSITIVE_TOKENS);
-                    q.addSearchField("grebi__description", 400, SearchType.WHOLE_FIELD);
-                    q.addSearchField("grebi__description", 250, SearchType.CASE_INSENSITIVE_TOKENS);
+                    q.addSearchField("grebi:name", 450, SearchType.CASE_INSENSITIVE_TOKENS);
+                    q.addSearchField("grebi:synonym", 420, SearchType.CASE_INSENSITIVE_TOKENS);
+                    q.addSearchField("grebi:description", 400, SearchType.WHOLE_FIELD);
+                    q.addSearchField("grebi:description", 250, SearchType.CASE_INSENSITIVE_TOKENS);
                     q.addSearchField("_text_", 1, SearchType.CASE_INSENSITIVE_TOKENS);
+                    q.addFilter("ols:isObsolete", Set.of("true"), SearchType.WHOLE_FIELD, true);
                     for(var param : ctx.queryParamMap().entrySet()) {
                         if(param.getKey().equals("q") ||
                                 param.getKey().equals("page") ||
@@ -88,15 +91,18 @@ public static void main(String[] args) throws ParseException, org.apache.commons
                         ) {
                             continue;
                         }
-                        q.addFilter(param.getKey(), param.getValue(), SearchType.WHOLE_FIELD);
+                        q.addFilter(param.getKey(), param.getValue(), SearchType.WHOLE_FIELD, false);
+                    }
+                    for(var facetField : ctx.queryParams("facet")) {
+                        q.addFacetField(facetField);
                     }
                     var page_num = ctx.queryParam("page");
                     if(page_num == null) {
                         page_num = "0";
                     }
                     var size = ctx.queryParam("size");
                     if(size == null) {
-                        size = "100";
+                        size = "10";
                     }
                     var page = PageRequest.of(Integer.parseInt(page_num), Integer.parseInt(size));
                     var res = solr.searchNodesPaginated(q, page);

diff --git a/grebi_api/src/main/java/uk/ac/ebi/grebi/db/GrebiSolrClient.java b/grebi_api/src/main/java/uk/ac/ebi/grebi/db/GrebiSolrClient.java
@@ -51,7 +51,7 @@ public GrebiFacetedResultsPage<SolrDocument> searchSolrPaginated(GrebiSolrQuery
                     valueToCount.put(count.getName(), count.getCount());
                 }
 
-                facetFieldToCounts.put(facetField.getName(), valueToCount);
+                facetFieldToCounts.put(facetField.getName().replace("__", ":"), valueToCount);
             }
         }
 

diff --git a/grebi_api/src/main/java/uk/ac/ebi/grebi/db/GrebiSolrQuery.java b/grebi_api/src/main/java/uk/ac/ebi/grebi/db/GrebiSolrQuery.java
@@ -45,8 +45,8 @@ public void addFacetField(String propertyName) {
         this.facetFields.add(propertyName);
     }
 
-    public void addFilter(String propertyName, Collection<String> propertyValues, SearchType searchType) {
-        this.filters.add(new Filter(propertyName, propertyValues, searchType));
+    public void addFilter(String propertyName, Collection<String> propertyValues, SearchType searchType, boolean negate) {
+        this.filters.add(new Filter(propertyName, propertyValues, searchType, negate));
     }
 
     public SolrQuery constructQuery() {
@@ -107,6 +107,10 @@ public SolrQuery constructQuery() {
                 fq.append("{!tag=grebifacet}");
             }
 
+            if(f.negate) {
+                fq.append("-");
+            }
+
             fq.append( ClientUtils.escapeQueryChars(getSolrPropertyName(f.propertyName, f.searchType)) );
             fq.append(":(");
 
@@ -127,8 +131,9 @@ public SolrQuery constructQuery() {
 
         if(facetFields.size() > 0) {
             for(String facetField : facetFields) {
-                query.addFacetField("{!ex=grebifacet}" + facetField);
+                query.addFacetField("{!ex=grebifacet}" + facetField.replace(":", "__"));
             }
+            query.setFacetMinCount(1);
         }
 
         return query;
@@ -139,11 +144,13 @@ private class Filter {
         String propertyName;
         Collection<String> propertyValues; // all values to search for ("OR")
         SearchType searchType;
+        boolean negate;
 
-        public Filter(String propertyName, Collection<String> propertyValues, SearchType searchType) {
+        public Filter(String propertyName, Collection<String> propertyValues, SearchType searchType, boolean negate) {
             this.propertyName = propertyName;
             this.propertyValues = propertyValues;
             this.searchType = searchType;
+            this.negate = negate;
         }
     }
 
@@ -180,9 +187,9 @@ public BoostField(String propertyName, String propertyValue, int weight, SearchT
     private String getSolrPropertyName(String propertyName, SearchType searchType) {
         switch(searchType) {
             case CASE_INSENSITIVE_TOKENS:
-                return propertyName;
+                return propertyName.replace(":", "__");
             case WHOLE_FIELD:
-                return "str_" + propertyName;
+                return "str_" + propertyName.replace(":", "__");
             default:
                 throw new RuntimeException("unknown filter accuracy");
         }

diff --git a/grebi_api/src/main/java/uk/ac/ebi/grebi/db/ResolverClient.java b/grebi_api/src/main/java/uk/ac/ebi/grebi/db/ResolverClient.java
@@ -8,8 +8,11 @@
 import com.google.gson.JsonElement;
 import java.util.List;
 import java.util.Map;
+import java.util.stream.Collectors;
+
 import com.google.gson.JsonElement;
 import com.google.gson.Gson;
+import com.google.gson.internal.LinkedTreeMap;
 import org.apache.http.HttpEntity;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.HttpClient;
@@ -31,7 +34,7 @@ public static String getResolverHost() {
         return "http://localhost:8080/";
     }
 
-    public Map<String, Map<String,JsonElement>> resolve(Collection<String> ids) {
+    public Map<String, Map<String,JsonElement>> resolveToMap(Collection<String> ids) {
 
         Stopwatch timer = Stopwatch.createStarted();
 
@@ -65,4 +68,11 @@ public Map<String, Map<String,JsonElement>> resolve(Collection<String> ids) {
 
         return null;
     }
+
+    public List<Map<String, JsonElement>> resolveToList(Collection<String> ids) {
+
+        var resolved = resolveToMap(ids);
+
+        return ids.stream().map(id -> resolved.get(id)).collect(Collectors.toList());
+    }
 }
diff --git a/grebi_api/src/main/java/uk/ac/ebi/grebi/repo/GrebiNeoRepo.java b/grebi_api/src/main/java/uk/ac/ebi/grebi/repo/GrebiNeoRepo.java
@@ -65,7 +65,7 @@ public List<EdgeAndNode> getIncomingEdges(String nodeId) {
             .withParameters(Map.of("nodeId", nodeId))
             .withConfig(QueryConfig.builder().withDatabase("neo4j").build()).execute();
 
-        var resolved = resolver.resolve(
+        var resolved = resolver.resolveToMap(
                 res.records().stream().flatMap(record -> {
                     var props = record.asMap();
                     return List.of((String) props.get("otherId"), (String) props.get("edgeId")).stream();

diff --git a/grebi_api/src/main/java/uk/ac/ebi/grebi/repo/GrebiSolrRepo.java b/grebi_api/src/main/java/uk/ac/ebi/grebi/repo/GrebiSolrRepo.java
@@ -38,38 +38,29 @@ private GrebiFacetedResultsPage<Map<String,JsonElement>> resolveNodeIds(GrebiFac
 
         List<String> ids = solrDocs.map(doc -> doc.getFieldValue("grebi__nodeId").toString()).toList();
 
-        Map<String,Map<String,JsonElement>> idToEntity = resolver.resolve(ids);
-
-        List<Map<String,JsonElement>> vals = idToEntity.values().stream().collect(Collectors.toList());
+        List<Map<String,JsonElement>> vals = resolver.resolveToList(ids);
         assert(vals.size() == solrDocs.getSize());
 
         return new GrebiFacetedResultsPage<>(vals, solrDocs.facetFieldToCounts, solrDocs.getPageable(), solrDocs.getTotalElements());
     }
 
     private Map<String,JsonElement> resolveNodeId(SolrDocument solrDoc)  {
-
-        Map<String,Map<String,JsonElement>> idToEntity = resolver.resolve(List.of(solrDoc.getFieldValue("grebi__nodeId").toString()));
-
-        return idToEntity.values().iterator().next();
+        return resolver.resolveToList(List.of(solrDoc.getFieldValue("grebi__nodeId").toString())).iterator().next();
     }
 
     private GrebiFacetedResultsPage<Map<String,JsonElement>> resolveEdgeIds(GrebiFacetedResultsPage<SolrDocument> solrDocs) {
 
         List<String> ids = solrDocs.map(doc -> doc.getFieldValue("grebi__edgeId").toString()).toList();
 
-        Map<String, Map<String,JsonElement>> idToEntity = resolver.resolve(ids);
-
-        List<Map<String,JsonElement>> vals = idToEntity.values().stream().collect(Collectors.toList());
+        List<Map<String,JsonElement>> vals = resolver.resolveToList(ids);
         assert(vals.size() == solrDocs.getSize());
 
         return new GrebiFacetedResultsPage<>(vals, solrDocs.facetFieldToCounts, solrDocs.getPageable(), solrDocs.getTotalElements());
     }
 
     private Map<String,JsonElement> resolveEdgeId(SolrDocument solrDoc)  {
 
-        Map<String,Map<String,JsonElement>> idToEntity = resolver.resolve(List.of(solrDoc.getFieldValue("grebi__edgeId").toString()));
-
-        return idToEntity.values().iterator().next();
+        return resolver.resolveToList(List.of(solrDoc.getFieldValue("grebi__edgeId").toString())).iterator().next();
     }
 
 }
diff --git a/grebi_ui/src/App.tsx b/grebi_ui/src/App.tsx
@@ -13,9 +13,26 @@ import Search from "./pages/search/Search";
 import NodePage from "./pages/node/NodePage";
 import DownloadsPage from "./pages/downloads/Downloads";
 
+
+import MuiThemeProvider from '@mui/styles/ThemeProvider'
+import createTheme from '@mui/material/styles/createTheme'
+
+const theme = createTheme({
+  palette: {
+    primary: {
+      main: '#ff0000',
+    },
+    secondary: {
+      main: '#ff0000',
+    }
+  }
+});
+
+
 class App extends React.Component {
   render() {
     return (
+       <MuiThemeProvider theme={theme}>
       <Fragment>
         <Helmet>
           <meta charSet="utf-8" />
@@ -36,6 +53,7 @@ class App extends React.Component {
         {/* <Footer /> */}
       </BrowserRouter>
       </Fragment>
+      </MuiThemeProvider>
     );
   }
 }

diff --git a/grebi_ui/src/app/api.ts b/grebi_ui/src/app/api.ts
@@ -1,5 +1,20 @@
 
-type ReqParams = {[k:string]:string}|undefined 
+type ReqParams = {[k:string]:(string|string[])}|undefined 
+
+function buildSearchParams(reqParams:ReqParams):string {
+  let params = new URLSearchParams()
+  for(let key in reqParams) {
+    let val = reqParams[key]
+    if(Array.isArray(val)) {
+      for(let v of val) {
+        params.append(key, v)
+      }
+    } else {
+      params.append(key, val)
+    }
+  }
+  return params.toString()
+}
 
 export async function request(
   path: string,
@@ -9,7 +24,7 @@ export async function request(
 ): Promise<any> {
   const url = (apiUrl || process.env.REACT_APP_APIURL) + path;
   //const res = await fetch(url.replace(/([^:]\/)\/+/g, "$1"), {
-  const res = await fetch(url + (reqParams ? ('?' + new URLSearchParams(Object.entries(reqParams)).toString()) : ''), {
+  const res = await fetch(url + (reqParams ? ('?' + buildSearchParams(reqParams)) : ''), {
     ...(init ? init : {}),
     //headers: { ...(init?.headers || {}), ...getAuthHeaders() }
   });

diff --git a/grebi_ui/src/components/SearchBox.tsx b/grebi_ui/src/components/SearchBox.tsx
@@ -147,9 +147,8 @@ export default function SearchBox({
     .map((entry: GraphNode, i: number): SearchBoxEntry => {
           let name = entry.getName();
           let type = entry.extractType()?.short
-          const linkUrl = `/nodes/${encodeNodeId(entry.getNodeId())}`;
           return {
-            linkUrl,
+            linkUrl: entry.getLinkUrl(),
             li: (
               <li
                 key={randomString()}
@@ -164,7 +163,7 @@ export default function SearchBox({
                   onClick={() => {
                     setQuery("");
                   }}
-                  to={linkUrl}
+                  to={entry.getLinkUrl()}
                 >
                   <div className="flex justify-between">
 

diff --git a/grebi_ui/src/model/GraphNode.ts b/grebi_ui/src/model/GraphNode.ts
@@ -1,4 +1,5 @@
 import { pickBestDisplayName } from "../app/util";
+import encodeNodeId from "../encodeNodeId";
 import PropVal from "./PropVal";
 import Refs from "./Refs";
 
@@ -14,22 +15,30 @@ export default class GraphNode {
         return PropVal.arrFrom(this.props['grebi:name'] || []);
     }
 
+    getSynonyms():PropVal[] {
+        return PropVal.arrFrom(this.props['grebi:synonym'] || []);
+    }
+
     getName():string {
         return pickBestDisplayName(this.getNames().map(n => n.value)) || this.getId().value
     }
 
     getDescriptions():PropVal[] {
-        return PropVal.arrFrom(this.props['rdfs:comment'])
+        return PropVal.arrFrom(this.props['grebi:description'])
     }
 
-    getDescription():PropVal|undefined {
-        return PropVal.arrFrom(this.getDescriptions())[0]
+    getDescription():string|undefined {
+        return PropVal.arrFrom(this.getDescriptions())[0]?.value
     }
 
     getNodeId():string {
         return this.props['grebi:nodeId']
     }
 
+    getLinkUrl():string {
+        return `/nodes/${encodeNodeId(this.getNodeId())}`;
+    }
+
     getId():PropVal {
         if(this.props['ols:curie']){
             return PropVal.arrFrom(this.props['ols:curie'])[0]
@@ -62,6 +71,9 @@ export default class GraphNode {
         }
         if(types.indexOf('ols:Class') !== -1) {
             let ancestors:any[] = PropVal.arrFrom(this.props['ols:directAncestor']).map(a => a.value)
+            if(ancestors.indexOf("chebi:36080") !== -1) {
+                return {long:'Protein',short:'Protein'}
+            }
             if(ancestors.indexOf("chebi:24431") !== -1) {
                 return {long:'Chemical',short:'Chemical'}
             }
@@ -83,8 +95,13 @@ export default class GraphNode {
         return this.props['grebi:datasources'] || []
     }
 
-    isBold() { // idk yet
-        return false
+    isBoldForQuery(q:string) {
+        let allIdentifiers = [
+            ...this.getNames().map(p => p.value),
+            ...this.getSynonyms().map(p => p.value),
+            ...this.getIds().map(p => p.value),
+        ];
+        return allIdentifiers.indexOf(q) !== -1
     }
 
     isDeprecated() {
@@ -97,12 +114,28 @@ export default class GraphNode {
 
     getProps():{[key:string]:PropVal[]} {
         let res_props = {}
-        for(let k of Object.keys(this.props)) {
-            if( (k.startsWith('grebi:') || k === '_refs') && k !== 'grebi:type') {
+        let keys = Object.keys(this.props)
+
+        let sortOrder = [
+            'grebi:name',
+            'grebi:synonym',
+            'grebi:description',
+            'grebi:type'
+        ].filter(k => {
+            if(keys.indexOf(k) !== -1) {
+                keys.splice(keys.indexOf(k), 1)
+                return true
+            }
+        })
+        keys = sortOrder.concat(keys)
+        for(let k of keys) {
+            //if( (k.startsWith('grebi:') || k === '_refs') && k !== 'grebi:type') {
+            if(k === '_refs') {
                 continue;
             }
             res_props[k] = PropVal.arrFrom(this.props[k])
         }
         return res_props
     }
-}
+}
+
-Original file line number
+Diff line change
@@ Expand Up / @@ -18,4 +18,5 @@ graph.db @@
     *.txt
     *.swp
     .nextflow*
+    work