[risk=no] [PD-14784] Genetic Variant Search Changes and DOS applicati…

…on hang up fix (#1462) * survey queries for location data * survey queries for location data * survey queries for location data * survey queries for location data * survey queries for location data * trying to fix DOS breakage on < --------- Co-authored-by: Srushti Gangireddy <[email protected]>
all-of-us · Sep 19, 2024 · be94630 · be94630
1 parent 77f9e76
commit be94630
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Showing 13 changed files with 214 additions and 86 deletions.
diff --git a/public-api/src/main/java/org/pmiops/workbench/cdr/dao/ConceptService.java b/public-api/src/main/java/org/pmiops/workbench/cdr/dao/ConceptService.java
@@ -136,6 +136,7 @@ public static String modifyMultipleMatchKeyword(String query, SearchType searchT
     public Slice<DbConcept> searchConcepts(String query, StandardConceptFilter standardConceptFilter, List<Long> conceptIds, List<String> vocabularyIds, String domainId, int limit, int minCount, int page,
                                          TestFilter testFilter, OrderFilter orderFilter) {
 
+
         Specification<DbConcept> conceptSpecification =
                 (root, criteriaQuery, criteriaBuilder) -> {
                     List<Predicate> predicates = new ArrayList<>();
@@ -151,6 +152,7 @@ public Slice<DbConcept> searchConcepts(String query, StandardConceptFilter stand
                     Pattern regex = Pattern.compile("[$&+,:;=\\\\?@#|/'<>.^*()%!-]");
                     if (keyword != null && regex.matcher(keyword).find() && keyword.length() == 1) {
                         keyword = "\"" + keyword + "\"";
+                        keyword = escapeSpecialCharacters(keyword);
                     }
 
                     Expression<Double> matchExp = null;
@@ -261,10 +263,17 @@ public List<Concept> getSourceConcepts(Long conceptId, Integer count) {
                 .collect(Collectors.toList());
     }
 
+    // Escaping function to safely handle special characters
+    private String escapeSpecialCharacters(String input) {
+        return input.replaceAll("<", "\\<")  // Escape less-than
+                .replaceAll(">", "\\>"); // Escape greater-than
+    }
+
     public List<Long> getDrugIngredientsByBrand(String query) {
         Pattern regex = Pattern.compile("[$&+,:;=\\\\?@#|/'<>.^*()%!-]");
         if (query != null && regex.matcher(query).find() && query.length() == 1) {
            query = "\"" + query + "\"";
+           query = escapeSpecialCharacters(query);
         }
         return conceptDao.findDrugIngredientsByBrand(query);
     }

diff --git a/public-api/src/main/resources/application.properties b/public-api/src/main/resources/application.properties
@@ -1,7 +1,7 @@
 # Uncomment the following to turn on full SQL debugging
 #logging.level.org.hibernate.SQL=DEBUG
 #logging.level.org.hibernate.type.descriptor.sql.BasicBinder=TRACE
-spring.jpa.properties.hibernate.show_sql=true
+#spring.jpa.properties.hibernate.show_sql=true
 #spring.jpa.properties.hibernate.format_sql=true
 #spring.jpa.properties.hibernate.type=trace
 
@@ -31,11 +31,11 @@ spring.liquibase.enabled=false
 management.endpoints.enabled-by-default=false
 spring.jackson.serialization.write-dates-as-timestamps=false
 
-logging.level.org.springframework.security=DEBUG
+#logging.level.org.springframework.security=DEBUG
 
 spring.autoconfigure.exclude=org.springframework.boot.autoconfigure.security.SecurityAutoConfiguration
 
-spring.log.debug=true
-logging.level.root=DEBUG 
-logging.level.org.springframework.web=DEBUG
-logging.level.org.springframework.web.filter.CommonsRequestLoggingFilter=DEBUG
+#spring.log.debug=true
+#logging.level.root=DEBUG
+#logging.level.org.springframework.web=DEBUG
+#logging.level.org.springframework.web.filter.CommonsRequestLoggingFilter=DEBUG
diff --git a/public-ui/src/app/app-routing.tsx b/public-ui/src/app/app-routing.tsx
@@ -107,9 +107,10 @@ export const AppRoutingComponent: React.FunctionComponent = () => {
         path="/variants"
         component={() =>
           GenomicViewComponent({
+            selectionId: 2,
             routeData: {
-              title: "SNV/Indel Variants",
-              breadcrumb: { value: "SNV/Indel Variants" },
+              title: "Variants",
+              breadcrumb: { value: "Variants" },
             },
           })
         }
@@ -118,9 +119,34 @@ export const AppRoutingComponent: React.FunctionComponent = () => {
         path="/variants/:search"
         component={() =>
           GenomicViewComponent({
+            selectionId: 2,
             routeData: {
-              title: "SNVIndel Variants",
-              breadcrumb: { value: "SNV/Indel Variants" },
+              title: "Variants",
+              breadcrumb: { value: "Variants" },
+            },
+          })
+        }
+      />
+      <AppRoute
+        path="/structural-variants"
+        component={() =>
+          GenomicViewComponent({
+            selectionId: 4,
+            routeData: {
+              title: "Variants",
+              breadcrumb: { value: "Variants" },
+            },
+          })
+        }
+      />
+      <AppRoute
+        path="/structural-variants/:search"
+        component={() =>
+          GenomicViewComponent({
+            selectionId: 4,
+            routeData: {
+              title: "Variants",
+              breadcrumb: { value: "Variants" },
             },
           })
         }

diff --git a/public-ui/src/app/data-browser/databrowser-routing.module.ts b/public-ui/src/app/data-browser/databrowser-routing.module.ts
@@ -86,9 +86,9 @@ const routes: Routes = [
             component: AppRouting,
             canActivate: [IsSafeGuard],
             data: {
-              title: "SNV/Indel Variants",
+              title: "Variants",
               breadcrumb: {
-                value: "SNV/Indel Variants",
+                value: "Variants",
               },
             },
           },
@@ -97,9 +97,31 @@ const routes: Routes = [
             component: AppRouting,
             canActivate: [IsSafeGuard],
             data: {
-              title: "SNV/Indel Variants",
+              title: "Variants",
               breadcrumb: {
-                value: "SNV/Indel Variants",
+                value: "Variants",
+              },
+            },
+          },
+          {
+            path: "structural-variants",
+            component: AppRouting,
+            canActivate: [IsSafeGuard],
+            data: {
+              title: "Variants",
+              breadcrumb: {
+                value: "Variants",
+              },
+            },
+          },
+          {
+            path: "structural-variants/:search",
+            component: AppRouting,
+            canActivate: [IsSafeGuard],
+            data: {
+              title: "Variants",
+              breadcrumb: {
+                value: "Variants",
               },
             },
           },

diff --git a/public-ui/src/app/data-browser/views/ehr-view/ehr-view-react.component.tsx b/public-ui/src/app/data-browser/views/ehr-view/ehr-view-react.component.tsx
@@ -495,6 +495,7 @@ export const EhrViewReactComponent = withRouteData(
     }
 
     fetchConcepts(searchRequest: any, append: boolean) {
+      console.log('Fetching ????');
       dataBrowserApi()
         .searchConcepts(searchRequest)
         .then((results) => {

diff --git a/public-ui/src/app/data-browser/views/genomic-view/components/genomic-search.component.tsx b/public-ui/src/app/data-browser/views/genomic-view/components/genomic-search.component.tsx
@@ -68,7 +68,7 @@ export class GenomicSearchComponent extends React.Component<Props, State> {
     super(props);
     this.scrollDiv = React.createRef();
     this.state = {
-      searchTerm: null,
+      searchTerm: this.props.searchTerm || "",
       filterMetadata: this.props.filterMetadata,
       sortMetadata: this.props.sortMetadata,
       submittedFilterMetadata: this.props.submittedFilterMetadata,

diff --git a/public-ui/src/app/data-browser/views/genomic-view/components/variant-search.component.tsx b/public-ui/src/app/data-browser/views/genomic-view/components/variant-search.component.tsx
@@ -95,7 +95,7 @@ export class VariantSearchComponent extends React.Component<Props, State> {
   constructor(props: Props) {
     super(props);
     this.state = {
-      searchWord: "",
+      searchWord: this.props.searchTerm || "",
       filterShow: false,
       filteredMetadata: undefined,
       filteredMetaMap: undefined,
@@ -204,6 +204,8 @@ export class VariantSearchComponent extends React.Component<Props, State> {
     const variantListSizeDisplay = variantListSize
       ? variantListSize.toLocaleString()
       : 0;
+    console.log(searchWord);
+    console.log(searchWord.length);
     return (
       <React.Fragment>
         <style>{css}</style>