Fix for broken intersect with updated API

weng-lab · Jul 10, 2024 · c1ff685 · c1ff685
1 parent be8f6d1
commit c1ff685
Show file tree

Hide file tree

Showing 2 changed files with 14 additions and 11 deletions.
diff --git a/screen2.0/src/app/header.tsx b/screen2.0/src/app/header.tsx
@@ -8,6 +8,7 @@ import Link from "next/link"
 import Image from "next/image"
 import screenIcon from "../../public/screenLogo.png"
 import { MainSearch } from "./_mainsearch/mainsearch"
+import { A } from "logots-react"
 
 
 /*  
@@ -89,9 +90,9 @@ function ResponsiveAppBar() {
           <Toolbar disableGutters sx={{ justifyContent: "space-between" }}>
             {/* Logo, and desktop navigation */}
             <Box display='flex' flexGrow={1}>
-              <Link href={"/"}>
+              <a href={"/"}>
                 <Image src={screenIcon} alt="SCREEN Icon" height={40} width={90} style={{marginRight: '20px'}}/>
-              </Link>
+              </a>
               {/* Main navigation items for desktop, hide on small screen size */}
               <Box sx={{ display: { xs: "none", lg: "flex" }, alignItems: 'center' }}>
                 {pageLinks.map((page) => (
@@ -107,11 +108,11 @@ function ResponsiveAppBar() {
                       onMouseEnter={page.subPages ? (event) => handleOpenNavMenu_Dropdown(event, page.dropdownID) : undefined}
                     >
                       {/* Wrap in next/link to enable dyanic link changing from basePath in next.config.js */}
-                      <Link href={page.link}>
+                      <a href={page.link}>
                         <Typography variant="body1">
                           {page.pageName}
                         </Typography>
-                      </Link>
+                      </a>
                     </Button>
                     {/* Create popup menu if page has subpages */}
                     {page.subPages && (
@@ -141,9 +142,9 @@ function ResponsiveAppBar() {
                             page.subPages.map((subPage) => (
                               <MenuItem key={subPage.pageName} onClick={() => handleCloseNavMenu_Dropdown(page.dropdownID)}>
                                 {/* Wrap in next/link to enable dyanic link changing from basePath in next.config.js */}
-                                <Link href={subPage.link}>
+                                <a href={subPage.link}>
                                   <Typography textAlign="center">{subPage.pageName}</Typography>
-                                </Link>
+                                </a>
                               </MenuItem>
                             ))}
                         </Paper>
@@ -192,9 +193,9 @@ function ResponsiveAppBar() {
                 </MenuItem>
                 {pageLinks.map((page) => (
                   <MenuItem key={page.pageName} onClick={handleCloseNavMenu_Hamburger}>
-                    <Link href={page.link}>
+                    <a href={page.link}>
                       <Typography textAlign="center" textTransform="none">{page.pageName}</Typography>
-                    </Link>
+                    </a>
                   </MenuItem>
                 ))}
               </Menu>

diff --git a/screen2.0/src/common/lib/queries.ts b/screen2.0/src/common/lib/queries.ts
@@ -120,11 +120,10 @@ const cCRE_QUERY = gql`
   }
 `
 
-function cCRE_QUERY_VARIABLES(assembly: string, chromosome: string, start: number, end: number, biosample: string, nearbygenesdistancethreshold: number, nearbygeneslimit: number, accessions: string[], noLimit?: boolean) {
+function cCRE_QUERY_VARIABLES(assembly: string, coordinates: {chromosome: string, start: number, end: number}[], biosample: string, nearbygenesdistancethreshold: number, nearbygeneslimit: number, accessions: string[], noLimit?: boolean) {
   let vars = {
     uuid: null,
     assembly: assembly,
-    coordinates: [{chromosome, start, end}],
     gene_all_start: 0,
     gene_all_end: 5000000,
     gene_pc_start: 0,
@@ -149,6 +148,9 @@ function cCRE_QUERY_VARIABLES(assembly: string, chromosome: string, start: numbe
   if (accessions) {
     vars["accessions"] = accessions
   }
+  if (coordinates) {
+    vars["coordinates"] = coordinates
+  }
 
   return vars
 }
@@ -259,7 +261,7 @@ export async function MainQuery(assembly: string = null, chromosome: string = nu
   try {
     data = await getClient().query({
       query: cCRE_QUERY,
-      variables: cCRE_QUERY_VARIABLES(assembly, chromosome, start, end, biosample, nearbygenesdistancethreshold, nearbygeneslimit, accessions, noLimit),
+      variables: cCRE_QUERY_VARIABLES(assembly, chromosome ? [{chromosome, start, end}] : null, biosample, nearbygenesdistancethreshold, nearbygeneslimit, accessions, noLimit),
       //Telling it to not cache, next js caches also and for things that exceed the 2mb cache limit it slows down substantially for some reason
       fetchPolicy: "no-cache",
     })