Lncrnalyzr

README.md

@@ -35,10 +35,10 @@ Check out our [Next.js deployment documentation](https://nextjs.org/docs/deploym
 # CFDE-KX
 
 ## Install
-helm install cfde-gse maayanlab/docker-compose -f <(docker-compose config) -n cfde-gse --create-namespace 
+helm install lncrnalyzr maayanlab/docker-compose -f <(docker-compose config) -n lncrnalyzr --create-namespace 
 
 ## UPGRADE
-helm upgrade cfde-gse maayanlab/docker-compose -f <(docker-compose config) -n cfde-gse 
+helm upgrade lncrnalyzr maayanlab/docker-compose -f <(docker-compose config) -n lncrnalyzr 
 
 helm template cfde-gse maayanlab/docker-compose -f <(docker-compose config) -n cfde-gse 
 

app/api/enrichment/augment/route.ts

@@ -148,7 +148,7 @@ const enrichment = async ({
             query_list.push(query_part)
             if (gene_links && gene_links.length > 0) {
                 const geneLinksRelations = schema.edges.reduce((acc, i)=>{
-                    if (i.gene_link) return [...acc, ...i.match]
+                    if (i.hidden) return [...acc, ...i.match]
                     else return acc
                 }, [])
                 for (const i of geneLinksRelations) {
@@ -174,7 +174,7 @@ const enrichment = async ({
         }
         if (gene_links && gene_links.length > 0) {
             const geneLinksRelations = schema.edges.reduce((acc, i)=>{
-                if (i.gene_link) return [...acc, ...i.match]
+                if (i.hidden) return [...acc, ...i.match]
                 else return acc
             }, [])
             for (const i of geneLinksRelations) {

app/api/schema/route.ts

@@ -83,7 +83,7 @@ export interface UISchema {
             {
                 component: string,
                 props?: {
-                    [key:string]: string|number
+                    [key:string]: string|number|boolean
                 }
             }
         >>,

components/Enrichment/EnrichmentBar.tsx

@@ -40,10 +40,10 @@ const renderCustomizedLabel = (props) => {
 			<Card sx={{opacity:"0.8", textAlign: "left"}}>
 				<CardContent>
 					<Typography variant="subtitle2"><b>{enrichr_label}</b></Typography>
-					<Typography variant="subtitle2"><b>p-value:</b> {precise(pval)}</Typography>
-					<Typography variant="subtitle2"><b>q-value:</b> {precise(qval)}</Typography>
-					<Typography variant="subtitle2"><b>z-score:</b> {precise(zscore)}</Typography>
-					<Typography variant="subtitle2"><b>combined score:</b> {precise(combined_score)}</Typography>
+					{ pval && <Typography variant="subtitle2"><b>p-value:</b> {precise(pval)}</Typography>}
+					{ qval && <Typography variant="subtitle2"><b>q-value:</b> {precise(qval)}</Typography>}
+					{ zscore && <Typography variant="subtitle2"><b>z-score:</b> {precise(zscore)}</Typography>}
+					{ combined_score && <Typography variant="subtitle2"><b>combined score:</b> {precise(combined_score)}</Typography>}
 				</CardContent>
 			</Card>
 		)

components/Enrichment/form.tsx

@@ -528,9 +528,9 @@ const GeneSetForm = ({
                 { fullWidth &&
                     <Grid item xs={12} md={6}>
                         <Grid container spacing={1} justifyContent="flex-end">
-                            <Grid item xs={12}>
+                            {/* <Grid item xs={12}>
                                 <EnrichrTermSearch setInput={setInput}/>
-                            </Grid>
+                            </Grid> */}
                             <Grid item xs={12}>
                                 <Typography variant={'subtitle2'}>
                                     Select libraries to include

components/Footer/index.tsx

@@ -11,7 +11,7 @@ export default function Footer({style, layout, footer_text}: {
         {
             component: string,
             props?: {
-                [key:string]: string|number
+                [key:string]: string|number|boolean
             }
         }
     >>,

docker-compose.yml

@@ -5,15 +5,15 @@ services:
       context: .
       dockerfile: ./Dockerfile.next
     platform: linux/amd64
-    image: maayanlab/enrichr-kg:2.3.6.1
+    image: maayanlab/lncrnalyzr:2.3.8
     x-kubernetes:
       imagePullPolicy: IfNotPresent
       annotations:
-        maayanlab.cloud/ingress: https://enrichr-kg-dev.maayanlab.cloud
+        maayanlab.cloud/ingress: https://lncrnalyzr.maayanlab.cloud
     ports:
       - 3000:3000
     environment:
-      - NEXT_PUBLIC_NEO4J_URL=bolt://neo4j:7687
+      - NEXT_PUBLIC_NEO4J_URL=bolt://neo4j-v5:7687
       - NEXT_PUBLIC_ENRICHR_URL=https://maayanlab.cloud/Enrichr
       - NEXT_PUBLIC_GENESHOT_URL=https://maayanlab.cloud/geneshot
       - NEXT_PUBLIC_NEO4J_USER
@@ -26,12 +26,12 @@ services:
       - NEXT_PUBLIC_TURL
       - NEXT_PUBLIC_TURL_URL
 
-  neo4j:
-    image: neo4j:4.4
+  neo4j-v5:
+    image: neo4j:5.19
     x-kubernetes:
       imagePullPolicy: IfNotPresent
     environment:
-      - NEO4JLABS_PLUGINS='["apoc", "n10s"]'
+      - NEO4J_PLUGINS=["apoc", "n10s"]
       - NEO4J_AUTH=${NEXT_PUBLIC_NEO4J_USER}/${NEXT_PUBLIC_NEO4J_PASSWORD}
       - NEO4J_dbms_memory_heap_max__size=8G
       - NEO4J_dbms_memory_heap_initial__size=2G
@@ -40,14 +40,30 @@ services:
       - 7687:7687
       - 7474:7474
     volumes:
-      - enrichr-kg-neo4j:/data
-
+      -  lncrnalyzr-neo4j-v5:/data
+
+  enrichment:
+    image: maayanlab/independent_enrichment:0.0.9
+    ports:
+      - 5000:80
+    x-kubernetes:
+      imagePullPolicy: IfNotPresent
+      annotations:
+        maayanlab.cloud/ingress: https://lncrnalyzr.maayanlab.cloud/enrichment
+    environment:
+      - PREFIX
+      - LIBRARY_DOMAIN
+
 volumes:
-  enrichr-kg-neo4j:
+  lncrnalyzr-neo4j:
+    x-kubernetes:
+      size: 25Gi
+      class: gp2
+  lncrnalyzr-neo4j-v5:
     x-kubernetes:
       size: 25Gi
       class: gp2
 
 x-kubernetes:
-  name: enrichr-kg
-  namespace: enrichr-kg
+  name: lncrnalyzr
+  namespace: lncrnalyzr

package.json

@@ -1,6 +1,6 @@
 {
   "name": "cfde-knowledge-exchange",
-  "version": "2.3.6",
+  "version": "2.3.8",
   "private": true,
   "scripts": {
     "dev": "NODE_ENV=development next dev",

utils/math.ts

@@ -30,9 +30,9 @@ export const precise = (value: number | string) => {
     else {
       return convert_float(value)
     }
-  } else {
+  } else if (value) {
     if (value.split(".").length === 1) return value
     const val = Number.parseFloat(value)
     return convert_float(val)
-  }
+  } else return ''
 }