Prepare for 7.4.0 Release

cdk/amplify-production-stack.ts

@@ -29,6 +29,7 @@ export class AmplifyProductionStack extends cdk.Stack {
       { source: '/jbrowsedata/XenBaseXLJBrowse/<*>',   target: 'https://jbrowse.xenbase.org/XenJBrowse/data/xl9_2/<*>',                               status: amplify.RedirectStatus.REWRITE },
       { source: '/jbrowsedata/XenBaseData/<*>',        target: 'https://jbrowse.xenbase.org/XenJBrowse/<*>',                                          status: amplify.RedirectStatus.REWRITE },
       { source: '/jbrowsedata/RGDJBrowse/<*>',         target: 'https://rgd.mcw.edu/jbrowse2/<*>',                                                    status: amplify.RedirectStatus.REWRITE },
+      { source: '/jbrowsedata/XenBaseBigFtp/<*>',      target: 'https://bigftp.xenbase.org/pub/xenbase/genomics/<*>',                                 status: amplify.RedirectStatus.REWRITE },
       { source: '/jbrowse/worms/protein',              target: 'https://www.alliancegenome.org/jbrowse/worms/protein/',                               status: amplify.RedirectStatus.PERMANENT_REDIRECT },
       { source: '/jbrowse/worms/protein/',             target: 'https://main.djgvd7iswt7yy.amplifyapp.com/',                                          status: amplify.RedirectStatus.REWRITE },
       { source: '/jbrowse/worms/protein/<*>',          target: 'https://main.djgvd7iswt7yy.amplifyapp.com/<*>',                                       status: amplify.RedirectStatus.REWRITE },

cdk/amplify-stage-stack.ts

@@ -24,6 +24,7 @@ export class AmplifyStageStack extends cdk.Stack {
       { source: '/jbrowsedata/XenBaseXLJBrowse/<*>',   target: 'https://jbrowse.xenbase.org/XenJBrowse/data/xl9_2/<*>',                               status: amplify.RedirectStatus.REWRITE },
       { source: '/jbrowsedata/XenBaseData/<*>',        target: 'https://jbrowse.xenbase.org/XenJBrowse/<*>',                                          status: amplify.RedirectStatus.REWRITE },
       { source: '/jbrowsedata/RGDJBrowse/<*>',         target: 'https://rgd.mcw.edu/jbrowse2/<*>',                                                    status: amplify.RedirectStatus.REWRITE },
+      { source: '/jbrowsedata/XenBaseBigFtp/<*>',      target: 'https://bigftp.xenbase.org/pub/xenbase/genomics/<*>',                                 status: amplify.RedirectStatus.REWRITE },
       { source: '/jbrowse/worms/protein',              target: 'https://stage.alliancegenome.org/jbrowse/worms/protein/',                             status: amplify.RedirectStatus.PERMANENT_REDIRECT },
       { source: '/jbrowse/worms/protein/',             target: 'https://staging.djgvd7iswt7yy.amplifyapp.com/',                                       status: amplify.RedirectStatus.REWRITE },
       { source: '/jbrowse/worms/protein/<*>',          target: 'https://staging.djgvd7iswt7yy.amplifyapp.com/<*>',                                    status: amplify.RedirectStatus.REWRITE },

cdk/amplify-test-stack.ts

@@ -25,6 +25,7 @@ export class AmplifyTestStack extends cdk.Stack {
       { source: '/jbrowsedata/XenBaseXLJBrowse/<*>',   target: 'https://jbrowse.xenbase.org/XenJBrowse/data/xl9_2/<*>',                               status: amplify.RedirectStatus.REWRITE },
       { source: '/jbrowsedata/XenBaseData/<*>',        target: 'https://jbrowse.xenbase.org/XenJBrowse/<*>',                                          status: amplify.RedirectStatus.REWRITE },
       { source: '/jbrowsedata/RGDJBrowse/<*>',         target: 'https://rgd.mcw.edu/jbrowse2/<*>',                                                    status: amplify.RedirectStatus.REWRITE },
+      { source: '/jbrowsedata/XenBaseBigFtp/<*>',      target: 'https://bigftp.xenbase.org/pub/xenbase/genomics/<*>',                                 status: amplify.RedirectStatus.REWRITE },
       { source: '/jbrowse/worms/protein',              target: 'https://test.alliancegenome.org/jbrowse/worms/protein/',                              status: amplify.RedirectStatus.PERMANENT_REDIRECT },
       { source: '/jbrowse/worms/protein/',             target: 'https://main.djgvd7iswt7yy.amplifyapp.com/',                                          status: amplify.RedirectStatus.REWRITE },
       { source: '/jbrowse/worms/protein/<*>',          target: 'https://main.djgvd7iswt7yy.amplifyapp.com/<*>',                                       status: amplify.RedirectStatus.REWRITE },

package.json

@@ -13,7 +13,7 @@
     "@fortawesome/free-solid-svg-icons": "^6.5.2",
     "@fortawesome/react-fontawesome": "^0.2.2",
     "@geneontology/curie-util-es5": "^1.2.4",
-    "@geneontology/wc-gocam-viz": "1.0.0",
+    "@geneontology/wc-gocam-viz": "1.0.1-beta.2",
     "@geneontology/wc-ribbon-strips": "0.0.37",
     "@geneontology/wc-ribbon-table": "0.0.57",
     "@testing-library/jest-dom": "^5.16.1",
@@ -96,4 +96,4 @@
   "devDependencies": {
     "ajv": "^8.16.0"
   }
-}
+}

src/containers/alzheimersPage/DiseasePortalSection.js

@@ -28,35 +28,34 @@ const DiseasePortalSection = () => {
             to='/disease/DOID:10652#associated-models'
             tooltip='View all associated models'
           >
-            [3000]<br />Models
+            213<br />Models
           </EntityButton>
           <EntityButton
             id='entity-genes'
             to='/disease/DOID:10652#associated-genes'
             tooltip='View all associated genes'
           >
-            [1221]<br />Genes
+            2,939<br />Genes
           </EntityButton>
           <EntityButton
             id='entity-alleles'
             to='/disease/DOID:10652#associated-alleles'
             tooltip='View all associated alleles'
           >
-            [1000]<br />Alleles
+            268<br />Alleles
           </EntityButton>
           <EntityButton
             id='entity-publications'
-            to=''
-            tooltip='View all associated publications'
+            to='/disease-portal/alzheimers-disease'
           >
-            [96000]<br />Publications
+            96,000<br />Publications
           </EntityButton>
           <EntityButton
             id='entity-species'
-            to=''
+            to='/about-us'
             tooltip='View all associated species'
           >
-            [9]<br />Species
+            9<br />Species
           </EntityButton>
         </div>
       </div>

src/containers/alzheimersPage/PapersSection.js

@@ -1,13 +1,33 @@
 import React from 'react';
 import style from './style.module.scss';
+import ExternalLink from '../../components/ExternalLink';
 
 const PapersSection = () => {
+  const publications = [
+    {pmid: '39143479', title: "Gene therapy in Aβ-induced cell and mouse models of Alzheimer's disease through compensating defective mitochondrial complex I function"},
+    {pmid: '38526283', title: "Activation of autophagy by Citri Reticulatae Semen extract ameliorates amyloid-beta-induced cell death and cognition deficits in Alzheimer's disease"},
+    {pmid: '38950494', title: "Nesfatin-1 ameliorates pathological abnormalities in Drosophila hTau model of Alzheimer's disease"},
+    {pmid: '38827230', title: "Aluminum chloride and D-galactose induced a zebrafish model of Alzheimer's disease with cognitive deficits and aging"},
+    {pmid: '37515920', title: "Discovery of triazole-bridged aryl adamantane analogs as an intriguing class of multifunctional agents for treatment of Alzheimer's disease"},
+    {pmid: '39009412', title: "c-KIT inhibitors reduce pathology and improve behavior in the Tg(SwDI) model of Alzheimer's disease"},
+    {pmid: '37736695', title: "Melatonin regulates the circadian rhythm to ameliorate postoperative sleep disorder and neurobehavioral abnormalities in aged mice"},
+  ];
+
   return (
     <section className={style.section}>
       <div className={style.contentContainer}>
         <div className='row'>
           <div className='col-lg-12'>
             <h2>Recent Papers</h2>
+              <div>
+                {publications.map((publication) => {
+                  return (
+                    <p>
+                      <ExternalLink href={'https://www.ncbi.nlm.nih.gov/pubmed/' + publication.pmid}>{publication.title}</ExternalLink>
+                    </p>
+                  )
+                })}
+              </div>
           </div>
         </div>
       </div>

src/containers/alzheimersPage/ResourcesSection.js

@@ -7,8 +7,10 @@ const ResourcesSection = () => {
   const resourceLinks = [
     {title: "Alzhemiers.gov", url: 'https://www.alzheimers.gov/'},
     {title: "Alzhemier's Association", url: 'https://www.alz.org/'},
+    {title: "Alzheimer's Disease Clinical Trials", url: 'https://www.clinicaltrials.gov/search?cond=Alzheimer%20Disease'},
     {title: "Alzhemier's Foundation of America", url: 'https://alzfdn.org/'},
     {title: "National Institute on Aging", url: 'https://www.nia.nih.gov/'},
+    {title: "OMIM", url: 'https://omim.org/entry/104300'},
   ];
 
   return (

src/containers/alzheimersPage/index.js

@@ -4,17 +4,22 @@ import PapersSection from './PapersSection';
 import ResourcesSection from './ResourcesSection';
 import DiseasePortalSection from './DiseasePortalSection';
 import MembersSection from '../../components/MembersSection';
+import { HELP_EMAIL } from '../../constants';
+
 
 
 const AlzheimersPage = () => {
   return (
     <div>
       <HeadMetaTags title="Alzheimer's Disease Portal" />
       <DiseasePortalSection />
-
       <PapersSection />
       <ResourcesSection />
 
+      <div>
+        <h4 className='mt-4 text-center'>Need Help? Contact Us: &nbsp;<a href={`mailto:${HELP_EMAIL}`}>{HELP_EMAIL}</a></h4>
+      </div>
+
       <MembersSection />
     </div>
   );