Add changes from test into stage.

.github/workflows/github-actions-PR-validation.yml

@@ -17,12 +17,12 @@ jobs:
           echo "Repository ${{ github.repository }}."
           echo "Trigger ref ${{ github.ref }}, base-ref ${{ github.base_ref }}, head_ref ${{ github.head_ref }}."
       - name: Check out repository code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Report files updated in PR
         run: |
           git fetch -q origin ${{ github.base_ref }} ${{ github.head_ref }}
           git diff --name-only origin/${{ github.base_ref }} origin/${{ github.head_ref }}
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: 18
       - name: Report runtime details

Makefile

@@ -15,11 +15,11 @@ endif
 all: install build test
 
 install:
-	npm install
+	npm install --legacy-peer-deps
 build:
 	npm run build
 test:
-	npm test
+	npm test -- --watchAll=false
 run:
 	npm start
 
@@ -42,13 +42,15 @@ prod-ui-deploy:
 	npx aws-cdk deploy agr-ui-production
 
 uirun:
-	npm start
+	REACT_APP_JBROWSE_AGR_RELEASE=${REACT_APP_JBROWSE_AGR_RELEASE} API_URL=${API_URL} npm start
 
+uirunstage: API_URL=https://stage.alliancegenome.org
 uirunstage:
-	API_URL=https://stage.alliancegenome.org npm start
+	@$(MAKE) --no-print-directory uirun API_URL=${API_URL}
 
+uiruntest: API_URL=https://test.alliancegenome.org
 uiruntest:
-	API_URL=https://test.alliancegenome.org npm start
+	@$(MAKE) --no-print-directory uirun API_URL=${API_URL}
 
 docker-build-nginx:
 	docker build -t ${REG}/agr_ui_server:${DOCKER_BUILD_TAG} --build-arg REG=${REG} --build-arg DOCKER_PULL_TAG=${DOCKER_PULL_TAG} .

src/constants.js

@@ -256,8 +256,6 @@ export const DEFAULT_TABLE_STATE = {
   filters: {},
 };
 
-const RELEASE = '7.0.0';
-
 export const SPECIES = [
   {
     taxonId: 'NCBITaxon:9606',
@@ -266,7 +264,7 @@ export const SPECIES = [
     apolloName: 'human',
     apolloTrack: '/All%20Genes/',
     jBrowseName: 'Homo sapiens',
-    jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/human/`,
+    jBrowsenclistbaseurltemplate: `https://s3.amazonaws.com/agrjbrowse/docker/{release}/human/`,
     jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
     jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001405.40_GRCh38.p14_genomic.fna.gz',
     jBrowsetracks: '_all_genes,_ht_variants',
@@ -282,7 +280,7 @@ export const SPECIES = [
     apolloName: 'mouse',
     apolloTrack: '/All%20Genes/',
     jBrowseName: 'Mus musculus',
-    jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/MGI/mouse/`,
+    jBrowsenclistbaseurltemplate: `https://s3.amazonaws.com/agrjbrowse/docker/{release}/MGI/mouse/`,
     jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
     jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001635.27_GRCm39_genomic.fna.gz',
     jBrowsetracks: '_all_genes,_ht_variants,_variants,_multiple-variant_alleles',
@@ -298,7 +296,7 @@ export const SPECIES = [
     apolloName: 'rat',
     apolloTrack: '/All%20Genes/',
     jBrowseName: 'Rattus norvegicus',
-    jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/RGD/rat/`,
+    jBrowsenclistbaseurltemplate: `https://s3.amazonaws.com/agrjbrowse/docker/{release}/RGD/rat/`,
     jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
     jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_015227675.2_mRatBN7.2_genomic.fna.gz',
     jBrowsetracks: '_all_genes,_ht_variants,_variants',
@@ -314,7 +312,7 @@ export const SPECIES = [
     apolloName: 'x_laevis',
     apolloTrack: '/All%20Genes/',
     jBrowseName: 'Xenopus laevis',
-    jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/XenBase/x_laevis/`,
+    jBrowsenclistbaseurltemplate: `https://s3.amazonaws.com/agrjbrowse/docker/{release}/XenBase/x_laevis/`,
     jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
     jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/XENLA_9.2_genome.fa.gz',
     jBrowsetracks: '_all_genes',
@@ -330,7 +328,7 @@ export const SPECIES = [
     apolloName: 'x_tropicalis',
     apolloTrack: '/All%20Genes/',
     jBrowseName: 'Xenopus tropicalis',
-    jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/XenBase/x_tropicalis/`,
+    jBrowsenclistbaseurltemplate: `https://s3.amazonaws.com/agrjbrowse/docker/{release}/XenBase/x_tropicalis/`,
     jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
     jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/XENTR_9.1_genome.fa.gz',
     jBrowsetracks: '_all_genes',
@@ -346,7 +344,7 @@ export const SPECIES = [
     apolloName: 'zebrafish',
     apolloTrack: '/All%20Genes/',
     jBrowseName: 'Danio rerio',
-    jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/zfin/zebrafish-11/`,
+    jBrowsenclistbaseurltemplate: `https://s3.amazonaws.com/agrjbrowse/docker/{release}/zfin/zebrafish-11/`,
     jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
     jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002035.6_GRCz11_genomic.fna.gz',
     jBrowsetracks: '_all_genes,_ht_variants,_variants',
@@ -362,7 +360,7 @@ export const SPECIES = [
     apolloName: 'fly',
     apolloTrack: '/All%20Genes/',
     jBrowseName: 'Drosophila melanogaster',
-    jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/FlyBase/fruitfly/`,
+    jBrowsenclistbaseurltemplate: `https://s3.amazonaws.com/agrjbrowse/docker/{release}/FlyBase/fruitfly/`,
     jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
     jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz',
     jBrowsetracks: '_all_genes,_ht_variants,_variants,_multiple-variant_alleles',
@@ -378,7 +376,7 @@ export const SPECIES = [
     apolloName: 'worm',
     apolloTrack: '/All%20Genes/',
     jBrowseName: 'Caenorhabditis elegans',
-    jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/WormBase/c_elegans_PRJNA13758/`,
+    jBrowsenclistbaseurltemplate: `https://s3.amazonaws.com/agrjbrowse/docker/{release}/WormBase/c_elegans_PRJNA13758/`,
     jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
     jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000002985.6_WBcel235_genomic.fna.gz',
     jBrowsetracks: '_all_genes,_ht_variants,_variants',
@@ -394,7 +392,7 @@ export const SPECIES = [
     apolloName: 'yeast',
     apolloTrack: '/All%20Genes/',
     jBrowseName: 'Saccharomyces cerevisiae',
-    jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/${RELEASE}/SGD/yeast/`,
+    jBrowsenclistbaseurltemplate: `https://s3.amazonaws.com/agrjbrowse/docker/{release}/SGD/yeast/`,
     jBrowseurltemplate: 'tracks/All_Genes/{refseq}/trackData.jsonz',
     jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000146045.2_R64_genomic.fna.gz',
     jBrowsetracks: '_all_genes,_ht_variants',
@@ -410,7 +408,7 @@ export const SPECIES = [
     apolloName: 'SARS-CoV-2',
     apolloTrack: '/Mature%20peptides/',
     jBrowseName: 'SARS-CoV-2',
-    jBrowsenclistbaseurl: `https://s3.amazonaws.com/agrjbrowse/docker/3.2.0/SARS-CoV-2/`,
+    jBrowsenclistbaseurltemplate: `https://s3.amazonaws.com/agrjbrowse/docker/3.2.0/SARS-CoV-2/`,
     jBrowseurltemplate: 'tracks/All Genes/{refseq}/trackData.jsonz',
     jBrowsefastaurl: 'https://s3.amazonaws.com/agrjbrowse/fasta/GCF_000001405.40_GRCh38.p14_genomic.fna.gz',
     jBrowsetracks: '_all_genes',

src/containers/alzheimersPage/PapersSection.js

@@ -7,7 +7,7 @@ const PapersSection = () => {
       <div className={style.contentContainer}>
         <div className='row'>
           <div className='col-lg-12'>
-            <p>Recent Papers</p>
+            <h2>Recent Papers</h2>
           </div>
         </div>
       </div>

src/containers/alzheimersPage/ResourcesSection.js

@@ -1,13 +1,31 @@
 import React from 'react';
 import style from './style.module.scss';
+import ExternalLink from '../../components/ExternalLink';
+
 
 const ResourcesSection = () => {
+  const resourceLinks = [
+    {title: "Alzhemiers.gov", url: 'https://www.alzheimers.gov/'},
+    {title: "Alzhemier's Association", url: 'https://www.alz.org/'},
+    {title: "Alzhemier's Foundation of America", url: 'https://alzfdn.org/'},
+    {title: "National Institute on Aging", url: 'https://www.nia.nih.gov/'},
+  ];
+
   return (
     <section className={style.section}>
       <div className={style.contentContainer}>
         <div className='row'>
           <div className='col-lg-12'>
-            <p>Community Resoures</p>
+            <h2>Community Resoures</h2>
+              <div>
+                {resourceLinks.map((resourceLink) => {
+                  return (
+                    <div>
+                      <ExternalLink href={resourceLink.url}>{resourceLink.title}</ExternalLink>
+                    </div>
+                  )
+                })}
+              </div>
           </div>
         </div>
       </div>

src/containers/genePage/sequencePanelWrapper.js

@@ -1,39 +1,50 @@
-import React, {Component} from 'react';
+import React from 'react';
 import PropTypes from 'prop-types';
 
 import { GenericGeneSeqPanel } from 'generic-sequence-panel';
 import { getSpecies } from '../../lib/utils';
 import { Buffer } from 'buffer';
 
+import { useRelease } from '../../hooks/ReleaseContextProvider';
+
 window.Buffer = Buffer
 
-class SequencePanel extends Component {
+const SequencePanel = ({species, gene, refseq, start, end}) => {
 
-  constructor(props) {
-    super(props);
+  const useGetReleaseVersion = () => {
+    const release = useRelease();
 
-    this.jBrowsenclistbaseurl = getSpecies(this.props.species).jBrowsenclistbaseurl;
-    this.jBrowseurltemplate   = getSpecies(this.props.species).jBrowseurltemplate;
-    this.jBrowsefastaurl      = getSpecies(this.props.species).jBrowsefastaurl;
+    if( !release.isLoading && !release.isError ){
+      return release.data.releaseVersion
+    }
+    else{
+      return 'unknown'
+    }
   }
 
-  render() {
-    var refseq = this.props.refseq;
-    if((this.props.species === 'NCBITaxon:559292' || this.props.species === 'NCBITaxon:8355') && !this.props.refseq.startsWith('chr') && !this.props.refseq.toLowerCase().startsWith('scaffold')){
-      refseq = 'chr' + refseq;
-    }
-    return (
-      <GenericGeneSeqPanel
-            refseq={refseq}
-            start={this.props.start}
-            end={this.props.end}
-            gene={this.props.gene}
-            nclistbaseurl={this.jBrowsenclistbaseurl}
-            urltemplate={this.jBrowseurltemplate}
-            fastaurl={this.jBrowsefastaurl} 
-      />
-    );
+  const contextReleaseVersion = useGetReleaseVersion()
+  const releaseVersion = process.env.REACT_APP_JBROWSE_AGR_RELEASE || contextReleaseVersion
+  console.info(`sequencePanelWrapper releaseVersion: ${releaseVersion}`)
+
+  const jBrowsenclistbaseurl = getSpecies(species).jBrowsenclistbaseurltemplate.replace('{release}', releaseVersion)
+  const jBrowseurltemplate   = getSpecies(species).jBrowseurltemplate;
+  const jBrowsefastaurl      = getSpecies(species).jBrowsefastaurl;
+
+  if((species === 'NCBITaxon:559292' || species === 'NCBITaxon:8355') && !refseq.startsWith('chr') && !refseq.toLowerCase().startsWith('scaffold')){
+    refseq = 'chr' + refseq;
   }
+
+  return (
+    <GenericGeneSeqPanel
+          refseq={refseq}
+          start={start}
+          end={end}
+          gene={gene}
+          nclistbaseurl={jBrowsenclistbaseurl}
+          urltemplate={jBrowseurltemplate}
+          fastaurl={jBrowsefastaurl}
+    />
+  );
 }
 
 SequencePanel.propTypes = {

src/lib/utils.js

@@ -1,5 +1,5 @@
-import { STRINGENCY_HIGH, STRINGENCY_MED } from '../components/homology/constants';
-import { DEFAULT_TABLE_STATE, SPECIES } from '../constants';
+import { STRINGENCY_HIGH, STRINGENCY_MED } from '../components/homology/constants.js';
+import { DEFAULT_TABLE_STATE, SPECIES } from '../constants.js';
 import { stringify } from 'qs';
 
 export function makeId(string) {