Skip to content

Commit

Permalink
Merge pull request #1310 from alliance-genome/stage
Browse files Browse the repository at this point in the history 
Release 7.1.0 into Test
  • Loading branch information
@oblodgett
oblodgett authored May 1, 2024
2 parents 7e2ee6d + be79cb9 commit b05013c
Show file tree
Hide file tree
Showing 40 changed files with 579 additions and 219 deletions.
5 changes: 5 additions & 0 deletions .dockerignore
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
node_modules
npm-debug.log
.git
dist
package-lock.json
13 changes: 13 additions & 0 deletions .editorconfig
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
# Editor configuration, see http://editorconfig.org
root = true

[*]
charset = utf-8
indent_style = space
indent_size = 2
insert_final_newline = true
trim_trailing_whitespace = true

[*.md]
max_line_length = off
trim_trailing_whitespace = false
23 changes: 23 additions & 0 deletions Dockerfile
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
ARG DOCKER_PULL_TAG=latest
ARG REG=100225593120.dkr.ecr.us-east-1.amazonaws.com
FROM ${REG}/agr_base_linux_env:${DOCKER_PULL_TAG} as build-stage

WORKDIR /workdir/agr_ui

ADD . .

RUN mkdir /workdir/agr_ui/build

ARG NODE_ENV=production
ENV NODE_ENV ${NODE_ENV}

RUN /bin/bash -c 'PS1=x && . /root/.profile && nvm install && nvm use && npm install --legacy-peer-deps && npm run build'

FROM nginx

WORKDIR /workdir/agr_ui/build

COPY --from=build-stage /workdir/agr_ui/build /workdir/agr_ui/build
COPY --from=build-stage /workdir/agr_ui/nginx.conf /etc/nginx/conf.d/default.conf

EXPOSE 3000
9 changes: 8 additions & 1 deletion cdk/amplify-production-stack.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,14 @@ export class AmplifyProductionStack extends cdk.Stack {
{ source: 'https://alliancegenome.org', target: 'https://www.alliancegenome.org', status: amplify.RedirectStatus.PERMANENT_REDIRECT },

{ source: '/api/<*>', target: 'https://prod-alb.alliancegenome.org/api/<*>', status: amplify.RedirectStatus.REWRITE },


{ source: '/jbrowse2', target: 'https://www.alliancegenome.org/jbrowse2/', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/jbrowse2/', target: 'https://main.dgaayxgqoarxf.amplifyapp.com/', status: amplify.RedirectStatus.REWRITE },
{ source: '/jbrowse2/<*>', target: 'https://main.dgaayxgqoarxf.amplifyapp.com/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/jbrowsedata/XenBaseXTJBrowse/<*>', target: 'https://jbrowse.xenbase.org/XenJBrowse/data/xt9_1/<*>', status: amplify.RedirectStatus.REWRITE },
{ 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: '/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 },
Expand Down
7 changes: 7 additions & 0 deletions cdk/amplify-stage-stack.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,13 @@ export class AmplifyStageStack extends cdk.Stack {

const stage_paths = [
{ source: '/api/<*>', target: 'https://stage-api.alliancegenome.org/api/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/jbrowse2', target: 'https://stage.alliancegenome.org/jbrowse2/', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/jbrowse2/', target: 'https://stage.dgaayxgqoarxf.amplifyapp.com/', status: amplify.RedirectStatus.REWRITE },
{ source: '/jbrowse2/<*>', target: 'https://stage.dgaayxgqoarxf.amplifyapp.com/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/jbrowsedata/XenBaseXTJBrowse/<*>', target: 'https://jbrowse.xenbase.org/XenJBrowse/data/xt9_1/<*>', status: amplify.RedirectStatus.REWRITE },
{ 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: '/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 },
Expand Down
7 changes: 7 additions & 0 deletions cdk/amplify-test-stack.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,13 @@ export class AmplifyTestStack extends cdk.Stack {
const test_paths = [
{ source: '/api/<*>', target: 'https://test-alb.alliancegenome.org/api/<*>', status: amplify.RedirectStatus.REWRITE },

{ source: '/jbrowse2', target: 'https://test.alliancegenome.org/jbrowse2/', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/jbrowse2/', target: 'https://stage.dgaayxgqoarxf.amplifyapp.com/', status: amplify.RedirectStatus.REWRITE },
{ source: '/jbrowse2/<*>', target: 'https://stage.dgaayxgqoarxf.amplifyapp.com/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/jbrowsedata/XenBaseXTJBrowse/<*>', target: 'https://jbrowse.xenbase.org/XenJBrowse/data/xt9_1/<*>', status: amplify.RedirectStatus.REWRITE },
{ 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: '/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 },
Expand Down
4 changes: 2 additions & 2 deletions cdk/cdk-app.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ new AmplifyALBStack(app, 'stage-alb-stack', {
new AmplifyALBStack(app, 'test-alb-stack', {
stackName: 'test-alb-stack',
dnsName: 'test',
targetInstanceId: 'i-003fafec7d050fd97',
targetInstanceId: 'i-0ccfdcd8c43104be5',
env: {
region: process.env.CDK_DEFAULT_REGION,
account: process.env.CDK_DEFAULT_ACCOUNT,
Expand All @@ -30,7 +30,7 @@ new AmplifyALBStack(app, 'test-alb-stack', {
new AmplifyALBStack(app, 'prod-alb-stack', {
stackName: 'prod-alb-stack',
dnsName: 'prod',
targetInstanceId: 'i-003fafec7d050fd97',
targetInstanceId: 'i-0ccfdcd8c43104be5',
env: {
region: process.env.CDK_DEFAULT_REGION,
account: process.env.CDK_DEFAULT_ACCOUNT,
Expand Down
7 changes: 7 additions & 0 deletions nginx.conf
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
server {
listen 3000;
root /workdir/agr_ui/build;
index index.html;

error_page 404 =200 /index.html;
}
4 changes: 2 additions & 2 deletions package.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
"@fortawesome/free-solid-svg-icons": "^6.4.2",
"@fortawesome/react-fontawesome": "^0.2.0",
"@geneontology/curie-util-es5": "^1.2.4",
"@geneontology/wc-gocam-viz": "0.0.51",
"@geneontology/wc-gocam-viz": "1.0.0",
"@geneontology/wc-ribbon-strips": "0.0.37",
"@geneontology/wc-ribbon-table": "0.0.57",
"@testing-library/jest-dom": "^5.16.1",
Expand All @@ -28,7 +28,7 @@
"custom-event-polyfill": "^1.0.6",
"d3-selection": "2.0.0",
"document-register-element": "1.13.1",
"generic-sequence-panel": "^1.4.0",
"generic-sequence-panel": "^1.4.1",
"html-react-parser": "^0.10.0",
"immutable": "^3.8.1",
"lodash.clone": "^4.5.0",
Expand Down
34 changes: 18 additions & 16 deletions src/components/dataTable/AnnotatedEntitiesPopupCuration.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,28 +22,30 @@ import AnnotationType from './AnnotationType';
import AssociationCellCuration from './AssociationCellCuration';
import AssertedGenes from './AssertedGenes';
import GeneticModifiersCellCuration from './GeneticModifiersCellCuration';
import { buildProviderWithUrl } from './utils';
import { buildProviderWithUrl, getIdentifier } from './utils';
import StrainBackground from './StrainBackground';

function renderLink(entity) {
const url = getResourceUrl(entity.subject.curie, entity.subject.type, entity.subject.subtype)
const curie = getIdentifier(entity.diseaseAnnotationSubject);
const url = getResourceUrl(curie, entity.diseaseAnnotationSubject.type, entity.diseaseAnnotationSubject.subtype)

if (entity.type === 'AlleleDiseaseAnnotation') {
const innerText = entity.subject.alleleSymbol ? entity.subject.alleleSymbol.displayText : entity.subject.name;
const innerText = entity.diseaseAnnotationSubject.alleleSymbol ? entity.diseaseAnnotationSubject.alleleSymbol.displayText : entity.diseaseAnnotationSubject.name;
const inner = <span dangerouslySetInnerHTML={{__html: innerText}}/>;
return <Link to={`/allele/${entity.subject.curie}`}>{inner}</Link>;
return <Link to={`/allele/${curie}`}>{inner}</Link>;
} else if(entity.type === 'GeneDiseaseAnnotation'){
const innerText = entity.subject.geneSymbol ? entity.subject.geneSymbol.displayText : entity.subject.name;
const innerText = entity.diseaseAnnotationSubject.geneSymbol ? entity.diseaseAnnotationSubject.geneSymbol.displayText : entity.diseaseAnnotationSubject.name;
const inner = <span dangerouslySetInnerHTML={{__html: innerText}}/>;
return <Link to={`/gene/${entity.subject.curie}`}>{inner}</Link>;
return <Link to={`/gene/${curie}`}>{inner}</Link>;
} else {
const inner = <span dangerouslySetInnerHTML={{__html: entity.subject.name}}/>;
return <ExternalLink href={url}>{inner}</ExternalLink>;
const inner = <span dangerouslySetInnerHTML={{__html: entity.diseaseAnnotationSubject.name}}/>;
return <ExternalLink href={url}>{inner}</ExternalLink>;
}
}

function AnnotatedEntitiesPopupCuration(props) {
const {children, entities, parentPage, mainRowCurie } = props;


function AnnotatedEntitiesPopupCuration({ children, entities, parentPage, mainRowCurie, pubModIds }) {

if (!entities || !entities.length) {
return null;
Expand All @@ -68,11 +70,11 @@ function AnnotatedEntitiesPopupCuration(props) {
<th>Name</th>
<th>Type</th>
<th className={style.associationCell}>Association</th>
{ parentPage === 'gene' ? <th>Additional implicated genes</th> : <></> }
{ parentPage === 'gene' || parentPage === 'disease' ? <th>Additional implicated genes</th> : <></> }
<th>Experimental condition</th>
<th></th>
<th>Genetic Modifiers</th>
{ parentPage === 'gene' ? <th>Strain Background</th> : <></> }
{ parentPage === 'gene' || parentPage === 'disease' ? <th>Strain Background</th> : <></> }
<th>Genetic Sex</th>
<th className={style.relatedNotes}>Notes</th>
<th>Annotation type</th>
Expand All @@ -88,19 +90,19 @@ function AnnotatedEntitiesPopupCuration(props) {
return (
<tr key={entity.id}>
<td>{renderLink(entity)}</td>
<td><TypeCellCuration subject={entity.subject}/></td>
<td><TypeCellCuration subject={entity.diseaseAnnotationSubject}/></td>
<td><AssociationCellCuration association={entity.relation?.name}/></td>
{ parentPage === 'gene' ? <td><AssertedGenes assertedGenes={entity.assertedGenes} mainRowCurie={mainRowCurie}/></td> : <></>}
{ parentPage === 'gene' || parentPage === 'disease' ? <td><AssertedGenes assertedGenes={entity.assertedGenes} mainRowCurie={mainRowCurie}/></td> : <></>}
<td><ExperimentalConditionCellCuration conditions={entity.conditionRelations}/></td>
<td><ExperimentalConditionCellCuration conditions={entity.conditionModifiers}/></td>
<td><GeneticModifiersCellCuration relation={entity.diseaseGeneticModifierRelation} modifiers={entity.diseaseGeneticModifiers}/></td>
{ parentPage === 'gene' ? <td><StrainBackground strainBackground={entity.sgdStrainBackground}/></td> : <></> }
{ parentPage === 'gene' || parentPage === 'disease' ? <td><StrainBackground strainBackground={entity.sgdStrainBackground}/></td> : <></> }
<td><GeneticSex geneticSex={entity.geneticSex}/></td>
<td><RelatedNotes className={style.relatedNotes} relatedNotes={entity.relatedNotes}/></td>
<td><AnnotationType annotationType={entity.annotationType}/></td>
<td><EvidenceCodesCellCuration evidenceCodes={entity.evidenceCodes}/></td>
<td><ProviderCellCuration provider={provider} /></td>
<td><SingleReferenceCellCuration singleReference={entity.singleReference}/></td>
<td><SingleReferenceCellCuration singleReference={entity.singleReference} pubModIds={pubModIds}/></td>
</tr>
)
})
Expand Down
9 changes: 5 additions & 4 deletions src/components/dataTable/AssertedGenes.js
View file
Original file line number Diff line number Diff line change
@@ -1,21 +1,22 @@
import CollapsibleList from '../collapsibleList/collapsibleList';
import ExternalLink from '../ExternalLink';
import { Link } from 'react-router-dom';
import { getIdentifier } from './utils';


function makeAssertedGeneLink(curie, geneSymbol) {
if(curie) {
const symbol = <span dangerouslySetInnerHTML={{__html: geneSymbol}}/>;
return <ExternalLink href={`https://www.alliancegenome.org/gene/${curie}`}>{symbol}</ExternalLink>;
return <Link to={`/gene/${curie}`}>{symbol}</Link>;
}
return null;
}

function AssertedGenes({assertedGenes, mainRowCurie}) {
const filteredAssertedGenes = assertedGenes?.filter(gene => gene.curie !== mainRowCurie);
const filteredAssertedGenes = assertedGenes?.filter(gene => getIdentifier(gene) !== mainRowCurie);
if(assertedGenes && assertedGenes.length > 1) {
return (
<CollapsibleList collapsedSize={assertedGenes.length}>
{filteredAssertedGenes.map(gene => makeAssertedGeneLink(gene.curie, gene.geneSymbol.displayText))}
{filteredAssertedGenes.map(gene => makeAssertedGeneLink(getIdentifier(gene), gene.geneSymbol.displayText))}
</CollapsibleList>
);
}
Expand Down
23 changes: 19 additions & 4 deletions src/components/dataTable/DataTable.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,8 @@ import HorizontalScroll from '../horizontalScroll';
import { buildTableQueryString } from '../../lib/utils';
import LoadingSpinner from '../loadingSpinner';
import DropdownNoDataFilter from './DropdownNoDataFilter';
import {DOWNLOAD_BUTTON_THRESHOLD} from '../../constants';
import { Link } from 'react-router-dom';

const DataTable = ({
className,
Expand Down Expand Up @@ -120,6 +122,8 @@ const DataTable = ({
onSizePerPageChange: scrollIntoView
});

let disabled = paginationObj.options?.totalSize > DOWNLOAD_BUTTON_THRESHOLD;

columns.forEach(column => {
const filterField = column.filterName || column.dataField;
const columnFilter = filters &&
Expand Down Expand Up @@ -221,10 +225,21 @@ const DataTable = ({
)
}
</PaginationProvider>
{downloadUrl &&
<DownloadButton
downloadUrl={`${downloadUrl}${downloadUrl.indexOf('?') < 0 ? '?' : '&'}${buildTableQueryString(tableState)}`}
/>
{
downloadUrl &&
<DownloadButton
downloadUrl={`${downloadUrl}${downloadUrl.indexOf('?') < 0 ? '?' : '&'}${buildTableQueryString(tableState)}`}
disabled={disabled}
/>
}
{
disabled &&
<div style={{color: 'red'}}>
The table above cannot be downloaded because there are too many rows in the unfiltered table.
Please apply filter(s) to limit the number of rows to less than {DOWNLOAD_BUTTON_THRESHOLD} to enable the Download button or visit our
<Link to="/downloads"> Downloads page </Link>
to download the entire data set.
</div>
}
</div>
);
Expand Down
4 changes: 2 additions & 2 deletions src/components/dataTable/DiseaseQualifiersColumn.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@ const DiseaseQualifiersColumn = ({qualifiers}) => {
if (!qualifiers || !qualifiers.length) {
return null;
}

return (
<CommaSeparatedList>
{qualifiers.map(qualifier => qualifier)}
{qualifiers.map(qualifier => qualifier.replaceAll("_", " "))}
</CommaSeparatedList>
);
};
Expand Down
8 changes: 5 additions & 3 deletions src/components/dataTable/GeneticModifiersCellCuration.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,28 +3,30 @@ import { CollapsibleList } from '../collapsibleList';
import ExternalLink from '../ExternalLink';
import { getResourceUrl } from './getResourceUrl';
import { Link } from 'react-router-dom';
import { getIdentifier } from './utils';


function GeneticModifierLink(modifier) {
const identifier = getIdentifier(modifier);
switch(modifier?.type) {
case 'Gene':
if (modifier.geneSymbol) {
return (
<Link to={`/gene/${modifier.curie}`} target='_blank'>
<Link to={`/gene/${identifier}`} target='_blank'>
<span dangerouslySetInnerHTML={{__html: modifier.geneSymbol.displayText}}/>
</Link>);
}
break;
case 'Allele':
if (modifier.alleleSymbol) {
return (
<Link to={`/allele/${modifier.curie}`} target='_blank'>
<Link to={`/allele/${identifier}`} target='_blank'>
<span dangerouslySetInnerHTML={{__html: modifier.alleleSymbol.displayText}}/>
</Link>);
}
break;
case 'AffectedGenomicModel':
let url = getResourceUrl(modifier.curie, modifier.type, modifier.subtype);
let url = getResourceUrl(identifier, modifier.type, modifier.subtype);
if (url && modifier.name) {
return (
<ExternalLink href={url}>
Expand Down
13 changes: 13 additions & 0 deletions src/components/dataTable/ReferencesCellViaOrthologyCuration.js
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
import React from 'react';

import ExternalLink from '../ExternalLink';

const ReferenceCellViaOrthologyCuration = () => {
const curie = "MGI:6194238";
const url = `http://www.informatics.jax.org/accession/${curie}`;
return (
<ExternalLink href={url} key={curie} title={curie}>{curie}</ExternalLink>
);
};

export default ReferenceCellViaOrthologyCuration;
Loading

0 comments on commit b05013c

Please sign in to comment.