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Release textpresso rules #1319

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merged 6 commits into from
May 7, 2024
Merged

Release textpresso rules #1319

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4d9d127
Added textpresso rewrites and redirects
valearna May 6, 2024
c11579f
Added textpresso rewrites to test
valearna May 6, 2024
6929eee
SCRUM-4012 add reference name lookup for mod references
adamgibs May 6, 2024
252e05a
Merge pull request #1318 from alliance-genome/SCRUM-4012
adamgibs May 6, 2024
101d3b5
Merge branch 'test' into textpresso_rewrites
valearna May 6, 2024
51fa387
Merge pull request #1317 from alliance-genome/textpresso_rewrites
valearna May 6, 2024
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13 changes: 11 additions & 2 deletions cdk/amplify-production-stack.ts
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Expand Up @@ -41,7 +41,7 @@ export class AmplifyProductionStack extends cdk.Stack {
{ source: '/jbrowse/worms/jbrowse2', target: 'https://www.alliancegenome.org/jbrowse/worms/jbrowse2/', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/jbrowse/worms/jbrowse2/', target: 'https://main.d2jjb0xowet5mr.amplifyapp.com/', status: amplify.RedirectStatus.REWRITE },
{ source: '/jbrowse/worms/jbrowse2/<*>', target: 'https://main.d2jjb0xowet5mr.amplifyapp.com/<*>', status: amplify.RedirectStatus.REWRITE },

{ source: '/agr_simplemine.cgi', target: 'https://caltech-curation.textpressolab.com/pub/cgi-bin/forms/agr_simplemine.cgi', status: amplify.RedirectStatus.REWRITE },

{ source: '/jbrowse/<*>', target: 'https://prod-alb.alliancegenome.org/jbrowse/<*>', status: amplify.RedirectStatus.REWRITE },
Expand All @@ -65,10 +65,19 @@ export class AmplifyProductionStack extends cdk.Stack {
{ source: '/textpresso/wb', target: 'https://www.alliancegenome.org/textpresso/wb/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/wb/', target: 'https://www.alliancegenome.org/textpresso/wb/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/wb/<*>', target: 'https://wb-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/textpresso/mgi', target: 'https://www.alliancegenome.org/textpresso/mgi/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/mgi/', target: 'https://www.alliancegenome.org/textpresso/mgi/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/mgi/<*>', target: 'https://mgi-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/textpresso/zfin', target: 'https://www.alliancegenome.org/textpresso/zfin/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/zfin/', target: 'https://www.alliancegenome.org/textpresso/zfin/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/zfin/<*>', target: 'https://zfin-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/textpresso/fb', target: 'https://www.alliancegenome.org/textpresso/fb/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/fb/', target: 'https://www.alliancegenome.org/textpresso/fb/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/fb/<*>', target: 'https://fb-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },

{ source: '/<*>', target: '/index.html', status: amplify.RedirectStatus.NOT_FOUND_REWRITE },
{ source: '</^[^.]+$/>', target: '/index.html', status: amplify.RedirectStatus.REWRITE }

];

const amplifyApp = new amplify.App(this, 'agr-ui-production', {
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13 changes: 12 additions & 1 deletion cdk/amplify-stage-stack.ts
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Expand Up @@ -19,7 +19,7 @@ export class AmplifyStageStack extends cdk.Stack {
{ 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: '/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 },
Expand Down Expand Up @@ -51,12 +51,23 @@ export class AmplifyStageStack extends cdk.Stack {
{ source: '/bluegenes', target: 'https://stage.alliancegenome.org/bluegenes/alliancemine', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/bluegenes/', target: 'https://stage.alliancegenome.org/bluegenes/alliancemine', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/bluegenes/<*>', target: 'https://stage-alliancemine.alliancegenome.org:444/bluegenes/<*>', status: amplify.RedirectStatus.REWRITE },

{ source: '/textpresso/sgd', target: 'https://stage.alliancegenome.org/textpresso/sgd/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/sgd/', target: 'https://stage.alliancegenome.org/textpresso/sgd/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/sgd/<*>', target: 'https://sgd-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/textpresso/wb', target: 'https://stage.alliancegenome.org/textpresso/wb/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/wb/', target: 'https://stage.alliancegenome.org/textpresso/wb/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/wb/<*>', target: 'https://wb-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/textpresso/mgi', target: 'https://stage.alliancegenome.org/textpresso/mgi/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/mgi/', target: 'https://stage.alliancegenome.org/textpresso/mgi/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/mgi/<*>', target: 'https://mgi-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/textpresso/zfin', target: 'https://stage.alliancegenome.org/textpresso/zfin/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/zfin/', target: 'https://stage.alliancegenome.org/textpresso/zfin/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/zfin/<*>', target: 'https://zfin-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/textpresso/fb', target: 'https://stage.alliancegenome.org/textpresso/fb/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/fb/', target: 'https://stage.alliancegenome.org/textpresso/fb/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/fb/<*>', target: 'https://fb-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },

{ source: '/<*>', target: '/index.html', status: amplify.RedirectStatus.NOT_FOUND_REWRITE },
{ source: '</^[^.]+$/>', target: '/index.html', status: amplify.RedirectStatus.REWRITE }
];
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16 changes: 16 additions & 0 deletions cdk/amplify-test-stack.ts
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Expand Up @@ -55,6 +55,22 @@ export class AmplifyTestStack extends cdk.Stack {
{ source: '/swagger-ui/<*>', target: 'https://test-alb.alliancegenome.org/swagger-ui/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/openapi', target: 'https://test-alb.alliancegenome.org/openapi', status: amplify.RedirectStatus.REWRITE },

{ source: '/textpresso/sgd', target: 'https://test.alliancegenome.org/textpresso/sgd/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/sgd/', target: 'https://test.alliancegenome.org/textpresso/sgd/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/sgd/<*>', target: 'https://sgd-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/textpresso/wb', target: 'https://test.alliancegenome.org/textpresso/wb/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/wb/', target: 'https://test.alliancegenome.org/textpresso/wb/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/wb/<*>', target: 'https://wb-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/textpresso/mgi', target: 'https://test.alliancegenome.org/textpresso/mgi/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/mgi/', target: 'https://test.alliancegenome.org/textpresso/mgi/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/mgi/<*>', target: 'https://mgi-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/textpresso/zfin', target: 'https://test.alliancegenome.org/textpresso/zfin/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/zfin/', target: 'https://test.alliancegenome.org/textpresso/zfin/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/zfin/<*>', target: 'https://zfin-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },
{ source: '/textpresso/fb', target: 'https://test.alliancegenome.org/textpresso/fb/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/fb/', target: 'https://test.alliancegenome.org/textpresso/fb/tpc', status: amplify.RedirectStatus.PERMANENT_REDIRECT },
{ source: '/textpresso/fb/<*>', target: 'https://fb-textpresso.alliancegenome.org/<*>', status: amplify.RedirectStatus.REWRITE },

{ source: '/<*>', target: '/index.html', status: amplify.RedirectStatus.NOT_FOUND_REWRITE },
{ source: '</^[^.]+$/>', target: '/index.html', status: amplify.RedirectStatus.REWRITE }
];
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6 changes: 5 additions & 1 deletion src/components/dataTable/AnnotatedEntitiesPopupCuration.js
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Expand Up @@ -27,7 +27,11 @@ import StrainBackground from './StrainBackground';

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

if (entity.type === 'AlleleDiseaseAnnotation') {
const innerText = entity.diseaseAnnotationSubject.alleleSymbol ? entity.diseaseAnnotationSubject.alleleSymbol.displayText : entity.diseaseAnnotationSubject.name;
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2 changes: 1 addition & 1 deletion src/components/dataTable/GeneticModifiersCellCuration.js
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Expand Up @@ -26,7 +26,7 @@ function GeneticModifierLink(modifier) {
}
break;
case 'AffectedGenomicModel':
let url = getResourceUrl(identifier, modifier.type, modifier.subtype);
let url = getResourceUrl({ curie: identifier, type: modifier.type, subtype: modifier.subtype});
if (url && modifier.name) {
return (
<ExternalLink href={url}>
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2 changes: 1 addition & 1 deletion src/components/dataTable/getResourceUrl.js
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@@ -1,6 +1,6 @@
import { resourceDescriptors } from "../../resourceDescriptors";

export const getResourceUrl = (curie, type, subtype ) => {
export const getResourceUrl = ({ curie, type, subtype }) => {
const [prefix, id] = curie.split(':');

let resource;
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7 changes: 6 additions & 1 deletion src/components/dataTable/utils.js
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Expand Up @@ -28,7 +28,12 @@ export const getIsViaOrthology = (annotation) => {
};

export const getSingleReferenceUrl = (pubModId) => {
const url = getResourceUrl(pubModId);
let url;
if(pubModId.includes("PMID")){
url = getResourceUrl({curie: pubModId});
} else {
url = getResourceUrl({curie: pubModId, type: "reference"});
}
return {pubModId, url};
}

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