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[DO NOT MERGE] CCF.OWL v1.x version of the code #984

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[DO NOT MERGE] CCF.OWL v1.x version of the code #984

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c79615a
HRA v1.3 Preview
bherr2 Dec 1, 2022
2142895
Point to the new ccf-api staging site
bherr2 Dec 1, 2022
bbca6ed
Update HRA v1.3 data
bherr2 Dec 2, 2022
eef1cc3
Merge branch 'main' of https://github.com/hubmapconsortium/ccf-ui int…
bherr2 Dec 6, 2022
5d04782
Merge branch 'main' of https://github.com/hubmapconsortium/ccf-ui int…
bherr2 Dec 6, 2022
6711e47
While out of band, use in-memory ccf database
bherr2 Dec 6, 2022
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2 changes: 1 addition & 1 deletion projects/ccf-api/ccf-cache/ccf.owl.n3store.json
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2 changes: 1 addition & 1 deletion projects/ccf-api/ccf-cache/cell-type-tree-model.json
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2 changes: 1 addition & 1 deletion projects/ccf-api/ccf-cache/ontology-tree-model.json
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2 changes: 1 addition & 1 deletion projects/ccf-api/ccf-cache/reference-organs.json
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4 changes: 2 additions & 2 deletions projects/ccf-body-ui/src/lib/util/process-reference-data.ts
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Expand Up @@ -10,9 +10,9 @@ import { processSpatialEntities } from './process-spatial-entities';


export const referenceDataConfig = {
extractionSitesUrl: 'http://localhost:8080/source_data/ASCT-B_3D_Models_Extraction_Sites.csv',
extractionSitesUrl: 'http://localhost:8080/source_data/asct-b-3d-models-extraction-sites.csv',
extractionSitesConfigUrl: 'http://localhost:8080/source_data/extraction-site-config.csv',
anatomicalStructuresUrl: 'http://localhost:8080/source_data/ASCT-B_3D_Models_Mapping.csv',
anatomicalStructuresUrl: 'http://localhost:8080/source_data/asct-b-3d-models-mapping.csv',
referenceOrganConfigUrl: 'http://localhost:8080/source_data/reference-organ-config.csv'
};

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3 changes: 3 additions & 0 deletions projects/ccf-database/src/lib/queries/ontology-tree-n3.ts
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Expand Up @@ -81,6 +81,9 @@ export function getAnatomicalStructureTreeModelSlowly(store: Store): OntologyTre
// 'http://purl.obolibrary.org/obo/FMA_24977', // Knee, R
'http://purl.obolibrary.org/obo/UBERON_0002107', // Liver
'http://purl.obolibrary.org/obo/UBERON_0002048', // Lungs
'http://purl.obolibrary.org/obo/UBERON_0001911', // Mammary Gland
// 'http://purl.obolibrary.org/obo/FMA_57991', // Mammary Gland, L
// 'http://purl.obolibrary.org/obo/FMA_57987', // Mammary Gland, R
'http://purl.obolibrary.org/obo/UBERON_0000992', // Ovary
// 'http://purl.obolibrary.org/obo/FMA_7214', // Ovary, L
// 'http://purl.obolibrary.org/obo/FMA_7213', // Ovary, R
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2 changes: 1 addition & 1 deletion projects/ccf-database/src/precompute-reference-data.ts
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Expand Up @@ -15,7 +15,7 @@ if (!(global as { fetch: unknown }).fetch) {

async function main(outputFile?: string): Promise<void> {
const db = new CCFDatabase({
ccfOwlUrl: 'http://localhost:8081/dist/ccf.owl',
ccfOwlUrl: 'http://localhost:8080/dist/ccf.owl',
ccfContextUrl: 'https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld',
hubmapDataService: 'search-api',
hubmapPortalUrl: 'https://portal.hubmapconsortium.org/',
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2 changes: 1 addition & 1 deletion projects/ccf-database/src/serialize-ccf-database.ts
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Expand Up @@ -12,7 +12,7 @@ if (!(global as { fetch: unknown }).fetch) {

async function main(outputFile?: string): Promise<void> {
const db = new CCFDatabase({
ccfOwlUrl: 'http://localhost:8081/dist/ccf.owl',
ccfOwlUrl: 'http://localhost:8080/dist/ccf.owl',
ccfContextUrl: 'https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld',
hubmapDataService: 'search-api',
hubmapPortalUrl: 'https://portal.hubmapconsortium.org/',
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1 change: 1 addition & 0 deletions projects/ccf-eui/src/app/core/store/icon-registry/default-icons.ts
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Expand Up @@ -50,6 +50,7 @@ export const DEFAULT_ICONS: DefaultIconDefinition[] = [
{ name: 'lung-right', namespace: 'app', url: 'assets/icons/organs/ico-organs-lung-right.svg' },
{ name: 'lung', namespace: 'app', url: 'assets/icons/organs/ico-organs-lung.svg' },
{ name: 'lymph-nodes', namespace: 'app', url: 'assets/icons/organs/ico-organs-lymph-nodes.svg' },
{ name: 'mammary-gland', namespace: 'app', url: 'assets/icons/organs/ico-organs-breast.svg' },
{ name: 'neuron', namespace: 'app', url: 'assets/icons/organs/ico-organs-neuron.svg' },
{ name: 'ovaries', namespace: 'app', url: 'assets/icons/organs/ico-organs-ovaries.svg' },
{ name: 'ovary-left', namespace: 'app', url: 'assets/icons/organs/ico-organs-ovary-left.svg' },
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2 changes: 1 addition & 1 deletion projects/ccf-eui/src/assets/ccf.owl.n3store.json
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1 change: 1 addition & 0 deletions projects/ccf-eui/src/assets/icons/organs/ico-organs-breast.svg
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2 changes: 1 addition & 1 deletion projects/ccf-eui/src/environments/environment.staging.ts
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Expand Up @@ -21,7 +21,7 @@ export const environment = {
hubmapToken: localStorage.getItem('HUBMAP_TOKEN') ?? '',

useRemoteApi: false,
remoteApiEndpoint: 'https://ccf-api--staging.herokuapp.com/v1'
remoteApiEndpoint: 'https://r5i95k35v5.us-east-2.awsapprunner.com/v1'
},
customization: {
theme: 'hubmap',
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4 changes: 2 additions & 2 deletions projects/ccf-eui/src/environments/environment.ts
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Expand Up @@ -26,8 +26,8 @@ export const environment = {
hubmapToken: localStorage.getItem('HUBMAP_TOKEN') ?? '',

useRemoteApi: false,
remoteApiEndpoint: 'https://ccf-api--staging.herokuapp.com/v1'
// remoteApiEndpoint: 'https://ccf-api.hubmapconsortium.org/v1',
remoteApiEndpoint: 'https://r5i95k35v5.us-east-2.awsapprunner.com/v1'
// remoteApiEndpoint: 'https://ccf-api.hubmapconsortium.org/v1'
// remoteApiEndpoint: 'http://localhost:8080/v1'
},
customization: {
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3 changes: 2 additions & 1 deletion projects/ccf-eui/src/index.html
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Expand Up @@ -13,8 +13,9 @@

<body class="mat-typography">
<ccf-eui
use-remote-api="true"
use-remote-api="false"
></ccf-eui>
<!-- Set use-remote-api back to "true" if it goes back into staging/production. -->
</body>

</html>
1 change: 1 addition & 0 deletions projects/ccf-rui/src/app/core/store/icon-registry/default-icons.ts
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Expand Up @@ -50,6 +50,7 @@ export const DEFAULT_ICONS: DefaultIconDefinition[] = [
{ name: 'lung-right', namespace: 'app', url: 'assets/icons/organs/ico-organs-lung-right.svg' },
{ name: 'lung', namespace: 'app', url: 'assets/icons/organs/ico-organs-lung.svg' },
{ name: 'lymph-nodes', namespace: 'app', url: 'assets/icons/organs/ico-organs-lymph-nodes.svg' },
{ name: 'mammary-gland', namespace: 'app', url: 'assets/icons/organs/ico-organs-breast.svg' },
{ name: 'neuron', namespace: 'app', url: 'assets/icons/organs/ico-organs-neuron.svg' },
{ name: 'ovaries', namespace: 'app', url: 'assets/icons/organs/ico-organs-ovaries.svg' },
{ name: 'ovary-left', namespace: 'app', url: 'assets/icons/organs/ico-organs-ovary-left.svg' },
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1 change: 1 addition & 0 deletions projects/ccf-rui/src/assets/icons/organs/ico-organs-breast.svg
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