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Remove biolucida #471

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67c0423
Remove biolucida image and segmentation.
alan-wu Feb 4, 2026
44288b4
Remove testing for segmentation.
alan-wu Feb 4, 2026
acc9d65
Remove neurolucida link environment variable.
alan-wu Feb 4, 2026
dd65b2e
Remove nlLinkPrefix
akhuoa Feb 4, 2026
2e6fe20
Merge pull request #12 from akhuoa/remove-biolucida
alan-wu Feb 5, 2026
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4 changes: 1 addition & 3 deletions cypress/component/MapContent.cy.js
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Expand Up @@ -208,7 +208,7 @@ describe('MapContent', () => {
cy.wait('@mouseDataset', {timeout: 20000});

//Check how many tags in the dataset
cy.get('.box-card .container button').should('have.length', 6);
cy.get('.box-card .container button').should('have.length', 5);

//Intercept the request and stub it with preloaded fixture
cy.get('@metadata').then((metadata) => {
Expand All @@ -232,8 +232,6 @@ describe('MapContent', () => {

//Check for plot and open it, should have four items in select now
cy.get('.open-tab > .el-icon').click();
cy.get('.box-card .container button').filter(':visible').contains('Segmentations (1)').click();
cy.get('.gallery-strip').contains('M54-8_03_20_20_Final.xml').should("exist");
cy.get('.box-card .container button').filter(':visible').contains('Plots (1)').click();
cy.get('.box-card :nth-child(1) > .details .el-button').filter(':visible').click();
cy.get('.gallery-strip').contains('RAGP_4subs_negdct.csv').should("exist");
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42 changes: 0 additions & 42 deletions cypress/fixtures/stubResponse.json
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Expand Up @@ -117,27 +117,6 @@
}
],
"additionalLinks": false,
"biolucida-3d": [
{
"additional_mimetype": {
"name": ""
},
"datacite": {},
"dataset": {
"identifier": "dataset:a523453f2-93218b5c7b31",
"path": "primary/sub-54-8/sam-TJU-3Scan-ratheart-54-8/TJU_3Scan_ratheart_54-8.jpx"
},
"description": "Image file associated with the accompanying subject 54-8 xml file, viewable in Tissue Mapper",
"file_type": {
"name": ".jpx"
},
"identifier": "package:170d03342134e214e5cd3cf61a",
"mimetype": {
"name": "image/jpx"
},
"name": "TJU_3Scan_ratheart_54-8.jpx"
}
],
"contributors": [
{
"affiliations": [
Expand All @@ -162,27 +141,6 @@
"description": "Test this",
"doi": "https://doi.org/10.26275/llxf-edeh",
"identifier": "N:dataset:a59a7c4c-0234534e24b31",
"mbf-segmentation": [
{
"additional_mimetype": {
"name": "application/vnd.mbfbioscience.metadata+xml"
},
"datacite": {},
"dataset": {
"identifier": "dataset:a59a7c4c-0978-45er2414b5c7b31",
"path": "derivative/sub-54-8/sam-TJU-3Scan-ratheart-54-8/M54-8_03_20_20_Final.xml"
},
"description": "XML file associated with the accompanying subject 54-8 jpx file, which illustrates the spatial distribution and location of marked neurons in context of segmented cardiac features denoted by different colored contours, created in and viewable in Tissue Mapper (SCR_017321)",
"file_type": {
"name": ".xml"
},
"identifier": "package:25fab6d9-cf21-234d245124e74a359",
"mimetype": {
"name": "application/xml"
},
"name": "M54-8_03_20_20_Final.xml"
}
],
"name": "Generic mouse colon scaffold",
"organisms": [
{
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3 changes: 1 addition & 2 deletions docs/demo.md
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Expand Up @@ -52,11 +52,10 @@
algoliaId: 'VITE_ALGOLIA_ID',
pennsieveApi: 'VITE_PENNSIEVE_API_LOCATION',
flatmapAPI: 'VITE_FLATMAPAPI_LOCATION',
nlLinkPrefix: 'VITE_NL_LINK_PREFIX',
rootUrl: 'meta.env.VITE_ROOT_URL',
}
}
}
}
</script>
```
```
1 change: 0 additions & 1 deletion src/App.vue
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Expand Up @@ -174,7 +174,6 @@ export default {
algoliaId: import.meta.env.VITE_ALGOLIA_ID,
pennsieveApi: import.meta.env.VITE_PENNSIEVE_API_LOCATION,
flatmapAPI: this.$route.query.flatmapserver ? this.$route.query.flatmapserver : import.meta.env.VITE_FLATMAPAPI_LOCATION,
nlLinkPrefix: import.meta.env.VITE_NL_LINK_PREFIX,
rootUrl: import.meta.env.VITE_ROOT_URL,
}
}
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1 change: 0 additions & 1 deletion src/components/ContentBar.vue
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Expand Up @@ -148,7 +148,6 @@ export default {
ALGOLIA_KEY: this.settingsStore.algoliaKey,
ALGOLIA_ID: this.settingsStore.algoliaId,
PENNSIEVE_API_LOCATION: this.settingsStore.pennsieveApi,
NL_LINK_PREFIX: this.settingsStore.nlLinkPrefix,
ROOT_URL: this.settingsStore.rootUrl,
};
},
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2 changes: 0 additions & 2 deletions src/components/ContentVuer.vue
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Expand Up @@ -173,9 +173,7 @@ export default {
...mapStores(useEntriesStore, useSplitFlowStore),
viewerType() {
switch (this.entry.type) {
case "Biolucida":
case "Iframe":
case "Segmentation":
return 'Iframe';
default:
return this.entry.type;
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1 change: 0 additions & 1 deletion src/components/MapContent.vue
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Expand Up @@ -406,7 +406,6 @@ export default {
this.options.algoliaId ? this.settingsStore.updateAlgoliaId(this.options.algoliaId) : null;
this.options.pennsieveApi ? this.settingsStore.updatePennsieveApi(this.options.pennsieveApi) : null;
this.options.flatmapAPI ? this.settingsStore.updateFlatmapAPI(this.options.flatmapAPI) : null;
this.options.nlLinkPrefix ? this.settingsStore.updateNLLinkPrefix(this.options.nlLinkPrefix) : null;
this.options.rootUrl ? this.settingsStore.updateRootUrl(this.options.rootUrl) : null;
}
this.settingsStore.updateAllClosable(this.allClosable);
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1 change: 0 additions & 1 deletion src/components/SplitFlow.vue
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Expand Up @@ -1026,7 +1026,6 @@ export default {
ALGOLIA_KEY: this.settingsStore.algoliaKey,
ALGOLIA_ID: this.settingsStore.algoliaId,
PENNSIEVE_API_LOCATION: this.settingsStore.pennsieveApi,
NL_LINK_PREFIX: this.settingsStore.nlLinkPrefix,
ROOT_URL: this.settingsStore.rootUrl,
FLATMAPAPI_LOCATION: this.settingsStore.flatmapAPI,
};
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4 changes: 0 additions & 4 deletions src/stores/settings.js
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Expand Up @@ -12,7 +12,6 @@ export const useSettingsStore = defineStore('settings', {
algoliaId: undefined,
pennsieveApi: undefined,
flatmapAPI: undefined,
nlLinkPrefix: undefined,
mapManager: undefined,
rootUrl: undefined,
facets: { species: [], gender: [], organ: [] },
Expand Down Expand Up @@ -114,9 +113,6 @@ export const useSettingsStore = defineStore('settings', {
updateMapManager(mapManager) {
this.mapManager = mapManager;
},
updateNLLinkPrefix(nlLinkPrefix) {
this.nlLinkPrefix = nlLinkPrefix;
},
updateRootUrl(rootUrl) {
this.rootUrl = rootUrl;
},
Expand Down