From 67c042378404c922fe1b791b4da2d00616e4a4c4 Mon Sep 17 00:00:00 2001 From: alan-wu Date: Wed, 4 Feb 2026 13:45:31 +1300 Subject: [PATCH 1/4] Remove biolucida image and segmentation. --- cypress/fixtures/stubResponse.json | 42 ------------------------------ src/components/ContentVuer.vue | 2 -- 2 files changed, 44 deletions(-) diff --git a/cypress/fixtures/stubResponse.json b/cypress/fixtures/stubResponse.json index 8d00e8fa..34d39dc2 100644 --- a/cypress/fixtures/stubResponse.json +++ b/cypress/fixtures/stubResponse.json @@ -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": [ @@ -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": [ { diff --git a/src/components/ContentVuer.vue b/src/components/ContentVuer.vue index ad99defb..aa548000 100644 --- a/src/components/ContentVuer.vue +++ b/src/components/ContentVuer.vue @@ -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; From 44288b4933cee296f7bddc0a5fa00540db2b33a7 Mon Sep 17 00:00:00 2001 From: alan-wu Date: Thu, 5 Feb 2026 11:28:13 +1300 Subject: [PATCH 2/4] Remove testing for segmentation. --- cypress/component/MapContent.cy.js | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/cypress/component/MapContent.cy.js b/cypress/component/MapContent.cy.js index 4d7deb58..492eade1 100644 --- a/cypress/component/MapContent.cy.js +++ b/cypress/component/MapContent.cy.js @@ -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) => { @@ -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"); From acc9d65bde14a5d4cb9eb8f25609a0f040b493bf Mon Sep 17 00:00:00 2001 From: alan-wu Date: Thu, 5 Feb 2026 11:38:47 +1300 Subject: [PATCH 3/4] Remove neurolucida link environment variable. --- src/App.vue | 1 - src/components/MapContent.vue | 1 - src/components/SplitFlow.vue | 1 - src/stores/settings.js | 4 ---- 4 files changed, 7 deletions(-) diff --git a/src/App.vue b/src/App.vue index 3eb3f87f..809cf1ba 100644 --- a/src/App.vue +++ b/src/App.vue @@ -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, } } diff --git a/src/components/MapContent.vue b/src/components/MapContent.vue index 14795497..0330d285 100644 --- a/src/components/MapContent.vue +++ b/src/components/MapContent.vue @@ -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); diff --git a/src/components/SplitFlow.vue b/src/components/SplitFlow.vue index 492333f3..79dc70db 100644 --- a/src/components/SplitFlow.vue +++ b/src/components/SplitFlow.vue @@ -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, }; diff --git a/src/stores/settings.js b/src/stores/settings.js index d330a0a6..510ee4b7 100644 --- a/src/stores/settings.js +++ b/src/stores/settings.js @@ -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: [] }, @@ -114,9 +113,6 @@ export const useSettingsStore = defineStore('settings', { updateMapManager(mapManager) { this.mapManager = mapManager; }, - updateNLLinkPrefix(nlLinkPrefix) { - this.nlLinkPrefix = nlLinkPrefix; - }, updateRootUrl(rootUrl) { this.rootUrl = rootUrl; }, From dd65b2ebb6679ffdab33cad5fd531c0bd3c34280 Mon Sep 17 00:00:00 2001 From: akhuoa Date: Thu, 5 Feb 2026 12:06:44 +1300 Subject: [PATCH 4/4] Remove nlLinkPrefix --- docs/demo.md | 3 +-- src/components/ContentBar.vue | 1 - 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/docs/demo.md b/docs/demo.md index ae41456f..5ca42bdb 100644 --- a/docs/demo.md +++ b/docs/demo.md @@ -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', } } } } -``` \ No newline at end of file +``` diff --git a/src/components/ContentBar.vue b/src/components/ContentBar.vue index 047205e4..16a823be 100644 --- a/src/components/ContentBar.vue +++ b/src/components/ContentBar.vue @@ -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, }; },