diff --git a/.gitignore b/.gitignore
index e66fee60..3d8fc175 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,4 +9,3 @@ docs/.vitepress/dist
docs/.vitepress/cache
docs/components
.DS_Store
-/.vitepress
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 97394c40..caa7aa4a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,162 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog).
-## [v1.3.1](https://github.com/alan-wu/flatmapvuer/compare/v1.3.0...v1.3.1)
-
-### Commits
-
-- Update map-utilties to version 1.3.0. [`013c45b`](https://github.com/alan-wu/flatmapvuer/commit/013c45b2de7d401dc9937b4b550b10071f820ba5)
-
-## [v1.3.0](https://github.com/alan-wu/flatmapvuer/compare/v1.2.0...v1.3.0) - 2024-07-10
-
-### Merged
-
-- Display connectivity info without obstructing current map view [`#175`](https://github.com/alan-wu/flatmapvuer/pull/175)
-- Revert "Fix PubMed URL issue" [`#177`](https://github.com/alan-wu/flatmapvuer/pull/177)
-- Fix PubMed URL issue [`#176`](https://github.com/alan-wu/flatmapvuer/pull/176)
-- Utilities package [`#174`](https://github.com/alan-wu/flatmapvuer/pull/174)
-
-### Commits
-
-- Replace local components by map-utilities package [`e59cf6e`](https://github.com/alan-wu/flatmapvuer/commit/e59cf6e284a99d3abae12248e6da6b7a4b1cbe33)
-- Update code for upcoming toolbar component [`94e38f4`](https://github.com/alan-wu/flatmapvuer/commit/94e38f47c48226f759b24c59f53ea119cce61331)
-- Update code for upcoming treecontrols component [`ab31662`](https://github.com/alan-wu/flatmapvuer/commit/ab316621cfeeee234eeaf5a7b54de039f4a09bd6)
-
-## [v1.2.0](https://github.com/alan-wu/flatmapvuer/compare/v1.1.1...v1.2.0) - 2024-06-24
-
-### Merged
-
-- Update to how modes are selected [`#170`](https://github.com/alan-wu/flatmapvuer/pull/170)
-- Switch to latest version of flatmap-viewer [`#173`](https://github.com/alan-wu/flatmapvuer/pull/173)
-- Update marker icon for help mode [`#6`](https://github.com/alan-wu/flatmapvuer/pull/6)
-
-### Commits
-
-- Switch the mode selector to a title/subtitle style [`13f1ff7`](https://github.com/alan-wu/flatmapvuer/commit/13f1ff79eb903ce2103d9d289b95dd4f161d1009)
-- Switch network discover mode to 'neuron connections' mode and add help text [`2d4f050`](https://github.com/alan-wu/flatmapvuer/commit/2d4f050ca1011c1272d1515e8be5993fbba5d8ca)
-- Maintain viewing modes order. [`bb1dc6a`](https://github.com/alan-wu/flatmapvuer/commit/bb1dc6ae5609869935e46c4fd235d9c2badfb1ea)
-
-## [v1.1.1](https://github.com/alan-wu/flatmapvuer/compare/v1.1.0...v1.1.1) - 2024-06-06
-
-### Merged
-
-- UI updates for FC map pathway container [`#171`](https://github.com/alan-wu/flatmapvuer/pull/171)
-- Now can handle single and double nodes at all times [`#169`](https://github.com/alan-wu/flatmapvuer/pull/169)
-
-### Commits
-
-- Add a fix to cypress testing. [`aa8de18`](https://github.com/alan-wu/flatmapvuer/commit/aa8de189572cb34ba584f99cc895926b79ed7d22)
-- Make improvements on TreeControls UI [`72fe2ee`](https://github.com/alan-wu/flatmapvuer/commit/72fe2ee54f6b257d870d3ff7bf4dbe336c2e98dd)
-- Update cypress testing. [`266c29c`](https://github.com/alan-wu/flatmapvuer/commit/266c29c28d2c25665f49267f7953abb6fcf46daa)
-
-## [v1.1.0](https://github.com/alan-wu/flatmapvuer/compare/v1.1.0-beta.3...v1.1.0) - 2024-05-29
-
-### Merged
-
-- Remove origins from highlight in network explorer mode: [`#144`](https://github.com/alan-wu/flatmapvuer/pull/144)
-- Toolbar icon style [`#168`](https://github.com/alan-wu/flatmapvuer/pull/168)
-- fix toolbar when Drawn By specified [`#167`](https://github.com/alan-wu/flatmapvuer/pull/167)
-- New draw feature for Annotator [`#142`](https://github.com/alan-wu/flatmapvuer/pull/142)
-- Refactor [`#14`](https://github.com/alan-wu/flatmapvuer/pull/14)
-- Add features alert [`#161`](https://github.com/alan-wu/flatmapvuer/pull/161)
-- Supports the old help mode without help dialog. [`#166`](https://github.com/alan-wu/flatmapvuer/pull/166)
-- Flatmap improvements - help text visible [`#165`](https://github.com/alan-wu/flatmapvuer/pull/165)
-
-### Commits
-
-- Update package-lock.json. [`4300265`](https://github.com/alan-wu/flatmapvuer/commit/4300265d0b175e003d937c225765466219d1663a)
-- Remove console message. [`eeaa6cc`](https://github.com/alan-wu/flatmapvuer/commit/eeaa6cc0f309b880fef4d66c01abd14eb804f1c0)
-- move dialog display control into draw tool component [`aafa7a8`](https://github.com/alan-wu/flatmapvuer/commit/aafa7a87e4cdbf5dc576f09534f6b21fc4f1eb93)
-
-## [v1.1.0-beta.3](https://github.com/alan-wu/flatmapvuer/compare/v1.0.2...v1.1.0-beta.3) - 2024-05-22
-
-### Merged
-
-- Highlight on species [`#127`](https://github.com/alan-wu/flatmapvuer/pull/127)
-- Add relation between drawn features [`#13`](https://github.com/alan-wu/flatmapvuer/pull/13)
-- Refactor annotator code [`#12`](https://github.com/alan-wu/flatmapvuer/pull/12)
-- Send item details when adding an annotation. [`#11`](https://github.com/alan-wu/flatmapvuer/pull/11)
-- A tidy up and pass more connection information to the annotation service [`#10`](https://github.com/alan-wu/flatmapvuer/pull/10)
-- Annotator further development [`#8`](https://github.com/alan-wu/flatmapvuer/pull/8)
-- Viewer changes merged [`#7`](https://github.com/alan-wu/flatmapvuer/pull/7)
-- pull requirements [`#6`](https://github.com/alan-wu/flatmapvuer/pull/6)
-- pull latest changes [`#4`](https://github.com/alan-wu/flatmapvuer/pull/4)
-- Merge new changes [`#3`](https://github.com/alan-wu/flatmapvuer/pull/3)
-- Vue3 migration [`#2`](https://github.com/alan-wu/flatmapvuer/pull/2)
-
-### Commits
-
-- Merged in annotationn changes. [`7b8cfcb`](https://github.com/alan-wu/flatmapvuer/commit/7b8cfcb0ba742711936d353759c86c2f7fa35887)
-- Merged in upstream changes. [`eeba37c`](https://github.com/alan-wu/flatmapvuer/commit/eeba37cb1c7c7efc3589c09fb6a2d1538debf023)
-- merged in upstream changes. [`77ddcf7`](https://github.com/alan-wu/flatmapvuer/commit/77ddcf73569a72613bd45de90bafbc5b74641ba6)
-
-## [v1.0.2](https://github.com/alan-wu/flatmapvuer/compare/v1.0.1...v1.0.2) - 2024-05-15
-
-### Merged
-
-- Bugfix - Help Mode Tooltips [`#164`](https://github.com/alan-wu/flatmapvuer/pull/164)
-- Add pathways checkbox events for data tracking [`#163`](https://github.com/alan-wu/flatmapvuer/pull/163)
-
-### Commits
-
-- Fix featured dataset tooltip and help mode [`883e6c5`](https://github.com/alan-wu/flatmapvuer/commit/883e6c5acf243abda7f0da047a80ff7af3677f95)
-- Open drawer to show tooltips inside when help mode is activated [`82b1ce6`](https://github.com/alan-wu/flatmapvuer/commit/82b1ce6405e6e6dac31f0e959010b06c7aa2f268)
-- Add open pubmed button click event [`782145d`](https://github.com/alan-wu/flatmapvuer/commit/782145d4641f173c992c36792eacf960b2456e3c)
-
-## [v1.0.1](https://github.com/alan-wu/flatmapvuer/compare/v1.0.0...v1.0.1) - 2024-05-02
-
-### Merged
-
-- Add species switch in component testing [`#150`](https://github.com/alan-wu/flatmapvuer/pull/150)
-
-### Commits
-
-- Update changelogs. [`164211a`](https://github.com/alan-wu/flatmapvuer/commit/164211aafed94962d79666caabe8e7df15726912)
-- Update test for species switch [`5cba70e`](https://github.com/alan-wu/flatmapvuer/commit/5cba70e6310fe5339017b8140c91d16e3b883b79)
-- Fix a typo. [`6feeab9`](https://github.com/alan-wu/flatmapvuer/commit/6feeab9a33e1ba2a4960a1a344442fa864a7c582)
-
-## [v1.0.0](https://github.com/alan-wu/flatmapvuer/compare/v0.5.9...v1.0.0) - 2024-04-24
-
-### Merged
-
-- Fix popup close error [`#160`](https://github.com/alan-wu/flatmapvuer/pull/160)
-- Fix tooltip arrow on top position [`#159`](https://github.com/alan-wu/flatmapvuer/pull/159)
-- Fix api docs demo for pinia [`#158`](https://github.com/alan-wu/flatmapvuer/pull/158)
-- Fix popup showing on switching viewingMode [`#157`](https://github.com/alan-wu/flatmapvuer/pull/157)
-- Popup UI Updates [`#156`](https://github.com/alan-wu/flatmapvuer/pull/156)
-- Fix tooltip arrows UI for corner positions [Bugfix] [UI] [`#153`](https://github.com/alan-wu/flatmapvuer/pull/153)
-- Update vitepress config with alias to resolve dir [`#148`](https://github.com/alan-wu/flatmapvuer/pull/148)
-- Update flatmapvuer. [`#147`](https://github.com/alan-wu/flatmapvuer/pull/147)
-- Add pinia in Cypress component test [`#4`](https://github.com/alan-wu/flatmapvuer/pull/4)
-- Annotation authentication [`#143`](https://github.com/alan-wu/flatmapvuer/pull/143)
-- Fix a bug causing annotation to not open the editing dialog. [`#9`](https://github.com/alan-wu/flatmapvuer/pull/9)
-- Update docs content [`#146`](https://github.com/alan-wu/flatmapvuer/pull/146)
-- Cleanup unused npm packages [`#137`](https://github.com/alan-wu/flatmapvuer/pull/137)
-- Make flatmap query helper functions more robust [`#141`](https://github.com/alan-wu/flatmapvuer/pull/141)
-- Change Flight Path Option [`#140`](https://github.com/alan-wu/flatmapvuer/pull/140)
-- Feature/3d fc map [`#139`](https://github.com/alan-wu/flatmapvuer/pull/139)
-- Hotfix - el-radio props incorrectly changed [`#136`](https://github.com/alan-wu/flatmapvuer/pull/136)
-- Cypress testing Vue 3 [`#134`](https://github.com/alan-wu/flatmapvuer/pull/134)
-- Update test and dependencies. [`#4`](https://github.com/alan-wu/flatmapvuer/pull/4)
-- APIs Documentation [`#133`](https://github.com/alan-wu/flatmapvuer/pull/133)
-- Update species selectbox style for hidden contents [`#135`](https://github.com/alan-wu/flatmapvuer/pull/135)
-- Fix svg being slighlty to big for its container [`#132`](https://github.com/alan-wu/flatmapvuer/pull/132)
-- Featured marker fix [`#128`](https://github.com/alan-wu/flatmapvuer/pull/128)
-- Add missing interface [`#131`](https://github.com/alan-wu/flatmapvuer/pull/131)
-- Add a property to disable UI elements [`#130`](https://github.com/alan-wu/flatmapvuer/pull/130)
-- Vue3 migration [`#126`](https://github.com/alan-wu/flatmapvuer/pull/126)
-- Remove warning [`#3`](https://github.com/alan-wu/flatmapvuer/pull/3)
-- fetch vue3 migration changes [`#1`](https://github.com/alan-wu/flatmapvuer/pull/1)
-- Allow html in "what's new": [`#125`](https://github.com/alan-wu/flatmapvuer/pull/125)
-- Featured marker legend name fix [`#124`](https://github.com/alan-wu/flatmapvuer/pull/124)
-
-### Commits
-
-- Add missing files [`219c3fe`](https://github.com/alan-wu/flatmapvuer/commit/219c3fe91fce576bc6314bd328f2ffaa89d89e3f)
-- Remove vuese/cli for npm security vulnerabilities [`bc46469`](https://github.com/alan-wu/flatmapvuer/commit/bc4646969051d750dc02a19c3226c067aea8b809)
-- Fix an issue with package-lock.json. [`1d9b9e5`](https://github.com/alan-wu/flatmapvuer/commit/1d9b9e57fc2765fd718ccaa6ac4ecae1aad43b72)
-
-## [v0.5.9](https://github.com/alan-wu/flatmapvuer/compare/v0.5.8...v0.5.9) - 2023-12-08
+## [v0.5.9](https://github.com/alan-wu/flatmapvuer/compare/v0.5.9-beta.0...v0.5.9)
### Merged
@@ -175,6 +20,14 @@ Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog).
- Reset version. [`5f10239`](https://github.com/alan-wu/flatmapvuer/commit/5f10239a05f33b9d6bb1b6c71d02605c0d1c0c58)
- Merge in changes. [`76ee249`](https://github.com/alan-wu/flatmapvuer/commit/76ee249280969445f48af38e9dfe8677d45faa00)
+## [v0.5.9-beta.0](https://github.com/alan-wu/flatmapvuer/compare/v0.5.8...v0.5.9-beta.0) - 2023-11-09
+
+### Commits
+
+- Add initial UI for annotation viewing/submitting dialog. [`b5d3263`](https://github.com/alan-wu/flatmapvuer/commit/b5d326303f83bba7c1c7f468aecee49d092e0b4d)
+- Restructure Tooltip component. Add in Annotational Tool component [`974f07e`](https://github.com/alan-wu/flatmapvuer/commit/974f07e6b242d11f3fb33469f0ae59246a5647e7)
+- Improve annotation UI based on feedbacks. [`c631c7a`](https://github.com/alan-wu/flatmapvuer/commit/c631c7a98e8b5baf070b02c3a7bdfbfcf999bd80)
+
## [v0.5.8](https://github.com/alan-wu/flatmapvuer/compare/v0.5.7...v0.5.8) - 2023-11-07
### Merged
@@ -259,18 +112,13 @@ Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog).
## [v0.4.6](https://github.com/alan-wu/flatmapvuer/compare/0.4.6-fixes-2...v0.4.6) - 2023-06-01
-## [0.4.6-fixes-2](https://github.com/alan-wu/flatmapvuer/compare/0.4.6-fixes-1...0.4.6-fixes-2) - 2023-06-05
-
-### Commits
-
-- Search will display the label and location of the highest score result. [`c3b2e47`](https://github.com/alan-wu/flatmapvuer/commit/c3b2e471ed3bb6eb61c078c903814f40d57ca3fa)
-
-## [0.4.6-fixes-1](https://github.com/alan-wu/flatmapvuer/compare/v0.4.6-fixes-0...0.4.6-fixes-1) - 2023-06-02
+## [0.4.6-fixes-2](https://github.com/alan-wu/flatmapvuer/compare/v0.4.6-fixes-0...0.4.6-fixes-2) - 2023-06-05
### Commits
- Version 0.4.6-fixes-1 [`e8b60c3`](https://github.com/alan-wu/flatmapvuer/commit/e8b60c3e9bf381f4af68bd95612cdd20ea3132d0)
- Rename mapboxgl in css rules to maplibregl. [`9040cc9`](https://github.com/alan-wu/flatmapvuer/commit/9040cc96d32bb076c14c05af52f79a7137cd2651)
+- Search will display the label and location of the highest score result. [`c3b2e47`](https://github.com/alan-wu/flatmapvuer/commit/c3b2e471ed3bb6eb61c078c903814f40d57ca3fa)
## [v0.4.6-fixes-0](https://github.com/alan-wu/flatmapvuer/compare/v0.4.5...v0.4.6-fixes-0) - 2023-06-01
@@ -326,8 +174,8 @@ Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog).
### Commits
- Create a new vue component for the selection controls. [`aed5e35`](https://github.com/alan-wu/flatmapvuer/commit/aed5e3598d4d1fc8d6dd34a0cb7541066d155751)
+- Add dynamic system legends. [`9c86414`](https://github.com/alan-wu/flatmapvuer/commit/9c8641476d61830f5f5141f3fe29c1a4c04b316f)
- update flatmap-viewer to 2.2.13 [`f8e0dc8`](https://github.com/alan-wu/flatmapvuer/commit/f8e0dc8473b37935dc24b9765569ed5c9d26604d)
-- Update flatmap-viewer. [`33c53dc`](https://github.com/alan-wu/flatmapvuer/commit/33c53dc53989823f934235e6ebbfe2a8bd1652a9)
## [v0.3.15](https://github.com/alan-wu/flatmapvuer/compare/v0.3.12...v0.3.15) - 2023-02-27
@@ -347,18 +195,29 @@ Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog).
## [v0.3.12](https://github.com/alan-wu/flatmapvuer/compare/v0.3.12-fixes-0...v0.3.12) - 2023-01-20
-## [v0.3.12-fixes-0](https://github.com/alan-wu/flatmapvuer/compare/v0.3.10...v0.3.12-fixes-0) - 2023-01-20
+## [v0.3.12-fixes-0](https://github.com/alan-wu/flatmapvuer/compare/v0.3.11...v0.3.12-fixes-0) - 2023-01-20
### Merged
- Permalink update [`#90`](https://github.com/alan-wu/flatmapvuer/pull/90)
-- Now search on model for pubmed ids [`#85`](https://github.com/alan-wu/flatmapvuer/pull/85)
### Commits
- Flatmapvuer now uses uuid to fetch the map when saved in state. [`af447d3`](https://github.com/alan-wu/flatmapvuer/commit/af447d3e73bb8324d636b4831d7527d821704a60)
+- Improve initialisation of the multi flatmap. [`c00e258`](https://github.com/alan-wu/flatmapvuer/commit/c00e2584f02e0e9d4fbb8507a5ebbabd0f2f9655)
+- Fix an issue with reactivity by assigning value directly into an object. [`f87757b`](https://github.com/alan-wu/flatmapvuer/commit/f87757b32f0566eb8d6355055d60cb4ff724b597)
+
+## [v0.3.11](https://github.com/alan-wu/flatmapvuer/compare/v0.3.10...v0.3.11) - 2022-12-16
+
+### Merged
+
+- Now search on model for pubmed ids [`#85`](https://github.com/alan-wu/flatmapvuer/pull/85)
+
+### Commits
+
- Cut down pubmedviewer, organise tooltip proccessing [`dde4b8b`](https://github.com/alan-wu/flatmapvuer/commit/dde4b8b62808475dac4e4cc2ecbbcc72c48d1196)
- Increment version number to 0.3.11. [`a7509fd`](https://github.com/alan-wu/flatmapvuer/commit/a7509fdbd4f6914f4362f2e526362ca8248b1a5e)
+- Remove older unused watch on the pubmedvuer [`a74efe6`](https://github.com/alan-wu/flatmapvuer/commit/a74efe6ea54380d36afdaeede339584697701d5b)
## [v0.3.10](https://github.com/alan-wu/flatmapvuer/compare/0.3.9...v0.3.10) - 2022-12-13
diff --git a/cypress/component/MultiFlatmapVuer.cy.js b/cypress/component/MultiFlatmapVuer.cy.js
index 48d642b3..1d9a7cba 100644
--- a/cypress/component/MultiFlatmapVuer.cy.js
+++ b/cypress/component/MultiFlatmapVuer.cy.js
@@ -9,25 +9,15 @@ import { createPinia, setActivePinia } from 'pinia';
describe('MultiFlatmapVuer', () => {
- Cypress.on('uncaught:exception', (err) => {
- // returning false here prevents Cypress from
- // failing the test
- if (err.message.includes('Source "markers" already exists.'))
- return false
- return true
- })
-
beforeEach(() => {
cy.viewport(1920, 1080);
- cy.fixture('MultiFlatmapProps.json').as('props');
});
//Load in some responses/assets before beginning the test
//This should prevent any async behaviours.
before(() => {
- // moved to beforeEach
- // cy.fixture('MultiFlatmapProps.json').as('props');
+ cy.fixture('MultiFlatmapProps.json').as('props');
})
it('Workflow testing', () => {
@@ -114,7 +104,7 @@ describe('MultiFlatmapVuer', () => {
}, [])
// Check the pop up has the same information as when the test was created
- cy.get('.subtitle').should('exist').contains('Studied in Rattus norvegicus species')
+ cy.get('.subtitle').should('exist').contains('Observed in Rattus norvegicus species')
cy.get('[origin-item-label="Twelfth thoracic ganglion"]').should('exist')
cy.get('[component-item-label="connective tissue, neck of urinary bladder"]').should('exist')
cy.get('[destination-item-label="wall of blood vessel, Arteriole in connective tissue of bladder dome"]').should('exist')
@@ -147,7 +137,7 @@ describe('MultiFlatmapVuer', () => {
// Click the open pubmed button and check that the window.open call was intercepted
cy.get('#open-pubmed-button').should('exist').click()
- cy.get('@Open').should('have.been.calledOnceWithExactly', Cypress.sinon.match(/^https:\/\/pubmed\.ncbi\.nlm\.nih\.gov(?:\/.*)/), '_blank')
+ cy.get('@Open').should('have.been.calledOnceWithExactly', 'https://pubmed.ncbi.nlm.nih.gov/?term=1358408%2C9622251%2C9442414%2C7174880', '_blank')
})
@@ -162,97 +152,11 @@ describe('MultiFlatmapVuer', () => {
})
- })
-
- })
- it('change different species', () => {
- // const resourceSelectedSpy = cy.spy().as('resourceSelectedSpy')
- cy.get('@props').then((props) => {
- console.log('flatmapAPI', props)
- cy.mount(CypressComponentWrapper, {
- propsData: {
- component: 'MultiFlatmapVuer',
- props: props,
- },
- global: {
- plugins: setActivePinia(createPinia())
- }
- }).then((vm) => {
- cy.wrap(vm).as('vm')
- window.vm = vm
-
- }).get('@vue').should('exist')
-
- // Now that we have the vue wrapper, check that the ready event is fired
- .then(() => {
- cy.get('@vue').should(wrapper => {
- expect(wrapper.emitted('ready')).to.be.ok
- Cypress.multiFlatmapVuerWrapper = wrapper
- })
- })
-
- })
-
- //Check if multiflatmap is mounted correctly
- cy.get('.content-container').should('exist');
-
- // Check if flatmap emits ready event
- cy.get('@vue').should(wrapper => {
- expect(wrapper.emitted('ready')).to.be.ok
- }).then(() => {
- const multiFlatmapVuer = window.Cypress.multiFlatmapVuer
- const speciesList = [
- {
- name: 'Human Female',
- taxon: 'NCBITaxon:9606'
- },
- {
- name: 'Rat (NPO)',
- taxon: 'NCBITaxon:10116'
- },
- {
- name: 'Functional Connectivity',
- taxon: 'FunctionalConnectivity'
- }
- ]
-
- // Switching species
- const switchSpeciesAndTest = (speciesId, speciesTaxo) => {
- multiFlatmapVuer.setSpecies(
- speciesId,
- multiFlatmapVuer.state ? multiFlatmapVuer.state.state : undefined,
- 1
- )
- }
-
- // Human Female
- switchSpeciesAndTest(speciesList[0].name, speciesList[0].taxon)
- expect(multiFlatmapVuer.activeSpecies).to.eq(speciesList[0].name)
- cy.get('#maplibre-minimap > .maplibregl-canvas-container > .maplibregl-canvas').should('exist');
- cy.get('.maplibregl-map').should('exist');
- cy.get('.pathway-location').should('exist');
-
- cy.wait(8000)
-
- // Rat (NPO)
- switchSpeciesAndTest(speciesList[1].name, speciesList[1].taxon)
- expect(multiFlatmapVuer.activeSpecies).to.eq(speciesList[1].name)
- cy.get('#maplibre-minimap > .maplibregl-canvas-container > .maplibregl-canvas').should('exist');
- cy.get('.maplibregl-map').should('exist');
- cy.get('.pathway-location').should('exist');
-
- cy.wait(8000)
-
- // Functional Connectivity
- switchSpeciesAndTest(speciesList[2].name, speciesList[2].taxon)
- expect(multiFlatmapVuer.activeSpecies).to.eq(speciesList[2].name)
- cy.get('#maplibre-minimap > .maplibregl-canvas-container > .maplibregl-canvas').should('exist');
- cy.get('.maplibregl-map').should('exist');
- cy.get('.pathway-location').should('exist');
})
})
+
});
diff --git a/cypress/fixtures/MultiFlatmapProps.json b/cypress/fixtures/MultiFlatmapProps.json
index ba40acbf..6c5c38e4 100644
--- a/cypress/fixtures/MultiFlatmapProps.json
+++ b/cypress/fixtures/MultiFlatmapProps.json
@@ -4,22 +4,6 @@
"Test": {
"taxo": "NCBITaxon:1",
"displayWarning": true
- },
- "Human Female": {
- "taxo": "NCBITaxon:9606",
- "biologicalSex": "PATO:0000383",
- "iconClass": "mapicon-icon_human",
- "displayWarning": true
- },
- "Rat (NPO)": {
- "taxo": "NCBITaxon:10116",
- "iconClass": "mapicon-icon_rat",
- "displayWarning": true,
- "displayLatestChanges": true
- },
- "Functional Connectivity": {
- "taxo": "FunctionalConnectivity",
- "displayWarning": true
}
},
"displayCloseButton": false,
diff --git a/docs/.vitepress/config.ts b/docs/.vitepress/config.ts
index 110337dc..71a79c64 100644
--- a/docs/.vitepress/config.ts
+++ b/docs/.vitepress/config.ts
@@ -1,4 +1,3 @@
-import path from 'path'
import { defineConfig } from 'vitepress'
import Components from 'unplugin-vue-components/vite'
import { ElementPlusResolver } from 'unplugin-vue-components/resolvers'
@@ -69,11 +68,6 @@ export default defineConfig({
},
},
},
- resolve: {
- alias: {
- '@': path.resolve(__dirname, '../../src'),
- }
- },
plugins: [
Components({
// allow auto load markdown components under `./src/components/`
diff --git a/docs/demo-flatmapvuer.md b/docs/demo-flatmapvuer.md
index b9a5ca3c..fedcf7c3 100644
--- a/docs/demo-flatmapvuer.md
+++ b/docs/demo-flatmapvuer.md
@@ -13,15 +13,9 @@
@@ -364,8 +306,6 @@ body {
.options-button {
z-index:100;
position: absolute;
- left: 50%;
- transform: translateX(-50%);
}
.options-container {
diff --git a/src/components.d.ts b/src/components.d.ts
index 2799c294..ad6b3ead 100644
--- a/src/components.d.ts
+++ b/src/components.d.ts
@@ -7,6 +7,7 @@ export {}
declare module 'vue' {
export interface GlobalComponents {
+ AnnotationTool: typeof import('./components/AnnotationTool.vue')['default']
DynamicLegends: typeof import('./components/legends/DynamicLegends.vue')['default']
ElAutocomplete: typeof import('element-plus/es')['ElAutocomplete']
ElButton: typeof import('element-plus/es')['ElButton']
@@ -16,8 +17,13 @@ declare module 'vue' {
ElIcon: typeof import('element-plus/es')['ElIcon']
ElIconArrowDown: typeof import('@element-plus/icons-vue')['ArrowDown']
ElIconArrowLeft: typeof import('@element-plus/icons-vue')['ArrowLeft']
+ ElIconArrowUp: typeof import('@element-plus/icons-vue')['ArrowUp']
+ ElIconClose: typeof import('@element-plus/icons-vue')['Close']
+ ElIconEdit: typeof import('@element-plus/icons-vue')['Edit']
ElIconWarning: typeof import('@element-plus/icons-vue')['Warning']
ElIconWarningFilled: typeof import('@element-plus/icons-vue')['WarningFilled']
+ ElInput: typeof import('element-plus/es')['ElInput']
+ ElMain: typeof import('element-plus/es')['ElMain']
ElOption: typeof import('element-plus/es')['ElOption']
ElPopover: typeof import('element-plus/es')['ElPopover']
ElRadio: typeof import('element-plus/es')['ElRadio']
@@ -25,10 +31,19 @@ declare module 'vue' {
ElRow: typeof import('element-plus/es')['ElRow']
ElSelect: typeof import('element-plus/es')['ElSelect']
ElSwitch: typeof import('element-plus/es')['ElSwitch']
+ ElTag: typeof import('element-plus/es')['ElTag']
+ ElTree: typeof import('element-plus/es')['ElTree']
+ ExternalResourceCard: typeof import('./components/ExternalResourceCard.vue')['default']
FlatmapVuer: typeof import('./components/FlatmapVuer.vue')['default']
+ IframeImageDialog: typeof import('./components/IframeImageDialog.vue')['default']
+ ImageGalleryPopup: typeof import('./components/ImageGalleryPopup.vue')['default']
+ ImagePopup: typeof import('./components/imagePopup.vue')['default']
MultiFlatmapVuer: typeof import('./components/MultiFlatmapVuer.vue')['default']
+ ProvenancePopup: typeof import('./components/ProvenancePopup.vue')['default']
SelectionsGroup: typeof import('./components/SelectionsGroup.vue')['default']
SvgLegends: typeof import('./components/legends/SvgLegends.vue')['default']
+ Tooltip: typeof import('./components/Tooltip.vue')['default']
+ TreeControls: typeof import('./components/TreeControls.vue')['default']
}
export interface ComponentCustomProperties {
vLoading: typeof import('element-plus/es')['ElLoadingDirective']
diff --git a/src/components/AnnotationTool.vue b/src/components/AnnotationTool.vue
new file mode 100644
index 00000000..11083e7b
--- /dev/null
+++ b/src/components/AnnotationTool.vue
@@ -0,0 +1,446 @@
+
+
+
+
+ Feature Annotations
+
+
+
+ {{ label }}: {{ annotationEntry[key] }}
+
+
+
+ Hide previous submissions
+
+
+ Show previous {{ prevSubs.length }} submission(s)
+
+
+
+ Previous submissions:
+
+
+
+ {{ formatTime(sub.created) }}
+ {{ sub.creator.name }}
+
+
+ Evidence:
+
+ {{ evidence }}
+
+
+
+ Comment: {{ sub.body.comment }}
+
+
+
+
+
+
+
+
+
+ Suggest changes:
+
+
+ Evidvence:
+
+
+
+ {{ evidence[index] }}
+
+
+
+
+
+
+
+
+
+
+ {{ item }}
+
+
+
+
+
+
+
+ Comment:
+
+
+
+
+
+ Submit
+
+
+
+
+ {{ errorMessage }}
+
+
+
+
+
+
+
+
+
+
diff --git a/src/components/ExternalResourceCard.vue b/src/components/ExternalResourceCard.vue
new file mode 100644
index 00000000..569b0909
--- /dev/null
+++ b/src/components/ExternalResourceCard.vue
@@ -0,0 +1,107 @@
+
+
+
+
+
+ Open publications in pubmed
+
+
+
+
+
+
+
+
diff --git a/src/components/FlatmapVuer.vue b/src/components/FlatmapVuer.vue
index 0d471f09..13692097 100644
--- a/src/components/FlatmapVuer.vue
+++ b/src/components/FlatmapVuer.vue
@@ -17,25 +17,20 @@
placement="right"
popper-class="warning-popper flatmap-popper"
:teleported="false"
- :visible="hoverVisibilities[7].value"
+ :visible="hoverVisibilities[6].value"
ref="warningPopover"
>
-
This is a legacy map, you may view the latest map instead.
This map displays the connectivity of individual neurons.
Specifically, those which align with (parts of) the neuron
@@ -54,7 +49,7 @@ Please use `const` to assign meaningful names to them...
SCKAN .
-
+
This map displays the connectivity of neuron populations.
Specifically, those from the primarily rat-based
@@ -99,22 +94,21 @@ Please use `const` to assign meaningful names to them...
:teleported="false"
trigger="manual"
popper-class="warning-popper flatmap-popper"
- :visible="hoverVisibilities[8].value"
- ref="whatsNewPopover"
+ :visible="hoverVisibilities[7].value"
>
What's new?
- Neuron Connection mode
+ Network discovery mode
You can now view the network of neurons connected to a selected
neuron. This mode is located in the settings at the bottom right.
@@ -142,28 +136,6 @@ Please use `const` to assign meaningful names to them...
@@ -191,17 +162,16 @@ Please use `const` to assign meaningful names to them...
:teleported="false"
trigger="manual"
width="70"
- popper-class="flatmap-popper"
- :visible="hoverVisibilities[2].value"
- ref="zoomOutPopover"
+ popper-class="flatmap-popper popper-zoomout"
+ :visible="hoverVisibilities[1].value"
>
@@ -212,8 +182,7 @@ Please use `const` to assign meaningful names to them...
trigger="manual"
width="70"
popper-class="flatmap-popper"
- :visible="hoverVisibilities[3].value"
- ref="zoomFitPopover"
+ :visible="hoverVisibilities[2].value"
>
Fit to
@@ -225,8 +194,8 @@ Please use `const` to assign meaningful names to them...
icon="fitWindow"
class="icon-button fitWindow"
@click="resetView()"
- @mouseover="showTooltip(3)"
- @mouseout="hideTooltip(3)"
+ @mouseover="showToolitip(2)"
+ @mouseout="hideToolitip(2)"
/>
@@ -236,9 +205,8 @@ Please use `const` to assign meaningful names to them...
placement="right"
:teleported="false"
trigger="manual"
- :offset="-18"
popper-class="flatmap-popper"
- :visible="hoverVisibilities[6].value"
+ :visible="hoverVisibilities[4].value"
ref="checkBoxPopover"
>
@@ -254,43 +222,37 @@ Please use `const` to assign meaningful names to them...
v-popover:checkBoxPopover
>
-
Viewing Mode
-
-
-
- {{ item.name }}
-
- {{ item.name }}
-
-
-
-
- {{ viewingModes[viewingModeIndex].description}}
-
-
-
- Drawn By*
-
-
-
-
- {{ item }}
-
-
-
-
- Annotated By*
-
-
+
-
-
- {{ item }}
-
-
-
-
-
+
+ {{ item }}
+
+
+
+
Flight path display
@@ -557,12 +452,11 @@ Please use `const` to assign meaningful names to them...
>
@@ -580,19 +474,18 @@ Please use `const` to assign meaningful names to them...
@@ -603,26 +496,34 @@ Please use `const` to assign meaningful names to them...
class="tooltip"
v-show="tooltipDisplay"
:annotationEntry="annotationEntry"
- :tooltipEntry="tooltipEntry"
- :annotationDisplay="viewingMode === 'Annotation'"
- @annotation="commitAnnotationEvent"
+ :entry="tooltipEntry"
+ :tooltipType="tooltipType"
+ :galleryItems="galleryItems"
+ @viewImage="viewIframeImage"
+ />
+
+
+
diff --git a/src/components/ImageGalleryPopup.vue b/src/components/ImageGalleryPopup.vue
new file mode 100644
index 00000000..c25144c4
--- /dev/null
+++ b/src/components/ImageGalleryPopup.vue
@@ -0,0 +1,344 @@
+
+
+
+
+
+ Hide images
+ View images at this location (Gallery)
+
+
+
+ {{ species.name }} ({{ species.count }})
+
+
+
+
+
+ View images at this location (iFrame)
+
+
+
+
+
+
+
diff --git a/src/components/MultiFlatmapVuer.vue b/src/components/MultiFlatmapVuer.vue
index 8723f93b..4f28f2fd 100644
--- a/src/components/MultiFlatmapVuer.vue
+++ b/src/components/MultiFlatmapVuer.vue
@@ -6,9 +6,8 @@
content="Select a species"
placement="right"
trigger="manual"
- popper-class="flatmap-popper flatmap-teleport-popper right-popper"
- width="max-content"
- :visible="activateTooltipByIndex(0)"
+ popper-class="flatmap-popper right-popper"
+ :visible="helpMode"
:teleported="false"
ref="selectPopover"
>
@@ -56,9 +55,6 @@
@resource-selected="resourceSelected"
@ready="FlatmapReady"
@pan-zoom-callback="panZoomCallback"
- :connectivityInfoSidebar="connectivityInfoSidebar"
- @connectivity-info-open="onConnectivityInfoOpen"
- @connectivity-info-close="onConnectivityInfoClose"
@open-map="
/**
* This event is emitted when the user chooses a different map option
@@ -66,15 +62,8 @@
* @arg $event
*/
$emit('open-map', $event)"
- @pathway-selection-changed="onSelectionsDataChanged"
:minZoom="minZoom"
- :helpMode="activeSpecies == key && helpMode"
- :helpModeActiveItem="helpModeActiveItem"
- :helpModeDialog="helpModeDialog"
- :helpModeInitialIndex="-2"
- @help-mode-last-item="onHelpModeLastItem"
- @shown-tooltip="onTooltipShown"
- @shown-map-tooltip="onMapTooltipShown"
+ :helpMode="helpMode"
:renderAtMounted="renderAtMounted"
:displayMinimap="displayMinimap"
:showStarInLegend="showStarInLegend"
@@ -131,15 +120,6 @@ export default {
EventBus.on('onActionClick', (action) => {
this.resourceSelected(action)
})
- EventBus.on('open-pubmed-url', (url) => {
- /**
- * This event is emitted when the user clicks
- * on "Open publications in pubmed" button
- * from provenance popup.
- * @arg url
- */
- this.$emit('open-pubmed-url', url);
- });
},
methods: {
/**
@@ -264,15 +244,6 @@ export default {
*/
this.$emit('pan-zoom-callback', payload)
},
- onConnectivityInfoClose: function () {
- this.$emit('connectivity-info-close');
- },
- onConnectivityInfoOpen: function (entryData) {
- this.$emit('connectivity-info-open', entryData);
- },
- onSelectionsDataChanged: function (data) {
- this.$emit('pathway-selection-changed', data);
- },
/**
* @vuese
* Function to show popup on map.
@@ -478,45 +449,6 @@ export default {
})
}
},
- /**
- * @vuese
- * Function to activate help mode tooltip by item index number
- */
- activateTooltipByIndex: function (index) {
- return (
- index === this.helpModeActiveItem
- && this.helpMode
- );
- },
- /**
- * @vuese
- * Function to check the last item of help mode
- */
- onHelpModeLastItem: function (isLastItem) {
- if (isLastItem) {
- this.$emit('help-mode-last-item', true);
- }
- },
- /**
- * @vuese
- * Function to emit event after a tooltip is shown.
- */
- onTooltipShown: function () {
- /**
- * This event is emitted after a tooltip in Flatmap is shown.
- */
- this.$emit('shown-tooltip');
- },
- /**
- * @vuese
- * Function to emit event after a tooltip on the map is shown.
- */
- onMapTooltipShown: function () {
- /**
- * This event is emitted after a tooltip on Flatmap's map is shown.
- */
- this.$emit('shown-map-tooltip');
- },
},
props: {
/**
@@ -548,29 +480,6 @@ export default {
type: Boolean,
default: false,
},
- /**
- * The active item index of help mode.
- */
- helpModeActiveItem: {
- type: Number,
- default: 0,
- },
- /**
- * The option to use helpModeDialog.
- * On default, `false`, clicking help will show all tooltips.
- * If `true`, clicking help will show the help-mode-dialog.
- */
- helpModeDialog: {
- type: Boolean,
- default: false,
- },
- /**
- * The last item of help mode.
- */
- helpModeLastItem: {
- type: Boolean,
- default: false,
- },
/**
* The option to display minimap at the top-right corner of the map.
*/
@@ -706,14 +615,7 @@ export default {
disableUI: {
type: Boolean,
default: false,
- },
- /**
- * The option to show connectivity information in sidebar
- */
- connectivityInfoSidebar: {
- type: Boolean,
- default: false,
- },
+ }
},
data: function () {
return {
@@ -827,4 +729,4 @@ export default {
--el-color-primary: #8300BF;
}
-
+
\ No newline at end of file
diff --git a/src/components/ProvenancePopup.vue b/src/components/ProvenancePopup.vue
new file mode 100644
index 00000000..505da3e8
--- /dev/null
+++ b/src/components/ProvenancePopup.vue
@@ -0,0 +1,558 @@
+
+
+
+
{{ capitalise(entry.title) }}
+
+ {{ provSpeciesDescription }}
+
+
+
+ {{ entry.featureId }}
+
+
+
+ Hide images
+ View images at this location (Gallery)
+
+
+
+
+ View images at this location (iFrame)
+
+
+
+ Hide path information
+
+
+ Show path information
+
+
+
+ {{ entry.paths }}
+
+
+ Origin
+
+
+
+
+ Origin {{ originDescription }}
+
+
+
+
+
+ {{ capitalise(origin) }}
+
+
+
+ Explore origin data
+
+
+
+
Components
+
+ {{ capitalise(component) }}
+
+
+
+
+
+ Destination
+
+
+
+
+ Destination is where the axons terminate
+
+
+
+
+ {{ capitalise(destination) }}
+
+
+
+ Explore destination data
+
+
+
+
+ Search for data on components
+
+
+
+
+
+
+
+
+
diff --git a/src/components/SelectionsGroup.vue b/src/components/SelectionsGroup.vue
index f629e7be..e4ced880 100644
--- a/src/components/SelectionsGroup.vue
+++ b/src/components/SelectionsGroup.vue
@@ -2,21 +2,7 @@
- {{ title }}
-
-
-
-
- {{ helpMessage }}
-
-
+ {{ title }}
Display all
@@ -42,15 +27,11 @@
:key="item[identifierKey]"
:label="item[identifierKey]"
>
-
+
@@ -73,13 +54,9 @@
+
+
diff --git a/src/components/TreeControls.vue b/src/components/TreeControls.vue
new file mode 100644
index 00000000..83cb3626
--- /dev/null
+++ b/src/components/TreeControls.vue
@@ -0,0 +1,231 @@
+
+
+
+
+ Systems
+
+
+
+
+
+
+
+ {{ node.label }}
+
+
+
+
+
+
+
+
+
+
diff --git a/src/components/imagePopup.vue b/src/components/imagePopup.vue
new file mode 100644
index 00000000..d05e60aa
--- /dev/null
+++ b/src/components/imagePopup.vue
@@ -0,0 +1,421 @@
+
+
+ Image gallery baby!
+
+
+
+ Hide images
+ View images at this location (Gallery)
+
+
+
+
+ View images at this location (iFrame)
+
+
+
+
+
+
+
diff --git a/src/components/index.js b/src/components/index.js
index f36c8efc..649161ad 100644
--- a/src/components/index.js
+++ b/src/components/index.js
@@ -1,6 +1,7 @@
// The Vue build version to load with the `import` command
// (runtime-only or standalone) has been set in webpack.base.conf with an alias.
-import FlatmapVuer from "./FlatmapVuer.vue";
-import MultiFlatmapVuer from "./MultiFlatmapVuer.vue";
+import FlatmapVuer from './FlatmapVuer.vue'
+import MultiFlatmapVuer from './MultiFlatmapVuer.vue'
+import Tooltip from './Tooltip.vue'
-export { FlatmapVuer, MultiFlatmapVuer };
+export { FlatmapVuer, MultiFlatmapVuer, Tooltip}
diff --git a/src/icons/flatmap-marker.js b/src/icons/flatmap-marker.js
index 0bc232b7..44f4dd58 100644
--- a/src/icons/flatmap-marker.js
+++ b/src/icons/flatmap-marker.js
@@ -1,9 +1 @@
-export default ``
+export default ''
diff --git a/src/icons/imageThumbnail1.js b/src/icons/imageThumbnail1.js
new file mode 100644
index 00000000..b6dd6014
--- /dev/null
+++ b/src/icons/imageThumbnail1.js
@@ -0,0 +1 @@
+export default '' +
'Featured dataset marker ' +
+ 'Featured dataset marker ' +
' '
diff --git a/src/mixins/flatmapImageMixin.js b/src/mixins/flatmapImageMixin.js
new file mode 100644
index 00000000..257f5fb5
--- /dev/null
+++ b/src/mixins/flatmapImageMixin.js
@@ -0,0 +1,105 @@
+export default {
+ // Note that the setting store is included in MapContent.vue
+ methods: {
+ populateFlatmapWithImages: function (mapImp, images) {
+ let anatomyList = []
+ console.log('images in populateflatmap', images)
+ images.images.forEach((image) => {
+ if (image.value && image.value.length > 0)
+ image.value.forEach((image) => {
+ if (image.anatomy && image.anatomy.length > 0) {
+ image.anatomy.forEach((anatomy) => {
+ if (!anatomyList.includes(anatomy.curie)) {
+ anatomyList.push(anatomy.curie)
+ this.createImageThumbnailMarkerUrl(mapImp, anatomy.curie, image.thumbnail)
+ }
+ })
+ }
+ })
+ })
+ },
+ findImagesForAnatomy: function (images, anatomyToFind) {
+ let imageList = []
+ images.images.forEach((image) => {
+ if (image.value && image.value.length > 0)
+ image.value.forEach((image) => {
+ if (image.anatomy && image.anatomy.length > 0) {
+ image.anatomy.forEach((anatomy) => {
+ if (anatomy.curie === anatomyToFind) {
+ imageList.push(image)
+ }
+ })
+ }
+ })
+ })
+ return imageList
+ },
+ findImagesForSpeciesFromGalleryItems: function (galleryItems, speciesToFind) {
+ let imageList = []
+ galleryItems.forEach((image) => {
+ if (image.species && image.species.length > 0) {
+ image.species.forEach((species) => {
+ if (species.species && species.species.curie === speciesToFind) {
+ imageList.push(image)
+ }
+ })
+ }
+ })
+ return imageList
+ },
+ findAllSpeciesFromGalleryItems: function (galleryItems) {
+ let speciesList = [];
+ let speciesSet = new Set();
+
+ galleryItems.forEach((image) => {
+ if (image.species && image.species.length > 0) {
+ image.species.forEach((species) => {
+ if (species.species) {
+ let ispc = species.species;
+ if (!speciesSet.has(ispc.curie)) {
+ speciesSet.add(ispc.curie);
+ speciesList.push({ 'taxon': ispc.curie, 'name': ispc.name, 'count': 1});
+ } else {
+ speciesList.forEach((sp) => {
+ if (sp.taxon === ispc.curie) sp.count++;
+ });
+ }
+ }
+ });
+ }
+ });
+
+ return speciesList;
+ },
+ createImageThumbnailMarkerUrl: function (mapImp, id, image) {
+ return new Promise((resolve, reject) => {
+ // create the image element
+ let wrapperElement = document.createElement("div");
+
+ // download image:
+ let img = new Image();
+ img.src = image;
+ img.style = "height: auto;width: 50px;margin-right: 80px;"
+ img.onload = function() {
+ wrapperElement.appendChild(img);
+
+ // add it to the flatmap
+ const markerIdentifier = mapImp.addMarker(id, {
+ element: wrapperElement,
+ className: "highlight-marker",
+ cluster: false,
+ type: "image",
+ });
+
+ const marker = mapImp.addMarker(id);
+ resolve(marker);
+ };
+
+ img.onerror = function() {
+ reject(new Error("Failed to load image at " + image));
+ };
+ });
+ },
+ }
+}
+
\ No newline at end of file
diff --git a/src/services/flatmapQueries.js b/src/services/flatmapQueries.js
index 0192621a..9dd9bed4 100644
--- a/src/services/flatmapQueries.js
+++ b/src/services/flatmapQueries.js
@@ -222,35 +222,23 @@ let FlatmapQueries = function () {
this.origins = []
this.components = []
if (!keastIds || keastIds.length == 0) return
-
- let prom1 = this.queryForConnectivity(keastIds, signal) // This on returns a promise so dont need 'await'
- let prom2 = await this.pubmedQueryOnIds(eventData)
- let results = await Promise.all([prom1, prom2])
- return results
- }
-
- this.queryForConnectivity = function (keastIds, signal, processConnectivity=true) {
const data = { sql: this.buildConnectivitySqlStatement(keastIds) }
- const headers = {
- method: 'POST',
- headers: {
- 'Content-Type': 'application/json',
- },
- body: JSON.stringify(data),
- ...(signal ? { signal: signal } : {}), // add signal to header if it exists
- }
- return new Promise((resolve) => {
- fetch(`${this.flatmapApi}knowledge/query/`, headers)
+ let prom1 = new Promise((resolve) => {
+ fetch(`${this.flatmapApi}knowledge/query/`, {
+ method: 'POST',
+ headers: {
+ 'Content-Type': 'application/json',
+ },
+ body: JSON.stringify(data),
+ signal: signal,
+ })
.then((response) => response.json())
.then((data) => {
if (this.connectivityExists(data)) {
let connectivity = JSON.parse(data.values[0][0])
- if (processConnectivity) {
- this.processConnectivity(connectivity).then((processedConnectivity) => {
- resolve(processedConnectivity)
- })
- }
- else resolve(connectivity)
+ this.processConnectivity(connectivity).then(() => {
+ resolve(true)
+ })
} else {
resolve(false)
}
@@ -260,6 +248,9 @@ let FlatmapQueries = function () {
resolve(false)
})
})
+ let prom2 = await this.pubmedQueryOnIds(eventData)
+ let results = await Promise.all([prom1, prom2])
+ return results
}
this.connectivityExists = function (data) {
@@ -275,32 +266,7 @@ let FlatmapQueries = function () {
}
}
- // This function is used to determine if a node is a single node or a node with multiple children
- // Returns the id of the node if it is a single node, otherwise returns false
- this.findIfNodeIsSingle = function (node) {
- if (node.length === 1) { // If the node is in the form [id]
- console.error("Server returns a single node", node)
- return node[0]
- } else {
- if (node.length === 2 && node[1].length === 0) { // If the node is in the form [id, []]
- return node[0]
- } else {
- return false // If the node is in the form [id, [id1, id2]]
- }
- }
- }
-
this.createLabelFromNeuralNode = function (node, lookUp) {
-
- // Check if the node is a single node or a node with multiple children
- let nodeIsSingle = this.findIfNodeIsSingle(node)
-
- // Case where node is in the form [id]
- if (nodeIsSingle) {
- return lookUp[nodeIsSingle]
- }
-
- // Case where node is in the form [id, [id1 (,id2)]]
let label = lookUp[node[0]]
if (node.length === 2 && node[1].length > 0) {
node[1].forEach((n) => {
@@ -356,18 +322,7 @@ let FlatmapQueries = function () {
this.createLabelFromNeuralNode(c, lookUp)
)
this.flattenAndFindDatasets(components, axons, dendrites)
- resolve({
- ids: {
- axons: axons,
- dendrites: dendrites,
- components: components,
- },
- labels: {
- destinations: this.destinations,
- origins: this.origins,
- components: this.components,
- }
- })
+ resolve(true)
})
})
}
@@ -386,6 +341,29 @@ let FlatmapQueries = function () {
return found.flat()
}
+ this.findComponents = function (connectivity) {
+ let dnodes = connectivity.connectivity.flat() // get nodes from edgelist
+ let nodes = removeDuplicates(dnodes)
+
+ let found = []
+ let terminal = false
+ nodes.forEach((node) => {
+ terminal = false
+ // Check if the node is an destination or origin (note that they are labelled dendrite and axon as opposed to origin and destination)
+ if (inArray(connectivity.axons, node)) {
+ terminal = true
+ }
+ if (inArray(connectivity.dendrites, node)) {
+ terminal = true
+ }
+ if (!terminal) {
+ found.push(node)
+ }
+ })
+
+ return found
+ }
+
this.stripPMIDPrefix = function (pubmedId) {
return pubmedId.split(':')[1]
}
@@ -467,8 +445,7 @@ let FlatmapQueries = function () {
this.pubmedSearchUrl = function (ids) {
let url = 'https://pubmed.ncbi.nlm.nih.gov/?'
let params = new URLSearchParams()
- const decodedIDs = ids.map((id) => decodeURIComponent(id));
- params.append('term', decodedIDs);
+ params.append('term', ids)
return url + params.toString()
}
}
diff --git a/src/services/scicrunchMixin.js b/src/services/scicrunchMixin.js
new file mode 100644
index 00000000..b9c21680
--- /dev/null
+++ b/src/services/scicrunchMixin.js
@@ -0,0 +1,89 @@
+/* eslint-disable no-alert, no-console */
+const imageQuery = '"*jp2* OR *vnd.ome.xml* OR *jpx*"';
+
+const generateShareLink = (datasetId, datasetVersion, filePath) => {
+ const prefix = 'https://sparc.biolucida.net';
+ return `${prefix}/dataviewer?datasetId=${datasetId}&version=${datasetVersion}&path=files/${filePath}`;
+}
+
+const getBiolucidaInfo = async function (sparcAPI, datasetId) {
+ return new Promise((resolve, reject) => {
+ const endpoint = `${sparcAPI}/image_search/${datasetId}`
+ fetch(endpoint)
+ .then((response) => response.json())
+ .then((data) => {
+ if (data.status == 'success') resolve(data);
+ })
+ })
+}
+
+export default {
+ // Note that the setting store is included in MapContent.vue
+ methods: {
+ getThumbnailURL: function(thumbnailId) {
+ console.log('thumbnail url', `${this.sparcAPI}/thumbnail/${thumbnailId}`)
+ return `${this.sparcAPI}/thumbnail/${thumbnailId}`
+ },
+
+ getSegmentationThumbnailURL: function(datasetId, datasetVersion, filePath, s3uri) {
+ console.log('thumbnail url', `${this.sparcAPI}/thumbnail/neurolucida?datasetId=${datasetId}&version=${datasetVersion}&path=files/${filePath}&s3uri=${s3uri}`)
+ return `${this.sparcAPI}/thumbnail/neurolucida?datasetId=${datasetId}&version=${datasetVersion}&path=files/${filePath}&s3uri=${s3uri}`;
+ },
+ getImagesFromScicrunch: async function () {
+ try {
+ const response = await fetch(`${this.sparcAPI}/multiple_dataset_info/using_multiple_mimetype/?${new URLSearchParams({q: imageQuery})}`);
+ const data = await response.json();
+ console.log('number of hits:', data.numberOfHits);
+ if (data.numberOfHits >= 1) {
+ let images = await this.processResults(data.results);
+ return {success: true, images: images};
+ }
+ return {success: false};
+ } catch (error) {
+ console.error('Error:', error);
+ return {success: false};
+ }
+ },
+
+ processResults: async function (results) {
+ try {
+ let images = [];
+ const dataType = 'segmentation';
+ console.log('starting promise list')
+ let promiseList = results.map(async (result, i) => {
+ if (i !== 8){
+ const datasetId = result.dataset_identifier;
+ const datasetVersion = result.dataset_version;
+ const s3uri = result.s3uri;
+ const biolucidaInfo = await getBiolucidaInfo(this.sparcAPI, datasetId);
+ return biolucidaInfo.dataset_images.map(bioImage => {
+ return {
+ resource: {
+ share_link: bioImage.share_link,
+ },
+ title: 'Image',
+ anatomy: result.organs,
+ species: result.organisms,
+ datasetId: datasetId,
+ datasetVersion: datasetVersion,
+ link: bioImage.share_link,
+ s3uri: s3uri,
+ type: dataType,
+ thumbnail: bioImage.thumbnail_url,
+ };
+ });}
+ });
+ console.log('promiseList:', promiseList);
+ let biolucidaInfos = await Promise.allSettled(promiseList);
+ images = biolucidaInfos.flat();
+ console.log('biolucidaInfos:', biolucidaInfos);
+ console.log('finished!')
+ return images;
+ } catch (error) {
+ console.error('Error:', error);
+ return [];
+ }
+ }
+ }
+}
+
\ No newline at end of file
diff --git a/vite.config.js b/vite.config.js
index 758f85e8..0023cef2 100644
--- a/vite.config.js
+++ b/vite.config.js
@@ -50,12 +50,11 @@ export default defineConfig(({ command, mode }) => {
fileName: 'flatmapvuer',
},
rollupOptions: {
- external: ["vue", "@abi-software/svg-sprite", "@abi-software/map-utilities"],
+ external: ["vue", "@abi-software/svg-sprite"],
output: {
globals: {
vue: "Vue",
- "@abi-software/svg-sprite": "@abi-software/svg-sprite",
- "@abi-software/map-utilities": "@abi-software/map-utilities"
+ "@abi-software/svg-sprite": "@abi-software/svg-sprite"
},
},
},
'
\ No newline at end of file
diff --git a/src/icons/imageThumbnail2.js b/src/icons/imageThumbnail2.js
new file mode 100644
index 00000000..32771fe5
--- /dev/null
+++ b/src/icons/imageThumbnail2.js
@@ -0,0 +1 @@
+export default '
'
\ No newline at end of file
diff --git a/src/icons/imageThumbnail3.js b/src/icons/imageThumbnail3.js
new file mode 100644
index 00000000..5f2ca2da
--- /dev/null
+++ b/src/icons/imageThumbnail3.js
@@ -0,0 +1 @@
+export default '
'
\ No newline at end of file
diff --git a/src/icons/yellowstar.js b/src/icons/yellowstar.js
index 24ad1e58..3ca279fe 100644
--- a/src/icons/yellowstar.js
+++ b/src/icons/yellowstar.js
@@ -1,5 +1,5 @@
export default ''
diff --git a/src/mixins/flatmapImageMixin.js b/src/mixins/flatmapImageMixin.js
new file mode 100644
index 00000000..257f5fb5
--- /dev/null
+++ b/src/mixins/flatmapImageMixin.js
@@ -0,0 +1,105 @@
+export default {
+ // Note that the setting store is included in MapContent.vue
+ methods: {
+ populateFlatmapWithImages: function (mapImp, images) {
+ let anatomyList = []
+ console.log('images in populateflatmap', images)
+ images.images.forEach((image) => {
+ if (image.value && image.value.length > 0)
+ image.value.forEach((image) => {
+ if (image.anatomy && image.anatomy.length > 0) {
+ image.anatomy.forEach((anatomy) => {
+ if (!anatomyList.includes(anatomy.curie)) {
+ anatomyList.push(anatomy.curie)
+ this.createImageThumbnailMarkerUrl(mapImp, anatomy.curie, image.thumbnail)
+ }
+ })
+ }
+ })
+ })
+ },
+ findImagesForAnatomy: function (images, anatomyToFind) {
+ let imageList = []
+ images.images.forEach((image) => {
+ if (image.value && image.value.length > 0)
+ image.value.forEach((image) => {
+ if (image.anatomy && image.anatomy.length > 0) {
+ image.anatomy.forEach((anatomy) => {
+ if (anatomy.curie === anatomyToFind) {
+ imageList.push(image)
+ }
+ })
+ }
+ })
+ })
+ return imageList
+ },
+ findImagesForSpeciesFromGalleryItems: function (galleryItems, speciesToFind) {
+ let imageList = []
+ galleryItems.forEach((image) => {
+ if (image.species && image.species.length > 0) {
+ image.species.forEach((species) => {
+ if (species.species && species.species.curie === speciesToFind) {
+ imageList.push(image)
+ }
+ })
+ }
+ })
+ return imageList
+ },
+ findAllSpeciesFromGalleryItems: function (galleryItems) {
+ let speciesList = [];
+ let speciesSet = new Set();
+
+ galleryItems.forEach((image) => {
+ if (image.species && image.species.length > 0) {
+ image.species.forEach((species) => {
+ if (species.species) {
+ let ispc = species.species;
+ if (!speciesSet.has(ispc.curie)) {
+ speciesSet.add(ispc.curie);
+ speciesList.push({ 'taxon': ispc.curie, 'name': ispc.name, 'count': 1});
+ } else {
+ speciesList.forEach((sp) => {
+ if (sp.taxon === ispc.curie) sp.count++;
+ });
+ }
+ }
+ });
+ }
+ });
+
+ return speciesList;
+ },
+ createImageThumbnailMarkerUrl: function (mapImp, id, image) {
+ return new Promise((resolve, reject) => {
+ // create the image element
+ let wrapperElement = document.createElement("div");
+
+ // download image:
+ let img = new Image();
+ img.src = image;
+ img.style = "height: auto;width: 50px;margin-right: 80px;"
+ img.onload = function() {
+ wrapperElement.appendChild(img);
+
+ // add it to the flatmap
+ const markerIdentifier = mapImp.addMarker(id, {
+ element: wrapperElement,
+ className: "highlight-marker",
+ cluster: false,
+ type: "image",
+ });
+
+ const marker = mapImp.addMarker(id);
+ resolve(marker);
+ };
+
+ img.onerror = function() {
+ reject(new Error("Failed to load image at " + image));
+ };
+ });
+ },
+ }
+}
+
\ No newline at end of file
diff --git a/src/services/flatmapQueries.js b/src/services/flatmapQueries.js
index 0192621a..9dd9bed4 100644
--- a/src/services/flatmapQueries.js
+++ b/src/services/flatmapQueries.js
@@ -222,35 +222,23 @@ let FlatmapQueries = function () {
this.origins = []
this.components = []
if (!keastIds || keastIds.length == 0) return
-
- let prom1 = this.queryForConnectivity(keastIds, signal) // This on returns a promise so dont need 'await'
- let prom2 = await this.pubmedQueryOnIds(eventData)
- let results = await Promise.all([prom1, prom2])
- return results
- }
-
- this.queryForConnectivity = function (keastIds, signal, processConnectivity=true) {
const data = { sql: this.buildConnectivitySqlStatement(keastIds) }
- const headers = {
- method: 'POST',
- headers: {
- 'Content-Type': 'application/json',
- },
- body: JSON.stringify(data),
- ...(signal ? { signal: signal } : {}), // add signal to header if it exists
- }
- return new Promise((resolve) => {
- fetch(`${this.flatmapApi}knowledge/query/`, headers)
+ let prom1 = new Promise((resolve) => {
+ fetch(`${this.flatmapApi}knowledge/query/`, {
+ method: 'POST',
+ headers: {
+ 'Content-Type': 'application/json',
+ },
+ body: JSON.stringify(data),
+ signal: signal,
+ })
.then((response) => response.json())
.then((data) => {
if (this.connectivityExists(data)) {
let connectivity = JSON.parse(data.values[0][0])
- if (processConnectivity) {
- this.processConnectivity(connectivity).then((processedConnectivity) => {
- resolve(processedConnectivity)
- })
- }
- else resolve(connectivity)
+ this.processConnectivity(connectivity).then(() => {
+ resolve(true)
+ })
} else {
resolve(false)
}
@@ -260,6 +248,9 @@ let FlatmapQueries = function () {
resolve(false)
})
})
+ let prom2 = await this.pubmedQueryOnIds(eventData)
+ let results = await Promise.all([prom1, prom2])
+ return results
}
this.connectivityExists = function (data) {
@@ -275,32 +266,7 @@ let FlatmapQueries = function () {
}
}
- // This function is used to determine if a node is a single node or a node with multiple children
- // Returns the id of the node if it is a single node, otherwise returns false
- this.findIfNodeIsSingle = function (node) {
- if (node.length === 1) { // If the node is in the form [id]
- console.error("Server returns a single node", node)
- return node[0]
- } else {
- if (node.length === 2 && node[1].length === 0) { // If the node is in the form [id, []]
- return node[0]
- } else {
- return false // If the node is in the form [id, [id1, id2]]
- }
- }
- }
-
this.createLabelFromNeuralNode = function (node, lookUp) {
-
- // Check if the node is a single node or a node with multiple children
- let nodeIsSingle = this.findIfNodeIsSingle(node)
-
- // Case where node is in the form [id]
- if (nodeIsSingle) {
- return lookUp[nodeIsSingle]
- }
-
- // Case where node is in the form [id, [id1 (,id2)]]
let label = lookUp[node[0]]
if (node.length === 2 && node[1].length > 0) {
node[1].forEach((n) => {
@@ -356,18 +322,7 @@ let FlatmapQueries = function () {
this.createLabelFromNeuralNode(c, lookUp)
)
this.flattenAndFindDatasets(components, axons, dendrites)
- resolve({
- ids: {
- axons: axons,
- dendrites: dendrites,
- components: components,
- },
- labels: {
- destinations: this.destinations,
- origins: this.origins,
- components: this.components,
- }
- })
+ resolve(true)
})
})
}
@@ -386,6 +341,29 @@ let FlatmapQueries = function () {
return found.flat()
}
+ this.findComponents = function (connectivity) {
+ let dnodes = connectivity.connectivity.flat() // get nodes from edgelist
+ let nodes = removeDuplicates(dnodes)
+
+ let found = []
+ let terminal = false
+ nodes.forEach((node) => {
+ terminal = false
+ // Check if the node is an destination or origin (note that they are labelled dendrite and axon as opposed to origin and destination)
+ if (inArray(connectivity.axons, node)) {
+ terminal = true
+ }
+ if (inArray(connectivity.dendrites, node)) {
+ terminal = true
+ }
+ if (!terminal) {
+ found.push(node)
+ }
+ })
+
+ return found
+ }
+
this.stripPMIDPrefix = function (pubmedId) {
return pubmedId.split(':')[1]
}
@@ -467,8 +445,7 @@ let FlatmapQueries = function () {
this.pubmedSearchUrl = function (ids) {
let url = 'https://pubmed.ncbi.nlm.nih.gov/?'
let params = new URLSearchParams()
- const decodedIDs = ids.map((id) => decodeURIComponent(id));
- params.append('term', decodedIDs);
+ params.append('term', ids)
return url + params.toString()
}
}
diff --git a/src/services/scicrunchMixin.js b/src/services/scicrunchMixin.js
new file mode 100644
index 00000000..b9c21680
--- /dev/null
+++ b/src/services/scicrunchMixin.js
@@ -0,0 +1,89 @@
+/* eslint-disable no-alert, no-console */
+const imageQuery = '"*jp2* OR *vnd.ome.xml* OR *jpx*"';
+
+const generateShareLink = (datasetId, datasetVersion, filePath) => {
+ const prefix = 'https://sparc.biolucida.net';
+ return `${prefix}/dataviewer?datasetId=${datasetId}&version=${datasetVersion}&path=files/${filePath}`;
+}
+
+const getBiolucidaInfo = async function (sparcAPI, datasetId) {
+ return new Promise((resolve, reject) => {
+ const endpoint = `${sparcAPI}/image_search/${datasetId}`
+ fetch(endpoint)
+ .then((response) => response.json())
+ .then((data) => {
+ if (data.status == 'success') resolve(data);
+ })
+ })
+}
+
+export default {
+ // Note that the setting store is included in MapContent.vue
+ methods: {
+ getThumbnailURL: function(thumbnailId) {
+ console.log('thumbnail url', `${this.sparcAPI}/thumbnail/${thumbnailId}`)
+ return `${this.sparcAPI}/thumbnail/${thumbnailId}`
+ },
+
+ getSegmentationThumbnailURL: function(datasetId, datasetVersion, filePath, s3uri) {
+ console.log('thumbnail url', `${this.sparcAPI}/thumbnail/neurolucida?datasetId=${datasetId}&version=${datasetVersion}&path=files/${filePath}&s3uri=${s3uri}`)
+ return `${this.sparcAPI}/thumbnail/neurolucida?datasetId=${datasetId}&version=${datasetVersion}&path=files/${filePath}&s3uri=${s3uri}`;
+ },
+ getImagesFromScicrunch: async function () {
+ try {
+ const response = await fetch(`${this.sparcAPI}/multiple_dataset_info/using_multiple_mimetype/?${new URLSearchParams({q: imageQuery})}`);
+ const data = await response.json();
+ console.log('number of hits:', data.numberOfHits);
+ if (data.numberOfHits >= 1) {
+ let images = await this.processResults(data.results);
+ return {success: true, images: images};
+ }
+ return {success: false};
+ } catch (error) {
+ console.error('Error:', error);
+ return {success: false};
+ }
+ },
+
+ processResults: async function (results) {
+ try {
+ let images = [];
+ const dataType = 'segmentation';
+ console.log('starting promise list')
+ let promiseList = results.map(async (result, i) => {
+ if (i !== 8){
+ const datasetId = result.dataset_identifier;
+ const datasetVersion = result.dataset_version;
+ const s3uri = result.s3uri;
+ const biolucidaInfo = await getBiolucidaInfo(this.sparcAPI, datasetId);
+ return biolucidaInfo.dataset_images.map(bioImage => {
+ return {
+ resource: {
+ share_link: bioImage.share_link,
+ },
+ title: 'Image',
+ anatomy: result.organs,
+ species: result.organisms,
+ datasetId: datasetId,
+ datasetVersion: datasetVersion,
+ link: bioImage.share_link,
+ s3uri: s3uri,
+ type: dataType,
+ thumbnail: bioImage.thumbnail_url,
+ };
+ });}
+ });
+ console.log('promiseList:', promiseList);
+ let biolucidaInfos = await Promise.allSettled(promiseList);
+ images = biolucidaInfos.flat();
+ console.log('biolucidaInfos:', biolucidaInfos);
+ console.log('finished!')
+ return images;
+ } catch (error) {
+ console.error('Error:', error);
+ return [];
+ }
+ }
+ }
+}
+
\ No newline at end of file
diff --git a/vite.config.js b/vite.config.js
index 758f85e8..0023cef2 100644
--- a/vite.config.js
+++ b/vite.config.js
@@ -50,12 +50,11 @@ export default defineConfig(({ command, mode }) => {
fileName: 'flatmapvuer',
},
rollupOptions: {
- external: ["vue", "@abi-software/svg-sprite", "@abi-software/map-utilities"],
+ external: ["vue", "@abi-software/svg-sprite"],
output: {
globals: {
vue: "Vue",
- "@abi-software/svg-sprite": "@abi-software/svg-sprite",
- "@abi-software/map-utilities": "@abi-software/map-utilities"
+ "@abi-software/svg-sprite": "@abi-software/svg-sprite"
},
},
},