diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 99591e561..33da97746 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -191,3 +191,11 @@ jobs: fi - name: Stop VFB server run: docker stop testServer + - uses: actions/upload-artifact@v2 + if: ${{ failure() }} + with: + name: test_fails + path: | + tests/jest/vfb/snapshots/*/*/__diff_output__/*.png + tests/jest/vfb/snapshots/*/*/*.png + retention-days: 5 diff --git a/actions/.Rhistory b/actions/.Rhistory new file mode 100644 index 000000000..e69de29bb diff --git a/components/configuration/VFBMain/searchConfiguration.js b/components/configuration/VFBMain/searchConfiguration.js index e0eea803d..859ef3327 100644 --- a/components/configuration/VFBMain/searchConfiguration.js +++ b/components/configuration/VFBMain/searchConfiguration.js @@ -95,7 +95,7 @@ var datasourceConfiguration = { "start": "0", "pf":"true", "fq": [ - "shortform_autosuggest:VFB* OR shortform_autosuggest:FB*" + "shortform_autosuggest:VFB* OR shortform_autosuggest:FB* OR facets_annotation:DataSet OR facets_annotation:pub" ], "rows": "100", "wt": "json", diff --git a/components/configuration/VFBOverview/quickHelp.json b/components/configuration/VFBOverview/quickHelp.json index 75d0ade4d..7b7d0b240 100644 --- a/components/configuration/VFBOverview/quickHelp.json +++ b/components/configuration/VFBOverview/quickHelp.json @@ -87,5 +87,43 @@ "icon" : "fa fa-quora", "label" : "Run term related queries" }] + },{ + "title": "This is the Term Context tab", + "image" : "geppetto/build/term-context.png", + "instructions": [{ + "icon" : "", + "label" : "Term Context displays grapical information on the currently selected term's location or classification" + },{ + "icon" : "fa fa-home", + "label" : "Home resets your view" + },{ + "icon" : "fa fa-search-plus", + "label" : "Use the zoom icons or scroll with the mouse to zoom in/out" + },{ + "icon" : "fa fa-refresh", + "label" : "Click to refresh to the current focus term" + },{ + "icon" : "fa fa-bars", + "label" : "Select either the location or the classification for the current term" + }] + },{ + "title": "This is the Circuit Browser tab", + "image" : "geppetto/build/circuit1.png", + "instructions": [{ + "icon" : "", + "label" : "The Circuit Browser allows you to find the strongest paths from one neuron (the source neuron) to another (the target neuron). The 'strongest' paths are the shortest/highest weighted paths. Paths are arranged from the 'strongest' at the bottom to the 'weakest' at the top. A detailed explanation for the algorithm used to determine path strengths can be found under help." + },{ + "icon" : "fa fa-dot-circle-o", + "label" : "Search for the source neuron to start from (Note: query is directional)" + },{ + "icon" : "fa fa-map-marker", + "label" : "Search for the target neuron" + },{ + "icon" : "fa fa-arrows-h", + "label" : "Maximum number of paths to return (only the 'strongest' paths will be returned)" + },{ + "icon" : "fa fa-balance-scale", + "label" : "A minimum weight for the synapse count of each connection can be applied, paths containing individual connections below this minimum will not be returned" + }] }] } diff --git a/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js b/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js index a85df3499..42d1711c6 100644 --- a/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js +++ b/components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js @@ -239,7 +239,7 @@ var toolbarMenu = { }, { label: "Term Context", - icon: "fas fa-project-diagram", + icon: "fa fa-sitemap", action: { handlerAction: "UIElementHandler", parameters: ["graphVisible"] @@ -247,7 +247,7 @@ var toolbarMenu = { }, { label: "Circuit Browser", - icon: "fa fa-cogs", + icon: "fa fa-connectdevelop", action: { handlerAction: "UIElementHandler", parameters: ["circuitBrowserVisible"] @@ -321,22 +321,85 @@ var toolbarMenu = { } }, { - label: "Adult VNC (FANC)", + label: "Adult VNC", icon: "", - trailerIcon: "fa fa-external-link", + position: "right-start", action: { - handlerAction: "openNewTab", - parameters: ["https://fanc.catmaid.virtualflybrain.org/?pid=1&zp=55260&yp=512482.5999999994&xp=173092.19999999998&tool=tracingtool&sid0=1&s0=9&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22publication%22%7D%7D,%200.6)"] - } + handlerAction: "submenu", + parameters: ["undefinedAction"] + }, + list: [ + { + label: "Adult VNC (FANC)", + icon: "", + trailerIcon: "fa fa-external-link", + action: { + handlerAction: "openNewTab", + parameters: ["https://fanc.catmaid.virtualflybrain.org/?pid=1&zp=55260&yp=512482.5999999994&xp=173092.19999999998&tool=tracingtool&sid0=1&s0=9&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22publication%22%7D%7D,%200.6)"] + } + }, + { + label: "Adult VNC (FANC) Aligned to JRC2018 VNC Female", + icon: "", + trailerIcon: "fa fa-external-link", + action: { + handlerAction: "openNewTab", + parameters: ["https://fanc.catmaid.virtualflybrain.org/?pid=2&zp=70800&yp=268000&xp=131600&tool=tracingtool&sid0=3&s0=1&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22publication%22%7D%7D,%200.6)"] + } + } + ] }, { - label: "Larval (L1EM)", + label: "Larval", icon: "", - trailerIcon: "fa fa-external-link", + position: "right-start", action: { - handlerAction: "openNewTab", - parameters: ["https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=108250&yp=82961.59999999999&xp=54210.799999999996&tool=tracingtool&sid0=1&s0=2.4999999999999996&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)"] - } + handlerAction: "submenu", + parameters: ["undefinedAction"] + }, + list: [ + { + label: "Larval (L1EM)", + icon: "", + trailerIcon: "fa fa-external-link", + action: { + handlerAction: "openNewTab", + parameters: ["https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=108250&yp=82961.59999999999&xp=54210.799999999996&tool=tracingtool&sid0=1&s0=2.4999999999999996&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)"] + } + }, + { + label: "Larval (L3VNC)", + icon: "", + action: { + handlerAction: "openNewTab", + parameters: ["https://l3vnc.catmaid.virtualflybrain.org/?pid=2&zp=0&yp=53578.49999999999&xp=71242.5&tool=tracingtool&sid0=2&s0=6&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)"] + } + }, + { + label: "Larval (ABD1.5)", + icon: "", + action: { + handlerAction: "openNewTab", + parameters: ["https://abd1.5.catmaid.virtualflybrain.org/?pid=1&zp=10485&yp=40560.65722061269&xp=42396.0789533435&tool=tracingtool&sid0=1&s0=4.5&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)"] + } + }, + { + label: "Larval Mutant (IAV-Robo)", + icon: "", + action: { + handlerAction: "openNewTab", + parameters: ["https://iav-robo.catmaid.virtualflybrain.org/?pid=1&zp=18360&yp=25383.555362060197&xp=40676.497110038756&tool=tracingtool&sid0=1&s0=4&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)"] + } + }, + { + label: "Larval Mutant (IAV-TNT)", + icon: "", + action: { + handlerAction: "openNewTab", + parameters: ["https://iav-tnt.catmaid.virtualflybrain.org/?pid=2&zp=0&yp=28633&xp=45094.6&sid0=2&s0=4&tool=tracingtool&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)"] + } + } + ] } ] }, @@ -372,6 +435,38 @@ var toolbarMenu = { handlerAction: "openNewTab", parameters: ["https://l1em.catmaid.virtualflybrain.org/apis/"] } + }, + { + label: "Larval (L3VNC)", + icon: "", + action: { + handlerAction: "openNewTab", + parameters: ["https://l3vnc.catmaid.virtualflybrain.org/apis/"] + } + }, + { + label: "Larval (ABD1.5)", + icon: "", + action: { + handlerAction: "openNewTab", + parameters: ["https://abd1.5.catmaid.virtualflybrain.org/apis/"] + } + }, + { + label: "Larval Mutant (IAV-Robo)", + icon: "", + action: { + handlerAction: "openNewTab", + parameters: ["https://iav-robo.catmaid.virtualflybrain.org/apis/"] + } + }, + { + label: "Larval Mutant (IAV-TNT)", + icon: "", + action: { + handlerAction: "openNewTab", + parameters: ["https://iav-tnt.catmaid.virtualflybrain.org/apis/"] + } } ] } @@ -384,7 +479,16 @@ var toolbarMenu = { position: "right-start", list: [ { - label: "Python (PyPi)", + label: "VFB_connect: A library for querying VFB", + icon: "", + trailerIcon: "fa fa-external-link", + action: { + handlerAction: "openNewTab", + parameters: ["https://vfb-connect.readthedocs.io/"] + } + }, + { + label: "Python (PiPy)", icon: "", trailerIcon: "fa fa-external-link", action: { @@ -657,25 +761,32 @@ var toolbarMenu = { list: [ { label: "F.A.Q.", - icon: "", - trailerIcon: "fa fa-external-link", + icon: "fa fa-comments-o", action: { handlerAction: "openNewTab", - parameters: ["https://groups.google.com/forum/embed/?place=forum/vfb-suport#!forum/vfb-suport"] + parameters: ["https://groups.google.com/g/vfb-suport"] } }, { label: "Support Forum", - icon: "", + icon: "fa fa-medkit", + action: { + handlerAction: "openNewTab", + parameters: ["https://groups.google.com/g/vfb-suport"] + } + }, + { + label: "Circuit Browser Query (Shortest Weighted Path Algorithm)", + icon: "fa fa-connectdevelop", trailerIcon: "fa fa-external-link", action: { handlerAction: "openNewTab", - parameters: ["https://groups.google.com/forum/#!forum/vfb-suport"] + parameters: ["https://github.com/VirtualFlyBrain/graph_queries/blob/main/weighted_path.md"] } }, { label: "Report an issue", - icon: "", + icon: "fa fa-bug", action: { handlerAction: "clickFeedback", parameters: [] diff --git a/images/circuit1.png b/images/circuit1.png new file mode 100644 index 000000000..6093780a9 Binary files /dev/null and b/images/circuit1.png differ diff --git a/images/term-context.png b/images/term-context.png new file mode 100644 index 000000000..27c0c2400 Binary files /dev/null and b/images/term-context.png differ diff --git a/tests/jest/vfb/batch1/.Rhistory b/tests/jest/vfb/batch1/.Rhistory new file mode 100644 index 000000000..e69de29bb diff --git a/tests/jest/vfb/batch1/menu-component-tests.js b/tests/jest/vfb/batch1/menu-component-tests.js index 9f65e6a63..0c256e321 100644 --- a/tests/jest/vfb/batch1/menu-component-tests.js +++ b/tests/jest/vfb/batch1/menu-component-tests.js @@ -105,7 +105,7 @@ describe('VFB Menu Component Tests', () => { await wait4selector(page, "ul.MuiList-root", { visible: true, timeout : 120000 }) // Check there's four elements in the drop down menu of 'Help' const dropDownMenuItems = await page.evaluate(async () => document.getElementsByClassName("MuiListItem-root").length); - expect(dropDownMenuItems).toEqual(4); + expect(dropDownMenuItems).toEqual(5); }) it('Help Modal FAQ Tab Opened', async () => { diff --git a/tests/jest/vfb/snapshots/term-context/medulla/term-context-tests-js-vfb-term-context-component-tests-add-medulla-snapshot-comparison-of-term-context-after-sync-trigger-graph-displays-medulla-1-snap.png b/tests/jest/vfb/snapshots/term-context/medulla/term-context-tests-js-vfb-term-context-component-tests-add-medulla-snapshot-comparison-of-term-context-after-sync-trigger-graph-displays-medulla-1-snap.png index 4d998c3c1..3ba5c2496 100644 Binary files a/tests/jest/vfb/snapshots/term-context/medulla/term-context-tests-js-vfb-term-context-component-tests-add-medulla-snapshot-comparison-of-term-context-after-sync-trigger-graph-displays-medulla-1-snap.png and b/tests/jest/vfb/snapshots/term-context/medulla/term-context-tests-js-vfb-term-context-component-tests-add-medulla-snapshot-comparison-of-term-context-after-sync-trigger-graph-displays-medulla-1-snap.png differ