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Merge pull request #1196 from VirtualFlyBrain/alpha
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Fine tuning for release
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@Robbie1977
Robbie1977 authored Oct 14, 2021
2 parents d95e877 + c98acd7 commit 3df00b4
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Showing 10 changed files with 178 additions and 21 deletions.
8 changes: 8 additions & 0 deletions .github/workflows/main.yml
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Expand Up @@ -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
Empty file added actions/.Rhistory
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2 changes: 1 addition & 1 deletion components/configuration/VFBMain/searchConfiguration.js
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Expand Up @@ -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",
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38 changes: 38 additions & 0 deletions components/configuration/VFBOverview/quickHelp.json
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Expand Up @@ -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"
}]
}]
}
149 changes: 130 additions & 19 deletions components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js
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Expand Up @@ -239,15 +239,15 @@ var toolbarMenu = {
},
{
label: "Term Context",
icon: "fas fa-project-diagram",
icon: "fa fa-sitemap",
action: {
handlerAction: "UIElementHandler",
parameters: ["graphVisible"]
}
},
{
label: "Circuit Browser",
icon: "fa fa-cogs",
icon: "fa fa-connectdevelop",
action: {
handlerAction: "UIElementHandler",
parameters: ["circuitBrowserVisible"]
Expand Down Expand Up @@ -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)"]
}
}
]
}
]
},
Expand Down Expand Up @@ -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/"]
}
}
]
}
Expand All @@ -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: {
Expand Down Expand Up @@ -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: []
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Empty file added tests/jest/vfb/batch1/.Rhistory
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2 changes: 1 addition & 1 deletion tests/jest/vfb/batch1/menu-component-tests.js
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Expand Up @@ -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 () => {
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