sync: development with development-sync-356b

.github/workflows/main.yml

@@ -26,8 +26,8 @@ jobs:
       # Decide based on branch which servers to use
       - name: Pass branch
         id: branch
-        run: echo "::set-output name=value::${GITHUB_REF#refs/heads/}";
-            echo "::set-output name=clean::$(echo ${GITHUB_REF#refs/heads/} | sed 's@[/\\]@-@g')";
+        run: echo "::set-output name=value::$(echo ${GITHUB_REF} | sed 's@refs/heads/@@g' | sed 's@refs/tags/@@g' )";
+            echo "::set-output name=clean::$(echo ${GITHUB_REF} | sed 's@refs/heads/@@g' | sed 's@refs/tags/@@g' | sed 's@[/\\]@-@g')";
       - name: Setup local servers
         id: local-servers
         shell: bash
@@ -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

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://github.com/VirtualFlyBrain/geppetto-vfb/workflows/CI/badge.svg)](https://github.com/Robbie1977/geppetto-vfb/actions?query=workflow%3ACI)[![Docker Hub](https://www.shippable.com/assets/images/logos/docker-hub.jpg)](https://hub.docker.com/r/virtualflybrain/geppetto-vfb/)
+[![Build Status](https://github.com/VirtualFlyBrain/geppetto-vfb/workflows/CI/badge.svg)](https://github.com/Robbie1977/geppetto-vfb/actions?query=workflow%3ACI)[![Docker Hub](https://d1q6f0aelx0por.cloudfront.net/product-logos/644d2f15-c5db-4731-a353-ace6235841fa-registry.png)](https://hub.docker.com/r/virtualflybrain/geppetto-vfb/)
 
 # geppetto-vfb
 Virtual Fly Brain project customised Geppetto build

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"
+		}]
 	}]
 }

components/configuration/VFBToolbar/vfbtoolbarMenuConfiguration.js

@@ -239,28 +239,20 @@ 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"]
           }
         },
-        {
-          label: "NBLAST Uploader",
-          icon: "fa fa-upload",
-          action: {
-            handlerAction: "uploaderContentsVisible",
-            parameters: []
-          }
-        },
         {
           label: "NBLAST",
           icon: "",
@@ -321,22 +313,85 @@ 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 +427,38 @@ 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 +471,16 @@ 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 +753,32 @@ 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: []