diff --git a/README.md b/README.md
index bfddaa8a59120b2c8c1835ac81a578b8cd9506fc..4b6613d49b827be7f5327db4ddfc1184f91a04a3 100644
--- a/README.md
+++ b/README.md
@@ -2,11 +2,12 @@ The Nyx project focuses on the neural activity and locomotion of the *Drosophila
# NyxUI.jl
-Web interface meant to be served at [nyx.pasteur.cloud](https://nyx.pasteur.cloud/).
+Web interface meant to be served at [nyx.pasteur.cloud](https://nyx.pasteur.cloud/) (public) and [nyx.dev.pasteur.cloud](https://nyx.dev.pasteur.cloud/) (internal).
-It features an app catalog, with currently a single available app:
+It features an app catalog, with the following apps:
-* an editor for muscular activity programs.
+* an editor for muscular activity programs,
+* [LarvaTagger.jl](https://gitlab.pasteur.fr/nyx/larvatagger.jl) without any automating tagging backends.
## Local installation
@@ -29,3 +30,9 @@ julia --project=. routes.jl
You may be asked whether to authorize ports 9284 and 9285; please give the app permission.
From there, in a web browser, open http://localhost:9284/ to access the app.
+
+Note that the generated files can be found somewhere in directory *storage/exports*.
+
+The download buttons in the LarvaTagger app will not work in the web browser.
+To make them work, the reverse proxy setup in the container image called *front* is required.
+If you have [Podman](https://podman.io/), as an alternative to the above installation procedure, you can simply run `front/build.sh --now` and, once the container is up and running, connect to http://localhost:8080/.
diff --git a/front/Manifest.toml b/front/Manifest.toml
index 39d0a4e6a058f4de88521428cbb002f5968aa685..7b87bea4414da2f15a4abc08c99fb472c32226cf 100644
--- a/front/Manifest.toml
+++ b/front/Manifest.toml
@@ -1120,11 +1120,11 @@ version = "1.0.0"
[[deps.NyxPlots]]
deps = ["Bonito", "Observables", "PlotlyBase"]
-git-tree-sha1 = "3d54e1c527baaf6a003e0d7a4fce5fcb9d3dd775"
+git-tree-sha1 = "796b76b7aa7d642cf41b60c2f4635f4140048db9"
repo-rev = "main"
repo-url = "https://gitlab.com/dbc-nyx/NyxPlots.jl"
uuid = "e8b8ccdb-0776-4145-b74f-57bbbfff4409"
-version = "0.1.2"
+version = "0.2.0"
[[deps.NyxWidgets]]
deps = ["Bonito", "Colors", "Format", "LazyArtifacts", "Observables"]
diff --git a/k8s/front-deployment.yaml b/k8s/front-deployment.yaml
deleted file mode 100644
index 6cdee87c1596605c2b807c2f750e789a7403b48f..0000000000000000000000000000000000000000
--- a/k8s/front-deployment.yaml
+++ /dev/null
@@ -1,38 +0,0 @@
-apiVersion: apps/v1
-kind: Deployment
-metadata:
- name: ${APP_NAME}-front
- labels:
- app: $APP_NAME
-spec:
- replicas: 1
- selector:
- matchLabels:
- app: $APP_NAME
- template:
- metadata:
- labels:
- app: $APP_NAME
- nyxui/component: front
- spec:
- containers:
- - name: $APP_NAME
- image: $FQ_IMAGE_NAME
- resources:
- limits:
- cpu: "2"
- ephemeral-storage: 1Gi
- memory: 4Gi
- requests:
- cpu: "2"
- ephemeral-storage: 1Gi
- memory: 4Gi
- ports:
- - name: http
- containerPort: 8080
- protocol: TCP
- securityContext:
- allowPrivilegeEscalation: false
- capabilities:
- drop:
- - ALL
\ No newline at end of file
diff --git a/k8s/front-service.yaml b/k8s/front-service.yaml
deleted file mode 100644
index 64f770f72932c56f81bed168bf45da31af8a6c3d..0000000000000000000000000000000000000000
--- a/k8s/front-service.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-apiVersion: v1
-kind: Service
-metadata:
- name: ${APP_NAME}-front
-spec:
- selector:
- app: $APP_NAME
- nyxui/component: front
- ports:
- - protocol: TCP
- port: 80
- targetPort: http
- name: http
diff --git a/k8s/ingress.yaml b/k8s/ingress.yaml
deleted file mode 100644
index cbaeb77f35b7d87eb9c0558c74e54e514c918842..0000000000000000000000000000000000000000
--- a/k8s/ingress.yaml
+++ /dev/null
@@ -1,19 +0,0 @@
-apiVersion: networking.k8s.io/v1
-kind: Ingress
-metadata:
- name: $APP_NAME
- labels:
- app: $APP_NAME
-spec:
- ingressClassName: internal
- rules:
- - host: $PUBLIC_URL
- http:
- paths:
- - path: /
- pathType: Prefix
- backend:
- service:
- name: ${APP_NAME}-front
- port:
- number: 80
diff --git a/nyxui/Chart.yaml b/nyxui/Chart.yaml
index 94afc3b14e04b5366844eab130c7c49b0e5bffc5..567ea86302b3a01ca09c28aa9ff20c3b221acfe9 100644
--- a/nyxui/Chart.yaml
+++ b/nyxui/Chart.yaml
@@ -15,10 +15,10 @@ type: application
# This is the chart version. This version number should be incremented each time you make changes
# to the chart and its templates, including the app version.
# Versions are expected to follow Semantic Versioning (https://semver.org/)
-version: 0.1.0
+version: 0.2.0
# This is the version number of the application being deployed. This version number should be
# incremented each time you make changes to the application. Versions are not expected to
# follow Semantic Versioning. They should reflect the version the application is using.
# It is recommended to use it with quotes.
-appVersion: "0.1"
+appVersion: "0.2.0"
diff --git a/src/apps/muscles/MuscleWidgets.jl b/src/apps/muscles/MuscleWidgets.jl
index 0c00d1059f142e6a92cb5a9907b378b69aa5a317..0c12617989856f547b119331022cb1afdbc5c42b 100644
--- a/src/apps/muscles/MuscleWidgets.jl
+++ b/src/apps/muscles/MuscleWidgets.jl
@@ -22,7 +22,6 @@ struct MuscleWidget
sequence::AbstractObservable
colormap::AbstractObservable
colorscheme::AbstractObservable
- setvalue::AbstractObservable
overview::Muscles.MultiSegmentMuscleWidget
individualsegments::Vector{Muscles.MuscleWidget}
heatmaps::Vector{Heatmap}
@@ -39,7 +38,6 @@ function MuscleWidget(sequence)
on(colormap) do c
colorscheme[] = scale2scheme(c)
end
- setvalue = Observable{Float64}(1)
editmode = Observable(false)
#
overview = Muscles.MultiSegmentMuscleWidget(; musclelabel=false, sidelabel=:right)
@@ -49,7 +47,7 @@ function MuscleWidget(sequence)
segmentlabel=true,
style="width: 40%; margin-top: 2rem;")
for segment in segments(overview)]
- moveto = clipboard = zlim = nothing
+ moveto = clipboard = zlim = setvalue = nothing
heatmaps = Heatmap[]
for segment in individualsegments
halfsegment = sequence[][segment.segment, segment.side]
@@ -61,10 +59,12 @@ function MuscleWidget(sequence)
pick=moveto,
clipboard=clipboard,
setvalue=setvalue,
- zlim=zlim)
+ zlim=zlim,
+ prompt_on_assign=true)
moveto = heatmap.pick
clipboard = heatmap.clipboard
zlim = heatmap.zlim
+ setvalue = heatmap.setvalue
push!(heatmaps, heatmap)
end
detailedviews = [Div(widget, heatmap; style=:row)
@@ -137,7 +137,7 @@ function MuscleWidget(sequence)
heatmaps[layer-1].editing[] = b
end
end
- return MuscleWidget(sequence, colormap, colorscheme, setvalue, overview,
+ return MuscleWidget(sequence, colormap, colorscheme, overview,
individualsegments, heatmaps, animation, editmode)
end
diff --git a/src/apps/muscles/app.jl b/src/apps/muscles/app.jl
index 082584919dcbe8e831b50d195d406f2e2ff249b1..30eb0d07a215825b8d56d59ee0258798ba59edf1 100644
--- a/src/apps/muscles/app.jl
+++ b/src/apps/muscles/app.jl
@@ -39,7 +39,6 @@ const bonito_app = NamedApp(:inherit, Backbone.app)
@out first_time_in_editmode = true # and in the heatmap view
@in editmode = false
@out editmode_disable = true
- @in setvalue = 1.0
@in series_length::Float64 = 21
@in time_interval = 0.05
@in start_time = 0.0
@@ -71,7 +70,6 @@ const bonito_app = NamedApp(:inherit, Backbone.app)
colormap = model.colormap[]
editmode = model.editmode[]
sequence_name = name
- setvalue = model.setvalue[]
seq = model.sequence[]
series_length = length(seq.times)
time_interval = step(seq.times)
@@ -221,6 +219,11 @@ const bonito_app = NamedApp(:inherit, Backbone.app)
end
@onchange editmode begin
+ if editmode && isempty(sequence_name)
+ @notify "Create a new program or load one first" :error
+ editmode = false
+ return
+ end
model = getmodel(back_session_id)
model.editmode[] = editmode
editmode_disable = !editmode
@@ -240,11 +243,6 @@ const bonito_app = NamedApp(:inherit, Backbone.app)
@notify "Toggle the \"edit mode\" off to browse the sequence with the heatmap" :info
end
- @onchange setvalue begin
- model = getmodel(back_session_id)
- model.setvalue[] = setvalue
- end
-
@onbutton export_sequence_click begin
filepath = exportsequence(back_session_id)
if isempty(filepath)
@@ -298,7 +296,7 @@ const bonito_app = NamedApp(:inherit, Backbone.app)
@notify "Selection copied! Press Ctrl while clicking to paste" :info
end
@onchange area_selected begin
- @notify "Click inside the selected area to assign the setvalue, or press Ctrl while clicking to copy the selection" :info
+ @notify "Click inside the selected area to assign a value, or press Ctrl while clicking to copy the selection" :info
end
@onbutton delete_sequence_click begin
@@ -331,6 +329,12 @@ const bonito_app = NamedApp(:inherit, Backbone.app)
# update the view
notify(sequence_names)
end
+
+ @onchange no_sequences_yet begin
+ if no_sequences_yet && editmode
+ editmode = false
+ end
+ end
end
function dropdown(key, options, label; margin=true, class=nothing)
@@ -366,8 +370,6 @@ function muscle_view(bonito_url=""; channel=":channel")
Html.div(class="edit-panel", style=col, [
toggle("Toggle edit mode", :editmode, color="blue"),
textfield("Motor program name", :sequence_name, disable=:editmode_disable),
- textfield("Set value", :setvalue, type="number", step="any",
- disable=:editmode_disable),
textfield("Number of time steps", :series_length, type="number", step="1",
disable=:editmode_disable),
textfield("Time interval", :time_interval, type="number", step="any",
diff --git a/src/apps/muscles/bonito.css b/src/apps/muscles/bonito.css
index 0feaf047580dcb279aa96fab0a9137f1febc2312..ca696314b5442f86ad184b63a4f0080ef30b64b6 100644
--- a/src/apps/muscles/bonito.css
+++ b/src/apps/muscles/bonito.css
@@ -1,4 +1,4 @@
-.nyx-animated-layers, .nyx-player select, .nyx-player span {
+.nyx-animated-layers, .nyx-player select, .nyx-player span, .nyx-segment-side-label-left, .nyx-segment-side-label-right {
font-family: Open Sans;
}