Atelier activetigger

docker-images-datalab/activetigger/Dockerfile

@@ -35,7 +35,7 @@ RUN Rscript /requirements.r
 
 
 # Install Miniconda
- RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
     bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \
     rm Miniconda3-latest-Linux-x86_64.sh
 

docker-images-datalab/activetigger/Dockerfile.rocker

@@ -0,0 +1,28 @@
+# Base
+FROM rocker/shiny
+
+# Copy requirements
+COPY requirements.py /
+COPY requirements.r /
+
+# Install system dependencies
+RUN apt-get update && \
+    apt-get install -y python3-pip libxml2-dev
+
+## Install packages
+RUN Rscript /requirements.r
+RUN pip3 install -r /requirements.py
+
+## Packages
+#RUN python -m spacy download fr_core_news_sm \
+#WORKDIR ~
+#RUN wget https://dl.fbaipublicfiles.com/fasttext/vectors-crawl/cc.fr.300.bin.gz \
+#    && gunzip cc.fr.300.bin.gz
+
+
+COPY activetigger ./activetigger
+# Expose the default Shiny port
+EXPOSE 3838
+
+# Command to run the Shiny app
+CMD ["R", "-e", "shiny::runApp('activetigger', port=3838, host='0.0.0.0')"]

docker-images-datalab/activetigger/requirements.py

@@ -0,0 +1,13 @@
+argparse
+datasets
+fasttext
+numpy
+pandas
+pyarrow
+scikit-learn
+torch
+transformers[torch]
+sentence_transformers
+typing-inspect==0.8.0
+typing_extensions==4.6.1
+spacy

docker-images-datalab/activetigger/requirements.r

@@ -1 +1,3 @@
-install.packages(c("arrow", "class", "data.table", "DT", "foreign", "glmnet", "haven", "LiblineaR", "Matrix", "Metrics", "quanteda", "quanteda.textmodels", "ranger", "readODS", "readxl", "RJSONIO", "rlang", "Rtsne", "shiny", "SparseM", "stringi", "uwot"))
+packages=c("arrow", "class", "data.table", "DT", "foreign", "glmnet", "haven", "LiblineaR", "Matrix", "Metrics", "quanteda", "quanteda.textmodels", "ranger", "readODS", "readxl", "RJSONIO", "rlang", "Rtsne", "shiny", "SparseM", "stringi", "uwot", "future","htmlTable","ggplot2")
+
+install.packages(setdiff(packages, rownames(installed.packages())))

helm-charts-datalab/helm-charts-test/charts/activetigger/template

@@ -0,0 +1,140 @@
+---
+# Source: activetigger/templates/serviceaccount.yaml
+apiVersion: v1
+kind: ServiceAccount
+metadata:
+  name: release-name-activetigger
+  labels:
+    helm.sh/chart: activetigger-0.1.0
+    app.kubernetes.io/name: activetigger
+    app.kubernetes.io/instance: release-name
+    app.kubernetes.io/version: "1.0.0"
+    app.kubernetes.io/managed-by: Helm
+automountServiceAccountToken: true
+---
+# Source: activetigger/templates/service.yaml
+apiVersion: v1
+kind: Service
+metadata:
+  name: release-name-activetigger
+  labels:
+    helm.sh/chart: activetigger-0.1.0
+    app.kubernetes.io/name: activetigger
+    app.kubernetes.io/instance: release-name
+    app.kubernetes.io/version: "1.0.0"
+    app.kubernetes.io/managed-by: Helm
+spec:
+  type: ClusterIP
+  ports:
+    - port: 8000
+      targetPort: http
+      protocol: TCP
+      name: http
+  selector:
+    app.kubernetes.io/name: activetigger
+    app.kubernetes.io/instance: release-name
+---
+# Source: activetigger/templates/deployment.yaml
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: release-name-activetigger
+  labels:
+    helm.sh/chart: activetigger-0.1.0
+    app.kubernetes.io/name: activetigger
+    app.kubernetes.io/instance: release-name
+    app.kubernetes.io/version: "1.0.0"
+    app.kubernetes.io/managed-by: Helm
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app.kubernetes.io/name: activetigger
+      app.kubernetes.io/instance: release-name
+  template:
+    metadata:
+      labels:
+        helm.sh/chart: activetigger-0.1.0
+        app.kubernetes.io/name: activetigger
+        app.kubernetes.io/instance: release-name
+        app.kubernetes.io/version: "1.0.0"
+        app.kubernetes.io/managed-by: Helm
+    spec:
+      serviceAccountName: release-name-activetigger
+      securityContext:
+        {}
+      containers:
+        - name: activetigger
+          securityContext:
+            {}
+          image: "code.groupe-genes.fr/datalab/activetigger:latest"
+          imagePullPolicy: IfNotPresent
+          ports:
+            - name: http
+              containerPort: 8000
+              protocol: TCP
+          livenessProbe:
+            httpGet:
+              path: /
+              port: http
+          readinessProbe:
+            httpGet:
+              path: /
+              port: http
+          resources:
+            {}
+---
+# Source: activetigger/templates/ingress.yaml
+apiVersion: networking.k8s.io/v1
+kind: Ingress
+metadata:
+  name: release-name-activetigger
+  labels:
+    helm.sh/chart: activetigger-0.1.0
+    app.kubernetes.io/name: activetigger
+    app.kubernetes.io/instance: release-name
+    app.kubernetes.io/version: "1.0.0"
+    app.kubernetes.io/managed-by: Helm
+spec:
+  rules:
+    - host: "activetigger.lab.groupe-genes.fr"
+      http:
+        paths:
+          - path: /
+            pathType: ImplementationSpecific
+            backend:
+              service:
+                name: release-name-activetigger
+                port:
+                  number: 8000
+    - host: "activetigger2.lab.groupe-genes.fr"
+      http:
+        paths:
+          - path: /
+            pathType: ImplementationSpecific
+            backend:
+              service:
+                name: release-name-activetigger
+                port:
+                  number: 8000
+---
+# Source: activetigger/templates/tests/test-connection.yaml
+apiVersion: v1
+kind: Pod
+metadata:
+  name: "release-name-activetigger-test-connection"
+  labels:
+    helm.sh/chart: activetigger-0.1.0
+    app.kubernetes.io/name: activetigger
+    app.kubernetes.io/instance: release-name
+    app.kubernetes.io/version: "1.0.0"
+    app.kubernetes.io/managed-by: Helm
+  annotations:
+    "helm.sh/hook": test
+spec:
+  containers:
+    - name: wget
+      image: busybox
+      command: ['wget']
+      args: ['release-name-activetigger:8000']
+  restartPolicy: Never

helm-charts-datalab/helm-charts-test/charts/activetigger/values.yaml

@@ -5,7 +5,7 @@
 replicaCount: 1
 
 image:
-  repository: https://code.groupe-genes.fr/dsit/datalab/src/branch/main/docker-images-datalab/activetigger
+  repository: code.groupe-genes.fr/datalab/activetigger:latest
   pullPolicy: IfNotPresent
   # Overrides the image tag whose default is the chart appVersion.
   tag: "latest"