WIP: MiniT4 w/Minio helm chart

.gitignore

@@ -39,3 +39,6 @@ registry/dpmd
 
 # Doc Build
 _build
+
+# Zip files
+**.tgz

api/python/t4/data_transfer.py

@@ -36,7 +36,15 @@
     # Linux only allows users to modify user.* xattrs.
     HELIUM_XATTR = 'user.%s' % HELIUM_XATTR
 
-s3_client = boto3.client('s3')
+#s3_client = boto3.client('s3')
+
+s3_client = boto3.client('s3',
+                         endpoint_url='http://localhost:9000',
+                         aws_access_key_id='AKIAIOSFODNN7EXAMPLE',
+                         aws_secret_access_key='wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY',
+                         config=Config(signature_version='s3v4'),
+                         region_name='us-east-1')
+
 try:
     # Ensure that user has AWS credentials that function.
     # quilt-example is readable by anonymous users, if the head fails
@@ -47,6 +55,14 @@
     # Use unsigned boto if credentials can't head the default bucket
     s3_client = boto3.client('s3', config=Config(signature_version=UNSIGNED))
 
+if True: # switch to env variable
+    s3_client = boto3.client('s3',
+                            endpoint_url='http://localhost:9000',
+                            aws_access_key_id='AKIAIOSFODNN7EXAMPLE',
+                            aws_secret_access_key='wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY',
+                            config=Config(signature_version='s3v4'),
+                            region_name='us-east-1')
+
 s3_transfer_config = TransferConfig()
 s3_threads = 4
 

catalog/app/utils/AWS/S3.js

@@ -17,7 +17,13 @@ const Ctx = React.createContext();
 export const Provider = composeComponent('AWS.S3.Provider',
   Config.inject(),
   withPropsOnChange(['awsConfig'], ({ awsConfig }) => ({
-    client: new S3(awsConfig),
+    client: new S3({
+      accessKeyId: 'AKIAIOSFODNN7EXAMPLE' , //Preferably read from an env variable
+      secretAccessKey: 'wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY' ,  //Preferably read from an env variable
+      endpoint: 'http://127.0.0.1:9000' ,
+      s3ForcePathStyle: true, // needed with minio?
+      signatureVersion: 'v4'
+}),
   })),
   provide(Ctx, 'client'));
 

charts/Chart.yaml

@@ -0,0 +1,12 @@
+apiVersion: v1
+name: miniT4
+version: 0.0.1
+description: A single-sentence description of this project (optional)
+keywords:
+  - Datascience
+home: https://quiltdata.com/
+sources:
+  - https://github.com/quiltdata/t4/
+maintainers: # (optional)
+  - name: Michael Sindelar
+    email: sindelar@quiltdata.io

charts/README.md

@@ -0,0 +1,14 @@
+Create a Secret in the cluster that holds your authorization token
+A Kubernetes cluster uses the Secret of docker-registry type to authenticate with a container registry to pull a private image.
+
+Create this Secret, naming it regcred:
+
+kubectl create secret docker-registry regcred --docker-server=<your-registry-server> --docker-username=<your-name> --docker-password=<your-pword> --docker-email=<your-email>
+where:
+
+<your-registry-server> is your Private Docker Registry FQDN. (https://index.docker.io/v1/ for DockerHub)
+<your-name> is your Docker username.
+<your-pword> is your Docker password.
+<your-email> is your Docker email.
+You have successfully set your Docker credentials in the cluster as a Secret called regcred.
+

charts/t4/.helmignore

@@ -0,0 +1,22 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

charts/t4/Chart.yaml

@@ -0,0 +1,5 @@
+apiVersion: v1
+appVersion: "1.0"
+description: A Helm chart for Kubernetes
+name: t4
+version: 0.1.0

charts/t4/requirements.lock

@@ -0,0 +1,9 @@
+dependencies:
+- name: elasticsearch
+  repository: https://helm.elastic.co
+  version: 6.4.2
+- name: minio
+  repository: https://kubernetes-charts.storage.googleapis.com
+  version: 2.3.5
+digest: sha256:af3ac95048e13e3b42fc79b4e1fc808fb771037220fed621234dc63dc5c26be6
+generated: 2019-01-23T13:49:18.248497-08:00

charts/t4/requirements.yaml

@@ -0,0 +1,13 @@
+dependencies:
+  - name: elasticsearch
+    repository: https://helm.elastic.co
+    version: '6.4.2'
+  - name: minio
+    repository: https://kubernetes-charts.storage.googleapis.com
+    version: '2.3.5'
+
+# knative installations?
+# helm install riff-incubator/istio --name istio --namespace istio-system --values http://riff-incubator.cfapps.io/values/values-istio-knative.yaml --set ingressgateway.service.type=NodePort
+# helm install riff-incubator/knative-istio --name knative-istio --namespace istio-system --set knative.ingressgateway.service.type=NodePort
+# helm install riff-incubator/knative-build --name knative-build --namespace knative-build
+# helm install riff-incubator/knative-serving --name knative-serving --namespace knative-serving

charts/t4/templates/NOTES.txt

@@ -0,0 +1,21 @@
+1. Get the application URL by running these commands:
+{{- if .Values.ingress.enabled }}
+{{- range $host := .Values.ingress.hosts }}
+  {{- range $.Values.ingress.paths }}
+  http{{ if $.Values.ingress.tls }}s{{ end }}://{{ $host }}{{ . }}
+  {{- end }}
+{{- end }}
+{{- else if contains "NodePort" .Values.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "t4.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get svc -w {{ include "t4.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "t4.fullname" . }} -o jsonpath='{.status.loadBalancer.ingress[0].ip}')
+  echo http://$SERVICE_IP:{{ .Values.service.port }}
+{{- else if contains "ClusterIP" .Values.service.type }}
+  export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "t4.name" . }},app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+  echo "Visit http://127.0.0.1:8080 to use your application"
+  kubectl port-forward $POD_NAME 8080:80
+{{- end }}

charts/t4/templates/_helpers.tpl

@@ -0,0 +1,32 @@
+{{/* vim: set filetype=mustache: */}}
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "t4.name" -}}
+{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
+{{- end -}}
+
+{{/*
+Create a default fully qualified app name.
+We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
+If release name contains chart name it will be used as a full name.
+*/}}
+{{- define "t4.fullname" -}}
+{{- if .Values.fullnameOverride -}}
+{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
+{{- else -}}
+{{- $name := default .Chart.Name .Values.nameOverride -}}
+{{- if contains $name .Release.Name -}}
+{{- .Release.Name | trunc 63 | trimSuffix "-" -}}
+{{- else -}}
+{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}}
+{{- end -}}
+{{- end -}}
+{{- end -}}
+
+{{/*
+Create chart name and version as used by the chart label.
+*/}}
+{{- define "t4.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
+{{- end -}}

charts/t4/templates/deployment.yaml

@@ -0,0 +1,51 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "t4.fullname" . }}
+  labels:
+    app.kubernetes.io/name: {{ include "t4.name" . }}
+    helm.sh/chart: {{ include "t4.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app.kubernetes.io/name: {{ include "t4.name" . }}
+      app.kubernetes.io/instance: {{ .Release.Name }}
+  template:
+    metadata:
+      labels:
+        app.kubernetes.io/name: {{ include "t4.name" . }}
+        app.kubernetes.io/instance: {{ .Release.Name }}
+    spec:
+      containers:
+        - name: {{ .Chart.Name }}
+          image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          ports:
+            - name: http
+              containerPort: 3000
+              protocol: TCP
+          livenessProbe:
+            httpGet:
+              path: /
+              port: http
+          readinessProbe:
+            httpGet:
+              path: /
+              port: http
+          resources:
+            {{- toYaml .Values.resources | nindent 12 }}
+      {{- with .Values.nodeSelector }}
+      nodeSelector:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+    {{- with .Values.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+    {{- end }}
+    {{- with .Values.tolerations }}
+      tolerations:
+        {{- toYaml . | nindent 8 }}
+    {{- end }}

charts/t4/templates/ingress.yaml

@@ -0,0 +1,40 @@
+{{- if .Values.ingress.enabled -}}
+{{- $fullName := include "t4.fullname" . -}}
+{{- $ingressPaths := .Values.ingress.paths -}}
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: {{ $fullName }}
+  labels:
+    app.kubernetes.io/name: {{ include "t4.name" . }}
+    helm.sh/chart: {{ include "t4.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+  {{- with .Values.ingress.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+spec:
+{{- if .Values.ingress.tls }}
+  tls:
+  {{- range .Values.ingress.tls }}
+    - hosts:
+      {{- range .hosts }}
+        - {{ . | quote }}
+      {{- end }}
+      secretName: {{ .secretName }}
+  {{- end }}
+{{- end }}
+  rules:
+  {{- range .Values.ingress.hosts }}
+    - host: {{ . | quote }}
+      http:
+        paths:
+	{{- range $ingressPaths }}
+          - path: {{ . }}
+            backend:
+              serviceName: {{ $fullName }}
+              servicePort: http
+	{{- end }}
+  {{- end }}
+{{- end }}

charts/t4/templates/service.yaml

@@ -0,0 +1,19 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ include "t4.fullname" . }}
+  labels:
+    app.kubernetes.io/name: {{ include "t4.name" . }}
+    helm.sh/chart: {{ include "t4.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+spec:
+  type: {{ .Values.service.type }}
+  ports:
+    - port: {{ .Values.service.port }}
+      targetPort: http
+      protocol: TCP
+      name: http
+  selector:
+    app.kubernetes.io/name: {{ include "t4.name" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}

charts/t4/templates/tests/test-connection.yaml

@@ -0,0 +1,18 @@
+apiVersion: v1
+kind: Pod
+metadata:
+  name: "{{ include "t4.fullname" . }}-test-connection"
+  labels:
+    app.kubernetes.io/name: {{ include "t4.name" . }}
+    helm.sh/chart: {{ include "t4.chart" . }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+  annotations:
+    "helm.sh/hook": test-success
+spec:
+  containers:
+    - name: wget
+      image: busybox
+      command: ['wget']
+      args:  ['{{ include "t4.fullname" . }}:{{ .Values.service.port }}']
+  restartPolicy: Never

charts/t4/values.yaml

@@ -0,0 +1,52 @@
+# Default values for t4.
+# This is a YAML-formatted file.
+# Declare variables to be passed into your templates.
+
+replicaCount: 1
+
+image:
+  repository: quiltdata/catalog
+  tag: minio-test
+  pullPolicy: IfNotPresent
+  imagePullSecrets:
+  - name: regcred
+
+nameOverride: ""
+fullnameOverride: ""
+
+service:
+  type: NodePort
+  port: 3000
+
+ingress:
+  enabled: false
+  annotations: {}
+    # kubernetes.io/ingress.class: nginx
+    # kubernetes.io/tls-acme: "true"
+  paths: []
+  hosts:
+    - chart-example.local
+  tls: []
+  #  - secretName: chart-example-tls
+  #    hosts:
+  #      - chart-example.local
+
+resources: {}
+
+nodeSelector: {}
+
+tolerations: []
+
+affinity: {}
+
+# pre-install hook to setup PV for minio PVC?
+
+elasticsearch:
+    replicas: 1
+
+minio:
+    accessKey: AKIAIOSFODNN7EXAMPLE
+    secretKey: wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY
+    defaultBucket:
+        enabled: True
+        name: config