Adds Helm chart repository to Github Actions

Closes #394

.github/lintconfig.yaml

@@ -0,0 +1,8 @@
+chart-dirs: helm
+check-version-increment: true
+debug: false
+remote: origin
+target-branch: main
+validate-chart-schema: true
+validate-maintainers: false
+validate-yaml: true

.github/workflows/lint_helm.yaml

@@ -0,0 +1,35 @@
+name: Lint Helm Charts
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ ]
+  pull_request: []
+
+
+jobs:
+  lint-test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Helm
+        uses: azure/setup-helm@v2
+        with:
+          version: v3.4.0
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.7
+
+      - name: Helm Chart Testing
+        uses: helm/[email protected]
+
+      - name: Run chart-testing (lint)
+        run: |
+          CHANGED=`ct list-changed --config .github/lintconfig.yaml;`;
+          LINTCONF=$CT_CONFIG_DIR/lintconf.yaml;
+          for c in $CHANGED; do echo "$c/Chart.yaml"; yamllint  --config-file $LINTCONF  $c/Chart.yaml;  echo "$c/values.yaml"; yamllint  --config-file $LINTCONF  $c/values.yaml; done;

.github/workflows/sphinx.yaml → .github/workflows/pages.yaml

@@ -1,9 +1,10 @@
-name: Deploy Sphinx site to Pages
+name: Deploy Pages
+# Builds and deploys docs and helm charts
 
 on:
-  # Runs on pushes targeting the default branch
-  push:
-    branches: [ "main" ]
+  # Runs on publication of a release or prerelease
+  release:
+    types: [ released, prereleased ]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -33,10 +34,16 @@ jobs:
           python-version: "3.9"
       - name: Install dependencies
         run: |
-          sudo apt-get update 
+          sudo apt-get update
           sudo apt-get install -y python-dev-is-python3 libldap2-dev libsasl2-dev libssl-dev
           python -m pip install --upgrade pip
-          pip install -r docs/requirements.txt
+          pip install -e ".[docs]"
+      - name: Build with Charts
+        # Outputs to the './_site' directory by default
+        run: |
+          helm dependency update helm
+          helm package -d ./_site/charts helm
+          helm repo index ./_site/charts
       - name: Setup Pages
         id: pages
         uses: actions/configure-pages@v2

README.md

@@ -1,6 +1,7 @@
 [![.github/workflows/tests.yml](https://github.com/NGEET/ngt-archive/actions/workflows/tests.yml/badge.svg)](https://github.com/NGEET/ngt-archive/actions/workflows/tests.yml)
 [![Deploy Sphinx site to Pages](https://github.com/NGEET/ngt-archive/actions/workflows/sphinx.yaml/badge.svg)](https://github.com/NGEET/ngt-archive/actions/workflows/sphinx.yaml)
 [![Docker Image CI](https://github.com/NGEET/ngt-archive/actions/workflows/docker-image.yaml/badge.svg?branch=main)](https://github.com/NGEET/ngt-archive/actions/workflows/docker-image.yaml)
+[![Lint Helm Charts](https://github.com/NGEET/ngt-archive/actions/workflows/lint_helm.yaml/badge.svg)](https://github.com/NGEET/ngt-archive/actions/workflows/lint_helm.yaml)
 
 # NGEE Tropics Archive Service
 

docs/helm_chart.rst

@@ -0,0 +1,4 @@
+.. _helmchart:
+
+.. include:: ../helm/README.md
+   :parser: myst_parser.docutils_

docs/index.rst

@@ -13,6 +13,7 @@ Contents:
 
    intro
    quickstart
+   helm_chart
    releases
    contact
    license

helm/.helmignore

@@ -0,0 +1,23 @@
+# 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
+*.orig
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

helm/Chart.yaml

@@ -0,0 +1,23 @@
+apiVersion: v2
+name: ngt-archive
+description: NGEE-Tropics Archive
+
+# A chart can be either an 'application' or a 'library' chart.
+#
+# Application charts are a collection of templates that can be packaged into versioned archives
+# to be deployed.
+#
+# Library charts provide useful utilities or functions for the chart developer. They're included as
+# a dependency of application charts to inject those utilities and functions into the rendering
+# pipeline. Library charts do not define any templates and therefore cannot be deployed.
+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: 2.0.0
+
+# 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.
+appVersion: 3.0.0-p119

helm/README.md

@@ -0,0 +1,167 @@
+# Helm Chart
+
+Next-Generation Ecosystem Experiments–Tropics (NGEE-Tropics) is a DOE-funded,
+multi-institutional project led by Berkeley Lab, focused on how
+tropical forests interact with Earth’s climate. This helm chart deploys the 
+The NGEE-Tropics archive service sits in the middle of the *NGEE Tropics data workflow*.
+
+* Place to upload datasets and metadata.
+* Datasets should consist of related data collections, not individual files (e.g. Sapflow collected at Manaus)
+* Datasets will receive a DOI, and can be updated with new data.
+* Datasets will be available for search to NGEE Tropics team, and (if policy allows) to public
+* Makes NGEE-Tropics compliant with DOE Data Management Plan
+
+
+## Get Access
+
+```bash
+$ helm repo add ngt-archive https://ngeet.github.io/ngt-archive/charts/
+$ helm search repo ngt-archive
+```
+
+## Introduction
+
+This chart bootstraps a **NGEE-Tropics Archive** deployment on either a [Kubernetes](http://kubernetes.io) 
+or [Rancher](https://rancher.com/) cluster using the [Helm](https://helm.sh) package manager.
+
+## Installing the Chart
+
+To install the chart with the release name `<release name>`:
+
+```bash
+$ helm upgrade --install <release name> ngt-archive/ngt-archive
+```
+
+The command deploys ESS-DIVE Fusion Database on the Kubernetes cluster in the default configuration. 
+
+> **Tip**: List all releases using `helm ls`
+
+## Uninstalling the Chart
+
+To uninstall/delete the `<release name>` deployment:
+
+```bash
+$ helm delete <release name>
+```
+
+The command removes all the Kubernetes components associated with the chart and deletes the release.
+
+
+## Configuration
+
+The following table lists the configurable parameters of the ESS-DIVE Fusion Db chart and their default values.
+
+| Parameter                | Description             | Default        |
+| :----------------------- | :---------------------- | -------------- |
+| `ka8.creatorId` |  Kubernetes user id | `""` |
+| `k8.clustername` |  Kubernates cluster name | `""` |
+| `uid` |  User id of the ngt-archive containers | `""` |
+| `gid` |  Group id of the ngt-archive containers | `""` |
+| `readOnly` |  Is the archive in read-only mode?  | `"false"` |
+| `teamEmail` | The email address for the - No Reply <[email protected]>  | `""` |
+| `celeryConcurrency` | The concurrency number for the celery worker  | `3` |
+| `emailSubjectPrefix` |  Subject prefix for emails sent by the application | `""` |
+| `image.repository` | docker image for this helm chart | `"registry.nersc.gov/m2690/ngt-archive"` |
+| `image.tag` | docker image tag. Overrides the image tag whose default is the chart appVersion. | `""` |
+| `imagePullSecrets` | Global registries for image pull secrets | `[]` |
+| `nameOverride` | overrides ngt-archive.name template | `""` |
+| `fullnameOverride` | The name of the service account to use. If not set and create is true, a name is generated using the fullname template | `""` |
+| `restore.importFile` | Restore from a backup. Set the name of the file to import. | `""` |
+| `secretName.application` | Application secrets (auth-bind-ldap-password, google-maps-key, secret-key) | `""` |
+| `secretName.database` |  Database Password (db-password) | `""` |
+| `secretName.certificate` | The secret that points to the certificate for this deployment (ngt-data) | `""` |
+| `volume.dbClaim` | Postgres db volume name (change this name when restoring from backups) | `""` |
+| `volume.backupDirectory` | the postgres db backup directory | `""` |
+| `volume.importDirectory` | the directory under the backup to import (e.g. 20221016T230006) | `""` |
+| `volume.dataDirectory` | directory where archive data is stored | `""` |
+| `volume.dataImportDirectory` | directory where archive data is imported from | `""` |
+| `ingress.name` | Name of the ingres. (Defaults to fullname) | `""` |
+| `ingress.enabled` | manage external access to services (https://kubernetes.io/docs/concepts/services-networking/ingress/) | `false` |
+| `ingress.annotations` | annotations for this ingress | `{}` |
+| `ingress.hosts` | list of hosts for the ingress | `[{"host": "chart-example.local", "paths": []}]` |
+| `ingress.tls` | transport layer security | `[]` |
+| `env` | environment variables for deployment | `"[]"` |
+| `web.serverName` | The server name of this host | `"localhost"` |
+| `web.realIp.enabled` | enable configuration for real ips | `false` |
+| `web.realIp.fromIps` | the list subnet addresses to accept real ips from (e.g. [ '10.42.0.0/16', '144.44.138.155/25' ]) | `[]` |
+| `web.locations.root` | root location declarations (e.g. `[{"name": "proxy_set_header", "value": "X-Forwarded-Proto https", "comment": "Set protocol to HTTPS"}]`) | `[]` |
+
+
+### Examples
+The examples below are minimal installations. You will likely need to configure more parameters. 
+
+Basic installation.
+
+```bash
+$ helm install <release name> ngt-archive/ngt-archive
+```
+
+## People
+
++ [Contributors](https://github.com/NGEET/ngt-archive/graphs/contributors)
+
+## Copyright
+
+NGEE Tropics Archive (NGT Archive) Copyright (c) 2017, The
+Regents of the University of California, through Lawrence Berkeley National
+Laboratory (subject to receipt of any required approvals from the U.S.
+Dept. of Energy).  All rights reserved.
+
+If you have questions about your rights to use or distribute this software,
+please contact Berkeley Lab's Intellectual Property Office at
+[email protected].
+
+NOTICE.  This Software was developed under funding from the U.S. Department
+of Energy and the U.S. Government consequently retains certain rights.  As
+such, the U.S. Government has been granted for itself and others acting on
+its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the
+Software to reproduce, distribute copies to the public, prepare derivative
+works
+
+# License
+
+```
+NGEE Tropics Archive (NGT Archive) Copyright (c) 2017, 
+The Regents of the University of California, through 
+Lawrence Berkeley National Laboratory (subject to receipt of any required 
+approvals from the U.S. Dept. of Energy).  All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+(1) Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+(2) Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+(3) Neither the name of the University of California, Lawrence Berkeley
+National Laboratory, U.S. Dept. of Energy nor the names of its contributors
+may be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+
+You are under no obligation whatsoever to provide any bug fixes, patches,
+or upgrades to the features, functionality or performance of the source
+code ("Enhancements") to anyone; however, if you choose to make your
+Enhancements available either publicly, or directly to Lawrence Berkeley
+National Laboratory, without imposing a separate written license agreement
+for such Enhancements, then you hereby grant the following license: a
+non-exclusive, royalty-free perpetual license to install, use, modify,
+prepare derivative works, incorporate into other computer software,
+distribute, and sublicense such enhancements or derivative works thereof,
+in binary and source code form.
+```

helm/config/error503.html

@@ -0,0 +1,24 @@
+<!DOCTYPE html>
+<html>
+    <head>
+        <title>NGEE-Tropics Archive Service -- Down For Maintenance</title>
+        <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+        <style>
+        h1 { font-size: 50px; }
+        body { text-align:center; font: 20px Helvetica, sans-serif; color: #333; }
+        #email { color:darkgreen;font-weight:bold }
+        </style>
+    </head>
+    <body>
+        <h1> NGEE-Tropics Data Service</h1>
+        <h2>Down For Maintenance</h2>
+	<p>Sorry for the inconvenience, but we are performing a maintenance at the moment.</p>
+	<p>We will be back online shortly!</p>
+    <p>For questions contact:
+        <span style="color:darkgreen;font-style:italic">
+            <span id="email">ngee-tropics-archive</span> at
+            <span id="email">lbl</span> dot
+            <span id="email">gov</span>
+        </span></p>
+    </body>
+</html>

helm/config/nginx.conf

@@ -0,0 +1,30 @@
+user  nginx;
+worker_processes  auto;
+
+error_log  /var/log/nginx/error.log notice;
+pid        /var/tmp/nginx.pid;
+
+events {
+    worker_connections  1024;
+}
+
+
+http {
+    include       /etc/nginx/mime.types;
+    default_type  application/octet-stream;
+
+    log_format  main  '$remote_addr - $remote_user [$time_local] "$request" '
+                      '$status $body_bytes_sent "$http_referer" '
+                      '"$http_user_agent" "$http_x_forwarded_for"';
+
+    access_log  /var/log/nginx/access.log  main;
+
+    sendfile        on;
+    #tcp_nopush     on;
+
+    keepalive_timeout  65;
+
+    #gzip  on;
+
+    include /etc/nginx/conf.d/*.conf;
+}