From 81210d79e7914c191317b707a2125150ff1e4b74 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Hampus=20N=C3=A4sstr=C3=B6m?= <hampus.nasstrom@gmail.com>
Date: Thu, 7 Mar 2024 15:55:51 +0100
Subject: [PATCH] Move files to top level and update README (#4)

* Moved nomad-oasis and docker-compose

* Updated initialize.yml workflow to new paths

* Updated both READMEs
---
 .github/workflows/initialize.yml              |   8 +-
 README.md                                     |  29 +++++--
 ...docker-compose.yaml => docker-compose.yaml |   0
 .../nomad-oasis.zip => nomad-oasis.zip        | Bin 4918 -> 4918 bytes
 .../nomad-oasis/configs/nginx.conf            |  82 ------------------
 .../nomad-oasis/configs/nomad.yaml            |  34 --------
 template_README.md                            |  36 +++++---
 7 files changed, 53 insertions(+), 136 deletions(-)
 rename nomad-oasis_files/nomad-oasis/docker-compose.yaml => docker-compose.yaml (100%)
 rename nomad-oasis_files/nomad-oasis.zip => nomad-oasis.zip (92%)
 delete mode 100644 nomad-oasis_files/nomad-oasis/configs/nginx.conf
 delete mode 100644 nomad-oasis_files/nomad-oasis/configs/nomad.yaml

diff --git a/.github/workflows/initialize.yml b/.github/workflows/initialize.yml
index 3420d03..40faec5 100644
--- a/.github/workflows/initialize.yml
+++ b/.github/workflows/initialize.yml
@@ -31,10 +31,12 @@ jobs:
           
       # Replaces the template repository name in the docker config file with the new one
       - name: Update docker-compose.yaml
-        working-directory: ./nomad-oasis_files
         run: |
-          sed -i "s|FAIRmat-NFDI/nomad-distribution-template|${{ github.repository }}|g" nomad-oasis/docker-compose.yaml
-          zip -r nomad-oasis.zip nomad-oasis
+          sed -i "s|FAIRmat-NFDI/nomad-distribution-template|${{ github.repository }}|g" docker-compose.yaml
+          mkdir nomad-oasis
+          cp docker-compose.yaml nomad-oasis
+          zip -ur nomad-oasis.zip nomad-oasis
+          rm -r nomad-oasis
 
       # Deletes this workflow file to prevent it from running on branch creation
       - name: Delete initialization workflow
diff --git a/README.md b/README.md
index 3647ce1..d5aec24 100644
--- a/README.md
+++ b/README.md
@@ -10,19 +10,18 @@ Click [here](https://github.com/new?template_name=nomad-distribution-template&te
 to use this template, or click the `Use this template` button in the upper right corner of
 the main GitHub page for this template.
 
-## Deploying the image
+## Deploying the distribution
 
-To deploy this NOMAD Oasis image you should follow the instructions on [nomad-lab.eu/prod/v1/docs/oasis/install.html](https://nomad-lab.eu/prod/v1/docs/oasis/install.html) but replace the Docker image in `docker-compose.yaml` with `ghcr.io/FAIRmat-NFDI/nomad-distribution-template:main` for the services `worker`, `app`, `north`, and `logtransfer`.
+Below are instructions for how to deploy this NOMAD Oasis distribution
+[for a new Oasis](#for-a-new-oasis) and [for an existing Oasis](#for-an-existing-oasis)
 
-Remember to also update the `nomad.yaml` config file to include the new plugins.
-
-### Quick-start
+### For a new Oasis
 
 - Find a linux computer.
 - Make sure you have [docker](https://docs.docker.com/engine/install/) installed.
 Docker nowadays comes with `docker compose` build in. Prior, you needed to
 install the stand alone [docker-compose](https://docs.docker.com/compose/install/).
-- Download the modified configuration files [nomad-oasis.zip](nomad-oasis_files/nomad-oasis.zip) from this repository.
+- Download the modified configuration files [nomad-oasis.zip](nomad-oasis.zip) from this repository.
 - Run the following commands (skip `chown` on MacOS and Windows computers)
 
 
@@ -42,3 +41,21 @@ the container has to be run under the docker group. You need to replace the defa
 id `991` in the `docker-compose.yaml`'s `hub` section with your systems docker group id.
 Run `id` if you are a docker user, or `getent group | grep docker` to find our your
 systems docker gid. The user id 1000 is used as the nomad user inside all containers.
+
+You can find more details on setting up and maintaining an Oasis in the NOMAD docs here:
+[nomad-lab.eu/prod/v1/docs/oasis/install.html](https://nomad-lab.eu/prod/v1/docs/oasis/install.html)
+
+### For an existing Oasis
+
+If you already have an Oasis running you only need to change the image being pulled in
+your `docker-compose.yaml` with `ghcr.io/GITHUB_REPOSITORY:main` for the services
+`worker`, `app`, `north`, and `logtransfer`.
+
+If you want to use the `nomad.yaml` from this repository you also need to comment out
+the inclusion of the `nomad.yaml` under the volumes key of those services in the
+`docker-compose.yaml`.
+
+```yaml
+    volumes:
+      # - ./configs/nomad.yaml:/app/nomad.yaml
+```
diff --git a/nomad-oasis_files/nomad-oasis/docker-compose.yaml b/docker-compose.yaml
similarity index 100%
rename from nomad-oasis_files/nomad-oasis/docker-compose.yaml
rename to docker-compose.yaml
diff --git a/nomad-oasis_files/nomad-oasis.zip b/nomad-oasis.zip
similarity index 92%
rename from nomad-oasis_files/nomad-oasis.zip
rename to nomad-oasis.zip
index 1d6684ef9dc7ab7c3a6d51f626071c9693330c97..75b59d7c3430634705f76c922c011685cd56a97c 100644
GIT binary patch
delta 100
zcmdm{woQ#Uz?+$civa|-2c}QtRbuySeVGcxllge0HU_w`G6RJtPiHlSiEqBln#}<g
gbmTK&1}R)GB(r$}pAsWja4WwvR8VKLx&S{j09Z94o&W#<

delta 77
zcmdm{woPra9FNpQDbdMWxfM4CxUe#3I;TyZ&T7hjRq9155O2QBn$0o!f`GteKR)Hj
eqJr|9C-5mTf>mwhcV@aOHMvnxceA<xKQjOh${B6|

diff --git a/nomad-oasis_files/nomad-oasis/configs/nginx.conf b/nomad-oasis_files/nomad-oasis/configs/nginx.conf
deleted file mode 100644
index 1b8531f..0000000
--- a/nomad-oasis_files/nomad-oasis/configs/nginx.conf
+++ /dev/null
@@ -1,82 +0,0 @@
-map $http_upgrade $connection_upgrade {
-    default upgrade;
-    ''      close;
-}
-
-server {
-    listen        80;
-    server_name   localhost;
-    proxy_set_header Host $host;
-
-    gzip_min_length     1000;
-    gzip_buffers        4 8k;
-    gzip_http_version   1.0;
-    gzip_disable        "msie6";
-    gzip_vary           on;
-    gzip on;
-    gzip_proxied any;
-    gzip_types
-        text/css
-        text/javascript
-        text/xml
-        text/plain
-        application/javascript
-        application/x-javascript
-        application/json;
-
-    location / {
-        proxy_pass http://app:8000;
-    }
-
-    location ~ /nomad-oasis\/?(gui)?$ {
-        rewrite ^ /nomad-oasis/gui/ permanent;
-    }
-
-    location /nomad-oasis/gui/ {
-        proxy_intercept_errors on;
-        error_page 404 = @redirect_to_index;
-        proxy_pass http://app:8000;
-    }
-
-    location @redirect_to_index {
-        rewrite ^ /nomad-oasis/gui/index.html break;
-        proxy_pass http://app:8000;
-    }
-
-    location ~ \/gui\/(service-worker\.js|meta\.json)$ {
-        add_header Last-Modified $date_gmt;
-        add_header Cache-Control 'no-store, no-cache, must-revalidate, proxy-revalidate, max-age=0';
-        if_modified_since off;
-        expires off;
-        etag off;
-        proxy_pass http://app:8000;
-    }
-
-    location ~ /api/v1/uploads(/?$|.*/raw|.*/bundle?$)  {
-        client_max_body_size 35g;
-        proxy_request_buffering off;
-        proxy_pass http://app:8000;
-    }
-
-    location ~ /api/v1/.*/download {
-        proxy_buffering off;
-        proxy_pass http://app:8000;
-    }
-
-    location /nomad-oasis/north/ {
-        client_max_body_size 500m;
-        proxy_pass http://north:9000;
-
-        proxy_set_header X-Real-IP $remote_addr;
-        proxy_set_header Host $host;
-        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
-
-        # websocket headers
-        proxy_http_version 1.1;
-        proxy_set_header Upgrade $http_upgrade;
-        proxy_set_header Connection $connection_upgrade;
-        proxy_set_header X-Scheme $scheme;
-
-        proxy_buffering off;
-    }
-}
diff --git a/nomad-oasis_files/nomad-oasis/configs/nomad.yaml b/nomad-oasis_files/nomad-oasis/configs/nomad.yaml
deleted file mode 100644
index 6b03954..0000000
--- a/nomad-oasis_files/nomad-oasis/configs/nomad.yaml
+++ /dev/null
@@ -1,34 +0,0 @@
-services:
-  api_host: 'localhost'
-  api_base_path: '/nomad-oasis'
-
-oasis:
-  is_oasis: true
-  uses_central_user_management: true
-
-north:
-  jupyterhub_crypt_key: '978bfb2e13a8448a253c629d8dd84ff89587f30e635b753153960930cad9d36d'
-
-meta:
-  deployment: 'oasis'
-  deployment_url: 'https://my-oasis.org/api'
-  maintainer_email: 'me@my-oasis.org'
-
-logstash:
-  enable: false
-
-mongo:
-    db_name: nomad_oasis_v1
-
-elastic:
-    entries_index: nomad_oasis_entries_v1
-    materials_index: nomad_oasis_materials_v1
-
-plugins:
-  options:
-    schemas/nomad_material_processing:
-      python_package: nomad_material_processing
-    schemas/nomad_measurements:
-      python_package: nomad_measurements
-    parsers/nomad_measurements/xrd:
-      python_package: nomad_measurements.xrd.parser
\ No newline at end of file
diff --git a/template_README.md b/template_README.md
index 2519b26..4334a0e 100644
--- a/template_README.md
+++ b/template_README.md
@@ -3,8 +3,8 @@
 # GITHUB_REPOSITORY_OWNER's NOMAD Oasis Distribution
 
 This is the NOMAD Oasis distribution of GITHUB_REPOSITORY_OWNER. 
-Below are instructions for how to [deploy this image](#deploying-the-image) and how to
-customize it through [adding plugins](#adding-a-plugin).
+Below are instructions for how to [deploy this distribution](#deploying-the-distribution)
+and how to customize it through [adding plugins](#adding-a-plugin).
 
 > [!IMPORTANT] 
 > Depending on the settings of the owner of this repository, the distributed image might
@@ -18,22 +18,18 @@ customize it through [adding plugins](#adding-a-plugin).
 > greatly appreciate it if you would add the topic `nomad-distribution` by clicking the
 > ⚙️ next to "About" on the main GitHub page for this repository.
 
-## Deploying the image
+## Deploying the distribution
 
-To deploy this NOMAD Oasis image you should follow the instructions on
-[nomad-lab.eu/prod/v1/docs/oasis/install.html](https://nomad-lab.eu/prod/v1/docs/oasis/install.html)
-but replace the Docker image in `docker-compose.yaml` with `ghcr.io/GITHUB_REPOSITORY:main` 
-for the services `worker`, `app`, `north`, and `logtransfer`.
-
-Remember to also update the `nomad.yaml` config file to include the new plugins.
+Below are instructions for how to deploy this NOMAD Oasis distribution
+[for a new Oasis](#for-a-new-oasis) and [for an existing Oasis](#for-an-existing-oasis)
 
-### Quick-start
+### For a new Oasis
 
 - Find a linux computer.
 - Make sure you have [docker](https://docs.docker.com/engine/install/) installed.
 Docker nowadays comes with `docker compose` build in. Prior, you needed to
 install the stand alone [docker-compose](https://docs.docker.com/compose/install/).
-- Download the modified configuration files [nomad-oasis.zip](nomad-oasis_files/nomad-oasis.zip) from this repository.
+- Download the modified configuration files [nomad-oasis.zip](nomad-oasis.zip) from this repository.
 - Run the following commands (skip `chown` on MacOS and Windows computers)
 
 
@@ -54,6 +50,24 @@ id `991` in the `docker-compose.yaml`'s `hub` section with your systems docker g
 Run `id` if you are a docker user, or `getent group | grep docker` to find our your
 systems docker gid. The user id 1000 is used as the nomad user inside all containers.
 
+You can find more details on setting up and maintaining an Oasis in the NOMAD docs here:
+[nomad-lab.eu/prod/v1/docs/oasis/install.html](https://nomad-lab.eu/prod/v1/docs/oasis/install.html)
+
+### For an existing Oasis
+
+If you already have an Oasis running you only need to change the image being pulled in
+your `docker-compose.yaml` with `ghcr.io/GITHUB_REPOSITORY:main` for the services
+`worker`, `app`, `north`, and `logtransfer`.
+
+If you want to use the `nomad.yaml` from this repository you also need to comment out
+the inclusion of the `nomad.yaml` under the volumes key of those services in the
+`docker-compose.yaml`.
+
+```yaml
+    volumes:
+      # - ./configs/nomad.yaml:/app/nomad.yaml
+```
+
 ## Adding a plugin
 
 To add a new plugin to the docker image you should add it to the [plugins.txt](plugins.txt) file.