From 4895d6cbe351e6c1ceb31c587fb4778f1979eb60 Mon Sep 17 00:00:00 2001
From: Martin Weise <martin.weise@tuwien.ac.at>
Date: Tue, 13 Jun 2023 16:39:25 +0200
Subject: [PATCH] Updated the docs

---
 .gitignore                    |  2 +-
 dockerhub/client/Dockerhub.py |  7 ++--
 dockerhub/release.py          |  5 ++-
 docs/get-started.md           | 56 ++++++++++++++++++++++++++------
 docs/system.md                |  2 +-
 misc/architecture.drawio      | 61 ++++++++++++++++++++++++++++++++---
 mkdocs.yml                    |  1 +
 7 files changed, 114 insertions(+), 20 deletions(-)

diff --git a/.gitignore b/.gitignore
index 26771e2..7a23556 100644
--- a/.gitignore
+++ b/.gitignore
@@ -35,7 +35,7 @@ id_rsa
 .idea/
 
 ## Docker Hub
-dockerhub/.env
+.env
 
 ## Virtual Environment
 venv/
diff --git a/dockerhub/client/Dockerhub.py b/dockerhub/client/Dockerhub.py
index 0f2d394..d8ede6e 100644
--- a/dockerhub/client/Dockerhub.py
+++ b/dockerhub/client/Dockerhub.py
@@ -5,7 +5,7 @@ class Dockerhub:
     """A simple Dockerhub client"""
     baseurl = "https://hub.docker.com"
     username = ""
-    registry = "registry-1.docker.io"
+    registry = "docker.io"
     workpath = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
     headers = {
         "Content-Type": "application/json",
@@ -14,6 +14,7 @@ class Dockerhub:
 
     def __init__(self):
         self.username = os.getenv("DOCKER_USERNAME")
+        print("docker username: %s" % self.username)
         response = rq.post(self.baseurl + "/v2/users/login", {
             "username": self.username,
             "password": os.getenv("DOCKER_PASSWORD")
@@ -28,7 +29,9 @@ class Dockerhub:
         header = self.__read__(self.workpath + "/_header.md").replace('REPOSITORY', repository)
         footer = self.__read__(self.workpath + "/_footer.md").replace('REPOSITORY', repository)
         body = self.__read__(self.workpath + "/fda-" + repository + ".md")
-        response = rq.patch(self.baseurl + "/v2/repositories/" + self.username + "/" + repository + "/", headers=self.headers,
+        url = self.baseurl + "/v2/repositories/dbrepo/" + repository + "/"
+        print("dispatch update: %s" % url)
+        response = rq.patch(url, headers=self.headers,
             json={
                 "description": "Official repository of DBRepo.",
                 "full_description": header + "\n\n" + body + "\n\n" + footer,
diff --git a/dockerhub/release.py b/dockerhub/release.py
index 9ea3e8c..42335de 100755
--- a/dockerhub/release.py
+++ b/dockerhub/release.py
@@ -8,8 +8,7 @@ dockerhub = Dockerhub()
 
 if __name__ == "__main__":
     for component in ["analyse-service", "authentication-service", "broker-service", "container-service",
-                      "database-service", "discovery-service", "gateway-service", "identifier-service",
-                      "metadata-db", "metadata-service", "query-service", "table-service", "ui", "semantics-service",
-                      "search-service"]:
+                      "database-service", "identifier-service", "metadata-db", "metadata-service", "query-service",
+                      "table-service", "ui", "semantics-service", "user-service"]:
         response = dockerhub.modify_description(component)
         print(response)
diff --git a/docs/get-started.md b/docs/get-started.md
index 5992112..2d75002 100644
--- a/docs/get-started.md
+++ b/docs/get-started.md
@@ -18,7 +18,7 @@ hide:
 ### Hardware
 
 For this small, local, test deployment any modern hardware would suffice, we recommend a dedicated virtual machine with
-the following settings. Note that most of the CPU and RAM resources will be needed for starting the infrastructure, 
+the following settings. Note that most of the CPU and RAM resources will be needed for starting the infrastructure,
 this is because of Docker.
 
 - 8 CPU cores
@@ -35,24 +35,28 @@ we only consider Debian.
 
 ### Docker Compose
 
-We maintain a rapid prototype deployment option through Docker Compose.
+We maintain a rapid prototype deployment option through Docker Compose (v2.17.0 and newer).
 
 Download the
-latest [`docker-compose.yml`](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/docker-compose.prod.yml)
+latest [`docker-compose.yml`](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/docker-compose.prod.yml),
+nginx reverse proxy
+conf [`dbrepo.conf`](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/dbrepo.conf)
 and [`.env`](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/.env.unix.example):
 
-    curl -o docker-compose.yml \
-      https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/docker-compose.prod.yml
-    curl -o .env \
-      https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/.env.unix.example
+    curl -o docker-compose.yml https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/docker-compose.prod.yml
+    curl -o dbrepo.conf https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/dbrepo.conf
+    curl -o .env https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/.env.unix.example
 
 Start the services:
 
-    docker-compose up -d
+    docker compose pull
+    docker compose up -d
 
 View the logs:
 
-    docker-compose logs -f
+    docker compose logs -f
+
+You should now be able to view the front end at <a href="http://127.0.0.1:80" target="_blank">http://127.0.0.1:80</a>
 
 Please be warned that the default configuration is not intended for public deployments. It is only intended to have a
 running system within minutes to play around within the system and explore features.
@@ -94,6 +98,40 @@ running system within minutes to play around within the system and explore featu
       [simple guide](http://nginx.org/en/docs/http/configuring_https_servers.html) on how to install a SSL/TLS
       certificate on NGINX.
 
+##### Migration from 1.2 to 1.3
+
+In case you have a previous deployment from version 1.2, shut down the containers and back them up manually. You can do
+this by using the `busybox` image. Replace `deadbeef` with your container name or hash:
+
+```console
+export NAME=dbrepo-userdb-xyz
+docker run --rm --volumes-from $NAME -v /home/$USER/backup:/backup busybox tar pcvfz /backup/$NAME.tar.gz /var/lib/mysql
+```
+
+!!! danger "Wipe all traces of DBRepo from your system"
+
+    To erase all traces of DBRepo from your computer or virtual machine, the following commands delete all containers,
+    volumes and networks that are present, execute the following **dangerous** command. It will **wipe** all information
+    about DBRepo from your system (excluding the images).
+    
+    ```console
+    docker container stop $(docker container ls -aq -f name=^/dbrepo-.*) || true
+    docker container rm $(docker container ls -aq -f name=^/dbrepo-.*) || true
+    docker volume rm $(docker volume ls -q -f name=^dbrepo-.*) || true
+    docker network rm $(docker network ls -q -f name=^dbrepo-.*) || true
+    ```
+
+You can restore the volume *after* downloading the new 1.3 images and creating the infrastructure:
+
+```console
+export NAME=dbrepo-userdb-xyz
+export PORT=12345
+docker container create -h $NAME --name $NAME -p $PORT:3306 -e MARIADB_ROOT_PASSWORD=mariadb --network userdb -v /backup mariadb:10.5
+docker run --rm --volumes-from $NAME -v /home/$USER/backup/.tar.gz:/backup/$NAME.tar.gz busybox sh -c 'cd /backup && tar xvfz /backup/$NAME.tar.gz && cp -r /backup/var/lib/mysql/* /var/lib/mysql'
+```
+
+Future releases will be backwards compatible and will come with migration scripts.
+
 ### Kubernetes
 
 We maintain a RKE2 Kubernetes deployment from version 1.3 onwards. More on that when the release date is fixed.
diff --git a/docs/system.md b/docs/system.md
index 23b1373..93e9623 100644
--- a/docs/system.md
+++ b/docs/system.md
@@ -66,7 +66,7 @@ the authentication will be through Keycloak.
     * Temporary passwords
 
 By default, the Authentication Service comes with a self-signed certificate valid 3 months from build date. For
-deployment it is *highly encouraged* to use your own certificate, properly issued by a trusted PKI, e.g. GEÁNT. For
+deployment it is *highly encouraged* to use your own certificate, properly issued by a trusted PKI, e.g. G&#201;ANT. For
 local deployments you can use the self-signed certificate. You need to accept the risk in most browsers when visiting
 the [admin panel](https://localhost:8443/admin/).
 
diff --git a/misc/architecture.drawio b/misc/architecture.drawio
index a688ab9..9e10ff5 100644
--- a/misc/architecture.drawio
+++ b/misc/architecture.drawio
@@ -1,6 +1,6 @@
-<mxfile host="Electron" modified="2023-06-01T06:09:08.990Z" agent="Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) draw.io/21.1.2 Chrome/106.0.5249.199 Electron/21.4.3 Safari/537.36" etag="-Z1STi4cUE9hBolYebCG" version="21.1.2" type="device" pages="3">
+<mxfile host="Electron" modified="2023-06-06T08:55:21.186Z" agent="Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) draw.io/21.1.2 Chrome/106.0.5249.199 Electron/21.4.3 Safari/537.36" etag="RoMWSCJjkYZ4h8t0DaKr" version="21.1.2" type="device" pages="4">
   <diagram name="Deployment" id="BS_rNRZWEkVqn4O3IFNu">
-    <mxGraphModel dx="1434" dy="822" grid="1" gridSize="10" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="840" pageHeight="509" math="0" shadow="0">
+    <mxGraphModel dx="2074" dy="1182" grid="1" gridSize="10" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="840" pageHeight="509" math="0" shadow="0">
       <root>
         <mxCell id="0" />
         <mxCell id="1" parent="0" />
@@ -206,7 +206,7 @@
     </mxGraphModel>
   </diagram>
   <diagram id="mvBsv1rP8O80Qe3yGnn_" name="Architecture">
-    <mxGraphModel dx="1434" dy="822" grid="1" gridSize="10" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="1169" pageHeight="827" math="0" shadow="0">
+    <mxGraphModel dx="2074" dy="1182" grid="1" gridSize="10" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="1169" pageHeight="827" math="0" shadow="0">
       <root>
         <mxCell id="0" />
         <mxCell id="1" parent="0" />
@@ -556,7 +556,7 @@
     </mxGraphModel>
   </diagram>
   <diagram name="Frontend" id="GYXS_N4ymJ7hX3zLKvDC">
-    <mxGraphModel dx="1434" dy="822" grid="1" gridSize="10" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="583" pageHeight="413" math="0" shadow="0">
+    <mxGraphModel dx="2074" dy="1182" grid="1" gridSize="10" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="583" pageHeight="413" math="0" shadow="0">
       <root>
         <mxCell id="ihsuRJ9dWuDPEHVUeUyY-0" />
         <mxCell id="ihsuRJ9dWuDPEHVUeUyY-1" parent="ihsuRJ9dWuDPEHVUeUyY-0" />
@@ -643,4 +643,57 @@
       </root>
     </mxGraphModel>
   </diagram>
+  <diagram id="-TYUtxSewH07omKFn9Rp" name="Kubernetes">
+    <mxGraphModel dx="1430" dy="815" grid="1" gridSize="10" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="1169" pageHeight="827" math="0" shadow="0">
+      <root>
+        <mxCell id="0" />
+        <mxCell id="1" parent="0" />
+        <mxCell id="z5OKJBfVE0389Lpc2gJH-7" value="80, 443" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;" edge="1" parent="1" source="z5OKJBfVE0389Lpc2gJH-1" target="z5OKJBfVE0389Lpc2gJH-2">
+          <mxGeometry relative="1" as="geometry" />
+        </mxCell>
+        <mxCell id="z5OKJBfVE0389Lpc2gJH-1" value="Ingress" style="sketch=0;html=1;dashed=0;whitespace=wrap;fillColor=#2875E2;strokeColor=#ffffff;points=[[0.005,0.63,0],[0.1,0.2,0],[0.9,0.2,0],[0.5,0,0],[0.995,0.63,0],[0.72,0.99,0],[0.5,1,0],[0.28,0.99,0]];verticalLabelPosition=bottom;align=center;verticalAlign=top;shape=mxgraph.kubernetes.icon;prIcon=ing" vertex="1" parent="1">
+          <mxGeometry x="20" y="390" width="50" height="48" as="geometry" />
+        </mxCell>
+        <mxCell id="z5OKJBfVE0389Lpc2gJH-8" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;entryX=0;entryY=0.5;entryDx=0;entryDy=0;entryPerimeter=0;" edge="1" parent="1" source="z5OKJBfVE0389Lpc2gJH-2" target="z5OKJBfVE0389Lpc2gJH-4">
+          <mxGeometry relative="1" as="geometry" />
+        </mxCell>
+        <mxCell id="z5OKJBfVE0389Lpc2gJH-2" value="dbrepo-ui" style="sketch=0;html=1;dashed=0;whitespace=wrap;fillColor=#2875E2;strokeColor=#ffffff;points=[[0.005,0.63,0],[0.1,0.2,0],[0.9,0.2,0],[0.5,0,0],[0.995,0.63,0],[0.72,0.99,0],[0.5,1,0],[0.28,0.99,0]];verticalLabelPosition=bottom;align=center;verticalAlign=top;shape=mxgraph.kubernetes.icon;prIcon=svc" vertex="1" parent="1">
+          <mxGeometry x="130" y="390" width="50" height="48" as="geometry" />
+        </mxCell>
+        <mxCell id="z5OKJBfVE0389Lpc2gJH-4" value="pod" style="sketch=0;html=1;dashed=0;whitespace=wrap;fillColor=#2875E2;strokeColor=#ffffff;points=[[0.005,0.63,0],[0.1,0.2,0],[0.9,0.2,0],[0.5,0,0],[0.995,0.63,0],[0.72,0.99,0],[0.5,1,0],[0.28,0.99,0]];verticalLabelPosition=bottom;align=center;verticalAlign=top;shape=mxgraph.kubernetes.icon;prIcon=pod" vertex="1" parent="1">
+          <mxGeometry x="240" y="390" width="50" height="48" as="geometry" />
+        </mxCell>
+        <mxCell id="z5OKJBfVE0389Lpc2gJH-13" value="Namespace dbrepo" style="sketch=0;html=1;dashed=0;whitespace=wrap;fillColor=#2875E2;strokeColor=#ffffff;points=[[0.005,0.63,0],[0.1,0.2,0],[0.9,0.2,0],[0.5,0,0],[0.995,0.63,0],[0.72,0.99,0],[0.5,1,0],[0.28,0.99,0]];verticalLabelPosition=bottom;align=center;verticalAlign=top;shape=mxgraph.kubernetes.icon;prIcon=ns" vertex="1" parent="1">
+          <mxGeometry x="40" width="50" height="48" as="geometry" />
+        </mxCell>
+        <mxCell id="z5OKJBfVE0389Lpc2gJH-14" value="dbrepo-&lt;br&gt;metadata-db" style="sketch=0;html=1;dashed=0;whitespace=wrap;fillColor=#2875E2;strokeColor=#ffffff;points=[[0.005,0.63,0],[0.1,0.2,0],[0.9,0.2,0],[0.5,0,0],[0.995,0.63,0],[0.72,0.99,0],[0.5,1,0],[0.28,0.99,0]];verticalLabelPosition=bottom;align=center;verticalAlign=top;shape=mxgraph.kubernetes.icon;prIcon=svc" vertex="1" parent="1">
+          <mxGeometry x="130" y="610" width="50" height="48" as="geometry" />
+        </mxCell>
+        <mxCell id="z5OKJBfVE0389Lpc2gJH-15" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;entryX=0;entryY=0.5;entryDx=0;entryDy=0;entryPerimeter=0;" edge="1" parent="1" target="z5OKJBfVE0389Lpc2gJH-18">
+          <mxGeometry relative="1" as="geometry">
+            <mxPoint x="180" y="634" as="sourcePoint" />
+          </mxGeometry>
+        </mxCell>
+        <mxCell id="z5OKJBfVE0389Lpc2gJH-16" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;startArrow=classic;startFill=1;endArrow=none;endFill=0;" edge="1" parent="1" source="z5OKJBfVE0389Lpc2gJH-17">
+          <mxGeometry relative="1" as="geometry">
+            <mxPoint x="192.66666666666663" y="634.3333333333334" as="targetPoint" />
+          </mxGeometry>
+        </mxCell>
+        <mxCell id="z5OKJBfVE0389Lpc2gJH-17" value="pod" style="sketch=0;html=1;dashed=0;whitespace=wrap;fillColor=#2875E2;strokeColor=#ffffff;points=[[0.005,0.63,0],[0.1,0.2,0],[0.9,0.2,0],[0.5,0,0],[0.995,0.63,0],[0.72,0.99,0],[0.5,1,0],[0.28,0.99,0]];verticalLabelPosition=bottom;align=center;verticalAlign=top;shape=mxgraph.kubernetes.icon;prIcon=pod" vertex="1" parent="1">
+          <mxGeometry x="240" y="530" width="50" height="48" as="geometry" />
+        </mxCell>
+        <mxCell id="z5OKJBfVE0389Lpc2gJH-18" value="pod" style="sketch=0;html=1;dashed=0;whitespace=wrap;fillColor=#2875E2;strokeColor=#ffffff;points=[[0.005,0.63,0],[0.1,0.2,0],[0.9,0.2,0],[0.5,0,0],[0.995,0.63,0],[0.72,0.99,0],[0.5,1,0],[0.28,0.99,0]];verticalLabelPosition=bottom;align=center;verticalAlign=top;shape=mxgraph.kubernetes.icon;prIcon=pod" vertex="1" parent="1">
+          <mxGeometry x="240" y="610" width="50" height="48" as="geometry" />
+        </mxCell>
+        <mxCell id="z5OKJBfVE0389Lpc2gJH-19" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;startArrow=classic;startFill=1;endArrow=none;endFill=0;" edge="1" parent="1" source="z5OKJBfVE0389Lpc2gJH-20">
+          <mxGeometry relative="1" as="geometry">
+            <mxPoint x="192.66666666666663" y="633.6666666666666" as="targetPoint" />
+          </mxGeometry>
+        </mxCell>
+        <mxCell id="z5OKJBfVE0389Lpc2gJH-20" value="pod" style="sketch=0;html=1;dashed=0;whitespace=wrap;fillColor=#2875E2;strokeColor=#ffffff;points=[[0.005,0.63,0],[0.1,0.2,0],[0.9,0.2,0],[0.5,0,0],[0.995,0.63,0],[0.72,0.99,0],[0.5,1,0],[0.28,0.99,0]];verticalLabelPosition=bottom;align=center;verticalAlign=top;shape=mxgraph.kubernetes.icon;prIcon=pod" vertex="1" parent="1">
+          <mxGeometry x="240" y="690" width="50" height="48" as="geometry" />
+        </mxCell>
+      </root>
+    </mxGraphModel>
+  </diagram>
 </mxfile>
diff --git a/mkdocs.yml b/mkdocs.yml
index e308b20..f23e3b6 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -31,6 +31,7 @@ theme:
     repo: fontawesome/brands/git-alt
   palette:
     scheme: default
+    primary: custom
     font:
       code: Roboto Mono
     toggle:
-- 
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