From 4a0850ed12c0af9eb43924d6a8f069c18735757f Mon Sep 17 00:00:00 2001
From: dasawanaka <michal.19.daniel.96@gmail.com>
Date: Wed, 17 May 2023 07:57:00 +0200
Subject: [PATCH 01/12] New docker compose

Signed-off-by: dasawanaka <michal.19.daniel.96@gmail.com>
---
 README.md                         | 93 +++++++++----------------------
 docker-compose.yaml               | 33 +++++------
 docker/init-onto-viewer.sh        |  3 +-
 docker/web/Dockerfile             | 43 ++++----------
 docker/web/init-web-and-strapi.sh | 27 +++++++++
 docker/web/nuxt.config.js         |  8 +--
 6 files changed, 83 insertions(+), 124 deletions(-)
 create mode 100644 docker/web/init-web-and-strapi.sh

diff --git a/README.md b/README.md
index 6dee6ad3..80571d42 100644
--- a/README.md
+++ b/README.md
@@ -36,91 +36,48 @@ java -jar app-v-0.1.0.war
 
 To run the application using Docker you have to install Docker and docker-compose on your local computer.  To install Docker see [here](https://docs.docker.com/get-docker/) and to install docker-compose see [here](https://docs.docker.com/compose/install/). 
 
-1. Create onto-viewer-web directory next to onto-viewer root folder.
-2. Install Strapi with the development database in the root directory. To this end, run `npx create-strapi-app@latest strapi-dashboard --quickstart --no-run`command.
-3. Copy files and folders from html-pages repository:
-- `html-pages/general/strapi/.tmp/` > `strapi-dashboard/.tmp/`
-- `html-pages/general/strapi/src/` > `strapi-dashboard/src/`
-- `html-pages/general` > `onto-viewer-web/`
-- `html-pages/general/strapi/Dockerfile` > `strapi-dashboard/Dockerfile`
-- `onto-viewer/docker/web/.dockerignore` > `strapi-dashboard/.dockerignore`
-- `onto-viewer/docker/web/nuxt.config.js` > `onto-viewer-web/nuxt.config.js`
-- `onto-viewer/docker/web/Dockerfile` > `onto-viewer-web/Dockerfile`
-4. In the `onto-viewer/docker/runtime/server/` folder, you must put configuration and ontologies files. You can find samples of these files in the `onto-viewer-config-loader/src/main/resources`. Note that the `onto-viewer/docker/runtime/ `folder is excluded from Git, so you can freely put there any file you want.
-The final folder system should look like shown below:
-
-```
-onto-viewer
-|   .gitignore
-|   CHANGELOG.md
-|   CODE_OF_CONDUCT.md
-|   CONTRIBUTING.md
-|   DCO
-|   docker-compose.yaml
-|   LICENSE
-|   pom.xml
-|   README.md   
-|   api-doc/
-|   docker/
-|   |   init-onto-viewer.sh
-|   runtime/
-|   |   server/ 
-|   |       config <- config files go here    
-|   |       ontologies <- ontologies go here
-|   server
-|   |   Dockerfile      
-|   web
-|   |   nuxt.config.js         
-|   onto-viewer-config-loader
-|   onto-viewer-core
-|   onto-viewer-toolkit
-|   onto-viewer-web-app 
-|   style          
-onto-viewer-web <- installed and configured general tempaltes from general directory
-|   .dockerignore
-|   ...
-|   Dockerfile
-|   jsconfig.json
-|   nuxt.config.js
-|   ...
-|   api
-|	...
-|   store
-|   strapi
-strapi-dashboard <- installed and configured Strapi
-|   .dockerignore
-|	...
-|   Dockerfile
-|   favicon.png
-|   package-lock.json
-|   package.json
-|   README.md
-|   yarn.lock
-|   .tmp/   
-|   config/
-|   database/
-|   public/
-|   src/
-```
-  
+ In the `onto-viewer/docker/runtime/server/` folder, you must put configuration and ontologies files. You can find samples of these files in the `onto-viewer-config-loader/src/main/resources`. Note that the `onto-viewer/docker/runtime/ `folder is excluded from Git, so you can freely put there any file you want.
 
 Then, from the `onto-viewer/` folder run the following command to start the applications:
 
 ```
 docker-compose up --build -d
 ```
-To list applications that have started, use ```docker-compose ps```.
 
 Please note that it takes a while to for all services to start depending on how many ontologies you provided.
 
 After all ontologies are loaded, the Onto viewer will be accessible from http://localhost:3000/dev/ontology. 
 
+
+You can see all running containers and their status:
+
+```
+$ docker compose ps
+
+NAME                   IMAGE                COMMAND                  SERVICE             CREATED             STATUS              PORTS
+html-pages-general-1   html-pages-general   "docker-entrypoint.s…"   general             20 seconds ago      Up 17 seconds       0.0.0.0:8081->3000/tcp
+html-pages-home-1      html-pages-home      "docker-entrypoint.s…"   home                7 hours ago         Up 4 minutes        0.0.0.0:8080->8080/tcp
+html-pages-strapi-1    html-pages-strapi    "docker-entrypoint.s…"   strapi              4 hours ago         Up 17 seconds       0.0.0.0:1337->1337/tcp
+```
+
+If you want to see logs from one container use:
+
+```
+# to view continuous log output
+$ docker logs --follow <container name>
+
+# to view specific amount of logs
+$ docker logs --tail <amount> <container name>
+```
+
 To stop the applications run:
 
 ```
 docker-compose down
 ```
 
+You could also run docker-compose without detached mode(without -d). If so, you'll just use '^C' to kill all containers.
+
 
 # Contributing
 Please read [CONTRIBUTING.md](CONTRIBUTING.md) and [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md) for details on our code of conduct, and the process for submitting pull requests to us.
diff --git a/docker-compose.yaml b/docker-compose.yaml
index 541a9969..bed45d6a 100644
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -12,11 +12,14 @@ version: "3.8"
 services:
   onto-viewer-server:
     container_name: onto-viewer-server
+    environment: 
+      - ONTPUB_FAMILY="${ONTPUB_FAMILY:-dev}"
     build:
       context: .
       dockerfile: ./docker/server/Dockerfile
     ports:
       - "6101:8080"
+
     volumes:
       - ./docker/init-onto-viewer.sh:/opt/develop/init-onto-viewer.sh
       - .:/opt/develop/src
@@ -24,26 +27,16 @@ services:
       - ./docker/runtime/server:/opt/develop/app_home
     networks:
       - default
-
-  onto-viewer-web:
-    container_name: onto-viewer-web
-    build:
-      context: ../onto-viewer-web
-      dockerfile: Dockerfile
-    ports:
-      - "3000:3000"
-    depends_on:
-      - onto-viewer-server
-      - strapi
-    networks:
-      - default
-
-  strapi:
-    container_name: onto-viewer-strapi
+  web-with-strapi: 
+    container_name: onto-viewer-web-with-strapi
+    environment: 
+      - PUBLIC_URL=0.0.0.0
+      - NUXT_PORT=3000
+      - ONTPUB_FAMILY=${ONTPUB_FAMILY:-dev}
     build:
-      context: ../strapi-dashboard
-      dockerfile: Dockerfile
-    ports:
-      - "1337:1337"
+      context: ./docker/web
+    ports: 
+      - 3000:3000
+      - 1337:1337
     networks:
       - default
\ No newline at end of file
diff --git a/docker/init-onto-viewer.sh b/docker/init-onto-viewer.sh
index b9e8c0f8..8ff19fec 100644
--- a/docker/init-onto-viewer.sh
+++ b/docker/init-onto-viewer.sh
@@ -19,4 +19,5 @@ cd "$INIT_DIR"
 cp "$INSTALL_DIR"/onto-viewer-web-app/target/onto-viewer-web-app-*.war app.war
 
 echo "[INFO] Starting app.war..."
-java -jar app.war --server.servlet.context-path=/dev/ontology --app.defaultHomePath="$INIT_DIR/app_home"
+exec java ${UPDATE_URL:+ -Dapp.config.ontologies.download_directory=download -Dapp.config.updateUrl=${UPDATE_URL}} -jar app.war --server.servlet.context-path=/dev/ontology --app.defaultHomePath="$INIT_DIR/app_home"
+#java -jar app.war --server.servlet.context-path=/$ONTPUB_FAMILY/ontology --app.defaultHomePath="$INIT_DIR/app_home"
diff --git a/docker/web/Dockerfile b/docker/web/Dockerfile
index ff88d1e2..80535979 100644
--- a/docker/web/Dockerfile
+++ b/docker/web/Dockerfile
@@ -1,31 +1,12 @@
-FROM node:16-alpine
-
-# create destination directory
-RUN mkdir -p /usr/src/nuxt-app
-WORKDIR /usr/src/nuxt-app
-
-# update and install dependency
-RUN apk update && apk upgrade
-RUN apk add git
-
-# copy the app, note .dockerignore
-COPY . /usr/src/nuxt-app/
-RUN npm install
-
-# build necessary, even if no static files are needed,
-# since it builds the server as well
- RUN npm run build
-
-# expose 3000 on container
-EXPOSE 3000
-
-# set app serving to permissive / assigned
-ENV PUBLIC_URL=0.0.0.0
-
-# set app port
-ENV NUXT_PORT=3000
-
-ENV ONTPUB_FAMILY=dev
-
-# start the app
-CMD [ "npm", "run" ,"dev" ]
+FROM node:16-alpine
+# Installing libvips-dev for sharp Compatibility
+RUN apk update && apk add --no-cache build-base gcc autoconf automake zlib-dev libpng-dev nasm bash vips-dev git
+ARG NODE_ENV=development
+ENV NODE_ENV=${NODE_ENV}
+WORKDIR /opt/
+COPY ./ .
+EXPOSE 1337
+EXPOSE 3000
+CMD ["sh", "init-web-and-strapi.sh"]
+# ENV HOST=0.0.0.0
+
diff --git a/docker/web/init-web-and-strapi.sh b/docker/web/init-web-and-strapi.sh
new file mode 100644
index 00000000..dfef113b
--- /dev/null
+++ b/docker/web/init-web-and-strapi.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+echo "[INFO] Clone html pages"
+git clone https://github.com/edmcouncil/html-pages.git
+
+cd /opt/html-pages/general/strapi
+
+echo "[INFO] Install strapi without run."
+npx create-strapi-app@latest strapi-dashboard --quickstart --no-run
+
+echo "[INFO] Copy database."
+mkdir ./strapi-dashboard/.tmp
+cp ./.tmp/data.db ./strapi-dashboard/.tmp/data.db
+
+echo "[INFO] Copy structures."
+cp -R ./src/ ./strapi-dashboard
+
+echo "[INFO] Run Strapi."
+cd strapi-dashboard
+npm run develop &
+
+echo "[INFO] Install and run general web pages"
+cd /opt/html-pages/general
+rm nuxt.config.js
+cp ../../nuxt.config.js .
+npm install
+npm run build
+npm run dev
diff --git a/docker/web/nuxt.config.js b/docker/web/nuxt.config.js
index 17870b01..e8932fe0 100644
--- a/docker/web/nuxt.config.js
+++ b/docker/web/nuxt.config.js
@@ -18,7 +18,7 @@ process.env.VUE_APP_TAG = process.env.TAG || process.env.TAG_NAME || "latest";
 process.env.VUE_DIST_DIR = `/${process.env.VUE_APP_PRODUCT}/${process.env.VUE_APP_BRANCH}/${process.env.VUE_APP_TAG}`;
 process.env.VUE_ASSETS_DIR = `${process.env.VUE_DIST_DIR}/_nuxt/`;
 
-process.env.VUE_ONTOLOGY_NAME = process.env.ONTPUB_FAMILY || "iof";
+process.env.VUE_ONTOLOGY_NAME = process.env.ONTPUB_FAMILY || "dev";
 process.env.VUE_BASE_URL =
   process.env.BASE_URL ||
   "https://spec." +
@@ -81,7 +81,7 @@ export default {
     base: `/${process.env.VUE_ONTOLOGY_NAME}`,
   },
 
-//to removed
+  //to removed
   generate: {
     dir: `dist/${process.env.VUE_ONTOLOGY_NAME}${process.env.VUE_DIST_DIR}`,
     routes() {
@@ -182,8 +182,8 @@ export default {
   },
 
   proxy: [
-        "http://onto-viewer-server:8080/dev/ontology/api",
-        "http://onto-viewer-server:8080/dev/ontology/*/api",
+    `http://onto-viewer-server:8080/${process.env.VUE_ONTOLOGY_NAME}/ontology/api`,
+    `http://onto-viewer-server:8080/${process.env.VUE_ONTOLOGY_NAME}/ontology/*/api`,
   ],
 
   styleResources: {

From 96630a3c5cc29166766f978bf9cb453cb3ff4b77 Mon Sep 17 00:00:00 2001
From: dasawanaka <michal.19.daniel.96@gmail.com>
Date: Wed, 17 May 2023 08:04:53 +0200
Subject: [PATCH 02/12] Fix Readme description

Signed-off-by: dasawanaka <michal.19.daniel.96@gmail.com>
---
 README.md | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 80571d42..46756a96 100644
--- a/README.md
+++ b/README.md
@@ -55,9 +55,8 @@ You can see all running containers and their status:
 $ docker compose ps
 
 NAME                   IMAGE                COMMAND                  SERVICE             CREATED             STATUS              PORTS
-html-pages-general-1   html-pages-general   "docker-entrypoint.s…"   general             20 seconds ago      Up 17 seconds       0.0.0.0:8081->3000/tcp
-html-pages-home-1      html-pages-home      "docker-entrypoint.s…"   home                7 hours ago         Up 4 minutes        0.0.0.0:8080->8080/tcp
-html-pages-strapi-1    html-pages-strapi    "docker-entrypoint.s…"   strapi              4 hours ago         Up 17 seconds       0.0.0.0:1337->1337/tcp
+onto-viewer-server-1   onto-viewer-server   "docker-entrypoint.s…"   onto-viewer-server  20 seconds ago      Up 17 seconds       0.0.0.0:8080->6101/tcp
+web-with-strapi-1      web-with-strapi      "docker-entrypoint.s…"   web-with-strapi     4 hours ago         Up 17 seconds       0.0.0.0:1337->1337/tcp
 ```
 
 If you want to see logs from one container use:

From b3b809acc1cfff9c23383ab22779ae47506e3c37 Mon Sep 17 00:00:00 2001
From: dasawanaka <michal.19.daniel.96@gmail.com>
Date: Fri, 19 May 2023 16:15:17 +0200
Subject: [PATCH 03/12] fix not working connection between ov and html-pages

Signed-off-by: dasawanaka <michal.19.daniel.96@gmail.com>
---
 README.md                         |  8 +++++---
 docker-compose.yaml               | 12 ++----------
 docker/init-onto-viewer.sh        |  4 ++--
 docker/web/init-web-and-strapi.sh |  2 +-
 4 files changed, 10 insertions(+), 16 deletions(-)

diff --git a/README.md b/README.md
index 46756a96..efa3946d 100644
--- a/README.md
+++ b/README.md
@@ -52,7 +52,7 @@ After all ontologies are loaded, the Onto viewer will be accessible from http://
 You can see all running containers and their status:
 
 ```
-$ docker compose ps
+$ docker-compose ps
 
 NAME                   IMAGE                COMMAND                  SERVICE             CREATED             STATUS              PORTS
 onto-viewer-server-1   onto-viewer-server   "docker-entrypoint.s…"   onto-viewer-server  20 seconds ago      Up 17 seconds       0.0.0.0:8080->6101/tcp
@@ -63,10 +63,12 @@ If you want to see logs from one container use:
 
 ```
 # to view continuous log output
-$ docker logs --follow <container name>
+# where "<container name>" is "onto-viewer-server" or "web-with-strapi"
+$ docker-compose logs --follow <container name> 
 
 # to view specific amount of logs
-$ docker logs --tail <amount> <container name>
+# where "<amount>" is amount of logs and "<container name>" is "onto-viewer-server" or "web-with-strapi"
+$ docker-compose logs --tail <amount> <container name>
 ```
 
 To stop the applications run:
diff --git a/docker-compose.yaml b/docker-compose.yaml
index bed45d6a..eab87f0e 100644
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -1,19 +1,11 @@
-# For this docker-compose.yaml file to work, the following folder outline is required:
-#
-#   aRootDir/
-#     onto-viewer/            (https://github.com/edmcouncil/onto-viewer)
-#       docker-compose.yaml   <- this file
-#         ...
-#     html-pages/             (https://github.com/edmcouncil/html-pages)
-#       ...
-
 version: "3.8"
 
 services:
   onto-viewer-server:
     container_name: onto-viewer-server
     environment: 
-      - ONTPUB_FAMILY="${ONTPUB_FAMILY:-dev}"
+      - ONTPUB_FAMILY=${ONTPUB_FAMILY:-dev}
+      - UPDATE_URL
     build:
       context: .
       dockerfile: ./docker/server/Dockerfile
diff --git a/docker/init-onto-viewer.sh b/docker/init-onto-viewer.sh
index 8ff19fec..7b4b8365 100644
--- a/docker/init-onto-viewer.sh
+++ b/docker/init-onto-viewer.sh
@@ -19,5 +19,5 @@ cd "$INIT_DIR"
 cp "$INSTALL_DIR"/onto-viewer-web-app/target/onto-viewer-web-app-*.war app.war
 
 echo "[INFO] Starting app.war..."
-exec java ${UPDATE_URL:+ -Dapp.config.ontologies.download_directory=download -Dapp.config.updateUrl=${UPDATE_URL}} -jar app.war --server.servlet.context-path=/dev/ontology --app.defaultHomePath="$INIT_DIR/app_home"
-#java -jar app.war --server.servlet.context-path=/$ONTPUB_FAMILY/ontology --app.defaultHomePath="$INIT_DIR/app_home"
+exec java ${UPDATE_URL:+ -Dapp.config.ontologies.download_directory=download -Dapp.config.updateUrl=${UPDATE_URL}} -jar app.war --server.servlet.context-path=/${ONTPUB_FAMILY:-dev}/ontology --app.defaultHomePath="$INIT_DIR/app_home"
+
diff --git a/docker/web/init-web-and-strapi.sh b/docker/web/init-web-and-strapi.sh
index dfef113b..cc90dbcb 100644
--- a/docker/web/init-web-and-strapi.sh
+++ b/docker/web/init-web-and-strapi.sh
@@ -9,7 +9,7 @@ npx create-strapi-app@latest strapi-dashboard --quickstart --no-run
 
 echo "[INFO] Copy database."
 mkdir ./strapi-dashboard/.tmp
-cp ./.tmp/data.db ./strapi-dashboard/.tmp/data.db
+cp ./.tmp/${ONTPUB_FAMILY:-data}.db ./strapi-dashboard/.tmp/data.db
 
 echo "[INFO] Copy structures."
 cp -R ./src/ ./strapi-dashboard

From 06a3ad1afcdfb2c702da3b9f9421e02e91419196 Mon Sep 17 00:00:00 2001
From: dasawanaka <michal.19.daniel.96@gmail.com>
Date: Fri, 19 May 2023 18:00:19 +0200
Subject: [PATCH 04/12] docker-compose -> docker compose

Signed-off-by: dasawanaka <michal.19.daniel.96@gmail.com>
---
 README.md | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index efa3946d..671477dc 100644
--- a/README.md
+++ b/README.md
@@ -34,14 +34,14 @@ java -jar app-v-0.1.0.war
  ## Running in Docker
 
 
-To run the application using Docker you have to install Docker and docker-compose on your local computer.  To install Docker see [here](https://docs.docker.com/get-docker/) and to install docker-compose see [here](https://docs.docker.com/compose/install/). 
+To run the application using Docker you have to install Docker and docker compose on your local computer.  To install Docker see [here](https://docs.docker.com/get-docker/) and to install docker compose see [here](https://docs.docker.com/compose/install/). 
 
  In the `onto-viewer/docker/runtime/server/` folder, you must put configuration and ontologies files. You can find samples of these files in the `onto-viewer-config-loader/src/main/resources`. Note that the `onto-viewer/docker/runtime/ `folder is excluded from Git, so you can freely put there any file you want.
 
 Then, from the `onto-viewer/` folder run the following command to start the applications:
 
 ```
-docker-compose up --build -d
+docker compose up --build -d
 ```
 
 Please note that it takes a while to for all services to start depending on how many ontologies you provided.
@@ -52,7 +52,7 @@ After all ontologies are loaded, the Onto viewer will be accessible from http://
 You can see all running containers and their status:
 
 ```
-$ docker-compose ps
+$ docker compose ps
 
 NAME                   IMAGE                COMMAND                  SERVICE             CREATED             STATUS              PORTS
 onto-viewer-server-1   onto-viewer-server   "docker-entrypoint.s…"   onto-viewer-server  20 seconds ago      Up 17 seconds       0.0.0.0:8080->6101/tcp
@@ -64,20 +64,20 @@ If you want to see logs from one container use:
 ```
 # to view continuous log output
 # where "<container name>" is "onto-viewer-server" or "web-with-strapi"
-$ docker-compose logs --follow <container name> 
+$ docker compose logs --follow <container name> 
 
 # to view specific amount of logs
 # where "<amount>" is amount of logs and "<container name>" is "onto-viewer-server" or "web-with-strapi"
-$ docker-compose logs --tail <amount> <container name>
+$ docker compose logs --tail <amount> <container name>
 ```
 
 To stop the applications run:
 
 ```
-docker-compose down
+docker compose down
 ```
 
-You could also run docker-compose without detached mode(without -d). If so, you'll just use '^C' to kill all containers.
+You could also run docker compose without detached mode(without -d). If so, you'll just use '^C' to kill all containers.
 
 
 # Contributing

From 63a78b1f8cb2733f562f0d22be3122e0bbe8772d Mon Sep 17 00:00:00 2001
From: dasawanaka <michal.19.daniel.96@gmail.com>
Date: Wed, 31 May 2023 05:42:32 +0200
Subject: [PATCH 05/12] Fix README

Signed-off-by: dasawanaka <michal.19.daniel.96@gmail.com>
---
 README.md | 17 +++++------------
 1 file changed, 5 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index 671477dc..3ba85c99 100644
--- a/README.md
+++ b/README.md
@@ -30,15 +30,15 @@ java -jar app-v-0.1.0.war
 ```
 
 
-
  ## Running in Docker
 
-
 To run the application using Docker you have to install Docker and docker compose on your local computer.  To install Docker see [here](https://docs.docker.com/get-docker/) and to install docker compose see [here](https://docs.docker.com/compose/install/). 
 
- In the `onto-viewer/docker/runtime/server/` folder, you must put configuration and ontologies files. You can find samples of these files in the `onto-viewer-config-loader/src/main/resources`. Note that the `onto-viewer/docker/runtime/ `folder is excluded from Git, so you can freely put there any file you want.
+The `onto-viewer/` folder is root/main project folder. All folders below are relative to this folder.
+
+ In the `docker/runtime/server/` folder, you must put configuration(in the `config` folder) and ontologies(in the `ontologies` folder) files if used. You can find samples of these files in the `onto-viewer-config-loader/src/main/resources`, you should rename the files - remove the default_ prefix. Note that the `docker/runtime/ `folder is excluded from Git, so you can freely put there any file you want.
 
-Then, from the `onto-viewer/` folder run the following command to start the applications:
+Then, from the root folder run the following command to start the applications:
 
 ```
 docker compose up --build -d
@@ -46,7 +46,7 @@ docker compose up --build -d
 
 Please note that it takes a while to for all services to start depending on how many ontologies you provided.
 
-After all ontologies are loaded, the Onto viewer will be accessible from http://localhost:3000/dev/ontology. 
+After all ontologies are loaded, the Onto Viewer will be accessible from http://localhost:3000/dev/ontology. 
 
 
 You can see all running containers and their status:
@@ -96,10 +96,3 @@ mvn -P integration-tests verify
 # License
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
 
-
-<!--
- # Release notes
-
-Please read [CHANGELOG.md](CHANGELOG.md) for details.
- -->
-

From 38d3657090847d717b0d940e3ffb2bb295606d37 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Przemys=C5=82aw=20Gr=C4=85dzki?= <przemek.gradzki@gmail.com>
Date: Tue, 6 Jun 2023 09:38:03 +0200
Subject: [PATCH 06/12] New docker compose
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Signed-off-by: Przemysław Grądzki <przemek.gradzki@gmail.com>
---
 Dockerfile.onto-viewer            | 23 ++++++++++++
 docker-compose.yaml               | 60 ++++++++++++++++---------------
 onto-viewer-web-app/entrypoint.sh | 14 ++++++++
 3 files changed, 68 insertions(+), 29 deletions(-)
 create mode 100644 Dockerfile.onto-viewer
 create mode 100644 onto-viewer-web-app/entrypoint.sh

diff --git a/Dockerfile.onto-viewer b/Dockerfile.onto-viewer
new file mode 100644
index 00000000..1eaf741e
--- /dev/null
+++ b/Dockerfile.onto-viewer
@@ -0,0 +1,23 @@
+FROM maven:3.8.1-jdk-11-openj9 AS build-onto-viewer
+SHELL ["/bin/bash", "-c"]
+RUN	apt-get update && \
+	apt-get -y install curl unzip zip
+RUN mkdir -p /opt/develop
+WORKDIR /opt/develop
+COPY .	/opt/develop/
+RUN	mvn clean package && cp -av onto-viewer-web-app/target/onto-viewer-web-app-*.war /app.war
+
+FROM	adoptopenjdk/openjdk11-openj9:alpine-slim
+ARG	ONTPUB_FAMILY	dev
+ARG	UPDATE_URL
+ENV	ONTPUB_FAMILY	${ONTPUB_FAMILY}
+ENV	UPDATE_URL	${UPDATE_URL}
+RUN	apk --no-cache add --upgrade bash curl jq && \
+	install -d /opt/viewer/{config,ontologies}
+WORKDIR	/opt/viewer
+COPY	./onto-viewer-web-app/entrypoint.sh		/opt/viewer/entrypoint.sh
+COPY	./onto-viewer-web-app/integration_tests	/opt/viewer/integration_tests
+COPY	./onto-viewer-web-app/staticOntologies	/opt/viewer/staticOntologies
+COPY --from=build-onto-viewer	/app.war	/app.war
+CMD	["sh", "entrypoint.sh"]
+HEALTHCHECK --start-period=60s --interval=15s --timeout=1s --retries=60 CMD curl -q http://localhost/${ONTPUB_FAMILY}/ontology/actuator/health | jq -e ".components.custom.details.INITIALIZATION_DONE"
\ No newline at end of file
diff --git a/docker-compose.yaml b/docker-compose.yaml
index eab87f0e..940035d3 100644
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -1,34 +1,36 @@
-version: "3.8"
-
 services:
-  onto-viewer-server:
-    container_name: onto-viewer-server
-    environment: 
-      - ONTPUB_FAMILY=${ONTPUB_FAMILY:-dev}
-      - UPDATE_URL
+  fibo-strapi:
+    image: edmcouncil/fibo-strapi:latest
+    volumes:
+      - opt:/opt
+  fibo-pages:
+    image: edmcouncil/fibo-pages:latest
+    environment:
+      - STRAPI_URL=http://fibo-strapi:1337
+    volumes:
+      - opt:/opt
+    depends_on:
+      - fibo-strapi
+  fibo-viewer:
+    image: edmcouncil/onto-viewer:latest
     build:
       context: .
-      dockerfile: ./docker/server/Dockerfile
+      dockerfile: ./Dockerfile.onto-viewer
+    environment:
+      - ONTPUB_FAMILY=fibo
+      - UPDATE_URL=${FIBO_UPDATE_URL:-https://spec.edmcouncil.org/fibo/ontology/etc/onto-viewer-web-app/config/}
+  spec:
+    image: edmcouncil/spec:latest
+    environment:
+      - FAMILY_REGEX=fibo
+    volumes:
+      - opt:/opt
+    depends_on:
+      - fibo-strapi
+      - fibo-pages
+      - fibo-viewer
     ports:
-      - "6101:8080"
+      - 8080:80
 
-    volumes:
-      - ./docker/init-onto-viewer.sh:/opt/develop/init-onto-viewer.sh
-      - .:/opt/develop/src
-      - ./docker/runtime/.m2:/opt/develop/.m2
-      - ./docker/runtime/server:/opt/develop/app_home
-    networks:
-      - default
-  web-with-strapi: 
-    container_name: onto-viewer-web-with-strapi
-    environment: 
-      - PUBLIC_URL=0.0.0.0
-      - NUXT_PORT=3000
-      - ONTPUB_FAMILY=${ONTPUB_FAMILY:-dev}
-    build:
-      context: ./docker/web
-    ports: 
-      - 3000:3000
-      - 1337:1337
-    networks:
-      - default
\ No newline at end of file
+volumes:
+  opt:
diff --git a/onto-viewer-web-app/entrypoint.sh b/onto-viewer-web-app/entrypoint.sh
new file mode 100644
index 00000000..5c34b8ae
--- /dev/null
+++ b/onto-viewer-web-app/entrypoint.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+for i in config/default_* ; do
+ test -e config/${i#config/default_} || cp -av ${i} config/${i#config/default_}
+done
+
+# if no UPDATE_URL and no ontology files in "ontologies" directory then copy ontology files from "integration_tests/ontologies/"
+if [ -z "${UPDATE_URL}" ] && [ $(find ontologies/ -type f | wc -l) -eq 0 ] ; then
+ find integration_tests/ontologies/ -type f -exec cp -av "{}" ontologies/ \;
+fi
+
+echo "[INFO] Starting app.war..."
+exec java -server -Xmx4G -XX:-UseGCOverheadLimit -Dserver.address=0.0.0.0 -Dserver.port=80 -Dserver.forward-headers-strategy=native -Dserver.tomcat.redirect-context-root=false \
+	${UPDATE_URL:+ -Dapp.config.ontologies.download_directory=download -Dapp.config.updateUrl=${UPDATE_URL}} -jar /app.war --server.servlet.context-path=/${ONTPUB_FAMILY:-dev}/ontology

From b6e70ce2a86777905004588e814cc7268fde14c0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Przemys=C5=82aw=20Gr=C4=85dzki?= <przemek.gradzki@gmail.com>
Date: Mon, 12 Jun 2023 09:28:12 +0200
Subject: [PATCH 07/12] New docker compose - fixes
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Signed-off-by: Przemysław Grądzki <przemek.gradzki@gmail.com>
---
 .gitignore                        |   2 +
 Dockerfile.onto-viewer            |  22 ++--
 README.md                         |  99 +++++++++-----
 docker-compose.dev.yaml           |  52 ++++++++
 docker-compose.yaml               |  30 +++--
 docker/init-onto-viewer.sh        |  23 ----
 docker/server/Dockerfile          |  13 --
 docker/web/.dockerignore          |   1 -
 docker/web/Dockerfile             |  12 --
 docker/web/init-web-and-strapi.sh |  27 ----
 docker/web/nuxt.config.js         | 206 ------------------------------
 onto-viewer-web-app/entrypoint.sh |   5 -
 12 files changed, 153 insertions(+), 339 deletions(-)
 create mode 100644 docker-compose.dev.yaml
 delete mode 100644 docker/init-onto-viewer.sh
 delete mode 100644 docker/server/Dockerfile
 delete mode 100644 docker/web/.dockerignore
 delete mode 100644 docker/web/Dockerfile
 delete mode 100644 docker/web/init-web-and-strapi.sh
 delete mode 100644 docker/web/nuxt.config.js

diff --git a/.gitignore b/.gitignore
index 0a8df84f..1e0b5ae6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -205,6 +205,7 @@ nbactions.xml
 **/api.key
 **/updateHistory.json
 /web-app/fiboMapper/fibo/**
+.env
 
 
 # Protege
@@ -216,6 +217,7 @@ docker/runtime/
 lucene_index/
 download/
 onto-viewer-web-app/config/
+onto-viewer-web-app/ontologies/*
 
 # Mac
 .DS_Store
\ No newline at end of file
diff --git a/Dockerfile.onto-viewer b/Dockerfile.onto-viewer
index 1eaf741e..86723b1b 100644
--- a/Dockerfile.onto-viewer
+++ b/Dockerfile.onto-viewer
@@ -1,23 +1,21 @@
 FROM maven:3.8.1-jdk-11-openj9 AS build-onto-viewer
-SHELL ["/bin/bash", "-c"]
+SHELL	["/bin/bash", "-c"]
 RUN	apt-get update && \
-	apt-get -y install curl unzip zip
-RUN mkdir -p /opt/develop
+	apt-get -y install curl unzip zip && \
+	mkdir -p /opt/develop
 WORKDIR /opt/develop
 COPY .	/opt/develop/
 RUN	mvn clean package && cp -av onto-viewer-web-app/target/onto-viewer-web-app-*.war /app.war
 
 FROM	adoptopenjdk/openjdk11-openj9:alpine-slim
-ARG	ONTPUB_FAMILY	dev
-ARG	UPDATE_URL
-ENV	ONTPUB_FAMILY	${ONTPUB_FAMILY}
-ENV	UPDATE_URL	${UPDATE_URL}
+ARG	ONTPUB_FAMILY=dev UPDATE_URL
+ENV	ONTPUB_FAMILY="${ONTPUB_FAMILY}" UPDATE_URL="${UPDATE_URL}"
 RUN	apk --no-cache add --upgrade bash curl jq && \
-	install -d /opt/viewer/{config,ontologies}
+	install -d /opt/viewer/config
 WORKDIR	/opt/viewer
-COPY	./onto-viewer-web-app/entrypoint.sh		/opt/viewer/entrypoint.sh
-COPY	./onto-viewer-web-app/integration_tests	/opt/viewer/integration_tests
-COPY	./onto-viewer-web-app/staticOntologies	/opt/viewer/staticOntologies
+COPY	./onto-viewer-web-app/entrypoint.sh			/opt/viewer/entrypoint.sh
+COPY	./onto-viewer-web-app/integration_tests/ontologies	/opt/viewer/
+COPY	./onto-viewer-web-app/staticOntologies			/opt/viewer/staticOntologies
 COPY --from=build-onto-viewer	/app.war	/app.war
 CMD	["sh", "entrypoint.sh"]
-HEALTHCHECK --start-period=60s --interval=15s --timeout=1s --retries=60 CMD curl -q http://localhost/${ONTPUB_FAMILY}/ontology/actuator/health | jq -e ".components.custom.details.INITIALIZATION_DONE"
\ No newline at end of file
+HEALTHCHECK --start-period=60s --interval=15s --timeout=1s --retries=60 CMD test "$(curl -q http://localhost/${ONTPUB_FAMILY}/ontology/actuator/health | jq -e ".components.custom.details.INITIALIZATION_DONE")" = "true"
\ No newline at end of file
diff --git a/README.md b/README.md
index 3ba85c99..aefc6365 100644
--- a/README.md
+++ b/README.md
@@ -30,55 +30,90 @@ java -jar app-v-0.1.0.war
 ```
 
 
- ## Running in Docker
-
-To run the application using Docker you have to install Docker and docker compose on your local computer.  To install Docker see [here](https://docs.docker.com/get-docker/) and to install docker compose see [here](https://docs.docker.com/compose/install/). 
-
-The `onto-viewer/` folder is root/main project folder. All folders below are relative to this folder.
-
- In the `docker/runtime/server/` folder, you must put configuration(in the `config` folder) and ontologies(in the `ontologies` folder) files if used. You can find samples of these files in the `onto-viewer-config-loader/src/main/resources`, you should rename the files - remove the default_ prefix. Note that the `docker/runtime/ `folder is excluded from Git, so you can freely put there any file you want.
-
-Then, from the root folder run the following command to start the applications:
+## Run with docker
+Requirements:
+- [git](https://git-scm.com/) ([install](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git))
+- [docker](https://www.docker.com/) - install:
+  * [Docker Desktop](https://docs.docker.com/desktop/) or ...
+  * [Docker Engine](https://docs.docker.com/engine/) with [Docker Compose plugin](https://docs.docker.com/compose/install/linux/)
+- free port **8080/tcp**
+
+How to start:
+Clone the [edmcouncil/onto-viewer](https://github.com/edmcouncil/onto-viewer) repository to the *onto-viewer* directory,
+go to the *onto-viewer* directory (run all subsequent commands inside this directory),
+then build the images (or pull from the registry if available) and run the containers:
+```bash
+# clone the repository
+git clone https://github.com/edmcouncil/onto-viewer onto-viewer
+
+# got to the onto-viewer directory
+cd onto-viewer
+
+# build images
+docker compose build
+# alternatively pull images from registry if available
+#docker compose pull --ignore-pull-failures
+
+# run the containers
+docker compose up -d
+```
 
+After some time, check the status of running containers:
 ```
-docker compose up --build -d
+docker compose ps
 ```
 
-Please note that it takes a while to for all services to start depending on how many ontologies you provided.
+if they work correctly, the following message will appear:
+```
+NAME                        IMAGE                           COMMAND                  SERVICE             CREATED             STATUS                   PORTS
+onto-viewer-fibo-pages-1    edmcouncil/fibo-pages:latest    "docker-entrypoint.s…"   fibo-pages          7 minutes ago       Up 6 minutes (healthy)   
+onto-viewer-fibo-strapi-1   edmcouncil/fibo-strapi:latest   "docker-entrypoint.s…"   fibo-strapi         7 minutes ago       Up 6 minutes (healthy)   
+onto-viewer-fibo-viewer-1   edmcouncil/onto-viewer:latest   "sh entrypoint.sh"       fibo-viewer         7 minutes ago       Up 6 minutes (healthy)   
+onto-viewer-spec-1          edmcouncil/spec:latest          "/docker-entrypoint.…"   spec                7 minutes ago       Up 6 minutes (healthy)   0.0.0.0:8080->80/tcp, :::8080->80/tcp
 
-After all ontologies are loaded, the Onto Viewer will be accessible from http://localhost:3000/dev/ontology. 
+```
 
+The services provide endpoints at the following URLs:
+- [http://localhost:8080](http://localhost:8080) :- [html-pages home page](https://github.com/edmcouncil/html-pages/blob/develop/home/README.md)
+- [http://localhost:8080/fibo](http://localhost:8080/fibo) :- [html-pages general template](https://github.com/edmcouncil/html-pages/tree/develop/general) for [FIBO](https://github.com/edmcouncil/fibo) ontology
+- [http://localhost:8080/fibo/ontology](http://localhost:8080/fibo/ontology) :- onto-viewer for [FIBO](https://github.com/edmcouncil/fibo) ontology
+- [http://localhost:8080/fibo/strapi/admin](http://localhost:8080/fibo/strapi/admin) :- [Strapi admin panel](https://docs.strapi.io/user-docs/intro#accessing-the-admin-panel) for for [FIBO](https://github.com/edmcouncil/fibo) ontology (Email: *edmc-strapi@dev.com*, Password: *devDBonly1*)
 
-You can see all running containers and their status:
+It is possible to run containers with the `dev` ontology (instead of `FIBO`):
+- use the `docker-compose.dev.yaml` file (instead of the default `docker-compose.yaml`):
+  ```
+  echo COMPOSE_FILE=docker-compose.dev.yaml >> .env
+  ```
 
-```
-$ docker compose ps
+- optionally place the ontology files in the `onto-viewer-web-app/ontologies` subdirectory
+  and uncomment the following entry 
+  (see [comment](./docker-compose.dev.yaml#L31) in the `docker-compose.dev.yaml` file):
+  ```
+     - ./onto-viewer-web-app/ontologies:/opt/viewer/ontologies
+  ```
 
-NAME                   IMAGE                COMMAND                  SERVICE             CREATED             STATUS              PORTS
-onto-viewer-server-1   onto-viewer-server   "docker-entrypoint.s…"   onto-viewer-server  20 seconds ago      Up 17 seconds       0.0.0.0:8080->6101/tcp
-web-with-strapi-1      web-with-strapi      "docker-entrypoint.s…"   web-with-strapi     4 hours ago         Up 17 seconds       0.0.0.0:1337->1337/tcp
-```
+- build the images and run the containers. After all ontologies are loaded,
+  the Onto Viewer will be accessible from `http://localhost:8080/dev/ontology`
 
-If you want to see logs from one container use:
 
-```
-# to view continuous log output
-# where "<container name>" is "onto-viewer-server" or "web-with-strapi"
-$ docker compose logs --follow <container name> 
+If you want to see the logs use:
+```bash
+# to view continuous log output for <SERVICE>=fibo-viewer
+docker compose logs --follow fibo-viewer
 
-# to view specific amount of logs
-# where "<amount>" is amount of logs and "<container name>" is "onto-viewer-server" or "web-with-strapi"
-$ docker compose logs --tail <amount> <container name>
+# to view *100* latest log lines for <SERVICE>=fibo-viewer
+docker compose logs --tail 100 fibo-strapi
 ```
 
-To stop the applications run:
-
-```
+Stop the services with the command:
+```bash
 docker compose down
 ```
 
-You could also run docker compose without detached mode(without -d). If so, you'll just use '^C' to kill all containers.
-
+Remove all images and volumes with the command:
+```bash
+docker compose down --rmi all -v
+```
 
 # Contributing
 Please read [CONTRIBUTING.md](CONTRIBUTING.md) and [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md) for details on our code of conduct, and the process for submitting pull requests to us.
diff --git a/docker-compose.dev.yaml b/docker-compose.dev.yaml
new file mode 100644
index 00000000..e153970e
--- /dev/null
+++ b/docker-compose.dev.yaml
@@ -0,0 +1,52 @@
+services:
+  dev-strapi:
+    image: edmcouncil/dev-strapi:${HTML_BRANCH:-latest}
+    build:
+      context: https://github.com/edmcouncil/html-pages.git#${HTML_BRANCH:-develop}:general/strapi
+      args:
+        - ONTPUB_FAMILY=dev
+        - BRANCH_NAME=${HTML_BRANCH:-develop}
+    volumes:
+      - spec_root:/opt/html-pages
+  dev-pages:
+    image: edmcouncil/dev-pages:${HTML_BRANCH:-latest}
+    build:
+      context: https://github.com/edmcouncil/html-pages.git#${HTML_BRANCH:-develop}:general
+      args:
+        - ONTPUB_FAMILY=dev
+        - BRANCH_NAME=${HTML_BRANCH:-develop}
+    environment:
+      - STRAPI_URL=http://dev-strapi:1337
+    volumes:
+      - spec_root:/opt/html-pages
+    depends_on:
+      - dev-strapi
+  dev-viewer:
+    image: edmcouncil/onto-viewer:${TAG:-latest}
+    build:
+      context: .
+      dockerfile: ./Dockerfile.onto-viewer
+    environment:
+      - ONTPUB_FAMILY=dev
+    # uncomment to use custom ontology files located in the "./onto-viewer-web-app/ontologies" directory
+    #volumes:
+    #  - ./onto-viewer-web-app/ontologies:/opt/viewer/ontologies
+  spec:
+    image: edmcouncil/spec:${HTML_BRANCH:-latest}
+    build:
+      context: https://github.com/edmcouncil/html-pages.git#${HTML_BRANCH:-develop}:home
+      args:
+        - BRANCH_NAME=${HTML_BRANCH:-develop}
+    environment:
+      - FAMILY_REGEX=dev
+    volumes:
+      - spec_root:/opt/html-pages
+    depends_on:
+      - dev-strapi
+      - dev-pages
+      - dev-viewer
+    ports:
+      - 8080:80
+
+volumes:
+  spec_root:
diff --git a/docker-compose.yaml b/docker-compose.yaml
index 940035d3..4b6ae2a4 100644
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -1,18 +1,28 @@
 services:
   fibo-strapi:
-    image: edmcouncil/fibo-strapi:latest
+    image: edmcouncil/fibo-strapi:${HTML_BRANCH:-latest}
+    build:
+      context: https://github.com/edmcouncil/html-pages.git#${HTML_BRANCH:-develop}:general/strapi
+      args:
+        - ONTPUB_FAMILY=fibo
+        - BRANCH_NAME=${HTML_BRANCH:-develop}
     volumes:
-      - opt:/opt
+      - spec_root:/opt/html-pages
   fibo-pages:
-    image: edmcouncil/fibo-pages:latest
+    image: edmcouncil/fibo-pages:${HTML_BRANCH:-latest}
+    build:
+      context: https://github.com/edmcouncil/html-pages.git#${HTML_BRANCH:-develop}:general
+      args:
+        - ONTPUB_FAMILY=fibo
+        - BRANCH_NAME=${HTML_BRANCH:-develop}
     environment:
       - STRAPI_URL=http://fibo-strapi:1337
     volumes:
-      - opt:/opt
+      - spec_root:/opt/html-pages
     depends_on:
       - fibo-strapi
   fibo-viewer:
-    image: edmcouncil/onto-viewer:latest
+    image: edmcouncil/onto-viewer:${TAG:-latest}
     build:
       context: .
       dockerfile: ./Dockerfile.onto-viewer
@@ -20,11 +30,15 @@ services:
       - ONTPUB_FAMILY=fibo
       - UPDATE_URL=${FIBO_UPDATE_URL:-https://spec.edmcouncil.org/fibo/ontology/etc/onto-viewer-web-app/config/}
   spec:
-    image: edmcouncil/spec:latest
+    image: edmcouncil/spec:${HTML_BRANCH:-latest}
+    build:
+      context: https://github.com/edmcouncil/html-pages.git#${HTML_BRANCH:-develop}:home
+      args:
+        - BRANCH_NAME=${HTML_BRANCH:-develop}
     environment:
       - FAMILY_REGEX=fibo
     volumes:
-      - opt:/opt
+      - spec_root:/opt/html-pages
     depends_on:
       - fibo-strapi
       - fibo-pages
@@ -33,4 +47,4 @@ services:
       - 8080:80
 
 volumes:
-  opt:
+  spec_root:
diff --git a/docker/init-onto-viewer.sh b/docker/init-onto-viewer.sh
deleted file mode 100644
index 7b4b8365..00000000
--- a/docker/init-onto-viewer.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/bash
-
-echo "[INFO] Starting 'init-onto-viewer' installer..."
-
-INIT_DIR=$(pwd)
-INSTALL_DIR="$INIT_DIR/install_dir"
-
-cp -r src/ "$INSTALL_DIR"
-if [ -d "$INSTALL_DIR" ]; then
-  cd "$INSTALL_DIR"
-  mvn clean package
-else
-  echo "$INSTALL_DIR hasn't been created. Exiting..."
-  exit 1
-fi
-
-echo "[INFO] Moving to $INIT_DIR..."
-cd "$INIT_DIR"
-cp "$INSTALL_DIR"/onto-viewer-web-app/target/onto-viewer-web-app-*.war app.war
-
-echo "[INFO] Starting app.war..."
-exec java ${UPDATE_URL:+ -Dapp.config.ontologies.download_directory=download -Dapp.config.updateUrl=${UPDATE_URL}} -jar app.war --server.servlet.context-path=/${ONTPUB_FAMILY:-dev}/ontology --app.defaultHomePath="$INIT_DIR/app_home"
-
diff --git a/docker/server/Dockerfile b/docker/server/Dockerfile
deleted file mode 100644
index a3c3d296..00000000
--- a/docker/server/Dockerfile
+++ /dev/null
@@ -1,13 +0,0 @@
-FROM maven:3.8.1-jdk-11-openj9
-
-SHELL ["/bin/bash", "-c"]
-
-RUN apt-get update
-RUN apt-get -y install curl \
-    unzip \
-    zip
-
-RUN mkdir -p /opt/develop
-WORKDIR /opt/develop
-
-CMD ["sh", "init-onto-viewer.sh"]
\ No newline at end of file
diff --git a/docker/web/.dockerignore b/docker/web/.dockerignore
deleted file mode 100644
index b512c09d..00000000
--- a/docker/web/.dockerignore
+++ /dev/null
@@ -1 +0,0 @@
-node_modules
\ No newline at end of file
diff --git a/docker/web/Dockerfile b/docker/web/Dockerfile
deleted file mode 100644
index 80535979..00000000
--- a/docker/web/Dockerfile
+++ /dev/null
@@ -1,12 +0,0 @@
-FROM node:16-alpine
-# Installing libvips-dev for sharp Compatibility
-RUN apk update && apk add --no-cache build-base gcc autoconf automake zlib-dev libpng-dev nasm bash vips-dev git
-ARG NODE_ENV=development
-ENV NODE_ENV=${NODE_ENV}
-WORKDIR /opt/
-COPY ./ .
-EXPOSE 1337
-EXPOSE 3000
-CMD ["sh", "init-web-and-strapi.sh"]
-# ENV HOST=0.0.0.0
-
diff --git a/docker/web/init-web-and-strapi.sh b/docker/web/init-web-and-strapi.sh
deleted file mode 100644
index cc90dbcb..00000000
--- a/docker/web/init-web-and-strapi.sh
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/bin/bash
-echo "[INFO] Clone html pages"
-git clone https://github.com/edmcouncil/html-pages.git
-
-cd /opt/html-pages/general/strapi
-
-echo "[INFO] Install strapi without run."
-npx create-strapi-app@latest strapi-dashboard --quickstart --no-run
-
-echo "[INFO] Copy database."
-mkdir ./strapi-dashboard/.tmp
-cp ./.tmp/${ONTPUB_FAMILY:-data}.db ./strapi-dashboard/.tmp/data.db
-
-echo "[INFO] Copy structures."
-cp -R ./src/ ./strapi-dashboard
-
-echo "[INFO] Run Strapi."
-cd strapi-dashboard
-npm run develop &
-
-echo "[INFO] Install and run general web pages"
-cd /opt/html-pages/general
-rm nuxt.config.js
-cp ../../nuxt.config.js .
-npm install
-npm run build
-npm run dev
diff --git a/docker/web/nuxt.config.js b/docker/web/nuxt.config.js
deleted file mode 100644
index e8932fe0..00000000
--- a/docker/web/nuxt.config.js
+++ /dev/null
@@ -1,206 +0,0 @@
-import axios from "axios";
-
-process.env.VUE_APP_TIMESTAMP =
-  process.env.TIMESTAMP || process.env.VUE_ONTOLOGY_NAME==='idmp'?"latest":"2022Q3";
-
-process.env.VUE_APP_PRODUCT =
-  process.env.PRODUCT ||
-  process.env.ontology_publisher_current_product ||
-  "pages";
-process.env.VUE_APP_BRANCH = (
-  process.env.BRANCH ||
-  (process.env.BRANCH_NAME === process.env.TAG_NAME
-    ? "develop"
-    : process.env.BRANCH_NAME || "develop")
-).toLowerCase();
-process.env.VUE_APP_TAG = process.env.TAG || process.env.TAG_NAME || "latest";
-
-process.env.VUE_DIST_DIR = `/${process.env.VUE_APP_PRODUCT}/${process.env.VUE_APP_BRANCH}/${process.env.VUE_APP_TAG}`;
-process.env.VUE_ASSETS_DIR = `${process.env.VUE_DIST_DIR}/_nuxt/`;
-
-process.env.VUE_ONTOLOGY_NAME = process.env.ONTPUB_FAMILY || "dev";
-process.env.VUE_BASE_URL =
-  process.env.BASE_URL ||
-  "https://spec." +
-    (process.env.VUE_ONTOLOGY_NAME === "idmp"
-      ? "pistoiaalliance"
-      : "edmcouncil") +
-    ".org/";
-
-process.env.VUE_RESOURCES_BASE_URL = process.env.VUE_BASE_URL + process.env.VUE_ONTOLOGY_NAME + "/ontology/";
-
-process.env.STRAPI_URL = process.env.STRAPI_URL || "http://localhost:1337";
-
-export default {
-  // target: 'static' description https://nuxtjs.org/announcements/going-full-static/
-  target: "static",
-  // Global page headers: https://go.nuxtjs.dev/config-head
-  head: {
-    title: process.env.VUE_ONTOLOGY_NAME.toUpperCase(),
-    htmlAttrs: {
-      lang: "en",
-    },
-    meta: [
-      { charset: "utf-8" },
-      { name: "viewport", content: "width=device-width, initial-scale=1" },
-      { hid: "description", name: "description", content: "" },
-      {
-        hid: "keywords",
-        name: "keywords",
-        content:
-          "ontology, Open Knowledge Graph, OKG, EDM Council, Enterprise Data Management Council",
-      },
-      { name: "format-detection", content: "telephone=no" },
-    ],
-    link: [{ rel: "icon", type: "image/x-icon", href: "/favicon.ico" }],
-    script: [
-      {
-        src: "https://cdn.jsdelivr.net/npm/jquery@3.5.1/dist/jquery.slim.min.js",
-        integrity:
-          "sha384-DfXdz2htPH0lsSSs5nCTpuj/zy4C+OGpamoFVy38MVBnE+IbbVYUew+OrCXaRkfj",
-        crossorigin: "anonymous",
-      },
-      {
-        src: "https://cdn.jsdelivr.net/npm/popper.js@1.16.1/dist/umd/popper.min.js",
-        integrity:
-          "sha384-9/reFTGAW83EW2RDu2S0VKaIzap3H66lZH81PoYlFhbGU+6BZp6G7niu735Sk7lN",
-        crossorigin: "anonymous",
-      },
-      {
-        src: "https://cdn.jsdelivr.net/npm/bootstrap@4.6.1/dist/js/bootstrap.min.js",
-        integrity:
-          "sha384-VHvPCCyXqtD5DqJeNxl2dtTyhF78xXNXdkwX1CZeRusQfRKp+tA7hAShOK/B/fQ2",
-        crossorigin: "anonymous",
-      },
-    ],
-  },
-  server: {
-    host: process.env.PUBLIC_URL || "localhost",
-  },
-  router: {
-    base: `/${process.env.VUE_ONTOLOGY_NAME}`,
-  },
-
-  //to removed
-  generate: {
-    dir: `dist/${process.env.VUE_ONTOLOGY_NAME}${process.env.VUE_DIST_DIR}`,
-    routes() {
-      return axios
-        .get(`${process.env.STRAPI_URL || "http://localhost:1337"}/api/pages`)
-        .then((res) => {
-          return res.data.data.map((page) => {
-            const slug = page.attributes.slug;
-            return `/page/${slug}`;
-          });
-        });
-    },
-  },
-
-  // loading bar
-  loading: {
-    color: "black",
-    height: "5px",
-  },
-
-  // Global CSS: https://go.nuxtjs.dev/config-css
-  css: ["./assets/scss/Ontology.scss"],
-
-  // Plugins to run before rendering page: https://go.nuxtjs.dev/config-plugins
-  plugins: [
-    { src: "~/plugins/vue-multiselect" },
-    { src: "~/plugins/v-clipboard" },
-  ],
-
-  // Auto import components: https://go.nuxtjs.dev/config-components
-  components: {
-    dirs: [
-      "~/components",
-      "~/components/Articles",
-      "~/components/chunks",
-      "~/components/Ontology",
-    ],
-  },
-
-  // Modules for dev and build (recommended): https://go.nuxtjs.dev/config-modules
-  buildModules: [
-    [
-      "@nuxtjs/google-fonts",
-      {
-        families: {
-          Inter: {
-            wght: [300, 400, 500],
-          },
-        },
-        display: "swap",
-        prefetch: false,
-        preconnect: false,
-        preload: false,
-        download: true,
-        base64: false,
-      },
-    ],
-  ],
-
-  // Modules: https://go.nuxtjs.dev/config-modules
-  modules: [
-    "@nuxtjs/style-resources",
-    "bootstrap-vue/nuxt",
-    "@nuxtjs/markdownit",
-    "@nuxtjs/proxy",
-  ],
-
-  // Build Configuration: https://go.nuxtjs.dev/config-build
-  build: {
-    standalone: true,
-    publicPath: process.env.VUE_ASSETS_DIR,
-    loaders: {
-      sass: {
-        implementation: require("sass"),
-      },
-      scss: {
-        implementation: require("sass"),
-      },
-    },
-    extend(config) {
-      config.resolve.alias.vue = "vue/dist/vue.common";
-    },
-  },
-
-  env: {
-    generateDir: `dist/${process.env.VUE_ONTOLOGY_NAME}`,
-    ontologyName: process.env.VUE_ONTOLOGY_NAME,
-    assetsDir: process.env.VUE_ASSETS_DIR,
-    distDir: process.env.VUE_DIST_DIR,
-    staticGenerationMode: process.env.NODE_ENV === "production",
-    ontologyResourcesBaseUri: process.env.VUE_RESOURCES_BASE_URL,
-    strapiBaseUrl: process.env.STRAPI_URL,
-    showTermsLinkOnFooter: process.env.SHOW_TERMS_LINK_ON_FOOTER || true,
-  },
-
-  http: {
-    proxy: process.env.NODE_ENV !== "production",
-  },
-
-  proxy: [
-    `http://onto-viewer-server:8080/${process.env.VUE_ONTOLOGY_NAME}/ontology/api`,
-    `http://onto-viewer-server:8080/${process.env.VUE_ONTOLOGY_NAME}/ontology/*/api`,
-  ],
-
-  styleResources: {
-    scss: [
-      "~assets/scss/_variables.scss",
-      "~assets/scss/_bootstrap-override.scss",
-      "~assets/scss/global.scss",
-      "~assets/scss/typography.scss",
-      "~assets/scss/highlight.scss",
-    ],
-  },
-
-  markdownit: {
-    preset: "default",
-    linkify: true,
-    breaks: true,
-    use: ["markdown-it-div", "markdown-it-attrs", "markdown-it-highlightjs"],
-    runtime: true,
-  },
-};
diff --git a/onto-viewer-web-app/entrypoint.sh b/onto-viewer-web-app/entrypoint.sh
index 5c34b8ae..61038a0f 100644
--- a/onto-viewer-web-app/entrypoint.sh
+++ b/onto-viewer-web-app/entrypoint.sh
@@ -4,11 +4,6 @@ for i in config/default_* ; do
  test -e config/${i#config/default_} || cp -av ${i} config/${i#config/default_}
 done
 
-# if no UPDATE_URL and no ontology files in "ontologies" directory then copy ontology files from "integration_tests/ontologies/"
-if [ -z "${UPDATE_URL}" ] && [ $(find ontologies/ -type f | wc -l) -eq 0 ] ; then
- find integration_tests/ontologies/ -type f -exec cp -av "{}" ontologies/ \;
-fi
-
 echo "[INFO] Starting app.war..."
 exec java -server -Xmx4G -XX:-UseGCOverheadLimit -Dserver.address=0.0.0.0 -Dserver.port=80 -Dserver.forward-headers-strategy=native -Dserver.tomcat.redirect-context-root=false \
 	${UPDATE_URL:+ -Dapp.config.ontologies.download_directory=download -Dapp.config.updateUrl=${UPDATE_URL}} -jar /app.war --server.servlet.context-path=/${ONTPUB_FAMILY:-dev}/ontology

From 080115f1428becad71df3114feadeb70c4dcbca4 Mon Sep 17 00:00:00 2001
From: mereolog <pawel.garbacz@makolab.com>
Date: Mon, 19 Jun 2023 11:12:31 +0200
Subject: [PATCH 08/12] dev config management

Signed-off-by: mereolog <pawel.garbacz@makolab.com>
---
 .gitignore                     | 1 +
 README.md                      | 9 ++++++++-
 docker-compose.dev.yaml        | 5 +++--
 onto-viewer-web-app/ontologies | 1 +
 4 files changed, 13 insertions(+), 3 deletions(-)
 create mode 160000 onto-viewer-web-app/ontologies

diff --git a/.gitignore b/.gitignore
index 1e0b5ae6..857e9fa0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -218,6 +218,7 @@ lucene_index/
 download/
 onto-viewer-web-app/config/
 onto-viewer-web-app/ontologies/*
+docker-compose.dev.yaml
 
 # Mac
 .DS_Store
\ No newline at end of file
diff --git a/README.md b/README.md
index aefc6365..e0d55e10 100644
--- a/README.md
+++ b/README.md
@@ -85,13 +85,20 @@ It is possible to run containers with the `dev` ontology (instead of `FIBO`):
   echo COMPOSE_FILE=docker-compose.dev.yaml >> .env
   ```
 
-- optionally place the ontology files in the `onto-viewer-web-app/ontologies` subdirectory
+- place the ontology files in the `onto-viewer-web-app/ontologies` subdirectory
   and uncomment the following entry 
   (see [comment](./docker-compose.dev.yaml#L31) in the `docker-compose.dev.yaml` file):
   ```
      - ./onto-viewer-web-app/ontologies:/opt/viewer/ontologies
   ```
 
+- place the config files in the `onto-viewer-web-app/config` subdirectory
+  and uncomment the following entry 
+  (see [comment](./docker-compose.dev.yaml#L31) in the `docker-compose.dev.yaml` file):
+  ```
+     - ./onto-viewer-web-app/ontologies:/opt/viewer/config
+  ```
+
 - build the images and run the containers. After all ontologies are loaded,
   the Onto Viewer will be accessible from `http://localhost:8080/dev/ontology`
 
diff --git a/docker-compose.dev.yaml b/docker-compose.dev.yaml
index e153970e..878fdc73 100644
--- a/docker-compose.dev.yaml
+++ b/docker-compose.dev.yaml
@@ -28,9 +28,10 @@ services:
       dockerfile: ./Dockerfile.onto-viewer
     environment:
       - ONTPUB_FAMILY=dev
-    # uncomment to use custom ontology files located in the "./onto-viewer-web-app/ontologies" directory
+    # uncomment to use custom ontology and config files located in, respectively, "./onto-viewer-web-app/ontologies" and "./onto-viewer-web-app/config" folders
     #volumes:
-    #  - ./onto-viewer-web-app/ontologies:/opt/viewer/ontologies
+      # - ./onto-viewer-web-app/ontologies:/opt/viewer/ontologies
+      # - ./onto-viewer-web-app/config:/opt/viewer/config
   spec:
     image: edmcouncil/spec:${HTML_BRANCH:-latest}
     build:
diff --git a/onto-viewer-web-app/ontologies b/onto-viewer-web-app/ontologies
new file mode 160000
index 00000000..487882fc
--- /dev/null
+++ b/onto-viewer-web-app/ontologies
@@ -0,0 +1 @@
+Subproject commit 487882fcdbacf78b74aa1c3c415da9af8e189c0a

From 09c2c84735a8eea33b5add482ca197df91f64308 Mon Sep 17 00:00:00 2001
From: mereolog <pawel.garbacz@makolab.com>
Date: Mon, 19 Jun 2023 11:14:35 +0200
Subject: [PATCH 09/12] dev config management

Signed-off-by: mereolog <pawel.garbacz@makolab.com>
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e0d55e10..6869bb69 100644
--- a/README.md
+++ b/README.md
@@ -96,7 +96,7 @@ It is possible to run containers with the `dev` ontology (instead of `FIBO`):
   and uncomment the following entry 
   (see [comment](./docker-compose.dev.yaml#L31) in the `docker-compose.dev.yaml` file):
   ```
-     - ./onto-viewer-web-app/ontologies:/opt/viewer/config
+     - ./onto-viewer-web-app/config:/opt/viewer/config
   ```
 
 - build the images and run the containers. After all ontologies are loaded,

From c2fe105c0f95bd6d99e8ba3c75b7233101918e2c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Przemys=C5=82aw=20Gr=C4=85dzki?= <przemek.gradzki@gmail.com>
Date: Thu, 22 Jun 2023 20:09:37 +0200
Subject: [PATCH 10/12] New docker compose - last fixes and cleanup
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Signed-off-by: Przemysław Grądzki <przemek.gradzki@gmail.com>
---
 .gitignore                           |  3 +--
 Dockerfile.onto-viewer => Dockerfile |  6 +++---
 README.md                            | 29 +++++++++-------------------
 docker-compose.dev.yaml              |  8 +++-----
 docker-compose.yaml                  |  1 -
 onto-viewer-web-app/config/.gitkeep  |  0
 onto-viewer-web-app/entrypoint.sh    |  6 +-----
 7 files changed, 17 insertions(+), 36 deletions(-)
 rename Dockerfile.onto-viewer => Dockerfile (87%)
 create mode 100644 onto-viewer-web-app/config/.gitkeep

diff --git a/.gitignore b/.gitignore
index 857e9fa0..f36087e6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -216,9 +216,8 @@ catalog-v001.xml
 docker/runtime/
 lucene_index/
 download/
-onto-viewer-web-app/config/
+onto-viewer-web-app/config/*
 onto-viewer-web-app/ontologies/*
-docker-compose.dev.yaml
 
 # Mac
 .DS_Store
\ No newline at end of file
diff --git a/Dockerfile.onto-viewer b/Dockerfile
similarity index 87%
rename from Dockerfile.onto-viewer
rename to Dockerfile
index 86723b1b..619a3eab 100644
--- a/Dockerfile.onto-viewer
+++ b/Dockerfile
@@ -5,7 +5,7 @@ RUN	apt-get update && \
 	mkdir -p /opt/develop
 WORKDIR /opt/develop
 COPY .	/opt/develop/
-RUN	mvn clean package && cp -av onto-viewer-web-app/target/onto-viewer-web-app-*.war /app.war
+RUN	mvn clean package && cp -av onto-viewer-web-app/target/onto-viewer-web-app-*.war /onto-viewer-web-app.war
 
 FROM	adoptopenjdk/openjdk11-openj9:alpine-slim
 ARG	ONTPUB_FAMILY=dev UPDATE_URL
@@ -14,8 +14,8 @@ RUN	apk --no-cache add --upgrade bash curl jq && \
 	install -d /opt/viewer/config
 WORKDIR	/opt/viewer
 COPY	./onto-viewer-web-app/entrypoint.sh			/opt/viewer/entrypoint.sh
-COPY	./onto-viewer-web-app/integration_tests/ontologies	/opt/viewer/
+COPY	./onto-viewer-web-app/integration_tests/ontologies	/opt/viewer/ontologies
 COPY	./onto-viewer-web-app/staticOntologies			/opt/viewer/staticOntologies
-COPY --from=build-onto-viewer	/app.war	/app.war
+COPY	--from=build-onto-viewer /onto-viewer-web-app.war	/opt/viewer/onto-viewer.war
 CMD	["sh", "entrypoint.sh"]
 HEALTHCHECK --start-period=60s --interval=15s --timeout=1s --retries=60 CMD test "$(curl -q http://localhost/${ONTPUB_FAMILY}/ontology/actuator/health | jq -e ".components.custom.details.INITIALIZATION_DONE")" = "true"
\ No newline at end of file
diff --git a/README.md b/README.md
index 6869bb69..20afe0e5 100644
--- a/README.md
+++ b/README.md
@@ -35,8 +35,7 @@ Requirements:
 - [git](https://git-scm.com/) ([install](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git))
 - [docker](https://www.docker.com/) - install:
   * [Docker Desktop](https://docs.docker.com/desktop/) or ...
-  * [Docker Engine](https://docs.docker.com/engine/) with [Docker Compose plugin](https://docs.docker.com/compose/install/linux/)
-- free port **8080/tcp**
+  * [Docker Engine](https://docs.docker.com/engine/) with [Docker Compose plugin](https://docs.docker.com/compose/)
 
 How to start:
 Clone the [edmcouncil/onto-viewer](https://github.com/edmcouncil/onto-viewer) repository to the *onto-viewer* directory,
@@ -80,28 +79,18 @@ The services provide endpoints at the following URLs:
 - [http://localhost:8080/fibo/strapi/admin](http://localhost:8080/fibo/strapi/admin) :- [Strapi admin panel](https://docs.strapi.io/user-docs/intro#accessing-the-admin-panel) for for [FIBO](https://github.com/edmcouncil/fibo) ontology (Email: *edmc-strapi@dev.com*, Password: *devDBonly1*)
 
 It is possible to run containers with the `dev` ontology (instead of `FIBO`):
-- use the `docker-compose.dev.yaml` file (instead of the default `docker-compose.yaml`):
-  ```
-  echo COMPOSE_FILE=docker-compose.dev.yaml >> .env
-  ```
-
 - place the ontology files in the `onto-viewer-web-app/ontologies` subdirectory
-  and uncomment the following entry 
-  (see [comment](./docker-compose.dev.yaml#L31) in the `docker-compose.dev.yaml` file):
-  ```
-     - ./onto-viewer-web-app/ontologies:/opt/viewer/ontologies
-  ```
+  and the config files in the `onto-viewer-web-app/config` subdirectory
 
-- place the config files in the `onto-viewer-web-app/config` subdirectory
-  and uncomment the following entry 
-  (see [comment](./docker-compose.dev.yaml#L31) in the `docker-compose.dev.yaml` file):
-  ```
-     - ./onto-viewer-web-app/config:/opt/viewer/config
+- using the `docker-compose.dev.yaml` compose file (instead of the default `docker-compose.yaml`),
+  build the images,then run the containers:
+  ```bash
+  echo COMPOSE_FILE=docker-compose.dev.yaml >> .env
+  docker compose build
+  docker compose up -d
   ```
 
-- build the images and run the containers. After all ontologies are loaded,
-  the Onto Viewer will be accessible from `http://localhost:8080/dev/ontology`
-
+  once all services are up and running, Onto Viewer will be available at `http://localhost:8080/dev/ontology`
 
 If you want to see the logs use:
 ```bash
diff --git a/docker-compose.dev.yaml b/docker-compose.dev.yaml
index 878fdc73..725fe368 100644
--- a/docker-compose.dev.yaml
+++ b/docker-compose.dev.yaml
@@ -25,13 +25,11 @@ services:
     image: edmcouncil/onto-viewer:${TAG:-latest}
     build:
       context: .
-      dockerfile: ./Dockerfile.onto-viewer
     environment:
       - ONTPUB_FAMILY=dev
-    # uncomment to use custom ontology and config files located in, respectively, "./onto-viewer-web-app/ontologies" and "./onto-viewer-web-app/config" folders
-    #volumes:
-      # - ./onto-viewer-web-app/ontologies:/opt/viewer/ontologies
-      # - ./onto-viewer-web-app/config:/opt/viewer/config
+    volumes:
+      - ./onto-viewer-web-app/ontologies:/opt/viewer/ontologies
+      - ./onto-viewer-web-app/config:/opt/viewer/config
   spec:
     image: edmcouncil/spec:${HTML_BRANCH:-latest}
     build:
diff --git a/docker-compose.yaml b/docker-compose.yaml
index 4b6ae2a4..b7beca36 100644
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -25,7 +25,6 @@ services:
     image: edmcouncil/onto-viewer:${TAG:-latest}
     build:
       context: .
-      dockerfile: ./Dockerfile.onto-viewer
     environment:
       - ONTPUB_FAMILY=fibo
       - UPDATE_URL=${FIBO_UPDATE_URL:-https://spec.edmcouncil.org/fibo/ontology/etc/onto-viewer-web-app/config/}
diff --git a/onto-viewer-web-app/config/.gitkeep b/onto-viewer-web-app/config/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/onto-viewer-web-app/entrypoint.sh b/onto-viewer-web-app/entrypoint.sh
index 61038a0f..5bc8b6ec 100644
--- a/onto-viewer-web-app/entrypoint.sh
+++ b/onto-viewer-web-app/entrypoint.sh
@@ -1,9 +1,5 @@
 #!/bin/bash
 
-for i in config/default_* ; do
- test -e config/${i#config/default_} || cp -av ${i} config/${i#config/default_}
-done
-
 echo "[INFO] Starting app.war..."
 exec java -server -Xmx4G -XX:-UseGCOverheadLimit -Dserver.address=0.0.0.0 -Dserver.port=80 -Dserver.forward-headers-strategy=native -Dserver.tomcat.redirect-context-root=false \
-	${UPDATE_URL:+ -Dapp.config.ontologies.download_directory=download -Dapp.config.updateUrl=${UPDATE_URL}} -jar /app.war --server.servlet.context-path=/${ONTPUB_FAMILY:-dev}/ontology
+	${UPDATE_URL:+ -Dapp.config.ontologies.download_directory=download -Dapp.config.updateUrl=${UPDATE_URL}} -jar onto-viewer.war --server.servlet.context-path=/${ONTPUB_FAMILY:-dev}/ontology

From 181a8fb7f1515234b26a09301ff898102dec74de Mon Sep 17 00:00:00 2001
From: Pawel Garbacz <mereolog@users.noreply.github.com>
Date: Fri, 23 Jun 2023 16:43:13 +0200
Subject: [PATCH 11/12] Update README.md

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 20afe0e5..2a6ed59a 100644
--- a/README.md
+++ b/README.md
@@ -78,8 +78,8 @@ The services provide endpoints at the following URLs:
 - [http://localhost:8080/fibo/ontology](http://localhost:8080/fibo/ontology) :- onto-viewer for [FIBO](https://github.com/edmcouncil/fibo) ontology
 - [http://localhost:8080/fibo/strapi/admin](http://localhost:8080/fibo/strapi/admin) :- [Strapi admin panel](https://docs.strapi.io/user-docs/intro#accessing-the-admin-panel) for for [FIBO](https://github.com/edmcouncil/fibo) ontology (Email: *edmc-strapi@dev.com*, Password: *devDBonly1*)
 
-It is possible to run containers with the `dev` ontology (instead of `FIBO`):
-- place the ontology files in the `onto-viewer-web-app/ontologies` subdirectory
+It is possible to run containers with any ontology (instead of `FIBO`):
+- place the ontology files of your choice in the `onto-viewer-web-app/ontologies` subdirectory
   and the config files in the `onto-viewer-web-app/config` subdirectory
 
 - using the `docker-compose.dev.yaml` compose file (instead of the default `docker-compose.yaml`),
@@ -90,7 +90,7 @@ It is possible to run containers with the `dev` ontology (instead of `FIBO`):
   docker compose up -d
   ```
 
-  once all services are up and running, Onto Viewer will be available at `http://localhost:8080/dev/ontology`
+  once all services are up and running, onto-viewer with your ontology will be available at `http://localhost:8080/dev/ontology`
 
 If you want to see the logs use:
 ```bash

From 17ef8363bc784460abf153fdc9c9241ee8642cb3 Mon Sep 17 00:00:00 2001
From: Pawel Garbacz <mereolog@users.noreply.github.com>
Date: Fri, 23 Jun 2023 16:45:17 +0200
Subject: [PATCH 12/12] Update README.md

---
 README.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/README.md b/README.md
index 2a6ed59a..784428fd 100644
--- a/README.md
+++ b/README.md
@@ -37,6 +37,8 @@ Requirements:
   * [Docker Desktop](https://docs.docker.com/desktop/) or ...
   * [Docker Engine](https://docs.docker.com/engine/) with [Docker Compose plugin](https://docs.docker.com/compose/)
 
+### ... with FIBO
+
 How to start:
 Clone the [edmcouncil/onto-viewer](https://github.com/edmcouncil/onto-viewer) repository to the *onto-viewer* directory,
 go to the *onto-viewer* directory (run all subsequent commands inside this directory),
@@ -78,6 +80,9 @@ The services provide endpoints at the following URLs:
 - [http://localhost:8080/fibo/ontology](http://localhost:8080/fibo/ontology) :- onto-viewer for [FIBO](https://github.com/edmcouncil/fibo) ontology
 - [http://localhost:8080/fibo/strapi/admin](http://localhost:8080/fibo/strapi/admin) :- [Strapi admin panel](https://docs.strapi.io/user-docs/intro#accessing-the-admin-panel) for for [FIBO](https://github.com/edmcouncil/fibo) ontology (Email: *edmc-strapi@dev.com*, Password: *devDBonly1*)
 
+
+### ... with an ontology of your choice
+
 It is possible to run containers with any ontology (instead of `FIBO`):
 - place the ontology files of your choice in the `onto-viewer-web-app/ontologies` subdirectory
   and the config files in the `onto-viewer-web-app/config` subdirectory