Docs and head tag fix

docker-compose.production.yaml

@@ -6,7 +6,7 @@ volumes:
 
 services:
   backend:
-    restart: unless-stopped
+    restart: always
     build:
       context: backend
       dockerfile: Dockerfile
@@ -20,6 +20,7 @@ services:
 
   nginx:
     container_name: nginx
+    restart: always
     image: nginx
     depends_on:
       - postgres
@@ -35,7 +36,7 @@ services:
 
   postgres:
     image: postgis/postgis:13-3.0
-    restart: unless-stopped
+    restart: always
     container_name: postgres
     volumes:
       - righttree-postgres-data:/var/lib/postgresql/data

docs/build-pdf.sh

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+
+# Uses https://gitlab.wgtn.cat-it.co.nz/nickg/pandoc-catalyst-template 
+# to build Markdown -> LaTeX -> PDF
+
+set -e
+
+docker run \
+    --rm \
+    -v $PWD:/source \
+    gitlab.wgtn.cat-it.co.nz:4567/nickg/pandoc-catalyst-template:latest \
+    userguide.md > rightplant-documentation.pdf

docs/userguide.md

@@ -0,0 +1,211 @@
+---
+mainfont: DejaVuSans
+documentclass: article
+geometry: margin=2.54cm
+title: Right Plant Systems Management Guide
+toc: true
+coverpage: true
+covertitle: Right Plant Systems Management Guide
+clientlogo: img/biosphere.png
+clientlogoheight: 1.5cm
+packed-figures: true
+---
+
+# Architecture
+
+Right Plant is built on a stack of a React frontend build in JavaScript, a simple Django REST API as a backend and PostGIS for data storage and persistence.
+
+All the components are configured to be deployed using `docker-compose`.
+
+# Running Configuration
+
+
+
+## OS and Supporting Software
+
+The Right Plant VM lives in the Hamilton (nz-hlz-1) region of Catalyst Cloud, with an IP address of 103.197.61.141.
+
+It runs a minimal version of 20.04, which will be supported until April 2025. Patching the server is as simple as `sudo apt update; sudo apt dist-upgrade -y` and a system reboot if required. It has not been configured for automatic upgrades.
+
+### SSH
+
+SSH is available on port 22 for Catalyst management purposes, and 43212 for general user access. SSH Keys are required to log into the server, password authentication should not be enabled.
+
+### Code
+The code and all configuration can be found on the VM in `/opt/rightplant`.
+
+Code is deployed as a git repository - any changes made will be tracked by git. It is not possible to push changes to the Catalyst stored git repository.
+
+### Observing running configuration
+
+Because Right Plant is deployed using Docker, the root user can access the docker daemon and execute CLI commands, such as `docker ps` to view running containers and `docker logs <container-name>` to view logs from the containers.
+
+In general, running `docker <command> --help` will get you useful information about how to interact with the docker CLI.
+
+
+\pagebreak
+
+# Developer README
+
+> This section has been lifted from the `README.md` file, that can be found in the git repository. It is aimed at developers and how to develop and run Right Plant.
+
+### Add shapefiles for database population
+
+Please unzip and add the following shapefiles to the `./backend/right_tree/api/data/resources` directory. It should include all the files required by the shapefile and use naming conventions as follows:
+
+**Ecological Districts Shapefile:**
+```
+backend/right_tree/api/data/resources/ecological_districts/
+- DOC_EcologicalDistricts_2021_08_02.cpg
+- DOC_EcologicalDistricts_2021_08_02.dbf
+- DOC_EcologicalDistricts_2021_08_02.prj
+- DOC_EcologicalDistricts_2021_08_02.sbn
+- DOC_EcologicalDistricts_2021_08_02.sbx
+- DOC_EcologicalDistricts_2021_08_02.shp
+- DOC_EcologicalDistricts_2021_08_02.shp.xml
+- DOC_EcologicalDistricts_2021_08_02.shx
+```
+
+**Ecological Districts Shapefile:**
+```
+backend/right_tree/api/data/resources/fundamental_soil_layers/
+- fundamental-soil-layers-new-zealand-soil-classification.cpg
+- fundamental-soil-layers-new-zealand-soil-classification.dbf
+- fundamental-soil-layers-new-zealand-soil-classification.prj
+- fundamental-soil-layers-new-zealand-soil-classification.shp
+- fundamental-soil-layers-new-zealand-soil-classification.shx
+- fundamental-soil-layers-new-zealand-soil-classification.xml
+```
+
+**Christchurch Zone Shapefile:**
+```
+backend/right_tree/api/data/resources/chch_zone/
+- Greater_Christchurch_Area.cpg
+- Greater_Christchurch_Area.shp
+- Greater_Christchurch_Area.dbf
+- Greater_Christchurch_Area.shx
+- Greater_Christchurch_Area.prj
+
+```
+### Add spreadsheet data for database population
+
+The plant spreadsheet should be renamed as `plant_data.xlsx` and placed in the `./backend/right_tree/api/data/resources` directory.
+
+## Running application for development
+
+### Initial build
+
+Builds the Django backend docker image. This may need to be re-run if any new dependencies are added.
+```
+./dev build
+```
+
+### Initialise database
+
+Creates `right_tree` database and installs `postgis` extensions.
+
+```
+./dev init_database
+```
+
+### Run web application
+
+Starts up the applications including the frontend, backend and database.
+
+```
+./dev start
+```
+
+Once running the components can be accessed as follows:
+
+| Application | Hosted |
+| --- | --- |
+| React Frontend | http://localhost:3000 |
+| Django Backend | http://localhost:8000 |
+| Database | postgis://localhost:5432 |
+
+## Available commands
+
+Other commands can be run using the following.
+```
+./dev <command>
+```
+
+A summary of available commands are outlined below. Note that if the command requires the application to be running (`Requires Run`) please execute `./dev start` in another terminal before running that command.
+
+| Command | Description | Requires Run |
+| --- | --- | --- |
+| `create_database` | Removes the existing database and data. Then it creates the `right_tree` database within a fresh postgis database instance. | No
+| `makemigrations` | Performs the django `makemigrations` command in the backend container. | Yes
+| `migrate` | Performs the django `migrate` command in the backend container. | Yes
+| `createsuperuser` | Performs the django `createsuperuser` command in the backend container. | Yes
+| `load_fixtures` | Performs the django `loaddata` command in the backend container. This loads all the fixtures found in the `/backend/right_tree/api/data/fixtures` directory. | Yes
+| `load_shapefiles` | Performs the custom `loadshapefiles` command in the backend container. This loads the ecological districts and soil layers shape files in `c`. | Yes
+| `create_plant_fixtures` | Performs the custom `createplantfixtures` command in the backend container. This loads the plant spreadsheet data from `/backend/right_tree/api/data/resources/plant_data.xlsx`. Requires the fixtures to be applied and shapefiles loaded. | Yes
+| `reset_plants` | Performs the custom `resetplants` command in the backend container. This removes all plant entries from the database. | Yes
+| `load_plant_fixtures` | Loads the `/backend/right_tree/api/data/fixtures/plants.json` fixture. Requires the `plants.json` file to be created (`./dev create_plant_fixtures`) and the plant table to be empty (`./dev reset_plants`). | Yes
+| `load_plants` | Creates plants fixtures and loads them into a fresh plant table in the database. Requires the fixtures to be applied and shapefiles loaded. | Yes
+| `load_sites_from_spreadsheet` | Loads site spreadsheet data the database initially (replaced with fixtures containing further information) | Yes
+| `populate_database` | Populates the `right_tree` database with base data (fixtures), provided shapefiles and plant spreadsheet data. Requires the database to be created. | No
+| `init_database` | Creates and populates the database | No
+| `reset_database` | Removes, recreates and populates the database | No
+| `build` | Builds required images | No
+| `start` | Runs all services including the frontend, backend and postgres database | No
+| `build` | Builds required images (frontend and backend) for development | No
+| `build_production` | Builds required images (frontend and backend) for production | No
+| `start_production` | Runs all services in production mode including the frontend, backend and postgres database | No
+| `renew_certificate` | Renews certificates for production | No
+| `process_svg_files` | Removes semi-colons from raw svg files to be compatible with the application | No
+
+## Creating zones for habitat images
+1. Create png image from original svg with approprate crop.
+2. Create zone polygons/rectangles on the original svg with divider lines anchor points as a guide
+3. Copy zone polygons/rectangles to png image and size to fit (this is to ensure the only paths on the image the selectable ones)
+4. Ensure all overlays have an almost transparent fill (lowest transparency value - in Inkscape this is 1) and no outline
+5. Add a 'label' (not an id) to each overlay to match with a column name relating to the zone segment, this may be repeated. In Inkscape this is under 'Object Properties'.
+6. Save the png with overlays as an svg (it may either be inkscape or plain svg)
+7. Place svg in relevant directory (`./frontend/src/assets/img/habitatSVG/`) in the frontend
+8. Find and replace any instance of colons (:) in property names for the raw svg i.e. inkscape:label -> inkscapelabel. A helper script has been written to do this automatically please run `python process_svg.py`.
+
+## Setting up and running the application for production
+
+1. Ensure the prerequisites are met as defined in [#Initial Setup]
+2. Create an `.env` file (if not done prior) in the root directory using `default.env` as an example. Uncomment values relating to production and fill in the values as appropriate.
+3. Build backend image `sudo ./dev build_production`
+4. Create the database `sudo ./dev create_database`
+5. Manually create postgres user with password and add the user to the `righttree` database with all permissions.
+
+Create an interactive terminal into the postgres container
+```bash
+sudo docker-compose -f docker-compose.production.yaml up -d postgres
+sudo docker exec -it postgres bash
+```
+
+Within the interactive terminal. Connect to the database, add the righttree_admin user and give permissions. Please use the same credentials as defined in .env.
+```bash
+psql -U postgres
+\c righttree
+CREATE USER righttree_admin;
+ALTER USER righttree_admin with encrypted password 'YOUR PASSWORD';
+GRANT ALL PRIVILEGES ON DATABASE righttree TO  righttree_admin;
+```
+
+Exit the container and stop postgres service:
+```
+[CTRL-D] - to exit psql THEN [CTRL-D] to exit container
+sudo docker-compose -f docker-compose.production.yaml down
+```
+
+6. Populate the database using `sudo ./dev populate_database`
+7. Build optimised frontend build and collect together staticfiles `sudo ./dev create_staticfiles`
+8. Create a django superuser for access to the admin interface. Please use the same credentials as defined in .env `sudo ./dev createsuperuser`
+9. Run the production application using `sudo ./dev start_production`
+
+### Setting up certificates
+
+Create certificate using certbot and letsencrypt, choose option 1 and provide an appropriate email.  Ensure port 80 and 443 are externally exposed for the domain before running this command. To retrieve a staging certificate, use the `--test-cert` flag.
+```
+sudo docker run -i --rm --name certbot -p 443:443 -p 80:80 \
+  -v /etc/letsencrypt:/etc/letsencrypt/ certbot/certbot certonly \
+  -d [YOUR DOMAIN] --logs-dir /etc/letsencrypt/logs
+```

frontend/public/index.html

@@ -6,7 +6,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta
       name="description"
-      content="Web site created using create-react-app"
+      content="Right Plant Right Place Plant Selector Tool for New Zealand."
     />
     <!--
       manifest.json provides metadata used when your web app is installed on a
@@ -28,7 +28,7 @@
       integrity="sha512-xodZBNTC5n17Xt2atTPuE1HxjVMSvLVW9ocqUKLsCC5CXdbqCmblAshOMAS6/keqq/sMZMZ19scR4PsZChSR7A=="
       crossorigin=""
     />
-    <title>Right Tree</title>
+    <title>Right Plant</title>
   </head>
   <body>
     <noscript>You need to enable JavaScript to run this app.</noscript>