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Indicia Warehouse

This is the repository for the Indicia Warehouse, the server-side component of Indicia, the online wildlife recording toolkit. Indicia accelerates development of wildlife recording websites and mobile applications. Documentation is available at https://indicia-docs.readthedocs.io/en/latest/index.html.

Details of the installation procedure are at http://indicia-docs.readthedocs.org/en/latest/administrating/warehouse/warehouse-installation.html.

The latest stable download of the warehouse code is available at https://github.com/Indicia-Team/warehouse/releases/latest

Details of the upgrade procedure are at http://indicia-docs.readthedocs.org/en/latest/administrating/warehouse/warehouse-upgrading.html.

Docker development

For those working in Linux, there is a set up script which will install and configure a 'complete' (work in progress) Indicia infrastructure using Docker. The code is in a shared volume so that you can see the effect of changes immediately and xdebug is set up so you can set breakpoints and single step through code.

Prerequisites

Naturally you'll need Docker installed.

Currently, a postgres client is needed on the host for the script to complete the set up of the indicia schema. E.g. on Ubuntu you can sudo apt install postgresql-client.

Starting

If you clone this repo, cd docker and execute ./compose.sh it will start 8 docker containers offering these services.

  1. A postgres database with postgis installed.
  2. pgAdmin for administering the database.
  3. A mock mail server.
  4. A webserver running the warehouse code.
  5. GeoServer for sharing spatial data in OGC standard format.
  6. Elasticsearch for storing an index of warehouse data.
  7. Kohana for exploring and managing Elasticsearch
  8. Logstash for populating Elasticsearch with warehouse data. On first run, it offers to initialise the indicia database schema. If you choose this option you will later login in as user admin having password password.

To reset your docker system to an entirely clean state, execute ./reset.sh from the docker folder. If you are going to immediately restart docker then delete cookies from your browser too.

Using

Once running you can browse the warehouse at http://localhost:8080. You can examine the database with pgAdmin at http://localhost:8070. Any mail sent by the warehouse can be viewed at http://localhost:8025. GeoServer can be configured at http://localhost:8090/geoserver. The Elasticsearch API is accessible at https://localhost:9200. Kohana is accessed by browsing https://localhost:5601.

PgAdmin

To log in , the default credentials are

To connect pgAdmin to the database, add a new server and configure the connection with

  • Host name: The docker container name e.g. indicia-postgres-1
  • Port: 5432
  • Username: postgres
  • Password: password To list the container names and ports you can execute the command docker container ls --format "table {{.Names}}\t{{.Ports}}"

GeoServer

To log in, the default credentials are:

  • Username: admin
  • Password: geoserver

Elasticsearch and Kohana

Note that security is enabled so use https. To log in the default credentials are

  • Username: elastic
  • Password: password

Unit testing

There is a separate Docker configuration for unit testing which can be run up by cd docker then ./phpunit.sh. This replicates the unit testing performed when you push commits to the repository, enabling you to create and debug tests locally. It uses its own volume for the database so won't overwrite any setup you have in your development system. You do have to stop your development containers before running unit testing though, as it uses the same ports and modifies configuration. Config files that are modified by testing are backed up and restored, provided the script runs to completion.