Biodiversity Browser

Tools to browse, analyze and visualize GBIF occurrence data from Elasticsearch.

Purposes:

• Test how much data can be handles efficiently with Elasticsearch and an inexpensive server
• Show species occurrence trends over the years
• Show species phenology
• Show species distribution on a map
• Show basic metadata about the data (sources, higher classification)
• Demonstrate Elasticsearch's signifigance search, which could be used to pinpoint uncommon occurences of species
• Find out uncommon traits of the data (check e.g. Circus aeroginosus yearly chart)

Data is indexed to Elasticsearch with https://github.com/mikkohei13/darwincore-php

Ideas

Done

• Species monthly chart
• Species yearly chart, compared to higher taxonomy
• Aggragation & interesting species for a given year & class and institution
• Clustered map

Could do

• Filter by country
• Filter by years
• Filter by month (to find e.g. breeding observations)
• Show proportional numbers on map
• Linkable URL's

Technical Todo

REFACTORING

• Navigation & URL routing
• Templates with Handlebars
• Modularize data fetching, map creation, chart creation

CHECK

• Browser requirements? (let?)
• default size in geohash queries??
• making two queries on arrival?
• Set slowlog threshold / delete old log files (/var/log/elasticsearch)
• use elastic on port 80? (https://gist.github.com/m5m1th/6870a54717c0387468c3)

SHOULD

• iOS 9 support?
• Test more with Chrome, FF, IE, Edge
• Refactor navigation, modularize
• Repo documentation
• Autocomplete species name (Elasticsearch suggestions?)
• Addresses for tabs & species (+browser history?)
• Templating (Handlebars/Ember)
• Refactor names:
  • getmonths -> getperiods
  • get -> do
  • use same div for all results (chart/map/class)?
  • total -> info

NICE

• Logging
• Map circle color, proportional to doc_count?
• URL Routing (Ember?)
• Favicon
• Mobile...

Logging

Log files at /var/log/elasticsearch

Enable slowlog:

curl -XPUT http://USER:PASS@213.32.16.197:9200/se-all/_settings -d '{ "index.search.slowlog.threshold.query.debug" : "100ms" }'

Disable slowlog:

curl -XPUT http://USER:PASS@213.32.16.197:9200/se-all/_settings -d '{ "index.search.slowlog.threshold.query.debug" : -1 }'