Catalogue of Life Backend

For source code contributions please see our developer guide. The COL backend is a Dropwizard application, that drives the COL ChecklistBank API. webservice is the maven module that builds the application.

Prerequisites

1. Java 11 JDK
2. Maven 3
3. Postgres 13

Run the COL WS application locally

1. cd into webservice
2. Run mvn clean install to build your application
3. create a local config.yml file
4. On the first run init a new, empty database & search index with java -jar target/webservice-1.0-SNAPSHOT.jar init --num 4 config.yml. --num 4 will configure the number of partitions to use for external datasets
5. Start application with java -jar target/webservice-1.0-SNAPSHOT.jar server config.yml
6. To check that your application is running enter url http://localhost:8080

For development tests you can also run the application straight from your IDE by executing the main WsServer.java class and passing it the right arguments server /path/to/config.yml

In order to avoid real authentication against the GBIF registry you can change the AuthBundle and use a LocalAuthFilter instead of the real AuthFilter. This authenticates every request with a test account with full admin privileges.

Health Check

To see your applications health enter url http://localhost:8081/healthcheck

Maven modules

api

The main API with model classes and shared common utilities classes.

dao

The postgres persistence layer.

doi

Code dealing with (dataset) DOI registration and management in DataCite.

parser

Various parsers/interpreters used mostly for importing. Contains a GBIF name parser wrapper.

webservice

The Dropwizard based JSON webservices, importer and assembly code.

Dataset imports

The admin server should be used to import known datasets from their registered data access URL. Imports are scheduled in an internal, non persistent queue. Scheduling a dataset for importing is done by POSTing an import request object to the importer resource like this:

curl -X POST -d "{'datasetKey'=1000, 'priority'=false}" "http://localhost:8080/importer/queue"

The priority parameter places the request on the beginning of the queue.

Data Normalizer

All data is normalized prior to inserting it into the database. This includes transforming a flat classification into a parent child hierarchy with just a single record for a uniue higher taxon.

Import behaviour

We have built the importer to fail early when encountering issue to not overwrite existing good data. Examples of data errors that cause the importer to abort are:

• unreadable data files (we only support UTF8, 16 and Latin1, Windows1552 & MacRoman as 8bit encodings)
• missing required fields (e.g. AcceptedSpeciesID or the scientific name)

The importer does gracefully handle empty lines and skip lines with less columns than expected (this shows as warning logs as bad delimiter escaping is often the root cause).

Issue flagging

The dataset import flags records that have problems. For each entire dataset import aggregate metrics are stored and can be retrieved even for historic versions for comparison and change analytics.

All potential issues that are handled can be found here: https://github.com/Sp2000/colplus-backend/blob/master/colplus-api/src/main/java/org/col/api/vocab/Issue.java#L6

For example:

• declared accepted taxa are missing in the sources (e.g. a synonym declaring an AcceptedSpeciesID which does not exist)