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Last pushed: 35 minutes ago
Short Description
Container holding the data-api and ingestion code
Full Description


This is the collection of code that makes up the iDigBio server side.


System Dependencies

Currently this project only works in python2.7.

The following library packages will need to be installed to run the api:

In Ubuntu 14.04:

apt-get install python2.7-dev libgeos-c1 libblas-dev liblapack-dev \
  libatlas-base-dev gfortran libgdal-dev

In Ubuntu 16.04:

apt-get install python2.7-dev libblas-dev liblapack-dev \
  libatlas-base-dev gfortran libgdal-dev libpq-dev libgeos-c1v5 \

For ingestion the following are also needed:

In Ubuntu 14.04:

apt-get install libxml2 libxslt1-dev libav-tools fonts-dejavu-core

In Ubuntu 16.04:

apt-get install libxml2 libxslt1-dev ffmpeg fonts-dejavu-core

Package installation

This package itself needs to be installed to generate the CLI
scripts. To install it editably (so that git pull continues to
updates everything) and include all dependencies:

pip install -r requirements.txt

To setup persistent tasks and cron tasks

systemctl link $PWD/etc/systemd/system/*
systemctl enable --now $(grep -l Install $PWD/etc/systemd/system/*)

For partial installation (without extra components) you can just run

pip install -e .

The available extra components are:

  • journal: Writes directly to systemd-journald
  • ingestion: the extra librs for running ingestion
  • test: the extra libs for testing

Docker Image

The idb-backend image
is built off of this repository.


The main entry point is the idb command; you can run idb --help to
see what subcommands are available. When invoking this script there is
no need to set the PYTHONPATH.

In any invocation an idigbio.json must be present in either $PWD,
$HOME, or /etc/idigbio.

Data API

This serves the interface

idb run-server

Celery worker

This package can also be run as a celery worker; this is used by the
data api that launches some tasks (most notably download building) via
celery to a background worker.

celery worker --app=idigbio_workers -l WARNING


To run tests:


Relies on having a local postgresql with user/pass test / test
that can connect to DB test_idigbio. The data in the DB will be
destroyed during the testing.

Create the local DB

createuser -l -e test -P
createdb -l 'en_US.UTF-8' -E UTF8 -O test -e test_idigbio;

# The schema obj is still owned by the user of the above
# statement, not the owner 'test'. Drop it so it will be recreated
# by the script appropriately
psql -c "DROP SCHEMA public CASCADE;" test_idigbio

Schema and data

Testing the DB uses the schema copied from the live DB with:

pg_dump --host --username idigbio \
    --format plain --schema-only --schema=public \
    --clean --if-exists \
    --no-owner --no-privileges --no-tablespaces --no-unlogged-table-data \
    --file tests/data/schema.sql \

The data has been built up to support the test suite; it is provided
in tests/data/testdata.sql

pg_dump --port 5432 --format plain --data-only --encoding UTF8 \
  --inserts --column-inserts --no-privileges --no-tablespaces \
  --verbose --no-unlogged-table-data  \
  --file tests/data/testdata.sql $DBNAME
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