idb-backend

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

Installation

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
#TODO figure out replacement for libgeos-c1

For ingestion the following are also needed:

In Ubuntu 14.04:

apt-get install libfontconfig-dev libxml2 libxslt1-dev libav-tools

In Ubuntu 16.04:

apt-get install libfontconfig1-dev libxml2 libxslt1-dev ffmpeg

Python Dependencies

Install all of the python dependencies, this will be very slow the first time, after that pip caches help.

pip install -r requirements.txt

For ingestion you will also need to run

pip install -r idigbio_ingestion/requirements.txt

For testing you will also need to run

pip install -r test-requirements.txt

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):

pip install -e .

To setup cron jobs symlink from etc/cron.d/* to /etc/cron.d/*

Running

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.

Testing

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.

Schema and data

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

pg_dump --host c18node8.acis.ufl.edu --port 5432 --username "idigbio" \
    --format plain --schema-only --no-owner --clean \
    --no-privileges --no-tablespaces --no-unlogged-table-data
    --file "~/projects/idigbio/idb-backend/idb/tests/data/schema.sql" \
    "idb_api_prod"

The data in the DB was built up, copying from the live DB and then snapshotted with:

pg_dump --port 5432 --format plain --data-only --encoding UTF8 \
  --inserts --column-inserts --no-privileges --no-tablespaces \
  --verbose --no-unlogged-table-data  \
  --file ~/projects/idigbio/idb-backend/idb/tests/data/testdata.sql \
  test_idigbio