README

Clef searches the Earth System Grid Federation datasets stored at the Australian National Computational Infrastructure, both data published on the NCI ESGF node as well as files that are locally replicated from other ESGF nodes.

Currently it searches for the following datasets:

  • CMIP5 raijin projects: rr3, where NCI is the primary publisher and al33 for replicas
  • CMIP6 raijin projects: 0i10 for replicas

The search returns both the path of data that is already available at NCI as well as information on data that is on external ESGF nodes but not yet available locally.

Install

Clef is pre-installed into a Conda environment at NCI. Load it with:

module use /g/data3/hh5/public/modules
module load conda/analysis3-unstable
We are constantly adding new features, the development version is available in a separate environment::
module use /g/data3/hh5/public/modules module load conda source activate clef-test

You can install it to your own environment with:

conda install -c coecms -c conda-forge clef

But note that the clef.nci.org.au database necessary for running clef can only be accessed from NCI systems

Use

clef cmip5

Find CMIP5 files matching the constraints:

clef cmip5 --model BCC-CSM1.1 --variable tas --experiment historical --table day

You can filter CMIP5 by the following terms:

  • ensemble/member
  • experiment
  • experiment-family
  • institution
  • model
  • table/cmor_table
  • realm
  • frequency
  • variable
  • cf-standard-name

See clef cmip5 --help for all available filters and their aliases

--latest will check the latest versions of the datasets on the ESGF

website, and will only return matching files

It will return a path for all the files available locally at NCI and a dataset-id for the ones that haven’t been downloaded yet.

You can use the flags --local and --missing to return respectively only the local paths or the missing dataset-id:

clef --local cmip5 --model MPI-ESM-LR --variable tas --table day
clef --missing cmip5 --model MPI-ESM-LR --variable tas --table day

NB these flags come immediately after the command “clef” and before the sub-command “cmip5” or “cmip6”. They are also clearly mutually exclusive. You can repeat arguments more than once:

clef --missing cmip5 --model MPI-ESM-LR -v tas -v tasmax -t day -t Amon

clef cmip6

You can filter CMIP6 by the following terms:

  • activity
  • experiment
  • institution
  • source_type
  • model
  • member
  • table
  • realm
  • frequency
  • variable
  • version

See clef cmip6 --help for all available filters

Develop

Development install:

conda env create -f conda/dev-environment.yml
source activate clef-dev
pip install -e '.[dev]'

The dev-environment.yml file is for speeding up installs and installing packages unavailable on pypi, requirements.txt is the source of truth for dependencies.

To work on the database tables you may need to start up a test database.

You can start a test database either with Docker:

docker-compose up # (In a separate terminal)
psql -h localhost -U postgres -f db/nci.sql
psql -h localhost -U postgres -f db/tables.sql
# ... do testing
docker-compose rm

Or with Vagrant:

vagrant up
# ... do testing
vagrant destroy

Run tests with py.test (they will default to using the test database):

py.test

or connect to the production database with:

py.test --db=postgresql://clef.nci.org.au/postgres

Build the documentation using Sphinx:

python setup.py build_sphinx
firefox docs/_build/index.html

New releases are packaged and uploaded to anaconda.org by CircleCI when a new Github release is made

Documentation is available on ReadTheDocs, both for stable and latest versions.

CleF can only return datasets which are listed in the ESGF database system for remote results and on the NCI clef database for local results. This means that potentially some of the datasets might not be returned in the following cases:
  • One or more of the ESGF nodes are offline: this can affect clef returning results for the models which are hostedworks which are offline. It is usually easy to verify if this is the case since a query on the browser should show a reduced list of models. In such cases using the –local flag will use a query method completely independent and will return at least what is available locally.
  • The NCI ESGF node is offline then nothing will be returned by the default or remote queries, again using –local should work.
  • The checksums stored in the ESGF database are different from the actual file checksums. CleF uses the checksums to match the files available remotely if even one file does not match it will flag the dataset as missing. Using the –local flag should still return the datasets regardless because it doesn’t compare them to what is available remotely.
  • A dataset has been recently donwloaded (up to a week before) and hasn’t yet been added to the NCI clef database. In such case it might not show locally even if it has been downloaded. The NCI clef database is updated weekly so we cannot guarantee for clef to find data which is more recent than that. NCI also provides us with a list of datasets recently queued or downloaded. The default query will show this data as “queued” or “downloaded”, rather than missing. While this list aims to cover the gap in between database updates, we have no control on its frequency and it might not capture all the data.