ADAGUC / adaguc-checker

This checker extends the existing cfchecker by Rosalyn Hatcher (NCAS-CMS, Univ. of Reading, UK) at https://github.com/cedadev/cf-checker by extending the CFChecker class through inheritance.

Usage information will follow when the original checker's command line argument passing is merged with the ADAGUC specific command line argument parsing.

Getting started

Prerequisites

For the moment, you need a compiled binary of adaguc-server with the reporting capability. The output is not very meaningful as of yet. You can get adaguc-server with reporting capability here: https://github.com/saskiawagenaar/adaguc-server

Create a python virtual environment and initialize it.

virtualenv ./env-cf-checker
source ./env-cf-checker/bin/activate

Clone the existing checker repository:

git clone https://github.com/cedadev/cf-checker.git

or install it through pip:

pip install cfchecker

Pillow is also needed for some image processing. Install it with pip in the virtual environment:

pip install Pillow

Running the software

Assuming that the autowms toplevel directory is /data/autowms:

export INPUT_DIR=/tmp
export OUTPUT_DIR=/tmp
./adaguc-checker.py --checks=adaguc /nobackup/users/neutvd/data/autowms/S-O3M_GOME_ARP_02_M01_20171015063857Z_20171015073557Z_N_O_20171015134801Z.nc
CHECKING NetCDF FILE: /nobackup/users/neutvd/data/autowms/S-O3M_GOME_ARP_02_M01_20171015063857Z_20171015073557Z_N_O_20171015134801Z.nc
=====================
Using CF Checker Version 3.0.5
Checking against CF Version CF-1.6
Using Standard Name Table Version 49 (2018-02-13T08:44:33Z)
Using Area Type Table Version 6 (22 February 2017)

Checking ADAGUC extensions

For now it is required that the file is located in the autowms directory of the adaguc-server and you must also supply the full path to the file on the command line. This is to satisfy both adaguc-server and the cfchecker library dependency.

If you wish to keep the images generated for all layers. Supply the --imagedir command line option:

$ ./adaguc-checker.py --checks=adaguc --imagedir=./ /nobackup/users/neutvd/data/autowms/S-O3M_GOME_ARP_02_M01_20171019065654Z_20171019075354Z_N_O_20171019144803Z.nc > output.json

The above command also redirects the JSON output to a file named output.json. Images are stored in the current directory with the following naming scheme input_filename.layername.png where the .nc extension is stripped from the input filename.

When using the adaguc-server docker started from the start-docker.sh script you probably want to supply the --baseurl command line arguement to set the base url to http://localhost:8090/adaguc-services/adagucserver?. The default is set for use in conjunction with a separate WPS wrapper using 2 docker instances in a network. Example:

./adaguc-checker.py --baseurl='http://localhost:8090/adaguc-services/adagucserver?'  --checks=adaguc --imagedir=./ /nobackup/users/neutvd/data/autowms/S-O3M_GOME_ARP_02_M01_20171019065654Z_20171019075354Z_N_O_20171019144803Z.nc

Running ADAGUC as Docker container

Configure

mkdir /tmp/input_dir
chmod 777 /tmp/input_dir
mkdir /tmp/output_dir
chmod 777 /tmp/output_dir

check adguc-checker.env: directories $INPUT_DIR and $OUTPUT_DIR should exist and have mods 777

source adaguc_checker.env

Build ADAGUC server docker image

git clone git@github.com:saskiawagenaar/adaguc-server.git  # For now, should be ADAGUC repo.
cd adaguc-server
git checkout checker

docker build -t $ADAGUC_CHECKER_IMAGE .
./start-docker-adaguc-checker                # maybe "docker rm adaguc-checker" first