IOOS Compliance Checker

The IOOS Compliance Checker is a python based tool for data providers to check
for completeness and community standard compliance of local or remote
netCDF files against
CF and
ACDD
file standards. The python module can be used as a command-line tool or as a
library that can be integrated into other software.

A web-based version of the Compliance
Checker was developed to enable a broader audience and improve accessibility for the
checker. With the web version, providers can simply provide a link or upload their
datasets and get the full suite of capabilities that Compliance Checker offers.

It currently supports the following sources and standards:

Advice to data providers

While the command-line version of this tool can be run in a loop, it is not necessary to check
every file if they are all created the same way. In short, this tool is not meant for
identifying bugs in your data processing stream. It is, however, intended to help you identify
your process procedure compliance to the standards. If you change your processing procedure
for any reason it would be worth your while to run one file through the Compliance Checker to
insure you procedure change does not impact your file’s compliance.

If you feel you will need to run a batch of files through the Compliance Checker, please contact
the IOOS Program Office Operations Division for assistance.

The Compliance Checker Web Tool

The IOOS Compliance Checker front end companion.

https://compliance.ioos.us/index.html

Source Code is available on GitHub:

https://github.com/ioos/compliance-checker-web

Usage

Select the test you want to run from the dropdown menu. Then, either upload your dataset or provide a url to a
remote dataset (OPeNDAP) and click 'Submit'.

The output of the Compliance Checker will give you a comprehensive list of issues and the actions needed to correct them.
You may download the Compliance Checker report as a text file by clicking the 'Download Report' button

API

In addition to a web-based front-end for the IOOS Compliance Checker project, an API is provided for
users interested in batch processing files hosted via OPeNDAP. Details on how to use the API are
available on the Compliance Checker Web wiki page.

Here are a couple examples:

HTML Output

https://compliance.ioos.us/index.htmlapi/run?report_format=html&test=acdd&url=http://sos.maracoos.org/stable/dodsC/hrecos/stationHRMARPH-agg.ncml

JSON Output

https://compliance.ioos.us/index.htmlapi/run?report_format=json&test=acdd&url=http://sos.maracoos.org/stable/dodsC/hrecos/stationHRMARPH-agg.ncml

The Compliance Checker Command Line Tool

Concepts & Terminology

Each compliance standard is executed by a Check Suite,
which functions similar to a Python standard Unit Test.
A Check Suite runs checks against a dataset based on a metadata standard,
returning a list of Results which are then aggregated into a summary.

Each Result has a (# passed / # total) score, a weight (HIGH/MEDIUM/LOW),
a computer-readable name, an optional list of human-readable messages,
and optionally a list of child Results.

A single score is then calculated by aggregating on the names,
then multiplying the score by the weight and summing them together.

The computer-readable name field controls how Results are aggregated together - in order to prevent the overall score for a Check Suite varying on the number of variables,
it is possible to group Results together via the name property.
Grouped results will only add up to a single top-level entry.

See the Development wiki page for more details on implementation.

Installation

Check out the Installation wiki for instructions on how to install.

Command Line Usage

The compliance-checker can work against local files (.nc files, .cdl
metadata files, .xml files of SOS GetCapabilities/DescribeSensor requests)
or against remote URLs (OPeNDAP data URLs, SOS GetCapabilities/DescribeSensor URLs).

If you are aiming to check a netCDF-dump, also known as a CDL file, the file
must be named to end with a .cdl for the check-suite to be able to correctly
parse it's contents.

WARNING The CF/ACDD checks will access data, so if using a remote OPeNDAP URL, please be sure the size is reasonable!

usage: cchecker.py [-h] [--test TEST] [--criteria {lenient,normal,strict}] [--verbose] [--describe-checks] [--skip-checks SKIP_CHECKS | --include-checks INCLUDE_CHECKS]
                   [-f {text,html,json,json_new}] [-o OUTPUT] [-O OPTION] [-V] [-l] [-d DOWNLOAD_STANDARD_NAMES]
                   [dataset_location ...]

positional arguments:
  dataset_location      Defines the location of the dataset to be checked. The location can be a local netCDF file, a remote OPeNDAP endpoint, a remote netCDF file which
                        returns content-type header of 'application/x-netcdf', or an ERDDAP TableDAP endpoint. Note that the ERDDAP TableDAP endpoint will currently attempt
                        to fetch the entire TableDAP dataset.

options:
  -h, --help            show this help message and exit
  --test, -t TEST       Select the Checks you want to perform. Defaults to 'acdd' if unspecified. Versions of standards can be specified via `-t <test_standard>:<version>`.
                        If `<version>` is omitted the latest version of the test standard is used.
  --criteria, -c {lenient,normal,strict}
                        Define the criteria for the checks. Either Strict, Normal, or Lenient. Defaults to Normal.
  --verbose, -v         Increase output. May be specified up to three times.
  --describe-checks, -D
                        Describes checks for checkers specified using `-t`. If `-t` is not specified, lists checks from all available checkers.
  --skip-checks, -s SKIP_CHECKS
                        Specifies tests to skip. Can take the form of either `<check_name>` or `<check_name>:<skip_level>`. The first form skips any checks matching the
                        name. In the second form <skip_level> may be specified as "A", "M", or "L". "A" skips all checks and is equivalent to calling the first form. "M"
                        will only show high priority output from the given check and will skip medium and low. "L" will show both high and medium priority issues, while
                        skipping low priority issues. Cannot be used with `-i`/`--include-checks` option.
  --include-checks, -i INCLUDE_CHECKS
                        Specifies checks to include. Can only take the form of `<check_name>`. Cannot be specified along with `-s`/`skip_checks`.
  -f, --format {text,html,json,json_new}
                        Output format(s). Options are 'text', 'html', 'json', 'json_new'. The difference between the 'json' and the 'json_new' formats is that the 'json'
                        format has the check as the top level key, whereas the 'json_new' format has the dataset name(s) as the main key in the output follow by any checks
                        as subkeys. Also, 'json' format can be only be run against one input file, whereas 'json_new' can be run against multiple files.
  -o, --output OUTPUT   Output filename(s). If '-' is supplied, output to stdout. Can either be one or many files. If one file is supplied, but the checker is run against
                        many files, all the output from the checks goes to that file (does not presently work with 'json' format). If more than one output file is supplied,
                        the number of input datasets supplied must match the number of output files.
  -O, --option OPTION   Additional options to be passed to the checkers. Multiple options can be specified via multiple invocations of this switch. Options should be
                        prefixed with a the checker name followed by the option, potentially followed by a value, e.g. '<checker>:<option_name>[:<option_value>]' Available
                        options: 'cf:enable_appendix_a_checks' - Allow check results against CF Appendix A for attribute location and data types.
  -V, --version         Display the IOOS Compliance Checker version information.
  -l, --list-tests      List the available tests
  -d, --download-standard-names DOWNLOAD_STANDARD_NAMES
                        Specify a version of the cf standard name table to download as packaged version. Either specify a version number (e.g. "72") to fetch a specific
                        version or "latest" to get the latest CF standard name table.

Examples

Check a local file against CF 1.6

compliance-checker --test=cf:1.6 compliance_checker/tests/data/examples/hycom_global.nc

--------------------------------------------------------------------------------
                         IOOS Compliance Checker Report
                                  cf:1.6 check
--------------------------------------------------------------------------------
                               Corrective Actions
hycom_global.nc has 9 potential issues


                                     Errors
--------------------------------------------------------------------------------
Name                                      Reasoning
§3.2 Either long_name or standard_name    Attribute long_name or/and standard_name
is highly recommended for variable time:  is highly recommended for variable time
§4.3.1 depth is a valid vertical          vertical coordinates not defining
coordinate:                               pressure must include a positive
                                          attribute that is either 'up' or 'down'


                                    Warnings
--------------------------------------------------------------------------------
Name                                   Reasoning
§2.6.1 Global Attribute Conventions    Conventions global attribute does not
includes CF-1.6:                       contain "CF-1.6". The CF Checker only
                                       supports CF-1.6 at this time.
§2.6.2 Recommended Attributes:         institution should be defined source
                                       should be defined references should be
                                       defined
§2.6.2 Recommended Global Attributes:  global attribute history should exist
                                       and be a non-empty string
§8.1 Packed Data defined by water_u    Attributes add_offset and scale_factor
contains valid packing:                are not of type float or double.
§8.1 Packed Data defined by water_v    Attributes add_offset and scale_factor
contains valid packing:                are not of type float or double.

Check a remote file against ACDD 1.3

The remote dataset url is taken from the Data URL section of an OPeNDAP endpoint.

compliance-checker --test=acdd:1.3 "http://sos.maracoos.org/stable/dodsC/hrecos/stationHRMARPH-agg.ncml"

Checking against remote ERDDAP Datasets

ERDDAP datasets are becoming a popular way to access data. Supply an ERDDAP TableDAP or GridDAP URL to the checker:

compliance-checker --test ioos:1.2 "https://pae-paha.pacioos.hawaii.edu/erddap/griddap/pibhmc_bathy_60m_guam"

Ensure to supply the URL without the format extension at the end (no .nc, .ncCF, etc.).

Some examples of ERDDAP datasets:

• https://pae-paha.pacioos.hawaii.edu/erddap/tabledap/aws_himb
• http://erddap.secoora.org/erddap/tabledap/edu_usf_marine_comps_1407d550
• http://erddap.cencoos.org/erddap/tabledap/bodega-bay-bml_wts
• http://erddap.cencoos.org/erddap/tabledap/fort-point
• http://erddap.cencoos.org/erddap/tabledap/edu_humboldt_humboldt
• http://erddap.cencoos.org/erddap/tabledap/edu_calpoly_marine_morro
• http://erddap.cencoos.org/erddap/tabledap/mlml_mlml_sea
• http://erddap.cencoos.org/erddap/tabledap/mlml_mlml_met
• http://erddap.cencoos.org/erddap/tabledap/mlml_monterey
• http://erddap.cencoos.org/erddap/tabledap/edu_humboldt_tdp

Write results to text file

compliance-checker --test=acdd:1.3 --format=text --output=/tmp/report.txt compliance_checker/tests/data/examples/hycom_global.nc

Write results to JSON file

compliance-checker --test=acdd:1.3 --format=json --output=/tmp/report.json compliance_checker/tests/data/examples/hycom_global.nc

Write results to HTML file

compliance-checker --test=acdd:1.3 --format=html --output=/tmp/report.html compliance_checker/tests/data/examples/hycom_global.nc

Output text from multiple input files to one output file

compliance-checker --test=cf:1.6 --format text --output=/tmp/combined_output.txt compliance_checker/tests/data/examples/hycom_global.nc compliance_checker/tests/data/examples/ww3.nc

Output html and text files from multiple input files (part 1)

In this case you'll get 2 files /tmp/combined_output.txt and /tmp/combined_output.html that contain cf check results for both input files because you only specified 1 output filename.

compliance-checker --test=cf:1.6 --format text --format html --output=/tmp/combined_output.txt compliance_checker/tests/data/examples/hycom_global.nc compliance_checker/tests/data/examples/ww3.nc

Output html and text files from multiple input files (part 2)

In this case you'll get 4 files /tmp/hycom.txt, /tmp/hycom.html, /tmp/ww3.txt, and /tmp/ww3.html that contain cf check results because you specified as many output filenames as input filenames.

compliance-checker --test=cf:1.6 --format text --format html --output=/tmp/hycom.txt --output=/tmp/ww3.txt compliance_checker/tests/data/examples/hycom_global.nc compliance_checker/tests/data/examples/ww3.nc

Download a particular CF standard names table for use in the test

Note
During the CF test, if a file has a particular version of the cf standard name table specified in the global attributes
(i.e. :standard_name_vocabulary = "CF Standard Name Table v30" ;) that doesn't match the packaged version, it will
try to download the specified version. If it fails, it will fall back to packaged version.

compliance-checker -d 35

Alternatively, you can specify an absolute path to a standard name table you may have locally in an environment variable named CF_STANDARD_NAME_TABLE and the compliance checker will use that version instead.

Python Usage

If you are interested in incorporating the IOOS Compliance Checker into your own python projects, check out the following python code example:

from compliance_checker.runner import ComplianceChecker, CheckSuite

# Load all available checker classes
check_suite = CheckSuite()
check_suite.load_all_available_checkers()

# Run cf and adcc checks
path = "/path/or/url/to/your/dataset"
checker_names = ["cf", "acdd"]
verbose = 0
criteria = "normal"
output_filename = "/output/report.json"
output_format = "json"
"""
Inputs to ComplianceChecker.run_checker

path            Dataset location (url or file)
checker_names   List of string names to run, should match keys of checkers dict (empty list means run all)
verbose         Verbosity of the output (0, 1, 2)
criteria        Determines failure (lenient, normal, strict)
output_filename Path to the file for output
output_format   Format of the output

@returns                If the tests failed (based on the criteria)
"""
return_value, errors = ComplianceChecker.run_checker(
    path,
    checker_names,
    verbose,
    criteria,
    output_filename=output_filename,
    output_format=output_format,
)

# Open the JSON output and get the compliance scores
with open(output_filename, "r") as fp:
    cc_data = json.load(fp)
    scored = cc_data[cc_test[0]]["scored_points"]
    possible = cc_data[cc_test[0]]["possible_points"]
    log.debug(f"CC Scored {scored} out of {possible} possible points")

Compliance Checker Plug-Ins

Separate Plug-ins have been developed to complement the Compliance Checker tool with
specifications for preparing data to be submitted to different data assembly centers.
The version numbering of these plug-ins are not necessarily link to the version of the
Compliance Checker, but they are all designed to run with the Compliance Checker tool.

Current Plug-in Releases:

• GliderDAC

This is a checker for GliderDAC files

• NCEI - link

This is a checker for NCEI netCDF Templates v1.1 and v2.0 files.

• UGRID

This is a checker for UGRID (https://ugrid-conventions.github.io/ugrid-conventions/)

These plug-ins must be installed separately but work on top of the base compliance checker software.

pip install cc-plugin-ncei

Check to see if it installed correctly, list the tests:

compliance-checker -l

You should see

 IOOS compliance checker available checker suites (code version):
 - ncei-grid (2.1.0)
 - ncei-grid:1.1 (2.1.0)
 - ncei-grid:2.0 (2.3.0)
 - ncei-grid:latest (2.1.0)
 - ncei-point (2.3.0)
 - ncei-point:1.1 (2.1.0)
 - ncei-point:2.0 (2.3.0)
 etc ....

Once installing the plug-in the usage is similar to the built in checkers.

Examples of how to use the Plug-Ins

1. Run the NCEI Point check on a THREDDS endpoint

compliance-checker -t ncei-point -v "https://data.nodc.noaa.gov/thredds/dodsC/testdata/mbiddle/GOLD_STANDARD_NETCDF/1.1/NODC_point_template_v1.1_2016-06-15_133710.844375.nc"

2. Run NCEI Trajectory Profile Orthogonal Check on local dataset

compliance-checker -t ncei-trajectory-profile-orthogonal -v ~/data/sample-trajectory-profile.nc

3. Outputting JSON from a gridded file check

compliance-checker -t ncei-grid -f json -o ~/Documents/sample_grid_report.json ~/Documents/sample_grid_report.nc

UGRID support

Compliance Checker does not support UGRID in the base package, although implicitly required by CF. If your needs include checking UGRID implementing files, we recommend that you either use an external checker such as the one maintained by the UK Met Office (https://github.com/pp-mo/ugrid-checks) or the Compliance Checker plugin listed above. (https://github.com/ioos/cc-plugin-ugrid)

Disclaimer

The objective of the IOOS Compliance Checker is to check your file against our interpretation of select dataset metadata standards to use as a guideline in generating compliant files. The compliance checker should not be considered the authoritative source on whether your file is 100% "compliant". Instead, we recommend that users use the results as a guide to work towards compliance. A table with the current CF feature support documenting implemented portions of CF is located here for reference: Feature Parity Matrix

Miscellaneous/Acknowledgements

Contributors

Portions of the CF checker are based on Michael Decker's work, http://repositories.iek.fz-juelich.de/hg/CFchecker/