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Checks Datasets and SOS endpoints for standards compliance

Project description

# IOOS Compliance Checker

[![Build Status](https://travis-ci.org/ioos/compliance-checker.svg)](https://travis-ci.org/ioos/compliance-checker)

The IOOS Compliance Checker is a Python tool to check local/remote datasets against a variety of compliance standards.
It is primarily a command-line tool (tested on OS X/Linux) and can also be used as a library import.

It currently supports the following sources and standards:

| Standard | Source | .nc/OPeNDAP | SOS |
| ---------------------------------------------------------------------------------------------------- | ----------- | ------ | ------------------------------- |
| [ACDD (1.1)](http://wiki.esipfed.org/index.php/Attribute_Convention_for_Data_Discovery_%28ACDD%29) | Built-in | X | - |
| [CF (1.6)](http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html) | Built-in | X | - |
| IOOS Asset Concept | Built-in | - | GetCapabilities, DescribeSensor |
| [Glider DAC](https://github.com/ioos/ioosngdac/wiki/NGDAC-NetCDF-File-Format-Version-2) | [ioos/cc-plugin-glider](https://github.com/ioos/cc-plugin-glider) | X | - |

## Concepts & Terminology

Each compliance standard is executed by a Check Suite,
which functions similar to a Python standard Unit Test.
A Check Suite runs one or more checks against a dataset,
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](//github.com/ioos/compliance-checker/wiki/Development) wiki page for more details on implementation.

## Usage (command line)

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).

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

```
usage: compliance-checker [-h] [--test TEST]
[--criteria [{lenient,normal,strict}]] [--verbose]
[--skip-checks SKIP_CHECKS] [-f {text,html,json}]
[-o OUTPUT] [-V] [-l] [-d DOWNLOAD_STANDARD_NAMES]
[dataset_location [dataset_location ...]]

positional arguments:
dataset_location Defines the location of the dataset to be checked.

optional arguments:
-h, --help show this help message and exit
--test TEST, -t TEST, --test= TEST, -t= TEST
Select the Checks you want to perform. Defaults to
'acdd' if unspecified
--criteria [{lenient,normal,strict}], -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.
--skip-checks SKIP_CHECKS, -s SKIP_CHECKS
Specifies tests to skip
-f {text,html,json}, --format {text,html,json}
Output format
-o OUTPUT, --output OUTPUT
Output filename
-V, --version Display the IOOS Compliance Checker version
information.
-l, --list-tests List the available tests
-d DOWNLOAD_STANDARD_NAMES, --download-standard-names DOWNLOAD_STANDARD_NAMES
Specify a version of the cf standard name table to
download as packaged version
```

```
$ compliance-checker --test=acdd compliance_checker/tests/data/ru07-20130824T170228_rt0.nc


--------------------------------------------------------------------------------
The dataset scored 69 out of 93 points
during the acdd check
--------------------------------------------------------------------------------
Scoring Breakdown:


High Priority
--------------------------------------------------------------------------------
Name :Priority: Score
Conventions :3: 1/2
keywords :3: 1/1
summary :3: 1/1
title :3: 1/1
varattr :3: 32/44


Medium Priority
--------------------------------------------------------------------------------
Name :Priority: Score
acknowledgment/acknowledgement :2: 1/1
comment :2: 1/1
creator_email :2: 1/1
creator_name :2: 1/1
creator_url :2: 1/1
date_created :2: 1/1
date_created_is_iso :2: 0/1
date_issued_is_iso :2: 0/1
date_metadata_modified_is_iso :2: 0/0
date_modified_is_iso :2: 0/1
geospatial_bounds :2: 0/1
geospatial_bounds_crs :2: 0/1
geospatial_bounds_vertical_crs :2: 0/1
geospatial_lat_extents_match :2: 1/2
geospatial_lat_max :2: 1/1
geospatial_lat_min :2: 1/1
geospatial_lon_extents_match :2: 1/2
geospatial_lon_max :2: 1/1
geospatial_lon_min :2: 1/1
geospatial_vertical_extents_match :2: 0/2
geospatial_vertical_max :2: 1/1
geospatial_vertical_min :2: 1/1
geospatial_vertical_positive :2: 1/1
history :2: 1/1
id :2: 1/1
institution :2: 1/1
license :2: 1/1
naming_authority :2: 1/1
no_blanks_in_id :2: 1/1
processing_level :2: 1/1
project :2: 1/1
publisher_email :2: 1/1
publisher_name :2: 1/1
publisher_url :2: 1/1
source :2: 1/1
standard_name_vocabulary :2: 1/1
time_coverage_duration :2: 0/1
time_coverage_end :2: 1/1
time_coverage_extents_match :2: 2/2
time_coverage_resolution :2: 1/1
time_coverage_start :2: 1/1


--------------------------------------------------------------------------------
Reasoning for the failed tests given below:


Name Priority: Score:Reasoning
--------------------------------------------------------------------------------
Conventions :3: 1/ 2 : Attr Conventions does not
contain 'ACDD-1.3'
varattr :3: 32/44 :
conductivity :3: 3/ 4 :
coverage_content_type :3: 0/ 1 : Var conductivity missing
attr coverage_content_type
density :3: 3/ 4 :
coverage_content_type :3: 0/ 1 : Var density missing attr
coverage_content_type
profile_id :3: 1/ 4 :
coverage_content_type :3: 0/ 1 : Var profile_id missing
attr coverage_content_type
var_std_name :3: 1/ 2 : Var profile_id missing
attr standard_name
var_units :3: 0/ 1 : Var profile_id missing
attr units
salinity :3: 3/ 4 :
coverage_content_type :3: 0/ 1 : Var salinity missing attr
coverage_content_type
segment_id :3: 1/ 4 :
coverage_content_type :3: 0/ 1 : Var segment_id missing
attr coverage_content_type
var_std_name :3: 1/ 2 : Var segment_id missing
attr standard_name
var_units :3: 0/ 1 : Var segment_id missing
attr units
temperature :3: 3/ 4 :
coverage_content_type :3: 0/ 1 : Var temperature missing
attr coverage_content_type
u :3: 3/ 4 :
coverage_content_type :3: 0/ 1 : Var u missing attr
coverage_content_type
v :3: 3/ 4 :
coverage_content_type :3: 0/ 1 : Var v missing attr
coverage_content_type
date_created_is_iso :2: 0/ 1 : Datetime provided is not
in a valid ISO 8601 format
date_issued_is_iso :2: 0/ 1 : Datetime provided is not
in a valid ISO 8601 format
date_modified_is_iso :2: 0/ 1 : Datetime provided is not
in a valid ISO 8601 format
geospatial_bounds :2: 0/ 1 : Attr geospatial_bounds not
present
geospatial_bounds_crs :2: 0/ 1 : Attr geospatial_bounds_crs
not present
geospatial_bounds_vertical_crs :2: 0/ 1 : Attr
geospatial_bounds_vertical
_crs not present
geospatial_lat_extents_match :2: 1/ 2 : Data for possible latitude
variables ({u'lat':
9.9692099683868702e+36,
u'lat_uv':
9.9692099683868702e+36})
did not match
geospatial_lat_max value
(34.85172)
geospatial_lon_extents_match :2: 1/ 2 : Data for possible
longitude variables
({u'lon_uv':
9.9692099683868702e+36,
u'lon':
9.9692099683868702e+36})
did not match
geospatial_lon_max value
(-120.78092)
geospatial_vertical_extents_match :2: 0/ 2 : geospatial_vertical_min !=
min(depth) values, 1.1 !=
0.11,
geospatial_vertical_max !=
max(depth) values, 1.1 !=
58.9
time_coverage_duration :2: 0/ 1 : Attr
time_coverage_duration not
present
creator_institution :1: 0/ 1 : Attr creator_institution
not present
creator_type :1: 0/ 2 : Attr creator_type not
present
date_metadata_modified :1: 0/ 1 : Attr
date_metadata_modified not
present
instrument :1: 0/ 1 : Attr instrument not
present
instrument_vocabulary :1: 0/ 1 : Attr instrument_vocabulary
not present
metadata_link :1: 0/ 1 : Attr metadata_link is
empty or completely
whitespace
metadata_link_valid :1: 0/ 1 : Metadata URL should
include http:// or
https://
platform :1: 0/ 1 : Attr platform not present
platform_vocabulary :1: 0/ 1 : Attr platform_vocabulary
not present
product_version :1: 0/ 1 : Attr product_version not
present
program :1: 0/ 1 : Attr program not present
publisher_institution :1: 0/ 1 : Attr publisher_institution
not present
publisher_type :1: 0/ 2 : Attr publisher_type not
present
references :1: 0/ 1 : Attr references is empty
or completely whitespace

```

```
$ compliance-checker --test=cf compliance_checker/tests/data/examples/hycom_global.nc


--------------------------------------------------------------------------------
The dataset scored 113 out of 122 points
during the cf check
--------------------------------------------------------------------------------
Scoring Breakdown:


High Priority
--------------------------------------------------------------------------------
Name :Priority: Score
§2.2 Valid netCDF data types :3: 6/6
§2.4 Unique dimensions :3: 6/6
§3.1 Variable depth contains valid CF u :3: 3/3
§3.1 Variable lat contains valid CF uni :3: 3/3
§3.1 Variable lon contains valid CF uni :3: 3/3
§3.1 Variable time contains valid CF un :3: 3/3
§3.1 Variable water_u contains valid CF :3: 3/3
§3.1 Variable water_v contains valid CF :3: 3/3
§3.3 Variable time has valid standard_n :3: 0/1
§4 depth contains a valid axis :3: 2/2
§4 lat contains a valid axis :3: 2/2
§4 lon contains a valid axis :3: 2/2
§4.1 Latitude variable lat has required :3: 1/1
§4.1 Longitude variable lon has require :3: 1/1
§4.3.1 depth is a valid vertical coordi :3: 1/2
§4.4 Time coordinate variable and attri :3: 2/2
§5.0 Variable water_u does not contain :3: 4/4
§5.0 Variable water_v does not contain :3: 4/4
§5.6 Grid Feature water_u is associated :3: 2/2
§5.6 Grid Feature water_v is associated :3: 2/2
§9.1 Dataset contains a valid featureTy :3: 1/1
§9.1 Feature Types are all the same :3: 1/1


Medium Priority
--------------------------------------------------------------------------------
Name :Priority: Score
cell_methods :2: 0/0
§2.3 Naming Conventions for attributes :2: 27/27
§2.3 Naming Conventions for dimensions :2: 4/4
§2.3 Naming Conventions for variables :2: 6/6
§2.3 Unique variable names :2: 6/6
§2.4 Dimension Order :2: 6/6
§2.5.1 Fill Values should be outside th :2: 0/0
§2.6.1 Global Attribute Conventions inc :2: 0/1
§2.6.2 Recommended Attributes :2: 0/3
§2.6.2 Recommended Global Attributes :2: 1/2
§4.1 Latitude variable lat defines eith :2: 1/1
§4.1 Latitude variable lat uses recomme :2: 1/1
§4.1 Longitude variable lon defines eit :2: 1/1
§4.1 Longitude variable lon uses recomm :2: 1/1
§5.0 multidimensional coordinate lat sh :2: 1/1
§5.0 multidimensional coordinate lon sh :2: 1/1
§8.1 Packed Data defined by water_u con :2: 1/1
§8.1 Packed Data defined by water_u con :2: 0/1
§8.1 Packed Data defined by water_v con :2: 1/1
§8.1 Packed Data defined by water_v con :2: 0/1


--------------------------------------------------------------------------------
Reasoning for the failed tests given below:


Name Priority: Score:Reasoning
--------------------------------------------------------------------------------
§3.3 Variable time has valid standard_n:3: 0/ 1 : variable time's attribute
standard_name must be a
non-empty string or it
should define a long_name
attribute.
§4.3.1 depth is a valid vertical coordi:3: 1/ 2 : vertical coordinates not
defining pressure must
include a positive
attribute that is either
'up' or 'down'
§2.6.1 Global Attribute Conventions inc:2: 0/ 1 : Conventions global
attribute does not contain
"CF-1.6"
§2.6.2 Recommended Attributes :2: 0/ 3 : institution should be
defined, source should be
defined, references should
be defined
§2.6.2 Recommended Global Attributes :2: 1/ 2 : global attribute history
should exist and be a non-
empty string
§8.1 Packed Data defined by water_u con:2: 0/ 1 : Attributes add_offset and
scale_factor are not of
type float or double.
§8.1 Packed Data defined by water_v con:2: 0/ 1 : Attributes add_offset and
scale_factor are not of
type float or double.



$ compliance-checker -d 35

Downloading cf-standard-names table version 35 from: http://cfconventions.org/Data/cf-standard-names/35/src/cf-standard-name-table.xml
```

## Installation

### Conda users

`compliance-checker` depends on many external C libraries,
so the easiest way to install it on MS-Windows/OS X/Linux is with `conda`.

```shell
$ conda install -c conda-forge compliance-checker
```

For more information on `conda` and installing the IOOS software stack see:

https://github.com/ioos/notebooks_demos/wiki/Installing-Conda-Python-with-the-IOOS-environment

### Pip users

When using pip the user must install the non-Python dependencies first.
Known C library dependencies include:
- UDUNITS (2.x series)
- HDF5
- NetCDF4
- libxml2/libxslt

Installation for these libraries will vary depending on your choice of operating system and method of installation
(i.e. binary packages versus compiling from source).
For more information on installing these libraries,
reference the documentation from the individual libraries.
(Check our [Ubuntu Install Guide](doc/ubuntu-install-guide.md) out.)

To install locally, set up a virtual environment (recommend using
[virtualenv-burrito](https://github.com/brainsik/virtualenv-burrito);

```
$ mkvirtualenv --no-site-packages compliance-checker
$ workon compliance-checker
```

The Python dependencies require several underlying system packages that most package managers should have.
See the [Installation](//github.com/ioos/compliance-checker/wiki/Installation) wiki page for more information.

```shell
$ pip install compliance-checker
```

## Usage (from Python code)

```python
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 with normal strictness, verbose text format to stdout
return_value, errors = ComplianceChecker.run_checker(
'/path/or/url/to/your/dataset',
['cf', 'acdd'], 0, 'normal', '-', 'text')
```


## Usage (Command Line)

```
compliance-checker <data-source> -t <test>[ <test>...]
```

The compliance checker command line tool will print out (to STDOUT) the test
results. The command line tool will also return 0 for a successful run and
non-0 for a failure.

## Available Test Suites

- [CF 1.6](http://cfconventions.org/)
- [ACDD 1.1, 1.3](http://www.unidata.ucar.edu/software/thredds/current/netcdf-java/metadata/DataDiscoveryAttConvention.html)
- [IOOS](http://ioos.noaa.gov/data/contribute-data/)

## Available Test Suites as Plugins

- [GliderDAC](https://github.com/ioos/ioosngdac/wiki/NGDAC-NetCDF-File-Format-Version-2) - [link](https://github.com/ioos/cc-plugin-glider)

## Development

The compliance-checker is designed to be simple and hackable to edit existing compliance suites or introduce new ones. See the [Development](https://github.com/ioos/compliance-checker/wiki/Development) wiki page for more information.

#### Testing

Please run any new code through `flake8` and `pep8`. You can easily do this by using `pylama` (config is already setup in `pytest.ini`).

```bash
$ pip install pylama
$ py.test --pylama
```

Take a look at the failed tests and fix accordingly. Travis does not run with the `--pylama` flag so you MUSt do this yourself!


## Resource materials

[Compliance checker Webinar](
https://mmancusa.webex.com/mmancusa/ldr.php?RCID=e5e6fc5b6d218307f9eec863111e6034)


## Roadmap

- Improved text output (\#12)
- UGRID compliance (\#33)

## Contributors

- [Dave Foster](https://github.com/daf) &lt;dave@axiomdatascience.com&gt;
- [Dan Maher](https://github.com/danieljmaher) &lt;daniel.maher@rpsgroup.com&gt;
- [Luke Campbell](https://github.com/lukecampbell) &lt;luke.campbell@rpsgroup.com&gt;
- [Kyle Wilcox](https://github.com/kwilcox) &lt;kyle@axiomdatascience.com&gt;
- [Ben Adams](https://github.com/benjwadams) &lt;ben.adams@rpsgroup.com&gt;

And many more testers!

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

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