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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 OSX/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>[ <test>...]]
[--criteria [{lenient,normal,strict}]] [--verbose]
[-f {stdout,html}] [-o OUTPUT] [-d]
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 {gliderdac|acdd|cf|ioos[:version]}[ gliderdac|acdd|cf|ioos[:version]...] -t {gliderdac|acdd|cf|ioos[:version]}[ gliderdac|acdd|cf|ioos[:version]...] --test= {gliderdac|acdd|cf|ioos[:version]}[ gliderdac|acdd|cf|ioos[:version]...], -t= {gliderdac|acdd|cf|ioos[:version]}[ gliderdac|acdd|cf|ioos[:version]...]
Select the Checks you want to perform. Versions may be specified by using a colon followed by a version number. Using a specification without a version number or with `:latest` will select the latest version of the standard. Multiple tests may be specified by separating with a comma
--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.
-f {stdout,html}, --format {stdout,html}
Output format
-o OUTPUT, --output OUTPUT
Output filename
-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
Running Compliance Checker on the dataset from: compliance_checker/tests/data/ru07-20130824T170228_rt0.nc


--------------------------------------------------------------------------------
The dataset scored 100 out of 188 points
during the acdd check
--------------------------------------------------------------------------------
Scoring Breakdown:


High Priority
--------------------------------------------------------------------------------
Name :Priority: Score
keywords :3: 1/1
summary :3: 1/1
title :3: 1/1
varattr :3: 69/150


Medium Priority
--------------------------------------------------------------------------------
Name :Priority: Score
acknowledgement :2: 0/1
cdm_data_type :2: 1/2
comment :2: 1/1
creator_email :2: 1/1
creator_name :2: 1/1
creator_url :2: 1/1
date_created :2: 1/1
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
history :2: 1/1
id :2: 1/1
institution :2: 1/1
keywords_vocabulary :2: 1/1
license :2: 1/1
naming_authority :2: 1/1
processing_level :2: 1/1
project :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
--------------------------------------------------------------------------------
varattr :3: 69/150 :
conductivity :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var conductivity missing
attr coverage_content_type
conductivity_qc :3: 2/ 5 :
var_coverage_content_type :3: 0/ 2 : Var conductivity_qc
missing attr
coverage_content_type
var_units :3: 0/ 1 : Var conductivity_qc
missing attr units
density :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var density missing attr
coverage_content_type
density_qc :3: 2/ 5 :
var_coverage_content_type :3: 0/ 2 : Var density_qc missing
attr coverage_content_type
var_units :3: 0/ 1 : Var density_qc missing
attr units
depth :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var depth missing attr
coverage_content_type
depth_qc :3: 2/ 5 :
var_coverage_content_type :3: 0/ 2 : Var depth_qc missing attr
coverage_content_type
var_units :3: 0/ 1 : Var depth_qc missing attr
units
instrument_ctd :3: 1/ 5 :
var_coverage_content_type :3: 0/ 2 : Var instrument_ctd missing
attr coverage_content_type
var_std_name :3: 0/ 1 : Var instrument_ctd missing
attr standard_name
var_units :3: 0/ 1 : Var instrument_ctd missing
attr units
lat :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var lat missing attr
coverage_content_type
lat_qc :3: 2/ 5 :
var_coverage_content_type :3: 0/ 2 : Var lat_qc missing attr
coverage_content_type
var_units :3: 0/ 1 : Var lat_qc missing attr
units
lat_uv :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var lat_uv missing attr
coverage_content_type
lon :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var lon missing attr
coverage_content_type
lon_qc :3: 2/ 5 :
var_coverage_content_type :3: 0/ 2 : Var lon_qc missing attr
coverage_content_type
var_units :3: 0/ 1 : Var lon_qc missing attr
units
lon_uv :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var lon_uv missing attr
coverage_content_type
platform :3: 1/ 5 :
var_coverage_content_type :3: 0/ 2 : Var platform missing attr
coverage_content_type
var_std_name :3: 0/ 1 : Var platform missing attr
standard_name
var_units :3: 0/ 1 : Var platform missing attr
units
pressure :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var pressure missing attr
coverage_content_type
pressure_qc :3: 2/ 5 :
var_coverage_content_type :3: 0/ 2 : Var pressure_qc missing
attr coverage_content_type
var_units :3: 0/ 1 : Var pressure_qc missing
attr units
profile_id :3: 1/ 5 :
var_coverage_content_type :3: 0/ 2 : Var profile_id missing
attr coverage_content_type
var_std_name :3: 0/ 1 : Var profile_id missing
attr standard_name
var_units :3: 0/ 1 : Var profile_id missing
attr units
salinity :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var salinity missing attr
coverage_content_type
salinity_qc :3: 2/ 5 :
var_coverage_content_type :3: 0/ 2 : Var salinity_qc missing
attr coverage_content_type
var_units :3: 0/ 1 : Var salinity_qc missing
attr units
segment_id :3: 1/ 5 :
var_coverage_content_type :3: 0/ 2 : Var segment_id missing
attr coverage_content_type
var_std_name :3: 0/ 1 : Var segment_id missing
attr standard_name
var_units :3: 0/ 1 : Var segment_id missing
attr units
temperature :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var temperature missing
attr coverage_content_type
temperature_qc :3: 2/ 5 :
var_coverage_content_type :3: 0/ 2 : Var temperature_qc missing
attr coverage_content_type
var_units :3: 0/ 1 : Var temperature_qc missing
attr units
time :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var time missing attr
coverage_content_type
time_qc :3: 2/ 5 :
var_coverage_content_type :3: 0/ 2 : Var time_qc missing attr
coverage_content_type
var_units :3: 0/ 1 : Var time_qc missing attr
units
time_uv :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var time_uv missing attr
coverage_content_type
trajectory :3: 1/ 5 :
var_coverage_content_type :3: 0/ 2 : Var trajectory missing
attr coverage_content_type
var_std_name :3: 0/ 1 : Var trajectory missing
attr standard_name
var_units :3: 0/ 1 : Var trajectory missing
attr units
u :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var u missing attr
coverage_content_type
u_qc :3: 2/ 5 :
var_coverage_content_type :3: 0/ 2 : Var u_qc missing attr
coverage_content_type
var_units :3: 0/ 1 : Var u_qc missing attr
units
v :3: 3/ 5 :
var_coverage_content_type :3: 0/ 2 : Var v missing attr
coverage_content_type
v_qc :3: 2/ 5 :
var_coverage_content_type :3: 0/ 2 : Var v_qc missing attr
coverage_content_type
var_units :3: 0/ 1 : Var v_qc missing attr
units
acknowledgement :2: 0/ 1 : Attr acknowledgement not
present
cdm_data_type :2: 1/ 2 : Attr cdm_data_type present
but not in expected value
list (['vector', 'grid',
'textTable', 'tin',
'stereoModel', 'video'])
geospatial_lat_extents_match :2: 1/ 2 : Data for possible latitude
variables ({u'lat':
9.969209968386869e+36,
u'lat_uv':
9.969209968386869e+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':
9.969209968386869e+36,
u'lon':
9.969209968386869e+36})
did not match
geospatial_lon_max value
(-120.78092)
geospatial_vertical_extents_match :2: 0/ 2 : Data for possible vertical
variables ({u'pressure':
0.10999999999999999,
u'depth':
0.10999999999999999}) did
not match
geospatial_vertical_min
value (1.1) Data for
possible vertical
variables ({u'pressure':
9.969209968386869e+36,
u'depth':
9.969209968386869e+36})
did not match
geospatial_vertical_max
value (589.0)
time_coverage_duration :2: 0/ 1 : Attr
time_coverage_duration not
present
contributor_role :1: 1/ 2 : Attr contributor_role
present but not in
expected value list
(['principalInvestigator',
'author'])



$ compliance-checker --test=cf compliance_checker/tests/data/sss20140107.v2.0cap.nc

Running Compliance Checker on the dataset from: compliance_checker/tests/data/sss20140107.v2.0cap.nc


--------------------------------------------------------------------------------
The dataset scored 12 out of 14 points
during the cf check
--------------------------------------------------------------------------------
Scoring Breakdown:


High Priority
--------------------------------------------------------------------------------
Name :Priority: Score
Variable names :3: 3/3
conventions :3: 0/1
data_types :3: 3/3
dimension_names :3: 3/3
units :3: 0/1


Medium Priority
--------------------------------------------------------------------------------
Name :Priority: Score
all_features_are_same_type :2: 0/0
contiguous_ragged_array :2: 0/0
coordinate_type :2: 2/2
coordinates_and_metadata :2: 0/0
feature_type :2: 0/0
incomplete_multidim_array :2: 0/0
indexed_ragged_array :2: 0/0
missing_data :2: 0/0
orthogonal_multidim_array :2: 0/0
var :2: 1/1


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


Name Priority: Score:Reasoning
--------------------------------------------------------------------------------
conventions :3: 0/ 1 : Conventions field is not
present
units :3: 0/ 1 :
sss_cap :3: 0/ 1 :
known :3: 0/ 1 : unknown units type (PSU)



$ 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

### Non-Python dependencies

A number of the Python modules used by the compliance checker such as NumPy
require linking against external C or Fortran libraries. If using an
installation method for Python dependencies such as pip below, these external
libraries will need to be installed beforehand prior to the installation of
the Python dependencies.
Known C library dependencies include:
- NetCDF4
- HDF5
- UDUNITS (2.x series)
- 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.

### Python dependencies with `pip`

To install locally, set up a virtual environment (recommend using
[virtualenv-burrito](https://github.com/brainsik/virtualenv-burrito);
however, do not use `virtualenv-burrito` if you are using Anaconda python.
[Instructions for Anaconda](#anaconda) appear below):

```
$ 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.

Install dependencies, numpy must be installed on its own:

```
$ pip install numpy
$ pip install compliance-checker
```

###<a name="anaconda"></a> Anaconda on linux

Assuming you have a standard Anaconda installation, run the following:

1. From the compliance-checker top-level directory create the virtual
environment (stay as far away from virtualenv's burrito as you possibly
can):
```
conda create --file requirements.txt -n compliance_checker
source activate compliance_checker
conda install compliance-checker
```

2. Test the installation using the following commands:
```
compliance-checker --help
compliance-checker --test=acdd compliance_checker/tests/data/ru07-20130824T170228_rt0.nc
compliance-checker --test=cf compliance_checker/tests/data/sss20140107.v2.0cap.nc
```

### MS-Windows

Before [creating the virtual environment and installing compliance-checker](https://github.com/ioos/compliance-checker#-anaconda-on-linux), the channel locations should be updated in the Anaconda configuration file `.condarc`; without that the `conda` command fails to find the required packages. If that file does not exist it should be created in the Anaconda root directory with the following text (the comments with "#" prefix are optional):

```
# channel locations. These override conda defaults, i.e., conda will
# search *only* the channels listed here, in the order given. Use "defaults" to
# automatically include all default channels. Non-url channels will be
# interpreted as binstar usernames (this can be changed by modifying the
# channel_alias key; see below).
channels:
- defaults
- IOOS

```

If after that conda still cannot find the required packages, the `binstar` package should be installed:

```
conda install binstar
```

### Ubuntu

Installing on Ubuntu? Check out the [Ubuntu Install Guide](doc/ubuntu-install-guide.md)

## 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'], True, '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://www.ioos.noaa.gov/data/contribute_data.html)

## 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 <dave@axiomdatascience.com>
- Dan Maher <dmaher@asascience.com>
- Luke Campbell <lcampbell@asascience.com>
- [Kyle Wilcox](https://github.com/kwilcox) <kyle@axiomdatascience.com>
- Ben Adams <ben.adams@rpsgroup.com>

And many more testers!

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

<!--
15 vim --version
17 python --version
23 git --version
27 wget http://09c8d0b2229f813c1b93-c95ac804525aac4b6dba79b00b39d1d3.r79.cf1.rackcdn.com/Anaconda-2.1.0-Linux-x86_64.sh
33 bash Anaconda-2.1.0-Linux-x86_64.sh
67 wget https://github.com/spf13/hugo/releases/download/v0.12/hugo_0.12_linux_amd64.tar.gz
70 git clone ssh://git@github.com/duncombe/dotfiles.git
82 git clone ssh://git@github.com/duncombe/centos-instance.git
106 git config --global user.name "Christopher Duncombe Rae"
108 git config --global user.email "christopher.duncombe.rae@noaa.gov"
278 git remote add origin ssh://git@github.com/duncombe/PROGS.git
344 git clone ssh://git@github.com/duncombe/system-test.git
348 git remote set-url upstream ssh://git@github.com/ioos/system-test.git
449 git submodule add ssh://git@github.com/duncombe/bash-git-prompt.git
749 git clone ssh://git@github.com/duncombe/unidata-python-workshop.git
750 git remote add upstream ssh://git@github.com/Unidata/unidata-python-workshop.git
783 git clone https://github.com/Unidata/unidata-python-workshop
784 conda config --add channels https://conda.binstar.org/rsignell
785 conda config --add channels https://conda.binstar.org/Unidata
791 conda create -n workshop python=2 numpy matplotlib cartopy ipython ipython-notebook netcdf4 owslib pyudl networkx basemap
836 compliance-checker --test=acdd compliance_checker/tests/data/test-data/ru07-20130824T170228_rt0.nc
837 compliance-checker --test=acdd compliance_checker/tests/data/ru07-20130824T170228_rt0.nc
838 compliance-checker --test=acdd compliance_checker/tests/data/ru07-20130824T170228_rt0.nc | less -S
839 compliance-checker --test=acdd test-data/ru07-20130824T170228_rt0.nc

-->

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