pdok-geopackage-validator 0.5.3

Validate Geopackage files

geopackage-validator

Table of Contents

• geopackage-validator
  • What does it do
  • Installation
    • Ubuntu
    • Windows
    • Docker
  • Usage
    • Validate
    • Show validations
    • Generate table definitions
  • Performance
  • Local development
    • Installation
    • Usage
    • Code style
    • Tests
    • Releasing

What does it do

The Geopackage validator can validate .gkpg files to see if they conform to a set of standards. The current checks are (see also the 'show-validations' command):

Validation code	Description
RQ1	Layer names must start with a letter, and valid characters are lowercase a-z, numbers or underscores.
RQ2	Layers must have at least one feature.
RQ3	Layer features should have an allowed geometry_type (one of POINT, LINESTRING, POLYGON, MULTIPOINT, MULTILINESTRING, or MULTIPOLYGON).
RQ4	The geopackage should have no views defined.
RQ5	Geometry should be valid.
RQ6	Column names must start with a letter, and valid characters are lowercase a-z, numbers or underscores.
RQ7	Tables should have a feature id column with unique index.
RQ8	Geopackage must conform to given JSON definitions.
RQ9	All geometry tables must have an rtree index.
RQ10	All geometry table rtree indexes must be valid.
RQ11	OGR indexed feature counts must be up to date.
RQ12	Only the following ESPG spatial reference systems are allowed: 28992, 3034, 3035, 3038, 3039, 3040, 3041, 3042, 3043, 3044, 3045, 3046, 3047, 3048, 3049, 3050, 3051, 4258, 4936, 4937, 5730, 7409.
RQ13	It is required to give all GEOMETRY features the same default spatial reference system.
RQ14	The geometry_type_name from the gpkg_geometry_columns table must be one of POINT, LINESTRING, POLYGON, MULTIPOINT, MULTILINESTRING, or MULTIPOLYGON.
RQ15	All table geometries must match the geometry_type_name from the gpkg_geometry_columns table.
RC1	It is recommended to name all GEOMETRY type columns 'geom'.
RC2	It is recommended to give all GEOMETRY type columns the same name.

Installation

This package requires GDAL version >= 3.0.4. And python >= 3.8 to run.

Ubuntu

Install GDAL:

sudo apt-get install gdal-bin

Install the validator with:

pip3 install pdok-geopackage-validator

Windows

Either use anaconda to install gdal:

conda install -c conda-forge gdal

Or download and install OSGeo4W. And download get-pip.py and run it in the OSGeo4W shell:

python3 get-pip.py

Install the validator with:

pip3 install pdok-geopackage-validator

Docker

Pull the latest version of the Docker image (only once needed, or after an update)

docker pull pdok/geopackage-validator:latest

Or build the Docker image from source:

docker build -t pdok/geopackage-validator .

The command is directly called so subcommands can be run in the container directly:

docker run -v ${PWD}:/gpkg --rm pdok/geopackage-validator validate -t /path/to/generated_definitions.json --gpkg-path /gpkg/tests/data/test_allcorrect.gpkg

Usage

RQ8 Validation

To validate RQ8 you have to generate definitions first.

geopackage-validator generate-definitions --gpkg-path /path/to/file.gpkg

Validate

Usage: geopackage-validator validate [OPTIONS]

  Geopackage validator validating a local file or from s3 storage

Options:
  --gpkg-path FILE                Path pointing to the geopackage.gpkg file
                                  [env var: GPKG_PATH]

  -t, --table-definitions-path FILE
                                  Path pointing to the table-definitions JSON
                                  file (generate this file by calling the
                                  generate-definitions command)

  --validations-path FILE         Path pointing to the set of validations to
                                  run. If validations-path and validations are
                                  not given, validate runs all validations
                                  [env var: VALIDATIONS_FILE]

  --validations TEXT              Comma-separated list of validations to run
                                  (e.g. --validations R1,R2,R3). If
                                  validations-path and validations are not
                                  given, validate runs all validations  [env
                                  var: VALIDATIONS]

  --s3-endpoint-no-protocol TEXT  Endpoint for the s3 service without protocol
                                  [env var: S3_ENDPOINT_NO_PROTOCOL]

  --s3-access-key TEXT            Access key for the s3 service  [env var:
                                  S3_ACCESS_KEY]

  --s3-secret-key TEXT            Secret key for the s3 service  [env var:
                                  S3_SECRET_KEY]

  --s3-bucket TEXT                Bucket where the geopackage is on the s3
                                  service  [env var: S3_BUCKET]

  --s3-key TEXT                   Key where the geopackage is in the bucket
                                  [env var: S3_KEY]

  -v, --verbosity LVL             Either CRITICAL, ERROR, WARNING, INFO or
                                  DEBUG

  --help                          Show this message and exit.

Examples:

pipenv run geopackage-validator validate -t /path/to/generated_definitions.json --gpkg-path tests/data/test_allcorrect.gpkg

Run with specific validations only

Specified in file:

pipenv run geopackage-validator validate --gpkg-path tests/data/test_allcorrect.gpkg --validations-path tests/validationsets/example-validation-set.json

Or specified on command line:

pipenv run geopackage-validator validate --gpkg-path tests/data/test_allcorrect.gpkg --validations R1,R2,R3

Show validations

Show all the possible validations that are executed in the validate command.

Usage: geopackage-validator show-validations [OPTIONS]

  Show all the possible validations that are executed in the validate
  command.

Options:
  -v, --verbosity LVL  Either CRITICAL, ERROR, WARNING, INFO or DEBUG
  --help               Show this message and exit.

Generate table definitions

Generate Geopackage table definition JSON from given local or s3 package. This command generates a definition that describes the Geopackage layout, in JSON format. This JSON, when saved in a file, can be used in the validation step to validate a Geopackage against these table definitions.

Usage: geopackage-validator generate-definitions [OPTIONS]

  Generate Geopackage table definition JSON from given local or s3 package.
  Use the generated definition JSON in the validation step by providing the
  table definitions with the --table-definitions-path parameter.

Options:
  --gpkg-path FILE                Path pointing to the geopackage.gpkg file
                                  [env var: GPKG_PATH]

  --s3-endpoint-no-protocol TEXT  Endpoint for the s3 service without protocol
                                  [env var: S3_ENDPOINT_NO_PROTOCOL]

  --s3-access-key TEXT            Access key for the s3 service  [env var:
                                  S3_ACCESS_KEY]

  --s3-secret-key TEXT            Secret key for the s3 service  [env var:
                                  S3_SECRET_KEY]

  --s3-bucket TEXT                Bucket where the geopackage is on the s3
                                  service  [env var: S3_BUCKET]

  --s3-key TEXT                   Key where the geopackage is in the bucket
                                  [env var: S3_KEY]

  -v, --verbosity LVL             Either CRITICAL, ERROR, WARNING, INFO or
                                  DEBUG

  --help                          Show this message and exit.

Performance

On a PC with 32GB memory and Intel Core i7-8850H CPU @ 2.6 ghz, the following performance has been measured:

Geopackage size	Time needed for validation	MB / minute
315 MB	0.5 minutes	630 MB / minute
6.3 GB	12.5 minutes	504 MB / minute
9.9 GB	17.5 minutes	565 MB / minute
15.7 GB	24 minutes	654 MB / minute

This is to give an indication of the performance and by no means a guarantee.

Local development

Pipenv installation

We're installed with pipenv, a handy wrapper around pip and virtualenv. Install that first with pip install pipenv.

Install the GDAL native library version 3.0.4 and development headers:

sudo apt-get update
sudo apt-get install gdal-bin libgdal-dev -y

Make sure you have GDAL version 3.0.4:

$ gdalinfo --version
GDAL 3.0.4, released 2020/01/28

Then install the dependencies of this project:

export CPLUS_INCLUDE_PATH=/usr/include/gdal
export C_INCLUDE_PATH=/usr/include/gdal
PIPENV_VENV_IN_PROJECT=1 pipenv install --python 3.8 --dev

In case you do not have python 3.8 on your machine, install python using pyenv and try the previous command again. See install pyenv below for instructions.

If you need a new dependency (like requests), add it in setup.py in install_requires. Afterwards, run install again to actually install your dependency:

pipenv install --dev

Pipenv usage

There will be a script you can run like this:

pipenv run geopackage-validator

Code style

In order to get nicely formatted python files without having to spend manual work on it, run the following command periodically:

pipenv run black geopackage_validator

Tests

Run the tests regularly. This also checks with pyflakes and black:

pipenv run pytest

Code coverage:

pipenv run pytest --cov=geopackage_validator  --cov-report html

Releasing

Release in github by creating and pushing a new tag to master and create a new release in github.

Install pyenv

We can install pyenv by running the following commands:

sudo apt-get install -y make build-essential libssl-dev zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev xz-utils tk-dev libffi-dev liblzma-dev
curl -L https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer | bash

Also make sure to put pyenv in your .bashrc or .zshrc as instructed by the previous commands.

Changelog of geopackage-validator

0.4.3 (unreleased)

• Nothing changed yet.

0.4.2 (2021-01-12)

• Move to pdok-geopackage-validator

0.4.1 (2020-12-23)

• Better logging.

0.3 (2020-10-09)

• Fix for PyPI.

0.2 (2020-10-09)

• Output refactor.

• Differentiate between requirements and recommendations in the validations.

• First PyPI release.

0.1 (2020-08-13)

• Initial project structure created with cookiecutter and https://github.com/PDOK/cookiecutter-python-base