pdok-geopackage-validator 0.4.2

Validate Geopackage files

Table of Contents

• geopackage-validator
  • Installation
    • GDAL
  • Usage
    • Usage through Docker (pull from Docker Hub)
    • Usage through Docker (local build)
  • Commands
    • Validate
    • Show validations
    • Generate table definitions
  • Performance
  • Development installation
  • Releasing
  • Install pyenv

geopackage-validator

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 a valid geometry (one of POINT, LINESTRING, POLYGON, MULTIPOINT, MULTILINESTRING, or MULTIPOLYGON). (random sample of up to 100)
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. (random sample of up to 100)
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

We are installed with:

pip3 install geopackage-validator

GDAL

This package uses Python bindings for GDAL) and has a runtime dependency on an installed GDAL (when not running through Docker, which is the recommended way of running this package.)

Usage

Usage through Docker (pull from Docker Hub)

Place your geopackage somewhere on disk or in an S3 storage repository.

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

docker pull pdok/geopackage-validator:latest

Run the Docker container, mounting the current directory to /gpkg (adjust where needed)

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

Usage through Docker (local build)

Place your geopackage somewhere on disk or in an S3 storage repository.

Build the Docker image (only once needed, or after an update)

docker build -t geopackage-validator .

Run the Docker container, mounting the current directory to /gpkg (adjust where needed)

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

Commands

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 --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.

Development 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.

There will be a script you can run like this:

pipenv run geopackage-validator

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

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

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

Releasing

Pipenv installs zest.releaser which allows you to release the package to a git(hub) repo. It has a fullrelease command that asks you a few questions, which you all respond to with <enter>:

pipenv run fullrelease

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

0.4.2 (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