pdok-geopackage-validator 0.8.5

Validate Geopackage files according to PDOK requirements and recommendations

PDOK geopackage-validator

Geopackages are a data format that have a deliberately broad application, so many of the requirements are dependend on your use.

The PDOK geopackage validator is used by PDOK. PDOK is part of the Dutch government. This geopackage validator is used to validate a set of requirements to make sure geopackages adhere to our standardized ETL pipeline. It is possible to use this for your own purposes as described here. The validations will not change (except for bugfixes); new validations are always added to the list.

Table of Contents

• geopackage-validator
  • Table of Contents
  • What does it do
  • Geopackage versions
  • Installation
    • Docker
  • Usage
    • RQ8 Validation
    • Show validations
    • Generate table definitions
  • Local development
    • Usage
    • Python console
    • Code style
    • Tests
    • Releasing

TL;DR Commands

Either run through docker or locally.

Docker

Validate a GeoPackage with the default set of validation rules:

gpkg_path=relative/path/to/the.gpkg
docker run -v "$(pwd)":/gpkg --rm pdok/geopackage-validator validate --gpkg-path "/gpkg/${gpkg_path}" 

Validate a GeoPackage with the default set of validation rules including a schema:

schema_path=relative/path/to/the/schema.json
gpkg_path=relative/path/to/the.gpkg
docker run -v "$(pwd)":/gpkg --rm pdok/geopackage-validator validate --gpkg-path "/gpkg/${gpkg_path}" --table-definitions-path "/gpkg/${schema_path}" 

Generate a schema:

schema_path=relative/path/to/the/schema.json
gpkg_path=relative/path/to/the.gpkg
docker run -v "$(pwd)":/gpkg --rm pdok/geopackage-validator generate-definitions --gpkg-path "/gpkg/${gpkg_path}" > "$schema_path" 

Local

For a local setup we require/tested against python > 3.6 and gdal = 3.4.

gpkg_path=relative/path/to/the.gpkg
geopackage-validator validate --gpkg-path "/gpkg/${gpkg_path}" 

Validate a GeoPackage with the default set of validation rules including a schema:

schema_path=relative/path/to/the/schema.json
gpkg_path=relative/path/to/the.gpkg
geopackage-validator validate --gpkg-path "/gpkg/${gpkg_path}" --table-definitions-path "/gpkg/${schema_path}" 

Generate a schema:

schema_path=relative/path/to/the/schema.json
gpkg_path=relative/path/to/the.gpkg
geopackage-validator generate-definitions --gpkg-path "/gpkg/${gpkg_path}" > "$schema_path" 

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
UNKNOWN_ERROR	No unexpected (GDAL) errors must occur.
RQ0	LEGACY: * Geopackage must conform to table names in the given JSON or YAML definitions.
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	LEGACY: * 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 or YAML 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 EPSG 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.
RQ16	All layer and column names shall not be longer than 53 characters.
RC17	It is recommended to name all GEOMETRY type columns 'geom'.
RC18	It is recommended to give all GEOMETRY type columns the same name.
RC19	It is recommended to only use multidimensional geometry coordinates (elevation and measurement) when necessary.
RC20	It is recommended that all (MULTI)POLYGON geometries have a counter-clockwise orientation for their exterior ring, and a clockwise direction for all interior rings.
UNKNOWN_WARNINGS	It is recommended that the unexpected (GDAL) warnings are looked into.

* Legacy requirements are only executed with the validate command when explicitly requested in the validation set.
** Since version 0.8.0 the recommendations are part of the same sequence as the requirements. From now on a check will always maintain the integer part of the code. Even if at a later time the validation type can shift between requirement and recommendation.

An explanation in Dutch with a reason for each rule can be found here.

Geopackage versions

The Geopackage validator support the following Geopackage versions:

• 1.3.1
• 1.3
• 1.2.1

Installation

This package requires:

• GDAL version >= 3.2.1.
• Spatialite version >= 5.0.0
• And python >= 3.8 to run.

We recommend using the docker image. When above requirements are met the package can be installed using pip (pip install pdok-geopackage-validator).

Docker Installation

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.

docker run -v ${PWD}:/gpkg --rm pdok/geopackage-validator geopackage-validator generate-definitions --gpkg-path /path/to/file.gpkg

Validate

Usage: geopackage-validator validate [OPTIONS]

  Geopackage validator validating a local file or a file from S3 storage.
  When the filepath is preceded with '/vsis3' or '/vsicurl' the gdal virtual
  file system will be used to access the file on S3 and will not be directly
  downloaded. See https://gdal.org/user/virtual_file_systems.html for
  further explanation how to use gdal virtual file systems. For convenience
  the gdal vsi environment parameters and optional parameters are provided
  with an S3_ instead of an AWS_ prefix. The AWS_ environment parameters
  will also work.

  Examples:

  viscurl:

  geopackage-validator validate --gpkg-path /vsicurl/http://minio-
  url.nl/bucketname/key/to/public.gpkg

  vsis3:

  geopackage-validator validate --gpkg-path
  /vsis3/bucketname/key/to/public.gpkg --s3-signing-region eu-central-1
  --s3-secret-key secret --s3-access-key acces-key --s3-secure=false
  --s3-virtual-hosting false --s3-endpoint-no-protocol minio-url.nl

  S3_SECRET_KEY=secret S3_ACCESS_KEY=acces-key S3_SIGNING_REGION=eu-
  central-1 S3_SECURE=false S3_VIRTUAL_HOSTING=false
  S3_ENDPOINT_NO_PROTOCOL=minio-url.nl geopackage-validator validate --gpkg-
  path /vsis3/bucketname/key/to/public.gpkg

  AWS_SECRET_ACCESS_KEY=secret AWS_ACCESS_KEY_ID=acces-key
  AWS_DEFAULT_REGION=eu-central-1 AWS_HTTPS=NO AWS_VIRTUAL_HOSTING=FALSE
  AWS_S3_ENDPOINT=minio-url.nl geopackage-validator validate --gpkg-path
  /vsis3/bucketname/key/to/public.gpkg

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
                                  or YAML 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 RQ1,RQ2,RQ3). If
                                  validations-path and validations are not
                                  given, validate runs all validations  [env
                                  var: VALIDATIONS]

  --exit-on-fail                  Exit with code 1 when validation success is
                                  false.

  --yaml                          Output yaml.
  --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]

  --s3-secure BOOLEAN             Use a secure TLS connection for S3.  [env
                                  var: S3_SECURE]

  --s3-virtual-hosting TEXT       TRUE value, identifies the bucket via a
                                  virtual bucket host name, e.g.:
                                  mybucket.cname.domain.com - FALSE value,
                                  identifies the bucket as the top-level
                                  directory in the URI, e.g.:
                                  cname.domain.com/mybucket. Convenience
                                  parameter, same as gdal AWS_VIRTUAL_HOSTING.
                                  [env var: S3_VIRTUAL_HOSTING]

  --s3-signing-region TEXT        S3 signing region. Convenience parameter,
                                  same as gdal AWS_DEFAULT_REGION.  [env var:
                                  S3_SIGNING_REGION]

  --s3-no-sign-request TEXT       When set, request signing is disabled. This
                                  option might be used for buckets with public
                                  access rights. Convenience parameter, same
                                  as gdal AWS_NO_SIGN_REQUEST.  [env var:
                                  S3_NO_SIGN_REQUEST]

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

  --help                          Show this message and exit.

Examples:

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

Run with specific validations only

Specified in file:

docker run -v ${PWD}:/gpkg --rm pdok/geopackage-validator validate --gpkg-path tests/data/test_allcorrect.gpkg --validations-path tests/validationsets/example-validation-set.json

Or specified on command line:

docker run -v ${PWD}:/gpkg --rm pdok/geopackage-validator validate --gpkg-path tests/data/test_allcorrect.gpkg --validations RQ1,RQ2,RQ3

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

Usage: geopackage-validator generate-definitions [OPTIONS]

  Generate table definition for a geopackage on local or S3 storage. Use the
  generated definition JSON or YAML in the validation step by providing the
  table definitions with the --table-definitions-path parameter. When the
  filepath is preceded with '/vsi' the gdal virtual file system method will
  be used to access the file on S3 and will not be directly downloaded. See
  https://gdal.org/user/virtual_file_systems.html for further explanation.
  For convenience the gdal vsi environment parameters and optional
  parameters are provided with an S3_ instead of an AWS_ prefix. The AWS_
  environment parameters will also work.

  Examples:

  viscurl:

  geopackage-validator validate --gpkg-path /vsicurl/http://minio-
  url.nl/bucketname/key/to/public.gpkg

  vsis3:

  geopackage-validator generate-definitions --gpkg-path
  /vsis3/bucketname/key/to/public.gpkg --s3-signing-region eu-central-1
  --s3-secret-key secret --s3-access-key acces-key --s3-secure=false
  --s3-virtual-hosting false --s3-endpoint-no-protocol minio-url.nl

  S3_SECRET_KEY=secret S3_ACCESS_KEY=acces-key S3_SIGNING_REGION=eu-
  central-1 S3_SECURE=false S3_VIRTUAL_HOSTING=false
  S3_ENDPOINT_NO_PROTOCOL=minio-url.nl geopackage-validator generate-definitions --gpkg-
  path /vsis3/bucketname/key/to/public.gpkg

  AWS_SECRET_ACCESS_KEY=secret AWS_ACCESS_KEY_ID=acces-key
  AWS_DEFAULT_REGION=eu-central-1 AWS_HTTPS=NO AWS_VIRTUAL_HOSTING=FALSE
  AWS_S3_ENDPOINT=minio-url.nl geopackage-validator generate-definitions --gpkg-path
  /vsis3/bucketname/key/to/public.gpkg

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

  --yaml                          Output yaml
  --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]

  --s3-secure BOOLEAN             Use a secure TLS connection for S3.  [env
                                  var: S3_SECURE]

  --s3-virtual-hosting TEXT       TRUE value, identifies the bucket via a
                                  virtual bucket host name, e.g.:
                                  mybucket.cname.domain.com - FALSE value,
                                  identifies the bucket as the top-level
                                  directory in the URI, e.g.:
                                  cname.domain.com/mybucket. Convenience
                                  parameter, same as gdal AWS_VIRTUAL_HOSTING.
                                  [env var: S3_VIRTUAL_HOSTING]

  --s3-signing-region TEXT        S3 signing region. Convenience parameter,
                                  same as gdal AWS_DEFAULT_REGION.  [env var:
                                  S3_SIGNING_REGION]

  --s3-no-sign-request TEXT       When set, request signing is disabled. This
                                  option might be used for buckets with public
                                  access rights. Convenience parameter, same
                                  as gdal AWS_NO_SIGN_REQUEST.  [env var:
                                  S3_NO_SIGN_REQUEST]

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

  --help                          Show this message and exit.

Local development

We advise using docker-compose for local development. This allows live editing and testing code with the correct gdal/ogr version with spatialite 5.0.0. First build the local image with your machines user id and group id:

docker-compose build --build-arg USER_ID=`id -u` --build-arg GROUP_ID=`id -g`

Usage

There will be a script you can run like this:

docker-compose run --rm validator geopackage-validator

This command has direct access to the files found in this directory. In case you want to point the docker-compose to other files, you can add or edit the volumes in the docker-compose.yaml

Python console

Ipython is available in the docker:

docker-compose run --rm validator ipython

Code style

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

docker-compose run --rm validator black .

Tests

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

docker-compose run --rm validator pytest

Releasing

Release in github by creating a new release in github.