* resolving case when lat dimensions are decreasing
CF conventions state only that a "coordinate variable must have values that are strictly monotonic (increasing or decreasing)." In the case of PRISM, the lat coordinates are decreasing. pygeoapi failed due to the lat dimension being empty with existing implementation; this update addresses the issue.
* remove blank space
* resolving case when lat dimensions are decreasing
CF conventions state only that a "coordinate variable must have values that are strictly monotonic (increasing or decreasing)." In the case of PRISM, the lat coordinates are decreasing. pygeoapi failed due to the lat dimension being empty with existing implementation; this update addresses the issue.
* remove blank space
* test decreasing latitude
The new test will now uncover if you can successfully serve data stored on S3 AND test if you can perform a cube query on data with monotonically decreasing latitude coordinates at the same time.
* flake8 py3 fixes
* read from s3 bucket
* fix formatting for build workflow
* add s3fs to provider requirements
* storage options for fsspec
* Revert "storage options for fsspec"
This reverts commit dcfaceedd78d0f0e0dc3e38610958671c27b06a6.
* Revert "storage options for fsspec"
This reverts commit dcfaceedd78d0f0e0dc3e38610958671c27b06a6.
* delete extraneous code for cloud storage read
* update documentation
* add ci testing
* update test suite config file
* update number of collections
* update test query for s3
* ci testing updates
* read from s3 bucket
* fix formatting for build workflow
* add s3fs to provider requirements
* storage options for fsspec
* Revert "storage options for fsspec"
This reverts commit dcfaceedd78d0f0e0dc3e38610958671c27b06a6.
* Revert "storage options for fsspec"
This reverts commit dcfaceedd78d0f0e0dc3e38610958671c27b06a6.
* delete extraneous code for cloud storage read
* update documentation
* add ci testing
* update test suite config file
* update number of collections
* update test query for s3
* ci testing updates
* documentation updates
* config updates
* flake8
* modify sfs3 version
installing requirements threw an error when specifying 2023.6.0 (only identifies up through 2023.1.0). Had added the sfs3 requirement to deal with issues thrown when the 2023.9.0 release came out.
* updated coverages documentation
* Fix for Django build, changes to documentation, and dev dependencies updated
* remove example configuration files
* Added readthedocs configuration file
* added section on building the documentation
* renamed docs/requirements-docs.txt to docs/requirements.txt
* renamed requirements file in readthedocs configuration
* Added documentation requirements installation to GitHub build workflow
* fixed pagination next page response
* fixed line too long
* Update get_collection_items test to accomodate last page fix
Note that this feature can't be tested with the CSV provider
because it uses the number of current items as numberMatched,
which doesn't seem correct but is an independent issue.
https://github.com/geopython/pygeoapi/blob/c7c07855e5cfa95b88d6d0d11f5c23111e38da95/pygeoapi/provider/csv_.py#L173
---------
Co-authored-by: Juan Pablo Duque <juan-pablo-duque@hotmail.com>
Co-authored-by: Juan Duque <juanpablo.duque@polimi.it>
* Process manager now knows about existing processes
* Move get_manager to base module
* Process manager now knows about existing processes
* Guard API from manager.get_job() errors
* Guard API from job-related errors
* fix flak8-related issue on tests
* moved process-related exceptions to pygeoapi.process.base
---------
Co-authored-by: Ricardo Garcia Silva <ricardo@kartoza.com>
* - Added conformance class for Mapbox Vector Tiles
* - updated number of conformance classes on tests
---------
Co-authored-by: doublebyte1 <info@doublebyte.net>
* update time handling for edr provider
* add logging for time parsing
* fix time handling errors
Convert times to np.datetime64 to allow greater than/less than comparison. If slicing over time, separate xarray sel into temporal and spatial component (cannot use method='nearest' for time slices).
* fix temporal query dictionary
* fix time error handling
* fix list handling for single timestep
* single timestep handling
* spatial-only query amendment
* code clean-up
* convert datetime
* move code to methods
for reuse between position and cube. #1239
* formatting fixes
#1239
* time query test
#1239
* clean-up
* move time querying tests to api testing
* Update test_api.py
* update time key
* modify test values
* updates for desired query behavior
#1239
* Update xarray_edr.py
* sanitize datetime_ parameter with Z
OpenAPI document provides RFC 3339 compliant examples (exclusively specify UTC as the timezone with a trailing Z; want to avoid confusion between allowed datetime query and the documentation. #1239
* requested changes from @webb-ben and @tomkralidis
#1247
* Added enum for requested process execution modes
* Added data dict as expected base process.execute param
* Modified base process manager to select execution mode
* Pass requested execution mode to process manager
* Refactored dummy process manager to deal with request execution mode
* Use num value in response headers
* fix bug with non-existent process response headers
* fix flake8 errors
* fix python version errors
* fix python version errors
* fix python version errors
* refactor failing test
* refactor failing test
* fix line length
* fix using tuple in type annotations
* update docs and add missing param docstring
* swapped double quotes for single quotes for consistency
* OGC API - Features Part 2 (groundwork+CRS-BBOX) from PR #1155 - contributes to issue #1128
* #1128 provide conformance class for OAPIF Part 2 in /conformance page
* #1128 bitten by flake8...
* #1128 configurability CRS Feature Providers with syntax, defaults and tests
* #1128 configurability CRS Feature Providers refine for default values
* #1128 display supported CRSs in HTML Collection template
* #1128 config, mmetadata and tests for storageCRS and storageCrsCoordinateEpoch
* #1128 WIP for bbox-crs parameter support
* #1128 utility function and tests for default/mandatory supprted CRS list
* #1128 default supported CRS adaptation to OAPIF Part 2 standard
* #1128 grr flake8 whitespace
* #1128 start adding full API tests OGR for bbox-crs and crs parms
* #1128 fix flake8
* #1128 fix flake8 - install GDAL in workflow main for OGR tests
* #1128 fix flake8 - install GDAL in workflow main for OGR tests - need pip package?
* #1128 fix flake8 - install GDAL in workflow main for OGR tests - using libgdal-dev gdal-bin
* #1128 fix SensorThings test for main.yml Workflow
* #1128 fix SensorThings test for main.yml Workflow nr 2
* #1128 make all OGR tests working again
* #1128 make all OGR tests working again - flake8
* #1128 make all OGR tests working again - GeoSolutions WFS bbox
* #1128#1155 add documentation for OGC OAPIF Part 2 CRS CRS BBOX support
* #1128#1155 refine documentation for OGC OAPIF Part 2 CRS CRS BBOX support
* #1128#1155 refine documentation to align with #1149
* #1128#1155 rework from review OAS and pygeoapi config schema
* #1128#1155 minor: compile Re for CRS URI only once as global var
* #1128 merge in changes from PR #1173 - fix missing import
* WIP Ogcapi features part 2 - Support for crs query parameter (#1149)
* feat(ogcapi_features_crs): start implementing crs support from ogcapi features part2
* Pass input and output CRSs WKT instead of crs transformation object
* fix longs lines and blank lines
* fix typo
* fix import for type annotation not supported by python version
* fix variable visibility in local scope
* fix tabs/spaces indentations
* Add support for the crs parameter to OGRProvider
* make flake8 happy
* Make crs transformation mechanism more consistent between PostgreSQL and OGR providers
* test(util): add two test functions in util.py
New functions: test_get_crs_from_uri and test_get_transform_from_crs
* fix too long lines...
* Update get_crs_from_uri and corresponding test function
* fix(get_crs_from_uri): make the error more explicit in if wrong crs uri format
* flake8 again...
* Keep support for source_srs/target_srs in config for OGRProvider
* revert changes made to pygeoapi-config-0.x.yml, overlap with PR 1155
* test: add test data and update test config file
* Extract 'crs' and 'storage_crs' and provider level instead of collection level
* feat(crs): new decorator to support coordinates transformation of feature collections
* feat(crs): 'crs' query parameter for CSVProvider
* test(crs): add tests for 'crs' query parameter
* test: update number of collections in test_describe_collections
* test: update number of collections in test_filter_dict_by_key_value
* fix(crs_transform): change the crs transformation decorator
Change the logic of the decorator so that it works for both functions that
return FeatureCollections and for functions tha return single Features.
* test: add tests for get_collection_item end-point with 'crs' parameter
* fix(test_get_collection_item_crs): id as path parameter, not query parameter
* test: unpack coordinates to create point geometry
* feat(crs): add suuport for crs query parameter for all providers of type 'feature'
* docs(crs): add documentation to illustrate use of 'crs' query parameters
* docs(crs): more data access examples
* fix typo and add new line
* refactor: specify None as default value for crs_transform_out parameter in _sqlalchemy_to_feature method
* changes for PR 1149, test_api and style formatting
* CRS84 as default crs also for test_get_collection_items_crs
* test(crs): test coordinates transformation implementation of PostgreSQLProvider
* test(crs): move tests to test_postgresql_provider
* fix test function calls
* change test to ensure returned features are the same
* add json format to request object
* test(crs): test coordinates transformation implementation of OGRProvider
* refactor(crs): make more compact get_collection_item and get_collection_items
Define two new static methods in API class, to create crs_transform_wkt and
setting content-crs header. These methods can be re-used in both
get_collection_item and get_collection_items methods and removes code
duplication.
---------
Co-authored-by: Just van den Broecke <just@justobjects.nl>
* #1178 fix flake8 error
* #1178 use EPSG:28992 i.s.o. 32631 - fix unit test OGR Shapefile
* #1174 use CRS-compliant Axis ordering for crs support
* #1174 fix and honour CRS 4258disable native CRS Transform in OGR Provider - Axis ordering not honoured...
* #1174 remove ADR tests rom test_util.py
* #1174 enable native CRS transform again in OGR Provider
* #1174 enable native CRS transform again in OGR Provider - fix config
* #1174 remove support for source/target_srs in OGRProvider - enforce transforms always based on storageCRS
* #1174 fix tests Postgresql Provider for Transforms
* #1174 fix tests Postgresql Provider for Transforms
* #1174 add tests for OGR Transformation and Axis Order
* #1174 Suppress potential axis-swapping in OGR ExportToJSON
* #1174 minor fix test - unassign spatialref before setgeom infeat
* #1174 minor fix test - unassign spatialref before setgeom infeat - flake8
* #1174 solve CI WFS test failures with GDAL HTTP config options
* #1174 bbox and bbox-crs defs local in openapi.py for CITE validators
* #1174 merge master - #1152#1203 etc
* #1174 small doc changes
* #1174 move GeomObject typedef to beginning of util.py
* #1174 added debug logging in transform Decorator func
---------
Co-authored-by: Mathieu Tachon <92298764+MTachon@users.noreply.github.com>
* API design rule support (#1134):
- Change config model
- Change Flask, Starlette, and Django apps for API rule adherence
- Add Flask and Starlette mock clients to test API rule adherence
- Add get_base_url() util function to replace all config['server']['url'] refs
- Ensure that any internal links have URL prefixes if needed
- Add tests and update docs
* Prevent fcntl import error (breaks tests when running locally on Windows)
* Prefer trailing slash in landing page URL when strict_slashes=True (#1134)
* bbox query parameter support for EDR cube queries
As per Requirement A.61 C, D and E, as well as A.7 in the EDR standard.
* bbox queries support z-axis dimension
* xarray-edr provider cube query support, edr cube unit tests
---------
Co-authored-by: Peter Garnæs <pga@dmi.dk>
* Render template if specified in config and provide example config
Update linked_data.py
Merge branch 'geopython:master' into jsonld
Rended from json-ld output
Render jinja2 json-ld template from json-ld output instead of json output
Merge branch 'geopython:master' into jsonld
Add documentation
- Add documentation
- Add test to workflow
Update pygeoapi-test-config.yml
Update test_api.py
Update api.py
Update linked_data.py
Move template declaration in configuration
Update docs
Update configuration.rst
Update configuration.rst
* Updates per requested changes
* Fix spelling
* Fix json-ld template pathing
* Remove root path for the templating
* Move json-ld template from api.py
- Move single item json-ld templating to inside geojson2jsonld
- Reformat json-ld configuration for context and item_template to children of json-ld block
- Update docs and example configurations
* Fix ref
* Use FileSystemLoader to control template search path
search for templates is in order of `template_paths` list
* s/json-ld/linked-data/ig
rename json-ld to more generic name
* Add pygeofilter, unpin psycopg2
* Add pygeofilter SQLAlchemy query demo
* Add note about primary key
* Add todos to script
* Make script generic
* Add (commented out) PostgreSQL provider hotosm_bdi_waterways to config
* Update to use local test database
* Return result as dictionary
* Pass GEOM_FIELD as variable
* Add offset and limt, fix two names
* Implement order by
* Use function for cql query
* Add cql query block to query and test
* Link up to db engine
* Convert WKB geometry to GeoJSON
* Add shapely as explicit dependency
* Add tests for CQL queries
* Add test using CROSSES with LINESTRING
* Uncomment Docker PostGIS test layer
* First pass at wiring up API
The CQL is read from the request but the parser fails to convert to
AST.
* Turn logging to DEBUG
Example query
http://localhost:5000/collections/hot_osm_waterways/items?cql=%27osm_id%20BETWEEN%2080800000%20AND%2080900000%20AND%20name%20IS%20NULL%27
* Create dedicated pygeoapi-config.yml for testing PostgreSQL
* Add test for PostgreSQL CQL
* Return 400 for bad CQL
* Tidy up old files
* Bring API error type tests together
* Only reflect the table of interest
* Add pygeofilter to requirements
* Remove local setup_env.sh from .gitignore
* Remove lark exception handling
* Remove lark codes from tests, docstring change
* Split cql test into good and error
* Rename cql parameter to filter
* Add optional filter-lang parameter with test
* Initial changes
* Rename cql text parser
* Use CQL-JSON POST for PostgreSQL query
* Refactor to get data early and handle errors
* Add error tests for CQL-JSON PostgreSQL
* Add tests for prev/next and provider instantiation
* As filter-lang is set the block in not needed
* Clarify test fixtures
* Use filterq only in all CQL calls
* Make engine and table_model attributes of provider
* Handle different instantiation failures
* Use SQLAlchemy for get_fields()
* Minor doc edits
* Use SQLAlchemy for get()
* Simplify _sqlalchemy_to_feature
* Store database parameters in dedicated function
* Strip out non-SQLAlchemy code
* Add draft query() based on CQL filters
* Add property filtering to query()
* Implement select_properties and skip_geometry
* Implement bbox filter
* Implement properties subset defined in config
* Clean up materialized view test
We only need to test the fields that are present to be sure that the
view has been accessed, so other checks have been removed.
* Flake8 fixes and tidy up
* Add combined test for CQL with bbox and properties
* Create sessions directly where required
* Add Engine store to allow connection reuse
* Replace cql_ast with filterq
* Tidy up tests by using fixture for api
* Add authors
* Use Session() as context manager
A session requires a connection to the database, as provided by the
SQLAlchemy engine. When the session goes out of scope, e.g. at exit
from the function when it was used, it should be garbage collected and
the connection freed. However, during load testing it was found that
this wasn't happening. This commit uses a context manager pattern to
start the session, which ensures that the session is closed at the end
of the `with` block.
* Return fields type as {'type': ...}
* Cache the table_model with the engine
Generating the table_model by "reflecting" the database is expensive but
the resulting model doesn't change. If we cache the table_model with
the engine we save on a round-trip to the database and speed up response
time.
* Use separate stores for Engine and table_models
Using a combined store based on both engine and table_model meant that
a pygeoapi serving multiple tables on the same database would maintain
a connection pool for each table. This could eventually saturate the
number of available connections. This commit separates the store into
two parts.
* Update documentation with example
* Manage or post items based on POST content type
* ghcr build action
* only ghcr job
* run criteria edit
* Update README.md
* job = main
* remove success requirememt
* add tag
* tags: bgs-cql
* Update main.yml
* Update README.md
* remove binary
* update
* Update actions to latest versions
* Dockerfile refactor
* Dockerfile refactor
* restore dockerhub
* fix pygeoif version
* # 3.6 test & dockerhub ref
* Pin pygeoif version to less than 1
* Replace psycopg-binary with psycopg
* Split Docker build into sections
* Pin click version >7,<=8
* Add further cql examples
* Update workflows to match GeoPython repo
* update flake python version
* Unquote PostgreSQL column names
* Update container workflow uses versions
* flake8 use python version 3.7
* Use pre ping to get db connection
* Test that properties are set in provider
* Amendments as requested by @tomkralidis
* Correction
* Fix reviewed changes in api code
Co-authored-by: Colin Blackburn <colb@bgs.ac.uk>
Co-authored-by: KoalaGeo <eddlewis85@gmail.com>
Co-authored-by: Edd <edlew@bgs.ac.uk>
Co-authored-by: Colin Blackburn <ximenesuk@users.noreply.github.com>
* Start a wip alignment
* Adding CRS to tile_matrix_set_links
* Refactor json structure tiles endpoint
* Link section in tileset
* Unit test
Co-authored-by: Francesco Bartoli <francesco.bartoli@geobeyond.it>
* Add gzip to API.py
* pytest for gzip
* fix pytest
* Update test_api.py
* Add gzip to server block of configuration files
* Update api.py to include gzip opts from config
Update logic behind gzip compression such that compression will only happen when gzip in the Accept-Encoding request header and config.server.gzip is True. Use server charset for encoding/decoding and include charset in Content-Type when compressed.
* Update pytest to use gzip config options
Update pytest to test with (gzip in Accept-Encoding & server.gzip = False), (gzip in Accept-Encoding & server.gzip = True), (gzip not in Accept-Encoding & server.gzip = True)
* Better Content Negotiation (#7)
* Change content negotiation in _get_format()
* Add to pytest and force h to always be string
* Force F_JSON to default response
* Update test_api.py for utf-16 encoding
* better content negotiation pytest.
* Add comments to pytest
* Fix flake 8
* Improve docstring for gzip decorator function
Sarah Jordan