8d377072b96265ec36ec3d3b61dca8d255c577fc
4 Commits
| Author | SHA1 | Message | Date | |
|---|---|---|---|---|
 Francesco Bartoli
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96cf72236a |
Improve postgres connection options (#1357)
* Add database connection options * Move under provider options Add docs for connection options Fix typo Use already existing provider options from config json schema Use already existing provider options from config json schema * Validate configuration of provider options * Replace pydantic validation with plain jsonschema |
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Just van den Broecke
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7c6993719d |
add CRS Support for OGC API Feature pygeoapi Provider (#1174)
* 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> |
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Mathieu Tachon
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1a1d6362c1 |
fix(automap): fixes naming conflicts for PostgreSQLProvider (#1184)
* fix(automap): fix naming conflicts for PostgreSQLProvider Automaping classes and relationships from database schema throws an error if a column name is the same as a relationship name (see https://docs-sqlalchemy.readthedocs.io/ko/latest/orm/extensions/automap.html#handling-simple-naming-conflicts). * renaming function name_for_scalar_relationship -> _name_for_scalar_relationship * test: test that PostgreSQL provider can handle naming conflicts Re-use data file from https://github.com/geopython/pygeoapi/pull/1185, and make to new and empty tables that create naming conflicts when queried. * Change test function post_collection_items -> get_collection_items * fix path to table |
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John A Stevenson
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644281359a |
Add CQL to PostgreSQL provider (via pygeofilter and sqlalchemy) (#964)
* 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> |