MySQL OAF provider (#2004)

* Mysql Provider (#6)

- mysql provider and associated tests
- refactor postgres and mysql to use a shared base class that they both inherit from
- handle geometry / encoding necessary to use mysql wity sqlalchemy

---------

Co-authored-by: Benjamin Webb <40066515+webb-ben@users.noreply.github.com>

* keep postgis instructions

* Apply suggestions from code review

Co-authored-by: Benjamin Webb <40066515+webb-ben@users.noreply.github.com>

* Update pygeoapi/provider/sql.py

Co-authored-by: Benjamin Webb <40066515+webb-ben@users.noreply.github.com>

* Update pygeoapi/provider/sql.py

Co-authored-by: Benjamin Webb <40066515+webb-ben@users.noreply.github.com>

* Fix MVT_postgres import

* Set default port for Postgres and MySQL provider

* Add MySQL documentation

* Fix typo

---------

Co-authored-by: Benjamin Webb <40066515+webb-ben@users.noreply.github.com>
Co-authored-by: Benjamin Webb <benjamin.miller.webb@gmail.com>

Author: C-Loftus

.github/workflows/main.yml

@@ -53,6 +53,17 @@ jobs:
       with:
         postgresql password: ${{ secrets.DatabasePassword || 'postgres' }}
         postgresql db: 'test'
+
+    - name: "Install and run MySQL 📦"
+      uses: mirromutth/mysql-action@v1.1
+      with:
+        host port: 3306 
+        mysql version: '8.0' 
+        mysql database: test_geo_app
+        mysql root password: mysql # This is a dummy password here; not actually used in prod
+        mysql user: pygeoapi 
+        mysql password: mysql 
+        
     - name: Install and run Elasticsearch 📦
       uses: getong/elasticsearch-action@v1.2
       with:
@@ -111,6 +122,7 @@ jobs:
         psql postgresql://postgres:${{ secrets.DatabasePassword || 'postgres' }}@localhost:5432/test -f tests/data/dummy_data.sql
         psql postgresql://postgres:${{ secrets.DatabasePassword || 'postgres' }}@localhost:5432/test -f tests/data/dummy_types_data.sql
         psql postgresql://postgres:${{ secrets.DatabasePassword || 'postgres' }}@localhost:5432/test -f tests/data/postgres_manager_full_structure.backup.sql
+        mysql -h 127.0.0.1 -P 3306 -u root -p'mysql' test_geo_app < tests/data/mysql_data.sql
         docker ps
         python3 tests/load_oracle_data.py
     - name: run unit tests ⚙️
@@ -142,6 +154,7 @@ jobs:
         pytest tests/test_oracle_provider.py
         pytest tests/test_parquet_provider.py
         pytest tests/test_postgresql_provider.py
+        pytest tests/test_mysql_provider.py
         pytest tests/test_rasterio_provider.py
         pytest tests/test_sensorthings_edr_provider.py 
         pytest tests/test_sensorthings_provider.py

docs/source/data-publishing/ogcapi-features.rst

@@ -25,6 +25,7 @@ parameters.
    `ESRI Feature Service`_,✅/✅,results/hits,✅,✅,✅,✅,❌,❌,❌,✅
    `GeoJSON`_,✅/✅,results/hits,❌,❌,❌,✅,❌,❌,❌,✅
    `MongoDB`_,✅/❌,results,✅,✅,✅,✅,❌,❌,❌,✅
+   `MySQL`_,✅/✅,results/hits,✅,✅,✅,✅,❌,✅,✅,✅
    `OGR`_,✅/❌,results/hits,✅,❌,❌,✅,❌,❌,❌,✅
    `OpenSearch`_,✅/✅,results/hits,✅,✅,✅,✅,❌,✅,✅,✅
    `Oracle`_,✅/✅,results/hits,✅,❌,✅,✅,❌,❌,❌,✅
@@ -222,6 +223,76 @@ Here `test` is the name of database , `points` is the target collection name.
          data: mongodb://localhost:27017/testdb
          collection: testplaces
 
+
+.. _MySQL:
+
+MySQL
+^^^^^
+
+.. note::
+   Requires Python packages sqlalchemy, geoalchemy2 and pymysql
+
+Must have MySQL installed.
+
+.. code-block:: yaml
+
+   providers:
+       - type: feature
+         name: MySQL
+         data:
+             host: 127.0.0.1
+             port: 3306 # Default 3306 if not provided
+             dbname: test_geo_app
+             user: mysql
+             password: mysql
+             search_path: [test_geo_app] # Same as dbname
+         id_field: locationID
+         table: location
+         geom_field: locationCoordinates
+
+A number of database connection options can be also configured in the provider in order to adjust properly the sqlalchemy engine client.
+These are optional and if not specified, the default from the engine will be used. Please see also `SQLAlchemy docs <https://docs.sqlalchemy.org/en/14/core/engines.html#custom-dbapi-connect-arguments-on-connect-routines>`_.
+
+.. code-block:: yaml
+
+    providers:
+       - type: feature
+         name: MySQL
+         data:
+             host: 127.0.0.1
+             port: 3306 # Default 3306 if not provided
+             dbname: test_geo_app
+             user: mysql
+             password: mysql
+             search_path: [test_geo_app] # Same as dbname
+         options:
+             # Maximum time to wait while connecting, in seconds.
+             connect_timeout: 10
+             # Number of *milliseconds* that transmitted data may remain
+             # unacknowledged before a connection is forcibly closed.
+             tcp_user_timeout: 10000
+             # Whether client-side TCP keepalives are used. 1 = use keepalives,
+             # 0 = don't use keepalives.
+             keepalives: 1
+             # Number of seconds of inactivity after which TCP should send a
+             # keepalive message to the server.
+             keepalives_idle: 5
+             # Number of TCP keepalives that can be lost before the client's
+             # connection to the server is considered dead.
+             keepalives_count: 5
+             # Number of seconds after which a TCP keepalive message that is not
+             # acknowledged by the server should be retransmitted.
+             keepalives_interval: 1
+         id_field: locationID
+         table: location
+         geom_field: locationCoordinates
+
+This provider has support for the CQL queries as indicated in the Provider table above.
+
+.. seealso::
+  :ref:`cql` for more details on how to use Common Query Language (CQL) to filter the collection with specific queries.
+
+
 OGR
 ^^^
 

pygeoapi/plugin.py

@@ -53,12 +53,13 @@
         'MVT-tippecanoe': 'pygeoapi.provider.mvt_tippecanoe.MVTTippecanoeProvider',  # noqa: E501
         'MVT-elastic': 'pygeoapi.provider.mvt_elastic.MVTElasticProvider',
         'MVT-proxy': 'pygeoapi.provider.mvt_proxy.MVTProxyProvider',
+        'MySQL': 'pygeoapi.provider.sql.MySQLProvider',
         'MVT-postgresql': 'pygeoapi.provider.mvt_postgresql.MVTPostgreSQLProvider',  # noqa: E501
         'OracleDB': 'pygeoapi.provider.oracle.OracleProvider',
         'OGR': 'pygeoapi.provider.ogr.OGRProvider',
         'OpenSearch': 'pygeoapi.provider.opensearch_.OpenSearchProvider',
         'Parquet': 'pygeoapi.provider.parquet.ParquetProvider',
-        'PostgreSQL': 'pygeoapi.provider.postgresql.PostgreSQLProvider',
+        'PostgreSQL': 'pygeoapi.provider.sql.PostgreSQLProvider',
         'rasterio': 'pygeoapi.provider.rasterio_.RasterioProvider',
         'SensorThings': 'pygeoapi.provider.sensorthings.SensorThingsProvider',
         'SensorThingsEDR': 'pygeoapi.provider.sensorthings_edr.SensorThingsEDRProvider',  # noqa: E501

pygeoapi/process/manager/postgresql.py

@@ -56,7 +56,7 @@
     ProcessorGenericError
 )
 from pygeoapi.process.manager.base import BaseManager
-from pygeoapi.provider.postgresql import get_engine, get_table_model
+from pygeoapi.provider.sql import get_engine, get_table_model
 from pygeoapi.util import JobStatus
 
 
@@ -92,13 +92,15 @@ def __init__(self, manager_def: dict):
             if isinstance(self.connection, str):
                 _url = make_url(self.connection)
                 self._engine = get_engine(
+                    'postgresql+psycopg2',
                     _url.host,
                     _url.port,
                     _url.database,
                     _url.username,
                     _url.password)
             else:
-                self._engine = get_engine(**self.connection)
+                self._engine = get_engine('postgresql+psycopg2',
+                                          **self.connection)
         except Exception as err:
             msg = 'Test connecting to DB failed'
             LOGGER.error(f'{msg}: {err}')

pygeoapi/provider/mvt_postgresql.py

@@ -40,7 +40,7 @@
     TileSetMetadata, TileMatrixSetEnum, LinkType)
 from pygeoapi.provider.base import ProviderConnectionError
 from pygeoapi.provider.base_mvt import BaseMVTProvider
-from pygeoapi.provider.postgresql import PostgreSQLProvider
+from pygeoapi.provider.sql import PostgreSQLProvider
 from pygeoapi.provider.tile import ProviderTileNotFoundError
 from pygeoapi.util import url_join