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fix(automap): fixes naming conflicts for PostgreSQLProvider (#1184)

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* 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
This commit is contained in:
Mathieu Tachon
2023-03-31 13:05:31 +02:00
committed by GitHub
parent e8acad7120
commit 1a1d6362c1
5 changed files with 130 additions and 8 deletions
Download Patch File Download Diff File Expand all files Collapse all files
.github/workflows/main.yml
+7 -6
View File
@@ -1,17 +1,17 @@
name: Build
on:
on:
push:
paths-ignore:
- '**.md'
- '**.md'
pull_request:
branches:
- master
paths-ignore:
- '!**.md'
paths-ignore:
- '!**.md'
release:
types:
- released
- released
jobs:
flake8_py3:
@@ -78,7 +78,7 @@ jobs:
- name: Install sqlite and gpkg dependencies
uses: awalsh128/cache-apt-pkgs-action@latest
with:
packages: libsqlite3-mod-spatialite
packages: libsqlite3-mod-spatialite
version: 4.3.0a-6build1
- name: Install requirements 📦
run: |
@@ -96,6 +96,7 @@ jobs:
python3 tests/load_es_data.py tests/cite/ogcapi-features/canada-hydat-daily-mean-02HC003.geojson IDENTIFIER
python3 tests/load_mongo_data.py tests/data/ne_110m_populated_places_simple.geojson
gunzip < tests/data/hotosm_bdi_waterways.sql.gz | psql postgresql://postgres:${{ secrets.DatabasePassword || 'postgres' }}@localhost:5432/test
psql postgresql://postgres:${{ secrets.DatabasePassword || 'postgres' }}@localhost:5432/test -f tests/data/dummy_data.sql
- name: run unit tests ⚙️
env:
POSTGRESQL_PASSWORD: ${{ secrets.DatabasePassword || 'postgres' }}
pygeoapi/provider/postgresql.py
+21 -1
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@@ -319,11 +319,31 @@ class PostgreSQLProvider(BaseProvider):
raise ProviderQueryError(msg)
Base = automap_base(metadata=metadata)
Base.prepare()
Base.prepare(
name_for_scalar_relationship=self._name_for_scalar_relationship,
)
TableModel = getattr(Base.classes, self.table)
return TableModel
@staticmethod
def _name_for_scalar_relationship(
base, local_cls, referred_cls, constraint,
):
"""Function used when automapping classes and relationships from
database schema and fixes potential naming conflicts.
"""
name = referred_cls.__name__.lower()
local_table = local_cls.__table__
if name in local_table.columns:
newname = name + '_'
LOGGER.debug(
f'Already detected column name {name!r} in table '
f'{local_table!r}. Using {newname!r} for relationship name.'
)
return newname
return name
def _sqlalchemy_to_feature(self, item):
feature = {
'type': 'Feature'
tests/data/dummy_data.sql
+56
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@@ -0,0 +1,56 @@
CREATE SCHEMA IF NOT EXISTS dummy AUTHORIZATION postgres;
CREATE EXTENSION IF NOT EXISTS postgis WITH SCHEMA dummy;
-- table with multiple geometry columns
CREATE TABLE IF NOT EXISTS dummy.buildings(
gid serial PRIMARY KEY,
centroid geometry(POINT, 25833),
contours geometry(POLYGON, 25833)
);
INSERT INTO dummy.buildings(centroid, contours)
VALUES (ST_GeomFromText('POINT (473449 7463146)', 25833),
ST_GeomFromText('POLYGON ((473447.9967755177 7463140.685534775, 473453.51980463834 7463143.029921546, 473450.0032244818 7463151.314465227, 473444.4801953612 7463148.970078456, 473447.9967755177 7463140.685534775))', 25833)),
(ST_GeomFromText('POINT (473458 7463104)', 25833),
ST_GeomFromText('POLYGON ((473460.9359104787 7463106.762323238, 473457.1106914547 7463107.931810057, 473455.06408952177 7463101.237676765, 473458.88930854574 7463100.068189946, 473460.9359104787 7463106.762323238))', 25833)),
(ST_GeomFromText('POINT (473446 7463144)', 25833),
ST_GeomFromText('POLYGON ((473446.09474694915 7463138.853056925, 473450.31999101397 7463146.79958526, 473445.9052530499 7463149.146943075, 473441.6800089851 7463141.20041474, 473446.09474694915 7463138.853056925))', 25833)),
(ST_GeomFromText('POINT (473449 7463142)', 25833),
ST_GeomFromText('POLYGON ((473452.3381955018 7463138.820935548, 473452.65221123956 7463144.812712757, 473445.6618044963 7463145.179064451, 473445.3477887586 7463139.187287242, 473452.3381955018 7463138.820935548))', 25833)),
(ST_GeomFromText('POINT (473443 7463137)', 25833),
ST_GeomFromText('POLYGON ((473447.7083111685 7463135.5571535295, 473440.9159249468 7463141.46168479, 473438.2916888306 7463138.44284647, 473445.0840750523 7463132.538315209, 473447.7083111685 7463135.5571535295))', 25833)),
(ST_GeomFromText('POINT (473433 7463125)', 25833),
ST_GeomFromText('POLYGON ((473432.73905580025 7463120.082489641, 473436.8249702975 7463128.10154836, 473433.2609442007 7463129.917510359, 473429.1750297034 7463121.898451641, 473432.73905580025 7463120.082489641))', 25833)),
(ST_GeomFromText('POINT (473451 7463140)', 25833),
ST_GeomFromText('POLYGON ((473454.99435667787 7463139.456755368, 473453.4959303038 7463143.165490787, 473447.00564332213 7463140.543244633, 473448.5040696962 7463136.834509214, 473454.99435667787 7463139.456755368))', 25833)),
(ST_GeomFromText('POINT (473438 7463144)', 25833),
ST_GeomFromText('POLYGON ((473438.99554283824 7463137.7143898895, 473444.28561010957 7463144.995542839, 473437.00445716083 7463150.28561011, 473431.7143898895 7463143.00445716, 473438.99554283824 7463137.7143898895))', 25833)),
(ST_GeomFromText('POINT (473474 7463101)', 25833),
ST_GeomFromText('POLYGON ((473474.83006438427 7463097.491297516, 473477.55805782415 7463100.416712323, 473473.1699356148 7463104.508702483, 473470.441942174 7463101.583287676, 473474.83006438427 7463097.491297516))', 25833)),
-- gid 10
(NULL,
ST_GeomFromText('POLYGON ((473464.1495667333 7463116.574655892, 473461.1307284124 7463119.1988920085, 473457.85043326765 7463115.425344108, 473460.8692715885 7463112.8011079915, 473464.1495667333 7463116.574655892))', 25833)),
-- gid 11
(ST_GeomFromText('POINT (473461 7463116)', 25833),
NULL),
-- gid 12
(NULL,
NULL);
/* Two tables which create a naming conflict
The name of relationship or referred table is the same as the name of an
existing column. Example adapted from
https://docs-sqlalchemy.readthedocs.io/ko/latest/orm/extensions/automap.html#handling-simple-naming-conflicts
*/
CREATE TABLE IF NOT EXISTS dummy.referred_table(
id INTEGER PRIMARY KEY
);
CREATE TABLE IF NOT EXISTS dummy.naming_conflicts_table(
id INTEGER PRIMARY KEY,
point_geom geometry(POINT, 4326),
referred_table INTEGER,
FOREIGN KEY(referred_table) REFERENCES dummy.referred_table(id)
);
tests/pygeoapi-test-config-postgresql.yml
+32 -1
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@@ -134,4 +134,35 @@ resources:
search_path: [osm, public]
id_field: osm_id
table: hotosm_bdi_waterways
geom_field: foo_geom
geom_field: foo_geom
dummy_naming_conflicts:
type: collection
title: Dummy data
description: Dummy data creating naming conflicts
keywords:
- dummy
links:
- type: text/html
rel: canonical
title: Source instructions for loading data
href: https://github.com/geopython/pygeoapi/blob/master/pygeoapi/provider/postgresql.py
hreflang: en-UK
extents:
spatial:
bbox: [-180, -90, 180, 90]
crs: http://www.opengis.net/def/crs/OGC/1.3/CRS84
temporal:
begin: null
end: null # or empty (either means open ended)
providers:
- type: feature
name: PostgreSQL
data:
host: localhost
dbname: test
user: postgres
password: postgres
search_path: [dummy]
id_field: id
table: naming_conflicts_table
geom_field: point_geom
tests/test_postgresql_provider.py
+14
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@@ -570,3 +570,17 @@ def test_post_collection_items_postgresql_cql_bad_cql(pg_api_, bad_cql):
error_response = json.loads(response)
assert error_response['code'] == 'InvalidParameterValue'
assert error_response['description'].startswith('Bad CQL string')
def test_get_collection_items_postgresql_automap_naming_conflicts(pg_api_):
"""
Test that PostgreSQLProvider can handle naming conflicts when automapping
classes and relationships from database schema.
"""
req = mock_request()
rsp_headers, code, response = pg_api_.get_collection_items(
req, 'dummy_naming_conflicts')
assert code == HTTPStatus.OK
features = json.loads(response).get('features')
assert len(features) == 0