Merge branch 'master' into add-nginx-container

Author: gadomski

.github/workflows/cicd.yaml

@@ -1,27 +1,30 @@
 name: stac-fastapi
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.8', '3.9', '3.10']
+        python-version: ["3.8", "3.9", "3.10"]
     timeout-minutes: 10
 
     services:
       db_service:
-        image: bitner/pgstac:0.2.7
+        image: ghcr.io/stac-utils/pgstac:v0.6.12
         env:
           POSTGRES_USER: username
           POSTGRES_PASSWORD: password
           POSTGRES_DB: postgis
           POSTGRES_HOST: localhost
           POSTGRES_PORT: 5432
+          PGUSER: username
+          PGPASSWORD: password
+          PGDATABASE: postgis
           ALLOW_IP_RANGE: 0.0.0.0/0
         # Set health checks to wait until postgres has started
         options: >-
@@ -118,9 +121,69 @@ jobs:
           POSTGRES_HOST_READER: localhost
           POSTGRES_HOST_WRITER: localhost
           POSTGRES_PORT: 5432
+
+  validate:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        backend: ["sqlalchemy", "pgstac"]
+    services:
+      pgstac:
+        image: ghcr.io/stac-utils/pgstac:v0.6.11
+        env:
+          POSTGRES_USER: username
+          POSTGRES_PASSWORD: password
+          POSTGRES_DB: postgis
+          PGUSER: username
+          PGPASSWORD: password
+          PGDATABASE: postgis
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - name: Setup Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+          cache: pip
+          cache-dependency-path: stac_fastapi/pgstac/setup.cfg
+      - name: Install stac-fastapi and stac-api-validator
+        run: pip install ./stac_fastapi/api ./stac_fastapi/types ./stac_fastapi/${{ matrix.backend }}[server] stac-api-validator==0.4.1
+      - name: Run migration
+        if: ${{ matrix.backend == 'sqlalchemy' }}
+        run: cd stac_fastapi/sqlalchemy && alembic upgrade head
+        env:
+          POSTGRES_USER: username
+          POSTGRES_PASS: password
+          POSTGRES_DBNAME: postgis
+          POSTGRES_HOST: localhost
+          POSTGRES_PORT: 5432
+      - name: Load data and validate
+        run: python -m stac_fastapi.${{ matrix.backend }}.app & ./scripts/wait-for-it.sh localhost:8080 && python ./scripts/ingest_joplin.py http://localhost:8080 && ./scripts/validate http://localhost:8080
+        env:
+          POSTGRES_USER: username
+          POSTGRES_PASS: password
+          POSTGRES_DBNAME: postgis
+          POSTGRES_HOST_READER: localhost
+          POSTGRES_HOST_WRITER: localhost
+          POSTGRES_PORT: 5432
+          PGUSER: username
+          PGPASSWORD: password
+          PGHOST: localhost
+          PGDATABASE: postgis
+          APP_HOST: 0.0.0.0
+          APP_PORT: 8080
+
   test-docs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - name: Test generating docs
-        run: make docs
+        run: make docs

CHANGES.md

@@ -1,16 +1,21 @@
 # Changelog
 
-## Unreleased
+## [Unreleased]
 
 ### Added
 
 ### Changed
 
+* Updated CI to test against [pgstac v0.6.12](https://github.com/stac-utils/pgstac/releases/tag/v0.6.12) ([#511](https://github.com/stac-utils/stac-fastapi/pull/511))
+
 ### Removed
 
 ### Fixed
 
-## [2.4.3]
+* Allow url encoded values for `query` in GET requests ([#504](https://github.com/stac-utils/stac-fastapi/pull/504))
+* Fix path in `register_update_item` docstring ([507](https://github.com/stac-utils/stac-fastapi/pull/507))
+
+## [2.4.3] - 2022-11-25
 
 ### Added
 
@@ -22,8 +27,7 @@
 
 ### Fixed
 
-
-## [2.4.2]
+## [2.4.2] - 2022-11-25
 
 ### Added
 
@@ -44,7 +48,7 @@
 * Fix pgstac backend for /queryables endpoint to return 404 for non-existent collections ([#482](https://github.com/stac-utils/stac-fastapi/pull/482))
 * `/collection/{collection_id}/items` endpoints now return geojson media type ([#488](https://github.com/stac-utils/stac-fastapi/pull/488))
 
-## [2.4.1]
+## [2.4.1] - 2022-08-05
 
 ### Added
 
@@ -56,7 +60,7 @@
 
 * `ciso8601` fails to build in some environments, instead use `pyiso8601` to parse datetimes.
 
-## [2.4.0]
+## [2.4.0] - 2022-08-04
 
 ### Added
 
@@ -102,7 +106,7 @@
 * PGStac Backend Transactions endpoints return added Item/Collection instead of Item/Collection from request ([#424](https://github.com/stac-utils/stac-fastapi/pull/424))
 * Application no longer breaks on startup when pagination extension is not included ([#444](https://github.com/stac-utils/stac-fastapi/pull/444))
 
-## [2.3.0]
+## [2.3.0] - 2022-01-18
 
 ### Added
 
@@ -135,7 +139,7 @@
 * Expanded on tests to ensure properly testing get and post searches ([#318](https://github.com/stac-utils/stac-fastapi/pull/318))
 * Ensure invalid datetimes result in 400s ([#323](https://github.com/stac-utils/stac-fastapi/pull/323))
 
-## [2.2.0]
+## [2.2.0] - 2021-10-19
 
 ### Added
 
@@ -148,7 +152,7 @@
 * Update pgstac to 0.4.0 ([#308](https://github.com/stac-utils/stac-fastapi/pull/308))
 * Update get_item in sqlalchemy backend to allow for querying for items with same ids but in different collections. ([#275](https://github.com/stac-utils/stac-fastapi/pull/275))
 
-## [2.1.1]
+## [2.1.1] - 2021-09-23
 
 ### Added
 
@@ -165,7 +169,7 @@
 * Add `stac_version` to default search attributes ([#268](https://github.com/stac-utils/stac-fastapi/pull/268))
 * pgstac backend specifies collection_id when fetching a single item ([#279](https://github.com/stac-utils/stac-fastapi/pull/270))
 
-## [2.1.0]
+## [2.1.0] - 2021-08-26
 
 ### Added
 
@@ -195,17 +199,13 @@
 * Correct response codes for bad/unusable bboxes ([#235](https://github.com/stac-utils/stac-fastapi/pull/235))
 * Update pgstac to return 400 on invalid date parameter ([#240](https://github.com/stac-utils/stac-fastapi/pull/240))
 
-## [2.0.0]
-
-_2021-07_
+## [2.0.0] - 2021-07-26
 
 * Refactor stac-fastapi into submodules ([#106](https://github.com/)stac-utils/stac-fastapi/pull/106)
 * Add pgstac backend ([#126](https://github.com/stac-utils/stac-fastapi/pull/126))
 * Upgrade to stac-pydantic 2.0.0 and stac-spec 1.0.0 ([#181](https://github.com/stac-utils/stac-fastapi/pull/181))
 
-## [1.1.0]
-
-_2021-01-28_
+## [1.1.0] - 2021-01-28
 
 * Improve how the library declares API extensions ([#54](https://github.com/stac-utils/arturo-stac-api/pull/54))
 * Add postgres bulk transactions client ([#59](https://github.com/stac-utils/arturo-stac-api/pull/59))
@@ -214,12 +214,16 @@ _2021-01-28_
 * Remove postgres database connection from API layer ([#74](https://github.com/stac-utils/arturo-stac-api/pull/74))
 * Fix `pre-commit` config ([#75](https://github.com/stac-utils/arturo-stac-api/pull/75))
 
-## [1.0.0]
-
-_2020-09-25_
+## [1.0.0] - 2020-09-28
 
 * First PyPi release!
 
+[Unreleased]: <https://github.com/stac-utils/stac-fastapi/compare/2.4.3..master>
+[2.4.3]: <https://github.com/stac-utils/stac-fastapi/compare/2.4.2..2.4.3>
+[2.4.2]: <https://github.com/stac-utils/stac-fastapi/compare/2.4.1..2.4.2>
+[2.4.1]: <https://github.com/stac-utils/stac-fastapi/compare/2.4.0..2.4.1>
+[2.4.0]: <https://github.com/stac-utils/stac-fastapi/compare/2.3.0..2.4.0>
+[2.3.0]: <https://github.com/stac-utils/stac-fastapi/compare/2.2.0..2.3.0>
 [2.2.0]: <https://github.com/stac-utils/stac-fastapi/compare/2.1.1..2.2.0>
 [2.1.1]: <https://github.com/stac-utils/stac-fastapi/compare/2.1.0..2.1.1>
 [2.1.0]: <https://github.com/stac-utils/stac-fastapi/compare/2.1.0..main>

docker-compose.yml

@@ -38,8 +38,7 @@ services:
       - ./scripts:/app/scripts
     depends_on:
       - database
-    command:
-      bash -c "./scripts/wait-for-it.sh database:5432 && python -m stac_fastapi.sqlalchemy.app"
+    command: bash -c "./scripts/wait-for-it.sh database:5432 && python -m stac_fastapi.sqlalchemy.app"
 
   app-pgstac:
     container_name: stac-fastapi-pgstac
@@ -71,12 +70,11 @@ services:
       - ./scripts:/app/scripts
     depends_on:
       - database
-    command:
-      bash -c "./scripts/wait-for-it.sh database:5432 && python -m stac_fastapi.pgstac.app"
+    command: bash -c "./scripts/wait-for-it.sh database:5432 && python -m stac_fastapi.pgstac.app"
 
   database:
     container_name: stac-db
-    image: ghcr.io/stac-utils/pgstac:v0.6.10
+    image: ghcr.io/stac-utils/pgstac:v0.6.12
     environment:
       - POSTGRES_USER=username
       - POSTGRES_PASSWORD=password

scripts/validate

@@ -0,0 +1,28 @@
+#!/usr/bin/env sh
+#
+# Validate a STAC server using [stac-api-validator](https://github.com/stac-utils/stac-api-validator).
+#
+# Assumptions:
+#
+#   - You have stac-api-validator installed, e.g. via `pip install stac-api-validator`
+#   - You've loaded the joplin data, probably using `python ./scripts/ingest_joplin.py http://localhost:8080``
+#
+# Currently, item-search is not checked, because it crashes stac-api-validator (probably a problem on our side).
+
+set -e
+
+if [ $# -eq 0 ]; then
+    root_url=http://localhost:8080
+else
+    root_url="$1"
+fi
+geometry='{"type":"Polygon","coordinates":[[[-94.6884155,37.0595608],[-94.6884155,37.0332547],[-94.6554565,37.0332547],[-94.6554565,37.0595608],[-94.6884155,37.0595608]]]}'
+
+stac-api-validator --root-url "$root_url" \
+    --conformance core \
+    --conformance collections \
+    --conformance features \
+    --conformance filter \
+    --collection joplin \
+    --geometry "$geometry"
+    # --conformance item-search # currently breaks stac-api-validator

stac_fastapi/api/stac_fastapi/api/app.py

@@ -158,12 +158,12 @@ def register_get_item(self):
             name="Get Item",
             path="/collections/{collection_id}/items/{item_id}",
             response_model=Item if self.settings.enable_response_models else None,
-            response_class=self.response_class,
+            response_class=GeoJSONResponse,
             response_model_exclude_unset=True,
             response_model_exclude_none=True,
             methods=["GET"],
             endpoint=create_async_endpoint(
-                self.client.get_item, ItemUri, self.response_class
+                self.client.get_item, ItemUri, GeoJSONResponse
             ),
         )
 

stac_fastapi/extensions/stac_fastapi/extensions/core/transaction.py

@@ -73,7 +73,7 @@ def register_create_item(self):
         )
 
     def register_update_item(self):
-        """Register update item endpoint (PUT /collections/{collection_id}/items)."""
+        """Register update item endpoint (PUT /collections/{collection_id}/items/{item_id})."""
         self.router.add_api_route(
             name="Update Item",
             path="/collections/{collection_id}/items/{item_id}",

stac_fastapi/pgstac/setup.py

@@ -31,7 +31,7 @@
         "httpx",
     ],
     "docs": ["mkdocs", "mkdocs-material", "pdocs"],
-    "server": ["uvicorn[standard]==0.17.0"],
+    "server": ["uvicorn[standard]==0.17.0.post1"],
     "awslambda": ["mangum"],
 }
 

stac_fastapi/pgstac/stac_fastapi/pgstac/core.py

@@ -2,7 +2,7 @@
 import re
 from datetime import datetime
 from typing import Any, Dict, List, Optional, Union
-from urllib.parse import urljoin
+from urllib.parse import unquote_plus, urljoin
 
 import attr
 import orjson
@@ -18,7 +18,12 @@
 from starlette.requests import Request
 
 from stac_fastapi.pgstac.config import Settings
-from stac_fastapi.pgstac.models.links import CollectionLinks, ItemLinks, PagingLinks
+from stac_fastapi.pgstac.models.links import (
+    CollectionLinks,
+    ItemCollectionLinks,
+    ItemLinks,
+    PagingLinks,
+)
 from stac_fastapi.pgstac.types.search import PgstacSearch
 from stac_fastapi.pgstac.utils import filter_fields
 from stac_fastapi.types.core import AsyncBaseCoreClient
@@ -286,7 +291,7 @@ async def item_collection(
             **clean,
         )
         item_collection = await self._search_base(req, **kwargs)
-        links = await CollectionLinks(
+        links = await ItemCollectionLinks(
             collection_id=collection_id, request=kwargs["request"]
         ).get_links(extra_links=item_collection["links"])
         item_collection["links"] = links
@@ -372,7 +377,7 @@ async def get_search(
             "bbox": bbox,
             "limit": limit,
             "token": token,
-            "query": orjson.loads(query) if query else query,
+            "query": orjson.loads(unquote_plus(query)) if query else query,
         }
 
         if filter:

stac_fastapi/pgstac/stac_fastapi/pgstac/models/links.py

@@ -206,6 +206,27 @@ def link_items(self) -> Dict:
         )
 
 
+@attr.s
+class ItemCollectionLinks(CollectionLinksBase):
+    """Create inferred links specific to collections."""
+
+    def link_self(self) -> Dict:
+        """Return the self link."""
+        return dict(
+            rel=Relations.self.value,
+            type=MimeTypes.geojson.value,
+            href=self.resolve(f"collections/{self.collection_id}/items"),
+        )
+
+    def link_parent(self) -> Dict:
+        """Create the `parent` link."""
+        return self.collection_link(rel=Relations.parent.value)
+
+    def link_collection(self) -> Dict:
+        """Create the `collection` link."""
+        return self.collection_link()
+
+
 @attr.s
 class ItemLinks(CollectionLinksBase):
     """Create inferred links specific to items."""