Updates to the sparql provider to match the mainstem query (#22)

* Query Mainstems and Gages with SPARQL provider (7261757324) * Update SPARQL provider * Use pygeoapi root image * updates to the sparql provider to match the mainstem query * updated docker compose * update readme * Update pygeoapi.config.yml Co-authored-by: Benjamin Webb <[email protected]> * Update docker-compose.yml Co-authored-by: Benjamin Webb <[email protected]> * reversions * indent * indent again for diff * update sparql config * change back to error * add indent * Update pygeoapi.config.yml --------- Co-authored-by: Benjamin Webb <[email protected]>
internetofwater · Sep 17, 2024 · ec6fb38 · ec6fb38
1 parent 57dd55f
commit ec6fb38
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diff --git a/.gitignore b/.gitignore
@@ -158,3 +158,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+
+*.sql.gz
diff --git a/Dockerfile b/Dockerfile
@@ -1,12 +1,11 @@
 FROM geopython/pygeoapi:latest
 #pygeoapi last updated 2023-07-31
 
-#add requirements and mods
-COPY ./pygeoapi.config.yml /pygeoapi/local.config.yml
-
 # COPY ./schemas.opengis.net /opt/schemas.opengis.net
 COPY ./pygeoapi-skin-dashboard /skin-dashboard
 
+COPY ./pygeoapi.config.yml /pygeoapi/local.config.yml
+
 RUN pip3 install https://github.com/cgs-earth/pygeoapi-plugins/archive/refs/heads/master.zip
 
 COPY ./sitemap /sitemap

diff --git a/README.md b/README.md
@@ -70,11 +70,23 @@ These reference features are intended to be ["community reference locations"](ht
 
 ## Install
 
-Generate a SQL Dump of the Hydroshare resource using [Hydrodump Action](https://github.com/cgs-earth/hydrodump-action).
-
-Then use docker compose to bring up the containers:
+Use docker compose to bring up the containers:
 
 ```
 docker compose up -d database
 docker compose up -d pygeoapi
 ```
+
+Then generate a SQL Dump of the Hydroshare resource using [Hydrodump Action](https://github.com/cgs-earth/hydrodump-action).
+
+```
+docker compose up -d hydrodump
+```
+
+If you have a local hydrodump `reference.sql.gz` file, you can use that instead of regenerating the dump using
+
+```
+docker compose up -d local
+```
+
+
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,11 +1,11 @@
-# dont need this anymore, but useful for test deployment
-# requires separate service providing postgres database
 services:
   pygeoapi:
     build: .
     container_name: reference-geoconnex-us
     ports:
       - 5000:80
+    volumes:
+      - ./pygeoapi.config.yml:/pygeoapi/local.config.yml
     env_file:
       - .env
 
@@ -14,10 +14,36 @@ services:
     image: postgis/postgis:14-3.2-alpine
     env_file:
       - .env
+    volumes:
+      - db_data:/var/lib/postgresql/data
 
   hydrodump:
     container_name: hydrodump
     image: ghcr.io/cgs-earth/hydrodump-action:latest
     command: ["hydrodump", "run"]
     env_file:
       - .env
+
+  local:
+  # Instead of using a remote hydrodump, you can source a local database dump, reference.sql.gz
+    container_name: local
+    image: postgis/postgis:14-3.2-alpine
+    depends_on:
+      - database
+    volumes:
+      - ./reference.sql.gz:/docker-entrypoint-initdb.d/reference.sql.gz
+    entrypoint: >
+      sh -c "
+      export PGPASSWORD=${POSTGRES_PASSWORD} && \
+      echo 'Waiting for database to be ready...' && \
+      while ! pg_isready -h ${POSTGRES_HOST} -U ${POSTGRES_USER} -d ${POSTGRES_DB}; do
+        sleep 1
+      done && \
+      echo 'Database is ready. Starting migration...' && \
+      gunzip -c /docker-entrypoint-initdb.d/reference.sql.gz | psql -h ${POSTGRES_HOST} -U ${POSTGRES_USER} -d ${POSTGRES_DB}
+      "
+    env_file:
+      - .env
+
+volumes:
+  db_data:
diff --git a/pygeoapi-skin-dashboard/templates/collections/items/item.html b/pygeoapi-skin-dashboard/templates/collections/items/item.html
@@ -172,4 +172,4 @@ <h2 class="mx-auto">Datasets</h2>
     map.addLayer(items);
     map.fitBounds(items.getBounds(), {maxZoom: 10});
     </script>
-{% endblock %}
+{% endblock %}
diff --git a/pygeoapi-skin-dashboard/templates/jsonld/hu06.jsonld b/pygeoapi-skin-dashboard/templates/jsonld/hu06.jsonld
@@ -18,4 +18,4 @@
     ],
     "gsp:hasGeometry": {{ data['gsp:hasGeometry'] | to_json }},
     "geo": {{ data['schema:geo'] | to_json | safe }}
-}
+}
diff --git a/pygeoapi.config.yml b/pygeoapi.config.yml
@@ -404,62 +404,57 @@ resources:
                 bind:
                   name: uri
                   variable: '?mainstem'
-                select: '?mainstem ?monitoringLocation ?siteName ?datasetDescription ?type ?url ?variableMeasured ?variableUnit ?measurementTechnique ?temporalCoverage ?wkt'
+                select: '?mainstem ?monitoringLocation ?siteName ?datasetDescription ?type ?url ?variableMeasured ?variableUnit ?measurementTechnique ?temporalCoverage ?distributionName ?distributionURL ?distributionFormat ?wkt'
                 where:
                   - subject: '?monitoringLocation'
-                    predicate: hyf:referencedPosition/hyf:HY_IndirectPosition/hyf:linearElement
-                    object: '?mainstem'
+                    predicate: 'hyf:HydroLocationType'
+                    object: '?type'
                   - subject: '?monitoringLocation'
-                    predicate: schema:name
-                    object: '?siteName'
+                    predicate: 'hyf:referencedPosition/hyf:HY_IndirectPosition/hyf:linearElement'
+                    object: '?mainstem'
                   - subject: '?monitoringLocation'
-                    predicate: schema:subjectOf
+                    predicate: 'schema:subjectOf'
                     object: '?dataset'
+                  - subject: '?monitoringLocation'
+                    predicate: 'gsp:hasGeometry/gsp:asWKT'
+                    object: '?wkt'
                   - subject: '?dataset'
-                    predicate: schema:url
+                    predicate: 'schema:variableMeasured'
+                    object: '?var'
+                  - subject: '?dataset'
+                    predicate: 'schema:url'
                     object: '?url'
                   - subject: '?dataset'
-                    predicate: schema:distribution
+                    predicate: 'schema:distribution'
                     object: '?distribution'
-                  - subject: '?distribution'
-                    predicate: schema:name
-                    object: '?distributionName'
-                  - subject: '?distribution'
-                    predicate: schema:contentUrl
-                    object: '?distributionURL'
-                  - subject: '?distribution'
-                    predicate: schema:encodingFormat
-                    object: '?distributionFormat'
                   - subject: '?dataset'
-                    predicate: schema:description
+                    predicate: 'schema:description'
                     object: '?datasetDescription'
-                  - subject: '?monitoringLocation'
-                    predicate: hyf:HydroLocationType
-                    object: '?type'
                   - subject: '?dataset'
-                    predicate: 'schema:variableMeasured'
-                    object: '?variableMeasured_'
-                  - subject: '?variableMeasured_'
+                    predicate: 'schema:temporalCoverage'
+                    object: '?temporalCoverage'
+                  - subject: '?dataset'
+                    predicate: 'schema:name'
+                    object: '?siteName'
+                  - subject: '?var'
                     predicate: 'schema:name'
                     object: '?variableMeasured'
-                  - subject: '?variableMeasured_'
+                  - subject: '?var'
                     predicate: 'schema:unitText'
                     object: '?variableUnit'
-                  - subject: '?variableMeasured_'
+                  - subject: '?var'
                     predicate: 'schema:measurementTechnique'
                     object: '?measurementTechnique'
-                  - subject: '?variableMeasured_'
-                    predicate: 'schema:name'
-                    object: '?variableMeasured'
-                  - subject: '?dataset'
-                    predicate: 'schema:temporalCoverage'
-                    object: '?temporalCoverage'
-                  - subject: '?dataset'
-                    predicate: 'schema:provider'
-                    object: '?provider'
-                  - subject: '?provider'
+                  - subject: '?distribution'
                     predicate: 'schema:name'
-                    object: '?datasetProvider'
+                    object: '?distributionName'
+                  - subject: '?distribution'
+                    predicate: 'schema:contentUrl'
+                    object: '?distributionURL'
+                  - subject: '?distribution'
+                    predicate: 'schema:encodingFormat'
+                    object: '?distributionFormat'
+
     dams: # updated 2024-04-23
         type: collection
         title: Reference Dams