Improve pygeoapi configuration (#19)

* Update pygeoapi configuration * Update Docker entrypoint Separate out source alignment from server startup * Hide fix pygeoapi link in landing page
internetofwater · Sep 27, 2023 · 47d66b8 · 47d66b8
1 parent a51d16f
commit 47d66b8
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Showing 6 changed files with 60 additions and 35 deletions.
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -33,9 +33,9 @@ services:
       NLDI_DB_HOST: nldi-db
       NLDI_DB_PORT: 5432
       NLDI_DB_NAME: nldi
-      NLDI_DB_USERNAME: read_only_user
+      NLDI_DB_USERNAME: nldi
       NLDI_DB_PASSWORD: changeMe
-      pygeoapiUrl: "https://labs.waterdata.usgs.gov/api/nldi/pygeoapi/"
+      PYGEOAPI_URL: https://labs.waterdata.usgs.gov/api/nldi/pygeoapi/
     networks:
       - nldi
 

diff --git a/docker/default.source.yml b/docker/default.source.yml
@@ -30,14 +30,17 @@
 server:
   url: ${NLDI_URL}
   pretty_print: false
-  pygeoapi: true
   data:
     host: ${NLDI_DB_HOST}
     port: ${NLDI_DB_PORT}
     dbname: ${NLDI_DB_NAME}
     user: ${NLDI_DB_USERNAME}
     password: ${NLDI_DB_PASSWORD}
 
+pygeoapi: 
+  enabled: true
+  gdp_url: ${PYGEOAPI_URL}
+
 logging:
   level: ERROR
   # logfile: /tmp/nldi.log

diff --git a/docker/entrypoint.sh b/docker/entrypoint.sh
@@ -53,31 +53,44 @@ entry_cmd=${1:-run}
 
 # Shorthand
 function error() {
-	echo "ERROR: $@"
-	exit -1
+        echo "ERROR: $@"
+        exit -1
 }
 
 # Workdir
 cd ${NLDI_HOME}
 
-echo "Trying to generate openapi.yml"
-pygeoapi openapi generate ${PYGEOAPI_CONFIG} --output-file ${PYGEOAPI_OPENAPI}
-nldi config align-sources ${NLDI_CONFIG}
-nldi openapi generate ${NLDI_CONFIG} --output-file ${NLDI_OPENAPI}
+case ${entry_cmd} in
+# Align source table
+align)
+        nldi config align-sources ${NLDI_CONFIG}
+        ;;
 
-[[ $? -ne 0 ]] && error "openapi.yml could not be generated ERROR"
+# Run NLDI Server
+run)
+        echo "Trying to generate openapi.yml"
+        pygeoapi openapi generate ${PYGEOAPI_CONFIG} --output-file ${PYGEOAPI_OPENAPI}
+        nldi openapi generate ${NLDI_CONFIG} --output-file ${NLDI_OPENAPI}
 
-echo "openapi.yml generated continue to nldi"
+        [[ $? -ne 0 ]] && error "openapi.yml could not be generated ERROR"
 
-# SCRIPT_NAME should not have value '/'
-[[ "${SCRIPT_NAME}" = '/' ]] && export SCRIPT_NAME="" && echo "make SCRIPT_NAME empty from /"
+        echo "openapi.yml generated continue to nldi"
 
-echo "Start gunicorn name=${CONTAINER_NAME} on ${CONTAINER_HOST}:${CONTAINER_PORT} with ${WSGI_WORKERS} workers and SCRIPT_NAME=${SCRIPT_NAME}"
-exec gunicorn --workers ${WSGI_WORKERS} \
-        --worker-class=${WSGI_WORKER_CLASS} \
-        --timeout ${WSGI_WORKER_TIMEOUT} \
-        --name=${CONTAINER_NAME} \
-        --bind ${CONTAINER_HOST}:${CONTAINER_PORT} \
-        nldi.flask_app:APP
+        # SCRIPT_NAME should not have value '/'
+        [[ "${SCRIPT_NAME}" = '/' ]] && export SCRIPT_NAME="" && echo "make SCRIPT_NAME empty from /"
+
+        echo "Start gunicorn name=${CONTAINER_NAME} on ${CONTAINER_HOST}:${CONTAINER_PORT} with ${WSGI_WORKERS} workers and SCRIPT_NAME=${SCRIPT_NAME}"
+        exec gunicorn --workers ${WSGI_WORKERS} \
+                --worker-class=${WSGI_WORKER_CLASS} \
+                --timeout ${WSGI_WORKER_TIMEOUT} \
+                --name=${CONTAINER_NAME} \
+                --bind ${CONTAINER_HOST}:${CONTAINER_PORT} \
+                nldi.flask_app:APP
+        ;;
+
+*)
+        error "unknown command arg: must be run (default) or align"
+        ;;
+esac
 
 echo "END /entrypoint.sh"
diff --git a/nldi/api.py b/nldi/api.py
@@ -157,9 +157,14 @@ def flowline_lookup(self) -> FlowlineLookup:
     def pygeoapi_lookup(self) -> PygeoapiLookup:
         """pygeoapi Lookup Provider"""
         if self._pygeoapi_lookup is None:
+            try:
+                PYGEOAPI_URL = self.config['pygeoapi']['gdp_url']
+            except KeyError:
+                PYGEOAPI_URL = 'https://labs.waterdata.usgs.gov/api/nldi/pygeoapi'  # noqa
             self._pygeoapi_lookup = \
                 self.load_plugin('PygeoapiLookup',
-                                 catchment_lookup=self.catchment_lookup)
+                                 catchment_lookup=self.catchment_lookup,
+                                 pygeoapi_url=PYGEOAPI_URL)
         return self._pygeoapi_lookup
 
     @pre_process
@@ -197,13 +202,16 @@ def landing_page(self, request: Union[APIRequest, Any]
             }]
         }
 
-        if self.config['server']['pygeoapi'] is True:
-            content['links'].append({
-                'rel': 'data',
-                'type': 'text/html',
-                'title': 'pygeoapi for the NLDI',
-                'href': f'{self.base_url}/pygeoapi?f=html'
-            })
+        try:
+            if self.config['pygeoapi']['enabled'] is True:
+                content['links'].append({
+                    'rel': 'data',
+                    'type': 'text/html',
+                    'title': 'pygeoapi for the NLDI',
+                    'href': f'{self.base_url}/pygeoapi?f=html'
+                })
+        except KeyError:
+            LOGGER.debug('Omitting pygeoapi link')
 
         return headers, HTTPStatus.OK, to_json(content, self.pretty_print)
 

diff --git a/nldi/flask_app.py b/nldi/flask_app.py
@@ -224,8 +224,11 @@ def get_navigation(source_name=None, identifier=None, nav_mode=None, data_source
         request, source_name, identifier, nav_mode, data_source))
 
 
-if CONFIG['server']['pygeoapi'] is True:
-    from pygeoapi.flask_app import BLUEPRINT as PYGEOAPI_BLUEPRINT
-    APP.register_blueprint(PYGEOAPI_BLUEPRINT, url_prefix='/pygeoapi')
+try:
+    if CONFIG['pygeoapi']['enabled'] is True:
+        from pygeoapi.flask_app import BLUEPRINT as PYGEOAPI_BLUEPRINT
+        APP.register_blueprint(PYGEOAPI_BLUEPRINT, url_prefix='/pygeoapi')
+except KeyError:
+    LOGGER.info('Not including pygeoapi templates')
 
 APP.register_blueprint(BLUEPRINT)
diff --git a/nldi/lookup/pygeoapi.py b/nldi/lookup/pygeoapi.py
@@ -29,7 +29,6 @@
 
 import json
 import logging
-import os
 from requests import Session as HTTPSession
 from shapely import wkt
 from sqlalchemy import func
@@ -42,8 +41,6 @@
 
 LOGGER = logging.getLogger(__name__)
 
-PYGEOAPI_URL = os.getenv(
-    'PYGEOAPI_URL', 'https://labs.waterdata.usgs.gov/api/nldi/pygeoapi')
 DEFAULT_PROPS = {
     'identifier': '', 'navigation': '', 'measure': '',
     'reachcode': '', 'name': '', 'source': 'provided',
@@ -66,6 +63,7 @@ def __init__(self, provider_def):
         """
         LOGGER.debug('Initialising Pygeoapi Lookup.')
         self.catchment_lookup = provider_def['catchment_lookup']
+        self.pygeoapi_url = provider_def['pygeoapi_url']
         self.base_url = provider_def['base_url']
         self.http = HTTPSession()
 
@@ -90,7 +88,7 @@ def get_hydrolocation(self, coords: str) -> dict:
         }
 
         LOGGER.debug('Making OGC API - Processes request')
-        url = url_join(PYGEOAPI_URL, 'processes/nldi-flowtrace/execution')
+        url = url_join(self.pygeoapi_url, 'processes/nldi-flowtrace/execution')
         response = self._get_response(url, data=data)
 
         LOGGER.debug('Getting feature intersection')