Improve pygeoapi configuration (#19)

* Update pygeoapi configuration

* Update Docker entrypoint

Separate out source alignment from server startup

* Hide fix pygeoapi link in landing page

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
 

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

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"

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)
 

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)

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')