Updates for ES8 and Python 3.8.10

- Pin pygeoapi to 0.16.1.
- Update debian/control
- Update flake8.yml for Python 3.8, updated actions/checkout and actions/setup-python version. Run flake8 on current diurectory and all subdirectories
- Update README and deploy-nightly.sh
- Use custom ES provider instead of pygeoapi ES provider, subclassed from pygeoapi ElasticsearchProvider
- Update config.yml to use WOUDC_API_ES_INDEX_PREFIX env
- Improved deploy-nightly.sh script
- Permission changes to deploy

.github/workflows/flake8.yml

@@ -7,11 +7,11 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.8]
 
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
       name: Set up Python ${{ matrix.python-version }}
       with:
         python-version: ${{ matrix.python-version }}
@@ -20,6 +20,6 @@ jobs:
         python3 -m pip install --upgrade pip
         pip3 install flake8
     - name: run flake8 ⚙️
-      run: | 
-        flake8
+      run: |
+        flake8 .
 

README.md

@@ -27,8 +27,8 @@ are automatically installed during installation.
 
 ```bash
 # setup virtualenv
-python3 -m venv --system-site-packages woudc-api
-cd woudc-api
+python3 -m venv --system-site-packages woudc-api_env
+cd woudc-api_env
 source bin/activate
 
 # setup local OGC schemas (i.e. WOUDC_API_OGC_SCHEMAS_LOCATION in default.env)
@@ -38,21 +38,32 @@ curl -O http://schemas.opengis.net/SCHEMAS_OPENGIS_NET.zip && unzip ./SCHEMAS_OP
 # clone pygeoapi codebase and install
 git clone https://github.com/geopython/pygeoapi.git
 cd pygeoapi
-python setup.py install
+git checkout 0.16.1
+pip3 install -r requirements.txt
+python3 setup.py install
+cd ..
+
+# clone woudc-extcsv and install
+git clone https://github.com/woudc/woudc-extcsv.git
+cd woudc-extcsv
+python3 setup.py install
 cd ..
 
 # clone woudc-api codebase and install
 git clone https://github.com/woudc/woudc-api.git
 cd woudc-api
-python setup.py install
+python3 setup.py install
 
 # set system environment variables
 cp default.env local.env
 vi local.env  # edit accordingly
 . local.env
 
 # generate openapi document
-pygeoapi openapi generate -c $PYGEOAPI_CONFIG > $PYGEOAPI_OPENAPI
+pygeoapi openapi generate ${PYGEOAPI_CONFIG} -f json --output-file ${PYGEOAPI_OPENAPI}
+
+# optional: validate openapi document
+pygeoapi openapi validate ${PYGEOAPI_OPENAPI}
 
 # run the server
 woudc-api serve  # server runs on http://localhost:5000

debian/control

@@ -4,12 +4,12 @@ Priority: optional
 Maintainer: Tom Kralidis <[email protected]>
 Build-Depends: debhelper (>= 9), python3, python3-setuptools, curl, unzip
 Standards-Version: 3.9.5
-X-Python-Version: >= 3.6
+X-Python-Version: >= 3.8
 Vcs-Git: https://github.com/woudc/woudc-api.git
 
 Package: woudc-api
 Architecture: all
-Depends: elasticsearch (>=7), elasticsearch (<8), libapache2-mod-wsgi-py3, python3, python3-flask, python3-pygeoapi, woudc-extcsv
-Suggests: python3-elasticsearch (>=7), python3-elasticsearch (<8)
+Depends: elasticsearch (>=8), elasticsearch (<9), libapache2-mod-wsgi-py3, python3, python3-flask, python3-pygeoapi, woudc-extcsv
+Suggests: python3-elasticsearch (>=8), python3-elasticsearch (<9)
 Homepage: https://woudc.org
 Description: WMO WOUDC REST API

debian/postinst

@@ -1,6 +1,6 @@
 #!/bin/sh
 
-set -e 
+set -e
 
 USERNAME="woudcuser"
 GROUP="www-data"

default.env

@@ -1,7 +1,10 @@
 export WOUDC_API_BIND_HOST=0.0.0.0
 export WOUDC_API_BIND_PORT=5000
 export WOUDC_API_URL=http://localhost:5000/oapi
-export WOUDC_API_ES_URL=http://localhost:9200
+export WOUDC_API_ES_USERNAME=elasticsearch
+export WOUDC_API_ES_PASSWORD=<secret>
+export WOUDC_API_ES_URL=http://${WOUDC_API_ES_USERNAME}:${WOUDC_API_ES_PASSWORD}@localhost:9200
+export WOUDC_API_ES_INDEX_PREFIX=woudc_data_registry
 export WOUDC_API_OGC_SCHEMAS_LOCATION=/opt/woudc-api/schemas.opengis.net
 export PYGEOAPI_CONFIG=/path/to/woudc-api-config.yml
 export PYGEOAPI_OPENAPI=/path/to/woudc-api-openapi.yml