Swc loc depths

.github/workflows/build_push_concH2oSoilSalinity_position_history_loader.yml

@@ -6,6 +6,8 @@ on:
       - 'master'
     paths:
       - 'modules/concH2oSoilSalinity_position_history_loader/**'
+      - 'modules/data_access/**'
+      - 'modules/common/**'
   workflow_dispatch: {} # Allows trigger of workflow from web interface
 
 env:

modules/concH2oSoilSalinity_position_history_loader/Dockerfile

@@ -0,0 +1,47 @@
+####
+#
+# This dockerfile builds the concH2oSoilSalinity position-history loader.
+# Must be built from the project root so common/ and data_access/ are in context:
+#   docker build --no-cache \
+#     -t concH2oSoilSalinity_position_history_loader:latest \
+#     -f modules/concH2oSoilSalinity_position_history_loader/Dockerfile .
+#
+###
+FROM registry.access.redhat.com/ubi8/ubi-minimal
+
+ARG MODULE_DIR="./modules"
+ARG APP_DIR="concH2oSoilSalinity_position_history_loader"
+ARG COMMON_DIR="common"
+ARG DATA_ACCESS_DIR="data_access"
+ARG CONTAINER_APP_DIR="/usr/src/app"
+ENV PYTHONPATH="${PYTHONPATH}:${CONTAINER_APP_DIR}"
+
+WORKDIR ${CONTAINER_APP_DIR}
+
+COPY ${MODULE_DIR}/${APP_DIR}/requirements.txt ${CONTAINER_APP_DIR}/${APP_DIR}/app-requirements.txt
+COPY ${MODULE_DIR}/${DATA_ACCESS_DIR}/requirements.txt ${CONTAINER_APP_DIR}/${APP_DIR}/data-access-requirements.txt
+
+RUN update-ca-trust && \
+    microdnf update -y --disableplugin=subscription-manager && \
+    microdnf install -y --disableplugin=subscription-manager \
+            shadow-utils \
+            gcc \
+            libzstd  \
+            python39 \
+            python39-pip \
+            python39-wheel \
+            python39-devel \
+            python39-setuptools && \
+    python3 -mpip install --no-cache-dir --upgrade pip setuptools wheel && \
+    python3 -mpip install --no-cache-dir -r ${CONTAINER_APP_DIR}/${APP_DIR}/app-requirements.txt && \
+    python3 -mpip install --no-cache-dir -r ${CONTAINER_APP_DIR}/${APP_DIR}/data-access-requirements.txt && \
+    microdnf remove -y --disableplugin=subscription-manager gcc cpp && \
+    microdnf clean all --disableplugin=subscription-manager && \
+    groupadd -g 9999 appuser && \
+    useradd -r -u 9999 -g appuser appuser
+
+COPY ${MODULE_DIR}/${APP_DIR} ${CONTAINER_APP_DIR}/${APP_DIR}
+COPY ${MODULE_DIR}/${COMMON_DIR} ${CONTAINER_APP_DIR}/${COMMON_DIR}
+COPY ${MODULE_DIR}/${DATA_ACCESS_DIR} ${CONTAINER_APP_DIR}/${DATA_ACCESS_DIR}
+
+USER appuser

modules/concH2oSoilSalinity_position_history_loader/concH2oSoilSalinity_position_history_loader_main.py

@@ -0,0 +1,45 @@
+#!/usr/bin/env python3
+from contextlib import closing
+from functools import partial
+from pathlib import Path
+
+import environs
+import structlog
+
+import common.log_config as log_config
+from data_access.db_config_reader import read_from_mount
+from data_access.db_connector import DbConnector
+from data_access.get_enviroscan_asset_installs import get_enviroscan_asset_installs
+from data_access.get_enviroscan_cvald1_calibrations import get_enviroscan_cvald1_calibrations
+from data_access.get_enviroscan_cfgloc_vers import get_enviroscan_cfgloc_vers
+from data_access.get_named_location_geolocations import get_named_location_geolocations
+from data_access.get_named_location_parents import get_named_location_parents
+
+import concH2oSoilSalinity_position_history_loader.concH2oSoilSalinity_position_history_loader as loader
+
+log = structlog.get_logger()
+
+
+def main() -> None:
+    env = environs.Env()
+    out_path: Path = env.path('OUT_PATH')
+    err_path: Path = env.path('ERR_PATH')
+    log_level: str = env.log_level('LOG_LEVEL', 'INFO')
+    log_config.configure(log_level)
+    log.debug(f'out_path: {out_path}')
+
+    db_config = read_from_mount(Path('/var/db_secret'))
+    with closing(DbConnector(db_config)) as connector:
+        loader.write_files(
+            get_asset_installs=partial(get_enviroscan_asset_installs, connector),
+            get_calibrations=partial(get_enviroscan_cvald1_calibrations, connector),
+            get_cfgloc_vers=partial(get_enviroscan_cfgloc_vers, connector),
+            get_geolocations=partial(get_named_location_geolocations, connector),
+            get_parents=partial(get_named_location_parents, connector),
+            out_path=out_path,
+            err_path=err_path,
+        )
+
+
+if __name__ == '__main__':
+    main()

modules/concH2oSoilSalinity_position_history_loader/requirements.txt

@@ -0,0 +1,4 @@
+structlog==21.5.0
+environs==11.0.0
+marshmallow==3.21.3
+geojson==2.4.1