Updated build process for DISP-S1 PGE to isoloate grib_to_netcdf depe…

…ndencies in their own conda environment
nasa · Jan 16, 2024 · cf66eeb · cf66eeb
1 parent 4907bbf
commit cf66eeb
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Showing 3 changed files with 8 additions and 4 deletions.
diff --git a/.ci/docker/Dockerfile_disp_s1 b/.ci/docker/Dockerfile_disp_s1
@@ -52,12 +52,15 @@ RUN set -ex \
     && chmod +x ${CONDA_ROOT}/bin/*_entrypoint.sh \
     && source /usr/local/bin/_activate_current_env.sh \
     && ${MAMBA_EXE} install --yes --channel conda-forge --file ${PGE_DEST_DIR}/opera/requirements.txt \
-    && ${MAMBA_EXE} install --yes --channel conda-forge eccodes jpeg \
     && chmod 775 ${PGE_DEST_DIR} \
+    # Create a separate conda environment for the eccodes install needed to run grib_to_netcdf
+    && ${MAMBA_EXE} create -n eccodes \
+    && ${MAMBA_EXE} install -n eccodes --yes --channel conda-forge eccodes jpeg \
+    # Install grib_to_netcdf and make it available to the eccodes conda env
     && curl -o /tmp/eccodes-2.28.1-1.x86_64.rpm https://artifactory-fn.jpl.nasa.gov:443/artifactory/general/gov/nasa/jpl/opera/sds/pge/disp_s1/eccodes/eccodes-2.28.1-1.x86_64.rpm \
     && dnf install -y /tmp/eccodes-2.28.1-1.x86_64.rpm \
     && rm -rf /tmp/eccodes-2.28.1-1.x86_64.rpm \
-    && ln -sf /opt/eccodes/bin/grib_to_netcdf /opt/conda/bin/
+    && ln -sf /opt/eccodes/bin/grib_to_netcdf /opt/conda/envs/eccodes/bin/
 
 # Set the Docker entrypoint and clear the default command
 ENTRYPOINT ["sh", "-c", "source /usr/local/bin/_activate_current_env.sh;exec ${CONDA_ROOT}/bin/pge_docker_entrypoint.sh \"${@}\"", "--"]

diff --git a/src/opera/pge/disp_s1/disp_s1_pge.py b/src/opera/pge/disp_s1/disp_s1_pge.py
@@ -93,13 +93,14 @@ def convert_troposphere_model_files(self):
                 grib_file_name = tropo_file
                 subprocess.run(
                     [
-                        "grib_to_netcdf",
+                        "/opt/conda/envs/eccodes/bin/grib_to_netcdf",
                         "-D",
                         "NC_FLOAT",
                         "-o",
                         netcdf_file,
                         grib_file_name[:-4],
                     ],
+                    env={'ENV_NAME': 'eccodes', 'LD_LIBRARY_PATH': '/opt/conda/envs/eccodes/lib'},
                     shell=False,
                     check=False,
                 )

diff --git a/src/opera/test/pge/disp_s1/test_disp_s1_pge.py b/src/opera/test/pge/disp_s1/test_disp_s1_pge.py
@@ -41,7 +41,7 @@ def mock_grib_to_netcdf(*popenargs, input=None, capture_output=False, timeout=No
     here we do not want this mocked version to run.
 
     """
-    if popenargs[0][0] == "grib_to_netcdf":
+    if popenargs[0][0].endswith("grib_to_netcdf"):
         output_path = popenargs[0][4]
         open(output_path, 'w').close()
     else: