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Add scripts meant to replace some of the actions inside Dockerfiles so that this installation steps can be done inside of an interactive Jupyterlab.
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‎.dockerignore‎

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# Ignore certain files when copying that are large and unneeded for the build context
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src/**/acctest/**/in/**/*.cdl
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src/**/acctest/**/in/**/*.nc
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src/**/acctest/**/in/**/*.orig
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src/**/acctest/**/in/**/*.PDS
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src/**/acctest/**/expected
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src/**/unittest
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src/**/unittests

‎Dockerfile.common‎

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This file was deleted.

‎docker-compose.yml‎

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# ${DOCKER_GROUP} and ${DOCKER_TAG} default values defined in the .env file
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version: '3'
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services:
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sips_base:
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image: ${DOCKER_GROUP}/sounder_sips_base:${DOCKER_TAG}
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hostname: local
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build:
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context: base/
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dockerfile: $PWD/base/Dockerfile
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spss_pge_common:
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image: ${DOCKER_GROUP}/sounder_sips_pge_common:${DOCKER_TAG}
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hostname: local
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build:
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context: spss/
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dockerfile: $PWD/spss/Dockerfile.common
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spss_l1a_pge:
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l1a_pge:
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image: ${DOCKER_GROUP}/sounder_sips_l1a_pge:${DOCKER_TAG}
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hostname: local
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build:
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context: spss/
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dockerfile: $PWD/spss/Dockerfile.l1a
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spss_l1b_pge:
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dockerfile: $PWD/Dockerfile.l1a
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l1b_pge:
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image: ${DOCKER_GROUP}/sounder_sips_l1b_pge:${DOCKER_TAG}
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hostname: local
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build:
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context: spss/
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dockerfile: $PWD/spss/Dockerfile.l1b
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dockerfile: $PWD/Dockerfile.l1b

‎install/build_common.sh‎

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#!/bin/bash
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# Parallel build can cause the build to failr
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export NUM_COMPILE_JOBS=1
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usage () {
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echo "Usage:"
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echo "$0 <source_code_directory>"
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exit 1
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}
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src_dir=$1
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if [ -z "$src_dir" ]; then
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usage
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fi
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# PGE common directories
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cd $src_dir/src/common/make && make -j $NUM_COMPILE_JOBS
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cd $src_dir/src/shared_io/make && make -j $NUM_COMPILE_JOBS
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cd $src_dir/src/shared_alg/make && make -j $NUM_COMPILE_JOBS
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cd $src_dir/src/pge_wrapper/make && make -j $NUM_COMPILE_JOBS
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# MetExtractor compilation
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cd $src_dir/src/scf_shared/make && make -j $NUM_COMPILE_JOBS
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cd $src_dir/src/scf_pge/make && make -j $NUM_COMPILE_JOBS
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cd $src_dir/src/scf_metextractors/make && make -j $NUM_COMPILE_JOBS

‎install/build_l1a.sh‎

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#!/bin/bash
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# Parallel build can cause the build to failr
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export NUM_COMPILE_JOBS=1
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usage () {
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echo "Usage:"
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echo "$0 <source_code_directory> [<destination_binary_directory>]"
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exit 1
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}
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src_dir=$1
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dst_dir=$2
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if [ -z "$src_dir" ]; then
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usage
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fi
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cd $src_dir/src/sips_pge/l1a_atms/make && make -j $NUM_COMPILE_JOBS
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if [ ! -z "$dst_dir" ]; then
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mkdir -p $dst_dir
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cp $src_dir/src/sips_pge/l1a_atms/pge/bin/L1AMw_main $dst_dir
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cp $src_dir/src/scf_metextractors/main/bin/MetExtractor $dst_dir
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fi

‎install/create_l1a_static_config.sh‎

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#!/bin/bash
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script_dir=$(dirname $0)
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src_dir=$1
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dst_dir=$2
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static_dir=$3
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if [ -z "$src_dir" ]; then
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usage
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fi
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if [ -z "$dst_dir" ]; then
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usage
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fi
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if [ ! -e "$dst_dir" ]; then
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mkdir -p $dst_dir
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fi
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if [ -z "$static_dir" ]; then
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static_dir=$DEFAULT_STATIC_FILES_DIR
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fi
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# Copy SDPTK toolkit files
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cp $script_dir/../ephemeris/leapsec.dat $dst_dir
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cp $script_dir/../ephemeris/utcpole.dat $dst_dir
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# Copy files from acceptance test directories, these are referenced by the input XML file
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cp $src_dir/src/sips_pge/l1a_atms_snpp/acctest/in/pcf/SNDR.PGSToolkit_ProcessControlFile.pcf $dst_dir
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cp $src_dir/src/sips_pge/l1a_atms_snpp/acctest/in/SNDR.SNPP.ATMS.L1A.sfif_201214135000.xml $dst_dir
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cp $src_dir/src/sips_pge/l1a_atms_snpp/acctest/in/SNDR.SchemaParameterfile.060401120000.xsd $dst_dir
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# Modify SFIF file to point to destination paths
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sed -i 's|../../../static|'$dst_dir'|' $dst_dir/SNDR.SNPP.ATMS.L1A.sfif_201214135000.xml
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# Modify to point leapsec.dat and utcpole.dat to our configuration static dir
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sed -i -e 's|utcpole_20201220.dat|utcpole.dat|' \
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-e 's|../../in/pcf|'$dst_dir'|' \
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-e 's|~/database/common/TD|'$dst_dir'|' \
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$dst_dir/SNDR.PGSToolkit_ProcessControlFile.pcf
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# Modify to point DEMs to a path controlled by Docker
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sed -i -e 's|/peate/support/static/dem|'$static_dir'/dem|' \
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-e 's|/ref/devstable/STORE/mcf|'$static_dir'/mcf|' \
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$dst_dir/SNDR.PGSToolkit_ProcessControlFile.pcf
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# Static files referenced in SFIF file
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cp $src_dir/src/sips_pge/l1a_atms_snpp/static/SNDR.SNPP.ATMS.L1A.template.v02_02_08_201214135000.nc $dst_dir
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cp $src_dir/src/sips_pge/l1a_atms_snpp/static/ATMS-SDR-CC_npp_20131201000000Z_20140101000000Z_ee00000000000000Z_PS-1-O-CCR-14-1487-JPSS-DPA-008-SIDEA-PE_noaa_all_all-_all.xml $dst_dir
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cp $src_dir/src/sips_pge/l1a_atms_snpp/static/SNDR.SNPP.ATMS.L1A.calibration_data_200204184500.csv $dst_dir
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cp $src_dir/src/sips_pge/l1a_atms_snpp/static/SNDR.SNPP.ATMS.APID_531_ENGHSKP_v11_200204184500.xml $dst_dir
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cp $src_dir/src/sips_pge/l1a_atms_snpp/static/SNDR.SNPP.ATMS.L1A.apf_180412120000.xml $dst_dir
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cp $src_dir/src/sips_pge/l1a_atms_snpp/static/SNDR.SIPS.SNPP.ATMS.L1A.SPDCMetConstants_170905120000.pev $dst_dir
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cp $src_dir/src/sips_pge/l1a_atms_snpp/static/SNDR.SIPS.ATMS.L1A.SPDCMetStructure_161130151628.xml $dst_dir
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cp $src_dir/src/sips_pge/l1a_atms_snpp/static/SNDR.SIPS.SNPP.ATMS.L1A.SPDCMetMappings_170905120000.xml $dst_dir
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# Template PGE configuration file to be modified by the Jupyter notebook
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cp $src_dir/src/sips_pge/l1a_atms_snpp/acctest/spdc_nominal2/in/SNDR.SNPP.ATMS.L1A.nominal2.config_201214135000.xml $dst_dir/pge_config_template.xml

‎interface/run_l1a_pge.ipynb‎

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"from xml.dom import minidom"
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]
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},
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{
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"cell_type": "markdown",
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"id": "1fc21ce3-a47a-40f9-8039-d04970151ef5",
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"metadata": {},
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"source": [
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"## Constants"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "40c333f0-aff0-4813-9a59-5fdff4681bcf",
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"metadata": {},
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"outputs": [],
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"source": [
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"# Base path where configuration and executables have been installed\n",
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"install_base_path = \"/pge\"\n",
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"\n",
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"# Where PGE static config files\n",
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"config_static_path = os.path.join(install_base_path, \"static\")\n",
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"\n",
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"# Where PGE binaries are located\n",
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"pge_bin_path = os.path.join(install_base_path, \"bin\")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "0f1c1c7e",
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"outputs": [],
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"source": [
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"# Location of input L0 files\n",
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"input_path = \"/pge/in\"\n",
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"input_path = \"/tmp/in\"\n",
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"\n",
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"# Where PGE output files and log files get written\n",
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"output_path = \"/pge/out\"\n",
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"output_path = \"/tmp/out\"\n",
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"\n",
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"# Location of dem and mcf static files\n",
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"data_static_path = \"/tmp/static\"\n",
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"id": "e80baccd",
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"metadata": {},
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"source": [
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"## Constants"
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"## Configuration"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"# Where PGE static config files\n",
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"config_static_path = \"/pge/static\"\n",
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"\n",
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"# Source XML file to be modified with execution parameters\n",
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"config_template_filename = \"/pge/static/pge_config_template.xml\"\n",
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"config_template_filename = os.path.join(config_static_path, \"pge_config_template.xml\")\n",
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"\n",
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"# Where config file gets written\n",
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"config_output_filename = os.path.join(output_path, \"l1a_config.xml\")\n",
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"log_filename = os.path.join(output_path, \"L1AMw_main.log\")\n",
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"\n",
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"# Location of PGE executable\n",
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"pge_executable = \"/pge/bin/L1AMw_main\"\n",
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"pge_executable = os.path.join(pge_bin_path, \"L1AMw_main\")\n",
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"\n",
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"# Location of MetExtractor executable\n",
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"met_extractor_executable = \"/pge/bin/MetExtractor\""
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"met_extractor_executable = os.path.join(pge_bin_path, \"MetExtractor\")"
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]
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},
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{
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"\n",
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"dem_dst_path = \"/tmp/static/dem\"\n",
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"mcf_dst_path = \"/tmp/static/mcf\"\n",
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"\n",
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" \n",
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"for src_path, dst_path in [(dem_src_path, dem_dst_path), (mcf_src_path, mcf_dst_path)]:\n",
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" # Only error if the destination path exists and is not the same as the source\n",
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" if os.path.exists(dst_path) and not os.path.realpath(src_path) == os.path.realpath(dst_path):\n",
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.8"
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"version": "3.10.5"
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}
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},
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"nbformat": 4,

‎test/common/copy_l1a_input.sh‎

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# Copy input files from SPSS repo
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acc_case_in_dir=$(realpath $(dirname $0)/../src/src/sips_pge/l1a_atms_snpp/acctest/spdc_nominal2/in/)
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acc_case_in_dir=$(realpath $(dirname $0)/../../src/src/sips_pge/l1a_atms_snpp/acctest/spdc_nominal2/in/)
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# Copy the input files referenced by the test XML file1
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for src_fn in $acc_case_in_dir/atms_science $acc_case_in_dir/ephatt; do

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