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MarkusKonkbgruening
MarkusKonk
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bgruening
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solve incompatible environment in cmems and ccds tool (#205)
* add bc package * solve incompatible environment in cmems and ccds tool * increase version * some fixes * Update cmems_download_ic_bc.xml * add bc to requirements * add bc to requirements for cmems * change ccds tool from username,password to token * adapt to latest copernicus renaming --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
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Lines changed: 39 additions & 39 deletions

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‎tools/ccds_download_era5_af/ccds_download_era5_af.xml‎

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@@ -1,40 +1,39 @@
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<tool id="ccds_download_era5_af" name="Copernicus CDS Downloader for AquaINFRA marine model" version="1.0.0" profile="22.05">
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<tool id="ccds_download_era5_af" name="Copernicus CDS Downloader for AquaINFRA marine model" version="1.0.1" profile="22.05">
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<description>
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Download ERA5 data from the Copernicus Climate Data Store to provide as input to the AquaINFRA marine model. Products: ERA5 hourly data on single levels from 1940 to present, Reanalysis.
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</description>
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<creator>
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<organization name="EOSC AquaINFRA" url="https://aquainfra.eu/"/>
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</creator>
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<requirements>
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<requirement type="package" version="1.41.0">boto3</requirement>
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<requirement type="package" version="1.41.0">botocore</requirement>
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<requirement type="package" version="3.11">python</requirement>
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<requirement type="package" version="2.2.5">copernicusmarine</requirement>
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<requirement type="package" version="1.41.2">boto3</requirement>
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<requirement type="package" version="1.41.2">botocore</requirement>
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<requirement type="package" version="5.2.37">bash</requirement>
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<requirement type="package" version="3.14.0">python</requirement>
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<requirement type="package" version="2.3.3">pandas</requirement>
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<requirement type="package" version="0.7.7">cdsapi</requirement>
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<requirement type="package" version="1.8.1">jq</requirement>
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<requirement type="package" version="1.7.3">netcdf4</requirement>
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<requirement type="package" version="1.7.3">bc</requirement>
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<!--<credentials name="cds_api" version="1.0">
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<variable name="token" inject_as_env="CDS_TOKEN" />
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</credentials>-->
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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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bash '$cmems_credentials' &&
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source '$cds_token_api' &&
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bash '$__tool_directory__/ccds_download_era5_af.sh' \
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"$min_lat" "$max_lat" \
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"$min_lon" "$max_lon" \
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"$start_date" "$end_date"
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]]></command>
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bash '$__tool_directory__/ccds_download_era5_af.sh' \
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"$min_lat" "$max_lat" \
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"$min_lon" "$max_lon" \
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"$start_date" "$end_date"
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]]></command>
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<configfiles>
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<configfile name="cmems_credentials">
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<configfile name="cds_token_api">
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#import os
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#set $cmems_username = $__user__.extra_preferences.get('cmems_username', "")
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#set $cmems_password = $__user__.extra_preferences.get('cmems_password', "")
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#if $cmems_username == "" or $cmems_password == ""
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#set $cmems_username = os.getenv('CMEMS_USERNAME', '')
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#set $cmems_password = os.getenv('CMEMS_PASSWORD', '')
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#set $c3s_cds_apikey = $__user__.extra_preferences.get('c3s_account|c3s_cds_apikey', "")
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#if $c3s_cds_apikey == ""
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echo "Error. Set your credentials via: C3S CDS API Key"
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#end if
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export CMEMS_USERNAME='$cmems_username'
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export CMEMS_PASSWORD='$cmems_password'
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export CDS_TOKEN='$c3s_cds_apikey'
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</configfile>
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</configfiles>
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<inputs>

‎tools/cmems_download_ic_bc/cmems_download_ic_bc.sh‎

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Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@ echo ">> startdate: ${START_DATE}"
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echo ">> Tool directory set to: ${TOOL_DIR}"
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# Define dataset IDs
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REANALYSIS_TEM_DATASET_ID="med-cmcc-tem-rean-d"
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REANALYSIS_TEM_DATASET_ID="cmems_mod_med_phy-temp_my_4.2km_P1D-m"
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FCANALYSIS_TEM_DATASET_ID="cmems_mod_med_phy-tem_anfc_4.2km_P1D-m"
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# Define functions
@@ -127,15 +127,13 @@ check_product_availability(){
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select_datasets() {
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if check_product_availability "$REANALYSIS_TEM_DATASET_ID" "$START_DATE" "$END_DATE"; then
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cm_tem_daily_product="$REANALYSIS_TEM_DATASET_ID"
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cm_sal_daily_product="med-cmcc-sal-rean-d"
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cm_cur_daily_product="med-cmcc-cur-rean-d"
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prod_version="202012"
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cm_sal_daily_product="cmems_mod_med_phy-sal_my_4.2km_P1D-m"
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cm_cur_daily_product="cmems_mod_med_phy-cur_my_4.2km_P1D-m"
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echo ">> Using Copernicus Mediterranean Sea Physics Reanalysis product for ${START_DATE} to ${END_DATE}"
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else
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cm_tem_daily_product="$FCANALYSIS_TEM_DATASET_ID"
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cm_sal_daily_product="cmems_mod_med_phy-sal_anfc_4.2km_P1D-m"
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cm_cur_daily_product="cmems_mod_med_phy-cur_anfc_4.2km_P1D-m"
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prod_version="202411"
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echo ">> Using Copernicus Mediterranean Sea Physics Analysis and Forecast product for ${START_DATE} to ${END_DATE}"
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fi
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}
@@ -157,7 +155,6 @@ download_ic(){
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esac
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copernicusmarine subset \
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--dataset-id "$DATASET" \
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--dataset-version "${prod_version}" \
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--minimum-longitude "$cm_xmin" \
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--maximum-longitude "$cm_xmax" \
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--minimum-latitude "$cm_ymin" \
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copernicusmarine subset \
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--dataset-id "$DATASET" \
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--dataset-version "${prod_version}" \
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--minimum-longitude "$cm_xmin" \
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--maximum-longitude "$cm_xmax" \
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--minimum-latitude "$cm_ymin" \
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esac
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copernicusmarine subset \
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--dataset-id "$DATASET" \
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--dataset-version "${prod_version}" \
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--minimum-longitude "$cm_bc_xmin" \
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--maximum-longitude "$cm_bc_xmax" \
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--minimum-latitude "$cm_bc_ymin" \
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copernicusmarine subset \
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--dataset-id "$DATASET" \
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--dataset-version "${prod_version}" \
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--minimum-longitude "$cm_bc_xmin" \
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--maximum-longitude "$cm_bc_xmax" \
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--minimum-latitude "$cm_bc_ymin" \

‎tools/cmems_download_ic_bc/cmems_download_ic_bc.xml‎

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Original file line numberDiff line numberDiff line change
@@ -1,20 +1,26 @@
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<tool id="cmems_download_ic_bc" name="Copernicus CMEMS Downloader for AquaINFRA marine model" version="1.0.0" profile="22.05">
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<description>Download data from the Copernicus Marine Service to provide as input to the AquaINFRA marine model. Products: Mediterranean Sea Physics Analysis and Forecast or Mediterranean Sea Physics Reanalysis, depending on the selected temporal period.</description>
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<tool id="cmems_download_ic_bc" name="Copernicus CMEMS Downloader for AquaINFRA marine model" version="1.0.1" profile="22.05">
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<description>
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Download data from the Copernicus Marine Service to provide as input to the AquaINFRA marine model. Products: Mediterranean Sea Physics Analysis and Forecast or Mediterranean Sea Physics Reanalysis, depending on the selected temporal period.
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</description>
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<creator>
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<organization name="EOSC AquaINFRA" url="https://aquainfra.eu/"/>
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</creator>
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<requirements>
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<requirement type="package" version="2.0">copernicusmarine</requirement>
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<requirement type="package" version="1.41.0">boto3</requirement>
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<requirement type="package" version="1.41.0">botocore</requirement>
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<requirement type="package" version="3.11">python</requirement>
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<requirement type="package" version="2.2.5">copernicusmarine</requirement>
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<requirement type="package" version="1.41.2">boto3</requirement>
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<requirement type="package" version="1.41.2">botocore</requirement>
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<requirement type="package" version="5.2.37">bash</requirement>
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<requirement type="package" version="1.8.1">jq</requirement>
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<requirement type="package" version="3.14.0">python</requirement>
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<requirement type="package" version="1.7.3">netcdf4</requirement>
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<requirement type="package" version="1.7.3">bc</requirement>
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<!--<credentials name="copernicus_marine" version="2.0">
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<variable name="username" inject_as_env="CMEMS_USERNAME" />
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<variable name="password" inject_as_env="CMEMS_PASSWORD" />
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</credentials>-->
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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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bash '$cmems_credentials' &&
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source '$cmems_credentials' &&
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bash "$__tool_directory__/cmems_download_ic_bc.sh" \
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"$min_lat" "$max_lat" \
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<configfiles>
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<configfile name="cmems_credentials">
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#import os
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#set $cmems_username = $__user__.extra_preferences.get('cmems_username', "")
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#set $cmems_password = $__user__.extra_preferences.get('cmems_password', "")
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#set $cmems_username = $__user__.extra_preferences.get('cmems_account|cmems_username', "")
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#set $cmems_password = $__user__.extra_preferences.get('cmems_account|cmems_password', "")
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#if $cmems_username == "" or $cmems_password == ""
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#set $cmems_username = os.getenv('CMEMS_USERNAME', '')
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#set $cmems_password = os.getenv('CMEMS_PASSWORD', '')
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</test>
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</tests>
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<help format="markdown"><![CDATA[
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This tool downloads data subsets from the **Copernicus Marine Service (CMEMS)** using the **Copernicus Marine Toolbox** v2.0, to give later as input to the AquaINFRA marine model.
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This tool downloads data subsets from the **Copernicus Marine Service (CMEMS)** using the **Copernicus Marine Toolbox** v2.0, to give later as input to the AquaINFRA marine model.
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Products: Mediterranean Sea Physics Analysis and Forecast or Mediterranean Sea Physics Reanalysis, depending on the selected temporal period.
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### Requirements
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