A Guide to hdar package

Introduction

The hdar R package provides seamless access to the WEkEO Harmonised Data Access (HDA) API, enabling users to efficiently query, download, and process data from the HDA platform.

Accessing the HDA Service

To utilize the HDA service and library, you must first register for a WEkEO account. The HDA service is available at no cost to all WEkEO users. Creating an account allows you full access to our services, ensuring you can leverage the full capabilities of HDA seamlessly. Registration is straightforward and can be completed through the following link: Register for WEkEO. Once your account is set up, you will be able to access the HDA services immediately.

Setup

To start using the hdar package, you first need to install and load it in your R environment.

# Install stable hdar from CRAN
if(!require("hdar")){install.packages("hdar")}
# or develop version from GitHub
# devtools::install_github("eea/hdar@develop")

# Load the hdar package
library(hdar)

Authentication

To interact with the HDA service, you need to authenticate by providing your username and password. The Client class allows you to pass these credentials directly and optionally save them to a configuration file for future use. If credentials are not specified as parameters, the client will read them from the ~/.hdarc file.

Creating and Authenticating the Client

You can create an instance of the Client class by passing your username and password directly. TThe initialization method has an optional parameter save_credentials that specifies whether the provided credentials should be saved in the ~/.hdarc configuration file. By default, save_credentials is set to FALSE.

Example: Pass User/Password at Initialization

Here is an example of how to authenticate by passing the user and password, and optionally saving these credentials:

# Define your username and password
username <- "your_username"
password <- "your_password"

# Create an instance of the Client class and save credentials to a config file
# The save_credentials parameter is optional and defaults to FALSE
client <- Client$new(username, password, save_credentials = TRUE)

If the save_credentials parameter is set to TRUE, the credentials will be saved in the ~/.hdarc file, making it easier to authenticate in future sessions without passing the credentials again.

Example: Using Saved Credentials

Once the credentials are saved, you can initialize the Client class without passing the credentials. The client will read the credentials from the ~/.hdarc file:

# Create an instance of the Client class without passing credentials
client <- Client$new()

Checking Authentication

Once the client is created, you can check if it has been authenticated properly by calling a method token() that verifies authentication. For example:

# Example method to check authentication by getting the auth token
client$get_token()

Copernicus Terms and Conditions (T&C)

Copernicus data is free to use and modify, still T&Cs must be accepted in order to download the data. hdarc offers a confortable functionality to read and accept/reject T&C of the individual Copernicus service:

client$show_terms()

Will open a browser where you can read all the available T&Cs. To accept/reject individual T&Cs or all at once use:

client$terms_and_conditions()
                                              term_id accepted
1                           Copernicus_General_License     TRUE
2                          Copernicus_Sentinel_License     TRUE
3                       EUMETSAT_Core_Products_Licence     TRUE
4                     EUMETSAT_Copernicus_Data_Licence     TRUE
5  Copernicus_DEM_Instance_COP-DEM-GLO-90-F_Global_90m     TRUE
6  Copernicus_DEM_Instance_COP-DEM-GLO-30-F_Global_30m     TRUE
7                             Copernicus_ECMWF_License     TRUE
8       Copernicus_Land_Monitoring_Service_Data_Policy     TRUE
9            Copernicus_Marine_Service_Product_License     TRUE
10                        CNES_Open_2.0_ETALAB_Licence     TRUE

Finding Datasets

WEkEO offers a vast amount of different products. To find what you need the Client class provides a method called datasets that lists available datasets, optionally filtered by a text pattern.

Basic Usage

The basic usage of the datasets method is straightforward. You can retrieve a list of all datasets available on WEkEO by calling the datasets method on an instance of the Client class.

# retrieving the full list can take about 2 minutes!
all_datasets <- client$datasets()

# list all datasets IDs on WEkEO
sapply(filtered_datasets,FUN = function(x){x$dataset_id})

Filtering Datasets

You can also filter the datasets by providing a text pattern. This is useful when you are looking for datasets that match a specific keyword or phrase.

pattern <- "Seasonal Trajectories"
filtered_datasets <- client$datasets(pattern)

# list dataset IDs
sapply(filtered_datasets,FUN = function(x){x$dataset_id})
[1] "EO:EEA:DAT:CLMS_HRVPP_VPP-LAEA" "EO:EEA:DAT:CLMS_HRVPP_ST"       "EO:EEA:DAT:CLMS_HRVPP_ST-LAEA" 
[4] "EO:EEA:DAT:CLMS_HRVPP_VPP" 

pattern <- "Baltic"
filtered_datasets <- client$datasets(pattern)

# list dataset IDs
sapply(filtered_datasets,FUN = function(x){x$dataset_id})
 [1] "EO:MO:DAT:BALTICSEA_ANALYSISFORECAST_BGC_003_007:cmems_mod_bal_bgc-pp_anfc_P1D-i_202311"               
 [2] "EO:MO:DAT:NWSHELF_MULTIYEAR_PHY_004_009:cmems_mod_nws_phy-sst_my_7km-2D_PT1H-i_202112"                 
 [3] "EO:MO:DAT:OCEANCOLOUR_BAL_BGC_L4_MY_009_134:cmems_obs-oc_bal_bgc-plankton_my_l4-multi-1km_P1M_202211"  
 [4] "EO:MO:DAT:SST_BAL_PHY_SUBSKIN_L4_NRT_010_034:cmems_obs-sst_bal_phy-subskin_nrt_l4_PT1H-m_202211"       
 [5] "EO:MO:DAT:BALTICSEA_MULTIYEAR_PHY_003_011:cmems_mod_bal_phy_my_P1Y-m_202303"                           
 [6] "EO:MO:DAT:OCEANCOLOUR_BAL_BGC_L3_NRT_009_131:cmems_obs-oc_bal_bgc-transp_nrt_l3-olci-300m_P1D_202207"  
 [7] "EO:MO:DAT:BALTICSEA_MULTIYEAR_BGC_003_012:cmems_mod_bal_bgc_my_P1Y-m_202303"                           
 [8] "EO:MO:DAT:SST_BAL_SST_L4_REP_OBSERVATIONS_010_016:DMI_BAL_SST_L4_REP_OBSERVATIONS_010_016_202012"      
 [9] "EO:MO:DAT:BALTICSEA_ANALYSISFORECAST_PHY_003_006:cmems_mod_bal_phy_anfc_PT15M-i_202311"                
[10] "EO:MO:DAT:OCEANCOLOUR_BAL_BGC_L3_MY_009_133:cmems_obs-oc_bal_bgc-plankton_my_l3-multi-1km_P1D_202207"  
[11] "EO:MO:DAT:SST_BAL_PHY_L3S_MY_010_040:cmems_obs-sst_bal_phy_my_l3s_P1D-m_202211"                        
[12] "EO:MO:DAT:SEAICE_BAL_SEAICE_L4_NRT_OBSERVATIONS_011_004:FMI-BAL-SEAICE_THICK-L4-NRT-OBS"               
[13] "EO:MO:DAT:SEAICE_BAL_PHY_L4_MY_011_019:cmems_obs-si_bal_seaice-conc_my_1km_202112"                     
[14] "EO:MO:DAT:BALTICSEA_ANALYSISFORECAST_WAV_003_010:cmems_mod_bal_wav_anfc_PT1H-i_202311"                 
[15] "EO:MO:DAT:BALTICSEA_REANALYSIS_WAV_003_015:dataset-bal-reanalysis-wav-hourly_202003"                   
[16] "EO:MO:DAT:OCEANCOLOUR_BAL_BGC_L4_NRT_009_132:cmems_obs-oc_bal_bgc-plankton_nrt_l4-olci-300m_P1M_202207"
[17] "EO:MO:DAT:SST_BAL_SST_L3S_NRT_OBSERVATIONS_010_032:DMI-BALTIC-SST-L3S-NRT-OBS_FULL_TIME_SERIE_201904"

Understanding the Results

The datasets method returns a list containing datasets and associated information. This information may include dataset names, descriptions, and other metadata.

client$datasets("EO:ECMWF:DAT:DERIVED_NEAR_SURFACE_METEOROLOGICAL_VARIABLES")
[[1]]
[[1]]$terms
[[1]]$terms[[1]]
[1] "Copernicus_ECMWF_License"

[[1]]$dataset_id
[1] "EO:ECMWF:DAT:DERIVED_NEAR_SURFACE_METEOROLOGICAL_VARIABLES"

[[1]]$title
[1] "Near surface meteorological variables from 1979 to 2019 derived from bias-corrected reanalysis"

[[1]]$abstract
[1] "This dataset provides bias-corrected reconstruction of near-surface meteorological variables derived from the fifth generation of the European Centre for Medium-Range Weather Forecasts  (ECMWF) atmospheric reanalyses (ERA5). It is intended to be used as a meteorological forcing dataset for land surface and hydrological models. \nThe dataset has been obtained using the same methodology used to derive the widely used water, energy and climate change (WATCH) forcing data, and is thus also referred to as WATCH Forcing Data methodology applied to ERA5 (WFDE5). The data are derived from the ERA5 reanalysis product that have been re-gridded to a half-degree resolution. Data have been adjusted using an elevation correction and monthly-scale bias corrections based on Climatic Research Unit (CRU) data (for temperature, diurnal temperature range, cloud-cover, wet days number and precipitation fields) and Global Precipitation Climatology Centre (GPCC) data (for precipitation fields only). Additional corrections are included for varying atmospheric aerosol-loading and separate precipitation gauge observations. For full details please refer to the product user-guide.\nThis dataset was produced on behalf of Copernicus Climate Change Service (C3S) and was generated entirely within the Climate Data Store (CDS) Toolbox. The toolbox source code is provided in the documentation tab.\n\nVariables in the dataset/application are:\nGrid-point altitude, Near-surface air temperature, Near-surface specific humidity, Near-surface wind speed, Rainfall flux, Snowfall flux, Surface air pressure, Surface downwelling longwave radiation, Surface downwelling shortwave radiation"

[[1]]$doi
NULL

[[1]]$thumbnails
[1] "https://datastore.copernicus-climate.eu/c3s/published-forms-v2/c3sprod/derived-near-surface-meteorological-variables/overview.jpg"

Creating a Query Template

To search for a specific product, you need to create a query template. You can either use the WEkEO viewer and copy paste the JSON query:

query <- '{
  "dataset_id": "EO:ECMWF:DAT:CEMS_GLOFAS_HISTORICAL",
  "system_version": [
    "version_4_0"
  ],
  "hydrological_model": [
    "lisflood"
  ],
  "product_type": [
    "consolidated"
  ],
  "variable": [
    "river_discharge_in_the_last_24_hours"
  ],
  "hyear": [
    "2024"
  ],
  "hmonth": [
    "june"
  ],
  "hday": [
    "01"
  ],
  "format": "grib",
  "bbox": [
    11.77115199576009,
    44.56907885098417,
    13.0263737724595,
    45.40384015467251
  ],
  "itemsPerPage": 200,
  "startIndex": 0
}'

or use the query template function generate_query_template for a given dataset.

Basic Usage

The generate_query_template function generates a template of a query for a specified dataset. This function fetches information about existing parameters, default values, etc., from the /queryable endpoint of the HDA service.

Example: Generating a Query

Here is an example of how to generate a query template for the dataset with the ID “EO:EEA:DAT:CLMS_HRVPP_ST”:

# client <- Client$new()
query_template <- client$generate_query_template("EO:EEA:DAT:CLMS_HRVPP_ST")
query_template
{
  "dataset_id": "EO:EEA:DAT:CLMS_HRVPP_ST",
  "uid": "__### Value of string type with pattern: [\\w-]+",
  "productType": "PPI",
  "platformSerialIdentifier": "S2A, S2B",
  "tileId": "__### Value of string type with pattern: [\\w-]+",
  "productVersion": "__### Value of string type with pattern: [\\w-]+",
  "resolution": "10",
  "processingDate": "__### Value of string",
  "start": "__### Value of string",
  "end": "__### Value of string",
  "bbox": [
    -180,
    -90,
    180,
    90
  ]
}

Modify and use the generated Query Template

You can and should customize the generated query template to fit your specific needs. Fields starting with __### are placeholders indicating possible values. If these placeholders are left unchanged, they will be automatically removed before sending the query to the HDA service.

To modify the query, it is often easier to transform the JSON into an R list using the jsonlite::fromJSON() function:

# convert to list for easier manipulation in R
library(jsonlite)
query_template <- fromJSON(query_template, flatten = FALSE)
query_template
$dataset_id
[1] "EO:EEA:DAT:CLMS_HRVPP_ST"

$uid
[1] "__### Value of string type with pattern: [\\w-]+"

$productType
[1] "PPI"

$platformSerialIdentifier
[1] "S2A, S2B"

$tileId
[1] "__### Value of string type with pattern: [\\w-]+"

$productVersion
[1] "__### Value of string type with pattern: [\\w-]+"

$resolution
[1] "10"

$processingDate
[1] "__### Value of string"

$start
[1] "__### Value of string"

$end
[1] "__### Value of string"

$bbox
[1] -180  -90  180   90

Here is an example of how to use the query template in a search:

# set a new bbox
query_template$bbox <- c(11.1090, 46.6210, 11.2090, 46.7210)

# limit the time range
query_template$start <- "2018-03-01T00:00:00.000Z"
query_template$end   <- "2018-05-31T00:00:00.000Z"
query_template
$dataset_id
[1] "EO:EEA:DAT:CLMS_HRVPP_ST"

$uid
[1] "__### Value of string type with pattern: [\\w-]+"

$productType
[1] "PPI"

$platformSerialIdentifier
[1] "S2A, S2B"

$tileId
[1] "__### Value of string type with pattern: [\\w-]+"

$productVersion
[1] "__### Value of string type with pattern: [\\w-]+"

$resolution
[1] "10"

$processingDate
[1] "__### Value of string"

$start
[1] "2018-03-01T00:00:00.000Z"

$end
[1] "2018-05-31T00:00:00.000Z"

$bbox
[1] 11.109 46.621 11.209 46.721

Once you have made the necessary modifications, you can convert the list back to JSON format with the jsonlite::toJSON() function. It’s crucial to use the auto_unbox = TRUE flag when converting back to JSON. This ensures that the JSON is correctly formatted, particularly for arrays with a single element, due to the way jsonlite handles serialization.

# convert to JSON format
query_template <- toJSON(query_template, auto_unbox = TRUE) # don't forget to put auto_unbox = TRUE

Searching and Downloading Data

To search for data in the HDA service, you can use the search function provided by the Client class. This function allows you to search for datasets based on a query and optionally limit the number of results. The search results can then be downloaded using the download method of the SearchResults class.

Searching for Data

The search function takes a query and an optional limit parameter, which specifies the maximum number of results you want to retrieve. The function only searches for data and does not download it. The output of this function is an instance of the SearchResults class.

Here is an example of how to search for data using a query and limit the results to 5:

# Assuming 'client' is already created and authenticated, 'query' is defined
matches <- client$search(query_template)
[1] "Found 9 files"
[1] "Total Size 1.8 GB"

sapply(matches$results,FUN = function(x){x$id})
[1] "ST_20180301T000000_S2_T32TPS-010m_V101_PPI" "ST_20180311T000000_S2_T32TPS-010m_V101_PPI"
[3] "ST_20180321T000000_S2_T32TPS-010m_V101_PPI" "ST_20180401T000000_S2_T32TPS-010m_V101_PPI"
[5] "ST_20180411T000000_S2_T32TPS-010m_V101_PPI" "ST_20180421T000000_S2_T32TPS-010m_V101_PPI"
[7] "ST_20180501T000000_S2_T32TPS-010m_V101_PPI" "ST_20180511T000000_S2_T32TPS-010m_V101_PPI"
[9] "ST_20180521T000000_S2_T32TPS-010m_V101_PPI"

Downloading the files

The SearchResults class has a public field results and a method called download that is responsible for downloading the found data. The download() function takes an output directory (which is created if it doesn’t already exist) and includes an optional force parameter. When force is set to TRUE, the function will re-download the files even if they already exist in the output directory, overwriting the existing files. If force is set to FALSE (the default), the function will skip downloading files that already exist, saving time and bandwidth.

# Assuming 'matches' is an instance of SearchResults obtained from the search
odir <- tempdir()
matches$download(odir)
The total size is 1.8 GB . Do you want to proceed? (Y/N):
y
[1] "[Download] Start"
[1] "[Download] Downloading file 1/9"
[1] "[Download] Downloading file 2/9"
[1] "[Download] Downloading file 3/9"
[1] "[Download] Downloading file 4/9"
[1] "[Download] Downloading file 5/9"
[1] "[Download] Downloading file 6/9"
[1] "[Download] Downloading file 7/9"
[1] "[Download] Downloading file 8/9"
[1] "[Download] Downloading file 9/9"
[1] "[Download] DONE"

# Assuming 'matches' is an instance of SearchResults obtained from the search
list.files(odir)
[1] "ST_20180301T000000_S2_T32TPS-010m_V101_PPI.tif" "ST_20180311T000000_S2_T32TPS-010m_V101_PPI.tif"
[3] "ST_20180321T000000_S2_T32TPS-010m_V101_PPI.tif" "ST_20180401T000000_S2_T32TPS-010m_V101_PPI.tif"
[5] "ST_20180411T000000_S2_T32TPS-010m_V101_PPI.tif" "ST_20180421T000000_S2_T32TPS-010m_V101_PPI.tif"
[7] "ST_20180501T000000_S2_T32TPS-010m_V101_PPI.tif" "ST_20180511T000000_S2_T32TPS-010m_V101_PPI.tif"
[9] "ST_20180521T000000_S2_T32TPS-010m_V101_PPI.tif"

unlink(odir,recursive = TRUE)