Code Examples

Setup

The following code examples require installation of certain packages and authentication from your ESS-DIVE account. Follow the instructions for setting up the Dataset API for your preferred coding language before trying out the search code examples:

Setup and Troubleshoot

---

Create Metadata

The metadata example provided here is from the ESS-DIVE sandbox site: https://data-sandbox.ess-dive.lbl.gov/#view/doi:10.3334/CDIAC/spruce.001.

Python

Format JSON-LD Metadata in Python

Setup the JSON for the “provider”, which includes details about the project. Simply update the "value" to use the desired project identifier, lookup project identifiers via ESS-DIVE's project list: https://data.ess-dive.lbl.gov/projects. The project will be listed as the publisher in the citation.

provider_spruce = {
    "identifier": {
        "@type": "PropertyValue",
        "propertyID": "ess-dive",
        "value": "1e6d50d3-9532-43fb-a63f-bdcb4350bf0c"
    }
 }

Prepare the dataset authors in the order that you would like them to appear in the citation. Please add the ORCID for all authors, especially the first author, if possible.

creators =  [
   {
     "@id": "http://orcid.org/0000-0001-7293-3561",
     "givenName": "Paul J",
     "familyName": "Hanson",
     "affiliation": "Oak Ridge National Laboratory",
     "email": "[email protected]"
   },
   {
     "givenName": "Jeffrey",
     "familyName": "Riggs",
     "affiliation": "Oak Ridge National Laboratory"
   },
   {
     "givenName": "C",
     "familyName": "Nettles",
     "affiliation": "Oak Ridge National Laboratory"
   },
   {
     "givenName": "William",
     "familyName": "Dorrance",
     "affiliation": "Oak Ridge National Laboratory"
   },
   {
     "givenName": "Les",
     "familyName": "Hook",
     "affiliation": "Oak Ridge National Laboratory"
   }
 ]

Create the rest of the JSON-LD object

json_ld = {
 "@context": "http://schema.org/",
 "@type": "Dataset",
 "@id": "http://dx.doi.org/10.3334/CDIAC/spruce.001",
 "name": "SPRUCE S1 Bog Environmental Monitoring Data: 2010-2016",
 "description": [
   "This data set reports selected ambient environmental monitoring data from the S1 bog in Minnesota for the period June 2010 through December 2016. Measurements of the environmental conditions at these stations will serve as a pre-treatment baseline for experimental treatments and provide driver data for future modeling activities.",
   "The site is the S1 bog, a Picea mariana [black spruce] - Sphagnum spp. bog forest in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF). There are/were three monitoring sites located in the bog: Stations 1 and 2 are co-located at the southern end of the bog and Station 3 is located north central and adjacent to an existing U.S. Forest Service monitoring well.",
   "There are eight data files with selected results of ambient environmental monitoring in the S1 bog for the period June 2010 through December 2016. One file has the ",
   "other seven have the available data for a given calendar year. Not all measurements started in June 2010 and EM3 measurements ended in May 2014.",
   "Further details about the data package are in the attached pdf file (SPRUCE_EM_DATA_2010_2016_20170620)."
 ],
 "creator": creators,
 "datePublished": "2015",
 "keywords": [
   "EARTH SCIENCE > BIOSPHERE > VEGETATION",
   "Climate Change"
 ],
 "variableMeasured": [
   "EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC TEMPERATURE > SURFACE TEMPERATURE > AIR TEMPERATURE",
   "EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC WATER VAPOR > WATER VAPOR INDICATORS > HUMIDITY > RELATIVE HUMIDITY",
   "EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC PRESSURE > SEA LEVEL PRESSURE",
   "EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC TEMPERATURE > SURFACE TEMPERATURE > DEW POINT TEMPERATURE > DEWPOINT DEPRESSION",
   "EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC WINDS > SURFACE WINDS > WIND SPEED",
   "EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC WINDS > SURFACE WINDS > WIND DIRECTION",
   "EARTH SCIENCE > BIOSPHERE > VEGETATION > PHOTOSYNTHETICALLY ACTIVE RADIATION",
   "EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC RADIATION > NET RADIATION",
   "EARTH SCIENCE > LAND SURFACE > SURFACE RADIATIVE PROPERTIES > ALBEDO",
   "EARTH SCIENCE > LAND SURFACE > SOILS > SOIL TEMPERATURE",
   "Precipitation (Total)",
   "Irradiance",
   "Groundwater Temperature",
   "Groundwater Level",
   "Volumetric Water Content",
   "surface_albedo"
 ],
 "license": "http://creativecommons.org/licenses/by/4.0/",
 "spatialCoverage": [
   {
     "description": "Site ID: S1 Bog Site name: S1 Bog, Marcell Experimental Forest Description: The site is the 8.1-ha S1 bog, a Picea mariana [black spruce] - Sphagnum spp. ombrotrophic bog forest in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF). The S1 bog was harvested in successive strip cuts in 1969 and 1974 and the cut areas were allowed to naturally regenerate. Stations 1 and 2 are located in a 1974 strip that is characterized by a medium density of 3-5 meter black spruce and larch trees with an open canopy. The area was suitable for siting a monitoring station for representative meteorological conditions on the S1 bog. Station 3 is located in a 1969 harvest strip that is characterized by a higher density of 3-5 meter black spruce and larch trees with a generally closed canopy. Measurements at this station represent conditions in the surrounding stand. Site Photographs are in the attached document",
     "geo": [
       {
         "name": "Northwest",
         "latitude": 47.50285,
         "longitude": -93.48283
       },
       {
         "name": "Southeast",
         "latitude": 47.50285,
         "longitude": -93.48283
       }
     ]
   }
 ],
 "funder": {
   "@id": "http://dx.doi.org/10.13039/100006206",
   "name": "U.S. DOE > Office of Science > Biological and Environmental Research (BER)"
 },
 "temporalCoverage": {
   "startDate": "2010-07-16",
   "endDate": "2016-12-31"
 },
 "editor": {
   "@id": "http://orcid.org/0000-0001-7293-3561",
   "givenName": "Paul J",
   "familyName": "Hanson",
   "email": "[email protected]"
 },
 "provider": provider_spruce,
 "measurementTechnique": [
   "The stations are equipped with standard sensors for measuring meteorological parameters, solar radiation, soil temperature and moisture, and groundwater temperature and elevation. Note that some sensor locations are relative to nearby vegetation and bog microtopographic features (i.e., hollows and hummocks). See Table 1 in the attached pdf (SPRUCE_EM_DATA_2010_2016_20170620) for a list of measurements and further details. Sensors and data loggers were initially installed and became operational in June, July, and August of 2010. Additional sensors were added in September 2011. Station 3 was removed from service on May 12, 2014.",
   "These data are considered at Quality Level 1. Level 1 indicates an internally consistent data product that has been subjected to quality checks and data management procedures. Established calibration procedures were followed."
 ]
}

Please refer to the API documentation to understand the schema and navigate through any errors: https://api-sandbox.ess-dive.lbl.gov

R

Java

Submit Dataset

The following lines of code submits and validates JSON-LD metadata for a single dataset.

Metadata Only

Python

Submit Metadata Only in Python

Submit the JSON-LD object with the Dataset API

post_packages_url = "{}{}".format(base,endpoint)
post_package_response = requests.post(post_packages_url,
                                      headers={"Authorization":header_authorization},
                                      json=json_ld)

if post_package_response.status_code == 201:
    # Success
    response=post_package_response.json()
    print(f"View URL:{response['viewUrl']}")
    print(f"Name:{response['dataset']['name']}")
else:
    # There was an error
    print(post_package_response.text)

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Single Data File

Python

Submit Metadata and Single Data File in Python

To submit the JSON-LD object along with data files, you need to create a folder named files and add your desired file to upload inside it.

files_tuples_array = []
upload_file = “path/to/your_file”

files_tuples_array.append((("json-ld", json.dumps(json_ld))))
files_tuples_array.append(("data", open(upload_file ,'rb')))

post_packages_url = "{}{}".format(base,endpoint)
post_package_response = requests.post(post_packages_url,
                                    headers={"Authorization":header_authorization},
                                    files= files_tuples_array)

if post_package_response.status_code == 201:
    # Success
    response=post_package_response.json()
    print(f"View URL:{response['viewUrl']}")
    print(f"Name:{response['dataset']['name']}")
else:
    # There was an error
    print(post_package_response.text)

Remember to change the file directories & file names to your actual names. The directory variable can be left blank if your API is already located in the same directory as your file.

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Java

Many Data Files

Python

Submit Metadata and Many Data Files in Python

In case you have many files to be uploaded, you can place them all inside the files directory and use the following code:

files_tuples_array = []
files_upload_directory = "your_upload_directory/"
files = os.listdir(files_upload_directory)

files_tuples_array.append((("json-ld", json.dumps(json_ld))))

for filename in files:
   file_directory = files_upload_directory + filename
   files_tuples_array.append((("data", open(file_directory, 'rb'))))

post_packages_url = "{}{}".format(base,endpoint)
post_package_response = requests.post(post_packages_url,
                                    headers={"Authorization":header_authorization},
                                    files= files_tuples_array)

if post_package_response.status_code == 201:
   # Success
   response=post_package_response.json()
   print(f"View URL:{response['viewUrl']}")
   print(f"Name:{response['dataset']['name']}")
else:
   # There was an error
   print(post_package_response.text)

R

Java

---

Edit Dataset

Metadata Only

Python

Edit Metadata in Python

Use the PUT function to update the metadata of a dataset. This example updates the name of a dataset.

dataset_id = "<Enter an ESS-DIVE Identifier here>"

put_package_url = "{}{}/{}".format(base,endpoint, dataset_id)

metadata_update_dict = {"name": "Updated Dataset Name"}

put_package_response = requests.put(put_package_url,
                                    headers={"Authorization":header_authorization},
                                    json=metadata_update_dict)

Check the results for the changed metadata attribute

# Check for errors
if put_package_response.status_code == 200:
   # Success
   response=put_package_response.json()
   print(f"View URL:{response['viewUrl']}")
   print(f"Name:{response['dataset']['name']}")
else:
   # There was an error
   print(put_package_response.text)

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Java

Metadata and Data

Python

Edit Metadata and Data in Python

Use the PUT function to update a dataset. This example updates the date published to 2019 of a dataset and adds a new data file.

dataset_id = "<Enter an ESS-DIVE Identifier here>"

files_tuples_array = []
upload_file = "path/to/your_file"
files_tuples_array.append((("json-ld", json.dumps(metadata_update_dict))))
files_tuples_array.append(("data", open(upload_file ,'rb')))

put_package_url = "{}{}/{}".format(base,endpoint, dataset_id)



put_package_response = requests.put(put_package_url,
                                   headers={"Authorization":header_authorization},
                                   files= files_tuples_array)

Check the results for the changed metadata attribute and newly uploaded file

# Check for errors
if put_package_response.status_code == 200:
    # Success
    response=put_package_response.json()
    print(f"View URL:{response['viewUrl']}")
    print(f"Date Published:{response['dataset']['datePublished']}")
    print(f"Files In Dataset:{response['dataset']['distribution']}")
else:
   # There was an error
   print(put_package_response.text)

get_packages_url = "{}{}".format(base,endpoint)
get_packages_response = requests.get(get_packages_url, 
    headers={"Authorization":header_authorization})

if get_packages_response.status_code == 200:
   #Success
   print(get_packages_response.json())
else:
   # There was an error
   print(get_packages_response.text)

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Java